biochem lecture 12 and 13

nucleotide

-building block of nucleic acid

-parts; phosphate, (deoxy)ribose sugar, heterocyclic nitrogenous base

purine (nitrogenous base)

-adenine and guanine

-larger and double ringed

pyrimidine (nitrogenous base)

-thymine(DNA only), cytosine, and uracil(RNA only)

-smaller and single ringed

base structural features

-heterocyclic amine

-nitrogen containing

-H bond donors and acceptors

-Aromatic planar

condensation

molecules combine by removing water

hydrolysis

molecules split by adding water

nucleoside

-sugar+base

-condensation

-similar to acetal formation but with secondary amine

nucleotide

-phosphate+base

-condensation

-phosphate ester formation

-phosphate usually on carbon 5

multiple phosphates

-AMP→monophosphate

-ADP→diphosphate

-ATP→triphosphate

dinucleotide formation (condensation reaction)

-phosphate ester formation

-O on carbon 3 connects with phosphate on carbon 5

-phospodiester

polynucleotides

-nucleic acids

-linear chain of multiple nucleotides

-connected by phosphodiester bonds

-5 prime phosphate end to 3 prime alcohol end

DNA

-A,T, C, G

-deoxyribose

-double stranded

RNA

-A, U, C, G

-ribose

-single stranded

nucleic acid/nucleotide function

-store and decode genetic information

-cofactor, carrier, and messenger

-energy transfer

-structural/catalytic roles

3D structure of DNA

-double helix

-antiparallel

-negative phosphate backbone towards outside

-bases towards center

-bases perpendicular to backbone

-A & T= 2 bonds

-C & G= 3 bonds

structural stability

-dispersion forces between stacked planar bases stabilize helical structure

-stronger for C & G versus A & T

-dispersion forces btwn stacked aromatic electron clouds of bases provide stabilizing force

-bases form H-bonds which determines specificity

DNA and protein interactions

salt bridge form between basic amino acids and negatively charged backbone phosphates

chromatin

orderly tangle of DNA present in non-dividing cells→ chromatin is loose until supercoiled/twisted into chromatin

centromere and telomere

centromere: middle of chromosome

telomere: end of chromosome

gene

segment of DNA that directs synthesis of a single polypeptide

nucleosomes

-beads on a string

-DNA wrapped around histones

-coiled into chromatin

histones

-proteins in nucleosomes that DNA wraps around

-a lot of arg and lys

how do negatively charged phosphates pack together in DNA

the histones in nucleosomes form salt bridges with the phosphate

chargaff’s rules

complementarity

-A always bonds w/ T

-C always bonds w/G

same amounts of A and T

same amounts of C and G

reverse complement

central dogma

DNA mutation and mutagen

mutation→ change in DNA sequence

mutagen→ substance causing a mutation

mutations can change shape or H bonding groups of the base

semiconservative replication

-2 strands split and each one makes a new copy

-each ds product had one new and one old parent strand

what provides energy for nucleic acid synthesis

phosphoanhydride hydrolysis

it is spontaneous and exergonic

DNA polymerase reaction

DNA polymerase is the enzyme that catalyzes the synthesis of new DNA (replication)

-2 ATP equivalents/phosphoanhydrides are hydrolyzed to drive the reaction

primase

makes primer made of RNA so DNA polymerase knows where to start when making the new strand

helices

unwinds DNA double helix by hydrolyzing ATP

topoisomerase

removes strain on DNA, prevents supercoil

single stranded binding protein

coats ss region of DNA so that double helix does not re form

keeps strands separated

origin of replication

site where replication begins, mostly TATA (box) in the beginning

DNA initiation, elongation, termination

initiation→ RNA polymerase binds to promoter

elongation→ RNA polymerase moves along template strand

termination→ RNA polymerase reaches termination sequence

leading vs lagging strand

leading→ continuous from 5 prime to 3 prime

lagging→ Okazaki fragments, discontinuously in segments

DNA clamp

protects processivity→ polymerase can stay on template stand and add 1000s of nucleotides before dissociating

can form consecutive reactions on substate without releasing it

proofreading

DNA polymerase checks the last base added and removes it with exonuclease if wrong

endonuclease

pushes out the RNA primer when DNA polymerase reaches it

DNA ligase

joins Okazaki fragments together

telomeres

-3 prime end of linear ds cannot be copied so telomeres are added by telomerase to extend sequence and give DNA polymerase a longer template

-repetitive DNA sequences at the ends of linear chromosomes

extended by telomerase

-room for primate to make primer

dideoxynucleotides(ddNTPs)

-missing OH groups at both 2 and 3 prime positions

-DNA polymerase uses 5 prime phosphates to addd ddNTP to growing strand

mRNA

RNA product of transcription, carries information for translation/protein building

tRNA

carries amino acids to ribosome. Has anticodons to pair with codons on mRNA

rRNA

RNA that makes up the ribosome, catalyst for protein synthesis

RNA transcription complementarity

mRNA sequence is same as coding(sense) strand (but U instead of T)

mRNA is reverse complement of noncoding(antisense) strand

template strand

noncoding, antisense strand

RNA polymerase

enzyme that catalyzes the synthesis of RNA from DNA template

needs 2 phosphoanhydrides(2 ATP equivalents) hydrolyzed to drive the reaction

transcription initiation

transcription factors bind promoter sites and recruit helices to unwind DNA

acetyl groups added to his/lys to remove positive charge and no more salt bridge

what triggers transcription elongation

-phosphorylation of RNA polymerase disrupts interactions btwn RNA polymerase and transcription factors bound to promoter, which allows elongation to begin

how are RNA and DNA polymerase similar

-adds nucleotides to 3 prime end of strand with hydrolysis of 2 ATP equivalents

-proofreads

-processive

transcription termination

-signal leads to disruption of RNA polymerase

either…

RNA dependent→ RNA product forms short helix that disrupts RNA polymerase

protein dependent→protein Rho binds a sequence in RNA product and disrupts RNA polymerase

RNA splicing

mRNA not mature for translation until spliced

exons are kept, introns are removed