Genetics Midterm 2

mutations

heritable changes in the DNA

monomorphic genes

one common allele, the definition of “wild type” is more clear-cut, the allele found on the vast majority of chromosomes in the population

polymorphic genes

several common alleles in natural populations

the definition of “wild" type” is more difficult

forward mutation

a wt allele —> a different allele (dominant or recessive)

reverse mutation (reversion)

a mutant allele —> back to wt

substitution

replacement of a base by another base

transition mutation

purine (G and A) to another purine or

pyrimidine (C and T) to another pyrimidine

transversion mutation

purine to pyrimidine or

pyrimidine to purine

deletion

one or more bp lost

insertion

one or more bp added

point mutations

affect one bp

transitions, transversions, deletions, or insertions

can all be point mutations

large deletion and insertions are among the most complex mutations can reorganize genomes by changing

the order of genes, the number of genes in the genome, the number of chromosomes

multicellular organisms have

higher mutation risks

between zygote formation and meiosis in germ cells, there are

many cell division

more chances to accumulate mutation

rate of reversion is always

lower than the rate of forward mutation probably because there are several ways to cause a mutation but fewer ways to “undo” it

sperm cells have a

higher mutation rate than oocytes

resistance to virus occurs 

independently of the action of the virus

bacterial resistance arises from

mutations that existed before exposure to bacteriophages

replica plating verifies that bacterial resistance is the results of

preexisting mutations

how does a random mutation occur in the DNA

chemical reactions or irradiation

mistakes during replication

if a mutation is repaired it will not be

transmitted to daughter cells

if a mutation is not corrected before the next round of DNA replication

it will be inherited by daughter cells

depurination

hydrolysis of a purine base (G or A)

1000x/hr in every human cell

creates an apurinic site that cannot specify a complementary base

DNA replication introduces a random base opposite the apurinic site

a mutation in the newly synthesized DNA 75% of the time

deamination

removal of an amino (-NH2) group

can change C to U

U pairs with A

changes CG —> TA after replication

oxidative damage

can affect any of the four bases

8-oxodG mispairs with A

GC —> TA after replication

what breaks the sugar-phosphate backbone

cosmic rays and X-rays

UV light causes

adjacent thymine residues to form abnormal covalent bonds (thymine dimers)

base analogs

replace a base, their chemical structure almost identical to the normal base

hydroxylating agents

adds an -OH group

C:G

alkylating agents

adds a methyl or an ethyl group

G:C

deaminating agents

remove an amino (-NH2) group

C:G

C —> U

U:A

intercalating agents

flat molecules

can intercalate btw successive base pairs

deletions or insertions of a single bp

proofreading

decreases mistakes made during replication

function of DNA polymerase

3’-to-5’ exonuclease activity recognizes mispaired bases and excises them

error rate if the nuclease is removed, 1 mistake every 10^-4 nucleotides

trinucleotide repeats can

expand or contract during replication

up to ~50 repeats are OK

unstable trinucleotide repeats

Huntington’s Disease

expansion of CAG repeats in the HTT gene

CAG encodes glutamine

the number of CAG repeats determines the severity and the age of onset

involuntary movement

usually starts in the mid-40s

autosomal dominant

progressive and fatal

the number of trinucleotide repeats increases or decreases in

different somatic cells of an individual

during gamete production

repeat trinucleotide numbers change from

one generation to the next

larger repeat numbers ar emore unstable

pre-mutation alleles

some alleles with intermediate numbers of trinucleotide repeats

likely to expand or contract during replication

carriers of pre-mutation alleles can transmit

new disease alleles with an expanded number of repeats to their children

pre-mutation alleles of particular genes tend to expand either in

the male or in the female germ lines (BUT NOT IN BOTH) (fragile X syndrome from mother, huntington’s disease is almost always from the father)

expansion and contraction of triplet repeats occurs by

slipped mispairing during DNA replication

how is the slipped mispairing during DNA replication

DNA polymerase often pauses as it replicates through repeat regions, allowing one DNA strand to slip relative to the other one

the strands can pair out of register, form a loop, causes expansion or contraction of trinucleotide repeat number in both strands

muller experimental evidence that mutagens induce mutations

if the X-rays caused a recessive lethal mutation, the F1 females could NOT have non-bat-eyed songs, all male progeny should have Bar eyes

the greater the intensity of the X-ray, the greater the frequency of the recessive lethal mutation

clustered damage by a mutagen is more

dangerous than isolated dagma

the ames test is important to determine if a chemical is a

mutagen

ames test

monitors the rate at which the second mutation occurs

allows to also quantify mutagenicity

screens for chemicals that cause mutations, and therefore, might cause cancer

tests whether a particular chemical can induce histidine (his+) revertants from his- strains

only revertants can grow on a plate that lacks histidine

a carcinogen is not necessarily a 

mutagen

accurate DNA repair systems

reversal of DNA base alterations

homology-dependent repair

dsbreak repair

mismatch repair

alkyltransferase enzymes

can remove if methyl or ethyl mistakenly added to guanine

MGMT

reverses DNA damage in one step

leads to the irreversible inactivation of the alkyltransferase

“suicide enzymes”

its efficiency relies on the constant synthesis of MGMT

photolyase

hydrolyzes thymine dimers

requires visible light

light repair or photorepair

not present in placental mammals

base-excision repair

homology-based

particularly important for removing uracil from DNA

UvrA and UvrB complex

sensors

scan for distortions of the DNA (thymine dimers)

if DNA damage is detected, UvrA is released and UvrB stays associated with the DNA

the UvrC endonuclease is recruited, cleaves the DNA

UvrD helicase recmoves the fragment

DNA polymerase fills the gap

DNA ligase connects the ends

methyl-directed mismatch repair

a backup repair system

active only after DNA replication

the base on the unmethylated strand is repaired

SOS system

bacteria

used when replication forks stalled because of unrepaired DNA damage

uses a “sloppy” DNA polymerase

adds random nucleotides opposite damaged bases

what hereditary diseases are due to mutations in DNA repair genes

xeroderma pigmentosum

hereditary forms of colorectal cancer

hereditary forms of breast cancer

changes in chromosome number and structure are important for the

emergence of new species

sutton concluded that the X and Y chromosomes determine

sex

klinefelter syndrome

47, XXY

if a Y is present a male will develop even with 2 X chromosomes

Turner syndrome

46, XO

Turner syndrome

Sterile females

short stature

lack of secondary sexual characteristics

neck webbing

if Y is absent X will develop the embryo towards a female

SRY Gene

primary determinant of maleness

sex determining region of Y

SRY is always present in

XX males

SRY is always nonfunctional in

XY females

MSY region (male-specific region of the Y) includes

SRY

3 genes required for spermatogenesis

8 genes shared with X

PARs

pseudoautosomal regions at the ends

allow X and Y to pair during meiosis I

the similarity in the PARs suggest that

the Y chromosome may have evolved from the X chromosome in an ancient mammal

when transgenic mice that were phenotypically male mated with female mice, it indicated that

SRY alone is sufficient to determine maleness and the human SRY could not replace mouse SRY

four-generation pedigree example in 1928

the grandfather has red-green color blindness and hemophilia A (X chromosome)

those who inherited one condition also inherited the other

the mutant alleles did not sort independently during meiosis

syntenic genes

genes on the same chromosome

the frequency of recombination is independent of the

arrangement of alleles

if there is linkage in autosomal genes, the expected 9:3:3:1 ratio is

altered

2 major roles of chiasmata during meiosis

1. exchange of genetic material

2. proper chromosome segregation

the generation of tension not only requires pulling forces exerted by the microtubules but also a

counteracting force (generated by the chiasmata)

recombination frequencies

% of total progeny that were recombinant types

could be used as a measure of the physical distance between two genes on the same chromosome

recombinant gametes are less frequent than parental gametes when geres are

linked

what leads to a recombination frequency of 50%?

1. independent assortment (if genes located on nonhomologous chromosomes)

2. if there is a crossover between the centromere and one gene

genes located very far also show a RF of

~50% (never exceeds 50%)

when 2 genes are close together, two types of meiosis

NCO (no crossover) - 0% recombinant gametes

SCO (single crossover) - 50% recombinant gametes

when 2 genes are further apart, SCO events are more

frequent, DCO (double crossover) also possible

Linked genes must be

syntenic and sufficiently close together on the same chromosome so that they do not assort independently

parentals > recombinants (RF < 50%)

unlinked genes

occurs either when two genes are on different chromosomes or when they are sufficiently far apart on the same chromosome that at least one crossover occurs between them in every meiosis

parentals = recombinants (RF=50%)

1:1:1:1 ratio of gametes

locus (plural loci)

gene/chromosome maps assign a gene to a specific chromosomal location

identification of a gene’s locus is important because

it can be used to isolate its DNA

it can help understand gene function

limitations of two-point crosses

difficult to determine gene order if two genes are closer together

actual distances between genes do not always add up

pairwise crosses are time and labor consuming

in three-point crosses we also see

double-crossovers

positive interference

a crossover inhibits the formation of another crossover in an adjacent region

coefficient of coincidence

comparing observed and expect frequencies of double crossovers (DCO) to quantify the amount of interference

coefficient of coincidence = observed DCO frequency / expect DCO frequency

interference = 1- coefficient of coincidence

chi square test

determines if an observed result may have occurred merely by chance

measures how well observed results conform to predicted ones

pinpoints the probability that ratios are evidence of linkage

cannot prove a hypothesis, only allows researchers to reject a hypothesis

critical requirement of the chi square test

null hypothesis - no significant difference occurs between the observed and the expected values

null hypothesis

no linkage (1:1:1:1, RF = 50%)

p-value

the numerical probability that observed results represent a chance deviation from the predicted values

information needed for the chi-square test

1. use data from breeding experiment

2. calculate number of offspring expected in each class (if there is no linkage (1:1:1:1 segregation)

degrees of freedom (df)

the number of independently varying parameters

df = N - 1 (where N is the number of classes)

if p > 0.10 we

cannot reject the null hypothesis for p < 0.05

there is no linkage

if p < 0.01, we have to

reject the null hypothesis

there is linkage

mutations in different genes

wild-type phenotype

complementation

mutations in the same gene

mutant phenotype

no complementation

complementation group

a collection of mutations that do not complement each other

complementation test examines individuals with:

one homologous chromosome carrying one mutation

the other homologous chromosome carrying the other mutation

benzer showed that 2 different mutations did not complement each other but rather

changed different parts of the same gene, crosses between homologous chromosomes carrying different mutations can generate the wild-type allele