Genetics Module 3

loss of function mutations

recessive

gain of function mutations

dominant

effects of point mutations at protein level

missense

nonsense

silent

readthrough

missense

changes amino acid (can have neutral effect)

nonsense

changes codon so that it becomes a stop codon

silent (synonymous)

codes for the same amino acid

eg AGG mutates to CGG but both code for Arginine

Readthrough

stop codon is changed to a codon that codes for amino acid resulting in a longer protein

point mutation example

Sickle cell anemia

one amino acid substiution

Spontaneous Point mutations

Depurination

Deamination of cytosine

Wobble base pairing

Depurination

Removes glycosidic bond at eithe

r G or A, results in missing purine

Deamination of cytosine

results in Uracil

causes GC to AT transition

wobble base pairing

mispairing due to flexibility in helix

results in transitions after replication

Chemically Induced Mutations

Base Analogs

Alkylating Agents

Deamination

Hydroxylamine

Oxidative Reactions

Intercalating Agents

Base Analogs Cause Transitions After Replication

5-bromouracil normally pairs with A, but can also pair with G.

2-aminopurine normally pairs with T, but can also pair with C

Oxidating Agents Damage DNA

Oxidative reaction converts guanine into 8-oxyguanine.

8-Oxyguanine pairs with A instead of C during replication

Frameshift Mutation example

Cystic Fibrosis

Mutation in a structural protein

Due to a defective CFTR protein- a chloride channel

abnormal salt transport across membranes

Causes of frameshift mutations

Intercalating Agents

Strand Slippage

Unequal Crossing Over

Repeat Regions

Intercalating Agents mutation

Large, planar molecules that slip between base pairs of DNA. This distorts the helix, causing template slippage during replication.

unequal crossing over mutation

Unequal crossing over can cause insertions and deletions

Misalignment of homologous chromosomes during crossing over can lead one product having an insertion and the other having a deletion.

Repeat Regions mutation

repeats may occur via hairpin formation during replication.

direct repair types

in bacteria- photoreactivation repair of pyrimidine dimers

methyltransferase restores correct form to incorrectly methylated G

mismatch repair

nucleotide excision repair

base excision repair

double strand base repair

direct repair

Corrects structure of abnormal nucleotide without replacing the nucleotide.

mismatch repair

Mismatch repair proteins recognize abnormal helical structure and identify the incorrect base. Exonucleases remove an area of the new strand from the methylated sequence to the mismatch. DNA polymerase fills in the gap and ligase seals the nick. • Does not remove lesions (damaged DNA).

nucleotide excision repair

Removes bulky lesions (damaged DNA)

Enzyme cleaves sugar phosphate bonds on both sides of lesion removing several nucleotides

DNA polymerase fills in gap, DNA ligase seals nick

Can remove lesions unlike MMR.

base excision repair

Removes modified bases

Glycosylases bases recognize and remove defective resulting in an AP site

Then AP endonuclease cleaves the phosphodiester bond next to the missing base (causes a nick) and then removes the rest of the nucleotide

DNA polymerase fills in the gap, DNA ligase seals the nick

double strand break repair

Homologous Recombination Repair

-Uses the sister chromatid to repair the break

Nonhomologous end joining

-Joins broken ends

-Often leads to translocations, deletions and insertions

translesion DNA polymerases

deletion types

terminal- acentric fragment lost in cell division

interstitial- 2 breaks

cri du chat

missing part of chromosome 5

deletion effects

haploinsufficiency- single copy not enough for wild type phenotype to occur

pseudodominance- expression of normally recessive phenotype because no homologous allele

duplication types

evolutionary significance of inversions

inversions may lead to speciation

translocation types

Reciprocal

Non-Reciprocal

Robertsonian

Reciprocal Translocations

Two nonhomologous chromosomes exchange arms (or parts of arms).

No gain or loss of DNA.

Non-Reciprocal Translocations

A segment from one chromosome is moved to a nonhomologous chromosome.

No gain or loss of DNA.

Robertsonian Translocations

• Two telocentric/nearly telocentric chromosomes combine to make one larger, more metacentric chromosome.

• Some small amount of DNA is lost but often not noticeable.

• Isochromosomes – two chromosomes joined are homologs.

Familial Down Syndrome

4% of Down Syndrome cases are familial.

• Chromosome with Robertsonian translocation joining 14 and 21 information

if a person is heterozygous for a reciprocal translocation, what % of their meiotic products will result in nonviable gametes?

50 percent

Burkitt’s Lymphoma

Abnormal function of B cells

Reciprocal translocation between chromosomes 8 and 14 places c myc (oncogene that promotes cell division) next to an enhancer which normally stimulates production of antibodies.

Cell division is stimulated in B cells.

Same genes are present, but chromosomal location alters the phenotype

Regulatory Mechanisms for Transcription

rapid turn on and rapid turn off

sequential cascades of gene expression

constitutive expression/housekeeping- always on

lac operon

negative inducible with lactose, positive inducible with cAMP (not glucose)

active repressor binds and turns it off, but when lactose present gene is turned on

I-

repressor cannot bind operator due to repressor’s bad binding site

I^s

super repressor, always on

can’t bind to lactose

lac operon and glucose

high glucose = low cAMP = lac operon is repressed = no transcription

Tryptophan Operon

negative repressible

tryptophan low

no tryptophan so repressor stays inactive, can’t bind to operator so transcription takes place

tryptophan high

tryptophan binds to the repressor and activates it

trp repressor binds to operator and shuts transcription off

Tryptophan Operon Attenuation

Premature termination of transcription

Attenuator – located in the leader sequence and responsible for decreasing transcription when trp is present

When trp high, transcription ends really fast

Puff DNA

loosely coiled and more transcription

how does chromatin change before transcription

decondenses to 11nm fibers beforehand

DNasel

chews up loose DNA

histone modification

acetylation and methylation

what does acetylation do

neutralizes positive charge on histones which loosens DNA and turns on gene

what does deacetylation do

turns off gene

what does DNA methylation do

decreases transcription

changes in histone modification and flowering

FLC gene suppresses flowering

Acetylation of FLC gene turns it on which prevents flowering

Deacetylation of FLC gene turns it off which allows flowering

epigenetic methylation of bees

female bees that eat royal jelly become queens

royal jelly suppresses Dnmt3

Dnmt3 adds methyl groups to DNA

Bees w/ suppressed DNmt3 have less methylation and genes that are normally silenced are expressed

Primary Immune response

Secondary immune response

Antibody structure

2 chains heavy and light

-each has a constant and variable region

Antigen binds to the variable region

antibody diversity- how are millions made

somatic recombination in B cells during B cell differentiation

alternative sites for recombination

somatic mutations

development

regulated growth resulting from interaction of genome, cytoplasm, and environment

programmed sequence of events

not reversible

differentiation

aspect of development

forming different types of cells, organs through specific regulation of gene expression

dorsal

up

ventral

down

Maternal drosophila genes

egg polarity genes- establish anterior/posterior polarity and dorsal/ventral polarity

When are Maternal drosophila genes transcribed?

during egg development

When are Maternal drosophila genes translated?

after fertilization

drosophila segmentation genes

affect number and polarity of segments

-gap genes

-pair rule genes

-segment polarity genes

homeotic genes

determine identity of each segment

bicoid maternal gene

bicoid mRNA anchored at ANTERIOR end

nanos maternal gene

nanos mRNA anchored at POSTERIOR end

egg from bcd+

normal larva

egg from bcd-

no anterior- headless

where is bicoid protein highest?

In anterior

Where is nanos protein highest?

In posterior

bicoid and caudal

bicoid represses translation of caudal mRNA

affects POSTERIOR

bicoid and hunchback

bicoid stimulates hunchback expression

in ANTERIOR

Nanos and hunchback

Nanos inhibits hunchback translation in ANTERIOR

homeotic genes

give specific identity to each segment

genes in order from anterior to posterior

each gene is on only in specific segments based on concentration of earlier gene products

homeotic drosophila mutation example

Ubx green in T3

When deleted, Antp red extends into T3 causing extra wings

homeotic homeoboxes

Region of the protein formed from the homeobox DNA is called homeodomain

Proteins containing homeodomain are DNA binding proteins

Homeodomain binds to specific DNA sequences and regulates transcription

apoptosis

removal of tissue between fingers

creation of joints

neural pruning

plant homeotic genes

Class A= whorl 1 sepal and whorl 2 petal

Class B= whorl 2 petal and whorl 3 stamen

Class C= whorl 3 stamen and whorl 4 carpel

normal chromosomes

2n=8

nullisomic

2n-2=6

The correct sequence of segmentation gene action in the development of the Drosophila embryo is

1. Gap

2. Pair rule

3. Segment polarity

whorl 1

sepal

whorl 2

petal

whorl 3

stamen

whorl 4

carpel

gap genes

divide embryo into broad segment

are a type of segmentation gene

eurkaryotic regulation

Changes in Chromatin

initiation of transcription

RNA processing and stability

Protein modification

In eukaryotes, repressors can function by:

A plant species is described as 2n=20.

 

How many chromosomes present in a triploid cell from this plant?

n=10

nx3= 30

In eukaryotes, repressors can function by: