3.1 Metabolism and energetics Flashcards
what are the 2 functions that all cells have regarding metabolism and energetics?
- genetic function (DNA, transcription, translation, replication)
- catalytic function (enzymes, energy conservation, synthesis of macromolecules)
METABOLISM; microorganisms must to what for survival, growth and replication?
- define anabolism vs catabolism. reducing/oxidizing power from what?
microorgs must be able to use the nutrients available from their environment to produce all the macromolecules and chemicals required for survival, growth and replication
ANABOLISM:
- production of macromolecules and chemicals from “building blocks” and energy (ATP)
- reducing power provided by NAD(P)H + H+
CATBOLISM:
- generation of energy (ATP) and reducing power (NAD(P)H + H+) by breaking down large molecules into smaller ones
- byproducts of catabolism may be used as precursor molecules for anabolism (“waste” = building blocks)
is e.coli gram positive or negative?
gram negative!
which elements from the periodic table are essential for all microorgs? (7)
- which trace metals are essential?
- metabolism of most nutrients (3) is relatively simple –> explain
- in contrast, sources of _______ and ______usually what?
- hydrogen, carbon (50%), nitrogen, oxygen, phosphate, sulfur, selenium
- iron! cobalt, nickel, copper, zinc, manganese…
- N, S and P –> relatively simple –> slight modifications are needed before incorporation into cellular material
- sources of carbon and energy usually undergo many transformations
- what is the difference btw chemoorganotrophs vs chemolithotrophs?
- difference between defined culture medium and complex culture medium?
CHEMOORGANOTROPHS:
- use organic source of carbon (ie glucose) for energy and electrons
CHEMOLITHOTROPH:
- do not use organic carbon as carbon/energy source –> can use CO2 from air as carbon source + sulfur are E source
DEFINED CULTURE MEDIUM:
- you know exactly what you’re putting in the medium (ie how many grams of each specific aa)
- can be very different based on species: ie E.coli can make everything from scratch VS leuconostoc mesenteroides = very fastidious: needs all the aa, and purines, etc.
COMPLEX CULTURE MEDIUM
- not well defined: don’t know exactly what’s in it, but know that both E.coli and L. Mesenteroides can grow in it
- ie yeast extract (you don’t know exactly which aa, purines and how much are in there), peptone…
anabolism or catabolism?
- ATP –> ADP + Pi
- NAD(P)+ –> NAD(P)H + H+
- ADP + Pi –> ATP
- NAD(P)H + H+ –> NAD(P)+
- anabolism
- catabolism
- catabolism
- anabolism
define:
- activation energy
- catalyst
- enzyme
- exergonic vs endergonic
*positive or negative free energy
*anabolism or catabolism?
ACTIVATION ENERGY:
- energy needed to put all molecules in a reactive state
CATALYST:
- substance that lowers the activation energy. does not affect the free energy (delta H), affects the rate
ENZYME:
- biological catalyst –> protein catalyst that decreases activation E
EXERGONIC:
- releases energy (negative free energy/delta H)
- products have lower E level than reactants
- catabolism
ENDERGONIC:
- absorbs energy (positive free energy)
- products have higher E level than reactants
- anabolism
oxidation vs reduction –> remove or add electrons?
- can involve what?
- redox reactions occur in ______ WHY?
OXIDATION: removal of electrons
REDUCTION: addition of electrons
leo the lion says ger
lose e- oxidation, give e- reduction
- can involve just e- or and e- and a proton (H+)
- redox rxns occur in pairs bc electrons cannot exist in solution –> oxidation of one substance is linked to the reduction of another substance –> always in pairs!
2 H+ / H2
- which is oxidized form vs reduced form?
- electron donor/acceptor = E source
- the chemical rxn in which e- donor and e- acceptor participate _________ energy –> what is important?
2H+ = oxidized form
H2 = reduced form
- donor = energy source
- releases energy –> difference btw donor and acceptor is important!
*the more space between the substances (on the tower), the more energy can be produced!
NAD+ vs NADH + H+
- which is oxidized form vs reduced form?
- what is an electron carrier?
- NAD+ = oxidized form
- NADH + H+ = reduced form –> gained electrons
- electron carrier = brings e- to dif places!
ie pink substrate gives e- to NAD+ through enzyme 1 –> produces NADH and oxidized pink substrate –> than, NADH gives e- to green substrate (electron acceptor) through enzyme 2 –> green substance is than reduced (bc accepted e-)
give examples of 5 energy-rich compounds and what makes the compound energy rich?
- adenosine triphosphate (ATP) –> E in anhydride bonds (btw phosphate groups) + ester bond
- glucose-6-P: ester bond
- phosphoenolpyruvate: anhydride bond
- acetyl phosphate: anhydride bond
- acetyl-coA: thioester bond (btw C of Acetyl and S of coA)
REVIEW:
1. how many rings in flagellum of gram positive vs gram negative bacteria?
2. mechanism of assembly of fimbriae/pilli in gram negative vs gram positive?
3. function of cell inclusions?
4. purpose of endospore? metabolically active?
5. name of picky organisms that need specific nutrients?
6. function of redox tower ish?
- gram pos = 3, gram neg = 4
- gram neg: chaperone and usher, attach fimbriae to outer membrane + strand exchange VS gram pos: sortase, attach subunit to peptidoglycan layer and to each other using covalent bond
- keep what you want inside the cell
- survival vessel, holds DNA in proper state for long term storage in harsh conditions –> NOT metabolically active
- fastidious organisms
- generate energy by stripping electron from substance high on the tower (ie glu) and give electron to substance very low on tower
in most organisms (what type?), 3 basic anabolic/catabolic pathways are all that is required to produce all of the precursors needed for anabolism/catabolism (2)
- name the 3
- what are the 2 series of reactions? explain
- in chemoorganotrophs, 3 basic catabolic pathways –> needed for anabolism (carbon compounds and energy)
a) glycolytic pathways: glycolysis or embden-meyerhof pathway
b) pentose phosphate pathway (hexose monophosphate pathway)
c) tricarboxylic acid pathway (TCA, citric acid cycle, Krebs cycle)
1) fermentation: organic compounds are electron donors and electron acceptors –> ATP is produced by substrate level phosphorylation
*less energetic than 2)
2) respiration: organic compounds are oxidized to CO2 with O2 (or substitue) as electron acceptor –> MOST of the ATP is produced by oxidative phosphorylation
*using proton motive force!
- what is another name for the most common glycolysis pathway?
- WHAT is oxidized/reduced into WHAT (very general)
- net yield?
- ATP is produced by which pathway ish?
- Embden-Meyerhof-Parnas EMP
- 1 glucose (6C) oxidized to yield 2 pyruvate (2 x 3C)
- net yield: 2 ATP + 2 NADH + H+
*use 2 ATP in investment phase and yield 4 ATP in payoff phase - ATP is produced by substrate level phosphorylation
FATE of PYRUVATE
- during _________, pyruvate can be fully oxidized/reduced to (2)
- what is the first reaction ish? –> then the product goes through which pathway, and becomes what?
- what are the end products of TCA cycle?
- during respiration –> pyruvate fully oxidized to CO2 and H2O
- pyruvate is first oxidized to acetyl-coA and Co2 by pyruvate dehydrogenase complex
- Acetyl-CoA is then fed into the TCA cycle which fully oxidizes acetyl-coA into CO2!
- what is the main purpose ish of the TCA cycle?
- what can GTP do? (2)
- what is another role of the TCA cycle? Name?
- what must be regenerated,? otherwise the TCA cycle will stop?
- fully oxidize acetyl-CoA into CO2 (ie strip e- from acetyl group) AND produce NADH & FADH2 and GTP (via substrate level phosphorylation)
- GTP can be used to phosphorylate ADP to produce ATP and GDP AND can also be used for some anabolic reactions
- intermediates of the TCA cycles are used as substrate for anabolic reactions (ie to make amino acids!) –> ANAPLEROTIC pathways = pathways that feed the TCA cycle with intermediates
- some microorgs can also use aa and feed them into the TCA cycle, to burn them as energy
- oxaloacetate must be regenerated
- what are the net products of 1 turn of the TCA cycle, from the complete oxidation of ____________
- what about the net products of pyruvate conversion to acetyl-coa?
- how do NADH and FADH2 participate in respiration? explain
- compared aerobic and anaerobic respiration (who is the terminal e- acceptor)
- process that uses energy produced by respiration to synthesize ATP is called what?
- 2 CO2 + 1 GTP/ATP + 3 NADH+H+ + 1 FADH2
- 1 more NADH+H+ and 1 CO2
- oxidation of NADH+H+ and FADH2 (lower on the tower) is coupled to the reduction of a terminal electron acceptor = respiration –> E released is used to drive synthesis of ATP
AEROBIC: O2 is the terminal e- acceptor
ANAEROBIC: other compounds act as terminal e- acceptors, under anoxic conditions
- oxidative phosphorylation
- describe the respiratory chain
- the electron transport chain is organized in which specific order?
- explain the 4 steps of NADH+H+ to the final e- acceptor ish in terms of electron/hydrogen carriers
- series of hydrogen and electron carriers that can undergo oxidation-reduction
- from high energy to lower energy
- when a reduced substrate is oxidized (NADH+H+), the hydrogens are transferred to a hydrogen carrier (FMN) –> hydrogens are then transferred to the next carrier in the sequence
- if the next carrier is an e- carrier, only the e- will be accepted and the protons will be released to the outer phase
- VS if the next carrier is a hydrogen carrier, 2 protons must be taken from the inner phase
- in the final steps, 2 e- and 2 protons form the inner phase are used to reduce oxygen to water –> o2 is the final e- acceptor
do all organisms pump the same number of protons in the ETC?
NO! DIFFERENCES IN THE respiratory chain result in less protons being pumped out
- ie in E.coli, only 8 protons per NADH+H+ and 4 protons per succinate, bc of different cytochromes
- proton motive force is generated as a result of what?
- pmf is used to do what?
- synthesis of ATP using pmf is called what?
- how many protons are necessary to phosphorylate 1 ADP to ATP?
- what are the 2 forces at play to maintain the pmf?
- respiration results in the generation of a transmembrane proton gradient, a potential source of energy, called the proton motive force
- used to drive other energy requiring reactions: flagellum rotation (in bacteria), transport across membrane and synthesis of ATP
- 3-4 protons -> so 1 NADH pumps 10 protons = 3 ATP ish
- membrane potential (difference in charge) and transmembrane pH gradient (concentration of protons)
what is the net yield of energy from respiration?
GLYCOLYSIS
TRANSITION
KREBS
TOTAL
GLYCOLYSIS
- 2 NADH –> 6 ATP
- 2 ATP
- TOTAL = 8 ATP
TRANSITION
- 2 x 1 NADH = 6 ATP
- TOTAL 6 ATP
KREBS
- 2 x 3 NADH = 18 ATP
- 2 x 1 FADH2 = 4 ATP
- 2 x 1 GTP/ATP = 2 ATP
- TOTAL 24 ATP
TOTAL: 38 ATP
how can cyanide, carbon monoxide and rotenone act as poisons and potentially kill you?
they targe electron transport chain!
CYANIDE: targets complex 4, blocking the chain –> all cells stop respiration = you die quickly
CARBON MONOXIDE: stops O2 transport by erythrocyte –> no more O2 = no more respiration –> slower death
ROTENONE: targets complex 1 –> used as piscicide and insecticide
- if no terminal electron acceptor is available, what happens?
- does glycolytic pathway still function in fermentation?
- in fermentation, what serves as e- donor vs final acceptor of e-
- succinate cannot be oxidized by succinate dehydrogenase in the respiratory chain
- can still function, provided that the NADH+H+ can be oxidized back to NAD+
*bc usually during aerobic respiration, glycolysis and TCA cycle convert NAD+ to NADH –> ETC converts NADH back to NAD+
BUT when no O2, NADH accumulates bc no respiration –> so fermentation allows to convert the NADH back to NAD+ (ie by converting acetaldehyde to ethanol) - an organic compound serves as the electron donor and an organic degradation product serves as the final acceptor of e-
does yeast grow faster with O2 or without O2? explain
in yeast, production of ethanol and CO2 is inversely proportional to the concentration of O2. (??)
- in the absence of O2, yeast population grows very slowly bc fermentation yields only a fraction of ATP produced by respiration
compare max yield of ATP molecules from
AEROBIC RESPIRATION
ANAEROBIC RESPIRATION
FERMENTATION
+ give example of bacteria
+ what is the final e- acceptor?
AEROBIC RESPIRATION
- 1 glu = 2 + 2 + 34 = 38
- staphylococcus aureus
- O2
ANAEROBIC RESPIRATION
- 2 (glycolysis) + 2 (krebs) + 1 to 32 (electron transport + oxidative phosphorylation) = btw 5 and 36
*depending on which e- acceptor is used! the lower it is on the tower, the better!
- Paracoccus denitrificans
- S^0, NO3-, SO4^2-, Fe3+, organic e- acceptors, other inorganics
FERMENTATION
- 2 (glycolysis) + 0 from fermentation = 2 ATP
- Candida albicans
- final e- acceptor = organics (usually pyruvate)
all chemoorganotrophs, whether they do fermentation or respiration, use the _______ ________ pathway
- happens where?
- what is the important molecule? used as what?
- how is that molecule produced? (2)
- what is the end-product of this pathway? can be used for what (2)
PENTOSE PHOSPHATE PATHWAY!
- in cytoplasm (for both prokaryotes and eukaryotes)
- NADPH+H+! –> in most anabolic reactions, is used as the source of reducing power (to harvest electrons!)
- most cells can convert NADH into NADPH BUT most NADPH is produced by the PPP
- ribose 5-P –> may be used to produce ribose (and later, deoxyribose) and is a substrate for many anabolic pathways (ie to make DNA/RNA)
for eukaryotes:
- where are the enzymes for glycolysis, TCA cycle, respiratory chain, fermentation and PPP?
vs prokaryotes?
EUKARYOTES:
- TCA cycle and respiratory chain –> enzymes in mitochondria
- glycolysis and fermentation –> enzymes in cytoplasm
PPP occurs in cytoplasm in both prokaryotes and eukaryotes
PROKARYOTES: everything in cytoplasm bc no compartments
what can freely pass through cytoplasmic membrane? what cannot pass?
- how can molecules that are not permeable be transported across the membrane?
- water! can freely pass in both directions bc water is small and weakly polar –> rate of simple diffusion = 100
- bc glycerol = 0.1 = good
tryptophan & glucose = 0.001 = fair - sodium = 0.00000001 = extremely poor –> bc charged!
- through transmembrane (integral) proteins!
what are the 2 main types of transport events? describe. first one has 2 sub
for the first one: compare charged vs uncharged substrates
PASSIVE TRANSPORT:
a) SIMPLE DIFFUSION:
- crosses the membrane without channel
b) FACILITATED DIFFUSION
- transports using a porin/channel
- only transport solutes down a gradient (from high to low concentration)
- for uncharged substrates, concentration gradient alone will determine direction of flow
VS for charges substrates, charge AND concentration gradient (electrochemical gradient) determines direction of flow
ACTIVE TRANSPORT
- can transport solutes against the concentration (or electrochemical) gradient
*cells need to concentrate building blocks and energy-rich molecules
- needs energy!
what are 3 characteristics of transport systems? explain
- how do cells usually acquire nutrients:
a) multicellular orgs
b) vs unicellular orgs (bacteria, archaea and eukarya)
- saturable! rate of uptake becomes maximal and addition of more substrate does not increase the rate! –> theres a finite number of channels and speed is not unlimited
*rate of solute entry is much faster than simple diffusion! - specific! transport single molecule or a class/category of closely related molecules
- biosynthesis of transport systems are highly regulated by the cell (ie will make glu transporter if there is glu)
a) cells usually acquire nutrients by means of diffusion or facilitated diffusion (bc lots of nutrients in blood/plasma)
b) nutrients are usually acquired by active transport (bc live in a bad environment)
what are 2 types of channels for facilitated diffusion? explain
CHANNEL-mediated
- “pore/hole” in membrane
- specificity is relatively low –> whatever small enough can go
- can be closed by the cell (gated channel)
- no energy required
CARRIER-mediated:
- binding of the substrate on 1 side of the membrane induces conformational change in the carrier
- substrate is released on th eother side
- tends to be more specific than channel mediated diffusion –> only passes through if can bind to transporter
- no energy required
what are 3 types of active transport?
- which 2 are found in bacteria and archaea?
- simple transport –> ie proton motive force
- group translocation: substrate is modified: ie transfer of P group while passing through the channel
- ATP-binding cassette (ATP)
2 and 3 (but also 1…)
what are 3 types of simple transport?
- uniporter: only 1 molecule passes through in 1 direction
- symporter: 2 different molecules pass through same direction
- antiporter: one goes 1 way, and the other goes the other way
pmf dependent transport - bacteria and archaea
- under conditions where respiration is possible, what is present, so ___A_____ is generated?
- when respiration is not possible, ________ can be used to generate ___A_____ –> these are ____________
- pmf dependent transporters are ______a_____ or ____b_____ that use the __________ _________ –> give examples of a) and b)
- these transport systems are common in which organisms?
- terminal electron acceptor is present –> proton motive force is generated
- ATPases can be used to generate pmf –> burn ATP to pump proton out to make pmf! –> ATPases are reversible
*in both cases, pump H+ out = creates a pmf - symporters or antiporters that use the proton gradient
a) symporter: use proton gradient to bring H+ and X inside the cell!
b) pmf can be used to generate a gradient of Na+ –> used as source of E! (use pmf to pump sodium out (Na+-H+ antiporter) and use [sodium] to power a Na+-X symporter!) - Na+-dependent transport systems are common in marine organisms! bc live in salt water
for each substrate, name the transport mechanism, the net charge and the driving force!
for H+ transporter:
a) Cation (ie K+)
b) anion (ie sulfate)
c) X (neutral) (ie lactose)
for Na+ transporter:
a) anion (ie glutamate)
b) X (neutral) (ie melobiose)
for H+ transporter:
a) Cation (ie K+)
- cation uniporter, + net charge
- membrane potential!
b) anion (ie sulfate)
- proton-anion symporter, 0 charge
- proton gradient!
c) X (neutral) (ie lactose)
- proton-X symporter, + charge
- both membrane potential and proton gradient
for Na+ transporter:
a) anion (ie glutamate)
- Na+-anion symporter, 0 charge
- sodium gradient
b) X (neutral) (ie melobiose)
- Na+-X symporter, + charge
- membrane potential + sodium gradient
name the net charge + the energy that drives the transport:
a) POTASSIUM UNIPORTER
b) PHOSPHATE SYMPORTER (with H+)
c) SODIUM-PROTON ANTIPORTER
d) LACTOSE PERMEASE
a) POTASSIUM UNIPORTER
- +1 –> membrane potential
b) PHOSPHATE SYMPORTER (with 2 x H+)
- phosphate = -2, 2 x H+ = +2 –> net charge = 0
- proton gradient!
c) SODIUM-PROTON ANTIPORTER
- net charge = 0
- proton gradient
d) LACTOSE PERMEASE
- lactose = 0, H+ = 1 –> +1
- both membrane potential and proton gradient!
REVIEW:
- purpose of pentose phosphate pathway?
- purpose of fermentation?
- PPP: produce NADPH = reducing power used to anabolism!
- fermentation: regenerate pool of NAD+ when there are no final electron acceptor around
- what is an ABC transporter?
- what are the 3 components of ABC transporters? + functions
- how can substrate pass through? even at _____ concentrations
- where is the binding protein for gram-neg vs gram-pos?
- ATP binding cassette –> powered by ATP!
1. membrane spanning protein –> active transport carrier
2. ATP hydrolyzing protein (on cytoplasm side) –> provides energy needed for active transport
3. substrate specific binding protein (on periplasm side or “outside”): has very high affinity for a specific substrate - binding protein binds to its substrate and transfers it to the transporter –> binding protein can bind its substrate at very low concentrations: less and 10^-6M
- gram-neg: free in periplasm
- gram-pos: anchored in cytoplasmic membrane
what is the last type of transporter apart from simple transport and ABC transporter?
- describe how it work
- best known? used by who to transport what (3)
group translocation!
- substrate is modified as it passes
through the transporter, across the
membrane.
ie glu can diffuse freely across membrane/out of cell towards lower [ ] (although pretty slow) –> so glu transporter is phosphorylated through the group translocation (gets P from PEP) –> glu becomes glu-6-P = trapped in cell bc charged! (also 1st step of glycolysis) - phosphoenolpyruvate-dependent
sugar phosphotransferase system. - It is used by bacteria to transport
common monosaccharides such as
glucose, fructose and mannose
- where is the pmf in unicellular eukaryotes?
- what is the main transport system ish they use? consequence? –> how?
- describe which type of ATPase + how many H+/ATP for eukaryotes vs prokaryotes vs mitochondria
- in mitochondria!
- H+-substrate symporters are used! –> pmf needs to be created at the level of the cytoplasmic membrane!
- proton-translocating ATPase (P type ATPase) exists in cytoplasmic membrane –> uses ATP to pump protons out
- pmf generated at cytoplasmic membrane can now be used to power symporters in cytoplasmic membrane
EUKARYOTES: P-type ATPase –> 1H+ /ATP hydrolyzed
PROKARYOTES and mitochondria –> F-type ATPase –> 3 H+ /ATP hydrolyzed
what is a transport type that only eukaryotes can do?
- 3 types ish
- what is essential for it?
endocytosis! modify cytoplasmic membrane –> take something from outside to inside
1. phagocytosis: take a really big particle (ie another bacteria), bring it inside your cell
2. pinocytosis: same as 1) but for small molecules like glucose
3. receptor mediated endocytosis: only endocytosis if substance binds to receptor
- actin filaments! change structure of cytoplasmic membrane
