molecular exam 2

genome

genetic makeup of the organism

conservative passing

passes on genes & intergenic regions and chromosome packaging

chromosome

genetic info packaged into at least one very long DNA molecule

eukaryotes

linear chromosome

bacteria and archaea

circular chromosome

less complex organisms tend to have ____ ________ arranged genes

more densely

transposons

jumping genes

retrotransposons

retrovirus (DNA to RNA to DNA)

LINE

interspersed nuclear elements; highly repetitive sequences

make up their own proteins to move

SINE

rely on proteins to copy and paste themselves in a new spot

common disease caused by transposons

hemophilia

____ human births have transposition different than parents

1/200

nucleosomes

octamers of H2A/H2B and H3/H4

what amino acids are found in nucleosomes

lysine and arginine

NH₃ or NH₂

why is lysine and arginine good for packaging

the positive charge on the nitrogens attract the negatively charged DNA

length of DNA found in nucleosome

146 bp of DNA

length of DNA strand in between nucleosomes

50 bp

each core histone has an ___ __ _______ ____ that can be modified; tails interact with other nucleosomes

N=terminal tail

common breaks found on what histones

H2A.x

H2A.x

modified H2A produced in ds breaks and is a marker for cancer cells or damaged cells

two major modifications done to histones

acetylation and methylation

nucleosome width

10 nm fiber wide

solenoid

30 nm

what twists solenoids into an S-shape

H1

width of heterochromatin

700 nm

heterochromatin

tightly packed chromatin

euchromatin

loosely packed chromatin

heterochromatin transcription

low

euchromatin transcription

high

regions with rich heterochromatin

telomeres, centromeres, highly repetitive DNA sequences

chromatin structure affects…

transcription, replication, recombination, and chromosome transmission

recombination

breakign DNA and joining it in different molecules

heterochromatic regions experience _____ recombination which protects the genome

less

covalent modification done to histones

acetylation, methylation, phosphorylation, and ubiquitination

what do modification do for histones

recruit specific proteins to the chromatin; influences transcription, attracting and repelling proteins

example of a modification done to histones

adds phosphate to tyrosine, serine, and threonine

histone acetyltransferases (HATs)

add acetyl to lysine side chain and loses positive charge and falls apart

histone deacetylase (HDACs)

remove acetyl groups

histone methyltransferases (HMTs)

add methyl group to lysine and arginine side chains

histone demethylases

removes methyl groups

most chromatin has ________ _______

acetylated histones

which histone is mostly acetylated

H3/H4

euchromatin has more ___________ than heterochromatin

acetylation

acetylation is associated with…

active transcription

acetylation removes…

removes the positive charge from lysine side chain

affects negatively charged DNA

histone acetylation generates binding sites for…

bromodomains

bromodomains

binds to certain acetyl-lysines and binds acetylated proteins/histones and brings other mechanisms to it

recruits nucleosome remodeling complexes to move other nucleosomes

methylation is associated to _________ and _________ ____________, depending on the _______ that is methylated

repressing, activating transcription, residue

________ and _________ are significant for regulation

position and modification

methylation of lysine 9

H3 tail → silence gene expression

methylation of lysine 4

H3 tail → upregulates gene expression

chromodomains

binds to specific methylated lysines and are associated with transcription silencing

what do chromodomains prevent

polymerase from docking

phosphates are added by ________ and removed by ____________

kinases, phosphatases

H3 serine 10 phosphorylation

cell growth transcription

H3 serine 10 and 28 phosphorylation

chromosome condensation in mitosis

phosphorylation at serine 10

promotes acetylation of lysine 14

recruits a HAT

acetylation of lysine 14

inhibits methylation of lysine 9

ubiquitination

76 amino acid protein

adds small groups to H2A and H2B

ubiquitin is added by a chain of _________ _____________ and ________ by a deubiquitinating enzyme

enzymatic reactions, removed

Sumo

small, ubiquitin-like modifier

similar modifying protein similar to ubiquitin

Sumo and ubiquitin roles

transcription regulation and DNA repair

added to lysine to upregulate ubiquitination

how do ATP dependent nucleosome remodeling complexes increase access

sliding the histone octamer along the DNA

removing the histone octamer and transferring it elsewhere

introducing loops into the DNA wrapped round a histone core

SWI/SNF

disrupts positioning

ACF

positions during x-some assembly (ISWI family)

HSA

helicase → unwinds DNA

bromo

bromodomain → acetylated

DExx and HELICc

parts of ATPase domain → lysine

binds acetylated histones

breaks ATP for energy

CpG islands

in bacteria and eukaryotes

cytosine residues do what to DNA

methylation

deamination of methyl cytosine

to thymine → mispairing and DNA polymerase recognizes the change

DNA methylation in bacteria

new strands are not methylated but old strands are

unequal methylated DNA

why can bacteria detect foreign DNA

invading genomes are not methylated

DNA methylation patterns

fixes by restriction enzymes

methylation in eukaryotes is used to silence…

transcription → epigenetic silencing

where is eukaryotic methylation is usually found where?

CpG or CpxpG sites

CpG or CpxpG sites

highly methylated and inhibits the polymerase

up to what percentage of human CpGs are methylated

60

methylated states can be…

inherited

methylated states might…

recruit or inhibit

what DNA binding complexes bind to methylated DNA

histone modification enzymes and nucleosome remodeling complexes

DNA methyl-binding domain bring a deacetyltransferases that…

take acetyl groups off histones

DNA methyl-binding domains bring histone methyltransferase domain and…

methylate histones

chromodomains proteins bring DNA methyl-transferases

to methylate histones

nucleosome remodeling enzyme moves…

the nucleosome to somewhere else and turn heterochromatin to euchromatin

x-chromosome inactivation

one chromosome in each cell is inactivated in females so they have the amount fo gene product as in males → heavily modified by heterochromatin

imprinting

control expression of passed down genes like methylation

boundaries between euchromatin and heterochromatin

influence what gene gets expressed

these boundaries prevent

heterochromatin spreading

insulators

keep heterochromatin and euchromatin separate → anchored loops help

chromosome inversion in flies

doesn’t separate heterchromatin from euchromatin

origin of replication

required to direct replication in bacteria and eukaryotes

bacteria origin of replication

one per chromosome

determine distribution of replicated chromosomes to the daughter cells

bacteria termination

termination sequence specifies replication termination

replication is…

bidirectional

eukaryotes termination

telomeres

telomeres

consists of simple tandum repeats (TTAGGG) and protects ends from being lost

total length of telomeres

50-30,000 bp; depending on the species

why do telomeres shorten

primase cuts off ends because of polymerase doesn’t cut it off

senescence

not metabolically active