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BMSC 210 - PART 2

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tasnimjaisee's version from 2017-10-11 19:50

Lecture 7

Question Answer
Electron transport system oriented in cytoplasmic membrane exists for what usage of protons and electrons?Keep separation
Electron carriers are arranged in membrane according to what order?Reduction potential
Proton motive forceElectron transfer protons' (from NADH & water) released to exterior membrane - pH & electrochemical potential crosses membrane
In respiration, inside of cell stays in what conditions?negative and alkaline
In respiration, outside of cell stays in what conditions?positive and acidic
ATP synthase (ATPase) (2)Dissipates and also converts proton motive force into ATP; F1 and F0 – Reversible
F1multiprotein extramembrane complex; faces cytoplasm
F0proton‐conducting intramembrane channel
Organic acids can be metabolized in which versions by microbes?Electron donors & carbon sources
C4‐C6 citric acid cycle intermediatesNatural plant & fermentation products - Catibolaized through citric acid cycle- ex. citrate, malate
What are the ways microorganisms demonstrate a wide range of mechanisms for generating energy (5)Fermentation - Aerobic & Anerobic respiration - Chemolithotrophy - Phototrophy
What does anaerobic respiration depend on? (3)Electron transport - Proton motive force - ATPase
Chemolithotrophy uses ___ ___ as electron donorsinorganic chemicals
Begins with oxidation of inorganic electron donorChemolithotrophy
Is chemolithotrophy aerobic or anerobic?Aerobic
Chemolithotrophy uses which chain and force?Electron transport chain - Proton motive force
Chemolithotrophy joins which other -trophy?Autotrophic; uses CO2 as carbon source
PhototrophyLight as energy
Photophosphorylationlight‐mediated ATP synthesis
PhotoautotrophsATP assimilation of CO2 for biosynthesis
PhotoheterotrophsATP assimilation of organic carbon for biosynthesis
BiosynthesesAnabolic processes
Prokaryotic polysaccharides are synthesized from which type of glucose?Activated glucose
Adenosine diphosphoglucose (ADPG)Biosynthesizes glycogen
Uridine diphosphoglucose (UDPG)Biosynthesizes polysaccharides
Fatty acids are biosynthesized how many carbons at a time?2
Acyl carrier protein (ACP)Holds fatty acid while its being biosyntheized
In Bacteria and Eukarya, the final assembly of lipids involves addition of?fatty acids to glycerol
In Archaea, lipids contain _____ instead of fatty acidsphytanyl side chains
Who releases less energy aerobics of anaerobicsAnaerboics
What is an electron acceptor other than oxygen?Anerobic respiration
memorize

Lecture 8

Question Answer
Relaxed circular DNA2 strands
Relaxed nicked circular DNA2 strands with a break
Supercoiled circular DNACircles: Rotate 1 end of strand around helix sealed
Chromosomal DNA with supercoiled domainsSupercoiled tails with protein holding together (flower)
How does E.Coile strain K-12 replication work?Goes both directions from DNA replication origin
Dual replication fork is found in which kind of DNA?Circle DNA
DNA Gyrase: Negative super coiling (4)Circle laid over - Helix double contact - Unbroken helix passed through break - Reseal causes 2 negative supercoils
Replisome (4)2 copies of DNA polymerase & DNA gyrase - Primosome - single strand DNA binding proteins
What component removes DNA supercoils for replication?DNA gyrase
Which direction do polymerase work to replicate strands in replisomes?They work in opposite directions
Transcription (4)Sigma finds promoter/initiation site - RNA polymerase opens double helix - RNA chain grows until Termination site - Release
Inverted repeatsTranscribed DNA form RNA loops - terminating transcription followed by uracil run
3 elements are critical for promoter recognition in archaeaINIT - TATA - BRE
Translation: Initiation starts when mRNA and tRNA does what?Carries Met binds to ribosome
Where does energy for refolding come from?ATP
Intrinsic terminatorstranscription is terminated without additional factors
Rho‐dependent terminationRho protein recognizes specific DNA sequences & pause RNA polymerase
Unit of transcriptionUnit of chromosome bounded transcription sites
Three types of rRNA16S, 23S, and 5S
Are rRNA and tRNA stable or unstable?very stable
What is tRNA cotranscribed withrRNA or other tRNA
mRNAs have what kind of life limit?short half‐lives
In what form of way are prokaryotes genes transcribed?all at once as a single mRNA
Polycistronic mRNACotranscribed genes
OperonCotranscribed on a polycistronic mRNA - Expresses multiple genes coordination
TBPTATA binding protein
TFBTranscription factor B
Where does promoter site start working in Archaea?When TFB ‐ binds to the BRE and INIT
Where is signal sequencesFound at protein molecule's beginning (need transport)
Tat protein export systemFolded poteins to be exported are exported (ex. • Iron–sulfur proteins • Redox proteins)
Only Protein Types II and V depend on which exports?Sec or Tat
Signal recognition particle binds to which proteins?Proteins inserted into membrane
SecA binds to which proteins?Proteins secreted across cytoplasmic membrane
InjectisomeType 3 secreation system
What prevents complete folding of proteins?Signal sequence
memorize

Lecture 9

Question Answer
Most bacteria have shorter generation times than which type microbes?eukaryotes
Generation time is dependent on which 2 factors?growth medium - incubation conditions
Generation time of the exponentially growing population equation is?G=T/N
Typical growth curve for population of cells grown in a closed system is characterized by four phasesLag - Exponential - Stationary - Death
Continuous cultureOpen‐system microbial culture of fixed volume
ChemostatContinuous culture device - Dilution rate controls growth: independently limiting nutrient
Growth rate and population density of culture can be controlled independently or simultaneously?Both
Dilution rateFresh medium is pumped in - Spent medium is pumped out – Controls growth rate
Batch cultureConstantly changing growth conditions - Closed‐system microbial culture of fixed volume
What is continuous Culture sensitive to? (2)Dilution - Nutrient
What happens at too high dilution rate in continuous cultures?Organism washed out
What happens at too low dilution rate in continuous cultures?Starvation
What happens at increasing concentration of a limiting nutrient in continuous cultures?Greater biomass - Same growth rate
Measuring Growth: Microscopic count cons (3)Can't differ live & dead w/o stains - Motile cells immobilization - Debris
Which microscope is required to count cells if a stain is not used?Phase contrast microscope
Methods for enumerating cells in liquid samples?Microscopic counts - Flow Cytometer
Flow cytometerLasers - Dyes
Methods for plate counts?Spread-Plate - Pour-Plate
Spread-PlateSample onto agar - Spread evenly- Surface colonies seen all in same size
Pour-Plate (4)Sample onto sterile plate - Mixed with inoculum - Solidified & Incubated - Big surface & subsurface colonies
SpectrophotometryTurbidity measurements - Indirect and rapid measuring microbial growth
What is a spectrophotometer's measurement?optical density (OD)
Pros of spectrophotometryQuick & easy - Doesn't need destruction of sample
Cons of spectrophotometryClumped microbes - Liquid medium biofilms
Conditions Affecting GrowthTemperature • pH • Osmolarity • Oxygen availability
Cardinal temperaturesMin/optimum/maximum temperatures at which an organism grows
ExtremophilesOrganisms that grow under very hot or very cold conditions
PsychrophilesOrganisms with cold temperature optima - In permanently cold environments
PsychrotolerantCan grow at 0ºC but have optima of 20ºC to 40ºC
Production of enzymes that function optimally in the coldFlexibility • α‐helices>β‐sheets • Polar> and
Above ~65ºC, only which life forms exist?prokaryotic
ThermophilesOrganisms with growth temperature optima between 45ºC and 80ºC
Hyperthermophilesorganisms with optima greater than 80ºC
Which group are more widely distributed in nature than psychrophiles?Psychrotolerant
memorize

Lecture 10

Question Answer
In growing cultures, addition of arginine ___ ___ of enzymes needed to make arginineRepresses production
In growing cultures, addition of lactose ___ ___ of enzymes needed to make B-Galactosidaseinduces synthesis
Genes that are negatively controlled have a default of?"ON"
Negative control: If proteins that regulate the expression of the gene are removed, what would happen?The gene would be expressed
Negative control: RepressionTranscription is at procession initially - Transcription stops once repressor joins with corepressor
Negative control: InductionTranscription is at stop initially - Transcription continues once inducer joins repressor and pulls it away
Genes that are positively controlled have a default of?"OFF"
Positive control: if proteins that regulate the expression of the gene are removed, what would happen?The gene would NOT be express
Positive Control: Activatior (3)No Flow initially - RNA Polymerase, Maltose protein and Maltose inducer binds site for flow
Direct regulation of proteins are subject to? (3)Degradation - Modification - Allosteric regulation
Global control systemsExpresses different genes simultaneously (ex. Catabolite repression)
Unrelated catabolite enzyme synthesis is repressed if?Glucose is in growth medium
What controls catabolite repression?Lac operon
Diauxic growthtwo exponential growth phases
CRP Activator protein (2)Catabolite repression transcription - Regulatory nucleotide
Are activator proteins a form of positive or negative control?Positive
What are flagellar genes controlled by?Catabolite repression; no need to swim in search of food
Archaea use DNA‐binding proteins to control?Transcription
NrpRArchaeal repressor protein - Represses genes in nitrogen metabolism
Do Archaea use repressors?Yes
memorize

Lecture 11

Question Answer
Prokaryotes regulate cellular metabolism in response to?environmental fluctuations
Signal TransductionExternal signal detected - Transmits to regulatory machine
Sensor kinase (3)In cytoplasmic membrane - detects environmental signal & autophosphorylates
Response regulatorin cytoplasm - regulates transcription
Which organism has 50 different two‐component systems?E.Coli
Can some signal transduction systems have multiple regulatory elements?Yes
Can Archaea have 2 component regulatory systems?Yes
In chemotaxis, modified two‐component system usages are? (2)Flaggerllar rotation - Detect temporal changes in attractants/replicants
Response to signal: Main stepsSensory cytoplasmic membrane proteins sense attractants & repellents (MCPs) - Controlling flagellar rotation (CheY & CheY-P) - Adaptation (Feedback loop)
Methyl‐accepting chemotaxis proteins (MCPs) (2)Bind attractant or repellent - Initiate flagellar rotation
CheYCouter clockwise rotations - Runs
CheY-PClockwise rotation - Tumbling
Feedback loop (2)System resets to continue sensing - Modifyies MCPs
Phototaxismovement toward light - Light sensor replaces MCPs
Aerotaxismovement toward oxygen - Redox protein monitors O2
Quorum sensingBacteria assessing their population density - Ensures cells count before initiating response that requires a certain cell density (ex. Pathogenic bacterium toxin production)
Autoinducer molecule (3)Diffuses - High concentrations if many cells near - Triggers transcription
Which operon encodes bioluminescence?Lux operon
What was the first autoinducer to be identifiedAcyl Homoserine lactone (AHL)
Examples of quorum sensing Virulence factors - Free-living to biofilm
Global Control NetworksAerobic, anaerobic and catabolic respiration - Nitrogen utilization - Oxidative stress - SOS & Heat shock response
What is heat shock (HS) response controlled by?Alternative sigma factors
Heat shock proteins (2)Counteracts denatured proteins damage - Temperature stress recovering
Signal Transduction (2)External signal sensored - Transmitted to regulatory machine
memorize

Lecture 14

Question Answer
Regulatory RNAsSmall RNAs and Antisense RNA – Riboswitches – Attenuation
Regulation of Enzymes and ProteinsFeedback Inhibition – Post‐translational Modification
Regulatory RNA molecules exert their effects by?base pairing with mRNA
Once bound to their target mRNA they can (2)...Block/Open up RBS – Increase/Decrease mRNA degregation
antisense RNAsSmall RNAs made by transcribing nontemplate strand of gene
antisense RNA transcription is enhanced when...Its target genes need to be off
Some antisense RNAs are able to enhance translation of?target mRNA
Trans‐sRNAs are encoded in the ___ regionintergenic
Binding of trans‐sRNA to targets depends on?RNA chaperones
HfqRNA chaperone example - binds to RNA molecules and ribonuclease E
What do trans‐sRNAs help small molecules maintain?correct structures
Are sRNAs are 100% complementary to their targets?No
RiboswitchesRNA domains in mRNA that bind small molecules controlling mRNA translation
Where and what are riboswitches located on?5' end of mRNA
Which organisms contain riboswitches?archaea, bacteria, fungi, and plants
AttenuationTranscriptional control that functions by premature termination of mRNA synthesis
Attenuation control is exerted after the ___ ___, but before its completiontranscription initiation
First example of attenuationtryptophan operon in E. coli
Determining factors in attenuationmRNA stem–loop structure - Synthesis of leader peptide
Which procaryote is attenuation in?Archea
Will attenuation work in eukaryotes?No, transcription and translation don't co-occur in eukaryotes
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