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Genetics > CHAPTER 11 & 19 > Flashcards

CHAPTER 11 & 19 Flashcards

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1
Q

What is the AT/GC rule in DNA replication?

A

-A pairs w/ T
-G pairs w/ C

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2
Q

Parental strands in DNA replication

A

They are the original DNA strands

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3
Q

Daughter Strands

A

Newly synthesized complementary strands

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4
Q

Three models of DNA replication were proposed in the 1950s

A
  1. Conservative Model
  2. Semiconservative Model (correct model)
  3. Dispersive Model
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5
Q

Semiconservative model of DNA replication.

A

Each double-stranded DNA molecule has one parental and one daughter strand after replication.

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6
Q

What did Meselson and Stahl use to differentiate between parental and daughter DNA strands?

A

Light and heavy nitrogen isotopes, 15N and 14N.

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7
Q

In E. coli, where does DNA replication begin?

A

At the origin of replication, termed oriC.

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8
Q

Name the three important DNA sequences in oriC.

A

-DnaA boxes
-At-rich regions
-GATC methylation sites

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9
Q

What role do GATC methylation sites play in replication?

A

Regulate replication by ensuring initiation occurs only on fully methylated DNA.

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10
Q

DNA helicase

A

Enzyme that separates the two DNA strands by breaking hydrogen bonds

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11
Q

Topoisomerase II (DNA gyrase)

A

Protein that alleviates positive supercoiling during replication

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12
Q

What is the function of RNA primers in DNA replication?

A

Primase synthesizes RNA primers to initiate DNA synthesis.

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13
Q

DNA polymerase III

A

Enzyme synthesizes the leading and lagging strands

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14
Q

Okazaki fragments

A

Short DNA segments are synthesized on the lagging strand during replication.

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15
Q

How are RNA primers removed and replaced with DNA?

A

DNA polymerase I excises RNA primers and fills the gaps with DNA.

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16
Q

What complex forms the replisome during DNA replication?

A

The primosome (helicase + primase) and two DNA polymerase holoenzymes.

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17
Q

What is the function of DNA ligase?

A

It connects Okazaki fragments by forming covalent bonds between DNA backbones.

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18
Q

What stops DNA replication at the termination sequences in E. coli?

A

The Tus protein binds to ter sequences, halting replication forks.

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19
Q

Catenanes

A

Intertwined circular DNA molecules that form post-replication, separated by topoisomerase II.

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20
Q

How does DNA polymerase III achieve processivity in E. coli?

A

The β subunit forms a clamp around DNA, allowing the enzyme to polymerize many nucleotides without detaching.

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21
Q

Why are temperature-sensitive (ts) mutants useful in studying DNA replication?

A

Ts mutants allow survival at permissive temperatures but inhibit growth at nonpermissive temperatures, revealing essential genes.

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22
Q

fidelity in DNA replication

A

High accuracy in DNA replication, with errors being extremely rare.

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23
Q

How often does DNA polymerase III make an error?

A

Approximately 1 error per 10⁸ bases.

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24
Q

What three main factors contribute to high fidelity in DNA replication?

A
  1. Base pairing stability
  2. Structure of the DNA polymerase active site
  3. Proofreading function of DNA polymerase
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25
Q

Why are complementary base pairs more stable?

A

They have higher stability than mismatched pairs, which partially accounts for fidelity.

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26
Q

How does DNA polymerase’s active site prevent errors?

A

Helix distortion from mispairing prevents incorrect nucleotides from fitting properly, reducing errors

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27
Q

What is the induced-fit mechanism in DNA polymerase?

A

The enzyme changes conformation to catalyze nucleotide addition, reducing the error rate.

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28
Q

How does DNA polymerase correct mismatched nucleotides?

A

-It uses 3’ to 5’ exonuclease activity to remove mismatches
-Resumes synthesis in the 5’ to 3’ direction.

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29
Q

Why is eukaryotic DNA replication more complex than bacterial replication?

A

-Larger linear chromosomes
-Packed chromatin
-Complex cell cycle regulation

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30
Q

Why do eukaryotes have multiple origins of replication?

A

To replicate large chromosomes quickly by forming bidirectional replication bubbles.

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31
Q

Which DNA polymerases are involved in eukaryotic DNA replication?

A

DNA polymerases alpha (⍺), delta (δ), epsilon (ε), and gamma (γ).

32
Q

DNA pol ε (epsilon)

A

Polymerase used for leading strand elongation

33
Q

DNA pol δ

A

Used for lagging strands

34
Q

DNA pol beta

A

removes incorrect bases from the DNA

35
Q

What are telomeres?

A

Repetitive DNA sequences at chromosome ends with bound proteins.

36
Q

What issue arises at the ends of linear chromosomes during replication?

A

DNA polymerase cannot fully replicate the 3’ ends, leading to potential shortening.

37
Q

How does telomerase prevent chromosome shortening?

A

DNA sequences are added to the telomere ends using RNA as a template.

38
Q

Mutation

A

A heritable change in the DNA sequence of a gene

39
Q

What are the types of point mutations?

A
  1. Transitions
  2. Transversions
40
Q

Mutations are changes in

A

-Chromosome structure
-Chromosome number
-DNA of a single gene

41
Q

missense mutation

A

A base substitution causes an amino acid change in a protein.

42
Q

frameshift mutation

A

Adding or deleting nucleotides not divisible by three alters the reading frame.

43
Q

nonsense mutation

A

A mutation that changes a normal codon to a stop codon, shortening the protein.

44
Q

Deleterious vs. Beneficial Mutations

A

-Deleterious mutations decrease survival chances
-Beneficial mutations enhance the survival chances

45
Q

conditional mutations

A

Mutations that affect phenotype only under specific conditions, like temperature-sensitive mutations.

46
Q

What is a position effect in gene expression?

A

A change in gene expression due to the gene’s new location after a chromosomal rearrangement, often near regulatory sequences or a heterochromatic region.

47
Q

What are the two main types of chromosomal rearrangements affecting gene expression?

A
  1. Movement next to regulatory sequences.
  2. Movement to a heterochromatic region.
48
Q

germ-line cells

A

Cells that give rise to gametes, such as eggs and sperm.

49
Q

somatic mutation

A

A mutation occurs in a body cell, not part of the germ line, and affects only specific areas.

50
Q

What is the difference between spontaneous and induced mutations?

A

-Spontaneous mutations arise from cellular processes
-Induced mutations are caused by environmental mutagens.

51
Q

Depurination

A

Removing a purine base from DNA can result in mutation if not repaired.

52
Q

What occurs during the deamination of cytosine?

A

Cytosine loses an amino group, potentially leading to a C-G to A-T mutation if repair fails.

53
Q

What are Reactive Oxygen Species (ROS), and how do they affect DNA?

A

ROS are byproducts of oxygen metabolism that can damage DNA and lead to mutations if not balanced by antioxidants.

54
Q

What is trinucleotide repeat expansion (TNRE)?

A

A mutation where the number of trinucleotide repeats in a gene increases.

55
Q

What is anticipation in TNRE disorders?

A

The phenomenon where TNRE disorders worsen in successive generations is influenced by whether the mutation is inherited from the mother or father.

56
Q

Base Modifiers

A

Chemical mutagens that covalently alter DNA bases, potentially leading to incorrect base pairing.

57
Q

Ames test

A

A test used to evaluate if a chemical agent is a mutagen

58
Q

Thymine dimers

A

DNA lesions caused by UV light create cross-links between adjacent thymine bases, potentially leading to mutations.

59
Q

How does a tautomeric shift cause mutations?

A

If not corrected, it temporarily changes the base structure, leading to incorrect base pairing during replication.

60
Q

Mutation frequency

A

The proportion of mutant genes in a population is calculated as the number of mutants divided by the total number of genes.

61
Q

What are the basic steps in the DNA repair process?

A
  1. Detect irregularity in DNA
  2. Remove abnormal DNA
  3. Synthesize normal DNA.
62
Q

Photolyase

A

Repairs thymine dimers by using visible light in a process called photoreactivation.

63
Q

What does alkyltransferase do, and what is unique about it?

A

Alkyltransferase removes alkyl groups from DNA bases and transfers them to itself, permanently inactivating the enzyme.

64
Q

What is the role of DNA glycosylases in Base Excision Repair (BER)?

A

DNA glycosylases recognize abnormal bases and cleave them from the sugar in the DNA strand.

65
Q

What type of DNA damage does Nucleotide Excision Repair (NER) address?

A

NER repairs bulky, helix-distorting lesions like thymine dimers and chemically modified bases.

66
Q

Name the key proteins involved in NER in E. coli.

A
  1. UvrA
  2. UvrB
  3. UvrC
  4. UvrD
67
Q

What human disorders are associated with defects in Nucleotide Excision Repair (NER)?

A

-Xeroderma pigmentosum (XP)
-Cockayne syndrome (CS)
-PIBIDS

68
Q

What does the Mismatch Repair (MMR) system correct?

A

MMR corrects base pair mismatches caused by DNA replication errors.

69
Q

In E. coli, which proteins detect and correct mismatches in DNA?

A

-MutL
-MutH
-MutS

70
Q

How does MutH distinguish between the parent and daughter DNA strands?

A

MutH identifies the parental strand by its methylation, which the new daughter strand lacks initially.

71
Q

What are the two main pathways for repairing double-strand breaks in DNA?

A

-Homologous recombination repair (HRR)
-Nonhomologous end joining (NHEJ)

72
Q

What are the pros and cons of homologous recombination repair (HRR)?

A

Pro: Error-free repair using sister chromatids.
Con: Only available in the S and G2 phases of the cell cycle.

73
Q

What is a disadvantage of Non-Homologous End Joining (NHEJ)?

A

NHEJ may result in deletions of small DNA segments.

74
Q

What type of polymerase is involved in translesion synthesis (TLS), and what is its downside?

A

Translesion DNA polymerases, which can bypass DNA lesions but have a high mutation rate.

75
Q

What is the Holliday model in homologous recombination?

A

A model describing the crossover of homologous DNA strands and the formation of a Holliday junction during recombination.

Genetics (10 decks)

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