Gen Mol Bio Midterm 2

Principle of segregation

Alleles separate during meiosis; each gamete gets one allele Aa → gamete A + gamete a

Independent assortment

alleles in one locus sort independently from alleles at another locus

AaBb = gametes AB:Ab:aB:ab 1:1:1:1 ratio of unlinked genes

Recombination

Alleles sort into new combinations; heart of crossing over in meiosis

Recomb. frequency: decreases as the genes get closer together

linked genes

DO NOT sort independently → skews the 1:1:1:1 ratio

gene measurement

A____B = centamorgan → the genes are close together => can determine gene mapping

complete linkage

no recombination occurs; only parental gametes produced

AABB x aabb → AB/ab

partial linkage

some recombination

AABB x aabb → Ab/aB

coupling (cis)

1 chromosome has the wild type allele, and 1 chromosome was the mutant allele

repulsion (trans)

wildtype and mutant allele are on the same chromosome

Deletion

loss of segments (ABEF)

→ gene loss, pseudodominance, haploinsufficiency

Duplication

Extra segments (ABCDEFEF)

→ gene dosage, imbalance, developmental issues

Inversions

segments flipped 180°

→ recombination suppression, fertility issues

paracentric inversion

Inversion does not involve the centromere AB•CFED

Pericentric inversion

Includes the centromere ADC•BEF

Translocation

segment moves to another chromosome

reciprocal translocation

exchange between chromosomes

Robertsonian translocation

fusion of acrocentric chromosomes => one long Chr, one short Chr.

Monosomy

2n-1 ex: turner syndrome

Trisomy

2n+1 ex: down syndrome

Tetrasomy 

2n+2 → rare, lethal

causes for aneuploidy

Nondisjunction, centromere deletion, translocation

polyploidy

addition of entire chromosome sets

→ common in plants, rare in animals

Autopolyploidy

from one species

Allopolyploidy

hybridization between species

Karyotyping

visualizing chromosomes in metaphase

G-Band

A-T rich regions

Q-Band

fluorescent

C-Band

centromeric heterochromatin

R-Band

G-C rich region

dark and light areas during karyotyping

Dark= gene poor regions

Light= gene rich regions

FISH and array CGH

detect microdeletions, duplications, and structural variants

gene dosage

imbalance affects development and metabolism

haploinsufficiency

one copy of a gene is insufficient for normal function

position effect

gene expression altered by chromosomal location

Pseudodominance

recessive allele expressed die to deletion of dominant allele

uniparental disomy

both chromosomes from one parent → imprinting disorders

Prokaryote

unicellular, no membrane-bound organelles

haploid genome

single chromosome with mutations directly expressed

Plasmid

1 circular DNA molecule, replicate independently

Episome

plasmids that can integrate into the bacterial chromosome

prototrophs

can synthesize all essential comounds

autotroph

require supplemented nutrients due to mutations

conjugation

DNA transfer via sex pilus, involves F plasmid

transformation

uptake free DNA from environment

transduction

DNA transfer via bacteriophages

has generalized and specialized

generalized transduction

any bacterial gene can transfer, only in the Lytic cycle

specialized transduction

speficic genes near prophage integrates in the Lysogenic cycle

Restriction - modification system

• restriction enzyme endonuclease protects from foreign DNA

• can modify host DNA to protect from self-cleavage

• can distinguish methylated DNA (self) and un-methylated DNA (non-self)

• Methyl-transferase activity: methylate host DNA to prevent self-cleavage

CRISPR-cas system

adaptive immune system in bacteria against viral DNA

CCRISPR-cas system; adaptation

bacteria infected by virus →

fragments of foreign virus captured →

captured fragments inserted into genome as space sequences → 

become short repeat space sequences

CRISPR-cas system; expression

DNA transcribed into CRISPR-RNA (long RNA molecule) →

CRISPR-RNA cleaved by cas proteins and processed into crRNA →

crRNA contains a spacer sequence (homologous to foreign DNA)

CRISPR-cas system; interference

foreign DNA enters bacteria again →

cas proteins cleave and degrade DNA

cas proteins

Cas9, Cas12, Cas13

used for genome editing and diagnosi

Cat1 protein

novel bacterial immune protein → depletes NAD+ to halt viral production

potential applications: biotechnology and cancer research 

retrovirus

RNA virus that integrates into host DNA via reverse transcriptase

→ can covert RNA into DNA

provirus

integrated viral genome in host DNA

F+

F factor is present as a separate circular plasmid

role in conjugation: donor

F-

F factor is absent

role in conjugation: recipient

Hfr

high frequency recombination bacterial strain. f factor is present and integrated into bacterial chromosome; behaves like F+

role in conjugation: high frequency donor

F’

F factor as separate circular plasmid, carrying some bacterial gene

role in conjugation: donor

F+ x F-

2x F+ cells

Hfr x F- 

no change, stays Hfr and F-

F’ x F-

2x F’ cells

Interrupted conjugation

time-based mapping of bacterial genes

Transformation

Contransformation rates indicate gene proximity

Transduction

contransduction used to map genes; close genes are more likely to be transferred together

Griffith

R and S strands of pneumoniae

R strain → nonvirulent (mouse survives)

S strain → virulent (mouse dies)

heat treated S strain → nonvirulent (mouse survives)

heat treated S strain + R strain → virulent (mouse dies)

DNA Double Helix Model

• 2 antiparallel strands (5’→3’ and 3’→5’)

• sugar-phosphate backbone

• nitrogenous bases: A=T (2 h-bonds), G=C (3-h-bonds)

• purines: Adenine and Guanine

• pyrimidines: Thymine and Cytosine

• Major and minor grooves: sites for protein binding

Chargaff’s rule

%A=%T

%G=%C

nucleotides composition, primary structure and secondary structure

deoxyribose sugar, phosphate group, and nitrogenous base

1° linked by phosphodiester bonds

2° help together by hydrogen bonds

B-DNA

most common, right-handed helix

10.5 bp per turn

very wide, deep major groove

shallow minor groove

A-DNA

more compact, right-handed

11 bp per turn

forms in dehydrated conditions

much tighter major groove

Z-DNA

left-handed helix

found in alternating purine and pyrimidine sequences

12 bp per turn

supercoiling

relaxed DNA: B-DNA

negative supercoiling → underwinding => assist separating strands

positive supercoiling → overwinding

adding and enzyme (topoisomerase) will tighten the coil → either negative/positive supercoiling

topoisomerase (I and II)

changes the coiling type → sense DNA and make tighter/longer

→directly influence supercoiling

type I: cuts one strand to relieve supercoiling

type II: cuts both strands, decatenates circular DNA

Hairpin loop

in single strand nucleotides when sequences od nucleotides on same strand are inverted complements (especially in RNA)

DNA Methylation

+CH3

→ regulates gene expression, chromatin structure, cellular identity

→ involved in imprinting, disease, environmental responses

Euchromatin

less condense

transcriptionally active

actively expressed

Heterochromatin

highly condensed

transcriptionally silent

suppressed DNA

constitutive or facultative

Constitutive Heterochromatin

always condensed

ex. centromeres

facultative heterochromatin

condensed only in some conditions

ex. inactive X chromosome

chromatin structure and highorder

Nucleosome: DNA wrapped around histone octamer, linker DNA: connect nucleosome, stabilized by H1 histone

High order: 20nm fiber → 300nm loops → 250 nm fiber → metaphase chromosome

DNase I sensitivity (chromatin remodeling)

indicated open chromatin and active transcription

Epigenetic changes (chromatin remodeling)

DNA methylation and histone modifications regulate accessibility

centromeres

site of spindle attachment during mitosis

→ chromosome fragments without centromeres are lost during cell division

Telomeres

repetitive sequences at chromosome ends (TTAGGG in humans)

prevent degradation and fusion

Sheltrin

binds to the telomeres and protects from being “repaired” as a double stranded break in the DNA

Telomerase

enzyme responsible for extending the telomeres

germ, cancer, and stem cells

C value paradox

a genome size in unequal to an organisms complexity

unique-sequence DNA

Encodes most proteins

Modernly repetitive DNA

includes rRNA and tRNA genes; tandem and interspersed repeats

highly repetitive DNA

short sequences; found in centromeres and telomeres

denaturation

exposing double stranded DNA to high heat → breaks H-bonds that hold the nucleotide strands together

melting temperature

the temperature of which ½ of the DNA is actually denatured

depends on the G-C value (3 H-bonds)

renaturation

single stranded DNA slowly cools→ ss collide and hydrogen bands will form → produces double-stranded DNA

hybridization

reannealing of complementary single stranded DNA from different species

Theta replication

• circular DNA (E. coli)

• single origin of replication; bidirectional replication

• produces 2 DNA molecules

rolling circle replication

• viruses and plasmids

• initiated by a nick in one strand; unidirectional

• produces 1 circular DNA and 1 linear DNA

• termination: one strand is cleaved

Linear Eukaryotic replication

multiple origins of replication

bidirectional replication; ends require telomerase

replication runs 5’ → 3’

leading strand: continuous replication

lagging strand: discontinuous replication

DNA ligase

seals the nicks of the okazaki fragments