Meselson and Stahl: DNA repllication is semiconservative, CsCl centrifuge Benzer: tRNA specificity from anticodon, not aa Ochoa:

discovered polynucleotide phosphorylase (string together nucleotides) could make own rRNA (comp only Khorana: exact relationsihp of 64 codons to 20 aa using ratios of bases Nirenberg and Leder: ribosome binding assay; specific nucleotide sequence determined, tRNA w/ no protein Rockefeller, Strasbourg, Sharp: HeLa cells to find proteins that bind to TATA Roberts and Sharp: genes divided into intro/exon Garrod: inborn diseases of metabolism Sharp, Chambon, Roeder: found the TF needed w/ HeLa

Carbonyl + amino = peptide bond Neutral, nonpolar: Tryptophan (Trp)(W), Phenylalanine (Phe)(F), Glycine (Gly)(G), Alanine (Ala)(A), Valine (Val)(V), Isoleucine (Ile)(I), Leucine (Leu)(L), Methionine (Met)(M), Proline (Pro)(P) Acidic (negative): Aspartic acid (Asp)(D), Glutamic Acid (Glu)(E) Basic (positive): Lysine (Lys)(K), Arginine (Arg)(R), Histidine (His)(H) Neutral, polar (hydrophobic): Tyrosine (Tyr)(Y), Serine (Ser)(S), Threonine (Thr)(T), Asparagine (Asn)(N), Glutamine (Gln)(Q), Cysteine (Cys)(C) Tyrosine, Serine and Threosine can be phosphorylated b/c they have an OH at the end -> regulate protein function. Cysteine- disulfide bond b/w Cys Minimal medium: salts (nitrogen), carbon, biotin Ways to Sequence DNA: Sanger Method (fluorescent ddNTP) CHIP= identifies sites in genome where proteins bind; formaldehyde, DNAse, immuno precipitation, antibody RNA sequencing= quantifies the abundance of mRNAs in a sample (is it expressed?) bead with poly T tail, reverse transcriptase, cDNA genome size, but not necessarily gene number, increases with organisms of increasing complexity IIR + IIIS Purine: AG, 9 member ring Pyrimidine: CUT, 6 member ring Protein synthesis: tRNA genes-> precursor tRNA (extra seq @ ends removed, 5'CCA3' added) -> tRNA -> aminoacyl-tRNA Griffith: there was a transforming principle IIR -> IIIS Avery, McCarty and MacLeod: DNA is the genetic material (DNAse -> rough) Hershey and Chase: DNA is the genetic material (T2 blender) Chargoff: A=T, C=G Franklin and Wilkins: DNA is a helix (xray diffraction) Watson and Crick: double helix structure of DNA

Replication 1.) Helicase unwinds 2.) Primase initiates 3.) DNA POL III replicates 4.) DNA POL I replaces RNA in primers w/ DNA 5.) Ligase connects Okazaki fragments Telomerase (RNA + protein) binds base pairs w/ telomeres to create an overhang; compensates for the shortening 3' to 5' exonuclease activity ("backspace key") Transcription: does NOT need a primer. Instead, w/ sigma factor, RNA polymerase finds promotoer, helicase, RNA polymerase synthesizes, hairpin, terminate RNA + NTP -> RNA + PP makes mRNA, tRNA, rRNA and snRNA In bacteria, promoter is upstream of 5' RNA coding seq Mutations: Intercalating agents: on template strand = insertion; on new strand = deletion RNA POL 1: rRNA RNA POL 2: mRNA, snRNA RNA POL 3: tRNA, snRNA, 5s rRNA Bacterial promoter sequences: TATAAT (-10, Pribnow Box), TTGACA (-35) RNA -RNA structure stronger than DNA- RNA Eukaryotes: Core Promoter: POLII can bind TATA Box (-30 bp) Initiatior: YYCAYYYY (Y=pyrimidine), helps position initiation site Promoter-proximal elements enhance transcription from core promoter. w/o, = only base level transcription enhancers: regioners where activators bind Transcription: TFIID binds to TATA Box

(TBP (TATA binding proteins) recognizes TATA) (TAF (TBP assoc factors) bind to TBP) TFIIA then TFIIB provide link b/w RNA POL and TAF TFIIF brings in RNA POL II (can get sm transc in tubes) TFIIE recruits TFIIH (only protein with enzymatic activity) Kinase phosphorolates RNA POL-> go signal -> helicase makes open complex --> Ready for transcription now!! E&H complete transcription initiation complex ABD not nec for elongation, stay w/ core promo Chromatin remodeling ATP dep chromatin remodeling: large # of protein in eukaryotes; use ATP as en to move histones; bind to DNA (minor groove) move histone away Histone Acetylation: hist are pos charged; adds acetyl groups to end points to disrupt interaction b/w histone and DNA (b/c DNA has phos backbone so neg charged) opens up chromatin; HATs (histone transferase) Histone deacetylation: reverses previous step; removes acetyl groups; HDAC: histone deacetylase modification of euk mRNA: modified at both ends; 5'-5'7 methyl guanine (5' to 5' linkage to protect, provide binding sites for proteins); poly A tail to 3'(polyadenylatoin): CPSF binds to polyadenylatoin signal and lots of protein made; CstF (CF stimulating factor binds to the mRNA; CF1 and CFII do the cleavage; PAP (poly A polymerase adds the A's), PAB II binds and stabilizes the newly added protein; buffer against exonucleases RNA POL III can have promoters inside the gene Splicing: mediated by snRNPs (snRNA+splicing proteins); recognize seq at 5' and 3' splice junctions, assemble into spliceosomses, process pre-mRNAs into mRNAs Intron: GU @5' end splice junction (U1 binds) AG @ 3' end splice junction A in the middle (branch point adenine) U2 binds cleavage at 5' junction; U4 and U6 bind cleavage of mRNA @ 5' force loop to form U5 makes it fold over 5G' to 2'A; 2' to 5' phosphodiester bond; 5' - 3' nucleotides Alternative splicing can skip exons; DSCAM: only 1 exon chosen from alternative groups, many more genes can be expressed need IF2 for 50S to bind 30S+50S=70S; 40S+60S=80S (rRNA + protein) MUTATIONS: tautomers: AT -> AC transition C-G -> C*-A; T-A -> T*-G; C-G -> T-G*; T-A->C-A* depurination: loss of purine by hydrolysis, sugar/puriene bond less stable; AP endonuclease, cleaves, DNA POL fills, very common in water deamination: removal of amino group C becomes U, 5mC becomes T (BAD) hard to save. Uracil glycolase fixes easy. Thymine dimers block DNA rep/transc: repaired by NucleotideExcision Repair Base modifying agents GC-> AT Intercalating agent on template= insertion; on new strand=delete Base analogs: chemicals that look like bases AT*->GC Replication slippage of DNA POL; looping in template = deletion in new; looping out of new = addition to new ketol- normal; enol- rare Silent mutations: 1) disrupt the ability of mRNA to form stem loop structure, affects stability 2) amount of translation, differing levels of tRNA; protein folding, if slow translation, protein can fold properly 3) alternative splicing, changes which exons chosen for splicing synon/ silent mutation: changing codon does not change the aa missense: change one amino acid to another neutral: change for a similar amino acid nonsense: change amino acid for stop codon deoxy =H