Week 5 -Wobble effect

-Genomes: the complete haploid collection of DNA – Chargaff’s rule 1:1

-Primary, Secondary, tertiary
-Sugar, Base, Phosphate, double helix, nucleosome
-Primary: phosphodiester bonds (backbone) + Stacking/hydrogen bond
(bases)
-Purines: A,G Pyrimidines: U,T,C
-Secondary: stacking/hydrophobic interactions
-Tertiary: DNA wraps around histones (nucleosomes) = Fully packed
Chromatin
-Bacteria Eukaryotes
Circular Linear + histones Week 9
Small Introns + big Positive and Negative Regulators
+ve = Transcription –ve = inhibits Transcription
Week 6 Operons: genes that are transcribed as one mRNA
-Semi conservative Repression: decreases in the gene expression
-DNA polymerase used since RNA poly don’t need primer Induction: increases in the gene expression
PCR Mutations
1.Denature 2.Anneal 3.elongate Missense = Point mutation in AA leads to change in protein
Nucleases and DNA polymerases repair mismatches after synthesis Nonsense= PM or +/- leads to early stop codon
Proof reading during DNA replication Silent = Point mutation in AA leads to no change in protein
Mismatch repair when DNA is complete Frameshift = new protein/ function overall
Damaged nucleotides from radiation = Nucleotide Metabolism: Enzyme catalyzed reactions
excision repair Anabolic: synthesis of macromolecules
Catabolic: break down of molecules (Car>fats>proteins)
Replication Vivo PCR Vitro just a part 2n
whole Mal Operon: Lac Operon:
Open helix helicase 95 -Positive regulation -Negative regulation
-Maltose present = transcription -Lactose present = transcription
Primer RNA by primase Specfic -MalPQ breaks down maltose -LacZYA breaks down maltose
oligonucleotides -Can’t make mRNA without changing -Inhibits by overlapping
Result Entire genome copied Short segment shape

Week 7 Week 10
-As the Gal 4 produces a reg protein, the Gal 80 attaches to the Gal 4 and in the
presence of galactose, the galactose binds to Gal 80 thus knocking it off and
Prokaryotes Eukaryotes
now Gal 4 can bind to the PPE. After it binds, the RNA pol11 binds onto the
Protien Sigma Basal transcription
promoter and can start transcription.
factors
Termination Hairpin forms Termination
sequence
Promoter -35 and -10 box TATA box
RNA processing Introns removed +
5’cap & 3’Poly A tail
DNA read 3’-5’ RNA Pol. I = rRNA
Leading strand into RNA Pol 2 = mRNA
replicationfork RNA Pol 3 = tRNA
made 5’-3’
Protein N-C DNA RNA
Template 3’-5’ A T
Coding 5’-3’ T U
C G
G C
Prokaryotes Eukaryotes
Glycolysis Cytoplasm Cytosol
1.Required to produce macromolecules
Pyruvate Cytoplasm Membrane
2.Required for structure and function
Processing
3.Required to enzymes
Krebs/Citric Cycle Plasma Mitochondrial 4.Required to reduce major bioelements in anabolism
Membrane matrix 5.Eergy to do work: Electrical/Concentration
Electron Plasma Inner membrane of
Transport Chain Membrane Mitochondria

Week 8
-Aminoacyl tRNA synthetases bind animo acid to tRNA
-Polyribosome: mRNA + ribosomes
Week 11-13
Cellular Respiration:
Glucose + 2NAD+ + 2ATP + 2ADP+ +2 Pi=> 2NADH + 4ATP + 2 Pyruvate
-Regulated byATP binding to phosphofructokinase
-Pyruvate to Acetyl CoA:
Pyruvate + coenzyme A + NAD+ => acetyl CoA + CO2 + NADH
-Additional catalysts: dehydrogenase
Fermentation:
Reuses NAD+ by reducing it and going back to glycolysis
Lactic acid (lactate) or alcohol fermentation (CO 2+Ethanol)
Cellular Respiration: (Krebs) Citric Cycle

Cellular Respiration: Electron Transport Chain (ETC) SLP

Anaerobic Respiration:
- Electron donor (NO3-,SO42-) and acceptors (H2,H2S,CH4, these are higher in
potential energy)
Chemiosmosis Hypothesis/Theory:
-Electron transport causes protons to be exported to the inter-membrane
space; the proton gradient/proton motive force created is harnessed by ATP
synthase to make ATP.
Endosymbiosis Theory
-came from anerobic bacteria

Identify the inputs and the outputs in the process of Calvin

cycle(stroma).
Input: RuBP, CO2, NADPH, ATP
Output: G3P, ADP, Pi, NADP+,
Identify the inputs and the outputs of the photophosphorylation.
Input: photons and water
Output: ATP, NADPH, O2
Identify the inputs and the outputs in the process of photosynthesis
inputs: carbon dioxide, water, light (photon)
outputs: carbohydrate(usually glucose), oxygen, heat