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march notes

by: Leila HD

march notes BIOCHM 307

Leila HD
GPA 3.7

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notes to first quiz after exam 1
Intro to biochemistry
Dr. Orla Hart
Class Notes
biology chemistry biochem
25 ?




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This 3 page Class Notes was uploaded by Leila HD on Thursday March 10, 2016. The Class Notes belongs to BIOCHM 307 at Purdue University taught by Dr. Orla Hart in Spring 2016. Since its upload, it has received 17 views. For similar materials see Intro to biochemistry in Biochemistry at Purdue University.

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Date Created: 03/10/16
3/4 3/7 3/9  Transcription is the process of making RNA from a DNA template  DNA replication is in the nucleus  New nucleic acid strands are always made in 5’ to 3’ direction  RNA polymerase: enzyme that makes RNA from DNA template  Helicases are involved in DNA replication  Promoters are involved in transcription  RNaseH is involved in DNA replication  Translation involves the stop codon  Splicing is involved in transcription  DNA is replicated semiconservatively o 2 parent strands go to 4 first generations  DNA double helix twist around itself supercoiling slightly underwound so has negative charge  Topoisomerases alter DNA by breaking the strand, untwisting, and breaking  Mitosis= cell cycle o G0 G1: growth and DNA synthesis prep S: DNA replication G2: mitosis prep and growth M phase: pro, met, ana, telo o Process is longer in euks than proks  Replication fork= site where DNA strands separate and new strands synthesize o Parental strands break open into 2 strands o Replication occurs in factories: foci in nucleus marking DNA presence  Proteins in DNA rep: o Helicase: converts dsDNA to ssDNA by unwinding o single stranded binding protein: single stranded DNA is bound to this o primase: help make RNA primers o DNA polymerase: antiparallel strands of DNA replicate simultaneously/ has proofreading abilities o RNase: ribonuclease: enzyme that catalyzes breakdown of RNA into smaller components o DNA ligase: seals Okazaki fragments by joining the 2 fragments  Helicase forms hexameric ring around DNA single strand/ pushes double stranded DNA apart  H bonds spontaneously bond to hold single stranded binding proteins together  DNA polymerase requires a primer/ can only extend a preexisting chain/ cannot initiate polynucleotide synthesis o RNA polymerase can initiate polynucleotide synthesis  Oligonucleotide: short stretch of nucleotide strand that DNA polymerase can look at to start  RNA primers are 10-60 nucleotides long  DNA synthesis is 5’ to 3’ direction  Synthesis can happen in 2 strands at once if DNA polymerases bind to each, the 2 polymerases work side by side, and if 1 strand loops back out  DNA rep: 2 strands in antiparallel directions w DNA polymerase on it new primer added leading strand is one but lagging strand is broken up into Okazaki fragments  Replication: o Helicase catalyzes 2 DNA strands to separate o DNA gyrase helps unwinding and rep fork o Exposed DNA strand protected w SSB proteins and complementary strand available o Primase produces RNA primer o DNA polymerase III synthesizes DNA starting w 3’ hydroxyl group of primer o Leading strand cont in direction of fork and laggin stops at each fragment o Primers removed 5’ to 3’ and gaps filled by DNA polymerase I o DNA ligase catalyzes formation of phosphodiester bond o Ends when 2 forks meet  DNA rep is by stationary protein complexes  DNA polymerase is accurate by ability to sense correctly paired nucleotides and mispairs  End prob of rep= daughter strands lack 3’end copy leading each round of rep to shorten the chromosome o Telomerase fix this by repeatedly adding nucleotides to 3’ end telomeres  DNA damage is unavoidable/ oxo is very damaging  Mutation: alteration in cell’s DNA o From nonenzymatic process, environment, rep errors o SNP evolved before mutation  Programmed cell death= apoptosis o Reactive O2 species cause DNA damage i.e. O2-, OH, H2O2  Free radicals cause aging bc damages DNA’s turn over effectiveness (ex crows ft)  Point mutation: substitute but still has same number of nucleotides o Transition: changes purine to diff purine (vice versa for pyrimadines) o Transvers: changes purine to pyrimidine (and vice versa)  Insertion/deletion: only not detrimental if does 3 nucleotides  Abasic mutation: removes DNA base and reading frame which is the order you read the 3 nucleotides o No chance for working protein  Deamination rxns alter base identity i.e. amino group chopped off  DNA backbone w thymine residues link across w self in thymine dimer form and cause recognition probs bc DNA polymerase may only see one and skip over  Methyltransferase can remove methyl grops from DNA base and can be part of DNA silencing  Mismatch repair protein= MutS= corrects nucleoside mispairings in E coli  Base excision repair corrects frequent DNA lesions o Dna glycosylase takes away damaged base leaving an open abasic site endonuclease cuts the strand open in the middle DNA polymerase and ligase binds strand back o Endonuclease breaks nucleic acids in the middle while exonuclease would on the ends  Ligase seals backbone by making phosphodiester bonds  Chromatin in euk nucleus: heterochromatin is red and euchromatin is yellow  Fundamental unit of DNA packing is the nucleosome: which is a pile of proteins that have DNA wrapped around twice o DNA wraps around histone to form nucleosome  Histones are covalently modified w/in nucleosome (4 inside) o They modify DNA interactions so acetylation of histones causes dissociation of DNA, increasing gene binding bc now histones are gone so other proteins have access  DNA undergoes covalent modification  Clusters of CpG sequences are CpG islands  Microbes have hella methylated DNA


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