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chapter 11 Flashcards

1
Q

What are Gene Mutations?

A

Random changes in the DNA sequence

Includes various types of mutations such as point mutations, insertions, and deletions.

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2
Q

What is a Point Mutation?

A

Substitution, insertion, or deletion of a single base pair in a gene

Often occurs during mistakes in DNA replication.

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3
Q

What is the mutation rate at the phenotype level?

A

~10-6 to 10-8 per individual

This rate indicates the frequency of observable mutations.

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4
Q

What is the mutation rate at the DNA sequence level?

A

~10-9 per base per replication

This rate indicates the frequency of mutations occurring at the DNA level.

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5
Q

What hypotheses did Luria and Delbrück test in 1943?

A
  1. Mutations are random
  2. Mutations arise from environmental triggers

They used bacteria and T1 phage to test these hypotheses.

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6
Q

What are Germ-line Mutations?

A

Mutations generated within gametes that can be passed onto the next generation

Important for evolutionary changes.

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7
Q

What are Somatic Mutations?

A

Mutations typically generated during mitosis that are not passed on but can affect the individual

Example includes cancerous tumors.

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8
Q

What is a Transition Mutation?

A

A mutation where a purine base is replaced by another purine, or a pyrimidine base is replaced by another pyrimidine

Examples include A-G and T-C substitutions.

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9
Q

What is a Transversion Mutation?

A

A mutation where a purine is replaced by a pyrimidine, or vice versa

Examples include A-T, A-C, G-T, G-C substitutions.

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10
Q

Which type of mutation occurs more frequently, transition or transversion?

A

Transition mutations

Transition mutations are generated at higher frequency than transversions.

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11
Q

What are Coding-Sequence Point Mutations?

A

Changes in a single nucleotide within the coding region of a gene

Includes synonymous, missense, nonsense, and frameshift mutations.

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12
Q

What is a Synonymous Mutation?

A

A mutation that results in no amino acid sequence change

Does not affect the protein product.

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13
Q

What is a Missense Mutation?

A

A mutation that changes one amino acid in the sequence

Can affect protein function depending on the amino acid change.

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14
Q

What is a Nonsense Mutation?

A

A mutation that creates a stop codon and terminates translation

Results in a truncated protein.

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15
Q

What is a Frameshift Mutation?

A

A mutation that causes a wrong sequence of amino acids

Typically caused by insertions or deletions that are not in multiples of three.

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16
Q

What are Regulatory Mutations?

A

DNA or RNA changes that alter the expression of genes

Affect how transcription factors bind to DNA and control mRNA production.

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17
Q

What is the role of a Promoter in regulatory mutations?

A

Changes the timing or amount of transcription

Influences gene expression levels.

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18
Q

What does Polyadenylation alter in regulatory mutations?

A

Alters the sequence of mRNA

Can affect mRNA stability and translation.

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19
Q

What happens at a Splice Site mutation?

A

Improperly retains an intron or excludes an exon

Can lead to abnormal protein products.

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20
Q

What is a DNA replication mutation?

A

Mutations like triplet-repeat expansion that increase or decrease the number of short repeats of DNA

Can lead to genetic disorders.

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21
Q

Do insertions/deletions always result in frameshift mutations?

A

No

If base pair insertions occur in multiples of three, the reading frame remains unaffected.

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22
Q

Fill in the blank: A 6 bp insertion results in _______.

A

two extra amino acids

The reading frame remains unaffected.

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23
Q

What is Forward Mutation?

A

wild type allele -> mutant allele

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24
Q

What is Reverse Mutation/Reversion?

A

mutant allele -> wild-type allele

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25
Define True reversion.
mutation restores exact wild-type DNA sequence
26
What is Intragenic reversion?
mutation elsewhere in same gene restores gene function
27
What is Second-site reversion/suppressor mutation?
mutation in a different gene compensates for original mutation, restoring wild-type phenotype
28
What are the mechanisms of Point Mutation?
* Mispaired nucleotides during replication * Spontaneous nucleotide base change * Mutagens (chemical or radiation)
29
What occurs due to Mispaired Nucleotides During Replication?
non-complementary base pairing can occur, leading to mutation
30
What is a common pairing error in Mispaired Nucleotides?
G:T pairing or C:A pairing
31
What is Depurination?
the loss of a purine leading to an apurinic site
32
What can happen if Depurination is not repaired?
DNA polymerase will put an adenine during replication
33
What is a common result of Depurination?
G -> A substitution
34
What is Deamination?
the loss of an amino group (NH2) from a nucleotide base
35
What can methylated cytosine undergo during Deamination?
it can become thymine
36
What is a common result of Deamination?
C-G pair can become T-A
37
How are Chemical Mutagens classified?
based on their mode of action on DNA
38
What are Nucleotide base Analogs?
a chemical with a similar structure to DNA that induces point mutation
39
What do Deaminating Agents do?
remove amino groups, stimulating C-G pair to become T-A
40
What do Alkylating Agents do?
add methyl or ethyl groups to nucleotide bases, causing distortion in DNA helix
41
What do Oxidizing Agents usually result in?
transversion mutation
42
What do Hydroxylating Agents do?
add hydroxyl groups to a nucleotide base, usually resulting in modified cytosine pairing with A
43
What are Intercalating Agents?
molecules that fit between DNA base pairs, leading to frameshift mutations
44
What is the Ames Test used for?
to verify if a chemical is a mutagen
45
What is the process of the Ames Test?
exposing bacteria to a chemical in the presence of enzymes from a mammalian liver
46
What do liver enzymes do in the Ames Test?
break down toxins into various byproducts for detoxification
47
What is the result if bacterial mutants grow in the Ames Test?
mutations occurred in mutated gene, allowing bacteria to synthesize histidine
48
Who discovered the mutagenic properties of radiation?
Hermann Muller
49
What types of radiation are considered mutagenic?
* Ultraviolet (UV) * X-rays * Gamma rays * Cosmic rays
50
What can excessive UV radiation exposure lead to?
thymine dimers
51
What are thymine dimers?
covalent bonds between C5-C6 or C4-C6 of adjacent thymines
52
What can happen if thymine dimers are not repaired?
disruption of DNA replication, inducing mutations
53
What is a primary cause of skin cancer associated with UV exposure?
strong association between excessive UV exposure and skin cancer
54
What is Base Excision Repair (BER) and Nick Translation?
Removal of an incorrect or damaged DNA base and repair by synthesis of a new strand segment. Nick: DNA polymerase initiates removal and replacement of nucleotides and DNA ligase seals sugar-phosphate backbone ## Footnote BER involves nick translation where DNA polymerase initiates removal and replacement of nucleotides.
55
What is Nucleotide Excision Repair (NER) and what is it used to repair?
Removal of a strand segment containing DNA damage and replacement by new DNA synthesis (sealed with DNA ligase). Used to repair UV-induced damage to DNA ## Footnote NER is often used to repair UV-induced damage to DNA.
56
What is the purpose of Mismatch Repair?
Removal of a DNA base-pair mismatch by excision of a segment of the newly synthesized strand followed by resynthesis of the excised strand.
57
During DNA replication, which strand is usually methylated?
Parental strand. ## Footnote The daughter strand is usually not methylated.
58
What role does the MutH protein play in Mismatch Repair?
Binds to unmethylated daughter strand.
59
explain mismatch repair steps
MutH binds to unmethylated daughter strand, MutS binds to basepair mismatch, MutL connects MutH to MutS, MutH cleaves daughter strand. Dna polymerase synthesizes gap.
60
What is Translesion DNA Synthesis?
An error-prone repair mechanism that allows DNA polymerase to bypass unrepaired DNA damage. When DNA polymerase III is blocked. Activated translesion DNA polymerase (pol V) that bypass these lesions and synthesizes short DNA segments. High mutation rate, no proof-reading abilities.
61
What triggers the SOS repair system (translesion DNA synthesis) in E. coli?
Massive DNA damage that blocks DNA polymerase III. DNA polymerase III cannot enter its active site to synthesize DNA, cant do its job.
62
What is the consequence of Double-Strand Breaks (DSBs)? and why are they hard to fix/extreme
Can cause chromosome instability, cell death, and cancer. -lack a template for DNA repair
63
What are the two mechanisms to repair Double-Strand Breaks?
* Nonhomologous end joining (NHEJ) - more error prone * Synthesis-dependent strand annealing (SDSA)
64
Describe Nonhomologous end joining (NHEJ).
An error-prone mechanism that can lead to mutation, where both strands of DNA are trimmed into blunt ends and rejoined. trimming leads to loss of nucleotides that cant be replaced. double stranded break due to x-ray/oxidative damage.
65
What is Synthesis-Dependent Strand Annealing (SDSA)?
An error-free process that uses an intact sister chromatid as a template to synthesize new DNA. strand invasion of sister chromatid creates D loop, replication fork assembles on loop and new strand synthesis occurs using available intact strand as template
66
What is CRISPR and its significance in gene editing?
relies on cells natural DNA repair mechanisms to facilitate genetic engineering. inject an embryo with plasmid or mRNA to express: - Cas9 nuclease enzyme - program/Guide RNA TO GUIDE Cas9 to genomic target (complementary to target site you want to cut) - donor template (synthetic DNA) if a "knock in" is required
67
What are Transposable Genetic Elements (TGE)?
DNA sequences that move within the genome through transposition, facilitated by transposase enzyme.
68
What are the two types of transposition?
* Non-replicative Transposition (cut & paste) * Replicative Transposition (copy & paste)
69
What is the structure of Transposable Genetic Elements?
They have terminal inverted repeats on their ends and are bracketed by flanking direct repeats. more transposable elements = more mutation generation potential
70
Transposition steps
1. staggered cuts cleave DNA strands of target sequence 2. single-stranded ends result from staggered cuts of target sequence 3. transposable element is inserted into target sequences and gaps filled by DNA polymerase
71
What are DNA transposons?
Transposable elements that transpose as DNA sequences. can be replicative: copy paste or non-replicative: cut and paste
72
How do retrotransposons transpose?
composed of DNA, transpose through RNA intermediate DNA -> RNA -> reverse transcribe back to DNA reverse transcribed DNA inserts into new location, enzyme reverse transcriptase is same enzyme used by retroviruses
73
What is a mutagenic effect of transposition?
TGEs can generate mutations when they insert themselves into crucial genetic regions.
74
Provide examples of diseases caused by transposition in humans, plants, drosophila.
Humans: * Hemophilia A * Coffin-Lowry syndrome Plants:round, wrinkled peas Drosophila: TGEs/P elements introduced in 1960s and quickly proliferated and remained (unaware of evolutionary implications/species interactions that could have caused this)
75
What are P-elements?
Transposable elements found in Drosophila, used in generating transgenic flies.
76
What was the process to generate transgenic flies using P-elements (old, before CRISPR)?
Clone gene of interest into plasmid flanked by inverted repeats, inject embryo with plasmid and transposase enzyme. gene of interest will randomly insert itself into genome of embryo

Genetics (13 decks)

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