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