MicroBio 305 Exam #2 WSU Fall 2018

Heterofermentative metabolism during heterolactic fermentation use?

- Uses pentose phosphate pathway initially - Uses heterolactic fermentation - Glucose ---> lactate + CO2 + ethanol

AraC transcriptional regulator

- When arabinose is absent, AraC represses expression of genes that break down arabinose - When arabinose is present, AraC activates those same genes

Amphibolic

- both catabolic and anabolic - in some catabolic pathways, useful intermediates are used as precursors in anabolic pathways

Conjugation of bacterial cells

- cell to cell contact via pilus from donor cell

How many ATP, NADH, and NADPH does Entner-Doudoroff make?

1 of each

Photolytic electron transport system

1. Antenna system 2. Reaction center 3. ETS

Operon control other examples

1. AraC transcriptional regulator (for CATABOLISM OF ARABINOSE) 2. the tryptophan operon (FOR ANABOLISM OF TRYPTOPHAN)

inhibition of DNA replication

SeqA

Plasmids occur in what types of cells during DNA replication?

bacterial, archaeal and eukaryotic microbes

Transduction

bacteriophages cay host DNA from one cell to another

what assembles the outer membrane proteins in the outer membrane in secretion?

beta barrel assembly machine complex

NADPH is used for?

biosynthesis

Calvin cycle carbons

bring in 3 and produces 3

Where does the ETC/ETC function within the prokaryotic membrane?

cell membrane

Chemo (energy source)

chemical electron donors are oxidized

what shape are plasmids

circular

Purine biosynthesis

comes from glutamine

Antenna system

complex of chlorophylls that captures photos and transfers their energy among photopigments until it reaches reaction center

Bacteriorhopdopsin (retinal)

conjugated double bonds absorb light

Transertion

coupling of transcription, translation, and insertion of membrane protein

Where are proteins made in the outer membrane in secretion

cytoplasm

start replicating too late

diving cell's septum guillotines the chromosome

Glutamine operon activation with high levels of glutamine

doesn't need to be turned on

What occurs from Photosystem II ETS?

drives synthesis of ATP

What happens during Photosystem I ETS

electrons from H2S are transferred to NADP+ to form NADPH

Respiration

electrons from a donor pass through ETC/ETS to terminal electron acceptor, making PMF used by ATP synthase to produce ATP

Biosynthesis Fatty acids are always odd or even

even because they are always added in groups of 2

Auxotrophs

fix carbon

Mutase

functional group shift

Sugar break down starts with?

glucose

reverse TCA cycle used by?

green sulfur phototrophs (chlorobium), thermophilic epsilonproteobacteria, sulfur-reducing bacteria

After replication oriC is

hemimethylated

Supercoiling

how nucleoids are formed

ATP anabolism

hydrolyze ATP to ADP (uses energy)

Litho (electron source)

inorganic molecules donate electrons

Rubisco

key enzyme in the calvin cycle that fixes CO2 in bacteria and chloroplasts

cyclic metabolic pathway

last step may regenerate a reactant for the first step

Photo (energy source)

light absorption captures energy and excites electrons

Photolysis

light absorption coupled to splitting a molecule

Photoionization

light absorption that causes electron separation

Photoexcitation

light absorption that raises an electron to a higher energy state

Translation

mRNA--> protein

ATP catabolism

make ATP to store energy (makes energy)

Secretion

movement of a protein out of the cytoplasm

Polysomes

multiple ribosomes translating a single mRNA, creating multiple peptide copies

Underwinding supercoil

negative

plasmids are positively or negatively supercoiled

negatively

Organo (Electron Source)

organic molecules donate electrons

DNA replication origin

oriC

where are proteins exported to from the outer membrane of secretion? (what transports it?)

periplasm; SecA- dependent secretion system

Kinase in Glycolysis

phosphotransferase

ETS

photoexcited electron enters an ETS

Photosynthesis

photolysis with CO2 fixation and biosynthesis

Reaction center

photon energy separates an electron from chlorophyll and replaced with electron from a small molecule or the ETS

overwinding supercoil

positive

Acetyl-coA pathway

produces 2 carbons

3-Hydroxypropionate cycle makes what?

produces 3 carbon molecule

Isomerase

rearrangement

Anaerobic photosystem I does?

receives electrons associated with hydrogens from H2S, HS-, or H2

What does Oxidative phosphorylation use the ETC for?

redox reactions conducted by membrane electron carriers

Dissimilatory denitrification

reduction of oxidized states of nitrogen for energy yield

Bidirectional plasmid replication

replication starts at single original and moves in two directions simultaneously

Anaerobic photosystem II does what?

returns electron from ETS to bacteriochlorophyll

mRNA goes to proteins via?

ribosomes

How do ribosomes find the right reading frame?

shine-dalgarno sequence

Paradigm

the lactose operon (for CATABOLISM OF LACTOSE)

Hydrogenotrophy

the use of molecular hydrogen (H2) as an electron donor

start replicating too early

too many copies of chromosomes

conjugation requires what kind of plasmids?

transferale

rolling-circle plasmid replication

unidirectional

how does fermentation happen?

use organic terminal electron acceptor (Pyruvate)

Aromatic Amino Acid Biosynthesis

uses chorismate to make either L-phentlalanine, L-Tyrosine, or L-Tryptophan

Glutamine operon activation with low levels of glutamine

will be turned on

DNA terminate at

(ter)- defined termination site

Bacteriorhopdopsin

- Absorb green light, reflecting blue and red (appear purple) - Photoexcitation coupled to pumping of H+ across membrane - Proton gradient drives ATP synthesis

Lactobacilli during heterolactic fermentation are found where and are?

- Acidophile - Found in intestinal flora and raw milk - Obligate fermenter - Aerotolerant anaerobe

What is produced/ pumped from Cytochrome bd oxidase (cyt bd) and is it aerobic or anaerobic?

- Aerobic - 2 quinol + oxygen 2 quinone + 2 water - Pumps 4H+ from 2 quinols

What is produced/ pumped from Cytochrome bo quinol oxidase (cyt bo) and is it aerobic or anaerobic?

- Aerobic - 2 quinol + oxygen 2 quinone + 2 water - Pumps 4H+ from 2 quinols plus 4H+ from bond energy

What are Pyruvate and NADH used for?

- Aerobic and anaerobic respiration - Fermentation

Fermentation happens when?

- Aerobic/Anaerobic respirers: if no inorganic terminal e- acceptor is available - Obligate fermenters: don't have ETC

Staphylococcus aureus

- Aerobic/anaerobic respiration and fermentation - Facultative anaerobe - Causes skin infections, food poisoning, pneumonia

What is produced/ pumped from Nitrate reductase and is it aerobic or anaerobic?

- Anaerobic - Quinol + nitrate quinone + nitrite - Pumps 2H+ from 1 quinol

Metabolic pathway reactions are catalyzed by? (including?)

- Enzymes - Include substrates, intermediates, and products

TAT (twin arginine translocase)

- Fully folded protein is transported across membrane - Powered by PMF

Homolactic fermentation

- Glucose ---> 2 pyruvate (via glycolysis) - 2 pyruvate + 2 NADH + 2H+ ---> 2 lactate + 2NAD+ [via lactate dehydrogenase]

Sugar breakdown pathways

- Glycolysis (Embden-Meyerhof-Parnas) - Entner-Doudoroff - Pentose Phosphate

transformation in bacterial cells

- Import free DNA into bacterial cells which requires transformasome complexes to be naturally competent. - Other species require chemical or physical laboratory induction of competence.

Oxygenic Z pathway does what?

- Includes homologues of photosystems I and II - H2O photolysis - Electrons flow from PSII into PSI, releasing O2 from H2O - Makes both NADPH and ATP, which are used to fix CO2

Dissimilatory metal reduction

- Iron - Manganese - Uranium

Proton motive force

- Make [H+]outside > [H+]inside across membrane - ATP synthase uses ~3H+ to make 1 ATP

Metabolic electron carriers (reducing power)

- NAD+/NADH (nicotinamide adenine dinucleotide) - NADP+/NADPH (nicotinamide adenine dinucleotide) - FAD/FADH2 (falvin adenine dinucleotide)

Oxidized forms of nitrogen

- Neisseria meningitis and Brucella - Bacillus

Metabolic pathways

- Not all chemical reactions are exothermic (favorable) - Organisms often link endothermic and exothermic reactions to drive overall equilibrium forward

Homofermentative metabolism

- Not really a pathway - just one enzyme - Glucose ---> 2 lactate

Three Terminal electron acceptors

- O2 - NO3- - Pyruvate

Clostridium fermentation (Clostridium perfringens)

- Obligate fermenter - Obligate anaerobe - Lives in intestines, soil, and aquatic environemnts - Causes necrosis (gangrene)

Streptococcus pyogenes

- Obligate fermentor - Aerotolerant anaerobe - Causes pharyngitis, rheumatic fever, mastitis, necrotizing fasciitis

Oxidized forms of sulfur

- Ocean bacteria and archaea - Salmonella enterica

what three ways can ATP be used?

- Phosphorylation of an organic molecule - Hydrolysis releasing phosphate - Hydrolysis releasing pyrophosphate

Proteins breakdown

- Proteases hydrolyze proteins into amino acids - Amino acids are decarboxylated and deaminated

SecA-dependent

- Protein is unfolded as it goes through membrane - ATP-driven

Phototrophy

- Simple phototrophy using bacteriorhodopsin in haloarchaea and proteorhodopsin in bacteria - ETS-based photolysis in bacteria and chloroplast

what are the three ways ATP can be made?

- Substrate-level phosphorylation - Oxidative phosphorylation - Photophosphorylation

Terminal oxidases

- Transfers 2e- from quinol(s) to terminal e- acceptor forming reduced e- acceptor and quinone - Each pumps 2H+ per quinol substrate

DNA replication termination happens by

- Tus binding to her which blocks DnaB helicase activity - One set of her sequences halts the clockwise polymerase and the other halts counter-clockwise polymerase.

Pyruvate is converted to what in fermentation?

1. Lactate ---> lactate dehydrogenase 2. Acetyl-CoA ---> (a.) Pyruvate dehydrogenase (b.) Pyruvate synthase (c.) Pyruvate formate

Heterolactic fermentation

1. Lactobacilli 2. Heterofermentative metabolism

Two different ETC electron sources

1. Litho 2. Organo

2 different ETC energy sources

1. Photo 2. Chemo

Periplasm in secretion two options

1. SecA-depend 2. TAT (twin arginine translocase)

Secretion inner membrane two pathways

1. Signal recognition particle (SRP) 2. Trigger factor Both converge on general secretion complex called SecYEG translocon (can export to periplasm or insert into membrane)

Glycolysis produces how many ATP and NADP?

2 ATP and 2 NADH

TCA cycle produces?

2 ATP, 6 NADPH, and 2 NADH

Pentose Phosphat sugar breakdown produces how many ATP, NADH, and NADPH?

2 of each

In sugar breakdown, glucose converts to?

2 pyruvate + energy carriers (ATP and NADH and/or NADPH)

Theoretical prokaryotic ATP yield

37 ATP per glucose (4 from substrate-level phosphorylation during Glycolysis and TCA cycle and 33 from oxidative phosphorylation)

Entner-Doudoroff has how many carbons?

6

Carbohydrates breakdown

Amylases hydrolyze starches into sugars

Metabolic energy carriers

ATP

Aldolase

Aldehyde + alcohol condensation

Acetyl-coA pathway used for?

Anaerobic soil bacteria and sulfate reducer bacteria; and methanogens (archaea)

Nucleoid

Bacterial DNA structure that has one chromosome packaged inside it because bacterial DNA do not have a nucleus.

Replication occurs in which direction

Bidirectionally

activation of DNA initiation

DnaA

Tricarboxylic Acid cycle converts acetyl- CoA to?

CO2

Oxygenic Z pathway occurs in what type of bacteria?

Cyanobacteria and chloroplasts

Calvin Cycle bacteria

Cyanobacteria, purple phototrophs, lithotrophs

Tricarboxylic Acid cycle happens in organisms with _____ only.

ETC

Fermentors don't use?

ETC- No oxidative phosphorylation, can only do substrate-level

Where are electrons stored>

Electron acceptors

Coupled Transcription/Translation

Ribosomes begin making protein from the 5' end of the mRNA before the RNA polymerase has finished ma

3-Hydroxypropionate cycle is used by?

Filamentous green bacteria and some archaea (aerobic sulfur oxidizers)

Chlorophylls are found in?

Found in chloroplasts in plants and in cyanobacteria (algae)

Dehydrogenase

Generate reducing power (NADH)

Arginine Biosynthesis Operon

Goes from glutamate to arginine

Extracellular space in the secretion process contains?

Gram (-) bacteria proteins such as proteases and toxins.

Photosystem I occurs in what kind of bacteria?

Green sulfur bacteria and filamentous green bacteria

Oxidative phosphorylation

Recycles electron carriers for more sugar breakdown

Lipid breakdown

Lipases hydrolyze lipids into glycerol and fatty acids

Catabolism

Metabolic pathways that break down molecules (complex), releasing (producing) energy.

Anabolism

Metabolic pathways that construct molecules, requiring (uses) energy. (Biosynthesis)

ATP is typically bound to which macronutrient?

Mg2+

Where does the ETC/ETS function within the Eukaryotic membrane?

Mitochondrial membrane

example of electron acceptors

NAD+ ---> NADH

Respiring organisms use what as electron donors into ETC?

NADH and FADH2

Biosynthesis of amino acids and nucleotides requires?

Nitrogen fixation and has to have ammonia

Glutamine operon activation

NtrC gets phosphorylated to activate

Lithotrophy

Reduced minerals and single-carbon compounds serve as electron donors for an ETS/ETC

Bacteriochlorophylls are found in what type of bacteria?

Purple

Photosystem II occurs in what kind of bacteria?

Purple nonsulfur bacteria

Pyruvate dehydrogenase complex

Pyruvate + CoA + NAD+ Acetyl-CoA + CO2 + NADH + 2 H+

Transcription initiation

RNA polymerase makes RNA copies of DNA template with each RNA polymerase having their own sigma factor which guide ENA polymerase to the beginning of genes.

linear metabolic pathway

Starting compound --> intermediate a --> intermediate b --> end product

branched metabolic pathway

Starting compound --> intermediate a --> intermediate b1 and b2 --> end product 1 and 2

Pyruvate dehydrogenase complex link sugar breakdown to?

TCA cycle or Fermentation

Kept positively supercoiled

Thermophilic and acidophilic archaeal cells - Harder to denature

Dehydrogenases

Transfers 2e- from reduced e- carrier to quinone, forming oxidized e- carrier and quinol

Reverse TCA cycle

Uses 4-5 ATP to fix 4 CO2 and generate oxaloacetate, which ultimately generates acetyl-coA for biosynthesis

What does NADH dehydrogenase 2 (NDH-2) use and how many H+ are pumped?

Uses NADH and 0 H+ are pumped

What does NADH dehydrogenase 1 (NDH-1) use and how many H+ are pumped?

Uses NADH and 4 H+ are pumped

What does Succinate dehydrogenase use and how many H+ are pumped?

Uses Succinate via FADH2 and 0 H+ are pumped

Entner-Doudoroff

Very common in bacteria and archaea

Kept negatively supercoiled

bacterial and some archaeal DNA - Easier access for transcription enzymes.

Chlorophyll does?

absorb light and contain chromophore, a light-absorbing electron carrier

Fatty acids

acetyl-coA units are cyclically added to make fatty acid chains