Genetics CH 20

mutation

heritable changes in genetic information

change from wt

some adv some disadv like disease

wt

what is observed most often in population

mutation is the source for _____ that is necessary for ____

genetic variation, evolution

genetic variation is good , as it helps population adapt

mutations can be :

1) large scale/ chromosomal

2) small scale/ point

large scale mutations

affect chromosome structure or #

can be detected by viewing chromosomes using light microscope

deletions, inversions, duplications, translocations, entire chromosome added/deleted.

small scale/ point mutations

single base pair/few nucleotides changed, added or deleted

What are the small scale mutations that DO alter structure and function of protein?

1) missense - neutral or have no effect

2) nonsense

3) frameshift

What are the small scale mutations that DONT alter structure and function of protein?

silent

Transitions and transversions are ____

point mutations

transition

purine → purine A → G , G→ A

pyrimidine → pyrimidine T → C, C → T

transversions

purine → pyr A → T, C ; G → T, C

pyr → purine T → A, G ; C → A, G

transversions and translocations

which is more common ? transition or transversion

transition

missense mutation

point mutation that leads to change in a single aa in product

considered neutral if no affect on protein function

eg) code for a neg aa, now codes for a dif neg aa → overall no effect in protein folding/ function

nonsense mutation

point mutation that changes sense (codes for aa) codon into non sense codon (STOP) → premature STOP → truncated/short protein that is nonfunctional

silent mutation

point mutation that changes on codon but aa stays same

frameshift mutation

adding or deleting one or more bp

which alters reading frame of the mRNA downstream of the change

usually puts nonsense into frame → shorter protein

A point mutation that changes a codon in the mRNA but not the amino acid at that position in the protein is:

silent mutation

ways to categorize mutations based on where they happened

• somatic mutations

• germline mutations

somatic mutations

body cells

not heritable/cant be passed on

cancer is usually somatic mutation → increased cell division

NOT in all cells in body of affected peron

but ARE present in all DAUGHTER cells of initial affected cell

Are somatic mutations across all cells in the body of the affected indv?

NO

but are present in the daughter cells that arise from initial affected cell in the affected individual (NOT present in progeny)

germline mutations

in gametes

heritable

ALL cells in affected individual have mutation

Are germline mutations across all cells in the body?

YES , passed onto progeny as well but not necessary that all the progeny are affected, but if affected then all cells affected

how can mutations happen?

1) spontaneous

2) induced

spontaneous mutation

during normal lifetime of cell

causes are :

1) errors made during DNA replication

2) normal biochem in cell, creating reactive forms of o2.

induced mutations

caused by external agent (mutagen)

mutagen examples

1) base analogues

2) base modifiers

3) intercalating agents

4) UV light

big butts in underwear

errors made during DNA replication

spontaneous

DNAP makes mistakes

usually corrected by 3’ → 5’ exonuclease activity

how do errors during DNA replication occur?

1) incorrect bases added due to wobble pairing

• h bonding btw non watson/crick bases can lead to permanent mutation after 2nd round of replication

2) frameshift mutation due to strand slippage

• common at repetitive seq

during errors made in DNA replication if proofreading does not correct the first error ____

a subsequent round of replication will establish a permanent change in genome

normal biochem in cell leading to …

spontaneous

• depurination

  • loss of purine

• deamination

  • loss of amine

depurination

loss of purine

only lose the base, sugar phosphate backbone stays intact

2 rounds of replication needed for this change to be permanent (if not correct by proofreading it will become permanent at second round)

DNAP puts A where something is missing

deamination

loss of amino group from base

1) amino group lost from cytosine

cytosine - amino group → uracil

U pair with A during synthesis

if not proofread then after 2 rounds becomes permanent

G/C → A/T transition

2) amino group lost from adenine

adenine - amino group → hypoxanthine (pairs with C)

A/T → G/C transition

permanent after 2 rounds of DNA replication

Test used to idenity mutagens

mutagens cause inducible mutations

Ames Test

Ames Test

used to identify mutagens/ chemical carcinogens

uses mutant bacterial strains that

• have no DNA repair system

• cannot make histidine (His-)

  • aka will only grow on minimal media supplemented with his

since test chemical is mixed with liver enzyme, we don’t know if the growth was caused by mutagen in test chemical or by mutagen byproduct of liver enzyme+ test chemical

this is why we run control of test chemical itself + his- bacteria and check for growth

what can be concluded if Ames test shows growth when chemical+liver enzyme+ bacteria his-

body metabolism converted the chemical into mutagen

You use the Ames test to study a chemical commonly found in plastic packaging materials.  You have 2 plates containing minimal media.  Untreated bacteria is added to Plate 1.  Bacteria mixed with the test chemical is added to Plate 2.  You observe no growth on Plate 1 and 150 colonies on Plate 2.  What do you conclude?

test chemical is mutagen

induced mutations 4 ways

big booty in underwear

base analog

chemical with structure similar to normal base

can be incorporated into the newly synthesized DNA, during S phase (as it looks like base)

DNAP cannot differentiate btw base analog and base

why is base analog a problem

as ionization of base analog will change bp properties during subsequent rounds of replication

base modifiers

add or remove chemical group from base → changes its bp properties → so it wont pair properly when it is a template

intercalating agents

flat, planar molecules that can insert themselves between stacked bases in DNA

causing contorted helical structure → leads to mistakes by DNAP

UV light

cause adjacent pyrimidines to bond tg

changing structure of helix

what stage do all inducible mutation mutagens act as mutagens or cause problems?

in actively DNA replicating cells

gene interaction epistasis = supressor mutation

supressor expressed at one locus of gene masks the phenotype expressed by another locus in gene

double mutant : individual has one mutation and a mutation at another locus supresses this mutation

mutant purple (p) eye in fly , wt red (p+)

supressor (ss) vs non supressor (s+ dom) makes red

1st mutation caused mutant phenotype purple, 2nd mutation at dif site supress the effect of first mutation and give wt

ppss → purple got supressed and became red

methods of supression

1) intergenic supression

mutation in 2 different genes

1st mutation gives mutant phenotpe

2nd supressor mutation restores to wt

2) intragenic supression

both mutations in same gene / single codon of gene

intergenic supression eg) eye color

indv that shows supression will be double mutant

1st mutation in gene that codes for eye color : nonsense mutation

2nd/ supressor mutation in gene that codes for tRNA

mutation 1 gives mutant phenotype of eye color

mutation 2 supresses mutant eyecolor and expresses wt

intergenic supression eg) enzyme

enzyme needs many subunits to function

1st mutation in code for subunit A : missense mutation

• subunit A and B cannot bind

2nd/ supressor mutation in gene that codes for subunit B

• restores binding btw A and B

at first mutation at red site

- → + so no longer binding as + vs +

at second mutation at green site

+ → - so now + and - can bind

intragenic supression eg) leu → phe → leu

both mutations in SINGLE codon of gene

intragenic supression eg) - → + → -

mutations in DIFFERENT codons of same gene

mutation 1 - → + so no longer folding correct

mutation 2 + → - now folding correct

2 wrongs → right

DNA repair mechanism

1) direct repair

2) excision repair

3) mismatch repair

dont envy me

2 strands of DNA

• 1 mutated , 1 template/ non mutated

What is true about BOTH intergenic suppression and intragenic suppression?

a double mutant shows wt phenotype

DNA repair mechanisms are ___ meaning?

redundant, many ways to repair all mutations

direct repair

reverse the change that happened to DNA

A) thymine dimers caused by UV light can be reversed using photolyase

UV light causes T to bond to neighbour T instead of complementary A

B) Methyltransferase

removes CH3 added by mutagen

photolyase

needs light to work

does direct repair and repairs thymine dimers caused by UV light

breaks T-T helping T-A form

Excision repair

1) nucleotide excision repair

2) base excision repair

nucleotide excision repair

remove multiple nucleotide

needs DNAP , DNA ligase

base excision repair

remove damaged base

Compare both the excision repair mechanisms

both use DNAP and DNA ligase

in first step nucleotide excision repair - removes nucl

in first step base excision repair - DNA glycosylase removes base

mismatch repair

during S phase as replication is happening

enzyme identifies old vs new strand

how to distinguish old and new DNA

many A’s in DNA are methylated after replication; but this takes time

so right after replication, new wont be methylated but old will be

Which repair is the only one that acts during DNA replication not after?

mismatch repair

Which repair acts on cells that are not actively dividing?

direct repair

excision repair