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Genetics III > Exam 3 Question Sample > Flashcards

Exam 3 Question Sample Flashcards

1
Q

Define: Restriction endonuclease

A

An enzyme that recognizes specific DNA sequences and cleaves them.

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2
Q

Define: Vector

A

A DNA molecule that carries foreign DNA and allows it to me replicated

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3
Q

Define: Genomic Library

A

A collection of clones, representing the entire genome of an organism

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4
Q

Define: Taq polymerase

A

A thermostable DNA polymerase used in PCR/

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5
Q

Define: Intercalating agent

A

A molecule that binds to DNA between base pairs and can cause frameshift mutations.

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6
Q

Mismatch repair enzymes can detect normal bases in DNA that are not correctly paired. However, something else must occur in order to ensure that the mismatch is repaired accurately. What is that?

A

Recognition of the new synthesized strand.

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7
Q

How are thymine dimers repaired before DNA replication? (except in mammals_

A

Photoreactivation uses the energy from blue light to enzymatically break the bonds holding the thymine dimer together.

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8
Q

What is the main reason for the difference in size between cDNA and a genomic clone of the same gene?

A

A cDNA clone lacks the Introns, compared to a genomic clone.

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9
Q

What is one advantage of PCR?

A

It’s sensitivity (low input DNA required)

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10
Q

What is one disadvantage of PCR?

A

It’s susceptible to contamination

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11
Q

In PCR, what process is the enzyme reverse transcriptase used?

A

Producing a cDNA library from mRNA

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12
Q

What are two ways double strand-breaks in DNA can be repaired?

A

homologous recombinational repair and nonhomologous end joining

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13
Q

If deamination is not repaired, it will lead to substitution mutation of which type?

A

Transitions

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14
Q

In deamination, if these mutations are in a protein-coding region of a gene, what are the three types of effect they can have?

A

Silent, missense, and nonsense.

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15
Q

What is a feature of nucleotide excision repair that distinguishes it from other types of excision repair?

A

Bulky lesions

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16
Q

Uracil DNA glycoslase is an enzyme that removes uracil bases from DNA. How does it happen that uracil is sometimes found in a DNA molecule?

A

Deamination of cytosine produces uracil.

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17
Q

Uracil DNA glycoslase is an enzyme that removes uracil bases from DNA. AFter removal of the uracil due to deamination, what is the next step in repair?

A

AP endonuclease removes the sugar phosphate from the DNA where the uracil has been removed.

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18
Q

If a nucleotide is deleted from a protein-coding region of a gene, the result will be a _________ mutation.

A

Frameshift

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19
Q

A single base change in a protein-coding region can produce either a ________ or a _______ mutation.

A

missense, nonsense, or silent

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20
Q

Transposons that move via a DNA intermediate can do so either _________
or ________ .

A

replicatively or nonreplicatively

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21
Q

___________ make up approximately 34% of the human genome.

A

Transposons

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22
Q

What are the different biological functions of the 5’ 3’ exonuclease and 3’ 5’ exonuclease activities of DNA Polymerase I?

A

The 5’ 3’ exonuclase is for primer removal, while the 3’ 5’ exonuclease proofreads

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23
Q

As a first step towards a complete genomic sequence of the aardvark, a complete genomic library would be made in a BAC vector. What is the advantage of using a BAC, rather than a plasmid, cosmid or bacteriophage vector?

A

BAC vectors allow much larger insert sizes than any of the alternatives mentioned.

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24
Q

How are thymine dimers repaired before DNA replication?

A

Photoreactivation uses the energy provided by blue light photons to reverse the
reaction and re-monomerize the thymines.

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25
Q

What are three essential components of a Polymerase Chain Reaction

A

DNA template
Primers
Deoxynucleotides
DNA polymerase (Taq)

26
Q

Deamination of cytosine to uracil is one of the most common forms of spontaneous DNA damage. What is the process that repairs this type of damage called?

A

Base excision repair

27
Q

What are three examples of sequences that are not represented in a cDNA library?

A

Introns, Promoters, Intergenic regions

28
Q

The process by which plasmids are introduced into host bacterial cells is called?

A

transformation

29
Q

List two essential features in any plasmid vector, and their purpose.

A

Origin of replication- To allow the plasmid to replicate in the host cell

Selectable marker- To allow all host cells lacking the plasmid to be killed

30
Q

What is epigenetics (one sentence)?

A

The study of how stable yet reversible changes in gene expression are initiated and maintained without DNA sequence changes.

31
Q

What are three essential components of a polymerase chain reaction (not including water, buffer and inorganic ions)?

A

Template DNA, primers, nucleotides, DNA polymerase

32
Q

The yeast GAL4 protein, like many transcription activators, has two domains with distinct functions. What are the two domains, and what is their function?

A

DNA binding-Binds to the enhancer sequences

Activation-Interacts with RNA polymerase to activate transcription

33
Q

The sex determination pathway of Drosophila is an example of gene regulation occurring at what step between gene and protein?

A

RNA splicing

34
Q

Define: Histone code

A

The complex patterns and interactions of histone modifications that change chromatin organization and gene expression

35
Q

Define: siRNA

A

short, double-stranded RNA molecules that regulate gene expression

36
Q

Define: Enhancer

A

A DNA sequence that binds transcription factors to activate transcription

37
Q

Predict the effect on inducibility of the lac operon of a mutation that deletes the crp gene that encodes the CAP protein (one sentence).

A

The lac operon will not be able to be induced by lactose, even when glucose is absent

38
Q

Methylation of cytosines in eukaryotic DNA, especially at CpG sequences, is usually associated with what genetic effect?

A

Silencing

39
Q

Who is Colin Pitchfork?

A

The first person to be convicted of murder based on DNA evidence

40
Q

What are two key differences between a genomic and a cDNA library?

A

A genomic library is prepared from total genomic DNA, whereas a cDNA library is prepared from mRNA

Genomic libraries contain much more sequence information and are much larger than libraries.

41
Q

List three important features contained in a plasmid vector & briefly explain what they are for.

A

Antibiotic resistance/selectable marker- to be able to screen for bacteria that took up the plasmid

Origin of replication- so that it can replicate

Polylinker- to be able to clone the DNA into the vector

42
Q

What is the difference between a missense and a nonsense mutation? Why do nonsense mutation often have more drastic phenotypic effects?

A

Missense mutations alter the coding sequence so that one amino acid is substituted for another. Nonsense mutations change a codon originally specifying an amino acid into a translation-termination codon.

43
Q

What is a common type of spontaneous DNA damage?

A

Deamination, pyrimidine dimers, tautomerization or depurination.

44
Q

What are the connections between histone deacelyation and gene regulation in eukaryotes?

A

When histones are deacetylated, they are tightly bound to DNA, resulting in no transcription. When they are acetylated, they are not tightly bound, resulting in transcription.

45
Q

Describe two major differences in the organization or content of prokaryotic and eukaryotic genomes.

A

Prokaryotic genomes generally have less DNA and fewer genes than eukaryotic genomes.

Most prokaryotic genomes are contained in one chromosome; while most eukaryotic genomes are contained in several.

46
Q

Genome sizes are highly variable. Name one thing that contributes to genome size variation.

A

Introns or repetitive elements.

47
Q

What are three essential components of a polymerase chain reaction?

A

Nucleotides, polymerase, and primers.

48
Q

PCR involves three steps that are cycled. The third step takes place at 72°C. What happens during this step?

A

Extension- nucleotides added to complete new strand.

49
Q

What is the main disadvantage of PCR?

A

Prone to contamination

50
Q

To inactivate a gene by RNAi, what information do you need about the gene?

A

The sequence of the RNA.

51
Q

The GAL4 protein, like many transcription factors, has two protein domains, what are they?

A

DNA binding domain and protein binding domain

52
Q

Name three cis elements in the GAL system.

A

UAS element, promoter of GAL1 and promoter of GAL10

53
Q

A mutation deletes the promoter region of the GAL80 gene. Would GAL10 be transcribed?

A

Yes, because GAL80 represses transcription, but here it cannot bind to GAL4.

54
Q

A different mutation deletes the entire GAL3 gene. Would GAL10 be transcribed?

A

No, because GAL80 is repressing it, and GAL3 can’t start up the transcription.

55
Q

Does the nucleotide sequence of a mutation tell you anything about its dominance or recessiveness? Explain.

A

Generally no, you would have to know something about the functional effects of the mutation.

56
Q

List the repair mechanism that a cell would use to repair the following damage: A double stranded break

A

Non homologous end joining or homologous recombination repair

57
Q

List the repair mechanism that a cell would use to repair the following damage: A change in the DNA sequence caused by DNA polymerase

A

Mismatch Repair

58
Q

List the repair mechanism that a cell would use to repair the following damage: A thymine-thymine dimer in the DNA of an actively dividing cell

A

Photoreactivation, NER, BER, SOS, Post replication

59
Q

What accounts for roughly half of the total DNA content of the human genome?

A

Repetitive DNA

60
Q

What is the annotated function of 40% of the protein coding genes in humans?

A

The 40% is unknown.

61
Q

You just obtained 100kb of platypus genomic sequence, What are the three methods you might use to identify potential genes in the 100kb?

A

BLAST, computer algorithm, or sequence cDNAs.

Genetics III (6 decks)

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