DNA structure

DNA is a polymer made of four monomers (A, T, G, C).Each monomer is contains:a. a nucleobase (nitrogeneous base) attached to a sugar

(deoxyribose) and a phosphate.b. a nucleobase (nitrogeneous base) attached to a sugar

(deoxyribose) and a lipidc. a nucleobase (nitrogeneous base) attached to an amino

acid and a phosphate.d. an amino acid attached to a sugar (deoxyribose) and a

phosphate.

True or False:

One end of a DNA strand is called the 5’-end and the other end is called the 3’-end.

The two strands of DNA are anti-parallel, meaning they run in opposite directions.

The backbone of DNA (the strands) are composed of sugars (deoxyribose) attached to each by phosphates.

If you know the sequence of one strand, you can figure out the sequence of the other.

If the sequence of one strand is 5’-ATGCAT-3’, what is the sequence of its complementary strand?

The two strands of DNA are held together by Hydrogen bonds between the nucleobases.

There are three hydrogen bonds holding together G:::C, and two hydrogen bonds holding together A::T.

Which of the following strands of DNA is most stable?

A. 5’GCGGCC-3’ 3’CGCCGG-5’

B. 5’AAAAAA-3’ 3’TTTTTT-5’

C. 5’TATATG-3’ 3’ATATAC-5’

D. 5’ATGCAT-3’ 3’TACGTA-5’

DNA replication

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What enzyme unzips (unwinds) the DNA molecule?

a. DNA polymeraseb. Helicasec. Primased. DNA ligasee. unzipase

Which of the following are limitations of DNA polymerase?

a. It can only add bases to the exposed 3’ end of a pre-existing strand

b. It can only replicate the leading strandc. It can only replicate the lagging strandd. None of the above

T or F:

The point where separation of the DNA occurs is called the replication fork.

Put the following events in the proper order:

a. DNA polymerase extends the RNA primer in opposite directions using monomers present in the cell.

b. DNA ligase joins together two adjacent strands of DNAc. Helicase unwinds/separates the two DNA strands c. RNA primase then adds a short complementary strand

of RNA (a RNA primer) to each strandd. DNA polymerase extends each strand until it runs into

another section that is already copied

Bidirectional DNA replication

DNA replication in bacteria begins at:

a. A single origin and proceeds in one directionb. A single origin and proceeds in both directionsc. Two origins and proceeds in both directionsd. Many origins and proceeds in one directione. Many origins and proceeds in two directions

True or False:

The bacterial chromosome is linear

mRNA synthesis (transcription)

Can you find a mistake in this animation?

The segment of the DNA molecule where mRNA synthesis begins is called the:

a. Promoter regionb. Sigma factorc. Transcription terminatord. Polymerasee. Template

The complementary mRNA stand that would be synthesized from the DNA sequence

5’-CTGAC-3’ would be:

a. 3’-GACTG-5’b. 3’-GACUG-5’c. 3’-CTGAC-5’d. 5’-CTGAC-3’

The name of the structure that causes the synthesis of mRNA to cease is called the:

a. Promoter regionb. Sigma factorc. Transcription terminatord. Polymerasee. Template

T or F:

The synthesis of mRNA is called translation.

The synthesis of mRNA is in the 5’ to 3’ direction.

The name of the enzyme that synthesizes mRNA is RNA polymerase

Exon Shuffling:

What is the name of the part of mRNA (in the primary transcript) that does not encode a protein, and is removed by splicing before a protein is made:

a. Exonb. Intronc. Gened. 5’cape. 3’polyA tail

The 5’-cap and 3’-polyA tails added to mRNA serve what purpose?

a. to make the mRNA more stableb. to make the mRNA longerc. to enable splicing out of intronsd. All of the above

One mRNA can be spliced many different ways, including all or just some of the exons. This allows 30,000 genes in humans to make over 100,000 different proteins.This is called:

a. Alternative splicingb. Intron shufflingc. Transcriptiond. translation

Processing of Gene Information: Prokaryotes vs Eukaryotes

Which of the following statements is true for eukaryotic mRNA, but not true for prokaryotic mRNA?

a. A cap is added to their 5’end.b. A poly-A tail is added to their 3’ end.c. Each usually specifies only a single protein.d. All of the above are true for eukaryotic mRNA, and false for prokaryotic mRNA.

T or F:

Prokaryotic mRNA can be translated by many ribosomes at the same time as it is being transcribed from DNA, but eukaryotic mRNA must first be processed and then transported from nucleus to the cytoplasm before it can be translated into a protein.

An operon consists of a set of related genes that are transcribed as a single mRNA and are found in eukaryotes.

Transposons:aka jumping genes

Does anyone know what a bacterial plasmid is?

Transposons are:

a. Segments of mRNAb. Plasmidsc. Segments of DNAd. Segments of transfer RNA (tRNA)

Transposons are transported between different cells by:

a. Transductionb. A sex pilusc. Conjugationd. Bacteriophagese. Plasmids

Which of the following is true about transposons (include all that are true)?

a. They are capable of moving from one cell to anotherb. They can move into the host cell genomec. They can more from one site in the host cell genome to

another sited. They can replicate themselves before moving

Addition and deletion mutations

The nucleic acid sequence in mRNA is determined by:

a. The order of amino acids in the proteinb. The nucleotide sequence in DNAc. The nucleotide sequence in tRNAd. All of the above

T or F:

One amino acid in a protein chain is encoded by three consecutive bases in RNA; the three bases in mRNA that code for one amino acid is called a codon.

Classify the following three “mutations” as either a point mutation or a frame-shift mutation.

If it is a frame-shift mutation, is it an addition or deletion?

Original THE BIG FAT CAT ATE ALL THE ICEmutant#1 THE BIG ATC ATA TEA LLT HEI CENmutant#2 THE BIG FAT CAT TAT EAL LTH EIC mutant#3 THE BIG CAT CAT ATE ALL THE ICE

What type of mutation has the least impact on the message?

If a frame-shift mutation creates a stop codon in the DNA sequence, then

a. The resulting protein will not be affectedb. The phenotype will change but not the genotypec. The resulting protein will be too short and non-functionald. The resulting protein will be too long and non-functional

A nucleotide deletion that occurs during DNA replication:

a. Causes one amino acid of the protein to be deletedb. Causes all of the amino acids of the protein to be incorrectc. Causes the amino acids after the deletion to be correctedd. Causes the amino acids before the deletion to be incorrecte. Has no effect on the resulting protein

Mutations in DNA, such as point mutations or frame-shift mutations, can be caused by:

a. Uncorrected errors during DNA replicationb. Mutagens such as the chemicals found in smokec. High energy particles such as radiation and UV lightd. Insertion of transposons into an exonic region e. All of the above

Restriction Endonucleases

Which of the following could NOT be the recognition site of a restriction endonuclease?

a. GAATTCCTTAAG

b. ATCGATTAGCTA

c. CTGCAGGACGTC

d. GCTTGCCGAACG

e. GGATCCCCTAGG

The single-stranded ends of DNA molecules can be joined together by:

a. Restriction endonucleasesb. DNA ligasec. DNA polymerased. Primasee. Helicase

Human DNA cut with restriction enzyme A will have the same sticky ends as (and can therefore be ligated/joined to) which of the following:

a. Human DNA cut with restriction enzyme Bb. Human DNA that is uncutc. Bacterial DNA that is uncutd. Corn DNA that is cut with restriction enzyme Ae. None of the above

T or F:

The ligating (joining) of sticky ends involves the formation of phosphodiester bonds.

If you have a piece of bacterial DNA that is 1280 bases long, and you add to it a restriction endonuclease that recognizes and cuts the following sequence:

5’-CATG-3’3’-GTAC-5’

approximately how many times will the bacterial DNA be cut?

Hint: if you flip a coin four times, how often to you expect to get heads four times in a row?

PCR: Polymerase Chain Reaction

PCR requires all of the following except:

a. Primersb. DNA ligasec. DNA polymerase (usually Taq DNA polymerase)d. At least one strand of DNA (polymer) to copy/amplifye. Deoxyribonucleotides (monomers)

The purpose of heating the DNA during each cycle of PCR is to

a. Activate the polymerase enzymeb. Speed up catalysis by the polymerase enzymec. Separate the two strands of DNA templated. Increase binding of primers to the DNA template

T or F:

Even though Taq polymerase is an enzyme from a bacteria, it can copy DNA from any species, including humans.

During the PCR, the hydrogen bonds holding the two strands of DNA molecules together are broken by the helicase enzyme.

You can determine which part of OJ Simpon’s DNA you wish to amplify by changing which of the following:

a. The sequence of the primerb. The temperature of the PCRc. The amount of polymerase

If you start with one drop of OJ Simpson’s blood, containing ten cells (and therefore ten copies of his DNA), and you amplify it by PCR for 10 cycles of “heat-cool-copy-repeat”, how many copies of the DNA have you made?

What temperature do you think your DNA polymerase works best at?

Do you think your DNA polymerase works at 95C (nearly the temperature of boiling water)?

Where do you think scientists found a polymerase that is active even at very high temperatures, such as Taq DNA polymerase?

Matthew CarriganResearch Fellow

Foundation for Applied Molecular Evolutionwww.ffame.org

Reconstruction of the Primate Alcohol Metabolic Pathway:

Did Ardi Party Hearty?

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OCH3C H

OHCH3C HH

ethanol

KrebscycleAdh1 O

CH3C OH

OCH3C OPO3=

OCH3C SCoA

ATP ADP

ATPconsumedacetaldehyde acetate acetyl phosphateacetyl-CoA

O2Aldh

Ethanol MetabolismEthanol can be a valuable source of energy

NADH+

NAD+

paleogenetics

paleogenetics

paleogenetics

paleogenetics

paleogenetics

ADH4: changes across phylogeny

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The most ancient ADH enzyme, node 44

time (seconds)

Amount of ethanol that is digested

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node 44 and 45

time (seconds)

Amount of ethanol that is digested

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node 44, 45, and 49

time (seconds)

Amount of ethanol that is digested

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node 44, 45, 49 and 52

time (seconds)

Amount of ethanol that is digested

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node 44, 45, 49, 52 and 53

time (seconds)

Amount of ethanol that is digested

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node 44, 45, 49, 52, 53 and YOU

time (seconds)

Amount of ethanol that is digested

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node 44, 45, 49, 52, 53 and YOU (and

tarsier)

time (seconds)

Amount of ethanol that is digested

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So are you saying we are adapted to drink ethanol?

OCH3C H

OHCH3C HH

ethanol

KrebscycleAdh1 O

CH3C OH

OCH3C OPO3=

OCH3C SCoA

ATP ADP

ATPconsumedacetaldehyde acetate acetyl phosphateacetyl-CoA

O2Aldh

Ethanol Metabolism

Ethanol can be a valuable source of energy…

…but if you have too much, a toxic intermediate can accumulate

NADH+

NAD+

…and if we (and orangutans) are adapted to drink ethanol…

then where are all the drunk monkeys?