10/4/2018

1

BIO 1101 Lec. 9, Part A (Guided Notes): Chapter 11 -- Gene Regulation

Gene Regulation

•

• An organism has many different kinds of cells the have different functions, but every body

cell has the _______________________

•

• If the DNA in every body cell is the same, how can cells be so different?

•

• An individual starts out as a single cell – a _________________

•

• That single cell divides by __________, making identical copies of itself

•

• As the organism continues to grow by mitosis, individual cells become ______________ –some genes become inactivated, while others are activated

• In this way, cells can become specialized

•

• The genes that are “__________________” are transcribed into mRNA, and then

translated into proteins

•

• Genes that are ___________________ aren’t transcribed or translated

•

• How does a cell turn on or off different genes?

Gene Regulation in Bacteria

• Bacteria can conserve resources by only expressing the genes they need

• E. coli bacteria can use the sugar ___________ as fuel if it is available in their environment

– Three enzymes needed to absorb and digest

– Genes located next to each other

– Genes that have related function and which can be simultaneously regulated form an

_______________

– E. coli have a _______________

•

•

• Control of an __________________

– _________________: a control sequence on DNA near the operon to which

____________________ can bind

– _________________: a sequence between the promoter and the genes of the operon;

_______________ can bind here to turn off transcription

• In the case of the lac operon, lactose interferes with the attachment of the lac

repressor to the operator; thus the presence of lactose turns on the operon

•

•

Gene Regulation in Eukarytoes

• In Eukaryotes (organisms other than bacteria and archea), several methods may be used:

– _________________: when DNA is in a condensed state (as when ready to divide), it

cannot be transcribed or translated

• Example: X chromosome inactivation in female cats

–

•

– Genes can be regulated at initiation of transcription

• Most important stage for regulating gene expression

• Most genes in eukaryotes, by default, are turned “______”

• Many proteins are involved in enhancing transcription of particular genes

• ______________ ______ are proteins that bind to enhancers and promoters of DNA

to activate multiple genes at the same time

• _____________________ may bind to DNA sequences called _______________ to inhibit transcription

•

• RNA Processing and Breakdown

– As we previously discussed, the initial mRNA transcript is edited to remove

____________ (intervening sequences) and __________ linked together before it leaves the nucleus and is translated

– Another way gene expression can be modified is through alternative ways of linking the

__________

• The exons of one gene may be linked in different ways to create different

__________________

– This is called _________________

•

•

– Not all RNAs code for protein

• Used to be considered “junk”

• Actually perform important functions

–microRNAs, for example

• miRNAs bind to one or more ____________

• Form a complex with mRNAs

• If the miRNA is complementary to the entire length of the mRNA, then the target

mRNA is ________________

• If the miRNA is only complementary to a part of the target mRNA, then the complex

_______________________________________

–Other ways genes can be regulated:

•

• By breaking down mRNA in the cytoplasm

•

• By regulating translation

•

• By altering the proteins produced in translation

•

• By breaking down the produced proteins

• The process of forming proteins from a DNA molecule involves many steps

•

• At each step, there are opportunities for gene regulation

•

• Cell Signaling and Homeotic Genes

– In multicellular organisms, information must be communicated between cells

– Chemicals like ____________ can be secreted by one cell and signal some activity in another cell

– The signal molecule acts by binding to a ___________________ on the target cell, initiating a ___________________________

– The binding activates a series of _______________, which ultimately activates a

________________, triggering the transcription of a specific gene

•

– _________________ are “master control genes” that regulate the expression of other groups of genes

– These are crucial in the process of embryonic development, when cells use chemical

signals to coordinate development

– A well-studied example of homeotic genes and their effects on development is seen in

fruit flies

• Certain homeotic genes in the fruit fly determine where ______________________

develop on the body

• One homeotic gene, when active, triggers legs to form on cells in the mid-body; this genes is inactive in other parts of the body

• A mutation in this homeotic genes can result in flies with legs coming out of their

heads, for example

• See video on experiments on homeotic genes in fruit flies:

https://www.youtube.com/watch?v=voQQ1dhCqZg

•

•

• 5-minute break

Cell Differentiation and the Science of Cloning

–

– Remember, the cells of an organism start out as undifferentiated – they have the

potential to become any type of cell

– As the organism grows, certain genes are turned on or left turned off, and the cell thus becomes differentiated

•

•

– Sometimes, cells that have become differentiated can “dedifferentiate” – allowing them

to grow into a new organism, or a new part of an organism

• Example: many plants can be propagated vegetatively

• Amphibians are famous for being able to re-generate lost limbs

•

• This process is relatively easy to do with plants

–Is used to make large numbers of “copies” of plants with desirable characteristics

• If a new organism is grown from the somatic (body) cells of an adult organism, the

result is a ____________ – it is genetically identical to the organism from whose cells it was grown

•

• _______________ = the production of identical copies of a cell, organism, or DNA molecule

–Doesn’t ONLY refer to making copies of entire organisms

–More common: cloning cells or molecules

– There are different types of cloning, and each has a different purpose

•

– “Reproductive Cloning”

•

• The egg of a female animal is extracted, its ______ is removed, and the DNA from a ___________ cell of the desired organism is placed into the egg

• After the egg divides and forms an early embryo, it can be implanted into a female

• Can be used to generate “copies” of desirable farm animals, or endangered species

•

•

•

• “Dolly” the sheep was the first mammal to be cloned (1997)

–Died in 2003 from a lung disease

–Was her relatively early death a result of cloning? Difficult to say, as lung diseases are fairly common among sheep raised indoors…

• In January of 2018, it was reported that the first primates (macaques) were cloned

– https://www.youtube.com/watch?v=oEXleYs58MY

•

– Therapeutic Cloning is another type of cloning

• Purpose is to generate __________________ (ES cells)

• Can divide indefinitely in culture, and have the potential to develop into any type of cell

• Certain growth factors can induce these cells to differentiate into specific kinds of cells

• May be used to treat or cure diseases or injured organs

• For example, there has been some success using stem cells to treat stroke victims or

Parkinson’s disease (inserting stem cells into brain)

• Embryonic stem cells are derived from embryos, and therein lies the controversy

•

– Adult stem cells are partially differentiated

• They may be able to differentiate into one of a few different types of cells, but are already set on a path to become one of a few types

• Less flexible than ES cells

• Example: stem cells in bone marrow can become any of the types of blood cells

• More difficult to culture in the lab

• Can be harvested from adults, so are less controversial

– New sources of stem cells…

• ______________________stem cells; can be created from somatic cells

Genetics of Cancer

• Cancer is the second-leading cause of death in industrialized countries; what causes it?

• __________________ – genes that cause cancer

• We carry many genes that are ____________________: that is, if changed in some way, they can turn into oncogenes

• Oncogenes can arise from insertion by a virus, or by mutation of a proto-oncogene

• Many _____________________ code for ______________________ – proteins that stimulate cell division

– Too much growth factor produced by a mutated gene can cause cancerous growth

• Some genes, called _____________________ genes, inhibit cell division

– If they are mutated, can also cause cancer

• _______________________ are substances that cause mutations to DNA that eventually lead to cancer

• Examples of carcinogens:

– UV radiation (sunlight or tanning beds); (skin cancer)

– Tobacco smoke (lung cancer)

– Alcohol (liver cancer)

• Prevention

•

– Compounds found in fruits and vegetables can reduce cancer risks

• __________________

– Can help reduce and repair DNA damage

– Some cancer-fighting foods include: cabbage, broccoli, brussels sprouts, kale, shiitake mushrooms, onions, red beans, cherries, raspberries, strawberries, blueberries, and

green tea

•

Bonus Activity

1. Explain how cells that look and behave so differently (like skin cells vs neurons) in the

same organism have the same genes.

2. What is an operon? Give an example.

3. A mutation in one gene may cause a major change in the body of a fruit fly, yet it takes many genes to produce a wing or leg. How can a change in one gene cause a big change, like legs coming out of the head? What are such genes called?

4.

Lec. 9 Part B: Chapter 12 - Biotechnology

• DNA technology has wide variety of uses

• We will focus on genetic engineering and forensics (pg. 218-229)

Genetic Engineering

– Through __________________________, genes from different sources can be

combined

– Examples:

• Genes for specific protein products have been inserted into bacteria; the bacteria can then be grown and used to produce large quantities of the desired protein (e.g.

insulin)

• Proteins that can be used as vaccines can be produced by bacteria

•

• Genetically modified foods (e.g. “Bt” corn with built-in pesticide; “Golden Rice” with

enhanced nutritional value; tomatoes with a longer shelf life; etc.)

–GE crops introduced in 1996; now widely used; 93% of soy and 88% corn crops in

US were genetically modified (as of 2012)

–Primarily used in crops (insect resistance; herbicide tolerance)

•

•

• How is it done?

•

– Use of bacterial ________________ (circular pieces of DNA) as __________ (gene

carriers)

• ________________ are small circular pieces of DNA

• Bacteria readily take them in

• When a desired gene is inserted into a plasmid, the plasmid can then be isolated, and

then exposed to bacteria, which absorb them

• The bacteria will then express the desired gene in the modified plasmid

•

•

• How are genes inserted into plasmids?

•

– Cutting and Pasting Genes with ______________ Enzymes

• Restriction enzymes recognize short nucleotide sequences and cut the DNA at that site

• Staggered cut results in “_______________”

–A single-stranded piece of DNA at the end of the double-stranded molecule, which will readily connect with a complementary sticky end

• Fragments can then be stuck back together using ____________________

•

• In order to generate “sticky ends,” the recognition sequence must be a palindrome

– That is, the same sequence can be read from opposite directions on BOTH strands

– Example:

–

GAATTC

CTTAAG

•

• Gene of interest is now inserted into ___________

• ___________ is absorbed by bacteria, which express the ___________

• Bacteria can be readily grown to make many, many copies of the gene, or to synthesize

the protein encoded by the gene

• Most commonly, recombinant DNA technology is used to modify ___________

– Insect-resistant corn and cotton

– Rice that produces more vitamins

–Disease-resistant papya and sweet potatoes

•

• Some more unusual uses:

– Glowing pet fish

– Allergen-free cats

• Glowing Puppies!

– http://www.youtube.com/watch?v=YXPnQvcqHkg&feature=related

• Gene Editing

– __________________ system is a new technique that allows nucleotide sequences of

genes to be edited in living cells

• May be used to reveal function of a gene, or to even correct a mutation

– Bacteria have a protein called _________ that can identify and cut our viral DNA from

their genome

• Will cut any DNA sequence that is complementary to a specific sequence of guiding _______

• A Cas9 protein with an RNA molecule complementary to a particular gene may be used to cut out a gene from a cell’s chromosomes

• Random DNA nucleotides are then inserted into the chromosome by DNA repair

enzymes; this “___________” the gene, making in non-functional

• Can therefore determine what the gene did in the cell

• To edit a gene, researchers can add a segment of a normal gene along with the Cas9-guide RNA complex

• After Cas9 cuts the target DNA, repair enzymes use the normal DNA as a template to

repair the target DNA (for example, a mutated gene)

• This allows researchers to potentially fix genetic mutations

• Researchers have used CRISP-Cas9 to fix a genetic defects in mice

• Video: https://www.youtube.com/watch?v=52jOEPzhpzc

•

Bonus Activity

• CRISPR is an exciting new technology and researchers are racing to find ways to use it. Do a Google search and find a recent news article talking about how CRISPR is being used.

Read the article, and then write 2-3 sentences summarizing the article.

•

• Break…

Forensics

The “scientific analysis of evidence for crime scene investigations and other legal proceedings”

– __________________ is one technique used in forensics, to compare DNA samples

– Every individual’s genetic makeup is unique

– A person’s “DNA Fingerprint” is his/her unique collection of DNA fragments generated

when restriction enzymes are used to cut up the DNA

•

•

• How do you generate a DNA fingerprint?

• First, DNA evidence must be collected

– Various tissues, such as blood, semen, skin, etc.

• Before DNA Fingerprints can be generated, often the DNA sample must be _____________

– A tiny spec of blood can provide enough information to run a test, if the DNA in that

spec is copied many times

– The _______________________ is used to copy DNA

•

•

– Genomes are quite large, and typically scientists only need to amplify a small region of

the genome

– To amplify only a specific sequence, scientists use _____________, a short single-

stranded DNA molecule

– _____________ are selected that are complementary to only to the sequences at the ends of the target sequence

• The primers thus flank to target sequence, marking the beginning and end of the sequence to be copied

• Only the DNA between the primers is thus amplified

–

• _______________________ enzymes can then be used to cut the DNA into pieces

–Many different kinds of restriction enzymes

– Each recognizes a specific sequence and cuts DNA at that location

• May cut straight across both strands

• May make a “staggered” cut

• Although all humans are >99% genetically identical, the size of the human genome allows

for enough variation that differences can be detected

– About 3 billion base pairs in our DNA

– 1 in 1000 difference between any two people

–about 3 million differences between any two people

• When DNA samples from two different people are “digested” with the same restriction enzyme (or set of restriction enzymes), they will produce different numbers and sizes of

DNA fragments

– These different sets of DNA pieces are called “_________________________________”

• Differences (polymorphisms) in the size of the fragments of DNA created by the

restriction enzymes

• ____________________________ can then be used to separate the fragments by size

–DNA is ____________ charged (due to the ___________ groups)

– Electrical current causes the fragments of DNA to move through a “gel”

– ____________ pieces migrate faster than ____________ ones

– Results in a unique banding pattern

•

•

• Another technique commonly used in forensics is _________________ (STR) Analysis

–Much of the DNA between genes is composed of ____________ sequences (for

example, perhaps the sequence AGAT may be repeated 12 times)

– Non-coding

– Close relatives more likely to have more similar patterns of STRs

– Standard STR analysis in forensics tests ___ different markers

• Chances of two different people being identical at all 13 markers is between

__________________________________________________________________________________________________

Bonus Activity 2

1. A carrier that moves DNA from one cell to another, such as a plasmid, is called a ___________. Plasmids are small, circular pieces of DNA from ___________.

2. In making recombinant DNA, what is the benefit of using a restriction enzyme that cuts

DNA in a staggered fashion?

3. A paleontologist has recovered a bit of organic material from the 400-year-old preserved

skin of an extinct dodo. She would like to compare DNA from the sample with DNA from living birds. The most useful method for initially increasing the amount of dodo DNA for

testing is _____________________.

4. What feature of DNA causes it to move through a gel during gel electrophoresis?

DNA Evidence in the News…

•

• Use of DNA evidence in criminal cases is relatively new

– First case was in 1986 in England

• A man confessed to a series of rape/murders; DNA evidence indicated he did not; another person was identified as the actual murderer, based on DNA evidence

– First used in the US in ______________

• Man convicted of rape based on DNA obtained from semen found in victim

• Recently, a number of people on death row have been found not guilty based on DNA

evidence

–

•

•

• Fatal Flaws: The Case of Earl Washington

–Washington spent 18 years in prison

– Came within nine days of being put to death in Virginia's electric chair.

– Years later, DNA evidence proved he was innocent, and after a long legal battle, he was set free

–Washington had been convicted largely based on his own confession to a rape and

murder

• His defenders say the confession was coerced

• Washington was mentally handicapped

•

• DNA testing is increasingly being made available in criminal cases

• 32 states mandate that compensation be awarded to people wrongfully convicted (as of 2017)

• >________ people have been exonerated (from death row) using DNA testing since 1989

(when DNA testing first became available)

• In 2013 Oklahoma became 50th (and final) state to guarantee right to DNA testing in cases

where DNA evidence could demonstrate innocence

•

• Conversely, DNA evidence can be used to prove guilt

• Jan 2009, this man, Benjamin Watta, convicted of 1980 rape/murder of Simone Sharp in California

• Was already in prison for attempted murder of his former girlfriend

• “Cold Case” solved

•

•

•

•

• Can DNA technology resolve all problems with accuracy in convicting criminals?

• In order to be accurate, DNA testing must be done properly

–DNA must be stored properly

– Contamination of DNA samples can invalidate results

– Sometimes, if enough DNA evidence is available, defense and prosecution conduct

independent tests, to ensure accuracy

– Sometimes, shoddy lab work can also lead to wrongful conviction

• Can’t resolve all problems, but it’s a good and important start

–

• All for now, except for…

•

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10/4/2018

2

BIO 1101 Lec. 9, Part A (Guided Notes): Chapter 11 -- Gene Regulation

Gene Regulation

•

• An organism has many different kinds of cells the have different functions, but every body

cell has the _______________________

•

• If the DNA in every body cell is the same, how can cells be so different?

•

• An individual starts out as a single cell – a _________________

•

• That single cell divides by __________, making identical copies of itself

•

• As the organism continues to grow by mitosis, individual cells become ______________ –some genes become inactivated, while others are activated

• In this way, cells can become specialized

•

• The genes that are “__________________” are transcribed into mRNA, and then

translated into proteins

•

• Genes that are ___________________ aren’t transcribed or translated

•

• How does a cell turn on or off different genes?

Gene Regulation in Bacteria

• Bacteria can conserve resources by only expressing the genes they need

• E. coli bacteria can use the sugar ___________ as fuel if it is available in their environment

– Three enzymes needed to absorb and digest

– Genes located next to each other

– Genes that have related function and which can be simultaneously regulated form an

_______________

– E. coli have a _______________

•

•

• Control of an __________________

– _________________: a control sequence on DNA near the operon to which

____________________ can bind

– _________________: a sequence between the promoter and the genes of the operon;

_______________ can bind here to turn off transcription

• In the case of the lac operon, lactose interferes with the attachment of the lac

repressor to the operator; thus the presence of lactose turns on the operon

•

•

Gene Regulation in Eukarytoes

• In Eukaryotes (organisms other than bacteria and archea), several methods may be used:

– _________________: when DNA is in a condensed state (as when ready to divide), it

cannot be transcribed or translated

• Example: X chromosome inactivation in female cats

–

•

– Genes can be regulated at initiation of transcription

• Most important stage for regulating gene expression

• Most genes in eukaryotes, by default, are turned “______”

• Many proteins are involved in enhancing transcription of particular genes

• ______________ ______ are proteins that bind to enhancers and promoters of DNA

to activate multiple genes at the same time

• _____________________ may bind to DNA sequences called _______________ to inhibit transcription

•

• RNA Processing and Breakdown

– As we previously discussed, the initial mRNA transcript is edited to remove

____________ (intervening sequences) and __________ linked together before it leaves the nucleus and is translated

– Another way gene expression can be modified is through alternative ways of linking the

__________

• The exons of one gene may be linked in different ways to create different

__________________

– This is called _________________

•

•

– Not all RNAs code for protein

• Used to be considered “junk”

• Actually perform important functions

–microRNAs, for example

• miRNAs bind to one or more ____________

• Form a complex with mRNAs

• If the miRNA is complementary to the entire length of the mRNA, then the target mRNA is ________________

• If the miRNA is only complementary to a part of the target mRNA, then the complex

_______________________________________

–Other ways genes can be regulated:

•

• By breaking down mRNA in the cytoplasm

•

• By regulating translation

•

• By altering the proteins produced in translation

•

• By breaking down the produced proteins

• The process of forming proteins from a DNA molecule involves many steps

•

• At each step, there are opportunities for gene regulation

•

• Cell Signaling and Homeotic Genes

– In multicellular organisms, information must be communicated between cells

– Chemicals like ____________ can be secreted by one cell and signal some activity in another cell

– The signal molecule acts by binding to a ___________________ on the target cell, initiating a ___________________________

– The binding activates a series of _______________, which ultimately activates a

________________, triggering the transcription of a specific gene

•

– _________________ are “master control genes” that regulate the expression of other groups of genes

– These are crucial in the process of embryonic development, when cells use chemical

signals to coordinate development

– A well-studied example of homeotic genes and their effects on development is seen in

fruit flies

• Certain homeotic genes in the fruit fly determine where ______________________

develop on the body

• One homeotic gene, when active, triggers legs to form on cells in the mid-body; this genes is inactive in other parts of the body

• A mutation in this homeotic genes can result in flies with legs coming out of their heads, for example

• See video on experiments on homeotic genes in fruit flies:

https://www.youtube.com/watch?v=voQQ1dhCqZg

•

•

• 5-minute break

Cell Differentiation and the Science of Cloning

–

– Remember, the cells of an organism start out as undifferentiated – they have the

potential to become any type of cell

– As the organism grows, certain genes are turned on or left turned off, and the cell thus becomes differentiated

•

•

– Sometimes, cells that have become differentiated can “dedifferentiate” – allowing them

to grow into a new organism, or a new part of an organism

• Example: many plants can be propagated vegetatively

• Amphibians are famous for being able to re-generate lost limbs

•

• This process is relatively easy to do with plants

–Is used to make large numbers of “copies” of plants with desirable characteristics

• If a new organism is grown from the somatic (body) cells of an adult organism, the

result is a ____________ – it is genetically identical to the organism from whose cells it was grown

•

• _______________ = the production of identical copies of a cell, organism, or DNA molecule

–Doesn’t ONLY refer to making copies of entire organisms

–More common: cloning cells or molecules

– There are different types of cloning, and each has a different purpose

•

– “Reproductive Cloning”

•

• The egg of a female animal is extracted, its ______ is removed, and the DNA from a ___________ cell of the desired organism is placed into the egg

• After the egg divides and forms an early embryo, it can be implanted into a female

• Can be used to generate “copies” of desirable farm animals, or endangered species

•

•

•

• “Dolly” the sheep was the first mammal to be cloned (1997)

–Died in 2003 from a lung disease

–Was her relatively early death a result of cloning? Difficult to say, as lung diseases are

fairly common among sheep raised indoors…

• In January of 2018, it was reported that the first primates (macaques) were cloned

– https://www.youtube.com/watch?v=oEXleYs58MY

•

– Therapeutic Cloning is another type of cloning

• Purpose is to generate __________________ (ES cells)

• Can divide indefinitely in culture, and have the potential to develop into any type of cell

• Certain growth factors can induce these cells to differentiate into specific kinds of cells

• May be used to treat or cure diseases or injured organs

• For example, there has been some success using stem cells to treat stroke victims or Parkinson’s disease (inserting stem cells into brain)

• Embryonic stem cells are derived from embryos, and therein lies the controversy

•

– Adult stem cells are partially differentiated

• They may be able to differentiate into one of a few different types of cells, but are already set on a path to become one of a few types

• Less flexible than ES cells

• Example: stem cells in bone marrow can become any of the types of blood cells

• More difficult to culture in the lab

• Can be harvested from adults, so are less controversial

– New sources of stem cells…

• ______________________stem cells; can be created from somatic cells

Genetics of Cancer

• Cancer is the second-leading cause of death in industrialized countries; what causes it?

• __________________ – genes that cause cancer

• We carry many genes that are ____________________: that is, if changed in some way, they can turn into oncogenes

• Oncogenes can arise from insertion by a virus, or by mutation of a proto-oncogene

• Many _____________________ code for ______________________ – proteins that stimulate cell division

– Too much growth factor produced by a mutated gene can cause cancerous growth

• Some genes, called _____________________ genes, inhibit cell division

– If they are mutated, can also cause cancer

• _______________________ are substances that cause mutations to DNA that eventually lead to cancer

• Examples of carcinogens:

– UV radiation (sunlight or tanning beds); (skin cancer)

– Tobacco smoke (lung cancer)

– Alcohol (liver cancer)

• Prevention

•

– Compounds found in fruits and vegetables can reduce cancer risks

• __________________

– Can help reduce and repair DNA damage

– Some cancer-fighting foods include: cabbage, broccoli, brussels sprouts, kale, shiitake mushrooms, onions, red beans, cherries, raspberries, strawberries, blueberries, and

green tea

•

Bonus Activity

1. Explain how cells that look and behave so differently (like skin cells vs neurons) in the

same organism have the same genes.

2. What is an operon? Give an example.

3. A mutation in one gene may cause a major change in the body of a fruit fly, yet it takes many genes to produce a wing or leg. How can a change in one gene cause a big

change, like legs coming out of the head? What are such genes called?

4.

Lec. 9 Part B: Chapter 12 - Biotechnology

• DNA technology has wide variety of uses

• We will focus on genetic engineering and forensics (pg. 218-229)

Genetic Engineering

– Through __________________________, genes from different sources can be

combined

– Examples:

• Genes for specific protein products have been inserted into bacteria; the bacteria can then be grown and used to produce large quantities of the desired protein (e.g.

insulin)

• Proteins that can be used as vaccines can be produced by bacteria

•

• Genetically modified foods (e.g. “Bt” corn with built-in pesticide; “Golden Rice” with

enhanced nutritional value; tomatoes with a longer shelf life; etc.)

–GE crops introduced in 1996; now widely used; 93% of soy and 88% corn crops in

US were genetically modified (as of 2012)

–Primarily used in crops (insect resistance; herbicide tolerance)

•

•

• How is it done?

•

– Use of bacterial ________________ (circular pieces of DNA) as __________ (gene

carriers)

• ________________ are small circular pieces of DNA

• Bacteria readily take them in

• When a desired gene is inserted into a plasmid, the plasmid can then be isolated, and

then exposed to bacteria, which absorb them

• The bacteria will then express the desired gene in the modified plasmid

•

•

• How are genes inserted into plasmids?

•

– Cutting and Pasting Genes with ______________ Enzymes

• Restriction enzymes recognize short nucleotide sequences and cut the DNA at that site

• Staggered cut results in “_______________”

–A single-stranded piece of DNA at the end of the double-stranded molecule, which will readily connect with a complementary sticky end

• Fragments can then be stuck back together using ____________________

•

• In order to generate “sticky ends,” the recognition sequence must be a palindrome

– That is, the same sequence can be read from opposite directions on BOTH strands

– Example:

–

GAATTC

CTTAAG

•

• Gene of interest is now inserted into ___________

• ___________ is absorbed by bacteria, which express the ___________

• Bacteria can be readily grown to make many, many copies of the gene, or to synthesize

the protein encoded by the gene

• Most commonly, recombinant DNA technology is used to modify ___________

– Insect-resistant corn and cotton

– Rice that produces more vitamins

–Disease-resistant papya and sweet potatoes

•

• Some more unusual uses:

– Glowing pet fish

– Allergen-free cats

• Glowing Puppies!

– http://www.youtube.com/watch?v=YXPnQvcqHkg&feature=related

• Gene Editing

– __________________ system is a new technique that allows nucleotide sequences of

genes to be edited in living cells

• May be used to reveal function of a gene, or to even correct a mutation

– Bacteria have a protein called _________ that can identify and cut our viral DNA from

their genome

• Will cut any DNA sequence that is complementary to a specific sequence of guiding _______

• A Cas9 protein with an RNA molecule complementary to a particular gene may be used to cut out a gene from a cell’s chromosomes

• Random DNA nucleotides are then inserted into the chromosome by DNA repair

enzymes; this “___________” the gene, making in non-functional

• Can therefore determine what the gene did in the cell

• To edit a gene, researchers can add a segment of a normal gene along with the Cas9-guide RNA complex

• After Cas9 cuts the target DNA, repair enzymes use the normal DNA as a template to

repair the target DNA (for example, a mutated gene)

• This allows researchers to potentially fix genetic mutations

• Researchers have used CRISP-Cas9 to fix a genetic defects in mice

• Video: https://www.youtube.com/watch?v=52jOEPzhpzc

•

Bonus Activity

• CRISPR is an exciting new technology and researchers are racing to find ways to use it. Do a Google search and find a recent news article talking about how CRISPR is being used.

Read the article, and then write 2-3 sentences summarizing the article.

•

• Break…

Forensics

The “scientific analysis of evidence for crime scene investigations and other legal proceedings”

– __________________ is one technique used in forensics, to compare DNA samples

– Every individual’s genetic makeup is unique

– A person’s “DNA Fingerprint” is his/her unique collection of DNA fragments generated

when restriction enzymes are used to cut up the DNA

•

•

• How do you generate a DNA fingerprint?

• First, DNA evidence must be collected

– Various tissues, such as blood, semen, skin, etc.

• Before DNA Fingerprints can be generated, often the DNA sample must be _____________

– A tiny spec of blood can provide enough information to run a test, if the DNA in that

spec is copied many times

– The _______________________ is used to copy DNA

•

•

– Genomes are quite large, and typically scientists only need to amplify a small region of

the genome

– To amplify only a specific sequence, scientists use _____________, a short single-

stranded DNA molecule

– _____________ are selected that are complementary to only to the sequences at the ends of the target sequence

• The primers thus flank to target sequence, marking the beginning and end of the sequence to be copied

• Only the DNA between the primers is thus amplified

–

• _______________________ enzymes can then be used to cut the DNA into pieces

–Many different kinds of restriction enzymes

– Each recognizes a specific sequence and cuts DNA at that location

• May cut straight across both strands

• May make a “staggered” cut

• Although all humans are >99% genetically identical, the size of the human genome allows

for enough variation that differences can be detected

– About 3 billion base pairs in our DNA

– 1 in 1000 difference between any two people

–about 3 million differences between any two people

• When DNA samples from two different people are “digested” with the same restriction enzyme (or set of restriction enzymes), they will produce different numbers and sizes of

DNA fragments

– These different sets of DNA pieces are called “_________________________________”

• Differences (polymorphisms) in the size of the fragments of DNA created by the

restriction enzymes

• ____________________________ can then be used to separate the fragments by size

–DNA is ____________ charged (due to the ___________ groups)

– Electrical current causes the fragments of DNA to move through a “gel”

– ____________ pieces migrate faster than ____________ ones

– Results in a unique banding pattern

•

•

• Another technique commonly used in forensics is _________________ (STR) Analysis

–Much of the DNA between genes is composed of ____________ sequences (for

example, perhaps the sequence AGAT may be repeated 12 times)

– Non-coding

– Close relatives more likely to have more similar patterns of STRs

– Standard STR analysis in forensics tests ___ different markers

• Chances of two different people being identical at all 13 markers is between

__________________________________________________________________________________________________

Bonus Activity 2

1. A carrier that moves DNA from one cell to another, such as a plasmid, is called a ___________. Plasmids are small, circular pieces of DNA from ___________.

2. In making recombinant DNA, what is the benefit of using a restriction enzyme that cuts

DNA in a staggered fashion?

3. A paleontologist has recovered a bit of organic material from the 400-year-old preserved

skin of an extinct dodo. She would like to compare DNA from the sample with DNA from living birds. The most useful method for initially increasing the amount of dodo DNA for

testing is _____________________.

4. What feature of DNA causes it to move through a gel during gel electrophoresis?

DNA Evidence in the News…

•

• Use of DNA evidence in criminal cases is relatively new

– First case was in 1986 in England

• A man confessed to a series of rape/murders; DNA evidence indicated he did not; another person was identified as the actual murderer, based on DNA evidence

– First used in the US in ______________

• Man convicted of rape based on DNA obtained from semen found in victim

• Recently, a number of people on death row have been found not guilty based on DNA

evidence

–

•

•

• Fatal Flaws: The Case of Earl Washington

–Washington spent 18 years in prison

– Came within nine days of being put to death in Virginia's electric chair.

– Years later, DNA evidence proved he was innocent, and after a long legal battle, he was set free

–Washington had been convicted largely based on his own confession to a rape and

murder

• His defenders say the confession was coerced

• Washington was mentally handicapped

•

• DNA testing is increasingly being made available in criminal cases

• 32 states mandate that compensation be awarded to people wrongfully convicted (as of 2017)

• >________ people have been exonerated (from death row) using DNA testing since 1989

(when DNA testing first became available)

• In 2013 Oklahoma became 50th (and final) state to guarantee right to DNA testing in cases

where DNA evidence could demonstrate innocence

•

• Conversely, DNA evidence can be used to prove guilt

• Jan 2009, this man, Benjamin Watta, convicted of 1980 rape/murder of Simone Sharp in California

• Was already in prison for attempted murder of his former girlfriend

• “Cold Case” solved

•

•

•

•

• Can DNA technology resolve all problems with accuracy in convicting criminals?

• In order to be accurate, DNA testing must be done properly

–DNA must be stored properly

– Contamination of DNA samples can invalidate results

– Sometimes, if enough DNA evidence is available, defense and prosecution conduct

independent tests, to ensure accuracy

– Sometimes, shoddy lab work can also lead to wrongful conviction

• Can’t resolve all problems, but it’s a good and important start

–

• All for now, except for…

•

Random Animal of the Day!

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BIO 1101 Lec. 9, Part A (Guided Notes): Chapter 11 -- Gene Regulation

Gene Regulation

•

• An organism has many different kinds of cells the have different functions, but every body

cell has the _______________________

•

• If the DNA in every body cell is the same, how can cells be so different?

•

• An individual starts out as a single cell – a _________________

•

• That single cell divides by __________, making identical copies of itself

•

• As the organism continues to grow by mitosis, individual cells become ______________ –some genes become inactivated, while others are activated

• In this way, cells can become specialized

•

• The genes that are “__________________” are transcribed into mRNA, and then

translated into proteins

•

• Genes that are ___________________ aren’t transcribed or translated

•

• How does a cell turn on or off different genes?

Gene Regulation in Bacteria

• Bacteria can conserve resources by only expressing the genes they need

• E. coli bacteria can use the sugar ___________ as fuel if it is available in their environment

– Three enzymes needed to absorb and digest

– Genes located next to each other

– Genes that have related function and which can be simultaneously regulated form an

_______________

– E. coli have a _______________

•

•

• Control of an __________________

– _________________: a control sequence on DNA near the operon to which

____________________ can bind

– _________________: a sequence between the promoter and the genes of the operon;

_______________ can bind here to turn off transcription

• In the case of the lac operon, lactose interferes with the attachment of the lac

repressor to the operator; thus the presence of lactose turns on the operon

•

•

Gene Regulation in Eukarytoes

• In Eukaryotes (organisms other than bacteria and archea), several methods may be used:

– _________________: when DNA is in a condensed state (as when ready to divide), it

cannot be transcribed or translated

• Example: X chromosome inactivation in female cats

–

•

– Genes can be regulated at initiation of transcription

• Most important stage for regulating gene expression

• Most genes in eukaryotes, by default, are turned “______”

• Many proteins are involved in enhancing transcription of particular genes

• ______________ ______ are proteins that bind to enhancers and promoters of DNA

to activate multiple genes at the same time

• _____________________ may bind to DNA sequences called _______________ to inhibit transcription

•

• RNA Processing and Breakdown

– As we previously discussed, the initial mRNA transcript is edited to remove

____________ (intervening sequences) and __________ linked together before it leaves the nucleus and is translated

– Another way gene expression can be modified is through alternative ways of linking the

__________

• The exons of one gene may be linked in different ways to create different

__________________

– This is called _________________

•

•

– Not all RNAs code for protein

• Used to be considered “junk”

• Actually perform important functions

–microRNAs, for example

• miRNAs bind to one or more ____________

• Form a complex with mRNAs

• If the miRNA is complementary to the entire length of the mRNA, then the target

mRNA is ________________

• If the miRNA is only complementary to a part of the target mRNA, then the complex _______________________________________

–Other ways genes can be regulated:

•

• By breaking down mRNA in the cytoplasm

•

• By regulating translation

•

• By altering the proteins produced in translation

•

• By breaking down the produced proteins

• The process of forming proteins from a DNA molecule involves many steps

•

• At each step, there are opportunities for gene regulation

•

• Cell Signaling and Homeotic Genes

– In multicellular organisms, information must be communicated between cells

– Chemicals like ____________ can be secreted by one cell and signal some activity in another cell

– The signal molecule acts by binding to a ___________________ on the target cell, initiating a ___________________________

– The binding activates a series of _______________, which ultimately activates a

________________, triggering the transcription of a specific gene

•

– _________________ are “master control genes” that regulate the expression of other groups of genes

– These are crucial in the process of embryonic development, when cells use chemical

signals to coordinate development

– A well-studied example of homeotic genes and their effects on development is seen in

fruit flies

• Certain homeotic genes in the fruit fly determine where ______________________

develop on the body

• One homeotic gene, when active, triggers legs to form on cells in the mid-body; this genes is inactive in other parts of the body

• A mutation in this homeotic genes can result in flies with legs coming out of their

heads, for example

• See video on experiments on homeotic genes in fruit flies: https://www.youtube.com/watch?v=voQQ1dhCqZg

•

•

• 5-minute break

Cell Differentiation and the Science of Cloning

–

– Remember, the cells of an organism start out as undifferentiated – they have the potential to become any type of cell

– As the organism grows, certain genes are turned on or left turned off, and the cell thus becomes differentiated

•

•

– Sometimes, cells that have become differentiated can “dedifferentiate” – allowing them

to grow into a new organism, or a new part of an organism

• Example: many plants can be propagated vegetatively

• Amphibians are famous for being able to re-generate lost limbs

•

• This process is relatively easy to do with plants

–Is used to make large numbers of “copies” of plants with desirable characteristics

• If a new organism is grown from the somatic (body) cells of an adult organism, the

result is a ____________ – it is genetically identical to the organism from whose cells it was grown

•

• _______________ = the production of identical copies of a cell, organism, or DNA molecule

–Doesn’t ONLY refer to making copies of entire organisms

–More common: cloning cells or molecules

– There are different types of cloning, and each has a different purpose

•

– “Reproductive Cloning”

•

• The egg of a female animal is extracted, its ______ is removed, and the DNA from a ___________ cell of the desired organism is placed into the egg

• After the egg divides and forms an early embryo, it can be implanted into a female

• Can be used to generate “copies” of desirable farm animals, or endangered species

•

•

•

• “Dolly” the sheep was the first mammal to be cloned (1997)

–Died in 2003 from a lung disease

–Was her relatively early death a result of cloning? Difficult to say, as lung diseases are

fairly common among sheep raised indoors…

• In January of 2018, it was reported that the first primates (macaques) were cloned

– https://www.youtube.com/watch?v=oEXleYs58MY

•

– Therapeutic Cloning is another type of cloning

• Purpose is to generate __________________ (ES cells)

• Can divide indefinitely in culture, and have the potential to develop into any type of cell

• Certain growth factors can induce these cells to differentiate into specific kinds of cells

• May be used to treat or cure diseases or injured organs

• For example, there has been some success using stem cells to treat stroke victims or

Parkinson’s disease (inserting stem cells into brain)

• Embryonic stem cells are derived from embryos, and therein lies the controversy

•

– Adult stem cells are partially differentiated

• They may be able to differentiate into one of a few different types of cells, but are already set on a path to become one of a few types

• Less flexible than ES cells

• Example: stem cells in bone marrow can become any of the types of blood cells

• More difficult to culture in the lab

• Can be harvested from adults, so are less controversial

– New sources of stem cells…

• ______________________stem cells; can be created from somatic cells

Genetics of Cancer

• Cancer is the second-leading cause of death in industrialized countries; what causes it?

• __________________ – genes that cause cancer

• We carry many genes that are ____________________: that is, if changed in some way, they can turn into oncogenes

• Oncogenes can arise from insertion by a virus, or by mutation of a proto-oncogene

• Many _____________________ code for ______________________ – proteins that stimulate cell division

– Too much growth factor produced by a mutated gene can cause cancerous growth

• Some genes, called _____________________ genes, inhibit cell division

– If they are mutated, can also cause cancer

• _______________________ are substances that cause mutations to DNA that eventually lead to cancer

• Examples of carcinogens:

– UV radiation (sunlight or tanning beds); (skin cancer)

– Tobacco smoke (lung cancer)

– Alcohol (liver cancer)

• Prevention

•

– Compounds found in fruits and vegetables can reduce cancer risks

• __________________

– Can help reduce and repair DNA damage

– Some cancer-fighting foods include: cabbage, broccoli, brussels sprouts, kale, shiitake mushrooms, onions, red beans, cherries, raspberries, strawberries, blueberries, and green tea

•

Bonus Activity

1. Explain how cells that look and behave so differently (like skin cells vs neurons) in the

same organism have the same genes.

2. What is an operon? Give an example.

3. A mutation in one gene may cause a major change in the body of a fruit fly, yet it takes many genes to produce a wing or leg. How can a change in one gene cause a big

change, like legs coming out of the head? What are such genes called?

4.

Lec. 9 Part B: Chapter 12 - Biotechnology

• DNA technology has wide variety of uses

• We will focus on genetic engineering and forensics (pg. 218-229)

Genetic Engineering

– Through __________________________, genes from different sources can be

combined

– Examples:

• Genes for specific protein products have been inserted into bacteria; the bacteria can then be grown and used to produce large quantities of the desired protein (e.g.

insulin)

• Proteins that can be used as vaccines can be produced by bacteria

•

• Genetically modified foods (e.g. “Bt” corn with built-in pesticide; “Golden Rice” with

enhanced nutritional value; tomatoes with a longer shelf life; etc.)

–GE crops introduced in 1996; now widely used; 93% of soy and 88% corn crops in

US were genetically modified (as of 2012)

–Primarily used in crops (insect resistance; herbicide tolerance)

•

•

• How is it done?

•

– Use of bacterial ________________ (circular pieces of DNA) as __________ (gene

carriers)

• ________________ are small circular pieces of DNA

• Bacteria readily take them in

• When a desired gene is inserted into a plasmid, the plasmid can then be isolated, and

then exposed to bacteria, which absorb them

• The bacteria will then express the desired gene in the modified plasmid

•

•

• How are genes inserted into plasmids?

•

– Cutting and Pasting Genes with ______________ Enzymes

• Restriction enzymes recognize short nucleotide sequences and cut the DNA at that site

• Staggered cut results in “_______________”

–A single-stranded piece of DNA at the end of the double-stranded molecule, which will readily connect with a complementary sticky end

• Fragments can then be stuck back together using ____________________

•

• In order to generate “sticky ends,” the recognition sequence must be a palindrome

– That is, the same sequence can be read from opposite directions on BOTH strands

– Example:

–

GAATTC

CTTAAG

•

• Gene of interest is now inserted into ___________

• ___________ is absorbed by bacteria, which express the ___________

• Bacteria can be readily grown to make many, many copies of the gene, or to synthesize

the protein encoded by the gene

• Most commonly, recombinant DNA technology is used to modify ___________

– Insect-resistant corn and cotton

– Rice that produces more vitamins

–Disease-resistant papya and sweet potatoes

•

• Some more unusual uses:

– Glowing pet fish

– Allergen-free cats

• Glowing Puppies!

– http://www.youtube.com/watch?v=YXPnQvcqHkg&feature=related

• Gene Editing

– __________________ system is a new technique that allows nucleotide sequences of genes to be edited in living cells

• May be used to reveal function of a gene, or to even correct a mutation

– Bacteria have a protein called _________ that can identify and cut our viral DNA from

their genome

• Will cut any DNA sequence that is complementary to a specific sequence of guiding _______

• A Cas9 protein with an RNA molecule complementary to a particular gene may be used to cut out a gene from a cell’s chromosomes

• Random DNA nucleotides are then inserted into the chromosome by DNA repair

enzymes; this “___________” the gene, making in non-functional

• Can therefore determine what the gene did in the cell

• To edit a gene, researchers can add a segment of a normal gene along with the Cas9-guide RNA complex

• After Cas9 cuts the target DNA, repair enzymes use the normal DNA as a template to

repair the target DNA (for example, a mutated gene)

• This allows researchers to potentially fix genetic mutations

• Researchers have used CRISP-Cas9 to fix a genetic defects in mice

• Video: https://www.youtube.com/watch?v=52jOEPzhpzc

•

Bonus Activity

• CRISPR is an exciting new technology and researchers are racing to find ways to use it. Do a Google search and find a recent news article talking about how CRISPR is being used.

Read the article, and then write 2-3 sentences summarizing the article.

•

• Break…

Forensics

The “scientific analysis of evidence for crime scene investigations and other legal proceedings”

– __________________ is one technique used in forensics, to compare DNA samples

– Every individual’s genetic makeup is unique

– A person’s “DNA Fingerprint” is his/her unique collection of DNA fragments generated

when restriction enzymes are used to cut up the DNA

•

•

• How do you generate a DNA fingerprint?

• First, DNA evidence must be collected

– Various tissues, such as blood, semen, skin, etc.

• Before DNA Fingerprints can be generated, often the DNA sample must be _____________

– A tiny spec of blood can provide enough information to run a test, if the DNA in that spec is copied many times

– The _______________________ is used to copy DNA

•

•

– Genomes are quite large, and typically scientists only need to amplify a small region of

the genome

– To amplify only a specific sequence, scientists use _____________, a short single-

stranded DNA molecule

– _____________ are selected that are complementary to only to the sequences at the ends of the target sequence

• The primers thus flank to target sequence, marking the beginning and end of the sequence to be copied

• Only the DNA between the primers is thus amplified

–

• _______________________ enzymes can then be used to cut the DNA into pieces

–Many different kinds of restriction enzymes

– Each recognizes a specific sequence and cuts DNA at that location

• May cut straight across both strands

• May make a “staggered” cut

• Although all humans are >99% genetically identical, the size of the human genome allows

for enough variation that differences can be detected

– About 3 billion base pairs in our DNA

– 1 in 1000 difference between any two people

–about 3 million differences between any two people

• When DNA samples from two different people are “digested” with the same restriction enzyme (or set of restriction enzymes), they will produce different numbers and sizes of DNA fragments

– These different sets of DNA pieces are called “_________________________________”

• Differences (polymorphisms) in the size of the fragments of DNA created by the

restriction enzymes

• ____________________________ can then be used to separate the fragments by size

–DNA is ____________ charged (due to the ___________ groups)

– Electrical current causes the fragments of DNA to move through a “gel”

– ____________ pieces migrate faster than ____________ ones

– Results in a unique banding pattern

•

•

• Another technique commonly used in forensics is _________________ (STR) Analysis

–Much of the DNA between genes is composed of ____________ sequences (for

example, perhaps the sequence AGAT may be repeated 12 times)

– Non-coding

– Close relatives more likely to have more similar patterns of STRs

– Standard STR analysis in forensics tests ___ different markers

• Chances of two different people being identical at all 13 markers is between

__________________________________________________________________________________________________

Bonus Activity 2

1. A carrier that moves DNA from one cell to another, such as a plasmid, is called a ___________. Plasmids are small, circular pieces of DNA from ___________.

2. In making recombinant DNA, what is the benefit of using a restriction enzyme that cuts

DNA in a staggered fashion?

3. A paleontologist has recovered a bit of organic material from the 400-year-old preserved

skin of an extinct dodo. She would like to compare DNA from the sample with DNA from living birds. The most useful method for initially increasing the amount of dodo DNA for

testing is _____________________.

4. What feature of DNA causes it to move through a gel during gel electrophoresis?

DNA Evidence in the News…

•

• Use of DNA evidence in criminal cases is relatively new

– First case was in 1986 in England

• A man confessed to a series of rape/murders; DNA evidence indicated he did not; another person was identified as the actual murderer, based on DNA evidence

– First used in the US in ______________

• Man convicted of rape based on DNA obtained from semen found in victim

• Recently, a number of people on death row have been found not guilty based on DNA

evidence

–

•

•

• Fatal Flaws: The Case of Earl Washington

–Washington spent 18 years in prison

– Came within nine days of being put to death in Virginia's electric chair.

– Years later, DNA evidence proved he was innocent, and after a long legal battle, he was set free

–Washington had been convicted largely based on his own confession to a rape and

murder

• His defenders say the confession was coerced

• Washington was mentally handicapped

•

• DNA testing is increasingly being made available in criminal cases

• 32 states mandate that compensation be awarded to people wrongfully convicted (as of 2017)

• >________ people have been exonerated (from death row) using DNA testing since 1989

(when DNA testing first became available)

• In 2013 Oklahoma became 50th (and final) state to guarantee right to DNA testing in cases

where DNA evidence could demonstrate innocence

•

• Conversely, DNA evidence can be used to prove guilt

• Jan 2009, this man, Benjamin Watta, convicted of 1980 rape/murder of Simone Sharp in California

• Was already in prison for attempted murder of his former girlfriend

• “Cold Case” solved

•

•

•

•

• Can DNA technology resolve all problems with accuracy in convicting criminals?

• In order to be accurate, DNA testing must be done properly

–DNA must be stored properly

– Contamination of DNA samples can invalidate results

– Sometimes, if enough DNA evidence is available, defense and prosecution conduct

independent tests, to ensure accuracy

– Sometimes, shoddy lab work can also lead to wrongful conviction

• Can’t resolve all problems, but it’s a good and important start

–

• All for now, except for…

•

Random Animal of the Day!

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10/4/2018

4

BIO 1101 Lec. 9, Part A (Guided Notes): Chapter 11 -- Gene Regulation

Gene Regulation

•

• An organism has many different kinds of cells the have different functions, but every body

cell has the _______________________

•

• If the DNA in every body cell is the same, how can cells be so different?

•

• An individual starts out as a single cell – a _________________

•

• That single cell divides by __________, making identical copies of itself

•

• As the organism continues to grow by mitosis, individual cells become ______________ –some genes become inactivated, while others are activated

• In this way, cells can become specialized

•

• The genes that are “__________________” are transcribed into mRNA, and then

translated into proteins

•

• Genes that are ___________________ aren’t transcribed or translated

•

• How does a cell turn on or off different genes?

Gene Regulation in Bacteria

• Bacteria can conserve resources by only expressing the genes they need

• E. coli bacteria can use the sugar ___________ as fuel if it is available in their environment

– Three enzymes needed to absorb and digest

– Genes located next to each other

– Genes that have related function and which can be simultaneously regulated form an

_______________

– E. coli have a _______________

•

•

• Control of an __________________

– _________________: a control sequence on DNA near the operon to which

____________________ can bind

– _________________: a sequence between the promoter and the genes of the operon;

_______________ can bind here to turn off transcription

• In the case of the lac operon, lactose interferes with the attachment of the lac

repressor to the operator; thus the presence of lactose turns on the operon

•

•

Gene Regulation in Eukarytoes

• In Eukaryotes (organisms other than bacteria and archea), several methods may be used:

– _________________: when DNA is in a condensed state (as when ready to divide), it

cannot be transcribed or translated

• Example: X chromosome inactivation in female cats

–

•

– Genes can be regulated at initiation of transcription

• Most important stage for regulating gene expression

• Most genes in eukaryotes, by default, are turned “______”

• Many proteins are involved in enhancing transcription of particular genes

• ______________ ______ are proteins that bind to enhancers and promoters of DNA

to activate multiple genes at the same time

• _____________________ may bind to DNA sequences called _______________ to inhibit transcription

•

• RNA Processing and Breakdown

– As we previously discussed, the initial mRNA transcript is edited to remove ____________ (intervening sequences) and __________ linked together before it leaves the nucleus and is translated

– Another way gene expression can be modified is through alternative ways of linking the

__________

• The exons of one gene may be linked in different ways to create different

__________________

– This is called _________________

•

•

– Not all RNAs code for protein

• Used to be considered “junk”

• Actually perform important functions

–microRNAs, for example

• miRNAs bind to one or more ____________

• Form a complex with mRNAs

• If the miRNA is complementary to the entire length of the mRNA, then the target

mRNA is ________________

• If the miRNA is only complementary to a part of the target mRNA, then the complex

_______________________________________

–Other ways genes can be regulated:

•

• By breaking down mRNA in the cytoplasm

•

• By regulating translation

•

• By altering the proteins produced in translation

•

• By breaking down the produced proteins

• The process of forming proteins from a DNA molecule involves many steps

•

• At each step, there are opportunities for gene regulation

•

• Cell Signaling and Homeotic Genes

– In multicellular organisms, information must be communicated between cells

– Chemicals like ____________ can be secreted by one cell and signal some activity in another cell

– The signal molecule acts by binding to a ___________________ on the target cell, initiating a ___________________________

– The binding activates a series of _______________, which ultimately activates a

________________, triggering the transcription of a specific gene

•

– _________________ are “master control genes” that regulate the expression of other groups of genes

– These are crucial in the process of embryonic development, when cells use chemical signals to coordinate development

– A well-studied example of homeotic genes and their effects on development is seen in

fruit flies

• Certain homeotic genes in the fruit fly determine where ______________________

develop on the body

• One homeotic gene, when active, triggers legs to form on cells in the mid-body; this genes is inactive in other parts of the body

• A mutation in this homeotic genes can result in flies with legs coming out of their

heads, for example

• See video on experiments on homeotic genes in fruit flies:

https://www.youtube.com/watch?v=voQQ1dhCqZg

•

•

• 5-minute break

Cell Differentiation and the Science of Cloning

–

– Remember, the cells of an organism start out as undifferentiated – they have the

potential to become any type of cell

– As the organism grows, certain genes are turned on or left turned off, and the cell thus becomes differentiated

•

•

– Sometimes, cells that have become differentiated can “dedifferentiate” – allowing them

to grow into a new organism, or a new part of an organism

• Example: many plants can be propagated vegetatively

• Amphibians are famous for being able to re-generate lost limbs

•

• This process is relatively easy to do with plants

–Is used to make large numbers of “copies” of plants with desirable characteristics

• If a new organism is grown from the somatic (body) cells of an adult organism, the

result is a ____________ – it is genetically identical to the organism from whose cells it was grown

•

• _______________ = the production of identical copies of a cell, organism, or DNA molecule

–Doesn’t ONLY refer to making copies of entire organisms

–More common: cloning cells or molecules

– There are different types of cloning, and each has a different purpose

•

– “Reproductive Cloning”

•

• The egg of a female animal is extracted, its ______ is removed, and the DNA from a ___________ cell of the desired organism is placed into the egg

• After the egg divides and forms an early embryo, it can be implanted into a female

• Can be used to generate “copies” of desirable farm animals, or endangered species

•

•

•

• “Dolly” the sheep was the first mammal to be cloned (1997)

–Died in 2003 from a lung disease

–Was her relatively early death a result of cloning? Difficult to say, as lung diseases are

fairly common among sheep raised indoors…

• In January of 2018, it was reported that the first primates (macaques) were cloned

– https://www.youtube.com/watch?v=oEXleYs58MY

•

– Therapeutic Cloning is another type of cloning

• Purpose is to generate __________________ (ES cells)

• Can divide indefinitely in culture, and have the potential to develop into any type of cell

• Certain growth factors can induce these cells to differentiate into specific kinds of cells

• May be used to treat or cure diseases or injured organs

• For example, there has been some success using stem cells to treat stroke victims or

Parkinson’s disease (inserting stem cells into brain)

• Embryonic stem cells are derived from embryos, and therein lies the controversy

•

– Adult stem cells are partially differentiated

• They may be able to differentiate into one of a few different types of cells, but are already set on a path to become one of a few types

• Less flexible than ES cells

• Example: stem cells in bone marrow can become any of the types of blood cells

• More difficult to culture in the lab

• Can be harvested from adults, so are less controversial

– New sources of stem cells…

• ______________________stem cells; can be created from somatic cells

Genetics of Cancer

• Cancer is the second-leading cause of death in industrialized countries; what causes it?

• __________________ – genes that cause cancer

• We carry many genes that are ____________________: that is, if changed in some way, they can turn into oncogenes

• Oncogenes can arise from insertion by a virus, or by mutation of a proto-oncogene

• Many _____________________ code for ______________________ – proteins that stimulate cell division

– Too much growth factor produced by a mutated gene can cause cancerous growth

• Some genes, called _____________________ genes, inhibit cell division

– If they are mutated, can also cause cancer

• _______________________ are substances that cause mutations to DNA that eventually lead to cancer

• Examples of carcinogens:

– UV radiation (sunlight or tanning beds); (skin cancer)

– Tobacco smoke (lung cancer)

– Alcohol (liver cancer)

• Prevention

•

– Compounds found in fruits and vegetables can reduce cancer risks

• __________________

– Can help reduce and repair DNA damage

– Some cancer-fighting foods include: cabbage, broccoli, brussels sprouts, kale, shiitake mushrooms, onions, red beans, cherries, raspberries, strawberries, blueberries, and

green tea

•

Bonus Activity

1. Explain how cells that look and behave so differently (like skin cells vs neurons) in the

same organism have the same genes.

2. What is an operon? Give an example.

3. A mutation in one gene may cause a major change in the body of a fruit fly, yet it takes many genes to produce a wing or leg. How can a change in one gene cause a big

change, like legs coming out of the head? What are such genes called?

4.

Lec. 9 Part B: Chapter 12 - Biotechnology

• DNA technology has wide variety of uses

• We will focus on genetic engineering and forensics (pg. 218-229)

Genetic Engineering

– Through __________________________, genes from different sources can be

combined

– Examples:

• Genes for specific protein products have been inserted into bacteria; the bacteria can then be grown and used to produce large quantities of the desired protein (e.g.

insulin)

• Proteins that can be used as vaccines can be produced by bacteria

•

• Genetically modified foods (e.g. “Bt” corn with built-in pesticide; “Golden Rice” with

enhanced nutritional value; tomatoes with a longer shelf life; etc.)

–GE crops introduced in 1996; now widely used; 93% of soy and 88% corn crops in

US were genetically modified (as of 2012)

–Primarily used in crops (insect resistance; herbicide tolerance)

•

•

• How is it done?

•

– Use of bacterial ________________ (circular pieces of DNA) as __________ (gene

carriers)

• ________________ are small circular pieces of DNA

• Bacteria readily take them in

• When a desired gene is inserted into a plasmid, the plasmid can then be isolated, and

then exposed to bacteria, which absorb them

• The bacteria will then express the desired gene in the modified plasmid

•

•

• How are genes inserted into plasmids?

•

– Cutting and Pasting Genes with ______________ Enzymes

• Restriction enzymes recognize short nucleotide sequences and cut the DNA at that site

• Staggered cut results in “_______________”

–A single-stranded piece of DNA at the end of the double-stranded molecule, which will readily connect with a complementary sticky end

• Fragments can then be stuck back together using ____________________

•

• In order to generate “sticky ends,” the recognition sequence must be a palindrome

– That is, the same sequence can be read from opposite directions on BOTH strands

– Example:

–

GAATTC

CTTAAG

•

• Gene of interest is now inserted into ___________

• ___________ is absorbed by bacteria, which express the ___________

• Bacteria can be readily grown to make many, many copies of the gene, or to synthesize

the protein encoded by the gene

• Most commonly, recombinant DNA technology is used to modify ___________

– Insect-resistant corn and cotton

– Rice that produces more vitamins

–Disease-resistant papya and sweet potatoes

•

• Some more unusual uses:

– Glowing pet fish

– Allergen-free cats

• Glowing Puppies!

– http://www.youtube.com/watch?v=YXPnQvcqHkg&feature=related

• Gene Editing

– __________________ system is a new technique that allows nucleotide sequences of

genes to be edited in living cells

• May be used to reveal function of a gene, or to even correct a mutation

– Bacteria have a protein called _________ that can identify and cut our viral DNA from

their genome

• Will cut any DNA sequence that is complementary to a specific sequence of guiding _______

• A Cas9 protein with an RNA molecule complementary to a particular gene may be used to cut out a gene from a cell’s chromosomes

• Random DNA nucleotides are then inserted into the chromosome by DNA repair

enzymes; this “___________” the gene, making in non-functional

• Can therefore determine what the gene did in the cell

• To edit a gene, researchers can add a segment of a normal gene along with the Cas9-guide RNA complex

• After Cas9 cuts the target DNA, repair enzymes use the normal DNA as a template to

repair the target DNA (for example, a mutated gene)

• This allows researchers to potentially fix genetic mutations

• Researchers have used CRISP-Cas9 to fix a genetic defects in mice

• Video: https://www.youtube.com/watch?v=52jOEPzhpzc

•

Bonus Activity

• CRISPR is an exciting new technology and researchers are racing to find ways to use it. Do a Google search and find a recent news article talking about how CRISPR is being used.

Read the article, and then write 2-3 sentences summarizing the article.

•

• Break…

Forensics

The “scientific analysis of evidence for crime scene investigations and other legal proceedings”

– __________________ is one technique used in forensics, to compare DNA samples

– Every individual’s genetic makeup is unique

– A person’s “DNA Fingerprint” is his/her unique collection of DNA fragments generated when restriction enzymes are used to cut up the DNA

•

•

• How do you generate a DNA fingerprint?

• First, DNA evidence must be collected

– Various tissues, such as blood, semen, skin, etc.

• Before DNA Fingerprints can be generated, often the DNA sample must be _____________

– A tiny spec of blood can provide enough information to run a test, if the DNA in that

spec is copied many times

– The _______________________ is used to copy DNA

•

•

– Genomes are quite large, and typically scientists only need to amplify a small region of

the genome

– To amplify only a specific sequence, scientists use _____________, a short single-

stranded DNA molecule

– _____________ are selected that are complementary to only to the sequences at the ends of the target sequence

• The primers thus flank to target sequence, marking the beginning and end of the sequence to be copied

• Only the DNA between the primers is thus amplified

–

• _______________________ enzymes can then be used to cut the DNA into pieces

–Many different kinds of restriction enzymes

– Each recognizes a specific sequence and cuts DNA at that location

• May cut straight across both strands

• May make a “staggered” cut

• Although all humans are >99% genetically identical, the size of the human genome allows

for enough variation that differences can be detected

– About 3 billion base pairs in our DNA

– 1 in 1000 difference between any two people

–about 3 million differences between any two people

• When DNA samples from two different people are “digested” with the same restriction enzyme (or set of restriction enzymes), they will produce different numbers and sizes of

DNA fragments

– These different sets of DNA pieces are called “_________________________________”

• Differences (polymorphisms) in the size of the fragments of DNA created by the

restriction enzymes

• ____________________________ can then be used to separate the fragments by size

–DNA is ____________ charged (due to the ___________ groups)

– Electrical current causes the fragments of DNA to move through a “gel”

– ____________ pieces migrate faster than ____________ ones

– Results in a unique banding pattern

•

•

• Another technique commonly used in forensics is _________________ (STR) Analysis

–Much of the DNA between genes is composed of ____________ sequences (for example, perhaps the sequence AGAT may be repeated 12 times)

– Non-coding

– Close relatives more likely to have more similar patterns of STRs

– Standard STR analysis in forensics tests ___ different markers

• Chances of two different people being identical at all 13 markers is between

__________________________________________________________________________________________________

Bonus Activity 2

1. A carrier that moves DNA from one cell to another, such as a plasmid, is called a ___________. Plasmids are small, circular pieces of DNA from ___________.

2. In making recombinant DNA, what is the benefit of using a restriction enzyme that cuts DNA in a staggered fashion?

3. A paleontologist has recovered a bit of organic material from the 400-year-old preserved

skin of an extinct dodo. She would like to compare DNA from the sample with DNA from living birds. The most useful method for initially increasing the amount of dodo DNA for

testing is _____________________.

4. What feature of DNA causes it to move through a gel during gel electrophoresis?

DNA Evidence in the News…

•

• Use of DNA evidence in criminal cases is relatively new

– First case was in 1986 in England

• A man confessed to a series of rape/murders; DNA evidence indicated he did not; another person was identified as the actual murderer, based on DNA evidence

– First used in the US in ______________

• Man convicted of rape based on DNA obtained from semen found in victim

• Recently, a number of people on death row have been found not guilty based on DNA

evidence

–

•

•

• Fatal Flaws: The Case of Earl Washington

–Washington spent 18 years in prison

– Came within nine days of being put to death in Virginia's electric chair.

– Years later, DNA evidence proved he was innocent, and after a long legal battle, he was set free

–Washington had been convicted largely based on his own confession to a rape and

murder

• His defenders say the confession was coerced

• Washington was mentally handicapped

•

• DNA testing is increasingly being made available in criminal cases

• 32 states mandate that compensation be awarded to people wrongfully convicted (as of 2017)

• >________ people have been exonerated (from death row) using DNA testing since 1989

(when DNA testing first became available)

• In 2013 Oklahoma became 50th (and final) state to guarantee right to DNA testing in cases

where DNA evidence could demonstrate innocence

•

• Conversely, DNA evidence can be used to prove guilt

• Jan 2009, this man, Benjamin Watta, convicted of 1980 rape/murder of Simone Sharp in California

• Was already in prison for attempted murder of his former girlfriend

• “Cold Case” solved

•

•

•

•

• Can DNA technology resolve all problems with accuracy in convicting criminals?

• In order to be accurate, DNA testing must be done properly

–DNA must be stored properly

– Contamination of DNA samples can invalidate results

– Sometimes, if enough DNA evidence is available, defense and prosecution conduct

independent tests, to ensure accuracy

– Sometimes, shoddy lab work can also lead to wrongful conviction

• Can’t resolve all problems, but it’s a good and important start

–

• All for now, except for…

•

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10/4/2018

5

BIO 1101 Lec. 9, Part A (Guided Notes): Chapter 11 -- Gene Regulation

Gene Regulation

•

• An organism has many different kinds of cells the have different functions, but every body

cell has the _______________________

•

• If the DNA in every body cell is the same, how can cells be so different?

•

• An individual starts out as a single cell – a _________________

•

• That single cell divides by __________, making identical copies of itself

•

• As the organism continues to grow by mitosis, individual cells become ______________ –some genes become inactivated, while others are activated

• In this way, cells can become specialized

•

• The genes that are “__________________” are transcribed into mRNA, and then

translated into proteins

•

• Genes that are ___________________ aren’t transcribed or translated

•

• How does a cell turn on or off different genes?

Gene Regulation in Bacteria

• Bacteria can conserve resources by only expressing the genes they need

• E. coli bacteria can use the sugar ___________ as fuel if it is available in their environment

– Three enzymes needed to absorb and digest

– Genes located next to each other

– Genes that have related function and which can be simultaneously regulated form an

_______________

– E. coli have a _______________

•

•

• Control of an __________________

– _________________: a control sequence on DNA near the operon to which

____________________ can bind

– _________________: a sequence between the promoter and the genes of the operon;

_______________ can bind here to turn off transcription

• In the case of the lac operon, lactose interferes with the attachment of the lac

repressor to the operator; thus the presence of lactose turns on the operon

•

•

Gene Regulation in Eukarytoes

• In Eukaryotes (organisms other than bacteria and archea), several methods may be used:

– _________________: when DNA is in a condensed state (as when ready to divide), it

cannot be transcribed or translated

• Example: X chromosome inactivation in female cats

–

•

– Genes can be regulated at initiation of transcription

• Most important stage for regulating gene expression

• Most genes in eukaryotes, by default, are turned “______”

• Many proteins are involved in enhancing transcription of particular genes

• ______________ ______ are proteins that bind to enhancers and promoters of DNA

to activate multiple genes at the same time

• _____________________ may bind to DNA sequences called _______________ to inhibit transcription

•

• RNA Processing and Breakdown

– As we previously discussed, the initial mRNA transcript is edited to remove

____________ (intervening sequences) and __________ linked together before it leaves the nucleus and is translated

– Another way gene expression can be modified is through alternative ways of linking the

__________

• The exons of one gene may be linked in different ways to create different

__________________

– This is called _________________

•

•

– Not all RNAs code for protein

• Used to be considered “junk”

• Actually perform important functions

–microRNAs, for example

• miRNAs bind to one or more ____________

• Form a complex with mRNAs

• If the miRNA is complementary to the entire length of the mRNA, then the target

mRNA is ________________

• If the miRNA is only complementary to a part of the target mRNA, then the complex

_______________________________________

–Other ways genes can be regulated:

•

• By breaking down mRNA in the cytoplasm

•

• By regulating translation

•

• By altering the proteins produced in translation

•

• By breaking down the produced proteins

• The process of forming proteins from a DNA molecule involves many steps

•

• At each step, there are opportunities for gene regulation

•

• Cell Signaling and Homeotic Genes

– In multicellular organisms, information must be communicated between cells

– Chemicals like ____________ can be secreted by one cell and signal some activity in another cell

– The signal molecule acts by binding to a ___________________ on the target cell, initiating a ___________________________

– The binding activates a series of _______________, which ultimately activates a

________________, triggering the transcription of a specific gene

•

– _________________ are “master control genes” that regulate the expression of other groups of genes

– These are crucial in the process of embryonic development, when cells use chemical

signals to coordinate development

– A well-studied example of homeotic genes and their effects on development is seen in fruit flies

• Certain homeotic genes in the fruit fly determine where ______________________

develop on the body

• One homeotic gene, when active, triggers legs to form on cells in the mid-body; this genes is inactive in other parts of the body

• A mutation in this homeotic genes can result in flies with legs coming out of their

heads, for example

• See video on experiments on homeotic genes in fruit flies:

https://www.youtube.com/watch?v=voQQ1dhCqZg

•

•

• 5-minute break

Cell Differentiation and the Science of Cloning

–

– Remember, the cells of an organism start out as undifferentiated – they have the

potential to become any type of cell

– As the organism grows, certain genes are turned on or left turned off, and the cell thus becomes differentiated

•

•

– Sometimes, cells that have become differentiated can “dedifferentiate” – allowing them

to grow into a new organism, or a new part of an organism

• Example: many plants can be propagated vegetatively

• Amphibians are famous for being able to re-generate lost limbs

•

• This process is relatively easy to do with plants

–Is used to make large numbers of “copies” of plants with desirable characteristics

• If a new organism is grown from the somatic (body) cells of an adult organism, the

result is a ____________ – it is genetically identical to the organism from whose cells it was grown

•

• _______________ = the production of identical copies of a cell, organism, or DNA molecule

–Doesn’t ONLY refer to making copies of entire organisms

–More common: cloning cells or molecules

– There are different types of cloning, and each has a different purpose

•

– “Reproductive Cloning”

•

• The egg of a female animal is extracted, its ______ is removed, and the DNA from a ___________ cell of the desired organism is placed into the egg

• After the egg divides and forms an early embryo, it can be implanted into a female

• Can be used to generate “copies” of desirable farm animals, or endangered species

•

•

•

• “Dolly” the sheep was the first mammal to be cloned (1997)

–Died in 2003 from a lung disease

–Was her relatively early death a result of cloning? Difficult to say, as lung diseases are

fairly common among sheep raised indoors…

• In January of 2018, it was reported that the first primates (macaques) were cloned

– https://www.youtube.com/watch?v=oEXleYs58MY

•

– Therapeutic Cloning is another type of cloning

• Purpose is to generate __________________ (ES cells)

• Can divide indefinitely in culture, and have the potential to develop into any type of cell

• Certain growth factors can induce these cells to differentiate into specific kinds of cells

• May be used to treat or cure diseases or injured organs

• For example, there has been some success using stem cells to treat stroke victims or

Parkinson’s disease (inserting stem cells into brain)

• Embryonic stem cells are derived from embryos, and therein lies the controversy

•

– Adult stem cells are partially differentiated

• They may be able to differentiate into one of a few different types of cells, but are already set on a path to become one of a few types

• Less flexible than ES cells

• Example: stem cells in bone marrow can become any of the types of blood cells

• More difficult to culture in the lab

• Can be harvested from adults, so are less controversial

– New sources of stem cells…

• ______________________stem cells; can be created from somatic cells

Genetics of Cancer

• Cancer is the second-leading cause of death in industrialized countries; what causes it?

• __________________ – genes that cause cancer

• We carry many genes that are ____________________: that is, if changed in some way, they can turn into oncogenes

• Oncogenes can arise from insertion by a virus, or by mutation of a proto-oncogene

• Many _____________________ code for ______________________ – proteins that stimulate cell division

– Too much growth factor produced by a mutated gene can cause cancerous growth

• Some genes, called _____________________ genes, inhibit cell division

– If they are mutated, can also cause cancer

• _______________________ are substances that cause mutations to DNA that eventually lead to cancer

• Examples of carcinogens:

– UV radiation (sunlight or tanning beds); (skin cancer)

– Tobacco smoke (lung cancer)

– Alcohol (liver cancer)

• Prevention

•

– Compounds found in fruits and vegetables can reduce cancer risks

• __________________

– Can help reduce and repair DNA damage

– Some cancer-fighting foods include: cabbage, broccoli, brussels sprouts, kale, shiitake mushrooms, onions, red beans, cherries, raspberries, strawberries, blueberries, and

green tea

•

Bonus Activity

1. Explain how cells that look and behave so differently (like skin cells vs neurons) in the same organism have the same genes.

2. What is an operon? Give an example.

3. A mutation in one gene may cause a major change in the body of a fruit fly, yet it takes many genes to produce a wing or leg. How can a change in one gene cause a big

change, like legs coming out of the head? What are such genes called?

4.

Lec. 9 Part B: Chapter 12 - Biotechnology

• DNA technology has wide variety of uses

• We will focus on genetic engineering and forensics (pg. 218-229)

Genetic Engineering

– Through __________________________, genes from different sources can be

combined

– Examples:

• Genes for specific protein products have been inserted into bacteria; the bacteria can then be grown and used to produce large quantities of the desired protein (e.g.

insulin)

• Proteins that can be used as vaccines can be produced by bacteria

•

• Genetically modified foods (e.g. “Bt” corn with built-in pesticide; “Golden Rice” with

enhanced nutritional value; tomatoes with a longer shelf life; etc.)

–GE crops introduced in 1996; now widely used; 93% of soy and 88% corn crops in

US were genetically modified (as of 2012)

–Primarily used in crops (insect resistance; herbicide tolerance)

•

•

• How is it done?

•

– Use of bacterial ________________ (circular pieces of DNA) as __________ (gene carriers)

• ________________ are small circular pieces of DNA

• Bacteria readily take them in

• When a desired gene is inserted into a plasmid, the plasmid can then be isolated, and

then exposed to bacteria, which absorb them

• The bacteria will then express the desired gene in the modified plasmid

•

•

• How are genes inserted into plasmids?

•

– Cutting and Pasting Genes with ______________ Enzymes

• Restriction enzymes recognize short nucleotide sequences and cut the DNA at that site

• Staggered cut results in “_______________”

–A single-stranded piece of DNA at the end of the double-stranded molecule, which will readily connect with a complementary sticky end

• Fragments can then be stuck back together using ____________________

•

• In order to generate “sticky ends,” the recognition sequence must be a palindrome

– That is, the same sequence can be read from opposite directions on BOTH strands

– Example:

–

GAATTC

CTTAAG

•

• Gene of interest is now inserted into ___________

• ___________ is absorbed by bacteria, which express the ___________

• Bacteria can be readily grown to make many, many copies of the gene, or to synthesize

the protein encoded by the gene

• Most commonly, recombinant DNA technology is used to modify ___________

– Insect-resistant corn and cotton

– Rice that produces more vitamins

–Disease-resistant papya and sweet potatoes

•

• Some more unusual uses:

– Glowing pet fish

– Allergen-free cats

• Glowing Puppies!

– http://www.youtube.com/watch?v=YXPnQvcqHkg&feature=related

• Gene Editing

– __________________ system is a new technique that allows nucleotide sequences of

genes to be edited in living cells

• May be used to reveal function of a gene, or to even correct a mutation

– Bacteria have a protein called _________ that can identify and cut our viral DNA from

their genome

• Will cut any DNA sequence that is complementary to a specific sequence of guiding _______

• A Cas9 protein with an RNA molecule complementary to a particular gene may be used to cut out a gene from a cell’s chromosomes

• Random DNA nucleotides are then inserted into the chromosome by DNA repair

enzymes; this “___________” the gene, making in non-functional

• Can therefore determine what the gene did in the cell

• To edit a gene, researchers can add a segment of a normal gene along with the Cas9-guide RNA complex

• After Cas9 cuts the target DNA, repair enzymes use the normal DNA as a template to repair the target DNA (for example, a mutated gene)

• This allows researchers to potentially fix genetic mutations

• Researchers have used CRISP-Cas9 to fix a genetic defects in mice

• Video: https://www.youtube.com/watch?v=52jOEPzhpzc

•

Bonus Activity

• CRISPR is an exciting new technology and researchers are racing to find ways to use it. Do a Google search and find a recent news article talking about how CRISPR is being used.

Read the article, and then write 2-3 sentences summarizing the article.

•

• Break…

Forensics

The “scientific analysis of evidence for crime scene investigations and other legal proceedings”

– __________________ is one technique used in forensics, to compare DNA samples

– Every individual’s genetic makeup is unique

– A person’s “DNA Fingerprint” is his/her unique collection of DNA fragments generated

when restriction enzymes are used to cut up the DNA

•

•

• How do you generate a DNA fingerprint?

• First, DNA evidence must be collected

– Various tissues, such as blood, semen, skin, etc.

• Before DNA Fingerprints can be generated, often the DNA sample must be _____________

– A tiny spec of blood can provide enough information to run a test, if the DNA in that

spec is copied many times

– The _______________________ is used to copy DNA

•

•

– Genomes are quite large, and typically scientists only need to amplify a small region of

the genome

– To amplify only a specific sequence, scientists use _____________, a short single-

stranded DNA molecule

– _____________ are selected that are complementary to only to the sequences at the ends of the target sequence

• The primers thus flank to target sequence, marking the beginning and end of the sequence to be copied

• Only the DNA between the primers is thus amplified

–

• _______________________ enzymes can then be used to cut the DNA into pieces

–Many different kinds of restriction enzymes

– Each recognizes a specific sequence and cuts DNA at that location

• May cut straight across both strands

• May make a “staggered” cut

• Although all humans are >99% genetically identical, the size of the human genome allows for enough variation that differences can be detected

– About 3 billion base pairs in our DNA

– 1 in 1000 difference between any two people

–about 3 million differences between any two people

• When DNA samples from two different people are “digested” with the same restriction enzyme (or set of restriction enzymes), they will produce different numbers and sizes of

DNA fragments

– These different sets of DNA pieces are called “_________________________________”

• Differences (polymorphisms) in the size of the fragments of DNA created by the

restriction enzymes

• ____________________________ can then be used to separate the fragments by size

–DNA is ____________ charged (due to the ___________ groups)

– Electrical current causes the fragments of DNA to move through a “gel”

– ____________ pieces migrate faster than ____________ ones

– Results in a unique banding pattern

•

•

• Another technique commonly used in forensics is _________________ (STR) Analysis

–Much of the DNA between genes is composed of ____________ sequences (for

example, perhaps the sequence AGAT may be repeated 12 times)

– Non-coding

– Close relatives more likely to have more similar patterns of STRs

– Standard STR analysis in forensics tests ___ different markers

• Chances of two different people being identical at all 13 markers is between

__________________________________________________________________________________________________

Bonus Activity 2

1. A carrier that moves DNA from one cell to another, such as a plasmid, is called a ___________. Plasmids are small, circular pieces of DNA from ___________.

2. In making recombinant DNA, what is the benefit of using a restriction enzyme that cuts

DNA in a staggered fashion?

3. A paleontologist has recovered a bit of organic material from the 400-year-old preserved skin of an extinct dodo. She would like to compare DNA from the sample with DNA from living birds. The most useful method for initially increasing the amount of dodo DNA for

testing is _____________________.

4. What feature of DNA causes it to move through a gel during gel electrophoresis?

DNA Evidence in the News…

•

• Use of DNA evidence in criminal cases is relatively new

– First case was in 1986 in England

• A man confessed to a series of rape/murders; DNA evidence indicated he did not; another person was identified as the actual murderer, based on DNA evidence

– First used in the US in ______________

• Man convicted of rape based on DNA obtained from semen found in victim

• Recently, a number of people on death row have been found not guilty based on DNA

evidence

–

•

•

• Fatal Flaws: The Case of Earl Washington

–Washington spent 18 years in prison

– Came within nine days of being put to death in Virginia's electric chair.

– Years later, DNA evidence proved he was innocent, and after a long legal battle, he was set free

–Washington had been convicted largely based on his own confession to a rape and

murder

• His defenders say the confession was coerced

• Washington was mentally handicapped

•

• DNA testing is increasingly being made available in criminal cases

• 32 states mandate that compensation be awarded to people wrongfully convicted (as of 2017)

• >________ people have been exonerated (from death row) using DNA testing since 1989

(when DNA testing first became available)

• In 2013 Oklahoma became 50th (and final) state to guarantee right to DNA testing in cases

where DNA evidence could demonstrate innocence

•

• Conversely, DNA evidence can be used to prove guilt

• Jan 2009, this man, Benjamin Watta, convicted of 1980 rape/murder of Simone Sharp in California

• Was already in prison for attempted murder of his former girlfriend

• “Cold Case” solved

•

•

•

•

• Can DNA technology resolve all problems with accuracy in convicting criminals?

• In order to be accurate, DNA testing must be done properly

–DNA must be stored properly

– Contamination of DNA samples can invalidate results

– Sometimes, if enough DNA evidence is available, defense and prosecution conduct

independent tests, to ensure accuracy

– Sometimes, shoddy lab work can also lead to wrongful conviction

• Can’t resolve all problems, but it’s a good and important start

–

• All for now, except for…

•

Random Animal of the Day!

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10/4/2018

6

BIO 1101 Lec. 9, Part A (Guided Notes): Chapter 11 -- Gene Regulation

Gene Regulation

•

• An organism has many different kinds of cells the have different functions, but every body

cell has the _______________________

•

• If the DNA in every body cell is the same, how can cells be so different?

•

• An individual starts out as a single cell – a _________________

•

• That single cell divides by __________, making identical copies of itself

•

• As the organism continues to grow by mitosis, individual cells become ______________ –some genes become inactivated, while others are activated

• In this way, cells can become specialized

•

• The genes that are “__________________” are transcribed into mRNA, and then

translated into proteins

•

• Genes that are ___________________ aren’t transcribed or translated

•

• How does a cell turn on or off different genes?

Gene Regulation in Bacteria

• Bacteria can conserve resources by only expressing the genes they need

• E. coli bacteria can use the sugar ___________ as fuel if it is available in their environment

– Three enzymes needed to absorb and digest

– Genes located next to each other

– Genes that have related function and which can be simultaneously regulated form an

_______________

– E. coli have a _______________

•

•

• Control of an __________________

– _________________: a control sequence on DNA near the operon to which

____________________ can bind

– _________________: a sequence between the promoter and the genes of the operon;

_______________ can bind here to turn off transcription

• In the case of the lac operon, lactose interferes with the attachment of the lac

repressor to the operator; thus the presence of lactose turns on the operon

•

•

Gene Regulation in Eukarytoes

• In Eukaryotes (organisms other than bacteria and archea), several methods may be used:

– _________________: when DNA is in a condensed state (as when ready to divide), it

cannot be transcribed or translated

• Example: X chromosome inactivation in female cats

–

•

– Genes can be regulated at initiation of transcription

• Most important stage for regulating gene expression

• Most genes in eukaryotes, by default, are turned “______”

• Many proteins are involved in enhancing transcription of particular genes

• ______________ ______ are proteins that bind to enhancers and promoters of DNA to activate multiple genes at the same time

• _____________________ may bind to DNA sequences called _______________ to inhibit transcription

•

• RNA Processing and Breakdown

– As we previously discussed, the initial mRNA transcript is edited to remove

____________ (intervening sequences) and __________ linked together before it leaves the nucleus and is translated

– Another way gene expression can be modified is through alternative ways of linking the

__________

• The exons of one gene may be linked in different ways to create different

__________________

– This is called _________________

•

•

– Not all RNAs code for protein

• Used to be considered “junk”

• Actually perform important functions

–microRNAs, for example

• miRNAs bind to one or more ____________

• Form a complex with mRNAs

• If the miRNA is complementary to the entire length of the mRNA, then the target

mRNA is ________________

• If the miRNA is only complementary to a part of the target mRNA, then the complex

_______________________________________

–Other ways genes can be regulated:

•

• By breaking down mRNA in the cytoplasm

•

• By regulating translation

•

• By altering the proteins produced in translation

•

• By breaking down the produced proteins

• The process of forming proteins from a DNA molecule involves many steps

•

• At each step, there are opportunities for gene regulation

•

• Cell Signaling and Homeotic Genes

– In multicellular organisms, information must be communicated between cells

– Chemicals like ____________ can be secreted by one cell and signal some activity in another cell

– The signal molecule acts by binding to a ___________________ on the target cell, initiating a ___________________________

– The binding activates a series of _______________, which ultimately activates a

________________, triggering the transcription of a specific gene

•

– _________________ are “master control genes” that regulate the expression of other groups of genes

– These are crucial in the process of embryonic development, when cells use chemical

signals to coordinate development

– A well-studied example of homeotic genes and their effects on development is seen in

fruit flies

• Certain homeotic genes in the fruit fly determine where ______________________ develop on the body

• One homeotic gene, when active, triggers legs to form on cells in the mid-body; this genes is inactive in other parts of the body

• A mutation in this homeotic genes can result in flies with legs coming out of their

heads, for example

• See video on experiments on homeotic genes in fruit flies:

https://www.youtube.com/watch?v=voQQ1dhCqZg

•

•

• 5-minute break

Cell Differentiation and the Science of Cloning

–

– Remember, the cells of an organism start out as undifferentiated – they have the

potential to become any type of cell

– As the organism grows, certain genes are turned on or left turned off, and the cell thus becomes differentiated

•

•

– Sometimes, cells that have become differentiated can “dedifferentiate” – allowing them

to grow into a new organism, or a new part of an organism

• Example: many plants can be propagated vegetatively

• Amphibians are famous for being able to re-generate lost limbs

•

• This process is relatively easy to do with plants

–Is used to make large numbers of “copies” of plants with desirable characteristics

• If a new organism is grown from the somatic (body) cells of an adult organism, the result is a ____________ – it is genetically identical to the organism from whose cells it was grown

•

• _______________ = the production of identical copies of a cell, organism, or DNA molecule

–Doesn’t ONLY refer to making copies of entire organisms

–More common: cloning cells or molecules

– There are different types of cloning, and each has a different purpose

•

– “Reproductive Cloning”

•

• The egg of a female animal is extracted, its ______ is removed, and the DNA from a ___________ cell of the desired organism is placed into the egg

• After the egg divides and forms an early embryo, it can be implanted into a female

• Can be used to generate “copies” of desirable farm animals, or endangered species

•

•

•

• “Dolly” the sheep was the first mammal to be cloned (1997)

–Died in 2003 from a lung disease

–Was her relatively early death a result of cloning? Difficult to say, as lung diseases are

fairly common among sheep raised indoors…

• In January of 2018, it was reported that the first primates (macaques) were cloned

– https://www.youtube.com/watch?v=oEXleYs58MY

•

– Therapeutic Cloning is another type of cloning

• Purpose is to generate __________________ (ES cells)

• Can divide indefinitely in culture, and have the potential to develop into any type of cell

• Certain growth factors can induce these cells to differentiate into specific kinds of cells

• May be used to treat or cure diseases or injured organs

• For example, there has been some success using stem cells to treat stroke victims or

Parkinson’s disease (inserting stem cells into brain)

• Embryonic stem cells are derived from embryos, and therein lies the controversy

•

– Adult stem cells are partially differentiated

• They may be able to differentiate into one of a few different types of cells, but are already set on a path to become one of a few types

• Less flexible than ES cells

• Example: stem cells in bone marrow can become any of the types of blood cells

• More difficult to culture in the lab

• Can be harvested from adults, so are less controversial

– New sources of stem cells…

• ______________________stem cells; can be created from somatic cells

Genetics of Cancer

• Cancer is the second-leading cause of death in industrialized countries; what causes it?

• __________________ – genes that cause cancer

• We carry many genes that are ____________________: that is, if changed in some way, they can turn into oncogenes

• Oncogenes can arise from insertion by a virus, or by mutation of a proto-oncogene

• Many _____________________ code for ______________________ – proteins that stimulate cell division

– Too much growth factor produced by a mutated gene can cause cancerous growth

• Some genes, called _____________________ genes, inhibit cell division

– If they are mutated, can also cause cancer

• _______________________ are substances that cause mutations to DNA that eventually lead to cancer

• Examples of carcinogens:

– UV radiation (sunlight or tanning beds); (skin cancer)

– Tobacco smoke (lung cancer)

– Alcohol (liver cancer)

• Prevention

•

– Compounds found in fruits and vegetables can reduce cancer risks

• __________________

– Can help reduce and repair DNA damage

– Some cancer-fighting foods include: cabbage, broccoli, brussels sprouts, kale, shiitake mushrooms, onions, red beans, cherries, raspberries, strawberries, blueberries, and

green tea

•

Bonus Activity

1. Explain how cells that look and behave so differently (like skin cells vs neurons) in the

same organism have the same genes.

2. What is an operon? Give an example.

3. A mutation in one gene may cause a major change in the body of a fruit fly, yet it takes many genes to produce a wing or leg. How can a change in one gene cause a big

change, like legs coming out of the head? What are such genes called?

4.

Lec. 9 Part B: Chapter 12 - Biotechnology

• DNA technology has wide variety of uses

• We will focus on genetic engineering and forensics (pg. 218-229)

Genetic Engineering

– Through __________________________, genes from different sources can be

combined

– Examples:

• Genes for specific protein products have been inserted into bacteria; the bacteria can then be grown and used to produce large quantities of the desired protein (e.g.

insulin)

• Proteins that can be used as vaccines can be produced by bacteria

•

• Genetically modified foods (e.g. “Bt” corn with built-in pesticide; “Golden Rice” with

enhanced nutritional value; tomatoes with a longer shelf life; etc.)

–GE crops introduced in 1996; now widely used; 93% of soy and 88% corn crops in

US were genetically modified (as of 2012)

–Primarily used in crops (insect resistance; herbicide tolerance)

•

•

• How is it done?

•

– Use of bacterial ________________ (circular pieces of DNA) as __________ (gene

carriers)

• ________________ are small circular pieces of DNA

• Bacteria readily take them in

• When a desired gene is inserted into a plasmid, the plasmid can then be isolated, and

then exposed to bacteria, which absorb them

• The bacteria will then express the desired gene in the modified plasmid

•

•

• How are genes inserted into plasmids?

•

– Cutting and Pasting Genes with ______________ Enzymes

• Restriction enzymes recognize short nucleotide sequences and cut the DNA at that site

• Staggered cut results in “_______________”

–A single-stranded piece of DNA at the end of the double-stranded molecule, which will readily connect with a complementary sticky end

• Fragments can then be stuck back together using ____________________

•

• In order to generate “sticky ends,” the recognition sequence must be a palindrome

– That is, the same sequence can be read from opposite directions on BOTH strands

– Example:

–

GAATTC

CTTAAG

•

• Gene of interest is now inserted into ___________

• ___________ is absorbed by bacteria, which express the ___________

• Bacteria can be readily grown to make many, many copies of the gene, or to synthesize the protein encoded by the gene

• Most commonly, recombinant DNA technology is used to modify ___________

– Insect-resistant corn and cotton

– Rice that produces more vitamins

–Disease-resistant papya and sweet potatoes

•

• Some more unusual uses:

– Glowing pet fish

– Allergen-free cats

• Glowing Puppies!

– http://www.youtube.com/watch?v=YXPnQvcqHkg&feature=related

• Gene Editing

– __________________ system is a new technique that allows nucleotide sequences of

genes to be edited in living cells

• May be used to reveal function of a gene, or to even correct a mutation

– Bacteria have a protein called _________ that can identify and cut our viral DNA from

their genome

• Will cut any DNA sequence that is complementary to a specific sequence of guiding _______

• A Cas9 protein with an RNA molecule complementary to a particular gene may be used to cut out a gene from a cell’s chromosomes

• Random DNA nucleotides are then inserted into the chromosome by DNA repair

enzymes; this “___________” the gene, making in non-functional

• Can therefore determine what the gene did in the cell

• To edit a gene, researchers can add a segment of a normal gene along with the Cas9-guide RNA complex

• After Cas9 cuts the target DNA, repair enzymes use the normal DNA as a template to

repair the target DNA (for example, a mutated gene)

• This allows researchers to potentially fix genetic mutations

• Researchers have used CRISP-Cas9 to fix a genetic defects in mice

• Video: https://www.youtube.com/watch?v=52jOEPzhpzc

•

Bonus Activity

• CRISPR is an exciting new technology and researchers are racing to find ways to use it. Do a Google search and find a recent news article talking about how CRISPR is being used.

Read the article, and then write 2-3 sentences summarizing the article.

•

• Break…

Forensics

The “scientific analysis of evidence for crime scene investigations and other legal proceedings”

– __________________ is one technique used in forensics, to compare DNA samples

– Every individual’s genetic makeup is unique

– A person’s “DNA Fingerprint” is his/her unique collection of DNA fragments generated

when restriction enzymes are used to cut up the DNA

•

•

• How do you generate a DNA fingerprint?

• First, DNA evidence must be collected

– Various tissues, such as blood, semen, skin, etc.

• Before DNA Fingerprints can be generated, often the DNA sample must be _____________

– A tiny spec of blood can provide enough information to run a test, if the DNA in that

spec is copied many times

– The _______________________ is used to copy DNA

•

•

– Genomes are quite large, and typically scientists only need to amplify a small region of

the genome

– To amplify only a specific sequence, scientists use _____________, a short single-

stranded DNA molecule

– _____________ are selected that are complementary to only to the sequences at the ends of the target sequence

• The primers thus flank to target sequence, marking the beginning and end of the sequence to be copied

• Only the DNA between the primers is thus amplified

–

• _______________________ enzymes can then be used to cut the DNA into pieces

–Many different kinds of restriction enzymes

– Each recognizes a specific sequence and cuts DNA at that location

• May cut straight across both strands

• May make a “staggered” cut

• Although all humans are >99% genetically identical, the size of the human genome allows

for enough variation that differences can be detected

– About 3 billion base pairs in our DNA

– 1 in 1000 difference between any two people

–about 3 million differences between any two people

• When DNA samples from two different people are “digested” with the same restriction enzyme (or set of restriction enzymes), they will produce different numbers and sizes of

DNA fragments

– These different sets of DNA pieces are called “_________________________________”

• Differences (polymorphisms) in the size of the fragments of DNA created by the

restriction enzymes

• ____________________________ can then be used to separate the fragments by size

–DNA is ____________ charged (due to the ___________ groups)

– Electrical current causes the fragments of DNA to move through a “gel”

– ____________ pieces migrate faster than ____________ ones

– Results in a unique banding pattern

•

•

• Another technique commonly used in forensics is _________________ (STR) Analysis

–Much of the DNA between genes is composed of ____________ sequences (for

example, perhaps the sequence AGAT may be repeated 12 times)

– Non-coding

– Close relatives more likely to have more similar patterns of STRs

– Standard STR analysis in forensics tests ___ different markers

• Chances of two different people being identical at all 13 markers is between

__________________________________________________________________________________________________

Bonus Activity 2

1. A carrier that moves DNA from one cell to another, such as a plasmid, is called a ___________. Plasmids are small, circular pieces of DNA from ___________.

2. In making recombinant DNA, what is the benefit of using a restriction enzyme that cuts

DNA in a staggered fashion?

3. A paleontologist has recovered a bit of organic material from the 400-year-old preserved

skin of an extinct dodo. She would like to compare DNA from the sample with DNA from living birds. The most useful method for initially increasing the amount of dodo DNA for testing is _____________________.

4. What feature of DNA causes it to move through a gel during gel electrophoresis?

DNA Evidence in the News…

•

• Use of DNA evidence in criminal cases is relatively new

– First case was in 1986 in England

• A man confessed to a series of rape/murders; DNA evidence indicated he did not; another person was identified as the actual murderer, based on DNA evidence

– First used in the US in ______________

• Man convicted of rape based on DNA obtained from semen found in victim

• Recently, a number of people on death row have been found not guilty based on DNA

evidence

–

•

•

• Fatal Flaws: The Case of Earl Washington

–Washington spent 18 years in prison

– Came within nine days of being put to death in Virginia's electric chair.

– Years later, DNA evidence proved he was innocent, and after a long legal battle, he was set free

–Washington had been convicted largely based on his own confession to a rape and

murder

• His defenders say the confession was coerced

• Washington was mentally handicapped

•

• DNA testing is increasingly being made available in criminal cases

• 32 states mandate that compensation be awarded to people wrongfully convicted (as of 2017)

• >________ people have been exonerated (from death row) using DNA testing since 1989

(when DNA testing first became available)

• In 2013 Oklahoma became 50th (and final) state to guarantee right to DNA testing in cases

where DNA evidence could demonstrate innocence

•

• Conversely, DNA evidence can be used to prove guilt

• Jan 2009, this man, Benjamin Watta, convicted of 1980 rape/murder of Simone Sharp in California

• Was already in prison for attempted murder of his former girlfriend

• “Cold Case” solved

•

•

•

•

• Can DNA technology resolve all problems with accuracy in convicting criminals?

• In order to be accurate, DNA testing must be done properly

–DNA must be stored properly

– Contamination of DNA samples can invalidate results

– Sometimes, if enough DNA evidence is available, defense and prosecution conduct

independent tests, to ensure accuracy

– Sometimes, shoddy lab work can also lead to wrongful conviction

• Can’t resolve all problems, but it’s a good and important start

–

• All for now, except for…

•

Random Animal of the Day!

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10/4/2018

7

BIO 1101 Lec. 9, Part A (Guided Notes): Chapter 11 -- Gene Regulation

Gene Regulation

•

• An organism has many different kinds of cells the have different functions, but every body

cell has the _______________________

•

• If the DNA in every body cell is the same, how can cells be so different?

•

• An individual starts out as a single cell – a _________________

•

• That single cell divides by __________, making identical copies of itself

•

• As the organism continues to grow by mitosis, individual cells become ______________ –some genes become inactivated, while others are activated

• In this way, cells can become specialized

•

• The genes that are “__________________” are transcribed into mRNA, and then

translated into proteins

•

• Genes that are ___________________ aren’t transcribed or translated

•

• How does a cell turn on or off different genes?

Gene Regulation in Bacteria

• Bacteria can conserve resources by only expressing the genes they need

• E. coli bacteria can use the sugar ___________ as fuel if it is available in their environment

– Three enzymes needed to absorb and digest

– Genes located next to each other

– Genes that have related function and which can be simultaneously regulated form an

_______________

– E. coli have a _______________

•

•

• Control of an __________________

– _________________: a control sequence on DNA near the operon to which

____________________ can bind

– _________________: a sequence between the promoter and the genes of the operon;

_______________ can bind here to turn off transcription

• In the case of the lac operon, lactose interferes with the attachment of the lac

repressor to the operator; thus the presence of lactose turns on the operon

•

•

Gene Regulation in Eukarytoes

• In Eukaryotes (organisms other than bacteria and archea), several methods may be used:

– _________________: when DNA is in a condensed state (as when ready to divide), it

cannot be transcribed or translated

• Example: X chromosome inactivation in female cats

–

•

– Genes can be regulated at initiation of transcription

• Most important stage for regulating gene expression

• Most genes in eukaryotes, by default, are turned “______”

• Many proteins are involved in enhancing transcription of particular genes

• ______________ ______ are proteins that bind to enhancers and promoters of DNA

to activate multiple genes at the same time

• _____________________ may bind to DNA sequences called _______________ to inhibit transcription

•

• RNA Processing and Breakdown

– As we previously discussed, the initial mRNA transcript is edited to remove

____________ (intervening sequences) and __________ linked together before it leaves the nucleus and is translated

– Another way gene expression can be modified is through alternative ways of linking the

__________

• The exons of one gene may be linked in different ways to create different

__________________

– This is called _________________

•

•

– Not all RNAs code for protein

• Used to be considered “junk”

• Actually perform important functions

–microRNAs, for example

• miRNAs bind to one or more ____________

• Form a complex with mRNAs

• If the miRNA is complementary to the entire length of the mRNA, then the target

mRNA is ________________

• If the miRNA is only complementary to a part of the target mRNA, then the complex

_______________________________________

–Other ways genes can be regulated:

•

• By breaking down mRNA in the cytoplasm

•

• By regulating translation

•

• By altering the proteins produced in translation

•

• By breaking down the produced proteins

• The process of forming proteins from a DNA molecule involves many steps

•

• At each step, there are opportunities for gene regulation

•

• Cell Signaling and Homeotic Genes

– In multicellular organisms, information must be communicated between cells

– Chemicals like ____________ can be secreted by one cell and signal some activity in another cell

– The signal molecule acts by binding to a ___________________ on the target cell, initiating a ___________________________

– The binding activates a series of _______________, which ultimately activates a

________________, triggering the transcription of a specific gene

•

– _________________ are “master control genes” that regulate the expression of other groups of genes

– These are crucial in the process of embryonic development, when cells use chemical

signals to coordinate development

– A well-studied example of homeotic genes and their effects on development is seen in

fruit flies

• Certain homeotic genes in the fruit fly determine where ______________________

develop on the body

• One homeotic gene, when active, triggers legs to form on cells in the mid-body; this genes is inactive in other parts of the body

• A mutation in this homeotic genes can result in flies with legs coming out of their

heads, for example

• See video on experiments on homeotic genes in fruit flies:

https://www.youtube.com/watch?v=voQQ1dhCqZg

•

•

• 5-minute break

Cell Differentiation and the Science of Cloning

–

– Remember, the cells of an organism start out as undifferentiated – they have the

potential to become any type of cell

– As the organism grows, certain genes are turned on or left turned off, and the cell thus becomes differentiated

•

•

– Sometimes, cells that have become differentiated can “dedifferentiate” – allowing them

to grow into a new organism, or a new part of an organism

• Example: many plants can be propagated vegetatively

• Amphibians are famous for being able to re-generate lost limbs

•

• This process is relatively easy to do with plants

–Is used to make large numbers of “copies” of plants with desirable characteristics

• If a new organism is grown from the somatic (body) cells of an adult organism, the

result is a ____________ – it is genetically identical to the organism from whose cells it was grown

•

• _______________ = the production of identical copies of a cell, organism, or DNA molecule

–Doesn’t ONLY refer to making copies of entire organisms

–More common: cloning cells or molecules

– There are different types of cloning, and each has a different purpose

•

– “Reproductive Cloning”

•

• The egg of a female animal is extracted, its ______ is removed, and the DNA from a ___________ cell of the desired organism is placed into the egg

• After the egg divides and forms an early embryo, it can be implanted into a female

• Can be used to generate “copies” of desirable farm animals, or endangered species

•

•

•

• “Dolly” the sheep was the first mammal to be cloned (1997)

–Died in 2003 from a lung disease

–Was her relatively early death a result of cloning? Difficult to say, as lung diseases are fairly common among sheep raised indoors…

• In January of 2018, it was reported that the first primates (macaques) were cloned

– https://www.youtube.com/watch?v=oEXleYs58MY

•

– Therapeutic Cloning is another type of cloning

• Purpose is to generate __________________ (ES cells)

• Can divide indefinitely in culture, and have the potential to develop into any type of cell

• Certain growth factors can induce these cells to differentiate into specific kinds of cells

• May be used to treat or cure diseases or injured organs

• For example, there has been some success using stem cells to treat stroke victims or

Parkinson’s disease (inserting stem cells into brain)

• Embryonic stem cells are derived from embryos, and therein lies the controversy

•

– Adult stem cells are partially differentiated

• They may be able to differentiate into one of a few different types of cells, but are already set on a path to become one of a few types

• Less flexible than ES cells

• Example: stem cells in bone marrow can become any of the types of blood cells

• More difficult to culture in the lab

• Can be harvested from adults, so are less controversial

– New sources of stem cells…

• ______________________stem cells; can be created from somatic cells

Genetics of Cancer

• Cancer is the second-leading cause of death in industrialized countries; what causes it?

• __________________ – genes that cause cancer

• We carry many genes that are ____________________: that is, if changed in some way, they can turn into oncogenes

• Oncogenes can arise from insertion by a virus, or by mutation of a proto-oncogene

• Many _____________________ code for ______________________ – proteins that stimulate cell division

– Too much growth factor produced by a mutated gene can cause cancerous growth

• Some genes, called _____________________ genes, inhibit cell division

– If they are mutated, can also cause cancer

• _______________________ are substances that cause mutations to DNA that eventually lead to cancer

• Examples of carcinogens:

– UV radiation (sunlight or tanning beds); (skin cancer)

– Tobacco smoke (lung cancer)

– Alcohol (liver cancer)

• Prevention

•

– Compounds found in fruits and vegetables can reduce cancer risks

• __________________

– Can help reduce and repair DNA damage

– Some cancer-fighting foods include: cabbage, broccoli, brussels sprouts, kale, shiitake mushrooms, onions, red beans, cherries, raspberries, strawberries, blueberries, and

green tea

•

Bonus Activity

1. Explain how cells that look and behave so differently (like skin cells vs neurons) in the

same organism have the same genes.

2. What is an operon? Give an example.

3. A mutation in one gene may cause a major change in the body of a fruit fly, yet it takes many genes to produce a wing or leg. How can a change in one gene cause a big change, like legs coming out of the head? What are such genes called?

4.

Lec. 9 Part B: Chapter 12 - Biotechnology

• DNA technology has wide variety of uses

• We will focus on genetic engineering and forensics (pg. 218-229)

Genetic Engineering

– Through __________________________, genes from different sources can be

combined

– Examples:

• Genes for specific protein products have been inserted into bacteria; the bacteria can then be grown and used to produce large quantities of the desired protein (e.g.

insulin)

• Proteins that can be used as vaccines can be produced by bacteria

•

• Genetically modified foods (e.g. “Bt” corn with built-in pesticide; “Golden Rice” with

enhanced nutritional value; tomatoes with a longer shelf life; etc.)

–GE crops introduced in 1996; now widely used; 93% of soy and 88% corn crops in

US were genetically modified (as of 2012)

–Primarily used in crops (insect resistance; herbicide tolerance)

•

•

• How is it done?

•

– Use of bacterial ________________ (circular pieces of DNA) as __________ (gene

carriers)

• ________________ are small circular pieces of DNA

• Bacteria readily take them in

• When a desired gene is inserted into a plasmid, the plasmid can then be isolated, and then exposed to bacteria, which absorb them

• The bacteria will then express the desired gene in the modified plasmid

•

•

• How are genes inserted into plasmids?

•

– Cutting and Pasting Genes with ______________ Enzymes

• Restriction enzymes recognize short nucleotide sequences and cut the DNA at that site

• Staggered cut results in “_______________”

–A single-stranded piece of DNA at the end of the double-stranded molecule, which will readily connect with a complementary sticky end

• Fragments can then be stuck back together using ____________________

•

• In order to generate “sticky ends,” the recognition sequence must be a palindrome

– That is, the same sequence can be read from opposite directions on BOTH strands

– Example:

–

GAATTC

CTTAAG

•

• Gene of interest is now inserted into ___________

• ___________ is absorbed by bacteria, which express the ___________

• Bacteria can be readily grown to make many, many copies of the gene, or to synthesize

the protein encoded by the gene

• Most commonly, recombinant DNA technology is used to modify ___________

– Insect-resistant corn and cotton

– Rice that produces more vitamins

–Disease-resistant papya and sweet potatoes

•

• Some more unusual uses:

– Glowing pet fish

– Allergen-free cats

• Glowing Puppies!

– http://www.youtube.com/watch?v=YXPnQvcqHkg&feature=related

• Gene Editing

– __________________ system is a new technique that allows nucleotide sequences of

genes to be edited in living cells

• May be used to reveal function of a gene, or to even correct a mutation

– Bacteria have a protein called _________ that can identify and cut our viral DNA from

their genome

• Will cut any DNA sequence that is complementary to a specific sequence of guiding _______

• A Cas9 protein with an RNA molecule complementary to a particular gene may be used to cut out a gene from a cell’s chromosomes

• Random DNA nucleotides are then inserted into the chromosome by DNA repair

enzymes; this “___________” the gene, making in non-functional

• Can therefore determine what the gene did in the cell

• To edit a gene, researchers can add a segment of a normal gene along with the Cas9-guide RNA complex

• After Cas9 cuts the target DNA, repair enzymes use the normal DNA as a template to

repair the target DNA (for example, a mutated gene)

• This allows researchers to potentially fix genetic mutations

• Researchers have used CRISP-Cas9 to fix a genetic defects in mice

• Video: https://www.youtube.com/watch?v=52jOEPzhpzc

•

Bonus Activity

• CRISPR is an exciting new technology and researchers are racing to find ways to use it. Do a Google search and find a recent news article talking about how CRISPR is being used.

Read the article, and then write 2-3 sentences summarizing the article.

•

• Break…

Forensics

The “scientific analysis of evidence for crime scene investigations and other legal proceedings”

– __________________ is one technique used in forensics, to compare DNA samples

– Every individual’s genetic makeup is unique

– A person’s “DNA Fingerprint” is his/her unique collection of DNA fragments generated

when restriction enzymes are used to cut up the DNA

•

•

• How do you generate a DNA fingerprint?

• First, DNA evidence must be collected

– Various tissues, such as blood, semen, skin, etc.

• Before DNA Fingerprints can be generated, often the DNA sample must be _____________

– A tiny spec of blood can provide enough information to run a test, if the DNA in that

spec is copied many times

– The _______________________ is used to copy DNA

•

•

– Genomes are quite large, and typically scientists only need to amplify a small region of the genome

– To amplify only a specific sequence, scientists use _____________, a short single-

stranded DNA molecule

– _____________ are selected that are complementary to only to the sequences at the ends of the target sequence

• The primers thus flank to target sequence, marking the beginning and end of the sequence to be copied

• Only the DNA between the primers is thus amplified

–

• _______________________ enzymes can then be used to cut the DNA into pieces

–Many different kinds of restriction enzymes

– Each recognizes a specific sequence and cuts DNA at that location

• May cut straight across both strands

• May make a “staggered” cut

• Although all humans are >99% genetically identical, the size of the human genome allows

for enough variation that differences can be detected

– About 3 billion base pairs in our DNA

– 1 in 1000 difference between any two people

–about 3 million differences between any two people

• When DNA samples from two different people are “digested” with the same restriction enzyme (or set of restriction enzymes), they will produce different numbers and sizes of

DNA fragments

– These different sets of DNA pieces are called “_________________________________”

• Differences (polymorphisms) in the size of the fragments of DNA created by the

restriction enzymes

• ____________________________ can then be used to separate the fragments by size

–DNA is ____________ charged (due to the ___________ groups)

– Electrical current causes the fragments of DNA to move through a “gel”

– ____________ pieces migrate faster than ____________ ones

– Results in a unique banding pattern

•

•

• Another technique commonly used in forensics is _________________ (STR) Analysis

–Much of the DNA between genes is composed of ____________ sequences (for

example, perhaps the sequence AGAT may be repeated 12 times)

– Non-coding

– Close relatives more likely to have more similar patterns of STRs

– Standard STR analysis in forensics tests ___ different markers

• Chances of two different people being identical at all 13 markers is between

__________________________________________________________________________________________________

Bonus Activity 2

1. A carrier that moves DNA from one cell to another, such as a plasmid, is called a ___________. Plasmids are small, circular pieces of DNA from ___________.

2. In making recombinant DNA, what is the benefit of using a restriction enzyme that cuts

DNA in a staggered fashion?

3. A paleontologist has recovered a bit of organic material from the 400-year-old preserved

skin of an extinct dodo. She would like to compare DNA from the sample with DNA from living birds. The most useful method for initially increasing the amount of dodo DNA for

testing is _____________________.

4. What feature of DNA causes it to move through a gel during gel electrophoresis?

DNA Evidence in the News…

•

• Use of DNA evidence in criminal cases is relatively new

– First case was in 1986 in England

• A man confessed to a series of rape/murders; DNA evidence indicated he did not; another person was identified as the actual murderer, based on DNA evidence

– First used in the US in ______________

• Man convicted of rape based on DNA obtained from semen found in victim

• Recently, a number of people on death row have been found not guilty based on DNA evidence

–

•

•

• Fatal Flaws: The Case of Earl Washington

–Washington spent 18 years in prison

– Came within nine days of being put to death in Virginia's electric chair.

– Years later, DNA evidence proved he was innocent, and after a long legal battle, he was set free

–Washington had been convicted largely based on his own confession to a rape and

murder

• His defenders say the confession was coerced

• Washington was mentally handicapped

•

• DNA testing is increasingly being made available in criminal cases

• 32 states mandate that compensation be awarded to people wrongfully convicted (as of 2017)

• >________ people have been exonerated (from death row) using DNA testing since 1989

(when DNA testing first became available)

• In 2013 Oklahoma became 50th (and final) state to guarantee right to DNA testing in cases

where DNA evidence could demonstrate innocence

•

• Conversely, DNA evidence can be used to prove guilt

• Jan 2009, this man, Benjamin Watta, convicted of 1980 rape/murder of Simone Sharp in California

• Was already in prison for attempted murder of his former girlfriend

• “Cold Case” solved

•

•

•

•

• Can DNA technology resolve all problems with accuracy in convicting criminals?

• In order to be accurate, DNA testing must be done properly

–DNA must be stored properly

– Contamination of DNA samples can invalidate results

– Sometimes, if enough DNA evidence is available, defense and prosecution conduct

independent tests, to ensure accuracy

– Sometimes, shoddy lab work can also lead to wrongful conviction

• Can’t resolve all problems, but it’s a good and important start

–

• All for now, except for…

•

Random Animal of the Day!

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10/4/2018

8

BIO 1101 Lec. 9, Part A (Guided Notes): Chapter 11 -- Gene Regulation

Gene Regulation

•

• An organism has many different kinds of cells the have different functions, but every body

cell has the _______________________

•

• If the DNA in every body cell is the same, how can cells be so different?

•

• An individual starts out as a single cell – a _________________

•

• That single cell divides by __________, making identical copies of itself

•

• As the organism continues to grow by mitosis, individual cells become ______________ –some genes become inactivated, while others are activated

• In this way, cells can become specialized

•

• The genes that are “__________________” are transcribed into mRNA, and then

translated into proteins

•

• Genes that are ___________________ aren’t transcribed or translated

•

• How does a cell turn on or off different genes?

Gene Regulation in Bacteria

• Bacteria can conserve resources by only expressing the genes they need

• E. coli bacteria can use the sugar ___________ as fuel if it is available in their environment

– Three enzymes needed to absorb and digest

– Genes located next to each other

– Genes that have related function and which can be simultaneously regulated form an

_______________

– E. coli have a _______________

•

•

• Control of an __________________

– _________________: a control sequence on DNA near the operon to which

____________________ can bind

– _________________: a sequence between the promoter and the genes of the operon;

_______________ can bind here to turn off transcription

• In the case of the lac operon, lactose interferes with the attachment of the lac

repressor to the operator; thus the presence of lactose turns on the operon

•

•

Gene Regulation in Eukarytoes

• In Eukaryotes (organisms other than bacteria and archea), several methods may be used:

– _________________: when DNA is in a condensed state (as when ready to divide), it

cannot be transcribed or translated

• Example: X chromosome inactivation in female cats

–

•

– Genes can be regulated at initiation of transcription

• Most important stage for regulating gene expression

• Most genes in eukaryotes, by default, are turned “______”

• Many proteins are involved in enhancing transcription of particular genes

• ______________ ______ are proteins that bind to enhancers and promoters of DNA

to activate multiple genes at the same time

• _____________________ may bind to DNA sequences called _______________ to inhibit transcription

•

• RNA Processing and Breakdown

– As we previously discussed, the initial mRNA transcript is edited to remove

____________ (intervening sequences) and __________ linked together before it leaves the nucleus and is translated

– Another way gene expression can be modified is through alternative ways of linking the

__________

• The exons of one gene may be linked in different ways to create different

__________________

– This is called _________________

•

•

– Not all RNAs code for protein

• Used to be considered “junk”

• Actually perform important functions

–microRNAs, for example

• miRNAs bind to one or more ____________

• Form a complex with mRNAs

• If the miRNA is complementary to the entire length of the mRNA, then the target mRNA is ________________

• If the miRNA is only complementary to a part of the target mRNA, then the complex

_______________________________________

–Other ways genes can be regulated:

•

• By breaking down mRNA in the cytoplasm

•

• By regulating translation

•

• By altering the proteins produced in translation

•

• By breaking down the produced proteins

• The process of forming proteins from a DNA molecule involves many steps

•

• At each step, there are opportunities for gene regulation

•

• Cell Signaling and Homeotic Genes

– In multicellular organisms, information must be communicated between cells

– Chemicals like ____________ can be secreted by one cell and signal some activity in another cell

– The signal molecule acts by binding to a ___________________ on the target cell, initiating a ___________________________

– The binding activates a series of _______________, which ultimately activates a

________________, triggering the transcription of a specific gene

•

– _________________ are “master control genes” that regulate the expression of other groups of genes

– These are crucial in the process of embryonic development, when cells use chemical

signals to coordinate development

– A well-studied example of homeotic genes and their effects on development is seen in

fruit flies

• Certain homeotic genes in the fruit fly determine where ______________________

develop on the body

• One homeotic gene, when active, triggers legs to form on cells in the mid-body; this genes is inactive in other parts of the body

• A mutation in this homeotic genes can result in flies with legs coming out of their heads, for example

• See video on experiments on homeotic genes in fruit flies:

https://www.youtube.com/watch?v=voQQ1dhCqZg

•

•

• 5-minute break

Cell Differentiation and the Science of Cloning

–

– Remember, the cells of an organism start out as undifferentiated – they have the

potential to become any type of cell

– As the organism grows, certain genes are turned on or left turned off, and the cell thus becomes differentiated

•

•

– Sometimes, cells that have become differentiated can “dedifferentiate” – allowing them

to grow into a new organism, or a new part of an organism

• Example: many plants can be propagated vegetatively

• Amphibians are famous for being able to re-generate lost limbs

•

• This process is relatively easy to do with plants

–Is used to make large numbers of “copies” of plants with desirable characteristics

• If a new organism is grown from the somatic (body) cells of an adult organism, the

result is a ____________ – it is genetically identical to the organism from whose cells it was grown

•

• _______________ = the production of identical copies of a cell, organism, or DNA molecule

–Doesn’t ONLY refer to making copies of entire organisms

–More common: cloning cells or molecules

– There are different types of cloning, and each has a different purpose

•

– “Reproductive Cloning”

•

• The egg of a female animal is extracted, its ______ is removed, and the DNA from a ___________ cell of the desired organism is placed into the egg

• After the egg divides and forms an early embryo, it can be implanted into a female

• Can be used to generate “copies” of desirable farm animals, or endangered species

•

•

•

• “Dolly” the sheep was the first mammal to be cloned (1997)

–Died in 2003 from a lung disease

–Was her relatively early death a result of cloning? Difficult to say, as lung diseases are

fairly common among sheep raised indoors…

• In January of 2018, it was reported that the first primates (macaques) were cloned

– https://www.youtube.com/watch?v=oEXleYs58MY

•

– Therapeutic Cloning is another type of cloning

• Purpose is to generate __________________ (ES cells)

• Can divide indefinitely in culture, and have the potential to develop into any type of cell

• Certain growth factors can induce these cells to differentiate into specific kinds of cells

• May be used to treat or cure diseases or injured organs

• For example, there has been some success using stem cells to treat stroke victims or Parkinson’s disease (inserting stem cells into brain)

• Embryonic stem cells are derived from embryos, and therein lies the controversy

•

– Adult stem cells are partially differentiated

• They may be able to differentiate into one of a few different types of cells, but are already set on a path to become one of a few types

• Less flexible than ES cells

• Example: stem cells in bone marrow can become any of the types of blood cells

• More difficult to culture in the lab

• Can be harvested from adults, so are less controversial

– New sources of stem cells…

• ______________________stem cells; can be created from somatic cells

Genetics of Cancer

• Cancer is the second-leading cause of death in industrialized countries; what causes it?

• __________________ – genes that cause cancer

• We carry many genes that are ____________________: that is, if changed in some way, they can turn into oncogenes

• Oncogenes can arise from insertion by a virus, or by mutation of a proto-oncogene

• Many _____________________ code for ______________________ – proteins that stimulate cell division

– Too much growth factor produced by a mutated gene can cause cancerous growth

• Some genes, called _____________________ genes, inhibit cell division

– If they are mutated, can also cause cancer

• _______________________ are substances that cause mutations to DNA that eventually lead to cancer

• Examples of carcinogens:

– UV radiation (sunlight or tanning beds); (skin cancer)

– Tobacco smoke (lung cancer)

– Alcohol (liver cancer)

• Prevention

•

– Compounds found in fruits and vegetables can reduce cancer risks

• __________________

– Can help reduce and repair DNA damage

– Some cancer-fighting foods include: cabbage, broccoli, brussels sprouts, kale, shiitake mushrooms, onions, red beans, cherries, raspberries, strawberries, blueberries, and

green tea

•

Bonus Activity

1. Explain how cells that look and behave so differently (like skin cells vs neurons) in the

same organism have the same genes.

2. What is an operon? Give an example.

3. A mutation in one gene may cause a major change in the body of a fruit fly, yet it takes many genes to produce a wing or leg. How can a change in one gene cause a big

change, like legs coming out of the head? What are such genes called?

4.

Lec. 9 Part B: Chapter 12 - Biotechnology

• DNA technology has wide variety of uses

• We will focus on genetic engineering and forensics (pg. 218-229)

Genetic Engineering

– Through __________________________, genes from different sources can be

combined

– Examples:

• Genes for specific protein products have been inserted into bacteria; the bacteria can then be grown and used to produce large quantities of the desired protein (e.g.

insulin)

• Proteins that can be used as vaccines can be produced by bacteria

•

• Genetically modified foods (e.g. “Bt” corn with built-in pesticide; “Golden Rice” with

enhanced nutritional value; tomatoes with a longer shelf life; etc.)

–GE crops introduced in 1996; now widely used; 93% of soy and 88% corn crops in

US were genetically modified (as of 2012)

–Primarily used in crops (insect resistance; herbicide tolerance)

•

•

• How is it done?

•

– Use of bacterial ________________ (circular pieces of DNA) as __________ (gene

carriers)

• ________________ are small circular pieces of DNA

• Bacteria readily take them in

• When a desired gene is inserted into a plasmid, the plasmid can then be isolated, and

then exposed to bacteria, which absorb them

• The bacteria will then express the desired gene in the modified plasmid

•

•

• How are genes inserted into plasmids?

•

– Cutting and Pasting Genes with ______________ Enzymes

• Restriction enzymes recognize short nucleotide sequences and cut the DNA at that site

• Staggered cut results in “_______________”

–A single-stranded piece of DNA at the end of the double-stranded molecule, which will readily connect with a complementary sticky end

• Fragments can then be stuck back together using ____________________

•

• In order to generate “sticky ends,” the recognition sequence must be a palindrome

– That is, the same sequence can be read from opposite directions on BOTH strands

– Example:

–

GAATTC

CTTAAG

•

• Gene of interest is now inserted into ___________

• ___________ is absorbed by bacteria, which express the ___________

• Bacteria can be readily grown to make many, many copies of the gene, or to synthesize

the protein encoded by the gene

• Most commonly, recombinant DNA technology is used to modify ___________

– Insect-resistant corn and cotton

– Rice that produces more vitamins

–Disease-resistant papya and sweet potatoes

•

• Some more unusual uses:

– Glowing pet fish

– Allergen-free cats

• Glowing Puppies!

– http://www.youtube.com/watch?v=YXPnQvcqHkg&feature=related

• Gene Editing

– __________________ system is a new technique that allows nucleotide sequences of

genes to be edited in living cells

• May be used to reveal function of a gene, or to even correct a mutation

– Bacteria have a protein called _________ that can identify and cut our viral DNA from

their genome

• Will cut any DNA sequence that is complementary to a specific sequence of guiding _______

• A Cas9 protein with an RNA molecule complementary to a particular gene may be used to cut out a gene from a cell’s chromosomes

• Random DNA nucleotides are then inserted into the chromosome by DNA repair

enzymes; this “___________” the gene, making in non-functional

• Can therefore determine what the gene did in the cell

• To edit a gene, researchers can add a segment of a normal gene along with the Cas9-guide RNA complex

• After Cas9 cuts the target DNA, repair enzymes use the normal DNA as a template to

repair the target DNA (for example, a mutated gene)

• This allows researchers to potentially fix genetic mutations

• Researchers have used CRISP-Cas9 to fix a genetic defects in mice

• Video: https://www.youtube.com/watch?v=52jOEPzhpzc

•

Bonus Activity

• CRISPR is an exciting new technology and researchers are racing to find ways to use it. Do a Google search and find a recent news article talking about how CRISPR is being used.

Read the article, and then write 2-3 sentences summarizing the article.

•

• Break…

Forensics

The “scientific analysis of evidence for crime scene investigations and other legal proceedings”

– __________________ is one technique used in forensics, to compare DNA samples

– Every individual’s genetic makeup is unique

– A person’s “DNA Fingerprint” is his/her unique collection of DNA fragments generated

when restriction enzymes are used to cut up the DNA

•

•

• How do you generate a DNA fingerprint?

• First, DNA evidence must be collected

– Various tissues, such as blood, semen, skin, etc.

• Before DNA Fingerprints can be generated, often the DNA sample must be _____________

– A tiny spec of blood can provide enough information to run a test, if the DNA in that

spec is copied many times

– The _______________________ is used to copy DNA

•

•

– Genomes are quite large, and typically scientists only need to amplify a small region of

the genome

– To amplify only a specific sequence, scientists use _____________, a short single-

stranded DNA molecule

– _____________ are selected that are complementary to only to the sequences at the ends of the target sequence

• The primers thus flank to target sequence, marking the beginning and end of the sequence to be copied

• Only the DNA between the primers is thus amplified

–

• _______________________ enzymes can then be used to cut the DNA into pieces

–Many different kinds of restriction enzymes

– Each recognizes a specific sequence and cuts DNA at that location

• May cut straight across both strands

• May make a “staggered” cut

• Although all humans are >99% genetically identical, the size of the human genome allows

for enough variation that differences can be detected

– About 3 billion base pairs in our DNA

– 1 in 1000 difference between any two people

–about 3 million differences between any two people

• When DNA samples from two different people are “digested” with the same restriction enzyme (or set of restriction enzymes), they will produce different numbers and sizes of

DNA fragments

– These different sets of DNA pieces are called “_________________________________”

• Differences (polymorphisms) in the size of the fragments of DNA created by the

restriction enzymes

• ____________________________ can then be used to separate the fragments by size

–DNA is ____________ charged (due to the ___________ groups)

– Electrical current causes the fragments of DNA to move through a “gel”

– ____________ pieces migrate faster than ____________ ones

– Results in a unique banding pattern

•

•

• Another technique commonly used in forensics is _________________ (STR) Analysis

–Much of the DNA between genes is composed of ____________ sequences (for

example, perhaps the sequence AGAT may be repeated 12 times)

– Non-coding

– Close relatives more likely to have more similar patterns of STRs

– Standard STR analysis in forensics tests ___ different markers

• Chances of two different people being identical at all 13 markers is between

__________________________________________________________________________________________________

Bonus Activity 2

1. A carrier that moves DNA from one cell to another, such as a plasmid, is called a ___________. Plasmids are small, circular pieces of DNA from ___________.

2. In making recombinant DNA, what is the benefit of using a restriction enzyme that cuts

DNA in a staggered fashion?

3. A paleontologist has recovered a bit of organic material from the 400-year-old preserved

skin of an extinct dodo. She would like to compare DNA from the sample with DNA from living birds. The most useful method for initially increasing the amount of dodo DNA for

testing is _____________________.

4. What feature of DNA causes it to move through a gel during gel electrophoresis?

DNA Evidence in the News…

•

• Use of DNA evidence in criminal cases is relatively new

– First case was in 1986 in England

• A man confessed to a series of rape/murders; DNA evidence indicated he did not; another person was identified as the actual murderer, based on DNA evidence

– First used in the US in ______________

• Man convicted of rape based on DNA obtained from semen found in victim

• Recently, a number of people on death row have been found not guilty based on DNA

evidence

–

•

•

• Fatal Flaws: The Case of Earl Washington

–Washington spent 18 years in prison

– Came within nine days of being put to death in Virginia's electric chair.

– Years later, DNA evidence proved he was innocent, and after a long legal battle, he was set free

–Washington had been convicted largely based on his own confession to a rape and

murder

• His defenders say the confession was coerced

• Washington was mentally handicapped

•

• DNA testing is increasingly being made available in criminal cases

• 32 states mandate that compensation be awarded to people wrongfully convicted (as of 2017)

• >________ people have been exonerated (from death row) using DNA testing since 1989

(when DNA testing first became available)

• In 2013 Oklahoma became 50th (and final) state to guarantee right to DNA testing in cases

where DNA evidence could demonstrate innocence

•

• Conversely, DNA evidence can be used to prove guilt

• Jan 2009, this man, Benjamin Watta, convicted of 1980 rape/murder of Simone Sharp in California

• Was already in prison for attempted murder of his former girlfriend

• “Cold Case” solved

•

•

•

•

• Can DNA technology resolve all problems with accuracy in convicting criminals?

• In order to be accurate, DNA testing must be done properly

–DNA must be stored properly

– Contamination of DNA samples can invalidate results

– Sometimes, if enough DNA evidence is available, defense and prosecution conduct

independent tests, to ensure accuracy

– Sometimes, shoddy lab work can also lead to wrongful conviction

• Can’t resolve all problems, but it’s a good and important start

–

• All for now, except for…

•

Random Animal of the Day!

1

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3

4

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10/4/2018

9

BIO 1101 Lec. 9, Part A (Guided Notes): Chapter 11 -- Gene Regulation

Gene Regulation

•

• An organism has many different kinds of cells the have different functions, but every body

cell has the _______________________

•

• If the DNA in every body cell is the same, how can cells be so different?

•

• An individual starts out as a single cell – a _________________

•

• That single cell divides by __________, making identical copies of itself

•

• As the organism continues to grow by mitosis, individual cells become ______________ –some genes become inactivated, while others are activated

• In this way, cells can become specialized

•

• The genes that are “__________________” are transcribed into mRNA, and then

translated into proteins

•

• Genes that are ___________________ aren’t transcribed or translated

•

• How does a cell turn on or off different genes?

Gene Regulation in Bacteria

• Bacteria can conserve resources by only expressing the genes they need

• E. coli bacteria can use the sugar ___________ as fuel if it is available in their environment

– Three enzymes needed to absorb and digest

– Genes located next to each other

– Genes that have related function and which can be simultaneously regulated form an

_______________

– E. coli have a _______________

•

•

• Control of an __________________

– _________________: a control sequence on DNA near the operon to which

____________________ can bind

– _________________: a sequence between the promoter and the genes of the operon;

_______________ can bind here to turn off transcription

• In the case of the lac operon, lactose interferes with the attachment of the lac

repressor to the operator; thus the presence of lactose turns on the operon

•

•

Gene Regulation in Eukarytoes

• In Eukaryotes (organisms other than bacteria and archea), several methods may be used:

– _________________: when DNA is in a condensed state (as when ready to divide), it

cannot be transcribed or translated

• Example: X chromosome inactivation in female cats

–

•

– Genes can be regulated at initiation of transcription

• Most important stage for regulating gene expression

• Most genes in eukaryotes, by default, are turned “______”

• Many proteins are involved in enhancing transcription of particular genes

• ______________ ______ are proteins that bind to enhancers and promoters of DNA

to activate multiple genes at the same time

• _____________________ may bind to DNA sequences called _______________ to inhibit transcription

•

• RNA Processing and Breakdown

– As we previously discussed, the initial mRNA transcript is edited to remove

____________ (intervening sequences) and __________ linked together before it leaves the nucleus and is translated

– Another way gene expression can be modified is through alternative ways of linking the

__________

• The exons of one gene may be linked in different ways to create different

__________________

– This is called _________________

•

•

– Not all RNAs code for protein

• Used to be considered “junk”

• Actually perform important functions

–microRNAs, for example

• miRNAs bind to one or more ____________

• Form a complex with mRNAs

• If the miRNA is complementary to the entire length of the mRNA, then the target

mRNA is ________________

• If the miRNA is only complementary to a part of the target mRNA, then the complex _______________________________________

–Other ways genes can be regulated:

•

• By breaking down mRNA in the cytoplasm

•

• By regulating translation

•

• By altering the proteins produced in translation

•

• By breaking down the produced proteins

• The process of forming proteins from a DNA molecule involves many steps

•

• At each step, there are opportunities for gene regulation

•

• Cell Signaling and Homeotic Genes

– In multicellular organisms, information must be communicated between cells

– Chemicals like ____________ can be secreted by one cell and signal some activity in another cell

– The signal molecule acts by binding to a ___________________ on the target cell, initiating a ___________________________

– The binding activates a series of _______________, which ultimately activates a

________________, triggering the transcription of a specific gene

•

– _________________ are “master control genes” that regulate the expression of other groups of genes

– These are crucial in the process of embryonic development, when cells use chemical

signals to coordinate development

– A well-studied example of homeotic genes and their effects on development is seen in

fruit flies

• Certain homeotic genes in the fruit fly determine where ______________________

develop on the body

• One homeotic gene, when active, triggers legs to form on cells in the mid-body; this genes is inactive in other parts of the body

• A mutation in this homeotic genes can result in flies with legs coming out of their

heads, for example

• See video on experiments on homeotic genes in fruit flies: https://www.youtube.com/watch?v=voQQ1dhCqZg

•

•

• 5-minute break

Cell Differentiation and the Science of Cloning

–

– Remember, the cells of an organism start out as undifferentiated – they have the potential to become any type of cell

– As the organism grows, certain genes are turned on or left turned off, and the cell thus becomes differentiated

•

•

– Sometimes, cells that have become differentiated can “dedifferentiate” – allowing them

to grow into a new organism, or a new part of an organism

• Example: many plants can be propagated vegetatively

• Amphibians are famous for being able to re-generate lost limbs

•

• This process is relatively easy to do with plants

–Is used to make large numbers of “copies” of plants with desirable characteristics

• If a new organism is grown from the somatic (body) cells of an adult organism, the

result is a ____________ – it is genetically identical to the organism from whose cells it was grown

•

• _______________ = the production of identical copies of a cell, organism, or DNA molecule

–Doesn’t ONLY refer to making copies of entire organisms

–More common: cloning cells or molecules

– There are different types of cloning, and each has a different purpose

•

– “Reproductive Cloning”

•

• The egg of a female animal is extracted, its ______ is removed, and the DNA from a ___________ cell of the desired organism is placed into the egg

• After the egg divides and forms an early embryo, it can be implanted into a female

• Can be used to generate “copies” of desirable farm animals, or endangered species

•

•

•

• “Dolly” the sheep was the first mammal to be cloned (1997)

–Died in 2003 from a lung disease

–Was her relatively early death a result of cloning? Difficult to say, as lung diseases are

fairly common among sheep raised indoors…

• In January of 2018, it was reported that the first primates (macaques) were cloned

– https://www.youtube.com/watch?v=oEXleYs58MY

•

– Therapeutic Cloning is another type of cloning

• Purpose is to generate __________________ (ES cells)

• Can divide indefinitely in culture, and have the potential to develop into any type of cell

• Certain growth factors can induce these cells to differentiate into specific kinds of cells

• May be used to treat or cure diseases or injured organs

• For example, there has been some success using stem cells to treat stroke victims or

Parkinson’s disease (inserting stem cells into brain)

• Embryonic stem cells are derived from embryos, and therein lies the controversy

•

– Adult stem cells are partially differentiated

• They may be able to differentiate into one of a few different types of cells, but are already set on a path to become one of a few types

• Less flexible than ES cells

• Example: stem cells in bone marrow can become any of the types of blood cells

• More difficult to culture in the lab

• Can be harvested from adults, so are less controversial

– New sources of stem cells…

• ______________________stem cells; can be created from somatic cells

Genetics of Cancer

• Cancer is the second-leading cause of death in industrialized countries; what causes it?

• __________________ – genes that cause cancer

• We carry many genes that are ____________________: that is, if changed in some way, they can turn into oncogenes

• Oncogenes can arise from insertion by a virus, or by mutation of a proto-oncogene

• Many _____________________ code for ______________________ – proteins that stimulate cell division

– Too much growth factor produced by a mutated gene can cause cancerous growth

• Some genes, called _____________________ genes, inhibit cell division

– If they are mutated, can also cause cancer

• _______________________ are substances that cause mutations to DNA that eventually lead to cancer

• Examples of carcinogens:

– UV radiation (sunlight or tanning beds); (skin cancer)

– Tobacco smoke (lung cancer)

– Alcohol (liver cancer)

• Prevention

•

– Compounds found in fruits and vegetables can reduce cancer risks

• __________________

– Can help reduce and repair DNA damage

– Some cancer-fighting foods include: cabbage, broccoli, brussels sprouts, kale, shiitake mushrooms, onions, red beans, cherries, raspberries, strawberries, blueberries, and green tea

•

Bonus Activity

1. Explain how cells that look and behave so differently (like skin cells vs neurons) in the

same organism have the same genes.

2. What is an operon? Give an example.

3. A mutation in one gene may cause a major change in the body of a fruit fly, yet it takes many genes to produce a wing or leg. How can a change in one gene cause a big

change, like legs coming out of the head? What are such genes called?

4.

Lec. 9 Part B: Chapter 12 - Biotechnology

• DNA technology has wide variety of uses

• We will focus on genetic engineering and forensics (pg. 218-229)

Genetic Engineering

– Through __________________________, genes from different sources can be

combined

– Examples:

• Genes for specific protein products have been inserted into bacteria; the bacteria can then be grown and used to produce large quantities of the desired protein (e.g.

insulin)

• Proteins that can be used as vaccines can be produced by bacteria

•

• Genetically modified foods (e.g. “Bt” corn with built-in pesticide; “Golden Rice” with

enhanced nutritional value; tomatoes with a longer shelf life; etc.)

–GE crops introduced in 1996; now widely used; 93% of soy and 88% corn crops in

US were genetically modified (as of 2012)

–Primarily used in crops (insect resistance; herbicide tolerance)

•

•

• How is it done?

•

– Use of bacterial ________________ (circular pieces of DNA) as __________ (gene

carriers)

• ________________ are small circular pieces of DNA

• Bacteria readily take them in

• When a desired gene is inserted into a plasmid, the plasmid can then be isolated, and

then exposed to bacteria, which absorb them

• The bacteria will then express the desired gene in the modified plasmid

•

•

• How are genes inserted into plasmids?

•

– Cutting and Pasting Genes with ______________ Enzymes

• Restriction enzymes recognize short nucleotide sequences and cut the DNA at that site

• Staggered cut results in “_______________”

–A single-stranded piece of DNA at the end of the double-stranded molecule, which will readily connect with a complementary sticky end

• Fragments can then be stuck back together using ____________________

•

• In order to generate “sticky ends,” the recognition sequence must be a palindrome

– That is, the same sequence can be read from opposite directions on BOTH strands

– Example:

–

GAATTC

CTTAAG

•

• Gene of interest is now inserted into ___________

• ___________ is absorbed by bacteria, which express the ___________

• Bacteria can be readily grown to make many, many copies of the gene, or to synthesize

the protein encoded by the gene

• Most commonly, recombinant DNA technology is used to modify ___________

– Insect-resistant corn and cotton

– Rice that produces more vitamins

–Disease-resistant papya and sweet potatoes

•

• Some more unusual uses:

– Glowing pet fish

– Allergen-free cats

• Glowing Puppies!

– http://www.youtube.com/watch?v=YXPnQvcqHkg&feature=related

• Gene Editing

– __________________ system is a new technique that allows nucleotide sequences of genes to be edited in living cells

• May be used to reveal function of a gene, or to even correct a mutation

– Bacteria have a protein called _________ that can identify and cut our viral DNA from

their genome

• Will cut any DNA sequence that is complementary to a specific sequence of guiding _______

• A Cas9 protein with an RNA molecule complementary to a particular gene may be used to cut out a gene from a cell’s chromosomes

• Random DNA nucleotides are then inserted into the chromosome by DNA repair

enzymes; this “___________” the gene, making in non-functional

• Can therefore determine what the gene did in the cell

• To edit a gene, researchers can add a segment of a normal gene along with the Cas9-guide RNA complex

• After Cas9 cuts the target DNA, repair enzymes use the normal DNA as a template to

repair the target DNA (for example, a mutated gene)

• This allows researchers to potentially fix genetic mutations

• Researchers have used CRISP-Cas9 to fix a genetic defects in mice

• Video: https://www.youtube.com/watch?v=52jOEPzhpzc

•

Bonus Activity

• CRISPR is an exciting new technology and researchers are racing to find ways to use it. Do a Google search and find a recent news article talking about how CRISPR is being used.

Read the article, and then write 2-3 sentences summarizing the article.

•

• Break…

Forensics

The “scientific analysis of evidence for crime scene investigations and other legal proceedings”

– __________________ is one technique used in forensics, to compare DNA samples

– Every individual’s genetic makeup is unique

– A person’s “DNA Fingerprint” is his/her unique collection of DNA fragments generated

when restriction enzymes are used to cut up the DNA

•

•

• How do you generate a DNA fingerprint?

• First, DNA evidence must be collected

– Various tissues, such as blood, semen, skin, etc.

• Before DNA Fingerprints can be generated, often the DNA sample must be _____________

– A tiny spec of blood can provide enough information to run a test, if the DNA in that spec is copied many times

– The _______________________ is used to copy DNA

•

•

– Genomes are quite large, and typically scientists only need to amplify a small region of

the genome

– To amplify only a specific sequence, scientists use _____________, a short single-

stranded DNA molecule

– _____________ are selected that are complementary to only to the sequences at the ends of the target sequence

• The primers thus flank to target sequence, marking the beginning and end of the sequence to be copied

• Only the DNA between the primers is thus amplified

–

• _______________________ enzymes can then be used to cut the DNA into pieces

–Many different kinds of restriction enzymes

– Each recognizes a specific sequence and cuts DNA at that location

• May cut straight across both strands

• May make a “staggered” cut

• Although all humans are >99% genetically identical, the size of the human genome allows

for enough variation that differences can be detected

– About 3 billion base pairs in our DNA

– 1 in 1000 difference between any two people

–about 3 million differences between any two people

• When DNA samples from two different people are “digested” with the same restriction enzyme (or set of restriction enzymes), they will produce different numbers and sizes of DNA fragments

– These different sets of DNA pieces are called “_________________________________”

• Differences (polymorphisms) in the size of the fragments of DNA created by the

restriction enzymes

• ____________________________ can then be used to separate the fragments by size

–DNA is ____________ charged (due to the ___________ groups)

– Electrical current causes the fragments of DNA to move through a “gel”

– ____________ pieces migrate faster than ____________ ones

– Results in a unique banding pattern

•

•

• Another technique commonly used in forensics is _________________ (STR) Analysis

–Much of the DNA between genes is composed of ____________ sequences (for

example, perhaps the sequence AGAT may be repeated 12 times)

– Non-coding

– Close relatives more likely to have more similar patterns of STRs

– Standard STR analysis in forensics tests ___ different markers

• Chances of two different people being identical at all 13 markers is between

__________________________________________________________________________________________________

Bonus Activity 2

1. A carrier that moves DNA from one cell to another, such as a plasmid, is called a ___________. Plasmids are small, circular pieces of DNA from ___________.

2. In making recombinant DNA, what is the benefit of using a restriction enzyme that cuts

DNA in a staggered fashion?

3. A paleontologist has recovered a bit of organic material from the 400-year-old preserved

skin of an extinct dodo. She would like to compare DNA from the sample with DNA from living birds. The most useful method for initially increasing the amount of dodo DNA for

testing is _____________________.

4. What feature of DNA causes it to move through a gel during gel electrophoresis?

DNA Evidence in the News…

•

• Use of DNA evidence in criminal cases is relatively new

– First case was in 1986 in England

• A man confessed to a series of rape/murders; DNA evidence indicated he did not; another person was identified as the actual murderer, based on DNA evidence

– First used in the US in ______________

• Man convicted of rape based on DNA obtained from semen found in victim

• Recently, a number of people on death row have been found not guilty based on DNA

evidence

–

•

•

• Fatal Flaws: The Case of Earl Washington

–Washington spent 18 years in prison

– Came within nine days of being put to death in Virginia's electric chair.

– Years later, DNA evidence proved he was innocent, and after a long legal battle, he was set free

–Washington had been convicted largely based on his own confession to a rape and

murder

• His defenders say the confession was coerced

• Washington was mentally handicapped

•

• DNA testing is increasingly being made available in criminal cases

• 32 states mandate that compensation be awarded to people wrongfully convicted (as of 2017)

• >________ people have been exonerated (from death row) using DNA testing since 1989

(when DNA testing first became available)

• In 2013 Oklahoma became 50th (and final) state to guarantee right to DNA testing in cases

where DNA evidence could demonstrate innocence

•

• Conversely, DNA evidence can be used to prove guilt

• Jan 2009, this man, Benjamin Watta, convicted of 1980 rape/murder of Simone Sharp in California

• Was already in prison for attempted murder of his former girlfriend

• “Cold Case” solved

•

•

•

•

• Can DNA technology resolve all problems with accuracy in convicting criminals?

• In order to be accurate, DNA testing must be done properly

–DNA must be stored properly

– Contamination of DNA samples can invalidate results

– Sometimes, if enough DNA evidence is available, defense and prosecution conduct

independent tests, to ensure accuracy

– Sometimes, shoddy lab work can also lead to wrongful conviction

• Can’t resolve all problems, but it’s a good and important start

–

• All for now, except for…

•

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10/4/2018

10

BIO 1101 Lec. 9, Part A (Guided Notes): Chapter 11 -- Gene Regulation

Gene Regulation

•

• An organism has many different kinds of cells the have different functions, but every body

cell has the _______________________

•

• If the DNA in every body cell is the same, how can cells be so different?

•

• An individual starts out as a single cell – a _________________

•

• That single cell divides by __________, making identical copies of itself

•

• As the organism continues to grow by mitosis, individual cells become ______________ –some genes become inactivated, while others are activated

• In this way, cells can become specialized

•

• The genes that are “__________________” are transcribed into mRNA, and then

translated into proteins

•

• Genes that are ___________________ aren’t transcribed or translated

•

• How does a cell turn on or off different genes?

Gene Regulation in Bacteria

• Bacteria can conserve resources by only expressing the genes they need

• E. coli bacteria can use the sugar ___________ as fuel if it is available in their environment

– Three enzymes needed to absorb and digest

– Genes located next to each other

– Genes that have related function and which can be simultaneously regulated form an

_______________

– E. coli have a _______________

•

•

• Control of an __________________

– _________________: a control sequence on DNA near the operon to which

____________________ can bind

– _________________: a sequence between the promoter and the genes of the operon;

_______________ can bind here to turn off transcription

• In the case of the lac operon, lactose interferes with the attachment of the lac

repressor to the operator; thus the presence of lactose turns on the operon

•

•

Gene Regulation in Eukarytoes

• In Eukaryotes (organisms other than bacteria and archea), several methods may be used:

– _________________: when DNA is in a condensed state (as when ready to divide), it

cannot be transcribed or translated

• Example: X chromosome inactivation in female cats

–

•

– Genes can be regulated at initiation of transcription

• Most important stage for regulating gene expression

• Most genes in eukaryotes, by default, are turned “______”

• Many proteins are involved in enhancing transcription of particular genes

• ______________ ______ are proteins that bind to enhancers and promoters of DNA

to activate multiple genes at the same time

• _____________________ may bind to DNA sequences called _______________ to inhibit transcription

•

• RNA Processing and Breakdown

– As we previously discussed, the initial mRNA transcript is edited to remove ____________ (intervening sequences) and __________ linked together before it leaves the nucleus and is translated

– Another way gene expression can be modified is through alternative ways of linking the

__________

• The exons of one gene may be linked in different ways to create different

__________________

– This is called _________________

•

•

– Not all RNAs code for protein

• Used to be considered “junk”

• Actually perform important functions

–microRNAs, for example

• miRNAs bind to one or more ____________

• Form a complex with mRNAs

• If the miRNA is complementary to the entire length of the mRNA, then the target

mRNA is ________________

• If the miRNA is only complementary to a part of the target mRNA, then the complex

_______________________________________

–Other ways genes can be regulated:

•

• By breaking down mRNA in the cytoplasm

•

• By regulating translation

•

• By altering the proteins produced in translation

•

• By breaking down the produced proteins

• The process of forming proteins from a DNA molecule involves many steps

•

• At each step, there are opportunities for gene regulation

•

• Cell Signaling and Homeotic Genes

– In multicellular organisms, information must be communicated between cells

– Chemicals like ____________ can be secreted by one cell and signal some activity in another cell

– The signal molecule acts by binding to a ___________________ on the target cell, initiating a ___________________________

– The binding activates a series of _______________, which ultimately activates a

________________, triggering the transcription of a specific gene

•

– _________________ are “master control genes” that regulate the expression of other groups of genes

– These are crucial in the process of embryonic development, when cells use chemical

signals to coordinate development

– A well-studied example of homeotic genes and their effects on development is seen in

fruit flies

• Certain homeotic genes in the fruit fly determine where ______________________

develop on the body

• One homeotic gene, when active, triggers legs to form on cells in the mid-body; this genes is inactive in other parts of the body

• A mutation in this homeotic genes can result in flies with legs coming out of their

heads, for example

• See video on experiments on homeotic genes in fruit flies:

https://www.youtube.com/watch?v=voQQ1dhCqZg

•

•

• 5-minute break

Cell Differentiation and the Science of Cloning

–

– Remember, the cells of an organism start out as undifferentiated – they have the

potential to become any type of cell

– As the organism grows, certain genes are turned on or left turned off, and the cell thus becomes differentiated

•

•

– Sometimes, cells that have become differentiated can “dedifferentiate” – allowing them

to grow into a new organism, or a new part of an organism

• Example: many plants can be propagated vegetatively

• Amphibians are famous for being able to re-generate lost limbs

•

• This process is relatively easy to do with plants

–Is used to make large numbers of “copies” of plants with desirable characteristics

• If a new organism is grown from the somatic (body) cells of an adult organism, the

result is a ____________ – it is genetically identical to the organism from whose cells it was grown

•

• _______________ = the production of identical copies of a cell, organism, or DNA molecule

–Doesn’t ONLY refer to making copies of entire organisms

–More common: cloning cells or molecules

– There are different types of cloning, and each has a different purpose

•

– “Reproductive Cloning”

•

• The egg of a female animal is extracted, its ______ is removed, and the DNA from a ___________ cell of the desired organism is placed into the egg

• After the egg divides and forms an early embryo, it can be implanted into a female

• Can be used to generate “copies” of desirable farm animals, or endangered species

•

•

•

• “Dolly” the sheep was the first mammal to be cloned (1997)

–Died in 2003 from a lung disease

–Was her relatively early death a result of cloning? Difficult to say, as lung diseases are

fairly common among sheep raised indoors…

• In January of 2018, it was reported that the first primates (macaques) were cloned

– https://www.youtube.com/watch?v=oEXleYs58MY

•

– Therapeutic Cloning is another type of cloning

• Purpose is to generate __________________ (ES cells)

• Can divide indefinitely in culture, and have the potential to develop into any type of cell

• Certain growth factors can induce these cells to differentiate into specific kinds of cells

• May be used to treat or cure diseases or injured organs

• For example, there has been some success using stem cells to treat stroke victims or

Parkinson’s disease (inserting stem cells into brain)

• Embryonic stem cells are derived from embryos, and therein lies the controversy

•

– Adult stem cells are partially differentiated

• They may be able to differentiate into one of a few different types of cells, but are already set on a path to become one of a few types

• Less flexible than ES cells

• Example: stem cells in bone marrow can become any of the types of blood cells

• More difficult to culture in the lab

• Can be harvested from adults, so are less controversial

– New sources of stem cells…

• ______________________stem cells; can be created from somatic cells

Genetics of Cancer

• Cancer is the second-leading cause of death in industrialized countries; what causes it?

• __________________ – genes that cause cancer

• We carry many genes that are ____________________: that is, if changed in some way, they can turn into oncogenes

• Oncogenes can arise from insertion by a virus, or by mutation of a proto-oncogene

• Many _____________________ code for ______________________ – proteins that stimulate cell division

– Too much growth factor produced by a mutated gene can cause cancerous growth

• Some genes, called _____________________ genes, inhibit cell division

– If they are mutated, can also cause cancer

• _______________________ are substances that cause mutations to DNA that eventually lead to cancer

• Examples of carcinogens:

– UV radiation (sunlight or tanning beds); (skin cancer)

– Tobacco smoke (lung cancer)

– Alcohol (liver cancer)

• Prevention

•

– Compounds found in fruits and vegetables can reduce cancer risks

• __________________

– Can help reduce and repair DNA damage

– Some cancer-fighting foods include: cabbage, broccoli, brussels sprouts, kale, shiitake mushrooms, onions, red beans, cherries, raspberries, strawberries, blueberries, and

green tea

•

Bonus Activity

1. Explain how cells that look and behave so differently (like skin cells vs neurons) in the

same organism have the same genes.

2. What is an operon? Give an example.

3. A mutation in one gene may cause a major change in the body of a fruit fly, yet it takes many genes to produce a wing or leg. How can a change in one gene cause a big

change, like legs coming out of the head? What are such genes called?

4.

Lec. 9 Part B: Chapter 12 - Biotechnology

• DNA technology has wide variety of uses

• We will focus on genetic engineering and forensics (pg. 218-229)

Genetic Engineering

– Through __________________________, genes from different sources can be

combined

– Examples:

• Genes for specific protein products have been inserted into bacteria; the bacteria can then be grown and used to produce large quantities of the desired protein (e.g.

insulin)

• Proteins that can be used as vaccines can be produced by bacteria

•

• Genetically modified foods (e.g. “Bt” corn with built-in pesticide; “Golden Rice” with

enhanced nutritional value; tomatoes with a longer shelf life; etc.)

–GE crops introduced in 1996; now widely used; 93% of soy and 88% corn crops in

US were genetically modified (as of 2012)

–Primarily used in crops (insect resistance; herbicide tolerance)

•

•

• How is it done?

•

– Use of bacterial ________________ (circular pieces of DNA) as __________ (gene

carriers)

• ________________ are small circular pieces of DNA

• Bacteria readily take them in

• When a desired gene is inserted into a plasmid, the plasmid can then be isolated, and

then exposed to bacteria, which absorb them

• The bacteria will then express the desired gene in the modified plasmid

•

•

• How are genes inserted into plasmids?

•

– Cutting and Pasting Genes with ______________ Enzymes

• Restriction enzymes recognize short nucleotide sequences and cut the DNA at that site

• Staggered cut results in “_______________”

–A single-stranded piece of DNA at the end of the double-stranded molecule, which will readily connect with a complementary sticky end

• Fragments can then be stuck back together using ____________________

•

• In order to generate “sticky ends,” the recognition sequence must be a palindrome

– That is, the same sequence can be read from opposite directions on BOTH strands

– Example:

–

GAATTC

CTTAAG

•

• Gene of interest is now inserted into ___________

• ___________ is absorbed by bacteria, which express the ___________

• Bacteria can be readily grown to make many, many copies of the gene, or to synthesize

the protein encoded by the gene

• Most commonly, recombinant DNA technology is used to modify ___________

– Insect-resistant corn and cotton

– Rice that produces more vitamins

–Disease-resistant papya and sweet potatoes

•

• Some more unusual uses:

– Glowing pet fish

– Allergen-free cats

• Glowing Puppies!

– http://www.youtube.com/watch?v=YXPnQvcqHkg&feature=related

• Gene Editing

– __________________ system is a new technique that allows nucleotide sequences of

genes to be edited in living cells

• May be used to reveal function of a gene, or to even correct a mutation

– Bacteria have a protein called _________ that can identify and cut our viral DNA from

their genome

• Will cut any DNA sequence that is complementary to a specific sequence of guiding _______

• A Cas9 protein with an RNA molecule complementary to a particular gene may be used to cut out a gene from a cell’s chromosomes

• Random DNA nucleotides are then inserted into the chromosome by DNA repair

enzymes; this “___________” the gene, making in non-functional

• Can therefore determine what the gene did in the cell

• To edit a gene, researchers can add a segment of a normal gene along with the Cas9-guide RNA complex

• After Cas9 cuts the target DNA, repair enzymes use the normal DNA as a template to

repair the target DNA (for example, a mutated gene)

• This allows researchers to potentially fix genetic mutations

• Researchers have used CRISP-Cas9 to fix a genetic defects in mice

• Video: https://www.youtube.com/watch?v=52jOEPzhpzc

•

Bonus Activity

• CRISPR is an exciting new technology and researchers are racing to find ways to use it. Do a Google search and find a recent news article talking about how CRISPR is being used. Read the article, and then write 2-3 sentences summarizing the article.

•

• Break…

Forensics

The “scientific analysis of evidence for crime scene investigations and other legal proceedings”

– __________________ is one technique used in forensics, to compare DNA samples

– Every individual’s genetic makeup is unique

– A person’s “DNA Fingerprint” is his/her unique collection of DNA fragments generated

when restriction enzymes are used to cut up the DNA

•

•

• How do you generate a DNA fingerprint?

• First, DNA evidence must be collected

– Various tissues, such as blood, semen, skin, etc.

• Before DNA Fingerprints can be generated, often the DNA sample must be _____________

– A tiny spec of blood can provide enough information to run a test, if the DNA in that

spec is copied many times

– The _______________________ is used to copy DNA

•

•

– Genomes are quite large, and typically scientists only need to amplify a small region of

the genome

– To amplify only a specific sequence, scientists use _____________, a short single-

stranded DNA molecule

– _____________ are selected that are complementary to only to the sequences at the ends of the target sequence

• The primers thus flank to target sequence, marking the beginning and end of the sequence to be copied

• Only the DNA between the primers is thus amplified

–

• _______________________ enzymes can then be used to cut the DNA into pieces

–Many different kinds of restriction enzymes

– Each recognizes a specific sequence and cuts DNA at that location

• May cut straight across both strands

• May make a “staggered” cut

• Although all humans are >99% genetically identical, the size of the human genome allows

for enough variation that differences can be detected

– About 3 billion base pairs in our DNA

– 1 in 1000 difference between any two people

–about 3 million differences between any two people

• When DNA samples from two different people are “digested” with the same restriction enzyme (or set of restriction enzymes), they will produce different numbers and sizes of

DNA fragments

– These different sets of DNA pieces are called “_________________________________”

• Differences (polymorphisms) in the size of the fragments of DNA created by the

restriction enzymes

• ____________________________ can then be used to separate the fragments by size

–DNA is ____________ charged (due to the ___________ groups)

– Electrical current causes the fragments of DNA to move through a “gel”

– ____________ pieces migrate faster than ____________ ones

– Results in a unique banding pattern

•

•

• Another technique commonly used in forensics is _________________ (STR) Analysis

–Much of the DNA between genes is composed of ____________ sequences (for example, perhaps the sequence AGAT may be repeated 12 times)

– Non-coding

– Close relatives more likely to have more similar patterns of STRs

– Standard STR analysis in forensics tests ___ different markers

• Chances of two different people being identical at all 13 markers is between

__________________________________________________________________________________________________

Bonus Activity 2

1. A carrier that moves DNA from one cell to another, such as a plasmid, is called a ___________. Plasmids are small, circular pieces of DNA from ___________.

2. In making recombinant DNA, what is the benefit of using a restriction enzyme that cuts

DNA in a staggered fashion?

3. A paleontologist has recovered a bit of organic material from the 400-year-old preserved

skin of an extinct dodo. She would like to compare DNA from the sample with DNA from living birds. The most useful method for initially increasing the amount of dodo DNA for

testing is _____________________.

4. What feature of DNA causes it to move through a gel during gel electrophoresis?

DNA Evidence in the News…

•

• Use of DNA evidence in criminal cases is relatively new

– First case was in 1986 in England

• A man confessed to a series of rape/murders; DNA evidence indicated he did not; another person was identified as the actual murderer, based on DNA evidence

– First used in the US in ______________

• Man convicted of rape based on DNA obtained from semen found in victim

• Recently, a number of people on death row have been found not guilty based on DNA

evidence

–

•

•

• Fatal Flaws: The Case of Earl Washington

–Washington spent 18 years in prison

– Came within nine days of being put to death in Virginia's electric chair.

– Years later, DNA evidence proved he was innocent, and after a long legal battle, he was set free

–Washington had been convicted largely based on his own confession to a rape and

murder

• His defenders say the confession was coerced

• Washington was mentally handicapped

•

• DNA testing is increasingly being made available in criminal cases

• 32 states mandate that compensation be awarded to people wrongfully convicted (as of 2017)

• >________ people have been exonerated (from death row) using DNA testing since 1989

(when DNA testing first became available)

• In 2013 Oklahoma became 50th (and final) state to guarantee right to DNA testing in cases

where DNA evidence could demonstrate innocence

•

• Conversely, DNA evidence can be used to prove guilt

• Jan 2009, this man, Benjamin Watta, convicted of 1980 rape/murder of Simone Sharp in California

• Was already in prison for attempted murder of his former girlfriend

• “Cold Case” solved

•

•

•

•

• Can DNA technology resolve all problems with accuracy in convicting criminals?

• In order to be accurate, DNA testing must be done properly

–DNA must be stored properly

– Contamination of DNA samples can invalidate results

– Sometimes, if enough DNA evidence is available, defense and prosecution conduct

independent tests, to ensure accuracy

– Sometimes, shoddy lab work can also lead to wrongful conviction

• Can’t resolve all problems, but it’s a good and important start

–

• All for now, except for…

•

Random Animal of the Day!

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10/4/2018

11

BIO 1101 Lec. 9, Part A (Guided Notes): Chapter 11 -- Gene Regulation

Gene Regulation

•

• An organism has many different kinds of cells the have different functions, but every body

cell has the _______________________

•

• If the DNA in every body cell is the same, how can cells be so different?

•

• An individual starts out as a single cell – a _________________

•

• That single cell divides by __________, making identical copies of itself

•

• As the organism continues to grow by mitosis, individual cells become ______________ –some genes become inactivated, while others are activated

• In this way, cells can become specialized

•

• The genes that are “__________________” are transcribed into mRNA, and then

translated into proteins

•

• Genes that are ___________________ aren’t transcribed or translated

•

• How does a cell turn on or off different genes?

Gene Regulation in Bacteria

• Bacteria can conserve resources by only expressing the genes they need

• E. coli bacteria can use the sugar ___________ as fuel if it is available in their environment

– Three enzymes needed to absorb and digest

– Genes located next to each other

– Genes that have related function and which can be simultaneously regulated form an

_______________

– E. coli have a _______________

•

•

• Control of an __________________

– _________________: a control sequence on DNA near the operon to which

____________________ can bind

– _________________: a sequence between the promoter and the genes of the operon;

_______________ can bind here to turn off transcription

• In the case of the lac operon, lactose interferes with the attachment of the lac

repressor to the operator; thus the presence of lactose turns on the operon

•

•

Gene Regulation in Eukarytoes

• In Eukaryotes (organisms other than bacteria and archea), several methods may be used:

– _________________: when DNA is in a condensed state (as when ready to divide), it

cannot be transcribed or translated

• Example: X chromosome inactivation in female cats

–

•

– Genes can be regulated at initiation of transcription

• Most important stage for regulating gene expression

• Most genes in eukaryotes, by default, are turned “______”

• Many proteins are involved in enhancing transcription of particular genes

• ______________ ______ are proteins that bind to enhancers and promoters of DNA

to activate multiple genes at the same time

• _____________________ may bind to DNA sequences called _______________ to inhibit transcription

•

• RNA Processing and Breakdown

– As we previously discussed, the initial mRNA transcript is edited to remove

____________ (intervening sequences) and __________ linked together before it leaves the nucleus and is translated

– Another way gene expression can be modified is through alternative ways of linking the

__________

• The exons of one gene may be linked in different ways to create different

__________________

– This is called _________________

•

•

– Not all RNAs code for protein

• Used to be considered “junk”

• Actually perform important functions

–microRNAs, for example

• miRNAs bind to one or more ____________

• Form a complex with mRNAs

• If the miRNA is complementary to the entire length of the mRNA, then the target

mRNA is ________________

• If the miRNA is only complementary to a part of the target mRNA, then the complex

_______________________________________

–Other ways genes can be regulated:

•

• By breaking down mRNA in the cytoplasm

•

• By regulating translation

•

• By altering the proteins produced in translation

•

• By breaking down the produced proteins

• The process of forming proteins from a DNA molecule involves many steps

•

• At each step, there are opportunities for gene regulation

•

• Cell Signaling and Homeotic Genes

– In multicellular organisms, information must be communicated between cells

– Chemicals like ____________ can be secreted by one cell and signal some activity in another cell

– The signal molecule acts by binding to a ___________________ on the target cell, initiating a ___________________________

– The binding activates a series of _______________, which ultimately activates a

________________, triggering the transcription of a specific gene

•

– _________________ are “master control genes” that regulate the expression of other groups of genes

– These are crucial in the process of embryonic development, when cells use chemical

signals to coordinate development

– A well-studied example of homeotic genes and their effects on development is seen in fruit flies

• Certain homeotic genes in the fruit fly determine where ______________________

develop on the body

• One homeotic gene, when active, triggers legs to form on cells in the mid-body; this genes is inactive in other parts of the body

• A mutation in this homeotic genes can result in flies with legs coming out of their

heads, for example

• See video on experiments on homeotic genes in fruit flies:

https://www.youtube.com/watch?v=voQQ1dhCqZg

•

•

• 5-minute break

Cell Differentiation and the Science of Cloning

–

– Remember, the cells of an organism start out as undifferentiated – they have the

potential to become any type of cell

– As the organism grows, certain genes are turned on or left turned off, and the cell thus becomes differentiated

•

•

– Sometimes, cells that have become differentiated can “dedifferentiate” – allowing them

to grow into a new organism, or a new part of an organism

• Example: many plants can be propagated vegetatively

• Amphibians are famous for being able to re-generate lost limbs

•

• This process is relatively easy to do with plants

–Is used to make large numbers of “copies” of plants with desirable characteristics

• If a new organism is grown from the somatic (body) cells of an adult organism, the

result is a ____________ – it is genetically identical to the organism from whose cells it was grown

•

• _______________ = the production of identical copies of a cell, organism, or DNA molecule

–Doesn’t ONLY refer to making copies of entire organisms

–More common: cloning cells or molecules

– There are different types of cloning, and each has a different purpose

•

– “Reproductive Cloning”

•

• The egg of a female animal is extracted, its ______ is removed, and the DNA from a ___________ cell of the desired organism is placed into the egg

• After the egg divides and forms an early embryo, it can be implanted into a female

• Can be used to generate “copies” of desirable farm animals, or endangered species

•

•

•

• “Dolly” the sheep was the first mammal to be cloned (1997)

–Died in 2003 from a lung disease

–Was her relatively early death a result of cloning? Difficult to say, as lung diseases are

fairly common among sheep raised indoors…

• In January of 2018, it was reported that the first primates (macaques) were cloned

– https://www.youtube.com/watch?v=oEXleYs58MY

•

– Therapeutic Cloning is another type of cloning

• Purpose is to generate __________________ (ES cells)

• Can divide indefinitely in culture, and have the potential to develop into any type of cell

• Certain growth factors can induce these cells to differentiate into specific kinds of cells

• May be used to treat or cure diseases or injured organs

• For example, there has been some success using stem cells to treat stroke victims or

Parkinson’s disease (inserting stem cells into brain)

• Embryonic stem cells are derived from embryos, and therein lies the controversy

•

– Adult stem cells are partially differentiated

• They may be able to differentiate into one of a few different types of cells, but are already set on a path to become one of a few types

• Less flexible than ES cells

• Example: stem cells in bone marrow can become any of the types of blood cells

• More difficult to culture in the lab

• Can be harvested from adults, so are less controversial

– New sources of stem cells…

• ______________________stem cells; can be created from somatic cells

Genetics of Cancer

• Cancer is the second-leading cause of death in industrialized countries; what causes it?

• __________________ – genes that cause cancer

• We carry many genes that are ____________________: that is, if changed in some way, they can turn into oncogenes

• Oncogenes can arise from insertion by a virus, or by mutation of a proto-oncogene

• Many _____________________ code for ______________________ – proteins that stimulate cell division

– Too much growth factor produced by a mutated gene can cause cancerous growth

• Some genes, called _____________________ genes, inhibit cell division

– If they are mutated, can also cause cancer

• _______________________ are substances that cause mutations to DNA that eventually lead to cancer

• Examples of carcinogens:

– UV radiation (sunlight or tanning beds); (skin cancer)

– Tobacco smoke (lung cancer)

– Alcohol (liver cancer)

• Prevention

•

– Compounds found in fruits and vegetables can reduce cancer risks

• __________________

– Can help reduce and repair DNA damage

– Some cancer-fighting foods include: cabbage, broccoli, brussels sprouts, kale, shiitake mushrooms, onions, red beans, cherries, raspberries, strawberries, blueberries, and

green tea

•

Bonus Activity

1. Explain how cells that look and behave so differently (like skin cells vs neurons) in the same organism have the same genes.

2. What is an operon? Give an example.

3. A mutation in one gene may cause a major change in the body of a fruit fly, yet it takes many genes to produce a wing or leg. How can a change in one gene cause a big

change, like legs coming out of the head? What are such genes called?

4.

Lec. 9 Part B: Chapter 12 - Biotechnology

• DNA technology has wide variety of uses

• We will focus on genetic engineering and forensics (pg. 218-229)

Genetic Engineering

– Through __________________________, genes from different sources can be

combined

– Examples:

• Genes for specific protein products have been inserted into bacteria; the bacteria can then be grown and used to produce large quantities of the desired protein (e.g.

insulin)

• Proteins that can be used as vaccines can be produced by bacteria

•

• Genetically modified foods (e.g. “Bt” corn with built-in pesticide; “Golden Rice” with

enhanced nutritional value; tomatoes with a longer shelf life; etc.)

–GE crops introduced in 1996; now widely used; 93% of soy and 88% corn crops in

US were genetically modified (as of 2012)

–Primarily used in crops (insect resistance; herbicide tolerance)

•

•

• How is it done?

•

– Use of bacterial ________________ (circular pieces of DNA) as __________ (gene carriers)

• ________________ are small circular pieces of DNA

• Bacteria readily take them in

• When a desired gene is inserted into a plasmid, the plasmid can then be isolated, and

then exposed to bacteria, which absorb them

• The bacteria will then express the desired gene in the modified plasmid

•

•

• How are genes inserted into plasmids?

•

– Cutting and Pasting Genes with ______________ Enzymes

• Restriction enzymes recognize short nucleotide sequences and cut the DNA at that site

• Staggered cut results in “_______________”

–A single-stranded piece of DNA at the end of the double-stranded molecule, which will readily connect with a complementary sticky end

• Fragments can then be stuck back together using ____________________

•

• In order to generate “sticky ends,” the recognition sequence must be a palindrome

– That is, the same sequence can be read from opposite directions on BOTH strands

– Example:

–

GAATTC

CTTAAG

•

• Gene of interest is now inserted into ___________

• ___________ is absorbed by bacteria, which express the ___________

• Bacteria can be readily grown to make many, many copies of the gene, or to synthesize

the protein encoded by the gene

• Most commonly, recombinant DNA technology is used to modify ___________

– Insect-resistant corn and cotton

– Rice that produces more vitamins

–Disease-resistant papya and sweet potatoes

•

• Some more unusual uses:

– Glowing pet fish

– Allergen-free cats

• Glowing Puppies!

– http://www.youtube.com/watch?v=YXPnQvcqHkg&feature=related

• Gene Editing

– __________________ system is a new technique that allows nucleotide sequences of

genes to be edited in living cells

• May be used to reveal function of a gene, or to even correct a mutation

– Bacteria have a protein called _________ that can identify and cut our viral DNA from

their genome

• Will cut any DNA sequence that is complementary to a specific sequence of guiding _______

• A Cas9 protein with an RNA molecule complementary to a particular gene may be used to cut out a gene from a cell’s chromosomes

• Random DNA nucleotides are then inserted into the chromosome by DNA repair

enzymes; this “___________” the gene, making in non-functional

• Can therefore determine what the gene did in the cell

• To edit a gene, researchers can add a segment of a normal gene along with the Cas9-guide RNA complex

• After Cas9 cuts the target DNA, repair enzymes use the normal DNA as a template to repair the target DNA (for example, a mutated gene)

• This allows researchers to potentially fix genetic mutations

• Researchers have used CRISP-Cas9 to fix a genetic defects in mice

• Video: https://www.youtube.com/watch?v=52jOEPzhpzc

•

Bonus Activity

• CRISPR is an exciting new technology and researchers are racing to find ways to use it. Do a Google search and find a recent news article talking about how CRISPR is being used.

Read the article, and then write 2-3 sentences summarizing the article.

•

• Break…

Forensics

The “scientific analysis of evidence for crime scene investigations and other legal proceedings”

– __________________ is one technique used in forensics, to compare DNA samples

– Every individual’s genetic makeup is unique

– A person’s “DNA Fingerprint” is his/her unique collection of DNA fragments generated

when restriction enzymes are used to cut up the DNA

•

•

• How do you generate a DNA fingerprint?

• First, DNA evidence must be collected

– Various tissues, such as blood, semen, skin, etc.

• Before DNA Fingerprints can be generated, often the DNA sample must be _____________

– A tiny spec of blood can provide enough information to run a test, if the DNA in that

spec is copied many times

– The _______________________ is used to copy DNA

•

•

– Genomes are quite large, and typically scientists only need to amplify a small region of

the genome

– To amplify only a specific sequence, scientists use _____________, a short single-

stranded DNA molecule

– _____________ are selected that are complementary to only to the sequences at the ends of the target sequence

• The primers thus flank to target sequence, marking the beginning and end of the sequence to be copied

• Only the DNA between the primers is thus amplified

–

• _______________________ enzymes can then be used to cut the DNA into pieces

–Many different kinds of restriction enzymes

– Each recognizes a specific sequence and cuts DNA at that location

• May cut straight across both strands

• May make a “staggered” cut

• Although all humans are >99% genetically identical, the size of the human genome allows

for enough variation that differences can be detected

– About 3 billion base pairs in our DNA

– 1 in 1000 difference between any two people

–about 3 million differences between any two people

• When DNA samples from two different people are “digested” with the same restriction enzyme (or set of restriction enzymes), they will produce different numbers and sizes of

DNA fragments

– These different sets of DNA pieces are called “_________________________________”

• Differences (polymorphisms) in the size of the fragments of DNA created by the

restriction enzymes

• ____________________________ can then be used to separate the fragments by size

–DNA is ____________ charged (due to the ___________ groups)

– Electrical current causes the fragments of DNA to move through a “gel”

– ____________ pieces migrate faster than ____________ ones

– Results in a unique banding pattern

•

•

• Another technique commonly used in forensics is _________________ (STR) Analysis

–Much of the DNA between genes is composed of ____________ sequences (for

example, perhaps the sequence AGAT may be repeated 12 times)

– Non-coding

– Close relatives more likely to have more similar patterns of STRs

– Standard STR analysis in forensics tests ___ different markers

• Chances of two different people being identical at all 13 markers is between

__________________________________________________________________________________________________

Bonus Activity 2

1. A carrier that moves DNA from one cell to another, such as a plasmid, is called a ___________. Plasmids are small, circular pieces of DNA from ___________.

2. In making recombinant DNA, what is the benefit of using a restriction enzyme that cuts

DNA in a staggered fashion?

3. A paleontologist has recovered a bit of organic material from the 400-year-old preserved skin of an extinct dodo. She would like to compare DNA from the sample with DNA from living birds. The most useful method for initially increasing the amount of dodo DNA for

testing is _____________________.

4. What feature of DNA causes it to move through a gel during gel electrophoresis?

DNA Evidence in the News…

•

• Use of DNA evidence in criminal cases is relatively new

– First case was in 1986 in England

• A man confessed to a series of rape/murders; DNA evidence indicated he did not; another person was identified as the actual murderer, based on DNA evidence

– First used in the US in ______________

• Man convicted of rape based on DNA obtained from semen found in victim

• Recently, a number of people on death row have been found not guilty based on DNA

evidence

–

•

•

• Fatal Flaws: The Case of Earl Washington

–Washington spent 18 years in prison

– Came within nine days of being put to death in Virginia's electric chair.

– Years later, DNA evidence proved he was innocent, and after a long legal battle, he was set free

–Washington had been convicted largely based on his own confession to a rape and

murder

• His defenders say the confession was coerced

• Washington was mentally handicapped

•

• DNA testing is increasingly being made available in criminal cases

• 32 states mandate that compensation be awarded to people wrongfully convicted (as of 2017)

• >________ people have been exonerated (from death row) using DNA testing since 1989

(when DNA testing first became available)

• In 2013 Oklahoma became 50th (and final) state to guarantee right to DNA testing in cases

where DNA evidence could demonstrate innocence

•

• Conversely, DNA evidence can be used to prove guilt

• Jan 2009, this man, Benjamin Watta, convicted of 1980 rape/murder of Simone Sharp in California

• Was already in prison for attempted murder of his former girlfriend

• “Cold Case” solved

•

•

•

•

• Can DNA technology resolve all problems with accuracy in convicting criminals?

• In order to be accurate, DNA testing must be done properly

–DNA must be stored properly

– Contamination of DNA samples can invalidate results

– Sometimes, if enough DNA evidence is available, defense and prosecution conduct

independent tests, to ensure accuracy

– Sometimes, shoddy lab work can also lead to wrongful conviction

• Can’t resolve all problems, but it’s a good and important start

–

• All for now, except for…

•

Random Animal of the Day!

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10/4/2018

12

BIO 1101 Lec. 9, Part A (Guided Notes): Chapter 11 -- Gene Regulation

Gene Regulation

•

• An organism has many different kinds of cells the have different functions, but every body

cell has the _______________________

•

• If the DNA in every body cell is the same, how can cells be so different?

•

• An individual starts out as a single cell – a _________________

•

• That single cell divides by __________, making identical copies of itself

•

• As the organism continues to grow by mitosis, individual cells become ______________ –some genes become inactivated, while others are activated

• In this way, cells can become specialized

•

• The genes that are “__________________” are transcribed into mRNA, and then

translated into proteins

•

• Genes that are ___________________ aren’t transcribed or translated

•

• How does a cell turn on or off different genes?

Gene Regulation in Bacteria

• Bacteria can conserve resources by only expressing the genes they need

• E. coli bacteria can use the sugar ___________ as fuel if it is available in their environment

– Three enzymes needed to absorb and digest

– Genes located next to each other

– Genes that have related function and which can be simultaneously regulated form an

_______________

– E. coli have a _______________

•

•

• Control of an __________________

– _________________: a control sequence on DNA near the operon to which

____________________ can bind

– _________________: a sequence between the promoter and the genes of the operon;

_______________ can bind here to turn off transcription

• In the case of the lac operon, lactose interferes with the attachment of the lac

repressor to the operator; thus the presence of lactose turns on the operon

•

•

Gene Regulation in Eukarytoes

• In Eukaryotes (organisms other than bacteria and archea), several methods may be used:

– _________________: when DNA is in a condensed state (as when ready to divide), it

cannot be transcribed or translated

• Example: X chromosome inactivation in female cats

–

•

– Genes can be regulated at initiation of transcription

• Most important stage for regulating gene expression

• Most genes in eukaryotes, by default, are turned “______”

• Many proteins are involved in enhancing transcription of particular genes

• ______________ ______ are proteins that bind to enhancers and promoters of DNA to activate multiple genes at the same time

• _____________________ may bind to DNA sequences called _______________ to inhibit transcription

•

• RNA Processing and Breakdown

– As we previously discussed, the initial mRNA transcript is edited to remove

____________ (intervening sequences) and __________ linked together before it leaves the nucleus and is translated

– Another way gene expression can be modified is through alternative ways of linking the

__________

• The exons of one gene may be linked in different ways to create different

__________________

– This is called _________________

•

•

– Not all RNAs code for protein

• Used to be considered “junk”

• Actually perform important functions

–microRNAs, for example

• miRNAs bind to one or more ____________

• Form a complex with mRNAs

• If the miRNA is complementary to the entire length of the mRNA, then the target

mRNA is ________________

• If the miRNA is only complementary to a part of the target mRNA, then the complex

_______________________________________

–Other ways genes can be regulated:

•

• By breaking down mRNA in the cytoplasm

•

• By regulating translation

•

• By altering the proteins produced in translation

•

• By breaking down the produced proteins

• The process of forming proteins from a DNA molecule involves many steps

•

• At each step, there are opportunities for gene regulation

•

• Cell Signaling and Homeotic Genes

– In multicellular organisms, information must be communicated between cells

– Chemicals like ____________ can be secreted by one cell and signal some activity in another cell

– The signal molecule acts by binding to a ___________________ on the target cell, initiating a ___________________________

– The binding activates a series of _______________, which ultimately activates a

________________, triggering the transcription of a specific gene

•

– _________________ are “master control genes” that regulate the expression of other groups of genes

– These are crucial in the process of embryonic development, when cells use chemical

signals to coordinate development

– A well-studied example of homeotic genes and their effects on development is seen in

fruit flies

• Certain homeotic genes in the fruit fly determine where ______________________

develop on the body

• One homeotic gene, when active, triggers legs to form on cells in the mid-body; this genes is inactive in other parts of the body

• A mutation in this homeotic genes can result in flies with legs coming out of their

heads, for example

• See video on experiments on homeotic genes in fruit flies:

https://www.youtube.com/watch?v=voQQ1dhCqZg

•

•

• 5-minute break

Cell Differentiation and the Science of Cloning

–

– Remember, the cells of an organism start out as undifferentiated – they have the

potential to become any type of cell

– As the organism grows, certain genes are turned on or left turned off, and the cell thus becomes differentiated

•

•

– Sometimes, cells that have become differentiated can “dedifferentiate” – allowing them

to grow into a new organism, or a new part of an organism

• Example: many plants can be propagated vegetatively

• Amphibians are famous for being able to re-generate lost limbs

•

• This process is relatively easy to do with plants

–Is used to make large numbers of “copies” of plants with desirable characteristics

• If a new organism is grown from the somatic (body) cells of an adult organism, the result is a ____________ – it is genetically identical to the organism from whose cells it was grown

•

• _______________ = the production of identical copies of a cell, organism, or DNA molecule

–Doesn’t ONLY refer to making copies of entire organisms

–More common: cloning cells or molecules

– There are different types of cloning, and each has a different purpose

•

– “Reproductive Cloning”

•

• The egg of a female animal is extracted, its ______ is removed, and the DNA from a ___________ cell of the desired organism is placed into the egg

• After the egg divides and forms an early embryo, it can be implanted into a female

• Can be used to generate “copies” of desirable farm animals, or endangered species

•

•

•

• “Dolly” the sheep was the first mammal to be cloned (1997)

–Died in 2003 from a lung disease

–Was her relatively early death a result of cloning? Difficult to say, as lung diseases are

fairly common among sheep raised indoors…

• In January of 2018, it was reported that the first primates (macaques) were cloned

– https://www.youtube.com/watch?v=oEXleYs58MY

•

– Therapeutic Cloning is another type of cloning

• Purpose is to generate __________________ (ES cells)

• Can divide indefinitely in culture, and have the potential to develop into any type of cell

• Certain growth factors can induce these cells to differentiate into specific kinds of cells

• May be used to treat or cure diseases or injured organs

• For example, there has been some success using stem cells to treat stroke victims or

Parkinson’s disease (inserting stem cells into brain)

• Embryonic stem cells are derived from embryos, and therein lies the controversy

•

– Adult stem cells are partially differentiated

• They may be able to differentiate into one of a few different types of cells, but are already set on a path to become one of a few types

• Less flexible than ES cells

• Example: stem cells in bone marrow can become any of the types of blood cells

• More difficult to culture in the lab

• Can be harvested from adults, so are less controversial

– New sources of stem cells…

• ______________________stem cells; can be created from somatic cells

Genetics of Cancer

• Cancer is the second-leading cause of death in industrialized countries; what causes it?

• __________________ – genes that cause cancer

• We carry many genes that are ____________________: that is, if changed in some way, they can turn into oncogenes

• Oncogenes can arise from insertion by a virus, or by mutation of a proto-oncogene

• Many _____________________ code for ______________________ – proteins that stimulate cell division

– Too much growth factor produced by a mutated gene can cause cancerous growth

• Some genes, called _____________________ genes, inhibit cell division

– If they are mutated, can also cause cancer

• _______________________ are substances that cause mutations to DNA that eventually lead to cancer

• Examples of carcinogens:

– UV radiation (sunlight or tanning beds); (skin cancer)

– Tobacco smoke (lung cancer)

– Alcohol (liver cancer)

• Prevention

•

– Compounds found in fruits and vegetables can reduce cancer risks

• __________________

– Can help reduce and repair DNA damage

– Some cancer-fighting foods include: cabbage, broccoli, brussels sprouts, kale, shiitake mushrooms, onions, red beans, cherries, raspberries, strawberries, blueberries, and

green tea

•

Bonus Activity

1. Explain how cells that look and behave so differently (like skin cells vs neurons) in the

same organism have the same genes.

2. What is an operon? Give an example.

3. A mutation in one gene may cause a major change in the body of a fruit fly, yet it takes many genes to produce a wing or leg. How can a change in one gene cause a big

change, like legs coming out of the head? What are such genes called?

4.

Lec. 9 Part B: Chapter 12 - Biotechnology

• DNA technology has wide variety of uses

• We will focus on genetic engineering and forensics (pg. 218-229)

Genetic Engineering

– Through __________________________, genes from different sources can be

combined

– Examples:

• Genes for specific protein products have been inserted into bacteria; the bacteria can then be grown and used to produce large quantities of the desired protein (e.g.

insulin)

• Proteins that can be used as vaccines can be produced by bacteria

•

• Genetically modified foods (e.g. “Bt” corn with built-in pesticide; “Golden Rice” with

enhanced nutritional value; tomatoes with a longer shelf life; etc.)

–GE crops introduced in 1996; now widely used; 93% of soy and 88% corn crops in

US were genetically modified (as of 2012)

–Primarily used in crops (insect resistance; herbicide tolerance)

•

•

• How is it done?

•

– Use of bacterial ________________ (circular pieces of DNA) as __________ (gene

carriers)

• ________________ are small circular pieces of DNA

• Bacteria readily take them in

• When a desired gene is inserted into a plasmid, the plasmid can then be isolated, and

then exposed to bacteria, which absorb them

• The bacteria will then express the desired gene in the modified plasmid

•

•

• How are genes inserted into plasmids?

•

– Cutting and Pasting Genes with ______________ Enzymes

• Restriction enzymes recognize short nucleotide sequences and cut the DNA at that site

• Staggered cut results in “_______________”

–A single-stranded piece of DNA at the end of the double-stranded molecule, which will readily connect with a complementary sticky end

• Fragments can then be stuck back together using ____________________

•

• In order to generate “sticky ends,” the recognition sequence must be a palindrome

– That is, the same sequence can be read from opposite directions on BOTH strands

– Example:

–

GAATTC

CTTAAG

•

• Gene of interest is now inserted into ___________

• ___________ is absorbed by bacteria, which express the ___________

• Bacteria can be readily grown to make many, many copies of the gene, or to synthesize the protein encoded by the gene

• Most commonly, recombinant DNA technology is used to modify ___________

– Insect-resistant corn and cotton

– Rice that produces more vitamins

–Disease-resistant papya and sweet potatoes

•

• Some more unusual uses:

– Glowing pet fish

– Allergen-free cats

• Glowing Puppies!

– http://www.youtube.com/watch?v=YXPnQvcqHkg&feature=related

• Gene Editing

– __________________ system is a new technique that allows nucleotide sequences of

genes to be edited in living cells

• May be used to reveal function of a gene, or to even correct a mutation

– Bacteria have a protein called _________ that can identify and cut our viral DNA from

their genome

• Will cut any DNA sequence that is complementary to a specific sequence of guiding _______

• A Cas9 protein with an RNA molecule complementary to a particular gene may be used to cut out a gene from a cell’s chromosomes

• Random DNA nucleotides are then inserted into the chromosome by DNA repair

enzymes; this “___________” the gene, making in non-functional

• Can therefore determine what the gene did in the cell

• To edit a gene, researchers can add a segment of a normal gene along with the Cas9-guide RNA complex

• After Cas9 cuts the target DNA, repair enzymes use the normal DNA as a template to

repair the target DNA (for example, a mutated gene)

• This allows researchers to potentially fix genetic mutations

• Researchers have used CRISP-Cas9 to fix a genetic defects in mice

• Video: https://www.youtube.com/watch?v=52jOEPzhpzc

•

Bonus Activity

• CRISPR is an exciting new technology and researchers are racing to find ways to use it. Do a Google search and find a recent news article talking about how CRISPR is being used.

Read the article, and then write 2-3 sentences summarizing the article.

•

• Break…

Forensics

The “scientific analysis of evidence for crime scene investigations and other legal proceedings”

– __________________ is one technique used in forensics, to compare DNA samples

– Every individual’s genetic makeup is unique

– A person’s “DNA Fingerprint” is his/her unique collection of DNA fragments generated

when restriction enzymes are used to cut up the DNA

•

•

• How do you generate a DNA fingerprint?

• First, DNA evidence must be collected

– Various tissues, such as blood, semen, skin, etc.

• Before DNA Fingerprints can be generated, often the DNA sample must be _____________

– A tiny spec of blood can provide enough information to run a test, if the DNA in that

spec is copied many times

– The _______________________ is used to copy DNA

•

•

– Genomes are quite large, and typically scientists only need to amplify a small region of

the genome

– To amplify only a specific sequence, scientists use _____________, a short single-

stranded DNA molecule

– _____________ are selected that are complementary to only to the sequences at the ends of the target sequence

• The primers thus flank to target sequence, marking the beginning and end of the sequence to be copied

• Only the DNA between the primers is thus amplified

–

• _______________________ enzymes can then be used to cut the DNA into pieces

–Many different kinds of restriction enzymes

– Each recognizes a specific sequence and cuts DNA at that location

• May cut straight across both strands

• May make a “staggered” cut

• Although all humans are >99% genetically identical, the size of the human genome allows

for enough variation that differences can be detected

– About 3 billion base pairs in our DNA

– 1 in 1000 difference between any two people

–about 3 million differences between any two people

• When DNA samples from two different people are “digested” with the same restriction enzyme (or set of restriction enzymes), they will produce different numbers and sizes of

DNA fragments

– These different sets of DNA pieces are called “_________________________________”

• Differences (polymorphisms) in the size of the fragments of DNA created by the

restriction enzymes

• ____________________________ can then be used to separate the fragments by size

–DNA is ____________ charged (due to the ___________ groups)

– Electrical current causes the fragments of DNA to move through a “gel”

– ____________ pieces migrate faster than ____________ ones

– Results in a unique banding pattern

•

•

• Another technique commonly used in forensics is _________________ (STR) Analysis

–Much of the DNA between genes is composed of ____________ sequences (for

example, perhaps the sequence AGAT may be repeated 12 times)

– Non-coding

– Close relatives more likely to have more similar patterns of STRs

– Standard STR analysis in forensics tests ___ different markers

• Chances of two different people being identical at all 13 markers is between

__________________________________________________________________________________________________

Bonus Activity 2

1. A carrier that moves DNA from one cell to another, such as a plasmid, is called a ___________. Plasmids are small, circular pieces of DNA from ___________.

2. In making recombinant DNA, what is the benefit of using a restriction enzyme that cuts

DNA in a staggered fashion?

3. A paleontologist has recovered a bit of organic material from the 400-year-old preserved

skin of an extinct dodo. She would like to compare DNA from the sample with DNA from living birds. The most useful method for initially increasing the amount of dodo DNA for

testing is _____________________.

4. What feature of DNA causes it to move through a gel during gel electrophoresis?

DNA Evidence in the News…

•

• Use of DNA evidence in criminal cases is relatively new

– First case was in 1986 in England

• A man confessed to a series of rape/murders; DNA evidence indicated he did not; another person was identified as the actual murderer, based on DNA evidence

– First used in the US in ______________

• Man convicted of rape based on DNA obtained from semen found in victim

• Recently, a number of people on death row have been found not guilty based on DNA

evidence

–

•

•

• Fatal Flaws: The Case of Earl Washington

–Washington spent 18 years in prison

– Came within nine days of being put to death in Virginia's electric chair.

– Years later, DNA evidence proved he was innocent, and after a long legal battle, he was set free

–Washington had been convicted largely based on his own confession to a rape and

murder

• His defenders say the confession was coerced

• Washington was mentally handicapped

•

• DNA testing is increasingly being made available in criminal cases

• 32 states mandate that compensation be awarded to people wrongfully convicted (as of 2017)

• >________ people have been exonerated (from death row) using DNA testing since 1989

(when DNA testing first became available)

• In 2013 Oklahoma became 50th (and final) state to guarantee right to DNA testing in cases

where DNA evidence could demonstrate innocence

•

• Conversely, DNA evidence can be used to prove guilt

• Jan 2009, this man, Benjamin Watta, convicted of 1980 rape/murder of Simone Sharp in California

• Was already in prison for attempted murder of his former girlfriend

• “Cold Case” solved

•

•

•

•

• Can DNA technology resolve all problems with accuracy in convicting criminals?

• In order to be accurate, DNA testing must be done properly

–DNA must be stored properly

– Contamination of DNA samples can invalidate results

– Sometimes, if enough DNA evidence is available, defense and prosecution conduct

independent tests, to ensure accuracy

– Sometimes, shoddy lab work can also lead to wrongful conviction

• Can’t resolve all problems, but it’s a good and important start

–

• All for now, except for…

•

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