E2 Flashcards
Site-specific inhibitors?
Carbon monoxide
cyanide
sodium azide
rotenone
antimycin A
amytal
- any compound that stops electron transport will stop breathing
Phosphorylation inhibitor?
Oligomycin
- Electron transport can be stopped by inhibiting ATP synthesis (blocking the proton channel)
Uncouplers?
DNP and FCCP
- breaking the connection between ATP synthesis and electron transport
How is the ETC electron flow effected by oligomycin
- not stopped
-PMF can be uncoupled from ATP synthesis by diversion to alternative integral membrane proteins
What do hydrogen sulfide and hydrogen cyanide do
-binding and inhibiting complex IV and electron flow
-preventing O2 reduction and respiration
Aerobic respiration steps?
Glucose –> 2 pyruvate (with oxygen)–> 36 ATP
- a lot produced in oxidative phosphorylation
Fermentation steps?
Glucose –> 2 pyruvate (without oxygen)–> 2 ATP
Aerobic vs Anaerobic respiration?
Aerobic
- requires O2
- complete substrate oxidation
- water formed as the end product
Anaerobic
- never requires O2
- Incomplete substrate oxidation
- water is not formed
Anaerobic Respiration (Denitrification) steps
NO3 –(nitrate reductase–> NO2 –(nitrite reductase)–> NO –(NO reductase)–> N20 –(N2O reductase)–> N2
Subunits of Nitrate Reductase?
alpha, beta, 2 gamma sheets
Nitrate reductase function?
gamma transfers electrons to quinol to Fe-S
alpha subunit catalyzes reduction of NO3- to NO2-
How is denitrification regulated?
- inhibited by O2 presence
What is the purpose of sulfate-reducing bacteria?
H2 or organic compounds usually serve as electron donors
Assimilatory NO3 reduction
If nitrogen is used for a new biomass
Dissimilatory NO3 reduction
if N2 gas is released
How to cells assimiliate N?
What is an ammoxosome?
- found in plantomyces bacteria
- structure that enabled PMF generation in the oceans
Nitrogen Fixation
- energetically demanding
- 16 ATP produced for every N2 reduced
Nitrogen fixation enzyme and function
Nitrogenase fixes N2 to ammonia
inactivated by O2
Ammonification
breaking down organic matter such as dead animals and plants and wastes like urea
Ammonification enzyme and funtion
Urease hydrolyzes urea to CO2 and ammonia
Nitrification performs what kind of respiration?
Aerobic respiration
- chemolithoautotrophic metabolism using NH3 for electrons for CO2 fixation
How is ammonia removal (nitrification) impacted by the environment?
- shocks (cold or hot spells)
- Toxicity (“slug” toxin from upstream)
- Solid loss (large rain event that can wash them out)
Denitrification
Progressive reduction of nitrate to N2 or N20
anaerobic respiration
dissimilatory
Strategies to prevent denitrification?
- Temporal separation
- High respiratory rate
- Spatial Separation
- Cellular Specialization
Aromatic Amino Acids
benzene ring derived from shikimate from condensation of PEP + Erythrose 4 phosphate
What is the key enzyme for aromatic AA synthesis?
EPSP synthase
Glyphosate function
- inhibits EPSP synthase
- inhbiting the production of aromatic amino acids
Nitrogen donor for most amino acids?
Glutamate
Nitrogen donor for tryptophan, Histidine, Asparagine, and nucleotides?
GlutamINE
Phosphoglycerate AA family
- 3 phosphoglycerate converted to serine then glycine to cysteine
Pyruvate AA family
- pyruvate transaminated to form alanine
- the enzyme is ALT (alanine amino transferase)
- important for catabolism of non- essential amino acids
Alpha-ketoglutarate AA family
Proline, Glutamate, Glutamine, Hisidine, Argenine
Glutamate dehydrogenase
converts alpha ketoglutarate and NH4 to glutamate
- used to transaminate and form various AA
- reversible enzyme
Transaminases
glutamate helps with the addition of amino group skeletons to synthesize most AA
- pyruvate: alanine, valine, leucine
- oxaloacetate to aspartate
Aspartate is used for the synthesis of
threonine
methionine
lysine
What is heme made of?
protoporporphoryn IX ring and iron
Leghemoglobin
A conjugated protein that combines apoprotein with heme prosthetic group to form a functional protein
- heme prosthetic group synthesized by rhizobium
How is heme related to central metabolism?
synthesized by succinyl CoA
What does ALA synthase do?
combines succinyl CoA and glycine to make ALA
- first enzyme in the process of making heme
Ferrochelatase function
Adding central iron to protoporphyrin IX to form heme
What enzyme links carb and lipid metabolism?
glycerol-3-phosphate dehydrogenase
Phases of lipid biosynthesis
- initiation
- formation of butyryl-ACP
- catalyzed by malonyl- COA:ACP transacylase - elongation
- termination
what enzyme is used in neutral lipid biosynthesis
DGAT
- catalyzes the formation of triglycerides from diacylglycerol and acyl CoA
Nucleotide biosynthesis pathways
- Salvage pathway
Activated ribose+ base - devnovo pathway
activated ribose+ amino acids+ ATP+ CO2
Mechanism of action of sulfa drugs
- inhibits bacterial folate synthesis
-folate needed for nucleic acid production so without it no DNA copied
Cons of sulfa drugs
- bacteriostatic instead of bactericidal
- allergic reactions comon
- not effective against all infections
- resistance happens fast in microbes by plasmid or spontaneous mutation
Peptidoglycan structure
sugar component made of alternating residues of beta-1,4 linked NAG and NAM
-NAM has short amino acid chain attached
What is the NAG/ NAM monomer?
Fructose 6-phosphate used to make activated monomers (UDP-NAG and UDP -NAM)
- UDP is a nucleoside diphosphate ester if pyrophosphoric acid with the nucleoside uridine
How is the NAG and NAM monomer made
- glutamine donates amino group to fructose 6-phosphate forming glucosamine-6-phosphate
- acetyl group is then transferred from acetyl CoA to amino group of glucosamine-6-phosphate making N- acetyl-glucosamine-6-phosphate
- NAG-6-phosphate isomerized to NAG-1- phosphate
- monophosphate site bunds to UTP
- UTP-NAG converted to UTP-NAM
-NADPH reduced to form NAM - peptides are attached to NAM only
MurG function?
- enzyme that makes lipid II by adding NGM to the NAM-peptide
What is the function of transglycosylase?
- catalyzes the polymerization step of the cell-wall biosynthesis
What part of the cell wall does penicillin target?
transpeptidase
What does transpeptidase do?
crosslinking peptides, solidifying cell wall
What is the central dogma?
DNA –(translation)–> RNA –(transcription)–> Protein
How do we overcome beta-lactam resistance?
beta- lactam antibiotics are given with beta lactamase inhibitors
Explain how drug resistance is formed via conjugation
- conjugated pili give plasmid from one bacteria to the next
Explain how drug resistance is formed via transformation
- put holes in the cell wall
- introduce plasmid so it can be absorbed
- close holes and select bacteria with new plasmid
Topoisomerase
uncoils DNA to prepare for replication fork
Topoisomerase
uncoils DNA to prepare for replication fork
Helicase
separating strands by breaking H bonds
DNA polymerase
catalyzes the correct base pairing and assembly of the complementary strand
- requires primer
Primase
adding short complementary bp to form a primer
What does a DNTP do?
gives energy to the new strand by forming a phosphodiester bond
DNA Pol IV
- an error-prone DNA repair system increasing the genetic diversity to make more mutants
What is a sigma factor?
direct gene expression in response to environmental conditions
