METABOLISM OVERVIEW

Student Edition 5/24/13 Version

Pharm. 304 Biochemistry

Fall 2014

Dr. Brad Chazotte 213 Maddox Hall

chazotte@campbell.edu

Web Site:

http://www.campbell.edu/faculty/chazotte

Original material only ©2000-14 B. Chazotte

Goals

• Understand that there is a chemical “logic” to metabolism.• Understand the thermodynamic logic of metabolism.• Understand the role of coupled reactions in metabolism• Understand how various mammalian organs interact metabolically

in the flow of energy (fuels).• Learn the various types of chemical reactions in metabolism.• Remember metabolically important electrophiles & nucleophiles.• Learn the principal ways metabolic processes are regulated

METABOLISM:• Metabolism comprises the entire network of chemical reactions in living

cells.

• Bioenergetics and metabolism are closely inter-related.

• Intermediary metabolism is a term applied to reactions involving low molecular weight molecules. These metabolites are the small molecules that are the intermediates in biopolymer synthesis or degradation.

• Reactions that degrade molecules to liberate smaller molecules and energy are called catabolic reactions.

• Reactions that synthesize molecules that the cell uses for growth reproduction and maintenance are called anabolic reactions. These reactions require energy.

Topic: Metabolism Horton et al., 2002 3rd p309

1. Performance of mechanical work in muscle contraction and other cellular movements.

2. Active transport of molecules and ions.

3. Synthesis of macromolecules and other biomolecules from simple precursors

Living organisms derive energy from the environment to maintain the organism in a thermodynamic state far from equilibrium

Living organisms require a continual input of energy for three major purposes:

• Metabolic Pathways are irreversible

The existence of independent interconversion routes is an important property of metabolic pathways because it allows independent control of rates of the two processes.

• Every metabolic pathway has a first committed step.

However, most of the component reactions are at or near equilibrium.

• All metabolic pathways are regulated.

Most metabolic pathways are controlled by regulating the enzymes that catalyze their first committed steps.

• Metabolic pathways in eukaryotic cells occur in specific cellular locations.

Voet ,Voet, & Pratt 2013 Fig. 14.4

Metabolic (Logic) Principles

The synthesis of metabolites in specific membrane-bounded subcellular compartments makes their transport between these compartments a vital part of eukaryotic metabolism.

Voet ,Voet, & Pratt 2013 p.444

COMMON THEMES FOR ORGANISMS IN METABOLISM:

• Cell membranes provide the physical barriers that form compartments and segregation from the external environment.

• Specific internal conc. of inorganic ions, metabolites & enzymes are maintained.

• Energy for Rx is extracted from external sources either by photosynthetic reactions or solely chemically from the ingestion & catabolism of energy-containing molecules.

• Metabolic pathways in each organism are specified by its genes.

• Interaction with the environment: activities of cells are geared to the availability of energy. Growth & reproduction occur in energy-rich environments. In energy-poor environments organism can temporarily reduce demand by slowing metabolic rates or use internals stores. Eventually they may die.

• Cells are dynamic. Many components are continually synthesized and degraded (turnover) while their concentrations are essentially static.

Topic: Metabolism Horton et al., 2002 3rd p311-312

TROPHIC STRATEGIES I:

The nutritional requirements of an organism are a reflection of its metabolic free energy source.

Autotrophs: synthesize all their cellular constituents from simple molecules: e.g. H2O, CO2, NH3 and H2S. - some prokaryotic organisms

Chemolithotrophs: obtain their free energy via the oxidation of inorganic compounds, e.g. NH3, H2S, and Fe2+.

Photoautotrophs: obtain their free energy via photosynthesis – light energy to produce carbohydrates from CO2.

Heterotrophs: obtain free energy via the oxidation of organic compounds, e.g. carbohydrates, lipids, proteins.

Topic: Metabolism Voet, Voet & Pratt, 2013 p437

TROPHIC STRATEGIES II:

Additional classification based on the oxidizing agent for nutrient breakdown.

Obligate Aerobes: must use O2, - includes animals

Aerobes: employ sulfate or nitrate as oxidizing agents.

Facultative anaerobes: can grow either in the presence of absence of O2. Example: E. Coli.

Obligate Anaerobes: grow in the absence of O2 and are in fact poisoned by oxygen.

Topic: Metabolism Voet, Voet & Pratt, 2013 p437

Nutrients, Organs, and Circulation

Matthews et al 2003 Fig 23.1

IN GENERAL: An organ specialized to produce a certain fuel lacks the enzymes to use that fuel.

Major fuel depots are:Triacylglycerols- stored mainly in adipose tissueProtein –most of it existing in skeletal muscles

Glycogen – which is stored primarily in liver and muscle

Major Events: Storage, Retrieval, & Use of “Fuels”

Matthews et al 2003 Fig 23.4

Metabolism and Thermodynamic Logic

Metabolism in some ways is concerned with the liberation of energy from molecules in order to do work, drive other reactions, or to help synthesize other molecules.

THERMODYNAMICSFREE ENERGY

Cramer & Knaff 1990

At constant temperature and pressure

DGp,T = DH -TDS

The free energy change can be defined as that portion of the total energy change which is available to do work as the system proceeds to equilibrium at constant temperature and pressure.

The conditions of constant temperature and pressure are typical of biological systems.

One can also state that for a reaction that :

DGreaction = DG products - DGreactants

THERMODYNAMICS: Free Energy 1Free Energy Change of Chemical Reactions:

Consider the relationship between a chemical reaction and its equilibrium constant.

reactants products

aA + bB cC + dD

Where a,b,c,d, are the number of molecules of A,B,C and D in the reaction. The free energy change at constant temperature and pressure is given by:

Cramer & Knaff 1990; Lehninger 1977

[C]c [D]d

DG = DG + RT ln [A]a [B]b

[ ] = molal concentrations

R = gas constant = 1.98 cal-1 mol-1 = 8.315 joules mole-1 deg-1

T = abs. Temp in K

DG is the standard free energy change of the reaction, here defined as at 298 ºK, at component concentrations of 1 M and 1.0 atm. pressure.

Coupled Reactions in Metabolism

Metabolism, at its most fundamental, is basically a series of linked chemical reactions that take one molecule and convert it to another molecule or molecules in a carefully defined fashion.

Berg, Tymoczko & Stryer, 2012 Fig. 15.1Metabolism Overview

Glucose Metabolism

Berg, Tymoczko & Stryer, 2012 Fig. 15.2

Chart of Metabolic Pathways

Berg, Tymoczko & Stryer, 2012 Fig. 15.10Metabolism Overview

Prominent Fuels

Complete Oxidation to Molecular OxygenGlucose Note: 1 cal =4.184J

C6H12O6 + 6 O2 6 CO2 + 6 H2O G° ’=-2823 kJ mole-1

Broken down into the half reactions:

C6H12O6 + 6 H2O 6CO2 + 24H+ + 24 e-

6 O2 + + 24H+ + 24 e- 12 H2O

Palmitic Acid

Palmitoyl-CoA + 23O2 + 131 Pi + 131 ADP CoA + 16CO2 + 146 H2O +131 ATP

Palmitic Acid + 23 O2 16 CO2 + 16 H2O G°’= -9790.5 kJ mole-1

129 ADP + 129Pi 129 ATP + 129 H2O G°’= +3941 kJ mole-1

129 ATP is the next yield since 2 ATP are needed to form palmitoyl-CoA from palmitic acid. To Form 1 ATP G°’= +30.54 kJ mole-1 = 7.3 kcal mole-1

Berg, Tymoczko & Stryer, 2012 Fig. 15.12Metabolism Overview

Stages of Catabolism

Reoccurring “Motifs” in Metabolic Pathways

Berg, Tymoczko & Stryer, 2002 Glycolysis

Modular Design & Economy: Activated Carriers

Economy of Metabolic Design: Six Reaction Types

Design of Metabolic Regulation: Three Control Mechanisms

Berg, Tymoczko & Stryer, 2012 Table. 15.2Metabolism Overview

Example of Metabolic Activated Carriers

Common Vitamin and Their Characteristics

Voet, Voet & Pratt 2013 Table 14.1 Berg, Tymoczko & Stryer, 2012 Table. 15.3, 15.4

CHEMICAL LOGIC IN METABOLISM and the Economy of Metabolic Design

Berg, Tymoczko & Stryer, 2012 Table. 15.5Metabolism Overview

Types of Metabolic Chemical Reactions

Modes of C-H Bond Breaking

Voet & Voet Biochemistry 1995 Fig 15.4Metabolism: Chemical Logic

Compound Types In Heterolytic Bond Cleavage

NUCLEOPHILES (“nucleus lovers”) – Electron-rich compounds that are negatively charged or contain unshared electron pairs that easily form covalent bonds with electron-deficient centers. Important groups: amino, hydroxyl, imidazole, and sulfhydral groups.

ELECTROPHILES (“electon lovers”)– Electron deficient compounds that can be positively-charged, contain an unfilled valence electron

shell, or contain an electronegative atom. Most common biological ones are: H+, metal ions, the carbon atoms of carbonyl groups and cationic imines.

Voet & Voet 1995, p416

Breaking a covalent bond where the electron pair of the covalent bonds remains with one of the atoms. (Homolytic:electron pair split between atoms.)

Metabolism: Chemical Logic

Biologically Important Nucleophilic Groups

Voet & Voet Biochemistry 1995 Fig. 15.5Metabolism: Chemical Logic

Nucleophilicity and Basicity are Closely Related Properties

Voet & Voet Biochemistry 1995 Chap 15 Fig. p416Metabolism: Chemical Logic

Biologically Important Electrophiles

Voet & Voet Biochemistry 1995 Fig. 15.6Metabolism: Chemical Logic

Group Transfer Reactions

Voet & Voet Biochemistry 1995 Chap 15 Fig. p417Metabolism: Chemical Logic

Types of Metabolic Group Transfer Reactions

Voet & Voet Biochemistry 1995 Fig. 15.7

Acyl group transfer

Phosphoryl group transfer

Glycosyl group transfer

Metabolism: Chemical Logic

carbonyl carbon

nucleophile Orig. acyl carrier

nucleophile Apical leaving group

Apical attacking group

C1 carbon

Oxidation-Reduction Rx’s

Voet & Voet Biochemistry 1995 Chap 15 Fig. P 418Metabolism: Chemical Logic

Possible Elimination Reactions Mechanisms(e.g., dehydration reaction)

Voet & Voet Biochemistry 1995 Fig. 15.9Metabolism: Chemical Logic

Note: Elimination reactions result in the formation of a double bond between two previously single-bonded, saturated centers.

ALDOSE-KETOSE ISOMERIZATION MECHANISM

Voet & Voet Biochemistry 1995 Fig 15.10Metabolism: Chemical Logic

Biochemical isomerizations involve the intramolecular shift of a hydrogen atom to change the location of a double bond.

Examples of C-C Bond Formation and Cleavage Reactions

Voet & Voet Biochemistry 1995 Fig 15.11Metabolism: Chemical Logic

Reactions that make and break C-C bonds forms the basis of both degradative and biosynthetic metabolism

Stabilization of Carbanions

Voet & Voet Biochemistry 1995 Fig. 15.12Metabolism: Chemical Logic

Regulation of Metabolic ProcessesPrincipal Ways

• The amount of enzymes

• The catalytic activities of the enzymes

• The accessibility of substrates

Berg, Tymoczko & Stryer, 2002 Metabolism OverviewMetabolism Overview

Control of the amount of enzyme

The amount of a particular enzyme depends on both its rate of synthesis (genetic control) and its degradation.

For most enzymes their level is primarily controlled by altering the rate of transcription of their genes. (In higher organism the response is on the order of hours or days.)

Example: Lac operon in E. Coli (lower organism) – in the the presence of lactose a 50-fold increase in the synthesis of -galactosidase occurs within minutes of exposure.

Berg, Tymoczko & Stryer, 2002 Metabolism Overview

Metabolism Overview

Control of enzyme catalytic activity• Reversible allosteric control

Allosteric effectors are often substrates, products or coenzymes. Consider that the first reaction of many biosynthetic pathways is inhibited by the ultimate product – for instance, cytidine triphosphate inhibits the enzyme aspartate transcarbamylase, an example of feedback inhibition which can be nearly instantaneous

• Reversible covalent modification

Typically phosphorylation or dephosphorylation is used. For instance, glycogen phosphorylase is activated by the phosphorylation of a specific serine residue at low glucose levels. Covalent modification may, in turn, be controlled by hormones.

• Hormones coordinate metabolic relations between different tissues.

This is frequently accomplished by regulating the reversible modification of key enzymes. For instance, epinephrine effect on muscle tissue or insulin promoting the uptake of glucose into many kinds of cells

Berg, Tymoczko & Stryer, 2002 Metabolism OverviewMetabolism Overview

Control of substrate flux

Regulation of the movement of substrates from one compartment to another can serve as a control point.

For instance, the movement of long-chain fatty acids from the cytosol to the mitochondrial matrix.

Berg, Tymoczko & Stryer, 2002 Metabolism OverviewMetabolism Overview

End of Lecture

Berg, Tymoczko & Stryer, 2002 Metabolism OverviewMetabolism Overview