BCHM 3050 Exam 2 Study Guide PDF

Preview

Summary

BCHM with Dr. Chandrasekeran, Exam 2 Study Guide, Spring 2017...

Description

BCHM 3050 Exam 2 Study Guide

Threobromine Caffeine Theophylline  Secondary metabolites of cocoa beans and tea leaves  Diuretic, cardiac stimulate, vasodilator, relax smooth muscles Caffeine  Stimulant, diuretic  Antagonist to adenosine (inhibitory NT, promotes sleepiness)

Theobromine

and

Theophylline

Cordycepin (3’-Deoxy Adenosine)  Antibiotic produced by “scarlet caterpillar fungus”  Inhibits the final step of RNA biosynthesis by termination of the ribonucleotide chain  “terminal step” = polyadenylation of mRNAs during processing, so it prevents the synthesis Cytokinins  Adenine ring system with an attached 5-carbon hydrophobic group at free NH2  Promote cell division in plants

NH 2 N

N

N

N HO O

OH

Cyclic AMP Originates from ATP ATP is the substrate of adenylate cyclase to make cAMP Signaling cascades Hormone signaling, apoptosis, disease rxns, neuron function

Cyclic GMP Originates from GTP GTP is the substrate of guanylate cyclase to make cGMP Nitric oxide signaling (pain) BP homeostasis, nerve impulse transmission, stress response in plants

DNA 1% of cell dry wt. Double-stranded Deoxy-ribose sugar ATCG

RNA 5-10% of cell dry wt. Single-stranded Ribose sugar AUCG (+ modified bases)

DNA Formation of phosphodiester linkage:  P---O---P  Connects two different nucleotides  Can only attach to a growing chaing; cannot just attach two free nucleotides  DNA polymerase: only job is to maintain DNA  Deoxyribonucleotide triphosphate is used as substrate to lengthen DNA, catalyzed by DNA polymerase  attaches 3’OH of previous nucleotide to the first phosphorous B-DNA  Watson & Crick  Represents most native DNA in the cell  Major groove: recognitions sites for transcription factors, promotes separation of DNA strands

  

Minor groove: often bind smaller, non-protein ligands; inhibits some cancers, antimicrobial activity 3.4nm = 1 turn = 10.4 bp 1bp = 0.34 nm

Levels of Structure 1. Primary = base sequence in complementary strands 2. Secondary = double helix coil  Linear: eukaryotic interphase chromosomes  Circular: prokaryotic chromosomes, plasmids, chloroplasts, mitochondria 3. Tertiary = super-coiled DNA  Heterochromatin – extremely condensed DNA in a metaphase chromosome (mitosis)  INACTIVE  Euchromatin – ACTIVE DNA o “Beads on a string” model o Nucleosome = basic unit of structure of eukaryotic chromosomes  8 core histones (basic: arg and lys, attach via electrostatic interactions)  DNA wraps around the nucleosome, H1 clips together  Linker DNA is exposed to the environment, will make proteins or interact with other proteins  Nucleosomes move around to change what DNA is exposed  140bp wrapped around nucleosome + 60bp of linker DNA between  200 bp per nucleosome total Stabilizing forces in DNA  Hydrogen bonds between base pairs  Hydrophobic interactions between bases (bases are non-polar, attract each other at center of double helix)  Electrostatic interactions o Improve solubility in water Chargaff’s Rule [A] = [T] and [G] = [C] RNA RNA is much more abundant than DNA because are are many more copies of RNAs made than the 2 copies of DNA  tRNA = 15% of total RNA  mRNA = 5%  rRNA = 80%  snRNA (small nuclear) = 1% U is replaced by T (methylated uracil), because T will only pair with A; U, however is the only base that can base pair with any of other others. Evolutionarily, this could not be “tolerated” to maintain the fidelity required in DNA base pairing

Griffith: some material gets transformed between bacteria  S strain = smooth capsule  R strain = no capsule/rough strain S strain  dies R strain  lives Heat killed S  lives (antigen is denatured and cannot infect) (by accident): Heat killed S + R  lives Conclusion: live R strain cells were transformed to S strain R cells absorb genetic material of S Avery-MacLeod-McCarty: the transforming material is DNA  Protein: heat shock s + r + protease  died  Carbohydrates: heat shock s + r + amulase  died  DNA: head shock s + r +DNAse  LIVES because transformation can’t take place without DNA  RNA: heat shock s + r +RNAse  died Conclusion: since the mouse lived when DNA was destroy, transformation wasn’t possible with DNA, meaning it was the transforming material Hershey & Chase: DNA is the genetic material and can be transferred down generations  “Blender experiment”  Labeled viral DNA, infected bacteria, bacteria passed on the labeled DNA o One virus tested proteins – sulfur is unique to proteins, so labeled vital proteins with radioactive sulfur o One virus tested DNA – Phosphorous is unique to DNA, so labeled vital DNA with radioactive phosphorous o Sent both viruses into a cell, tested to see what label would be stuck inside of the bacteria  phosphorous showed up inside the cell pellet  Can be exchanged across species Restriction Digestion  Restriction enzymes cut DNA o Originally used for defense by bacteria to chop up viral DNA o Seeks out certain sequences  Cruciform DNA – palindromes Genome Structure Prokaryotes Smaller Continuous, mostly coding Operons Plasmids

Eukaryotes Bigger Discontinuous, mostly non-coding, 45% repetitive Introns, exons, transposons Pseudogenes

Plasmis are small, can be used to transfer unique metabolic capabilities (antibiotic resistance, virulence genes, nitrogen fixation genes, degradation of unique carbon sources) Pseudogenes – lost necessity, but still in genome Prokaryotic genomes change a lot; mutations and adaptations Transposons – jumping genes (corn pigmentation); Alu

     

Eukaryotes have very few expressed regions in the genome E coli  majority is expressed Exons and introns alternate (introns have to be cut out) Lots of repeats in humans Prokaryotes has repeats too, but fewer Eukaryotes have more genes that code for tRNAs

DNA REPLICATION  5’  3’ direction ALWAYS  Semi-conservative  Spatially bidirectional (2 forks at once)  Semi-discontinous Meselson and Stahl: DNA replication is semi-conservative  Put bacterial cells in nutrient with labeled nitrogen, so that all of its nitrogen bases would be N15 (native is N14)

Origins – DNA sequence which signals where replication is beginning  Forms replication bubble with forks on each end that extend in both direction (bidirectional)

Leading and lagging strands are made at the same speed DNA Polymerase = enzyme DEOXYnucleoside TRIphosphate = substrate

Helicase – attracted to the origin by initiation factors, unwind dsDNA by breaking H-bonds, doesn’t leave until replication is over, defines fork Single stranded binding proteins – follow helicase and directly attaches to DNA; prevents two strands from coming back together after separation Primase – small type of RNA polymerase that can take two nucleotides and join then together; start with ~10 nucleotides so that DNA pol III can come in DNA Pol III – extends the chain that primase started, needed for both leading and lagging strands (DNA bends to get to pol III, which is a dimer  both strands @ same time)

DNA Pol I – cleans up after III; smaller and only seeks out RNA primers, takes them out, and replaces with DNA DNA ligase – forms phosphodiester bonds between gaps in okazaki fragments; doesn’t have to bring a nucleotide with it, just does to the already-positioned nucleotides and creates bonds Replisome = DNA pol III + primosome (primase + helicase) + ss binding protein 1. Initiation: unwind and stabilize the duplex DNA to form replication form  Initiation factors – bind to origin o Attracts helicase, leave after helicase comes  Helicase – catalyzes ATP-dependend unwinding of duplex DNA o Doesn’t directly bind to DNA  Topoisomerases – prevent supercoiling and tangling of DNA during unwinding o Bind ahead of fork, allows for uncoiling  ssDNA binding protein – prevents re-annealing of separated strands and protects against degradation 2. Elongation: 5’3’ synthesis of complementary DNA  Primase – synthesizes ~10 nucleotide primer  DNA pol III – extends RNA-primed chain

 DNA pol I – later replaces RNA with DNA 3. Termination of DNA replication (not well understood)  Prokaryotes: ter binding proteins o Bind to inverted repeat (ter sites) on opposite side of DNA loop, inhibit helicase and replisome falls off  Eukaryotes: o DNA polymerase runs off the ends of DNA o Replication bubbles fuse as polymerases collide



Telomere: a series of repeated TTAGGG at ends of linear eukaryotic chromosomes - Each time a cell divides, some of the telomere is lost due to exonuclease activity - Aging process - Premarue aging and death of clones are thought to be releated to cloning from cells with partly reduced telomeres - Telomerase – restores telomere sequence  cancer cells

Polymerase Chain Reaction (PCR)  Heating destroys H-bonds but not phosphodiester  Creates two single strands of DNA  Chemically synthesize a short stretch of RNA primer  Cooling allows for reformation of hydrogen bonds (annealing)  Treating both like leading strands  Extension – add DNA pol III (ONLY ENZYME NEEDED)  Adds dNTPS in equal proportions – substrates for DNA pol III  Exponential amplification...