Term
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Definition
*degradation
*nut and cell components broken down to salvage and make E
*complex metab > deg > simp products (make ATP and NADH)
* complex molecules = proteins, polysach, triacylglycerol |
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Term
|
Definition
*synthesis of complex molecules from simple
*simple products > biosynth > complex metabolites(generate NADP, use ATP -> ADP) |
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Term
| Locations of Metabolic Pathways |
|
Definition
CYTOSOL
*glycolysis
MITO
*CAC, ETC, Ox Phosp |
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Term
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Definition
*organs manage certain metabolic processes & can prod isozyme to use in metab process
LIVER: gluconeogen
ADIPOSES: store triacylglycerol |
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Term
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Definition
*different genes that create an enz that is similar to another enz in body but is organ specific
*can have own kinetic/ regulatory properties
*organ specific
EX: lactate dehydrogenase
M type in anarobic
H type in aerobic |
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Term
|
Definition
1) Which metabolic process
2) Which enz
3) Which cell compart
4) Which tissue
5) Which direction (relies on thermodyn) |
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Term
| Thermodynamics in Metabolism |
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Definition
RXN W/ REACTANTS PRESENT CLOSE TO EQUILIBRIUM
RXN W/ REACTANTS FAR FROM EQUIL |
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Term
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Definition
*changes in enz alter reaction rate
*binding of some other molecule to a place that is not the catalytic site |
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Term
| RXN W/ REACTANTS PRESENT CLOSE TO EQUILIBRIUM |
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Definition
*^G close to 0
*conc dependent rxns
*can go in either direction b/c close to equilibrium (easily revers)
*lot of react -> product, vise versa
*faster
*dependent on [S], [P] |
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Term
|
Definition
*rxns have enz w/ insufficient catalytic activity -> rxn rate slow -> accumulation of rreactants
*drives rxn in one direction so ^G<0
*energetically favorable
*irrevrsible rxns, foward direction
*changes in [substrate] have little effect (b/c so little enz that its sat at all conc)
*can have changes in enz
*enz act like dams b/c control subs flow |
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Term
| Glycolysis Free E Diagram |
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Definition
*glucose to Pyruvate
*large - Free E change help drive rxn foward
*free E changes has large drop offs (drive rate of flow through the process)
Hexonkinase- far from equil, slow rxn rate but spont (b/c lots gluc), lrg ^G
PFK- slow moving, lrg ^G
PK |
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Term
|
Definition
*rate of flow of metabolites through metab process
*need to know rxn near equil & which far
*most enx operate near, some far
*vf-vr
*set by rate determining step |
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Term
| Implication of Far from equil enz |
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Definition
1)Metabolic paths irreversible
- b/c lrg - ^G
-highly exergonic, goes to complete
-confer directionalty
-NO EQUIL - death b/c nothing processing
2)Every metabolic path has a first committed step
-glucose - gluc 6 (comits glgucose to go through series of rxn)
3) Differences in catabolic and anabolic paths
-metabolite converts to another metab by exergonic path, if need to convert back need free E
- 1 -> 2 (exergonic), 2-> 1 (require E)
-can take alternative routes (E more favorable) |
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Term
|
Definition
*open systems
*flux of intermediates through a path w/ steady, constat state
*take in nut, process, and release products |
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Term
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Definition
*product removed quickly by other steps after it b4 it can equilibrate w/ reactant
*far from equilibrium, and ^G <<0 |
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Term
| Altering Rate Determing Step |
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Definition
*alters flux of material through the entire pathway
*allows cells to control flux |
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Term
|
Definition
ALLOSTERIC CONTROL
COVALENT MODIFICATION
SUBSTARTE CYCLE
GENETIC CONTROL |
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Term
|
Definition
ALLOSTERIC CONTROL
-negative feedback regulation
- product binds somewhere on enz and changes shape of enz to affect catlytic site to prevent A->B |
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Term
|
Definition
*take enz and add covalent modification
*like phosphorylation, changes rate of rxn |
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Term
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Definition
*w/in rxn syst, have two enz(vf,vr) that are independently regulated
*vf & vr represented by 2 opposing non-equilibrium rxn catalyzed by diff enz
*if one speeds up/ slow down, effects other
*one enz take forward, other reverse |
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Term
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Definition
*if dont synth enz/ protein b/c genetics (silence of transcrip/lation)
*to make prot, cell needs to tramscribe gene into mRNA
*genes DNA must correct seq and regulatory seq must be present |
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Term
|
Definition
ANAEROBIC
1) ATP: used quick and recycled
2) PHOSPHOCREATINE: stores E, less quick (sprint)
3) GLYCOLYSIS: longer E (swim)
4) OX PHOS: most E, for more time
AEROBIC
4) OX PHOSP |
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Term
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Definition
E INVESTMENT
1)Hexokinase uses 1st ATP
2)Phosphoglucose Isomerase
3)Phosphofructose uses 2nd ATP
4)Aldolase-6C FBP to 3C GAP & DHAP
5)Triose Phosphate Isomerase (TIM)
E RECOVERY
6)GAPDH Forms 1st "High E" Intermediate
7)Phosphoglycerate Kinase (PGK) Generates 1st ATP
8)Phosphoglycerate Mutase (PGM) Interconverts 3PG & 2PG
9)Enolase Forms 2nd "High E" Intermediate
10) Pyruvate Kinase (PK) Generates 2nd ATP
*step 1 & 3 use E
*steps 7 + 10 recycle back |
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Term
|
Definition
STEP 1
RXN: phosphorylation of sugar
CONVERSION: gluc +ATP ⇌ gluc 6 phosp
ENZ: hexokinase (& Mg)
*glucokinase in liver
*gluc in musc > interact w/ hexokinase & Mg(works w/ ATP) > glucokinase adds phophate > phosp removed and add to gluc 6
*nuc attack cause trasnfer
*w/o Mg = inhibition |
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Term
|
Definition
STEP 2
RXN: isomerization, acid-base catalysis
CONVERSION:
gluc-6-phos(G6P) ⇌ fruct-6-phosp (F6P)
ENZ: phosphoglucose isomerase (PGI)
*enz takes proton and adds back, allows form again
*ring open b/c catalysis then concentrated acid-base catalysis (base then acid)-> transfer protons and closes ring |
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Term
| Phosphofructokinase Uses 2nd ATP |
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Definition
STEP 3
RXN: catalyzation
CONVERSION:
fruct-6-phosop (F6P) + ATP -> fruct-1,6-biphop (FBP)
ENZ: phosphofructokinase (PFK) & Mg
*PFK catalyze nuc atack of C1 OH of F6P (MgATP complex)
*PFK role in controlling glycolysis b/c cstslyzes a rate determin step |
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Term
| Aldolase 6C FBP to 3C GAP & DHAP |
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Definition
STEP 4
RXN: cleavage
CONVERSION:
*fruct-1,6-biphop (FBP) ⇌ dihydroxyacetone phosp (DHAP)
*fruct-1,6-biphop (FBP) ⇌ glycerald-3-phos (GAP)
ENZ: aldolase
*cleavge after C3 forms: 1-3 (DHAP), 4-6 (GAP)
*6C becomes two 3C
*aldolase cut 1/2 |
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Term
| Triose phosphate Isomerase (TIM) |
|
Definition
STEP 5
RXN: catalysis of interconversion
CONVERSION:
glycerald-3-phop(ald) ⇌ [enediol intermediate] ⇌ dihydroxyacetone phosphate
(ket)
ENZ: triose phosphate isomerase (TIM/TPI)
*enz catalyzes interconversion of GAP⇌enediol⇌DHAP
* @ equil, [DHAP] > [GAP]
*GAP rapidly sophoned away, replaced by DHAP
*GAP used right away to so DHAP convert to GAP
*end of Stage 1 |
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Term
| GAPDH Forms 1st "High E" Intermediate |
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Definition
STEP 6
RXN: ald oxidation
CONVERSION:
glyc-3-phosp(GAP) + NAD + Pi ⇌ 1,3 bipshophoglycerate (1,3 BPG)
ENZ: glyc-3-phosp dehydrogenase (GAPDH)
*exergonic (NAD red NADH) drives synth of high E acyl phosp(1,3 BPG)
*GAPDH gene control
*1st high E intermediate (1,3 BPG) |
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Term
| Phosphoglycerate Kinase (PGK) Generates 1st ATP |
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Definition
STEP 7
RXN: substrate level phosphorylation
CONVERSION:
1,3 biphpglycerate (1,3 BPG) + ADP ⇌ 3-phospoglycerate (3PG) + ATP
ENZ: phosphoglycerate kinase (PGK) & Mg
*GAPDH & PGK coupled so rxn forward
*2 phop to 1 phop structure
*1 rxn: ender; 2: exer (coupled rxn) |
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Term
| Phsophoglycerate Mutase (PGM) Interconverts 3PG & 2PG |
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Definition
STEP 8
RXN: catalyzation
CONVERSION:
3-phosphoglycerate (3PG) ⇌ 2-phosphoglycerate (2PG)
ENZ: phosphoglycerate mutase (PGM)
*need higher E interm
*molecule enters enz interact > give phos on C2 takes away on C3
*receives one and gives one away
*phosp His residue
*PG & PGM xchange phosp |
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Term
| Enolase Forms 2nd "High E" Intermediate |
|
Definition
STEP 9
RXN: dehydrogenation
CONVERSION:
2 phosphoglycerate (2PG) ⇌ phosphoenolpyruvate (PEP)
ENZ: enolase |
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Term
| Pyruvate Kinase (PK) Generates 2nd ATP |
|
Definition
STEP 10
RXN: clevage
CONVERSION:
phosphoenolpyruvate (PEP) + ADP -> Pyruvate +ATP
ENZ: pyruvate kinase (PK)
*pyruvate kinase generates ATP
*2 step process, both make ATP
*PK couples free E of PEP cleavage to ATP synth to form pyruvate |
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Term
|
Definition
*Part of Step 6
1) substrate bind
2) active site thiol addition
3) dehydrogenation (oxidation)
4) phosphate binding
5) Product release and NAD/NADH xchange
-becomes 1,3 BPG |
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Term
|
Definition
Part of Step 8
* enz catlyzing the transfer of func group from one positon to another on a molecule |
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Term
|
Definition
* formed as org go through catabolic rxn
*captured free E by org from nut degradation
*compounds like ATP
*subsequent breakdown used to power endergonic rxn
EX: ox metab
*E recovered in packets for for conservation of subsequent endergonic rxn
*molecules @ high E donate phosp to low E (catalyzed by kinase)
*not all ATP (thioester bond acetyl CoA) |
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Term
|
Definition
*high E compound
*related to the large - free E for hydrolysis of phophoanyhydride bonds
ATP + H2O ⇌ ADP + Pi
ATP + H2O ⇌ AMP + PPi
*continually hydrolyzed/regenerated'
*regenerated by coupling formation to exergonic rxn
*formed by subs-level phosp |
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Term
| Nature of E in High E compounds |
|
Definition
1) RESONANCE
PHOSPHOANHYDRIDE BONDS
*resonance stabilization is less than hydrolysis prod (b/c competition of lone pairs)
*more stable as product and more willing to form 2 sep phosphates b/c more stable ind
2) REPULSION
repulsion between charged groups (- O)
3)SOLVATION
destabilizing influence b/c sm solvation E compared to hydrol products (hydrolysis prod > solvation E, more willing to interact w/ water)
*3 things that describe high E nature |
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Term
| Outcome of ATP hydrolysis |
|
Definition
*coupled to endergonic to have favorable net rxn
STEP 1
GLUC -> GLUC 6 phosp = unfavorable
*coupled to ATP + H2O -> ADP + Pi = makes favorable
STEP 10?
PEP ⇌ PYRUVATE |
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Term
|
Definition
*leaves AMP
*when making tRNA
*ATP ⇌ AMP when pyrophosp removed |
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Term
|
Definition
*direct transfer of phosphoryl groups from compounds w/ high phosphoryl group transfer potentials to those w/ low phosphoryl group transfer potentials
*transfer phosp to ATP |
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Term
|
Definition
*high phosporyl group transfer pot lrgly from the competing resonances (guandino vs phosphoryl)
*ATP w/ creatine = phospcreatine + ADP
(costs E, but allows storage in phosphocreatine)
*allows ATP to serve as buffer for creatine kinase
*when body is creating xs E
*if have enough, give to ADP so ATP canbe used |
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Term
|
Definition
*allow phosphorylation of creatine
*CK
*when phosphorylated, musc get extra minutes of E |
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Term
|
Definition
ATP + NDP ⇌ ADP + NTP
AMP + ATP ⇌ 2 ADP
*converted for no E
*N can be C,G,T |
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Term
| Acetyl CoA thioester bond |
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Definition
*thioester bond in acetyl CoA = high E bond
*CoA is carrier
*when hydrolyzed produces lots E that can be coupled t endergonic |
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Term
| Oxidation- Reduction Rxns |
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Definition
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Term
|
Definition
*NAD+, FAD
*accept e- from reduced metabolites and transfer to other componds |
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Term
|
Definition
*reduced to FADH2
*undergo reversible reduction and accept e-
*1 e- at a time (semiquinone form)
*2 hydride pick up (hydrquinone) |
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Term
|
Definition
*left to right, e- left
*(oxidant) recieves e- = reduced
*gain electrons
* NAD+ -> NADH |
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Term
|
Definition
*left to right, e- right
*causes reduction of other (reductant) |
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Term
| Reductant (reducing agent) |
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Definition
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|
Term
| Oxidant (oxidizing agent) |
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Definition
|
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Term
|
Definition
| *work required to transfer n mols e- through electrical potential difference |
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Term
|
Definition
*electrical potential difference
*chnge in reduction potential (tend of subs to undergo reduct)
*in Nernst Eq
*the greater the reduction potential = the more likely spont
* +^E = - ^G (spont)
*need a combo of redox pairs where 1 wants to give e- and 1 want to take |
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Term
| The more + the standard red potential |
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Definition
1) the higher the affinity of the redox couples oxidized form for e-
- greater tendency for oxid form to accept e- (becomes reduced) |
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Term
| Standard Reduction Potentials |
|
Definition
*reduced - oxidized = V
* (acceptor)-(donor)
* +^E(in V) = - ^G
*every time theres a tranfer of e-, tranfers to a # that always has +^E (alows to transfer from complex to complex) |
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Term
|
Definition
*active state
*good
*allow rxn to happen
*lets Arg & F6P interact form ion pair (phosphate & sidecchain) |
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Term
|
Definition
*Arg sidechain unwind (in transition)
*movement away from Arg -> Glu replacement
*dec in F6P affinity for T St. Enz (PFK)
*ATP binds to allosteric activator w/ unwound helix |
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Term
|
Definition
INHIBITOR
ATP -> unwinding
ACTIVATOR
*AMP, ADP -> no unwind
*add lots of F6P
*relieve ATP inhibition (sm []s) |
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Term
|
Definition
EFFECTOR SITE BOUND W/ - EFFECTOR
*Glu faces into the substrate site
*prevents F6P from bind
EFFECTOR SITE BOUND W/ + EFFECTOR
*Arg faces into substrate site
*F6P binds
*P attracts Arg & encourages R St |
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Term
|
Definition
LOW ATP
*need glycolysis
*high flux (active musc)
HIGH ATP
*flux low (resting musc) |
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Term
|
Definition
*flux varies greatly depending on ATP need
*[ATP] vary small [effector] (rest -> exertion) |
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Term
|
Definition
| *Creatine kinase & adenylate kinase buffer |
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Term
|
Definition
CATALYZE: 2 ADP ⇋ ATP + AMP
*rapid equilibrating ADP from ATP hydrol (musc contract) to ATP + AMP
*[ATP] > [ADP] > [AMP]
*causes signal amplify -> lrg inc in PFK activity
*double amounts of activator = 100% inc
*ADPs being prod can result in AMP & create huge flux |
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Term
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Definition
*regulates PFK (provides alt pathway)
*in rest musc: cycles maintain glycolysis to keep ready to attack; short burst E |
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Term
| Hexoses Entry in Glycolysis |
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Definition
GALACT: G6P
MANNOSE: F6P
FRUCT: F6P (musc), GAP (liver)
*fruct liver = prob (can become glycerol back bone in fat) |
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Term
|
Definition
| *phosphorylates gluc, fruct, mannose NOT galac |
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Term
|
Definition
*a major fuel source found in fruit (sucrose)
MUSC: processed by hexokinase -> F6P (norm)
LIVER: F1P- chain -> chain opens -> glceryald -> 1) Glyc-3P (glycer kinase) 2)glyrcerol (w/ OH dehydrog) -> Glycerol3P (dehydrog) -> DHAP (triosphosisom) -> (((glyc3P)))) -> glycolysis
PROBS:
*bypasses certain steps
*forms backbone @ glycerol 3P |
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Term
|
Definition
PROB: req own kinase
*trade off - epimerization by NAD red NADH receive UDP (uridyl transferase)
*need epimerization 1st (b/c galac obtained from hydrolysis gluc)
* galac -> galac1P (galac1P UT) -> UDP galac (UDPgalac4epimerase) -> UDP gluc (galac1P UT) -> gluc1P (phosphogluc mutase) -> gluc6P -> glycolysis |
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Term
|
Definition
MANNOSE (hexokinase, ATP -> ADP) ->
MAN6P (phosphomannose isomerase) ->
F6P |
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Term
|
Definition
*series of 8 rxns
*oxidizes acetyl group (CoA -> CO2) & others
*conserves liberated free E in reduced compounds of NADH and FADH2
*1st prod: citrate
*hub of cellular metabolism
*2CO2 come from acetyl group previous round
*intermediates = precursors for biosynth of other compound
3NAD + FAD + GDP + Pi + ACoA -> 2CO2 + 3NADH + 1FADH2 + 1GTP + CoA |
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Term
|
Definition
*consumed in 1st step and regen in last
*oxidize unlimited number of acetyl groups |
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Term
|
Definition
*all CAC enz in mito
*all substrates (NAD, GDP) gen in mito/ trans in
*all products consumed in mito or trans out |
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Term
| Pyruvate Dehydrogenase (PDH) |
|
Definition
*multi enz complex
*catayzes 5part rxn
*E2, E1, E3
pyruvate + CoA + NAD -> acetyl CoA + CO2 + NADH |
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Term
| Advantages of multienz complex |
|
Definition
1) distance the subtrates diffuse between enz active sites are lessened
-inc rxn rate
2) channeling metabolic intermediates between successive enz reduces likelihood react w/ others in side rxn
3) coordinated control of rxns catalyzed |
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Term
|
Definition
CITRATE SYNTHASE
ENZ: citrate synthase
RXN: ACoA -> oxaloacetate
TYPE: condensation
*rxn is an ordered sequential kinetic mech
1) homo dimer (free E) open form
2) oxalo binds enz
3) closed form gen ACoA bind site
4) oxalo hide
= citrate |
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Term
|
Definition
ACONITASE
ENZ: aconitase
RXN: citrate ⇌ [cis-aconitase] ⇌ isocitrate
TYPE: reversible isomerization
*[4Fe-4S] cluster coordinates OH on citrate (facilitate elimination)
*rehydration of double bond produces specific steroisomer |
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Term
|
Definition
ISOCITRATE DEHYDROGENASE RELEASE 1st CO2
ENZ: isocitrate dehydrogenase
RXN: isocitrate ⇌ [oxalosuccinate] x2 ⇌ a-KETOGLUTARATE
TYPE: oxidative decarboxylation
*prod 1st CO2, NADH
*CO2 exit from oxalo, not acetyl
*NAD (w/ Mn/Mg: polarize newly formed caarbonyl) catalyze oxid of isocitrate (2* OH) -> oxalosuccinate (ketone) -> decarobxylation CnylB to ketone |
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Term
|
Definition
a-KETOGLUTARATE DEHYDROGENASE RESEMBLES PDH COMPLEX (2nd NADH)
ENZ: a-ketoglutarate dehydrogenation
RXN: a-keto -> succinyl CoA
TYPE: oxidative decarboxylation
*CoASH -> Co2, Nad -> NADH +H
*prod 2nd CO2, NADH
*excite CO2 -> oxalo
*multienz complex (like PDH)
*E1, E2, E3 |
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Term
|
Definition
SUCCINYL- CoA SYNTHETASE MECH
ENZ:
RXN: succinyl CoA ⇌ succinate
TYPE: synthetase
*3 part rxn
1) succinyl CoA -> succinylP (high E acylP)
2) HisEnz -> 3P His + succinate (high E interm)
3) GDP -> GTP (phosphoryl tranfer) |
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Term
|
Definition
SUCCINATE DEHYDROGENASE PROD FADH2
ENZ: succinate dehydrogenase
RXN: succinate +EFAD ⇌ fumarate + EFADH2
TYPE: stereospecific dehydrogenation
*inhibit by malonate (competitive inhibitor)
*FAD prothetic group on enz (covalently linked to His)
*FAD oxidizes alkanes to alkenes)
*can be in the memb |
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Term
|
Definition
FUMARASE
ENZ: fumarase
RXN: fumarate ⇌ [carbanion] ⇌ malate
TYPE: hydration
*hydration of double bond of fumarate by OH add before H add |
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Term
|
Definition
MALATE DEHYDROGENASE PRODUCES 3rd NADH
ENZ: malate dehydrgoenase
RXN: Malate + NAD ⇌ oxalo + NADH + H
TYPE: regeneration
*hydorxyl group oxidized (NAD dependent rxn)
*couple w/ 1st rxn gives E b/c rxn +^G (have more malate) |
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Term
|
Definition
1 ACoA -> 2 CO2 (need 4e- pairs):
*3NAD red NADH -> 3e- pairs
*1FAD red FADHs -> 1e- pair
*1 GTP
e- NADH,FADH -> ETC
*O2 red -> H2O
*1 NADH -> 2.5 ATP (ADP +pi)
*1 FADH2 -> 1.5 ATP
1 round = 10 ATP |
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Term
|
Definition
Gluc -> pyruvate (glycolysis): 2ATP + 2NADH
NADH e- transfer (ETC): 5ATP
pyruvate -> 2 ACoA (PDH complex): 2NADH
2NADH give rise: 5ATP
2 Round CAC: 20 ATP
--------------
~32 ATP
ANAEROBIC: 2ATP/ gluc |
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