Lecture 2 - Genetic variation in the human genome

what are the major mechanisms that cause SPONTANEOUS error? (3)

1. mismatches

2. insertions/deletions from replication errors

2. spontaneous deamination (radiation damage)

What are the 6 SPONTANEOUS errors we talked about. List:

1. dna replication error

2. slippage

3. crossing over errors

4. cytosine deamination

5. 5-methylcyosine deamination

6. transposable element insertions

DNA replication error:

- how they occur

- things that they can cause

- how they are fixed (may be multiple, list all).

- wrong addition of dna

- mismatch

- proofreading, mmr

slippage:

- how they occur

- things that they can cause

- how they are fixed (may be multiple, list all).

- insertions of loops

- insertions/deletions

- mmr

crossing over errors:

- how they occur

- things that they can cause

- how they are fixed (may be multiple, list all).

- crossing over between genes that are homologous but not equal.

- deletions, insertions, duplications

- MMR

cytosine deamination

- how they occur

- things that they can cause

- how they are fixed (may be multiple, list all).

- loss of amino group causes C --> U

- U bonds with A (NOT G)

- Creates CG --> TA mutation (once dna rep after)

- base excision repair

5-methylcyosine deamination:

- how they occur

- things that they can cause

- how they are fixed (may be multiple, list all).

- loss of amino group in methylcytosine --> thymine

- creates CG --> TA mutation

- MMR bc thymine looks normal so not unnatural

transposable element insertions:

- how they occur

- things that they can cause

- how they are fixed (may be multiple, list all).

- jump onto other genes though non-homologous recomination methods

- changes in insertions, deletions

- MMR, BER

are sponanteous errors easy or hard to fix

easy

explain mismatch error (how its created) and how it is fixed (2 ways)

- dna polymerase adds wrong base

- proofreading and mmr

explain proofreading process + when it occurs + how mutation is detected

- occurs during replication

- 3'->5' exonuclease cuts out and replaces incorrect base

- dna polymerase feels weird H-bond

explain mmr and when it occurs + how mutation is detected

- occurs post replication

- cuts out area with incorrect base and repaired using the other strand as a template

- lagging strand helps identify (in chunks)

what type of error is slippage

spontaneous error

How is slippage fixed

MMR

for insertion case, what strand does slippage occur and what is the effect for when MMR fails and when it works (3)

- slippage happened on new strand (bulge on new), causes an extra repeat

- MMR fails: bulge is incorrporated into new strand causing a repeat

- MMR works: buldge is cut out and no insertion

for deletion case, what strand does slippage occur and what is the effect for when MMR fails and when it works (3)

- slippage happens on template strand(buldge on old) causes one less repeat to be copied onto new strand

- MMR fails: new strand is short

- MMR works: mmr does not skip the bulge and new strand has correct length

3 types of crossing over errors + effect

interchromosomal: between 2 chromosomes

- insertion and deletion

intrachromosomal: in one linear strand

- deletion or inversion

base excision vs MMR (2)

- base excision repairs the strand with messed up C (regardless of new/template)

MMR ONLY FIXES NEW

- base excision happens anytime, MMR only after rep

explain base excision repair

enzyme detects and cuts chemical base damage and fills in corrected

what are transposons

highly repeated sequences (unknown purpose)

how are transposons inserted

double stranded break then inserted

What are the 5 types of NON SPONTANEOUS mutations we discussed

1. base analogs

2. alkylating agents

3. intercalating agents

4. UV

5. ionizing radiation(x-ray, gamma)

what causes non-spontaneous mutations

carcinogens

1. base analogs

- how they occur

- things that they can cause

- chemical mutagens

- frameshift and base substitutions

explain how base analog of 5-bromouracil occurs + its effect on genotype

- 5-bromouracil (KETO form) binds to adenine bc looks like thymine

- 5-bromouracil turns into ENOL form

- guanine binds to ENOL 5-bromouracil

- causes A-T --> G-C

2. alkylating agents

- how they occur

- things that they can cause

- EMS mutagens is added to bases making them alkylated

- can cause incorrect base pairing

3. intercalating agents

- how they occur

- things that they can cause

- things that sneak in between dna. DNA pol thinks its an extra base with no complementary base pair

- flat, rings

4. UV radiation

- how they occur

- things that they can cause

- how they are fixed (may be multiple, list all).

- uv rays can cause dimers (ie. thyine dimer) which creates a kink halting sna replication

- Leads to mismatches

- nucleotide excision repair, reconominational repair

what is recombinational repair?

use dna sequence on other chromosome to repair

5. ionizing radiation

- how they occur

- things that they can cause

- how they are fixed (may be multiple, list all).

- caused by x-rays, gamma rays

- can create double and single stranded breaks in DNA

- repair through religation or recombination, MMR, BER

what is religation

process of sticking ends together that are broken

Mutagen vs carcinogen

mutagen causes mutations and carcinogens cause cancer specifically

what is the ames test?

Test to see if something is a mutagen (if that substance causes a mutation)

what is a true revertant in ames test

After u use the mutagen tratment if the strain returned back to its originalwild type (ie. when His+ was able to grow without histidine). GENE mutation itself FIXED

what is the pseudorevertant in ames test?

Gene mutation is NOT fixed but something else is mutated to bring the substance back to wild type. more common

what is a suppressor

mutation that reverses phenotype caused by another mutation (can be partial.complete)

what is an intragenic supressor

when suppressor lays in gene gene as initial mutation

what is a extragenic supressor

supressor lies on different gene from initial mutation.

what is nuclear excision repair

distortion in the DNA helix that forces piece from single strand to be cut out. Gap is fillwed by DA synthesis