genetic info location eu vs pro

eu: inside nucleus

pro: inside nucleoid (pro have not membrane-enclosed organelles)

Purines

AG

double rings

Pyrimidines

CYU

pYrimidines: cYtosine, thYmine (and uracil)

single rings

nucleoside vs nucleotide

nucleoside=base+pentose (ribose or deoxyribose)

nucleotide=phosphorylated nucleoside=base+pentose+phosphate

Base pairing

A double bonds T

G triple bonds C

therfore, GC-rich sequences have higher melting points

charge of DNA/ stabilization

DNA is negatively charged (phosphate groups)-->electrostatic intrastrand repulsion

stabilized by cations (Mg²⁺)

DNA ligase

forms phosphodiester bonds between free 5' and 3' ends in open circle DNA

location and advantage of circular DNA

loc: bacteria, plasmids, mitochondria

protection from endonucleases

exonuclease vs endonuclease

exo: cleaves ends

endo: cleaves within strand (can be non-specific or cleave specific sequences--restriction endonucleases)

3 types of DNA

B-DNA: normal kind found in cells (R-handed)

A-DNA: form during transcription (DNA-RNA hybrid)

Z-DNA: form of DNA seq controlling gene transcription (L-handed)

DNA supercoils

circular DNA supercoils so it can be packed within cell

topoisomerase

-general function

-3 types

general fn: regulate superhelices, relieving supercoils in PROKARYOTES

type I: break 1 DNA strand, then ligate

type II: break both DNA strands, then reseal (REQ ATP)

gyrase: unwind supercoils w/o breaking DNA

Nalidixic acid

inhibits gyrase--antibiotic

novobiocin

antibiotic

blocks ATP binding of topoisomerase II, effectively inactivating it

DNA bending (why)

bends at site of proteins

photochemical damage also causes bending-->signal for DNA repair

cruciforms

regions of DNA in which interchain hydrogen bonds are disrupted and intrachain bonds form

function in control of replication/transcription

triplex (triple-stranded DNA with Hoogsteen base pairing)

string of purine bases

transcription control, initiation and term of replication, telomeres (stability)

third strand binds to major groove of B-DNA

triplex and HbF

triple helix shuts off HbF gene after birth, mutation assoc w hereditary persistance of HbF

quadruplex DNA

immunoglobulin genes that undergo recombination-->antibody diversity

also in telomeres

histones vs HU proteins

EU: histones

PRO: HU proteins

histone structure

eight proteins (2 each of H2A, H2B, H3, H4) +H1 which stabilizes DNA by wrapping around octamer

histones interact with acidic phosphates of minor groove

nucleosome vs chromatosome

nucleosome: histone octamer

chromatosome: histone octamer + H1

nucleofilament

linear array of nucleo/chromatosomes

linker DNA

DNA between nucleosomes

chromatin

2 types

DNA plus assoc proteins

euchromatin:loosely coied, transcriptionally active

heterochromatin: tightly packed, inactive

HU proteins

PRO equivalent of histones

organize DNA into nucleoids

inverted repeat

DNA is self-complementary within inverted region-->restriction endonuclease target

TCCAATTGGA

mirror repeat

GGGACCAGGG

direct repeat

CGGCGGCGG

PRO vs EU: Genes

-density

-overlap

-introns/exons

PRO: gene-dense, overlap, introns are rare

EU: less-dense in structural genes, no overlap (~40kb spacing), introns/exons