Control MechanismsControl Mechanisms

• Gene regulationGene regulation involves involves turning turning on or off specific genes depending on on or off specific genes depending on the needs of the organism.the needs of the organism.

• Transcription factors Transcription factors turn on turn on genes by binding to DNA and helping genes by binding to DNA and helping RNA polymerase bind.RNA polymerase bind.

• NOTE: NOTE: Housekeeping genesHousekeeping genes are are always needed and are constantly always needed and are constantly being transcribed and translated.being transcribed and translated.

5.5 Control Mechanisms5.5 Control Mechanisms• Every living cell has the ability to respond to Every living cell has the ability to respond to

its environment by changing the kinds and its environment by changing the kinds and amounts of polypeptides it produces. Cells amounts of polypeptides it produces. Cells have developed methods by which they can have developed methods by which they can control the transcription and translation of control the transcription and translation of genes, depending on their need. genes, depending on their need.

• Gene regulation can occur at different levels:Gene regulation can occur at different levels:• TranscriptionalTranscriptional: how fast/slow : how fast/slow transcription occurstranscription occurs• PosttranscriptionalPosttranscriptional:: how fast/slow how fast/slow RNA processing occursRNA processing occurs• TranslationalTranslational: how fast/slow mRNA is : how fast/slow mRNA is transcribedtranscribed• PosttranslationalPosttranslational: how fast/slow the : how fast/slow the protein becomes active protein becomes active and functionaland functional

OperonsOperons

• Operons = are clusters of genes Operons = are clusters of genes under the control of one promoter under the control of one promoter and one operator and one operator ex lac operon, ex lac operon, trp operontrp operon

• oo  Form of control only used in bacteriaForm of control only used in bacteria• oo  In bacteria such as In bacteria such as E.coliE.coli found in the found in the

digestive system of mamals, digestive system of mamals, β-galactosidase β-galactosidase is the enzyme responsible for breaking down is the enzyme responsible for breaking down lactose (enzyme is not always required)lactose (enzyme is not always required)

• oo  β-galactosidaseβ-galactosidase is part of an operon is part of an operon• oo    lacl protein lacl protein binds to operon blocking binds to operon blocking

transcriptiontranscription• oo    in the presence of lactose a repressorin the presence of lactose a repressor proteinprotein

(lacl protein) (lacl protein) normally bound to operon normally bound to operon leaves and binds to lactose leaves and binds to lactose transcription of transcription of the lac operon no longer blocked (no enzymes the lac operon no longer blocked (no enzymes are made) are made) see fig. 2 p. 256 see fig. 2 p. 256

• oo    Why? When there is no milk, no enzyme is Why? When there is no milk, no enzyme is neededneeded

•         E. coliE. coli bacterial cells that are in the intestines bacterial cells that are in the intestines of mammals can use the energy supplied by of mammals can use the energy supplied by lactose in order to grow by breaking the bonds lactose in order to grow by breaking the bonds between the two sugars.between the two sugars.

•       -galactosidase is the enzyme used to break -galactosidase is the enzyme used to break down lactose. But bacteria only produce it down lactose. But bacteria only produce it when they need to, so they must regulate the when they need to, so they must regulate the production of production of -galactosidase using a negative -galactosidase using a negative control system.control system.

•       The gene for The gene for -galactosidase is part of an -galactosidase is part of an operonoperon (cluster of genes under the control of (cluster of genes under the control of one promotor and one operator)one promotor and one operator)

•   The The laclac operon has three genes that code for operon has three genes that code for protein involved in the breakdown of lactose: protein involved in the breakdown of lactose: lacZ, lacY,lacZ, lacY, and and lacAlacA..

• The The lacZlacZ gene encodes the enzyme gene encodes the enzyme --galactosidasegalactosidase

•   The The lacY lacY gene encodes the gene encodes the --galactosidase permease (that causes galactosidase permease (that causes lactose to permeate the cell membrane lactose to permeate the cell membrane and enter the cell)and enter the cell)

• The The lacAlacA encodes a transacetylase (we encodes a transacetylase (we don’t know what it does though)don’t know what it does though)

• The The LacI proteinLacI protein is a is a repressor repressor proteinprotein that blocks the transcription of that blocks the transcription of the the -galactosidase by binding to the -galactosidase by binding to the lactose operator and getting in the way lactose operator and getting in the way of the RNA polymeraseof the RNA polymerase

• If lactose is introduced, the roadblock If lactose is introduced, the roadblock (LacI protein) must be removed. The (LacI protein) must be removed. The presence of lactose itself removes the presence of lactose itself removes the protein and is known as the protein and is known as the signal signal moleculemolecule or the or the inducerinducer. .

•     Lactose binds to the LacI protein, Lactose binds to the LacI protein, which changes the conformation of the which changes the conformation of the protein and it can no longer stay bound protein and it can no longer stay bound to the operator region of the to the operator region of the laclac operon. operon. The complex falls off the DNA and it The complex falls off the DNA and it allows the RNA polymerase to proceed allows the RNA polymerase to proceed and transcribe the and transcribe the laclac operon. operon.

The trp OperonThe trp Operon

    Works in the opposite manner to the lac Works in the opposite manner to the lac operonoperon

      tryptophantryptophan is an amino acid used by is an amino acid used by bacteria to produce proteins, when bacteria to produce proteins, when available in its environment bacteria stop available in its environment bacteria stop producing tryptophan and absorb it from producing tryptophan and absorb it from its environmentits environment

    operon acitivity is inhibited when the operon acitivity is inhibited when the concentration of tryptophan in the concentration of tryptophan in the environment increases environment increases tryptophan tryptophan binds to operator region of operon binds to operator region of operon see see fig. 3, p. 257fig. 3, p. 257

• The The trptrp operon operon is another example of is another example of coordinated regulation. coordinated regulation.

•     The The trptrp operon is repressed when high operon is repressed when high levels of tryptophan are present.levels of tryptophan are present.

• The The trptrp operon has five genes that code operon has five genes that code for five polypeptides that make for five polypeptides that make enzymes needed to make tryptophan. enzymes needed to make tryptophan.

• When tryptophan levels are high, the When tryptophan levels are high, the tryptophan molecule binds to the tryptophan molecule binds to the repressor protein, altering its shape and repressor protein, altering its shape and binds with the binds with the trptrp operator. operator.

•     Because tryptophan is needed itself to Because tryptophan is needed itself to inactivate the inactivate the trptrp operon, it is called a operon, it is called a corepressorcorepressor..

Negative Gene Regulation in the Negative Gene Regulation in the laclac Operon Operon

Co-Repression in theCo-Repression in the trptrp Operon Operon

SummarySummarylaclac Operon Operon• Transcription induced when high Transcription induced when high

levels of lactose present.levels of lactose present.•

trptrp Operon Operon• Transcription repressed when high Transcription repressed when high

levels of tryptophan present.levels of tryptophan present.•

5.6: Mutations5.6: Mutations

• Inherited errors Inherited errors made in the DNA made in the DNA sequence.sequence.

Mutations Can beMutations Can be

• 1. Negative:1. Negative: genetic genetic

disorders/diseasesdisorders/diseases• 2. Positive: natural selection (ex. Large 2. Positive: natural selection (ex. Large

human brain sizehuman brain size• 3. Have no effect3. Have no effect

Types of MutationsTypes of Mutations

There are 7 types we are going to There are 7 types we are going to review.review.

1. Silent1. Silent

• has no effecthas no effect• occur in noncoding regions (introns)occur in noncoding regions (introns)• base change codes for the original amino base change codes for the original amino

acidacid

2. Missense2. Missense

• base change leads to a different amino base change leads to a different amino acidacid

• ex. Sickle cell anemiaex. Sickle cell anemia

3. Nonsense3. Nonsense• base change causes a stop codon to replace base change causes a stop codon to replace

an amino acidan amino acid• these are often lethal to the cell because these are often lethal to the cell because

the required protein is not producedthe required protein is not produced

Animation Quiz 3 - Mutation by Base Substitution

4. Deletion4. Deletion

• one or more nucleotides are removed, one or more nucleotides are removed, results in defective proteinresults in defective protein

5. Insertion5. Insertion

• inserting extra nucleotides results in inserting extra nucleotides results in different amino acids being translated different amino acids being translated

Animation Quiz 4 - Addition and Deletion Mutations

6. Translocation6. Translocation• involves large segments of DNA involves large segments of DNA

(chromosomes)(chromosomes)• groups of base pairs relocate from one part of groups of base pairs relocate from one part of

the genome to anotherthe genome to another• a part of one chromosome breaks and is a part of one chromosome breaks and is

released while the same thing happens to released while the same thing happens to another (usually non-homologous another (usually non-homologous chromosome) and the two parts exchange chromosome) and the two parts exchange places.places.

• Some fragments of DNA called transposable Some fragments of DNA called transposable elements consistently move from one location elements consistently move from one location to another. If they land within a coding region, to another. If they land within a coding region, they will disrupt transcriptionthey will disrupt transcription

TranslocationTranslocation

7. Inversion7. Inversion

• a chromosomal segment that has a chromosomal segment that has reversed its orientation in the reversed its orientation in the chromosome.chromosome.

• No loss of genetic info, but genes may No loss of genetic info, but genes may be disrupted.be disrupted.

Key Points:Key Points:

• Missense and Silent mutations arise from Missense and Silent mutations arise from substitution of one base pair for another substitution of one base pair for another known as known as point mutationpoint mutation..

• Insertion and Deletion cause Insertion and Deletion cause frameshift frameshift mutationsmutations (reading frame is changed). (reading frame is changed).

• Translocation and Inversion involve the Translocation and Inversion involve the whole chromosome.whole chromosome.

CausesCauses

1. Spontaneous:1. Spontaneous:simple errorssimple errors

2. Induced2. Induced: caused by mutagenic : caused by mutagenic agents such as UV radiation, agents such as UV radiation, cosmic rays, x-rays and chemicalscosmic rays, x-rays and chemicals

5.7: Endosymbiosis5.7: Endosymbiosis

• Protein Synthesis: Prokaryotes vs. Protein Synthesis: Prokaryotes vs. EukaryotesEukaryotes

ProkaryotesProkaryotes EukaryotesEukaryotes

GenomeGenome

• Since prokaryotes do not possess a nuclear Since prokaryotes do not possess a nuclear membrane, trancription and translation can be membrane, trancription and translation can be coupled.coupled.

ProkaryotesProkaryotes EukaryotesEukaryotes

TranscriptionTranscription

TranslationTranslation

Endosymbiotic Relationships Endosymbiotic Relationships between Organelles and between Organelles and

CellsCells

• Mitochondria resemble prokaryotic Mitochondria resemble prokaryotic cells in the following way:cells in the following way:

•   1.  Both contain circular DNA that is 1.  Both contain circular DNA that is not enclosed in a nucleus.not enclosed in a nucleus.

• 2. Sequence of DNA is similar.2. Sequence of DNA is similar.•   3.  Both divide by fission.3.  Both divide by fission.•   4.  Mitochondria possess their own 4.  Mitochondria possess their own

process of DNA replication and protein process of DNA replication and protein synthesis.synthesis.

Differences between Differences between Eukaryotes and Eukaryotes and ProkaryotesProkaryotes

• 1.    1.    Prokaryotes do not posses a Prokaryotes do not posses a nuclear membrane. nuclear membrane. Coupled Coupled transcription-translationtranscription-translation

• 2.    Prokaryotes do not contain introns 2.    Prokaryotes do not contain introns (non-coding regions)(non-coding regions)

• Prokaryotes, ribosome recognizes a Prokaryotes, ribosome recognizes a unique protein-rich base known as the unique protein-rich base known as the Shine-Dalgarno sequence at the start of Shine-Dalgarno sequence at the start of mRNA. Eukaryotes, ribosomes recognize mRNA. Eukaryotes, ribosomes recognize 5’ cap.5’ cap.

Differences between EukaDifferences between Eukaryotes and Prokaryotesryotes and Prokaryotes • 5.    Eukaryotic ribosomes are larger.5.    Eukaryotic ribosomes are larger.• 6.    Methionine is the first amino acid in 6.    Methionine is the first amino acid in

both Prokaryotes and Eukaryotes. In both Prokaryotes and Eukaryotes. In prokaryotes it is tagges with a formyl prokaryotes it is tagges with a formyl group.group.

• 7.  Eukaryotes do not have operons.7.  Eukaryotes do not have operons.• 8   Prokaryotic genome is circular, 8   Prokaryotic genome is circular,

Eukaryotic genome is organized in Eukaryotic genome is organized in chromosomes.chromosomes.

5.8: Gene Organization and 5.8: Gene Organization and Chromosome StructureChromosome Structure