Genetics: DNA chemistry and Replication

what carbon do nitrogenous bases attach on the deoxyribose

C1

what carbon does the OH attach to on deoxyribose

C3

what carbon does PO4 attach to on deoxyribose

C5

sugar + base =

nucleoside

sugar + base + phosphate group=

nucleotide

how are monomers (nucleotides) linked to form a polymer (DNA)

they are covalently bonded at the 5’ PO4 and the 3’ OH

what is the bond between nucleotides called

phosphodiester bond

what direction is DNA synthesized

5’ → 3’

what type of bond holds two strands of DNA together

hydrogen bonds

what is bonding together between 2 strands of DNA

nitrogenous base pairs

DNA is polymerized into

complementary antiparallel strands

where are phosphodiester bonds formed

between 5’ PO4 and 3’ OH groups of nucleotides

shargoffs rules

A=T, C=G

how much space between bases on helical structure

3.4 angstrom

how long is one helical twist

34 angtrom

how many nitrogenous bases in 1 helical twist

10

how many major and minor grooves per helical turn

1 of each

what causes the helical twist

base stacking

define base stacking

stacked bases make parallel planes causing the sugar phosphate backbone to twist which is energetically favorable

4 reasons why DNA organization and compaction is important

fits large amounts of DNA into a tiny space (nucleus)

stabilizes and protects DNA molecules

allows for condensation during cell division

helps regulate gene transcription

how many chromosome(s) does most bacteria have

1

what is most bacteria’s chromosome shape

circular

are bacteria chromosomes diploid or haploid

haploid

define plasmids

extrachromosomal circular DNA in many bacteria

what is the range of bases in bacteria

1-5 million b

where is DNA stored in bacteria

nucleoid

how is DNA in bacteria organized

into loops

what are the proteins that create/organize DNA in bacteria

small nucleoid associated proteins and SMCs

what are the two small nucleoid associated proteins

HU and H-NS

the first loop of bacteria DNA is made by small nucleoid associated proteins, then what occurs

SMC proteins make smaller loops within the larger loops

what happens after the bacteria after all looping is completed

supercoiling of the circular chromosomes

what are the two types of supercoiling

negative supercoiling

positive supercoiling

what is negative supercoiling

twists DNA in the opposite direction of the helix

what is positive supercoiling

twists DNA in direction of helix

what type of supercoiling is most common

negative supercoiling

what makes up 25% of chromosome weight

histones

what are the 5 types of histones

H1, H2A, H2B, H3, H4

what histone proteins are in the histone octamers

H2A, H2B, H3, H4

what is DNA wrapped around a histone called

nucleosome

what does H1 do

helps fold nucleosomes into a more condensed structure, with H1 proteins in the center creating a circle surrounded by nucleosomes

what is the further condensation of chromosomes around the H1 proteins called

solenoid

what happens to the solenoid structure during the m phase of mitosis

further compacted by non-histone proteins to make loops like bacteria

chromosomes are divided into segments by the

centromere

the short are of a chromosome is the

p arm

the long arm of a chromosome is the

q arm

what determines the lengths of the arms

centromere location

metacentric

centromere is placed in the center of the chromosome with equal length p and q arms

submetacentric

centromere is placement on chromosome results in longer (q) arms and shorter (p) arms

acrocentric

centromere is places that there are no p arms

telocentric

centromere is placed that p arms are like ‘satellites’ not attached to centromere

graphic display of all chromosomes

karyotype

DNA replication is conservative, semiconservative, or dispersive

semiconservative

DNA is opened up at the

origin of replication

define the origin of replication in eukaryotes

a region of rich A-T base pairs that have weaker hydrogen bonds

hydrogen bond number between A-T

2

hydrogen bond number between G-C

3

what opens up DNA for replication

helicase

how does helicase open DNA up

helicase burns ATP energy allowing it to break the hydrogen bonds between base pairs

what does primase do

lays down a short complementary RNA primer on DNA template

how does DNA polymerase attach to the RNA primer complementary template

it attaches to the free 3’OH with a 5’ PO4

what does PCNA (proliferating cell nuclear antigen) do

binds to DNA polymerase to prevent it from falling of the DNA strand

what does PCNA displace

primase

what do single strand binding proteins (SSBPs) do

prevents hydrogen bonding between unzipped bases before the DNA polymerase adds the nucleotide base pair

what does topoisomerase do

prevents the DNA from getting tangled, relieves torsional stress by nicking the DNA

replication is ____ directional

bidirectional

two types of replicated DNA strands

leading, lagging

lagging strands are also known as

okazaki fragments

how do lagging strands occur/work

DNA opens up enough that an RNA primer can make complementary DNA that DNA polymerase then attaches too, happens repetitively in sections as DNA opens up

what removes primers on okazaki fragments

RNase H

what happens once the primer is removed by RNase H on okazaki fragments

DNA polymerase codes the complementary strand in those gaps

what fills the gap between DNA is and RNA primer was

DNA ligase

what type of bond does DNA ligase use

phosphodiester bond

what is the origin of replication in prokaryotic DNA

13 mer sequence (3 copies) —- origin of replication —- 9 mer sequences (4 copies)

once circular chromosomal DNA is copied in prokaryotes, what separates the two circles

topoisomerase

what proofreads the DNA template

DNA polymerase

what does incorrect base pairing trigger

exonuclease active site

how does DNA pol respond to a triggered exonuclease active site

it backs up in the 3’→5’ direction knocking off the incorrect base pair, then proceeds forward placing the correct base pair

why can we not synthesize in the 3’→5’ direction

when proofreading, if an incorrect base is knocked off, then there wouldn’t be enough energy to add correct base

in 3’→5’ direction, the phosphates that break off to form atp are on the strand, not the nucleotide so if used and then tried to be corrected energy gone already

what is replicative senescence

Lack of telomerase activity in somatic cells results in a limited life

span for the cells

what prevents shortening of chromosomes due to lagging strand being shorter

telomeres

what is a telomere

multiple copies of repeat sequence to end of

chromosome

human telomere sequence

GGGGTTA

what does telomere allow the primer to do

attach a nonsense region so when chromosomes get shorter nothing important is lost