Bio Quiz 6

What kind of repair fixes DNA polymerase errors?

strand-directed mismatch repair

What do mismatched nucleotides create?

bulge in the newly synthesized DNA

How does repair machinery know which strand is old DNA and which one is new DNA?

looks for nicks always present in newly synthesized strand and checks for the correct face of the sliding clamp

What is the protein that recognizes and locks onto the DNA mismatch?

MutS

Does MutS fix the DNA mismatch?

no, it only recognized it and signals for MutL

What does MutS interact with?

the sliding clamp following directly behind the polymerase at work

How are correctly matched nucleotides different from mismatched?

correctly matched are springy while mismatched are soft

What assumption does MutL have to make?

it assumes that new DNA is the wrong one and identifies new DNA by looking for nicks

How does MutL remove the mismatched nucleotide?

digests away the new strain from the nick to the mismatched nucleotide

What happens after the mismatched nucleotide is removed?

DNA polymerase delta fills in the missing nucleotides

Does MutL also work on leading strand?

yes, nicking enzyme follows leading strand and adds nicks

What results from replication errors?

trinucleotide repeat expansion

What are trinucleotides?

highly repetitive regions of DNA

What do trinucleotide repeats do?

they are unstable, so they can expand in number when passed from parent to child, resulting in disease

What happens have trinucleotides have been replicated?

they form hair pins

What do hairpins in trinucleotides cause?

the DNA polymerase stumbles and re replicates the hairpin, forming a longer strand

What effect would expansion of trinucleotide repeats have on the protein encoded by this gene?

it would add extra amino acids and protein would expand and will not do what it should

Will expansion still occur if the hairpin is not re-replicated?

yes

How will expansion still occur if the hairpin is not re replicated?

it will be expanded in the next round of replication

How is this property of DNA polymerase related to another type of trinucleotide repeat you learned about earlier in the course?

short tandem repeats; instability of polymerase are the reason we have STR’s and they could change from one generation to the next which is why we test 13 for serious cases

Why won’t single stranded binding proteins prevent the formation of these trinucleotide repeat hairpins as it did during replication or “regular” DNA sequences?

these proteins only occur in front of the replication fork and they only bind to the template strand

What disease do trinucleotide repeat expansions cause?

Huntington’s Disease

What is Huntington’s Disease caused by?

trinucleotide repeat expansion in the Huntington gene

Are there some repetitive regions in exons?

yes

What happens to the Huntington protein?

when too many repeats occur in the Huntington gene it aggregates and becomes sticky for itself

What would be the effect of a mutation in the nicking enzyme that is associated with the mismatch repair process?

there would be more mutations in the leading strand

DNA is strong but…

vulnerable

How is DNA prone to damage?

exogenous and endogenous errors

Are replication errors the only source of DNA damage?

no

What are exogenous problems that cause DNA damage?

UV radiation, oxygen radicals, chemicals, other organisms, environment

How does UV radiation light cause a mutation in DNA?

UV light causes pyrimidine bases to covalently link to one another

What happens when UV light causes pyrimidine bases to covalently link to one another?

results in a kink or bulge in the double stranded molecule

What can be dimers?

T-T, T-C, C-C

What are dimers?

two molecules interacting with each other

What do oxygen radicals have?

missing electrons

How are oxygen radicals produced?

mistake during cellular respiration or because of exposure to ionizing radiation

What is dangerous about oxygen radicals?

they are very reactive and damage DNA by ripping electrons off the molecule

What do antioxidants do?

accept electrons which neutralize electrons which call for a less chance of cancer

What do alkylating agents do?

attach methyl or ethyl groups to DNA bases

What does attaching methyl or ethyl groups to DNA bases do?

interferes with proper base pairing

What is an example of an alkylating agent?

mustard gas (nitrogen mustard)

Nitrogen mustard is considered to be a…

chemical weapon

What happens when base pairing is interfered with?

transcription and replication cannot occur

How can one be affected by mustard gas?

inhalation, touching it

What does nitrogen mustard do to Watson and Krick?

causes a covalent linkage instead of a H bond between Watson and Krick

What is an interstrand crosslink?

covalent linkage between 2 mismatch base pairs between Watson and Krick

What is the scientific name for Giant Hogweed?

Heracleum mantegazzianum

What plant produces psoralen which causes cross linking?

Giant Hogweed

What does Giant Hogweed produce?

psoralen

What does psoralen do?

binds irreversibly to DNA

What happens when psoralen binds irreversibly to DNA?

it destroys the cells of predators which contact the plant

What cross linkage occurs due to psoralent?

thymines link

Is psoralen dangeous subcutaneously?

no, only cutaneous

What dangerous molecule is found in cigarette smoke?

benzopyrene

What does benzopyrene do?

binds to DNA and causes alterations in genetic sequence

What does benzopyrene lead to?

cancer

What is benzopyrene?

molecule found in cigarette smoke that covalently links to DNA, adduct

What is an adduct?

molecule that covalently links to DNA

What does the adduct benzopyrene cause in DNA?

bulky lesion

What besides benzopyrene is also an adduct?

psoralen

Who had the first thought that smoking causes cancer, specifically scrotal cancer?

Sir Percival Pott

What did Sir Percival Pott observe?

many boy chimney sweeps coming in with scrotal cancer

What did Sir Percival Pott believe the scrotal cancer was coming from?

the chimney sweeps went in naked and when they were sweating soot got stuck in the rugae on their scrotum

What was the first time environmental factor was found to cause cancer?

Sir Percival Pott and benzopyrene

When did Sir Percival Pott discover this and where?

late 1700s, London

What are two examples of endogenous damage?

deamination and depurination

What does deamination do?

removed the NH2 group from cytosine which makes uracil

Does deamination always remove the NH2 from cytosine specifically?

usually, but not all of the time

If deamination is not fixed before replication…

it can be encoded in DNA

Why would mutS not fix deamination?

this occurs before replication

What is depurination?

loss of a purine; affects the adenine or guanine only

What is the most common type of DNA damage?

depurination

What happens after depurination occurs?

polymerase skips the blank space which causes deletions in DNA

What bond is broken with depurination?

glycoslaic

What fixes minor damage?

base excision

What is base excision?

fixing the mutated base

What does glycosylase do?

removed the base only, not the sugar or phosphate

How does glycosylase maintain DNA?

by scanning it and flipping out to check

What removed the sugar phosphate in base excision?

AP endonuclease

What fills in the gaps in base excision?

specialized DNA polymerase

How is the damage detected in base excision repair?

enzymes that patrol the DNA, which flip out every base and check it for damage

Some glycosylases do flipping and checking…

at the same time

Why does the cell have a variety of glycosylases?

each recognizes and removes a specific type of damaged base

What was does the activity of the mechanism of base excision repair go?

5’ to 3’ exonuclease activity

What is a disease of base excision repair?

familial adenomatous polyposis

What does FAP stand for?

familial adenomatous polyposis

What can FAP patients not produce?

MYH glycosylase

What is MYH glycosylase needed for?

BER

What does the lack of MYH glycosylase needed for BER lead to?

polyps, abnormal growths in the colon

When do polyps begin to grow with FAP?

as early as teenage years

When do FAP patients begin getting colonoscopies?

age 10

What can the polyps develop into if left untreated?

cancer

When is the onset age of cancer in FAP patients?

39

What does the specific location of the cancer tell you about where MYH glycosylase is most active?

all cells need glycosylase but use in different versions so this version is active in the colon and we developed a dependence on it

What fixes larger damage to DNA?

nucleotide excision repair

What does NER stand for?

nucleotide excision repair mechanism

What is the function of nuclease?

break phosphodiester bonds

What does excision nuclease do in NER?

clips on both sides of the lesion with extra room

What calls over excision nuclease?

enzyme complex

How is NER initiated?

enzyme complex scans DNA for bulges