Lecture 4 and 5 Microbial Metabolism Flashcards
What is metabolism?
Sum of chemical reactions in a cell
What are the two parts of metabolism?
Catabolism, anabolism/biosynthesis
What is catabolism
Processes that degrade compounds to release energy
- cells capture to make ATP
What is anabolism?
Assemble subunits of macromolecules
uses ATP to drive reactions
What is energy?
Capacity to do work
What is potential energy?
(chemical bonds, rock on a hill, water behind a dam)
Stored energy
What is kinetic energy?
Energy of motion
Photosynthetic organisms harvest energy in sunlight
- power synthesis of organic compounds from ______
- converts kinetic energy of _____ to potential energy of ____
CO2
photons, chemical bonds
_______ obtain energy from organic compounds
Chemoorganotrophs
Chemoorganotrophs depend on activities of ______
Chemolithoautotrophs
What is free energy?
Energy available to do work
- released when a chemical bond is broken
What is exergonic reactions
When reactants have more free energy than products
Is energy released in exergonic reactions?
yes
Endergonic reactions
Products have more free energy than reactants
In an endergonic reaction, the reaction requires what?
An input of energy
Change in free energy is the ______ regardless of number of steps involved
Same
Cells use multiple steps when _________ compounds
degrading
Energy released from _____ reactions power ______ reactions
Exergonic, endergonic
Metabolic pathway
Series of reactions that converts starting compounds to a product
Metabolic pathways may be….
Linear, branched, cyclical
What is the role of biological catalysts
Speeds up conversion of substrate into a product by LOWERING activation energy
What is ATP long form
Adenosine triphosphate
What is ATP
Energy currency of a cell
What is ATP composed of?
Ribose, adenine, three phosphate groups
Cells use energy to produce ATP by adding Pi to what?
Adenosine disphosphate (ADP)
How is energy released in a metabolic pathway?
removing Pi from ATP to yield ADP
What is substrate level phosphorylation?
energy generated in exergonic reactions
What process do some bacteria, especially steptococci, get their energy from?
Substrate-level phosphorylation
What is oxidative phosphorylation
Energy generated by proton motive force
What type of organisms use substrate level phosphorylation and oxidative phosphorylation
Chemoogranotrophs
What is photophosphorylation?
Sunlight used to create proton motive force
What type of organisms use photophosphorylation?
Photosynthetic organisms
What is an electron that has a low affinity for electrons called
energy source
What is a molecule that has a high affinity for electrons called
Terminal electron acceptor
How is energy release in terms of affinity?
electrons move from a molecule that has a low affinity to a molecule that has a high affinity
AKA energy source to terminal electron acceptors
More energy is released when the difference in ______ is greater
Electronegativity
Electronegativity is the same as ______
Affinity for electrons
Prokaryotes use diverse energy sources and ______
terminal electron acceptors
In prokaryotes, what compounds are used as energy soruce?
inorganic compounds
In prokaryotes, what compounds are used as terminal electron acceptors?
O2 and other moecuels
Electrons are removed through what process?
Redox reactions
Substances that loses electrons is ______
Oxidized
Substances that gains electrons is ______
Reduced
______ is transferred in a redox reaction
Electron proton pair or hydrogen atoms
What is dehydrogenation?
oxidation
What is hydrogenation?
Reduction
Electrons are initially transferred to what?
electron carriers
What are common electron carriers?
NAD/NADH, NADP/NADPH, FAD/FADH2
Reduced electron carriers represent what power?
Reducing
What is the role of reduced electron carriers?
Easily transfer electrons to chemicals with HIGHER affinity for electrons/electronegativity
Raise energy level of recipient molecules
drive synthesis of ATP or biosynthesis
What occurs in central metabolic pathways?
Oxidized glucose molecules generate ATP, reducing power (NADH, FADH2 and NADPH) and precursor metabolites
Transferring the electrons carried by NADH and FADH2 to the terminal electron acceptor which is done by either ________ or ________
cellular respiration or fermentation
What do central metabolic pathways do?
Oxidize glucose to CO2
The catabolic, but precursor metabolites and reducing power can be also used in biosynthesis
- this means it is called ________ because of dual role
Amphibolic
What does glycolysis do?
Splits glucose to two pyruvate molecules
What does glycolysis generate?
ATP, reducing power, precursors
What is the role of pentose phosphate patway?
production precursor metabolites, NADH
What does tricarboxylic acid (TCA) cycle do?
Oxidizes pyruvate, release CO2
What does TCA cycle generate?
Reducing power, precursor metabolites, ATP
What process transfers electrons from glucose to ETC to terminal electron acceptor?
Cellular respiration
What does electron transport chain generate?
proton motive forces
In aerobic respiration, what is the terminal electron acceptor?
O2
In anaerobic respiration, what is the terminal electron acceptor?
Molecule other than O2
Anaerobic respiration is a modified version of what?
TCA cycles
What does fermentation do?
recycles electron carriers in a cell that cannot respire so that it can continue to make ATP
What is the terminal electron acceptor in fermentation process?
Pyruvate or derivate
- receives H from NADH
Fermentation regenerates NAD so that
glycolysis can continue
What does glycolysis provide
small amount of ATP
What are enzymes and what do they do?
biological catalysts, increase the rate of a reaction
enzymes are highly specific ________
enzymes are not changed by a reaction so a single molecules can be used ________
substrates
again and again
________ on surface of enzymes binds substrates weakly
active site
What does the enzyme fitting in an active sit result in?
enzyme substrate complex that destabilizes existing bond or allows new ones to form
What does the enzyme substrate complex do to the activation energy?
lowers in
enzyme- catalyzed reactions are ________
reversible
- but free energy of some reactions prevents reversibility
What assists different enzymes?
cofactors
What are common cofactors?
magnesium, zinc, copper
What are coenzymes
Organic cofactors
What are examples of coenzymes
electron carriers FAD, NAD, NADP
-derived from enzymes
What are environmental factors that influence enzyme activity
Temp, pH, salt concentration
What happens to proteins at high temperatures?
They denature
What is the optimum condition for most enzymes?
Low salt, neutral pH
What does 10 degrees celsius increase do to the speed of enzyme reaction?
Doubles speed
What is allosteric regulation?
enzyme activity controlled by regulatory molecules binding to allosteric site
What does allosteric regulation do the the enzyme shape and binding of substrate to active site?
Distorts enzyme shape
Prevents or enhances binding of substrate
What is the regulatory molecule in a metabolic pathway?
The end product that allows feedback inhibition
What is competitive inhibition?
When the inhibitor binds to the active site
The chemical structure of inhibitor is similar to what?
Substrate
What happens in non-competitive inhibition?
inhibitor binds to a site other than the active site
In which non competitive inhibitor is the action reversible?
Allosteric inhibitors
Some are not reversible
Mercery oxidizes the S-H groups of amino acid cysteine and converts to ______
Cystine
- cystine cannot form important S-S bond, so enzyme changes shape and becomes nonfunctional
What do the central metabolic pathways generate?
ATP, reducing power NADH, NADPH, precursor metabolites
Glucose molecules can be completely oxidized to CO2 which does what?
Generates maximum ATP
Glucose molecules can bo siphoned off as ________ for use in biosynthesis
How much ATP does it produce?
Precursor metabolite
It won’t produce maximum ATP
What does glycolysis generate?
2 ATP by substrate level phosphorylation
2 NADH
2 H
6 different precursor metabolites
What does the pentose Phosphate Cycle generate?
NADPH
H
2 different precursor metabolites
What does the transition step repeated twice do?
oxidizes two molecules of pyruvate to acetyl -CoA
What does the transition step generate?
2 NADH
2H
1 precursor metabolite
What does the TCA cycle, repeated twice do?
incorporates two acetyl groups
What does the TCA cycle generate?
2 ATP by substrate level phosphorylation
6 NADH
6 H
2 FADH2
2 different precursor metabolites
Glycolysis converts what to what?
1 glucose to 2 pyruvates
net yield: 2 ATP, NADH
What happens in the investment phase of glycolysis?
2 ATP consumed
2 phosphate groups added
Glucose split to two 3-carbon molecules
What happens in the pay-off phase of glycolysis?
3-carbon molecules converted to pyruvate
generates 4 ATP, 2 NAD
What does the pentose phosphate pathway do?
Breaks down glucose?
What is pentose phosphate pathway important for?
biosynthesis for precursor metabolites
What are the precursor metabolites in pentose phosphate pathway?
Ribose 5-phosphate
erythrose 4-phosphate
What does pentose phosphate pathway generate variable amounts of?
NADPH
What is the product of pentose phosphate pathway
Glyceraldehyde-3-phosphate can enter glycolysis
What happens in the transition step ?
CO2 is removed from pyruvate
Electrons transfer to NAD ruding it to NADH and H
What happens with the 2-carbon acetyl group in the transition step?
joins coenzyme A to form Acetyl- CoA
- links previous pathways to TCA cycles
What does TCA cycle stand for?
Tricarboxylic Acid cycle
What does the TCA cycle do?
Completes oxidation of glucose
What does TCA cycle produce?
2 CO2
2 ATP
6 NADH
2FADH2
Precursor metabolites
What does oxidative phosphorylation do?
Uses reducing power (NADH, FADH2) generated by glycolysis, transition step, TCA cycle to syntehsize ATP
What are the two processes in oxidative phosphorylation?
- Electron transport chain uses reducing power of NADh, FADH2 to generate proton motive force
- ATP synthase uses energy of proton motive force to generate ATP
Who developed the oxidative phosphorylation process?
Peter Mitchell in 1961
Peter Mitchell received a Nobel Prize in 1978 for what?
Chemiosmotic theory
What is the electron transport chain?
series of membrane-embedded electrons carrier
What does the ETC accept electrons from?
NADH, FADH2
In ETC, energy released as ______ are passed from one carrier to the next
electrons
in ETC, energy pumps _______ across membrane
Protons
What is the membrane that protons are pumped across in prokaryotes?
Cytoplasmic membrane
What is the membrane that protons are pumped across in prokaryotes?
Inner mitochondrial membrane
ETC creates an electrochemical gradient called
Proton motive force
What are quinones
what do they do
Lipid-soluble; move freely in membrane
can transfer electrons between complexes
What do cytochromes contain?
Heme, molecule with iron atom
several types, can be used to distinguish bacteria
What are flavorpteins
Proteins to which a flavin is attached
FAD, other flavins synthesized from RIBOFLAVIN
Mechanism of proton pumps
- some carriers accept only _______
- some carriers accept only _______
Hydrogen atoms (proton-electron pairds)
electrons
In proton pumps, _______ arrangement in membrane shuttles protons outside of membrane
Spatial
In a proton pump, when hydrogen carriers ACCEPTS electron from electron carrier, it does what?
picks up proton from inside cell
In a proton pump, when hydrogen carrier PASSES electrons to electron carrier, it does whata?
protons are released to outside of cell
What is the net effect in a proton pump?
movement of protons across membrane
What is the ETC like of prokaryotes/
Variation, single species can have several alternate carriers
in aerobic respiration in E. coli can use 2 different _______
NADH dehydrogenases
In aerobic respiration of E. coli, _______ is equivalent to complex I of mitochondria
Proton pump
In aerobic respiration of E. coli, _______ is equivalent to complex II of mitochondria
Succinate dehydrogenase
In aerobic respiration of E.Coli, ther is a lack of equivalents for In aerobic respiration of E. coli, _______ is equivalent to complex I of mitochondria
Complex III or cytochrome c
In aerobic respiration in E.Coli, _______ shuttle electrons directly to functional equivalent of complex IV
Quinones
which harvests less energy, anaerobic respiration or aerobic respiration in E.Coli?
Anaerobic
Anaerobic respiration in E. Coli can synthesize terminal _______ that uses NITRATE as terminal electron acceptor
oxidoreductase
What does terminal oxidoreductase produce?
nitrite
E.coli converts nitrite to what?
less toxic ammonia
Selfate reducers use what as terminal electron acceptors?
SO24, sulfate
What do sulfate reducers produce as end product?
Hydrogen sulfide
what is the ATP yield of aerobic respiration in prokaryotes for substrate level phosphorylation?
2 ATP (from glycolysis; net gain)
2 ATP from TCA cycle
4 ATP TOTAL
What is the ATP yield of aerobic respiration in prokaryotes for oxidative phosphorylation?
6 ATP from reducing power gained in glycolysis
6 ATP from reducing power gained in transition step
22 ATP from reducing power gained in TCA cycle
34 ATP total
What is the total ATP gain in aerobic respiration for prokaryotes?
38 ATP
When is fermentation used?
When respiration is not an option/ when the cell doesn’t have an ETC
What type of of bacteria is E. Coli?
Facultative anaerobe
What does streptoccus pneumoniae lack?
ETC
What must strep. pneumoniae use for respiration?
fermentation
ATP generating reactions are only those of _______
Glycolysis
microbes other than glucose can secrete _______, transport subunits into a cell, degrade into _______
Enzymes, precursor metabolites
_______ and _______ are broken down by amylases, cellulases, disaccharides
Polysaccharides and disaccharides
for polysaccharides and disaccharides, _______ enters glycolysis directly, other _______ convert to precursor metabolites
glucose, monosaccharides
for lipids broken down my lipases, _______ converts to _______ and enters glycolysis
Glycerol, dihydroxyacetone phosphate
for lipids, fatty acids are degraded by _______ to enter _______ phase
B-oxidation, TCA cycle
Proteins are broken down by
Proteases
For proteins, amino group is _______
_______ convert to precursor metabolites
Deaminated
carbon skeletons
What are chemolithotrophs?
Prokaryotes who can use reduced inorganic compounds as energy sources
Hydrogen sulfide and ammonia are produced by _______ respiration when _______ molecules serve as terminal electron acceptors
Anaerobic respiration, inorganic
Hydrogen sulfide and ammonia are used as energy sources for _______ and _______
Sulfur bacteria and nitrifying bacteria
hydrogen bacteria can also use _______ compounds for energy
simple organic
Sulfur bacteria can live at a pH of _______
less than 1
iron bacteria have _______ in their sheaths
Iron oxide
Nitrifying bacteria are important in the _______ cycle
Nitrogen
prokaryotes similar in biosynthesis processes synthesize subunits using precursor metabolites formed in _______ pathways
central metabolic pathways
If enzymes are lacking, end product must be supplies
- _______ bacteria require many growth factors
Fastidious
Lipid synthesis requires _______ and _______
Fatty acids and glycerol
What are fatty acids made of?
2 carbon units added to acetyl group from acetyl-CoA
- usually 14, 16, 18 carbons
What is glycerol synthesized from?
Dihydroxyacetone phosphate generated during glycolysis
Synthesis of _______ provides mechanism for incorporation of nitrogen into organic material
Glutamate
what is commonly used via glutamate synthesis?
Ammonium
_______ can generate other amino acids in amino acid synthesis
Transamination
Aromatic amino acids: branching pathway
- precursors form _______ compound that enters branching pathway
- amino acids are _______ inhibitors of enzymes that directs branch to its own synthesis
- Amino acids also inhibit formation of _______
- Result is _______
7-carbon
feedback
original 7-carbon
cell does not make amino acids that are already present
in nucleotide synthesis, DNA, RNA are initially synthesized as _______
Ribonucleotides
What are purines?
Atoms added to ribose 5-phosphate to form ring
What are pyrimidines?
Ring made than attached to ribose 5-phosphate
