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BSC 310 Exam 2 Flashcards

by: Mallory Ivy

BSC 310 Exam 2 Flashcards BSC 310

Mallory Ivy
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About this Document

These notes cover genomics, replication, transcription, translation, and a brief overview on temperature classes of bacteria.
Dr. Olson
Class Notes
genomics, spread, plate, pour, replication, transcription, translation, MreB, Fts, Proteins, pribnow, prokarya, eukarya, archaea, Microbiology




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This 198 page Class Notes was uploaded by Mallory Ivy on Monday May 2, 2016. The Class Notes belongs to BSC 310 at University of Alabama - Tuscaloosa taught by Dr. Olson in Spring 2016. Since its upload, it has received 27 views. For similar materials see Microbiology in Biology at University of Alabama - Tuscaloosa.


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Date Created: 05/02/16
3 Characteristics of ALL electron carriers 1a 1. arranged in order of increasingly more positive (E0') reduction potential 2. alternate electron only and electron-plus-proton carriers 3. generation of PMF 1b acyl carrier protein 2a holds growing fatty acid during its synthesis 2b aerobic respiration 3a respiration with oxygen as the final electron acceptor 3b aminoacyl-tRNA synthetases 4a -requires ATP; links aminoi acids to its corresponding tRNA 4b anaerobic respiration 5a uses NO3-, Fe3+, SO4 2-, CO3 2-, or acetate instead of oxygen as the final electron acceptor; yields less energy than with aerobic respiration 5b archaeal RNA polymerase 6a archaeal cells has a single RNA pol that resembles eukaryotic RNA pol II and 11-12 subunits whereas eukaryotic cells have multiple RNA polymerases and 12+ subunits 6b ATPase in organism with ETC versus those without 7a with ETC- functions bidirectionally without ETC- functions unidirectionally 7b ATP synthase 8a 2 Components: -multiprotein (5) cytoplasmic complex called F1 that carries out ATP synthesis and a membrane integrated protein (3) component called F0 -uses 3 to 4 hydrogens per ATP 8b autolysin 9a enzyme that breaks the β-1,4 glycosidic bonds between N- acetylglucosamine and N- acetylmuramic acid in peptidoglycan and new peptidoglycan is inserted 9b bacterial promoters 10a -initiation sites on DNA recognized by sigma factors slightly upstream of gene -2 regions: Pribnow box and - 35 region 10b Bacterial Transcription Termination 11a GC-rich sequence and Rho protein 11b bacteriocin 12a protein produced by bacteria of one strain and active against those of a closely related strain -where we get most of our antibiotics 12b batch culture 13a organisms growing in closed system like a tube, flask, or Petri dish 13b Biosynthesis of Peptidoglycan 14a 1. transglycosylation= transglycosylases insert precursors (Bactoprenol) into growing cell wall and catalyze glycosidic bond formation 2. transpeptidation= final step that forms peptide cross-links 14b bonds between DNA strands 15a hydrogen bonds 15b bonds that hold DNA backbone together 16a phosphodiester bond 16b CAC has both bio_______ and bio_____ roles 17a synthetic and energetic 17b chaperones 18a -assist in folding/refolding partially denatured proteins -4 major ones in E. coli: Dna K, Dna J, Gro EL, Gro ES 18b chemostat 19a a continuous culture; growth and cell density are controlled 19b cytochrome 20a -proteins containing heme prosthetic groups -can form complexes with other cytochromes or with Fe- S proteins 20b deoxytriphosphates 21a sugar + base + 3 phosphate groups that are collectively attached to a growing chain using the 2 high energy anhydride bonds for the reaction 21b divisome 22a cell-division plane in center of the cell made by Fts Proteins 22b DNA Bacterial Polymerase Components 23a 5 subunits- β, β', α (2), ω, σ) however, sigma factor easily dissociates to find promoting region 23b DNA gyrase 24a removes supercoils ahead of DNA helicase which separates/unwinds the 2 strands 24b DNA helicase 25a -uses ATP to unwind dsDNA to expose short ss regions -separates strands in advance of replication fork 25b DNA ligase 26a joins strands/segments of lagging strand 26b DNA polymerase I 27a removes RNA primer and replaces it with DNA 27b DNA polymerase III 28a -replaces primase after primer is formed -has 2 sliding clamps and 1 clamp loader complex -cannot combine two separately synthesized stretches of DNA 28b DNA polymerases 29a -enzymes that catalyze the addition of deoxynucleotides -each species often has several with specific functions -cannot start a new chain 29b Fatty Acid Synthesis 30a -synthesized 2 C's at a time using acyl carrier proteins (ACP) which holds growing fatty acid -each C2 unit originates from malonate (C3) -low temperature environment results in short chain fatty acid whereas a high temperature results in a longer chain 30b fermentation 31a -anaerobic catabolism -organic compound is an electron donor and acceptor -uses substrate level phosphorylation 31b ferredoxin 32a Fe2S2 is an iron-sulfur containing protein that functions in electron transport 32b FtsA 33a -anchors FtsZ to cytoplasmic membrane -recruits other divisome proteins -related to actin 33b FtsI 34a -penicillin-binding protein that assist in PG synthesis 34b FtsK 35a -pulls 2 copies of chromosomes to each of their respective daughter cells 35b Fts Proteins 36a -filamentous temperature sensitive -found in all bacteria; archaea only have FtsZ -interact to form divisome 36b FtsZ 37a -forms membrane-associated ring in center of the cell -inhibited by nucleoid region 37b generation time equation 38a g= duration of exponential growth/ number of generations during exponential growth 38b glucogneogenesis 39a -synthesis of glucose -uses phosphoenolpyruvate (intermediate of glycolysis) and goes backwards 39b glycolysis 40a -breaks down glucose into pyruvate -anaerobic -3 stages: I + II all organisms; III- fermenting organisms only -net gain= 2 ATP 40b glycoxylate cycle 41a variation of CAC utilized when intermediates are siphoned off for other purposes; generates malonate to be made into oxaloacetate so that CAC can proceed 41b Growth Cycle 42a 1. lag phase 2. exponential growth phase (slope) 3. stationary phase (plateau) 4. death 42b heterocyst 43a a differentiated cell within cyanobacteria dedicated to N2-fixation 43b How ATPase works 44a -F1 + F0 are rotary motors -p+ move through F0 causing rotation of c proteins generating torque in F1 through rotation of γε subunits and results in conformational change of β subunits, allowing them to bind ADP + phosphate. Return to original conformation produces ATP. -synthesis: oxidative phosphorylation if PMF originates from respiration or photophosphorylation if it originates from photosynthesis 44b lipid biosynthesis 45a simple fats--> 3 glycerol Carbons are each "esterified" with a fatty acid phospholipid--> one C atom in glycerol has a phosphate group attached to it 45b Min proteins 46a -MinC and MinD accumulate at the poles -MinE forms in the center -ensures divisome only forms at cell center 46b Molecular Adaptations of Psychrophiles 47a -more alpha helices -cold shock proteins -more polar AA and less hydrophobic 47b MreB 48a -major shape-determining protein in Bacteria and likely archaea -forms spiral shaped bands just below the membrane and directs synthesis of new peptidoglycan (PG) -coccoid cells lack MreB gene indicating that coccoid cells are the 48b nitrogenase 49a -enzyme that catalyzes nitrogen fixation -2 protein components: dinitrogenase (iron and molybdenum aka FeMo-co) and dinitrogenase reductase (iron) -some nitrogenases use vandium and iron or only iron (latter is found in archaea) -irreversibly inactivated by O2 49b nitrogen fixation 50a -process of forming ammonia (NH3) from (N2) --NH3 is assimimilated into AA and nucleotides -not done by eukaryotes -energy-demanding; 8 electrons consumed (2 ATP consumed per electron so 16 ATP per N2) 50b nucleoside 51a nitrogenous base + sugar (no phosphate) 51b open reading frame 52a a start codon followed by codons and a stop codon in a single reading frame -considered a putative protein 52b operons 53a -multiple genes are transcribed together -only found in prokaryotes 53b optical density vs absorbance 54a OD is the amount of light passed through while absorbance is the amount of light scattered 54b origin of replication (OriC) 55a -bacteria have a single location on the chromosome where replication is initiated 55b oxaloacetate 56a binds to acetyl-CoA to begin citric acid cycle 56b oxidative phosphorylation 57a ATP synthesis that is driven by PMF produced during respiration 57b plate count methods 58a spread plate and pour plate; differ in that spread plate uses a greater volume of culture -goal is to get between 30-300 colonies 58b polycistronic mRNA 59a -mRNA encoding a group of cotranscribed genes that when translated creates several polypeptides 59b Polypeptide Structure 60a Primary- AA sequence Secondary- H bonds to form alpha helices and beta-pleated sheets Tertiary- interactions between R groups Quartenary- multiple ppc stabilized by disulfide bonds 60b polysome 61a multiple ribosomes can translate a single mRNA simultaneously 61b primase 62a RNA polymerizing enzyme that makes the RNA primer 62b primer 63a -nucleic acid molecule to which DNA polymerase can attach the first nucleotide -usually a short stretch of RNA -eventually removed and DNA poly I fills in missing nucleotides 63b primosome 64a helicase and primase complex that aids in replication process 64b products of the citric acid cycle 65a 1 pyruvate yields 3 CO2, 4 NADH, 1 FADH2, and 1 GTP 65b Promotors of Archaea and Eukarya 66a -TATA box -B recognition element (BRE) recognized by transcription factor B (TFB) -initiator element (INIT) recognized by TFB 66b Protein Synthesis 67a 3 steps: 1. initiation 2. elongation 3. termination 67b quinones (CoQ) 68a -non-protein electron carriers involved in ETC -hydrophobic -can accept 2 electrons and 2 protons but only transfer two electrons 68b redox enzymes that participate in ETC 69a -flavoproteins -cytochromes -NADH dehydrogenases -Fe-S proteins (Fe2S2=ferredoxin) 69b reduction potential 70a difference between 2 points on redox tower 70b replisome (6 components) 71a -complex of DNA pol III, helicase, primase, gyrase, single-stranded binding proteins, and tau proteins through which DNA is pulled during replication 71b respiration 72a -aerobic catabolism -compound oxidized with O2 -uses oxidative phosphorylation to produce ATP 72b Rho protein 73a binds to RNA and terminates transcription in bacteria 73b ribonuclease 74a removes archaeal spacers -only processing occurs for genes coding for rRNA and tRNA 74b ribosomes 75a -30S and 50S subunits in prokaryotes -30S recognizes tRNA, mRNA transcript, and initiation proteins then 50S subunit joins 75b RNA polymerase 76a -enzyme that carries out transcription -can initiate new strands on its own -transcribes genes on either strand of DNA -stops at transcription terminators 76b rRNA 77a creates 30S and 50S ribosomal subunits; has structural and catalytic (forms peptide bonds between AA of tRNA) roles 77b SecA Protein 78a binds proteins that are to be fully transported across membrane 78b Shine-Delgarno Sequence 79a found in untranslated region; aligns reading frame in bacterial RNAs 79b signal recognition particle (SRP) 80a -binds proteins that will be inserted into membrane -contains a signal protein and a small non-coding, not-to-be- folded RNA molecule 80b signal sequence 81a -marks proteins to be transported through membrane -usually have several (+) residues, central hydrophobic region, and more polar end region -keeps protein from completely folding -removed after transport 81b Start Codons 82a AUG; codes for modified methionine 82b Stop Codons 83a UAA, UAG, UGA 83b substrate-level phosphorylation 84a -ATP synthesized from energy-rich intermediates -[sugars] act as both electron donor and acceptor 84b supercoiling 85a more twisting of genome (-) form is predominant in nature (fewer turns) inserted or removed by topoisomerases 85b Tat system 86a -proteins that require cofactors but need to be secreted are folded inside cell (cofactors are difficult to find outside the cell) -TAT= twin arginine translocase -uses PMF for energy -TatBC carry protein to TatA which is the membrane transporter 86b tau protein 87a holds DNA pol III together and in place 87b Temperature Classes of Bacteria 88a psychrophile (optimal temperature= 4 degrees C) mesophile (OT= 39 degrees C) thermophile (OT= 68 degrees C) hyperthermophile (OT= 88 degrees C) hyperthermophile (OT= 106 degrees C) *yes, there are two types of hyperthermophiles 88b Ter site vs Tus proteins 89a termination (ter) sites recognized by Tus proteins, which block progress of the forks 89b tmRNA 90a -has both tRNA and mRNA character -free ribosome from mRNA lacking a stop codon 90b topoisomerase IV 91a cuts both strands to unlink 2 CIRCLES that were produced in replication 91b translocase 92a enzymes that transports proteins through and into cytoplasmic membrane 92b tRNA 93a carries anticodon that base pairs to an AA and mRNA codon -ssRNA with extensive secondary structure that creates a cloverleaf structure -anticodon loop and 3' acceptor end with 3 unpaired nucleotides 93b Type I versus Type II topoisomerase 94a Type I cuts one strand of DNA to either increase or decrease supercoiling and reseals whereas type II cuts both strands or cuts 2 loops at once 94b Types I-VI Secretion Systems 95a -Types I, III, IV, and VI require 1-step and have a channel through both membranes -Types II and V require 2 steps to move the protein through inner and outer membrane -Type III acts as a syringe 95b Types of Plasmids 96a -Resistance plasmids -Pathogenic -Bacteriocin producing 96b wobble 97a irregular base pairing at 3rd position of codon; allows for 64 codons to code for 22 amino acid 97b Yield of ATP in Fermentation vs Aerobic Respiration 98a fermentation yields 2 ATP while aerobic respiration yields 38 98b ZipA 99a -anchors FtsZ to cytoplasmic mebrane -related to tubulin 99b


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