Microbiology Exam 2

operon

cluster of genes and their regulatory elements

operator

repressor proteins bind to halt transcription

polycistronic mRNA

multiple start and stop codons, can encode multiple proteins

monocistronic

only one stop and start codon, encodes 1 gene only

promoter

RNAP binds to initiate transcription

DNA A

recognizes the origin, opens DNA at this location to initiate replication

SSB (single-stranded binding)

binds to one strand to prevent double stranded DNA from joining back together during replication

DNA primase

primes DNA with RNA primer so DNAP III can recognize and start replication

DnaB (helicase)

hydrogen bond breakers, break the bonds of DNA as the replication fork proceeds

DNA gyrase (topoisomerase)

unwinds DNA ahead of the replication fork by making a cut, weaving it through, then sealing (like untying a knot)

DNA polymerase III

responsible for the majority of DNA synthesis, only moves 5’-3’

DNA polymerase I

removes RNA primers and fills in the gaps with DNA

Ligase

seals gaps of okazaki fragments after DNA polym. I fills in gaps

DNA gyrase

target of ciprofloxacin (quinolone antibiotic)

RNA polymerase

core + sigma factors, creates RNA from DNA

sigma factors

proteins, direct core to promoters, ex: sigma79, sigmaS

bacterial RNA polymerase

target of Rifampin (treatment of TB)

mRNA

template for protein synthesis

tRNA

carries amino acids to ribosome during protein synthesis, has anticodon

rRNA

component of ribosomes

characteristics of RNA

ribose, uracil instead of thymine, usually single-stranded

terminator

where transcription ends

promoter

two subregions (-35 & -10)

-35 subregion

RNA polymerase recognition site

-10

RNA polymerase binding site (Pribnow box)

start codon

AUG

shine-dalgarno sequence

ribosomal binding site in bacterial and archaeal mRNA

1st component

sensor kinase & kinase domain with phosphorylated histidine

2nd component

response regulator with phosphorylated aspartic acid

sensor (histidine) kinase

in PM, recognizes signals like a change in temperature, osmolarity, and pH

kinase domain

extends into cytoplasm, when signal is recognized the histidine is phosphorylated

response regulator

phosphate on histidine gets transferred to the Asp, once phosphorylated, it can bind to a promoter so that RNAP knows to start transcription

regulon

a collection of genes and operons controlled by a global regulator protein

EnvZ/OmpR system

controls porin production of E. coli with a two-component signal transduction system by sensing osmolarity of the periplasm

EnvZ

the sensor kinase, when osmolarity change is sensed, it autophosphorylates, then transfers it to OmpR

OmpR

receives phosphoryl group from EnvZ, binds DNA, then suppresses ompF and induces ompC

ompF

porin of E. coli, “wide open”, used when food is plentiful

ompC

porin of E. coli, narrower, used when toxins or too much salt is in the environment

cap snatching

when viruses steal the 5’ cap off of a host’s RNAs and adds it to their own to be able to translate its genetic info

23S rRNA

a peptidyltransferase, catalyzes the formation of a peptide bond between amino acids

ribozyme

RNA molecule with enzymatic function

16S rRNA

aligns mRNA with ribosome, has a sequence complementary to a Shine-Dalgarno sequence

Stop codons

UGA, UAA, UAG

tRNA

brings amino acids to ribosomes, clover-leaf shape, 2 functional regions

synthetase

an enzyme that attaches an amino acid at the top of the tRNA, requires ATP

anticodon

complementary to mRNA codon

3 stages of translation

initiation, elongation, termination

E-site

tRNA detaches from mRNA

P-site

peptide bond forms here

A-site

aminoacyl/acceptor region, attach tRNA anticodon to mRNA

formylmethionine

the amino acid held by tRNA that binds the start codon of mRNA in the p-site

formyl group

ensures amino acids attach correctly, attacked by human immune systems (bacteria) or found in the mitochondria

tetracycline

an antibiotic that inhibits the binding of tRNA

krebs cycle

produces GTP

release factors

cleave the peptide bonds & release the polypeptide when a stop codon is recognized

transfer pathway of energy in microbes

glucose → diffusible characteries in cytoplasm → membrane-bound carriers → O2, or metals/oxidized N and S in anaerobic

autotrophs

CO2 as C source, synthesize organic compounds used by heterotrophs (plants, many microbes)

heterotrophs

organic compounds as C source (animals, many microbes), convert large amounts of C to CO2

organotrophs

organic molecules as electron donors (glucose)

lithotrophs

inorganic molecules as electron donors

organotrophs

many different energy sources are funneled into common degradative pathways, most pathways generate glucose or intermediates of the pathways used in glucose metabolism

aerobic respiration

completely catabolizes an organic energy source to CO2 using glycolytic pathways, tricarboxylic acid cycle (Krebs/CA), ETC w/ O2 as final electron acceptor, produces ATP

glycolysis

most common form of glucose breakdown, makes pyruvate, takes place in the cytoplasm, functions in the presence or absence of O2, 10 reactions in 2 stages

photolithoautotroph

energy from light, inorganic electron source, CO2 carbon source, purple/green sulfur bacteria, cyanobacteria, diatoms

photoorganoheterotroph

energy from light, organic electron source, organic carbon source, purple nonsulfur/green nonsulfur

chemolithoautotroph

inorganic chemicals for energy, inorganic electron source, CO2 carbon source, sulfur-oxidizing, hydrogen-oxidizing, methanogens, nitrifiying, iron-oxidizing

chemolithoheterotroph

inorganic chemicals for energy, inorganic electron source, organic carbon source, some sulfur-oxidizing bacteria

chemoorganoheterotroph

organic chemicals for energy (often same as C source), organic electron source, organic carbon source, most nonphotosynthetic microbes, including most pathogens, fungi, and many protists

2 forms of ATP generation

substrate level phosphorylation, oxidative phosphorylation

phosphoenolpyruvate

used in nutrient transport, phosphorylation cascade to eventually let the sugar across the membrane, then immediately phosphorylates the sugar to prevent it from leaking back out

G3P dehydrogenase

catalyzes the oxidation/phosphorylation of glyceraldehyde-3-phosphate, NAD+ is also reduced to NADH

3PG kinase

catalyzes the transformation of 1,3 bisphosphoglycerate to 3 phosphoglycerate, also SL phosphorylation to produce ATP

pyruvate kinase

phosphoenolpyruvate is made into pyruvate, and ADP is phosphorylated to ATP by a high energy metabolic substrate

net yield of 3 carbon stage

2 ATP, 2 NADH, 2 pyruvate

TCA cycle (Citric Acid/Kreb’s)

pyruvate is completely oxidized to CO2, generates numerous NADH and FADH2 (diffusable e- carriers)

key reactions of the TCA cycle

pryuvate is oxidized to AcetylCoA, which condenses w/ oxaloacetate to form citrate. NADH & CO2 are then oxidized and decarboxylated, then succinyl CoA transforms to succinate (generates high energy GTP by SL phosph.). Finally, NADH and FADH2 are formed by even more oxidations

net yield from glycolysis

2 ATP (directly from oxidation of glucose), most ATP is made when NADH and FADH2 are oxidized in ETCs

direction of flow for ETC

e- flow from carriers with more negative E0 to more positive E0, energy released used to make ATP by oxidative phosph., electron carriers include cytochromes and quinones

location of ETCs

mitochondrial membrane in eukarya, plasma membrane in bacteria and archaea

chemiosmotic hypothesis

discovered by Peter Mitchell, states energy released during e- transport is used to establish a proton gradient and charge difference across a membrane (proton motive force, PMF)

proton motive force and how it drives ATP synthesis

e- flow causes protons to move outward across a membrane, and ATP is made when they move back in.

F1FO (not zero) ATP synthase

multiprotein complex, uses proton movement to catalyze ATP synthesis

how an ETC generates a PMF

starts at the most negative end, movement of protons establishes PMF, ATP synthase uses proton flow down the gradient to make ATP (now at the most positive side)

FO portion of ATP synthase

alpha subunit: proton channel, ring of C subunits rotates

F1 portion of ATP synthase

gamma shaft rotates, conformation changes in the sphere of alpha and beta subunits

fermentation

endogenous organic EA (pyruvate), does not use electron transport system and a terminal acceptor. Occurs in the cytoplasm, electrons from NADH → pyruvate. Generates NAD+, ATP by SLP, and fermentation products (lactic acid, ethanol)

aerobic respiration

O2

anaerobic respiration

EA: NO3-, SO4(2-), CO2, fumarate, used by bacteria/archaea/a few eukarya, creates less energy than aerobic because the EAs have less positive reduction potentials than O2, resulting in a shorter ETC with fewer protons transported to the periplasm. The smaller PMF and ATP yield is why facultative anaerobes will use aerobic whenever possible.

chemolithotrophy

O2, SO4(2-), NO3-

denitrification

an example of anaerobic respiration, nitrate as the terminal electron acceptor, reduced to Nitrite, then to nitrogen gas (N2). This process depletes soil of nitrogen and is the basis of the nitrite strip test (diagnostic for UTIs)

mannitol salt agar

can be used to clinically identify microbes based on their fermentation products. S. aureus will grow in salty environments, but S. epidermidis does not

iron-oxidizing bacteria

ex. Acidithiobacillus, oxidizes iron compounds as e- source using O2 as EA, oxidation generates insoluble ferric hydroxide (toxic to aquatic life), yields little energy similar to why anaerobic resp. does (Fe2+ and Fe3+ are similar to O2, so there is not much of a drop to generate a PMF)

nitrifying bacteria

oxidize ammonia to nitrate. 2 genera: nitrosomonas (ammonia to nitrite), nitrobacter (nitrite to nitrate), used to remove ammonia in wastewater and fish tanks