Mutation

Question 1

Somatic mutations

Answer 1

Occur in somatic cells and are not passed to progeny

Question 2

Germinal mutations

Answer 2

Occur in gametes, are passed to progeny

Question 3

Phage mutants

Answer 3

Useful in genetic studies.

Question 4

Base substitution (transition)

Answer 4

Pyrimidine swapped for a pyrimidine or purine for purine

Question 5

Base substitution (transversion)

Answer 5

Pyrimidine swapped with purine (vice versa)

Question 6

Frameshift

Answer 6

Insertion or deletion of one or two bp that alters the reading frame of the gene downstream.

Question 7

Tautomeric shift

Answer 7

Movement of H atoms from one position in a purine of pyrimidine base to another.

E.G causes rare A:C (rare imino form) and G:T (rare enol form).

Question 8

Expanding nucleotide repeats

Answer 8

expansion of triplet repeats (i.e. CAG and others) is cause of numerous human diseases (e.g. huntington’s)
Mechanism of expansion involves DNA replication
In a region of many triplet repeats, polymerase may have some difficulty knowing where it is in the order of repeats so it pauses and slips backwards, forming a hairpin loop
Hairpin obviously elongates the DNA by a bit and then when that DNA has to be replicated, there’s more triplet repeats than before which exacerbates the issue, causes continual addition of unnecessary repeats
A “dynamic” mutation because repeat copy number is in flux with each round of replication

Question 9

Forward mutation

Answer 9

Genetic alteration that changes the wild-type into a mutant

Question 10

Reverse mutation

Answer 10

Mutated site back to wild-type

Question 11

Missense mutation

Answer 11

Base substitution that results in an AA change

Question 12

Nonsense mutation

Answer 12

Base substitution that results in a regular codon becoming a stop coding

Question 13

Silent mutation

Answer 13

Base substitution at the 3rd codon position that changes to codon to one still specifying the same AA

Question 14

Loss of function mutation

Answer 14

Causes complete or partial loss of normal protein function

Question 15

Gain of function mutation

Answer 15

Cell produces protein/gene product whose function is not normally present

Question 16

Suppressor mutation

Answer 16

Second site mutation that hides/suppresses the effect of the first mutation.

Question 17

Spontaneous DNA damage results from

Answer 17

DNA Replication errors - tautomeric shifts, wobble mispairing or strand slippage during replication

DNA replication pauses- Replication stalls at nick in DNA, unusual DNA structure or bulky lesion can generate broken DNA

Endogenous chemical reactions -
Depurination - spontaneous loss of purine base from a nt through hydrolysis of glycosidic bond ( ~10000 x/cell/day). Loss of pyrimidine is possible but less frequent. Leaves abasic site which is susceptible to replacement with A or C, creates transition or transversion
Deamination - spontaneous loss of –NH2 group on base, causes transition mutation. Deamination of 5MeC converts C to T, pairs to A
Oxidation - endogenous reactive oxygen species (ROS) damage DNA, can produce oxidized bases such as 8-oxoG which frequently mispairs with C or A, causes transversion mutations (G:C → T:A)
Alkylation - endogenous alkylating agents (i.e. S-adenosyl methionine or SAM) can add methyl groups to DNA bases and produces transition mutations (G:C → A:T)

Question 18

Induced DNA ramage results from

Answer 18

Chemicals that are mutagenic to replicating AND non-replicating DNA
Alkylating agents - mutagens that react with DNA bases and add methyl or ethyl groups and induce (directly or indirectly) transitions, transversions, frameshifts and chromosomal aberrations
Nitrous acid (HNO2) - deaminating agent, removes amino groups from A, C, and G, causes transition mutations (A:T to G:C)
Hydroxylamine - hydroxylates amino group of C and causes it to pair with A, leads to transition mutation (C:G → OHC:A → T:A)
Chemicals mutagenic to replicating DNA only
Base analogs - 5-bromouracil (resembles T) and 2-aminopurine (resembles A or G) can be incorporated into DNA during replication and later cause transition mutations through occurrence of rare tautomers
Acridines - intercalation of acridine dye (planar rings e.g. proflavine, ethidium bromide, acridine orange) into DNA structure causing frameshift mutation during DNA replication

Question 19

Radiation-induced mutations

Answer 19

UV light induces mutations through excitation
X-rays and shorter wavelengths induce mutations through ionization
Mutagenesis by UV radiation produces cross-linking of adjacent thymines, making thymine dimers (covalent bond of pyrimidine rings)
Blocks DNA replication, can cause double stranded DNA breaks (serious issue)
At peak hour sunlight, each human skin cell exposed to sun acquires ~4500 thymine dimers/h
X-ray ionizing radiation can cause DNA strand breaks and changes in chromosomal structure
Causes nicks and DSB in chromosomes
Faulty repair of strand breaks by recombination can cause gross chromosomal rearrangements such as deletions, duplications, inversions and translocations

Question 20

Direct reversal of DNA damage

Answer 20

Light-dependent repair - direct repair of thymine dimers (and other UV-induced photoproducts) by photolyase, also called photoreactivation, only found in prokaryotes
Enzymatic removal of alkyl groups from DNA bases (e.g. removal of methyl group from methylguanine so it returns to being just guanine and can pair with thymine)
Ligation of single-stranded nicks in DNA - occurs when there is a 5’ phosphate near a 3’ OH
Excision repair - base excision repair and nucleotide excision repair, same basic features:

Question 21

Excision repair

Answer 21

DNA repair endonuclease which can recognize damage to DNA, bind to it and excise damaged DNA
DNA polymerase - fills in gap using undamaged complementary strand of DNA as a template
DNA ligase seals the break left by DNA polymerase
Base excision repair (BER) - specifically recognizes and repairs DNA bases damaged by deamination, alkylation or oxidation, found in both prokaryotes and eukaryotes
DNA glycosylase detects and removes damaged base, breaks glycosidic bond
DNA endonuclease recognizes apurinic site left by DNA glycosylase and cleaves phosphodiester bonds on either side, removing deoxyribose sugar
DNA polymerase adds new nucleotides, complementary to template strand
Phosphodiester bonds reformed by DNA ligase
Nucleotide excision repair (NER) - acts to remove thymine dimers and other bulky forms of DNA damage that block DNA replication
Mechanism is similar for prokaryotes and eukaryotes but eukaryotes have a more complex process with more proteins
Enzyme complex removes a short tract of DNA around mutation and resynthesizes it
Mutation of human NER genes causes xeroderma pigmentosum - cells cannot remove pyrimidine dimers and patient is prone to skin cancer

Question 22

Mismatch repair

Answer 22

recognizes mismatched base in a newly-synthesized strand of DNA through ID of hemi-methylation GATC sequence

Question 23

Recombination

Answer 23

Homologous recombination (HR) - occurs during or after DNA replication, if one sister chromatid suffers a DSB, it can be repaired using identical (unbroken) sister chromatid
HR also used to ensure proper chromosome separation (disjunction) during meiosis
Replication either stops or leaves a gap when encountering a pyrimidine dimer
If dimer occurs on leading strand side, lagging strand is synthesized normally
HR uses lagging strand as a template for leading strand gap caused by dimer
Pyrimidine dimer remains in the strand, must still be excised by NER or MMR
Non-homologous end joining (NHEJ) - different set of proteins to repair DSB, occurs throughout cell cycle, unlike HR which only occurs in S/G2 phases

Question 24

Translesion synthesis

Answer 24

error-prone repair mechanism, uses TLS DNA polymerases
TLS DNA polymerases have lower fidelity of copying so they can replicate through damaged DNA, unlike normal polymerases which copy bulk of DNA in prokaryotes and eukaryotes
Pyrimidine dimers and other bulky DNA lesions block DNA pol. I and III, results in cell death
TLS DNA polymerase recruited to replicate through DNA damage, bypassing the lesion, and inserting random nucleotides in order to bypass it
TLS pol. swapped for pol. III once lesion is passed which properly copies rest of chromosome
Essentially TLS pol. Is a placeholder, but does cause mutations, is a last resort mech.
Some errors caused by TLS pol. can be fixed later by various DNA repair mechs.
SOS response - induced response to heavy mutation of bacterial chromosome which involves activation of DNA recombination, repair and replication proteins (including TLS polymerases)
In bacterial cells, an increase in mutation = possible adaptation
Eukaryotic cells have a similar response to damaged DNA