Biochemistry Final 2
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- Chemotrophs
- obtain chemical energy through oxidation of foodstuffs generated by phototrophs
- Phototrophs
- Use energy of sunlight to convert energy-poor molecules into energy-rich molecules from which energy can be derived.
- Catabolism
-
Convert energy into biologically useful fuels (carbohydrates, fats) --> (Carbon dioxide, water, useful energy)
BREAK DOWN - Anabolism
-
Reactions that require energy
useful energy + small molecules --> complex molecules.
BUILD UP - Kinases are coupled with:
- Usually Mg2+ (sometimes Mn2+)
- Structural Basis of the high phosphoryl transfer potential of ATP
-
1. Resonance Stabilization (ADP and Pi have greater resonance stabilization than ATP)
2. Electostatic Repulsion (fewer resonance structures because positive structure charges are next to each other. Also, at pH 7 there are four negative charges that repel each other)
3. Stabilization due to hydration - h2o can more effectively bind to adp and pi than ATP, stabilizing them. - Oxidants
- NAD+ and FAD
- NAD+ (reactive part?)
- nicotinamide ring, a pyridine derivative synthesized by the vitamin niacin
- FAD (reactive part?)
- isoalloxazine ring, a derivative of riboflavin
- Reductant
- NADPH
- NADPH (what is the tag that allows enzymes to distinguish between electrons for reduction and oxidation?)
- the extra-phosphoryl group
- Coenzyme A
- Important carrier of acyl groups; terminal sulfhydral group is the reactive site. Acetyl group linked to CoA by a thioester bond.
- Bronsted - Lowry Acid
- a substance that donates a proton (hydrogen ion, H+)
- Bronsted - Lowry Base
- a substance that accepts a proton (hydrogen ion, H+)
- Lewis Acid
- A substance that accepts an electron Pair
- Lewis Base
- A substance that donates an electron pair.
- Iron sulfur clusters can act as...
- Lewis Acids (Four Iron Atoms - three of which are coordinated to a sulfur and a cysteine - one can coordinate with oxygen).
- Electrophilic Addition Reactions can be used in the synthesis of...
- Terpenes
- Sn1 Reactions
- Proceed through a carbocation intermediate; synthesis of terpenes
- Sn2 reactions
- inversion of stereochemistry; The biosynthesis of epinephrine from norepinephrine occurs by an Sn2 reaction with SAM
- Pyruvate + PAP -->
- Imine
- Conjugate Addition
- Fumarate (plus water) to Malate
- Reactivity of Acyl Groups (from least to most)
-
amide
ester
thioester
acyl phosphate - Prochirality
- a molecule that can be converted from achiral to chiral in one step
- ATP is a coenzyme for
- phosphorylation
- Coenzyme A is a coenzyme for
- Acyl Transfers
- NAD+ is a coenzyme for
- oxidation/reduction
- FAD is a coenzyme for
- oxidation/reduction
- Tetrahydrofolate is a coenzyme for
- transfer of C1 units (derived from folic acid)
- Lipoic Acid is a coenzyme for
- acyl transfer
- Thiamine Diphosphate is a coenzyme for
- decarboxylation
- Biotin is a coenzyme for
- carboxylation
- SAM is a coenzyme for
- Methyl Transfer
- Many _____ reactions depend on PLP
- decarboxylation / amination/ deamination / Epimerization
- Net gain of how many ATP in glycolysis
- 2
- Net gain of how many NADH in glycolysis
- 2
- In glycolysis, glucose is broken down into
- pyruvate
- Glucose --> Glucose 6 phosphate
- catalyzed by hexokinase.
- What is the importance of hexokinase:
- keeps glucose from leaving the cell once it enters.
- What cofactor is required for hexokinase?
- Mg 2+
- Glucose + ___ --> Glucose - 6 - phosphate + ____
- ATP // ADP
- Phosphorylation of Glucose
-
- goes through a pentacoordinated intermediate
- inversion of configuration at the phosphorous - What residue on hexokinase acts as the base to deprotonate glucose
- Aspartyl
- Induced Fit
- Hexokinase; Substrate induced cleft is a feature of kinases
- G-6P --> F-6P
-
isomerization reaction; catalyzed by phosphoglucose isomerase; tautomerization mechanism
Goes from ring structure, to open chain, converted to fructose, closed chain - Phosphorylation of F-6P
-
Results in F - 1, 6 - BP.
Catalyzed by PFK
F-6P is in beta formation; must convert to alpha formation before forming alpha 1,6 BP - Phosphofructokinase
-
conversion of fructose-6-phosphate to fructose-1,6-bisphosphate.
Mg 2+ required as a cofactor.
Critical enzyme in metabolism; one of the rate-limiting enzymes. - 1,6 BP --> DHAP & GAP
- Catalyzed by Aldolase. its a retro-aldol conversion.
- DHAP v. GAP
- DHAP is much more abundant than GAP, though Le Chatlier's principle drives formation of GAP
- TIM
- 8 parallel beta strands form core; 8 alpha helices form outer ring. perfect enzyme (kinetics)
- What residue of TIM is the general acid-base catalyst?
- Glutamate 165
- What residue of TIM protonates the developing tetrahedral oxyanion
- His-95
- GAP --> 1,3 BPG
-
oxidation reaction; catalyzed by glyceraldehyde-3-phosphate dehydrogenase; results in the formation of 2 NADH (one for each 3 carbon molecule)
Involves an oxidation (energetically favorable) followed by a dehydration (not energetically favorable).
Thioester intermediate - 1,3 BPG --> 3-glycerate
- Catalyzed by phosphoglycerate kinase. 2 molecules of ATP produced (one for each 3 carbon molecule).
- ADP Phosphorylation from 1,3 BPG to 3-glycerate occurs via
- nucleophilic substitution
- 3PG --> 2 PG
-
Phsophoglycerate mutase catalyzes this reaction.
In animals and yeast, this reaction involves a histidine residue. - 2 PG --> phosphoenolpyruvate
-
catalyzed by enolase; loss of water.
The base that extracts thhe acidic alpha hydrogen is lysine 345. - PEP --> pyruvate
- pyruvate kinase catalyzes this reaction; ATP is formed
- Redox Balancing
- Must regenerate NAD-
- Pyruvate -> ethanol
-
Pyruvate --> acetaldehyde catalyzed by Pyruvate decarboxylase (release of CO2)
Acetaldehyde --> ethanol catalyzed by Alcohol dehydrogenase (release of NAD-) - Pyruvate Decarboxylase requires what cofactor?
- TPP
- Alcohol Dehydrogenase uses an active site ____ atom to polarize ____ of acetylaldehyde
- zinc; carbonyl
- Pyruvate --> lactate
- catalyzed by lactate dehydrogenase.
- TCA Cycle Dependent on
- the availability of oxygen as the ultimate acceptor of electrons and the electron transport chain to shuttle electrons to oxygen
- Acetyl CoA
- shuttles 2 carbon fragments to the TCA cycle.
- ___ (#) decarboxylations occur during the TCA cycle
- 2
- TCA cycles occur in
- the mitochondrial matrix
- Pyruvate is ______ to form Acetyl CoA
- decarboxylated
- Pyruvate Carrier
- Pyruvate is exchanged for hydroxide
- Pyruvate Dehydrogenase Complex
-
made up of E1, E2, & E3
Three Steps: Decarboxylation, Oxidation, and Transfer to Acetyl CoA - CoFactors for pyruvate dehydrogenase complex
- TPP, Lipoic Acid, NAD+, FAD, CoA
- TPP has a pKa of
- 10
- Decarboxylation of pyruvate depends on what cofactor:
- TPP; E1
- Acetyl group of the pyruvate is oxidized and transferred to
- lipoic acid; E1
- Acetyl Group Transfered to CoA
- E2; leaves a dihydrolipoamide
- dihydrolipoamide oxidized to ____. Depends on ____ as a cofactor. catalyzed by ___.
- lipoamide. FAD. E3.
- TCA cycle: oxaloacetate to citrate
-
oxaloacetate + acetyl CoA --> citryl CoA (aldol condensation)
citryl CoA --> citrate (hydrolysis)
catalyzed by citrate synthase. - coordinated kinetics
- oxaloacetate binds first; acetyl coA binds second - prevents hydrolysis of acetyl CoA.
- Citrate --> Isocitrate
- Dehydration followed by a hydration. Catalyzed by Aconitase, an Fe-S protein.
- Isocitrate --> alpha-ketoglutarate
-
oxidation reaction, catalyzed by isocitrate dehydrogenase.
isocitrate --> oxalosuccinate --> alpha-ketoglutarate
NAD+ is reduced to NADH; CO2 is released. - alpha-ketoglutarate --> succinyl coA
- oxidative decarboxylation, results in release of CO2 and NADH
- succinyl CoA --> Succinate
- GTP is synthesized from GDP and Pi. CoA is released
- Succinate --> fumarate ---> malate ---> oxaloacetate
-
dehydrogenation, hydration, oxidation.
succinate dehydrogenase is an iron sulfur protein. - Regulation of Pyruvate Dehydrogenase Complex
- Acetyl CoA inhibits complex
- ____, ____, & ____ inhibit oxidative decarboxylation of pyruvate to acetyl CoA
- ATP, NADH, and Acetyl CoA
- ___ and ___ inhibit conversion of isocitrate to alpha ketoglutarate
- ATP and NADH
- ____, ____, and ___ inhibit the coversion of alpha-ketoglutarate to succinyl coa
- ATP, NADH, and Succinyl CoA
- Oxaloacetate can be converted to
- AA, Purines and pyrimidines
- Succinyl CoA can be converted to
- Porphyrins
- Citrate can be converted to
- Fatty Acids and Sterols
- Alpha-Ketoglutarate can be convertd to
- AA & purines
- Pyruvate can be carboxylated to
- pyruvate carboxylase to regenerate oxaloacetate
- Arsenic Poisoning
- Arsenic reacts with thiols, such as dihydrolipoamide, to inactivate the pyruvate dehydrogenase complex
- Starch
- glucose polymer
- 2 main fractions of starch
-
Amylose (1,4 linkages) -- several hundred monomers
Amylopectin (1,4 linkages and 1,6 linkages every 25 monomers)- 5000 monomers - Alpha-Amylase
- begins digestion of 1,4 linkages in mouth
- Hydrolysis of glycosidic bonds
- catalyzed by glycosidases
- Inverting Glycosidases
- 1 Sn2 reaction; carboxylate acts as a general base to deprotonate water as it attacks oxonium ion.
- Retaining Glycosidases
- 2 Sn2 reactions; carboxylate adds to oxonium ion & water attacks from opposite side.
- Glycosidases proceed through an ________ intermediate
- oxonium ion
- Pentose Phosphate Pathway
- Allows metabolism of 5-carbon sugars; produces NADPH; produces ribose-5-phosphate
- Two stages of Pentose Phosphate Pathway
-
1. Oxidative
2. Non-Oxidative - Net Reaction of Pentose Phosphate Pathway
- 3Glucose-6-Phosphate + 6NADP+ + 3H2O --> 2 Fructose-6-Phosphate + GAP + 3 CO2 + 6NADPH/H+
- Step 1 of pentose phosphate pathway
- oxidation of G6P to 6 - phosphogluconolactone; NADPH released
- Step 2 of pentose phosphate pathway
- hydrolysis of lactone; forms an open chain carboxylate
- Step 3 of pentose phosphate pathway
- oxidation of c3 hydroxyl release NADPH and CO2
- Step 4 of pentose phosphate pathway
- isomerizations occure by keto-enol tautomerizations.
- Step 5 of pentose phosphate pathway
- xylulose 5-phosphate reacts with ribose-5-phosphate to give GAP and sedoheptulose 7 phosphate
- Step 6 of Pentose phosphate pathway
- GAP and sedoheputulose 7 phosphate exhange a c3 unit
- Step 7
- products exchange a c2 unit
- Oxidative Phosphorylation
- process by which reducing power from NADH and FADH2 is used to synthesize ATP; occurs in mitochondria; flow of protons out of matrix leads to a proton gradient, as they flow back into the matrix ATP is synthesized
- 3 electron-driven proton pumps create the proton motive force:
-
NADH - Q Oxidoreductase (complex 1)
Q-cytochrome c oxidoreductase (complex 3)
Cytochrome c oxidase (complex 4) - VDAC high conductance
- ATP and ions can enter
- VDAC low conductance
- ions can enter
- ____ terminus can regulate VDAC conductance
- amino
- Isoforms of VDAC in humans:
- VDAC1, VDAC2, VDAC3
- Coenzyme Q
-
ubiquinone
Quinone can be reduced by 1 e- to form semiquinone
Semiquinone can be reduced by 1 e- to form ubiquinol - Structure of complex 1
-
4 protons pumped out of matrix
NADH is oxidized
Q is reduced to QH2 - Mechanism of Complex 1
-
NADH binds to complex 1 (on vertical arm) and transfers 2 electrons to FMN.
The electrons are transferred through three 4fe-4s clusters to Q, which becomes QH2. This reduction causes 2 protons to be pupmed out of the matrix onto QH2. Electrons leave, protons leave QH2 to cytosol. Electrons transferred to mobile Q in membrane, 2 more protons pumped out. - Complex 2
-
transfer of electrons from FADH2 to ETC
FADH2 transfers 2 e-'s to Fe-S centers and then to Q. No protons transferred during this complex. - Complex 3
-
Three hemes (the 2 heme b's are not covalently attached to a protein; the heme c is covalently attached to a protein by a thioester linkage with a cystein). 2 Fe-S clusters present. Iron in cytochrome c alternates between +2 and +3 states
QH2 + 2 Cytc ox + 2H+ matrix --> Q + 2cytc red + 4 H+ imspace - complex IV
- oxidizes cyt c reduced by complex 3. reduces oxygen to water.
- ATP yield per molecule of glucose
-
about 30 molecules of ATP formed per molecule of glucose:
2 from glycolysis
2 from TCA cycle
26 from oxidative phosphorylation - lipids are broken down into:
- glycerol and fatty acids
- How is glycerol recovered?
- it is converted to DHAP, and intermediate in glycolysis
- Fatty acids are activated
- by coupling with CoA; occurs in mitochondrial matrix; driven by hydrolysis of ATP
- Carnitine
- used to carry activated (long chain) fatty acids into the mitochondrial matrix: Acyl Carnitine is exchanged for free carnitine
- B-oxidation of Fatty Acids
- FAD-dependent oxidation; Hydration; NAD+ dependent oxidation; thiolysis
- Ubiquitin: ___ terminus of ubiquitin is conjugated to proteins
- C
- Amino Acid degradation begins with removal of amino group - mediated by:
- PLP/PAP
- Fates of Carbon Skeletons of Amino Acids: Pyruvate
- ala, cys, gly, ser, thr, trp
- Fates of Carbon Skeletons of Amino Acids: Acetyl CoA
- Ile, Leu, Trp
- Fates of Carbon Skeletons of Amino Acids: Acetoacetyl CoA
- Leu, Lys, Phe, Trp, Tyr
- Fates of Carbon Skeletons of Amino Acids: AlphaKetoGlutarate
- arg, glu, gln, his, pro
- Fates of Carbon Skeletons of Amino Acids: Succinyl CoA
- Ile, Met, Thr, Val
- Fates of Carbon Skeletons of Amino Acids: Fumarate
- Asp, Phe, Tyr
- Fates of Carbon Skeletons of Amino Acids: Oxaloacetate
- Asp, Asn