Exam 1 Study Guide Questions Pt. 2

what is the favorable postiion for DNA bases within the same strand? unfavorable

stacked - van der waals forces, u - bases swinign out on th toher side of backbone

what can put DNA bases on same strand in unfavorable positions

DNA binding proteins

what are chargoff ratios

A=T, C=G, Purines (GA) = Pyrimidines (CT)

Does base composition of DNA vary depending on age, nutritional state, environment, or tissue type

only changes based of different species

how is it possible for a kidney cell to have the same DNA as a lung cell but have different funcitons

different genes within the DNA are expressed in different organs, gene expression does change with age time cell type environment

what is a major and minor groove in DNA

big vs. small

what happens in the major groove of DNA

allow proteins to bind with DNA

what is DNA anealing

2 DNA strands binding together

how do we differentiate between the replication and transcription polymerases

transcription polymerases = DNA dependent RNA pol, Replication polymerase= DNA dependent DNA pol

what is a hairpin and cruciform structure

bobby pin and cross structure

how does a hairpin and cruciform structure form

ssDNA and dsDNA inverted repeats

What is a palindrome

something the same forwards and backwards (same 5’ to 3’)

how are palindromes used by restriciton endo nulceases

its how it recognizes where to cut

why dont palindromes or mirror repeasts form hairpins or cruciforms

because there needs to be a 4 base space in between (P) and bases are the same so they wont bind (MR)

what is DNA recombination

during meiosis, specific sections of DNA are swapped between the male and the female chromosomes

mitosis

generates identical diploid cells for growth or replacement

meiosis

generates haploid cells contain half our genome, used for sexual reproduction

wha happens in G0

cell perfom specialized funciton without dividing

what happens in G1

cell is preparing for DNA replication, growing and making required proteins (cohesin, H2A H2B H3 H4)

what happens in S phase

DNA replication occurs

what happens in G2

the cell is preparing for mitosis, makes H1, seperase, condesin

what happens in interphase

G1 S and G2

what are homologous chromosomes

two chromosomes with the same genes but different expresions (mom vs. dad)

progressive levels of DNA/ chromosome condensation

DNA> DNA wrapped around histone > nucleosomes coiled into chromatin fiber > further condensation to chromatid > ]chromosome

most DNA in nucleus exists in what form

chromatin

sister chromatids

2 identical copies of genes (from same person)

what are the stages of mitosis

PMAT

prophase

DNA packed into chromosomes, nuclear membrane dissolves, spindle fibers emerge from centromeres

Metapahse

chromosomes line in middle, spindle fibers attach

anaphase

spindle fibers putt apart sister chromatids

telophase

nucleus is reformed, DNA returns to chromatin, cytokinesis

what is a centromere

region of a chromosome that joins two sister chromatids

what is a telomere

end of each chromosome with repeating sequence, protect genetic material

what is telomerase

telomerase specifically copies telomeres, don’t get tripped up by copies

how do bacteria package their genomes

circular dsDNA, DNA is looped in and out of core protein, plasmids are separate from genome- small rings of DNA free floating in bacteria

what is epigenetics

regulation of gene expression, histones largely control this

what are histones

8 protines - H2A H2B H3 H4

do bacteria have histones

no have nucleioids

how might endonulcease react with naked DNA vs. with chromatin

can cut naked DNA anywhere (shows as a smear), can only cut DNA where proteins aren’t (shows up as bands)

structure of nucleosome

histone with dna wrapped around

what is linker DNA

DNA in between nucleosomes

what makes H1 differen from other histone protiens

helps to condense, linker histone, turns genes on and off

why do histone protiens have a high proportion of lysine and arginine in thier N terminal tails

L and A are positive amino acids that can be modified to direct epigenetic changes and gene expression. and the positive interacts with the DNA on the next nucleosome

how do histones affect gene expression

high amount of H1 turn it off, low turns on

how do histone tails help nucleosomes to move

they can be modified (acetylation, methylation, ubiquitination) chromatin remodelers Replace, eject or reposition histones in order to open more linker DNA

what do chromodomains do

represses genes

what do bromodomaind do

activate gens

what is the histone fold and what does it do

interacts with minor groove of DNA

why is modification important with histone tailes

its key for gene expression though activation or repression

what types of modifications are there

acetylation, methylation, ubiquitination, phosphorylation

what is the purpose of remodiling

to make DNA avalible

what is the diffrence between remodeling and modificaiotn

makes DNA available vs. actually changing it

what is the difference between expression, supression , and repression

expression - activation, suppression - general reduction, repression - complete shut off