Review of Basic Metabolic Principles

A. Energy Currency of the Cell

Metabolic pathways can be classified as either:• energy generating (catabolic)…or• energy utilizing (anabolic)

The cell also uses two types of energy currency:

1. Phosphate anhydrides (compounds with high phosphate transfer potential)

General: hydrolysis of a phosphate ester

POR

O

OH

O

H2O

OHR P

O

OH

O

O H+ +

ATP hydrolysisO

PHO O

O

P

O

O

O P

O

CH2

OA

OH OH

O

HO P

O

O

O P

O

CH2

OA

OH OH

OO

PHO O

O

H2O

+ + H

ATP

Compound ∆G°’ (kcal/mol)

Phosphoenolpyruvate -14.8

Carbamoyl phosphate -12.3

Acetyl phosphate -10.3

Creatine phosphate -10.3

Pyrophosphate -8.0

ATP (to ADP) -7.3

Glucose 1-phosphate -5.0

Glucose 6-phosphate -3.3

Glycerol 3-phosphate -2.2

Free Energies of hydrolysis of some phosphorylatedcompounds

ATP is the most commonly used compound withhigh phosphate transfer potential• phosphoenolpyruvate & creatine phosphate

have enough energy to synthesize ATP• ATP can be used to synthesize glucose 6-

phosphate & similar compounds

GTP is sometimes used in place of ATP

ATP is called the energy currency of the cell

Foods ATP

Catabolism Anabolism

O2

CO2 + H2O [Energy]

Work

Heat

Biosynthesis

Definitions:• catabolism is the production of energy from

food• anabolism is the utilization of energy to provide

heat, do work, or drive biosynthetic reactions

2. Reducing equivalents (compounds with highelectron transfer potential)

Foods → NADH and FADH2 → ATP for Biosynthesis

The reducing equivalents in the foods we eat…• are transferred to NADH and FADH2 • NADH and FADH2 transfer their electrons to

the electron transport chain which..• uses the energy in those electrons to synthesize

ATP

Based on what you already know, you might predictthat:• catabolic pathways produce NADH, FADH2, &

ATP• anabolic pathways utilize ATP, NADH, & FADH2

However, that’s not quite true. In reality:• catabolic pathways produce NADH, FADH2, &

ATP• anabolic pathways utilize ATP, NADPH, & FADH2

B. Coenzymes

1. Definition

Coenzymes are small molecular weight compounds that are:a. necessary for the catalytic activity of

one or more enzymesb. present in very small amounts compared

to the substrates of the enzymec. used over & over in a catalytic manner

• most coenzymes exist free in solution• some coenzymes are bound to proteins

= prosthetic groups

2. Coenzymes carry some biologically important chemical group in an “activated” (high energy)form so that it can be used in biosyntheticreactions

Example = coenzyme A (carries acyl groups)

CCH3

O

SCoA + H20C

O

OH

CH2 + CoASH

acetyl CoA acetic acid

G = -7.5 kcal/mole

CR

O

SCoA

acyl CoA

+ H20C

O

OH

R+ CoASH

carboxylic acid

3. Coenzymes are sometimes derived from vitamins

Carrier Molecule

Group carried in activated form

Vitamin source of coenzyme

ATP Phosphoryl

NADH & NADPH

Electrons Niacin

FADH2 & FMNH2

Electrons Riboflavin

Coenzyme A Acyl Pantothenic acid

Lipoamide Acyl

Thiamine pyrophosphate

Aldehyde & Ketone

Thiamine

Biotin CO2 Biotin

Tetrahydro- folate

1-carbon units Folic acid

S-adenosyl- methionine

Methyl

UDP glucose Glucose

Some activated carriers in metabolism

C. What Does a Metabolic Pathway Look Like?• many reversible reactions• a few irreversible reactions that drive the

pathway• the irreversible reactions are important!

A B C D E FE1 E2 E3 E4 E5

D. Control of Metabolism1. Controls Which Operate at a Cellular Level

a. Which metabolites usually regulate pathways?

i. The precursor of a pathway usually stimulates the pathway

A B C D E+

ii. The end product of a pathway usuallyinhibits the pathway

A B C D E-

• regulation is by inhibitors & activators in cell

iii. The end product of a competing pathwayoften stimulates the other pathway

A B C D E+

G

HI

iv. Energy utilizing & producing pathwaysare often regulated on the basis of ATP supply in the cell

• Catabolic pathways are inhibited by ATP and/or stimulated by ADP or AMP

• Anabolic pathways are stimulated by ATP and/or inhibited by ADP or AMP

b. Where are pathways regulated?

i. At or near a branch point

A

B

D

C

*

*

ii. At 1st committed (irreversible) step

A B C D E*

2. Controls that operate at whole body level

• sites of regulation similar, but mechanisms different

a. Peptide hormones (glucagon, epinephrine,& insulin)

• act via second messenger (eg, cAMP)• result in phosphorylation or dephosphoryl-

ation• alter enzyme activity• are fast acting

b. Steroid hormones (cortisol)

• travel to nucleus & bind to DNA• affect amount of enzyme made• are slower acting

E. Glossary of Enzyme Names

Kinase: catalyzes the phosphorylation of somemetabolite, usually with ATP as the donor

Example = glucokinase or hexokinase

Phosphatase: catalyzes the hydrolytic removalof a phosphate group (also called dephosphorylation)

Example = glucose 6-phosphatase

glucose 6-phosphate + H2O → glucose + Pi

ATP + glucose → ADP + glucose 6-phosphate

Phosphorylase: catalyzes the phosphorolyticcleavage of a bond (phosphate is theattacking nucleophile)

Example = glycogen phosphorylase

+PiO

O

O O

O

O O

OHO

O

OPi

Hydrolase: catalyzes the hydrolytic cleavage ofsome bond (water is the attacking nucleophile)

Often subclassified according to bond cleavedEsterase: hydrolyzes ester bondPeptidase: hydrolyzes peptide bondPhospholipase: hydrolyses phospholipids

Dehydrogenase: catalyses oxidation-reductionreactions by the transfer of hydrogens (electrons). Generally use NAD+/NADH orFAD/FADH2.

Example = lactate dehydrogenase

Synthetase or synthase: catalyzes the joining oftwo molecules to create a larger molecule

Example: citrate synthase

oxaloacetate + acetylCoA + H2O → citrate + CoASH

(4 carbons) (2 carbons) (6 carbons)

CH3

C O

CO2-

Pyruvate + NADH + H+

+ NADH + H+NAD+ +

CH3

CHOH

CO2-

NAD+ + Lactate

Carboxylase: catalyzes the addition of CO2 to a molecule. Uses biotin as a coenzyme

Example = pyruvate carboxylase

pyruvate + CO2 + ATP + H2O OAA + ADP + Pi

Transferase: catalyzes the transfer of a group fromone molecule to another. Subclassifiedaccording to group transferred

Transaminase: transfers amino groups. Uses pyridoxal phosphate as a coenzyme.

+

-ketoglutarate Aspartate Glutamate

+

Oxaloacetate

Example = aspartate transaminase (AST)

CO2-

CH2

CH2

C O

CO2-

CH2

CH

CO2-

CO2-

NH3+

CO2-

CH2

CH2

CH NH3+

CO2-

CO2-

CH2

C O

CO2-

O

C

O

C

O

CH3

O

C

O

C

O

CH2 C

O

Opyruvate oxaloacetate

Transaldolase: transfers aldehyde groups. Usesthiamine pyrophosphate as a coenzyme

Transketolase: transfers ketone groups. Usesthiamine pyrophosphate as a coenzyme

Acyltransferase: transfers acyl (carboxylic acid)groups. Uses coenzyme A as a coenzyme

Methyltransferase: transfers methyl groups.

Decarboxylase: removes carboxyl groups as CO2

Isomerase: converts from one isomer to another

aldehyde:

ketone:

acyl (carboxylic acid):

R C CH3

O

R C

O

H

R C

OH

O