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1.) The equilibrium constant of an uncatalyzed reaction Keq is 0.5. If an enzyme having a Km of 0.01M and Vmax of 0.1 umoles/min is used to catalyze this same reaction, the Keq of the catalyzed reaction would be:

A.  5

B. 0.005 

C. 0.5

D. 0.05

2.) Addition of a competitive inhibitor to an enzymatically catalyzed reaction will 

A. increase the affinity the enzyme has for its substrate

B.  reduce the Vmax of the reaction 

C. increase the substrate concentration required to attain ½ Vmax

3.) The equation below describes the behavior of which of the following reactions obeying Michaelis-Menton kinetics?

Vo = Vmax [S] / (Km + a’ [S])

A. An uninhibited reaction

B. A non competitively inhibited reaction

C. None of the above answers are correct

D. competitively inhibited reaction

4.) Which of the following enzymes covalently modifies the FBP-2/PFK-2 enzyme complex?

A. PFK-2

B. protein kinase A

C. pyruvate kinase 

D. PFK-1 

5.) For each time (cycle) of the TCA cycle , how many molecules of ATP equivalents are produced ?

A. 24

B. 18

C. 6 

D. 12

6.) The first reaction of the tricarboxylic acid cycle condenses the acetyl group,  acetyl CoA with which of the following TCA cycle intermediates ?

A. pyruvate 

B. oxaloacetate

C. citrate

D. malate

7.) In the TCA cycle  TP is produced from CDP and Pi by which of the following mechanisms?

A. substrate level phosphorylation

B. cAMP- dependent kinase phosphorylation

C. reverse phosphorylation

8.) Succinate thiokinase (AKA succinyl – CoA synthetase) cleaves a high energy bond CoA this high energy bond is of which of the following types ?

A. Ester

B carboxylic acid 


D. thioester 

9.) The primary substrate in gluconeogenesis is which of the following  ?

A. glicerol

B. fatty acids 

C. amino acids 

D. glucose

10.)Which of the following results in a futile cycle ?

A.  glycolysis is inactive and glycogenesis is active 

B.  both glycolysis and gluconeogenesis are inactive 

C.  both glycolysis and gluconeogenesis are active 

D.  glycolysis is active and gluconeogenesis is inactive

11.) True/ False:  Oxaloacetate is permeable to inner mitochondrial membrane 



12.)The Cori Cycle is best described as which of the following?

A. glucose  converted to pyruvate and back to glucose 

B. glucose converted to glycogen and back to glucose 

C. glucose converted to ATP and back to glucose 

D. glucose converted to lactate and back to glucose 

13.) True /False the reaction : Acetyl – CoA+ oxaloacetate -> citrate is an anaplerotic reaction



14.) When initial reaction velocity is plotted as a function of substrate concentration the kinetics data of non allosterically regulated enzymes generate a curve with 

A. linear morphology

B.  Hyperbolic morphology

C.  zero order morphology

D. sigmoidal morphology

15.) Addition of a competitive inhibitor to an enzymatically catalyzed reaction will 

A. increase the affinity the enzyme has for its substrate

B.  reduce the Vmax of the reaction 

C. increase the substrate concentration required to attain ½ Vmax

Biochemistry II Lecture Notes Mark Mattie, MD, Ph.D.

TCA Cycle

Definition: The citric acid cycle (CAC) – also known as the TCA cycle (tricarboxylic acid cycle) or the Krebs cycle is a series of chemical reactions used by all aerobic organisms to release stored energy through the oxidation of acetyl-CoA derived from carbohydrates, fats, and proteins, into adenosine triphosphate (ATP) and carbon dioxide. In addition, the cycle provides precursors of certain amino acids, as well as the reducing agent NADH, that are used in numerous other reactions.

· TCA cycle overview

· Cycle provides energy in the form of reduced coenzymes for the production of ATP

· Nearly all CO2 produced by body is byproduct of TCA cycle and pyruvate dehydrogenase

· TCA cycle operates exclusively in mitochondria in proximity to e- transport chain and is considered to be part of the aerobic respiration pathway

· The cycle is a convergence pathway for oxidative metabolism of carbohydrates, AA’s, FA’s

· Carbon in molecules oxidized (burned) to CO2

· Removes e- from fat, carbohydrate, and protein to produce reduced coenzymes

· Coenzymes are then oxidized by e- transport chain to produce ATP


· TCA cycle can operate in two modes: catabolic and anabolic and is, therefore, described as being amphibolic

· Energy production (Catabolic mode)

· Carbohydrate, FAs, AA’s converted to acetyl-CoA

· Acetyl-CoA oxidized to produce:

· Reduced coenzymes by four redox reactions/cycle

· Three mitochondrial NADH molecules

· One mitochondrial FADH2 molecule

· One GTP by substrate level phosphorylation

· Biosynthesis (Anabolic mode)

· All biosynthetic reactions require input of carbons other than those contained in acetyl-CoA

· Input pathways are called anapleurotic (“filling up”) reactions

· TCA cycle intermediates are used for biosynthesis of:

· Glucose during starvation

· C’s taken from AA’s and lactate

· The conversion of carbohydrates to fat

· Nonessential AA’s

· E.g., Aspartate, glutamate

· Pyruvate is a substrate for many reactions in metabolism

· Pyruvate -> Lactate by lactate dehydrogenase

· Pyruvate -> Alanine by alanine aminotransferase (ALT)

· Pyruvate -> Oxaloacetate by pyruvate carboxylase

· Pyruvate carboxylase is homotetramer

· Carboxylases generally use CO2 and coenzyme biotin (aqueous vitamin) and ATP to drive carboxylation

· Each subunit contains allosteric binding site for acetyl-CoA

· Acetyl-CoA is a positive allosteric effector

· Acetyl-CoA produce by lipolysis during starvation will trigger production of oxaloacetate for gluconeogenesis

· Pyruvate -> Acetyl-CoA by pyruvate dehydrogenase complex

· Acetyl-CoA is a negative allosteric effector


· Pyruvate -> Acetyl-CoA catalyzed by pyruvate dehydrogenase complex

· Pyruvate dehydrogenase

· Catalyzes oxidative decarboxylation of pyruvate

· Multienzyme complex

· One of several α-ketoacid dehydrogenases

· Enzyme activity regulation

· Regulated by allosterism

· Negative allosteric effectors are Acetyl-CoA and NADH

· Regulated by and covalent modification

· Sequence of conversion

· Pyruvate transported from cytoplasm into mitosol via pyruvate-specific transporter

· Pyruvate converted to acetyl-CoA by pyruvate dehydrogenase complex located in the mitochondria

· Irreversible reaction

· Major source of acetyl-CoA for TCA cycle

· Multienzyme complex composition

· Functional Components

· (E1) Pyruvate dehydrogenase

· Coenzymes

· Thiamine pyrophosphate (TPP)

· Vit B1

· (E2) Dihydrolipoyl transacetylase

· Transfers acetyl group

· Transfers reducing equivalents to FAD

· Coenzymes

· Lipoic acid

· Coenzyme A

· (E3) Dihydrolipoyl dehydrogenase

· Transfers reduction equivalents to NAD+

· Coenzymes


· NAD+

· Regulation of complex

· Activate and deactivate E1 of pyruvate dehydrogenase

· Protein kinase

· Kinase phosphorylates and inhibits E1

· Kinase allosterically activated by high energy state compounds


· Acetyl-CoA


· Kinase allosterically inhibited by low energy state compounds:

· NAD+

· Coenzyme A

· Kinase inhibited by pyruvate

· Feedforward mechanism

· Phosphoprotein phosphatase

· Dephosphorylation action activates E1

· Phosphatase activated by Ca2+ in skeletal muscle

· In skeletal muscle, Ca2+ promotes activity of phosphatase -> produces energy by activating E1

· Other regulation methods

· Induction and repression of protein synthesis

· Proteolysis of enzyme proteins

· Pyruvate Dehydrogenase deficiency

· Most common enzymatic cause of congenital lactic acidosis

· Unable to convert pyruvate to acetyl-CoA

· Equilibrium shifted in favor of converting pyruvate to lactic acid by lactate dehydrogenase

· TCA cycle reactions

0. Acetyl group from acetyl-CoA condenses with oxaloacetate

· Acetyl-CoA may originate from

· Carbohydrates

· Oxidative decarboxylation of pyruvate

· Triacylglycerol

· Oxidation of glycerol & FFAs

· FA’s bypasses pyruvate formation

· Proteins/AA’s

1. Synthesis of citrate from acetyl-CoA and oxaloacetate

· Catalyzed by citrate synthase

· Aldol condensation reaction forming citrate

· Synthase allosterically regulated

· Activated by Ca2+, ADP

· Inhibited by ATP, NADH, succinyl-CoA, fatty acyl-CoA derivatives

· Primary mode of regulation

· Availability of substrates acetyl-CoA and oxaloacetate

2. Isomerization of citrate to isocitrate

· Catalyzed by aconitase

· Inhibited by fluoroacetate (rat poison)

· Converted to fluoroacetyl-CoA

· Condenses with oxaloacetate to form fluorocitrate

· Fluorocitrate is an inhibitor of aconitase

· Citrate accumulation

3. Oxidation and decarboxylation of isocitrate to α-Ketoglutarate

· Catalyzed by isocitrate dehydrogenase

· Allosterically activated by ADP, NAD+ and Ca2+

· Increase in energy demand results in accumulation of ADP and NAD which stimulate isocitrate dehydrogenase

· Allosterically inhibited by ATP and NADH

· Citrate accumulates in mitochondria after carbohydrate rich meal

· Exported to cytosol for lipogenesis

· FA exported from liver for storage in adipose tissue as triglycerides

· Citrate allosteric inhibitor of PFK-1 and activates acetyl-CoA carboxylase

· Irreversible oxidative decarboxylation of isocitrate

· Yields first NADH of three by the TCA cycle

· Releases CO2

· One of TCA cycle rate-limiting steps

4. Oxidative decarboxylation of α-ketoglutarate to succinyl-CoA

· Catalyzed by α-ketoglutarate dehydrogenase complex

· Oxidative decarboxylation of ketoglutarate

· Releases 2nd CO2 produces 2nd NADH

· Inhibited by ATP, GTP, NADH, succinyl-CoA

· Activated by Ca2+

· Not regulated by Phosphorylation/Dephosphorylation

· Coenzymes required, same as pyruvate dehydrogenase

· Thiamine pyrophosphate

· Lipoic acid


· NAD+

· Coenzyme A

· At this point in TCA cycle, the two C injected have been balanced by two removed in the form of CO2

· In two C in 2Acteyl-CoA -> out two C in 2CO2

· No net biosynthesis of intermediates when C sourced from acetyl-CoA

5. Cleavage of succinyl-CoA

· Catalyzed by succinate thiokinase (AKA succinyl-CoA synthetase)

· Cleaves high-energy thioester bond of succinyl-CoA

· Coupled to phosphorylation of GDP -> GTP

· Substrate level phosphorylation

· ATP and GTP are energetically interconvertible by nucleoside diphosphate kinase

· GTP + ADP <-> GDP + ATP

6. Oxidation of succinate to fumarate

· Catalyzed by succinate dehydrogenase

· Succinate dehydrogenase is also known as complex II of the e- chain

· Produces FADH2

· FAD -> FADH2

· FAD is the acceptor because reducing power of succinate insufficient to reduce NAD+

· FAD is the prosthetic group

7. Hydration of fumarate to malate

· Catalyzed by fumarase (fumarate hydratase)

8. Oxidation malate to oxaloacetate

· Catalyzed by malate dehydrogenase

· Produces 3rd and final NADH

· Energy produced by TCA cycle

· Two C enter cycle as acetyl group and converted to CO2

· As a result, there is no net production of TCA intermediates

· Total = 12 ATP/acetyl-CoA

· 11 ATP by oxidation of coenzymes

· Three mitochondrial NADH + H+ (production of 3 ATP)

· One mitochondrial FADH2 (production of 2 ATP)

· 1 ATP from GTP (via substrate level phosphorylation)

· Starting with one glucose molecule ending with e- transport chain results in the production of 36-38 ATP

· Variability result of use of malate vs. glycerol shuttle to transfer cytoplasmic redox equivalents of cytoplasmic NADH to mitochondrial matrix

1 Glucose Molecule



2 ATP -> 2 ATP

2 NADH cytosolic -> 2(2 to 3) ATP

Pyruvate DeH

2 NADH mitosolic -> 6 ATP


6 NADH mitosolic -> 18 ATP

2 FADH2 mitosolic -> 4

2 GTP -> 2 GTP


Total: 36-38 ATP/glucose

· TCA cycle regulation

· Rate regulated points of the TCA cycle

· Citrate synthase

· Isocitrate dehydrogenase

· α-ketoglutarate dehydrogenase complex

· Availability of oxaloacetate

· As NADH & FADH2 accumulate, oxidized forms become depleted and the TCA cycle is inhibited due to depletion of oxidized coenzymes


· Increases in ADP accelerates reactions generating ATP

· Oxidative phosphorylation stops if ADP is not available

· Oxidation and phosphorylation tightly coupled

· Anaplerotic (filling up) reactions

· Anaplerotic reactions provide source of C to produce a net increase in TCA intermediates

· Biosynthesis from TCA intermediates requires anaplerotic reactions supplying C, otherwise TCA cycle would stall when intermediates depleted

· E.g., Removal of succinyl-CoA for heme synthesis depletes mitochondrial oxaloacetate

· Acetyl-CoA does not provide any net increase in C for synthesis of TCA intermediates



Gluconeogenesis Definition: The formation of glucose from noncarbohydrates, such as protein or fat.

· Gluconeogenesis Overview

· Some tissues require a constant supply of glucose to remain viable. These include:


· RBCs

· Exercising muscle

· Sources of glucose

· Carbohydrate rich meal

· Provides source of glucose up to 3-4 hrs postprandial

· Liver stores glycogen

· Glycogenolysis supplies glucose for up to 10-18 after eating

· Gluconeogenesis (During prolonged fasting)

· Glucose synthesized from substrates, including:

· Lactate, pyruvate

· Glycerol from triglycerides

· α-ketoacids from glucogenic AA’s

· Glucose synthesized by gluconeogenic tissues

· First 12 hours of fasting

· Liver sources 90%

· Kidneys source 10%

· After first 12 hours of fasting

· Kidneys source 40%

· Substrates for gluconeogenesis

· All intermediates of glycolysis & TCA cycle

· Glycerol

· Liberated from triacylglycerols stored in adipose tissue by hydrolysis

· Lactate

· Released into blood by exercising muscle and RBCs which lack mitochondria

· Cori cycle converts lactate back to glucose

· Blood glucose converted to lactate by cells

· Lactate imported into hepatocyte and converted to glucose

· Glucose released by hepatocyte into circulation

· Glucogenic AA’s

· From catalysis of tissue proteins

· Primary source of glucose during a fast

· α-Keto acids derived from deamination of glucogenic AA’s

· Enter TCA cycle to form oxaloacetate or enter as α-Ketoglutarate

· Note:

· No net synthesis of glucose from Acetyl-CoA

· Reaction catalyzed by pyruvate dehydrogenase irreversible

· Reactions unique to gluconeogenesis:

· Gluconeogenesis is not a simple reversal of glycolysis

· Three reactions of glycolysis are irreversible

· These three reactions are bypassed by four unique reactions of gluconeogenesis for production of glucose

· Unique reactions #1 & #2 bypass pyruvate kinase

· Unique reaction #3 bypasses PFK-1

· Unique reaction #4 bypasses hexokinase

· #1) Carboxylation of pyruvate to oxaloacetate by pyruvate carboxylase

· Biotin is coenzyme

· Reaction occurs in mitochondria of liver and kidney

· Oxaloacetate transported to cytosol

· Gluconeogenic enzymes located in cytoplasm

· Oxaloacetate not permeable to inner mitochondrial membrane

· Reduced to malate by mitochondrial malate dehydrogenase

· Malate transported to cytoplasm

· Converted to oxaloacetate by cytoplasmic malate dehydrogenase

· Allosteric regulation

· Pyruvate carboxylase

· Activated by acetyl-CoA

· Deactivated by low levels of acetyl-CoA

· Pyruvate dehydrogenase is inhibited by acetyl-CoA

· When PDH active, acetyl-CoA used for TCA cycle energy production

· #2) Oxaloacetate converted to PEP by PEP carboxykinase (PEPCK)

· Driven by GTP hydrolysis

· Occurs in cytoplasm

· #3) Dephosphorylation of fructose 1,6-bisphosphate to Fructose 6-phosphate by fructose 1,6-bisphosphatase

· Glycolysic reactions are reversed until reaction reaches fructose 1,6-bisphosphate

· This reaction is the primary regulatory step in gluconeogenesis

· Allosteric regulation of fructose 1,6-bisphosphatase

· Regulated by intracellular energy levels

· Activated by ATP

· Inhibited by AMP (energy poor)

· Regulated by sugar levels of the blood

· When sugar levels increase and the hormone glucagon decreases, intracellular levels of Fructose 2,6-bisphosphate increase

· Levels of fructose 2,6-bisphosphate reflect blood glucose levels

· Levels of dependent on blood glucagon

· Fructose 1,6-bisphosphatase allosterically inhibited by fructose 2,6-bisphosphate

· PFK-1 activated by fructose 2,6-bisphosphate

· Allows for reciprocal control and prevents a futile cycle

· #4) Dephosphorylation of Glucose 6-P to glucose by glucose 6-phosphatase

· Dephosphorylation required for cell export, can’t export phosphorylated glucose

· Reaction produces glucose for export

· Activity of enzyme primarily found in ER of liver and kidney cells

· Glucose 6-phosphatase activity in ER only in gluconeogenic cells

· Hepatocytes and kidney release glucose into blood

· Note: Muscle lacks glucose 6-phosphatase

· Cannot supple blood with glucose by gluconeogenesis

· Glucose 6-P from glycogen can’t be dephosphorylated to yield glucose




· Enzyme naming nomenclature

· Systematic Name assigned by international union of biochemistry and molecular biology (IUBMB)

· Enzymes divided into six major classes

· Recommended Name, two derivations

· Substrate + “ase”

· e.g., Urase

· Reaction catalyzed + “ase”

· e.g., Lactate dehydrogenase

· Trivial/Historical Name

· Gives little or no operational information

· e.g., Pepsin, Trypsin

· Catalysts

· Types

· Metals

· Protein enzymes

· Ribozymes

· Protein enzyme properties

· Active Sites

· Binding site for substrate

· Forms [ES] = Enzyme substrate complex

· Enzyme site in which reaction takes place

· Contain AA side chains/ functional groups that help catalyze reaction

· Catalytic efficiency

· Can increase reaction velocity by 1×103 to 1×108 compared to uncatalyzed reaction

· Specificity

· Catalyst is specific when it utilizes a few select substrates

· The ability to discriminate between substrate & some other competing molecule

· Cofactors

· Additional chemical groups or components that may be required for enzyme activity

· Definitions

· Holoenzyme

· Hol-

· word-forming element meaning “whole, entire, complete,” from Greek holos

· Refers to catalytically active enzyme with cofactors

· Apoprotein (apoenzyme)

· Enzyme without cofactors

· Cofactors

· Inorganic ion

· e.g., Fe2+, Zn2+

· Coenzymes

· Organic or metalloorganic molecule

· Many are derivatives of vitamins

· Prosthetic group

· Tightly or covalently bound cofactor

· e.g., Heme

· Theory of operation

· Accelerates the completion of a reaction

· Does not change reaction equilibrium

· Energy changes during reaction

· Energy barrier of reaction = free energy of activation

· Energy difference between reactants and transition state (highest energy intermediate), T*

· Reaction rate determined by reaction step with the highest energy of activation

· Called rate limiting step

· E + S ↔ ES ↔ T* ↔ EP ↔ E + P

· Free energy of activation, ΔG‡

· Energy difference between reactants and transition state

· Higher ΔG‡ the slower the uncatalyzed reaction rate

· Enzymes increase rate of reaction

· Enzymes reduce ΔG‡

· Increases reaction rate

· Greater proportion molecules can reach transition state

· Enzymes do not alter free energies of reactants or products

· Enzymes do not alter reaction equilibrium

· Active site chemistry, mechanisms which facilitate conversion of substrate, S

· Active site binding forces S to assume geometry of transition state

· Stabilizes transition state for reaction

· AA side chains may function as catalytic groups

· Reaction velocity, V

· Usually expressed as μmol of product formed / min

· Variables affecting velocity

· Reactant concentration

· Rate increases with S concentration, [S], until Vmax approximately attained

· Kinetics curve

· Plot of initial velocity, Vo, vs. substrate concentration

· Hyperbolic shape

· Consistent with Michaelis-Menton kinetics

· Sigmoidal curve

· Allosteric enzymes

· e.g., oxygen dissociation curve of hemoglobin

· Temperature

· Velocity increases with temperature until peak reached

· The higher the temp, the greater the proportion of molecules of sufficient energy to overcome barrier

· Decrease in velocity after peak

· Temperature-induced denaturation of enzyme

· pH

· Changes may increase or decrease velocity

· Ionization state of reactants & enzymes change altering velocity

· Optimum pH for reaction velocity varies with enzyme

· e.g., Pepsin requires lower pH

· e.g., Alkaline phosphatase requires higher pH

· Enzymes which obey the Michaelis-Menten equation

· Reaction model:

· E_S_ESeq




· Where,

· E is enzyme

· S is substrate

· ES is the enzyme-substrate complex

· P is product

· k1, k-1, k2 are unimolecular rate constants

· Michaelis-Menten Equation

· MMeq




· Where,

· Km = Michaelis constant (M)

· Vo = Initial rxn velocity (μmol·min-1)

· Vmax = Maximum rxn velocity (μmol·min-1)

· [S] = Substrate concentration (Moles)

· Assumptions

· [S]>>[E]

· Substrate consumed is insignificant

· [ES] constant

· Rate of ES formation = ES breakdown

· System achieves steady state

· V0 measured at steady state

· Initial velocity used to analyze enzyme reactions

· Measured immediately after steady state achieved

· Called “Steady-state kinetics”

· Early in reaction [P] is negligible

· P -> S can be ignored, thus:

· V0 determined by breakdown rate of ES

· V0 = f([S]) = rectangular hyperbola

· Interpretation of variables

· Km = Michaelis constant

· Related to affinity of enzyme for substrate

· Practical definition

· Equal to [S] at which Vo = ½Vmax

· Lower Km implies higher affinity

· Higher Km implies lower affinity

· Reaction order

· When [S]<< Km

· V0([S]) is first order or linear

· When [S] >> Km

· V0([S]) = Vmax

· V0([S]) is zero order or constant

· Lineweaver-Burke plot (double-reciprocal plot)

· tmp


· FORM: y = mx + b

· X axis intercept = -1/Km

· Y axis intercept = 1/ Vmax

· Enzyme inhibitors

· Decrease velocity of enzymatically catalyzed reactions

· Mechanisms of inhibition

· Competitive inhibition

· Inhibitor binds reversibly to substrate binding site

· Increases apparent Km

· Greater [S] required to achieve Vmax

· Vmax unchanged

· e.g., Statin drugs – reduce cholesterol production

· Noncompetitive inhibition

· Inhibitor binds to site other than the substrate binding site

· Decreases Vmax

· No increase with increase in [S]

· Km does not change

· Does not alter affinity of S for E

· Example: ACE inhibitors decrease blood pressure

· Cellular regulation of enzyme activity

· Most cellular enzymes operate in an environment where with [S] ≈ Km

· Changes in [S] change rate of reaction

· Allosteric regulation

· Some enzymes regulated by allosteric effectors (modifiers)

· Bind noncovalently to site other than active site

· Effectors may modify substrate affinity, Vmax, or both

· Negative effectors – inhibit activity

· Positive effectors – enhance activity

· Example:

· Product of reaction can inhibit enzyme

· Example of negative feedback

· Regulation by covalent modification

· Phosphorylation may increase or decrease activity

· Phosphoprotein phosphatases cleave phosphate groups


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