Chapter 10: Introduction to Metabolism

Aspects of Metabolism Common to All Organisms

• Life obeys the laws of thermodynamics

• Cells obtain energy from their environment which is conserved in a form of ATO

• Redox reactions play a critical role in energy conservation

• Chemical reactions that occur in cells are organized into pathways

• Each reaction of a pathway is catalyzed by an enzyme

• Functioning of biochemical pathways is regulated

Cellular 'Work' and Energy Transfers

1. Chemical work

   1. Conversion of complex molecules

2. Transport work

   1. In and out of nutrients, wastes and ions

3. Mechanical work

   1. Cell motility and movement of structures within cells

• Source of energy

  • Sunlight and chemicals

  • Most commonly stored in ATP

Laws of Thermodynamics

Thermodynamics - energy changes in a cell and organisms

First Law of Thermodynamics

• Energy can neither be created nor destroyed

• Total energy in universe remains constant although it can be converted

Second Law of Thermodynamics

• Physical and chemical processes proceed in such a way that the entropy of the universe increases

• Not all energy can be used

  • Total energy = usable energy + unusable energy

Energy Units

• Calorie

  • Amount of heat needed to raise 1g of water 1C, specifically form 14.5 to 15.5C

• Joule

  • Unit of work capable of being done

  • 1 cal of heat = 4.184 J of work

Free Energy and Reactoins

DG = DH -TDS

• Relates change in energy that can occur in chemical reactions

• DF

  • Chane in free energy

  • Amount of energy available to do work

• DF

  • Change in enthalpy

• T

  • Temperature in K

• DS

  • Change in entropy

• Used to indicate if a reaction will proceed spontaneously

  • DG - , reaction is spontaneous

  • DG + , reaction is nonspontaneous

Chemical Equilibrium

• Equilibrium

  • Rate in both directions equal

• Equilibrium constant Keq

  • Relates equilibrium concentrations of products and reactants to one another

Role of ATP in Metabolism

Exergonic breakdown of high-energy ATP is coupled with endergonic reactions to make them more favorable

ATP + H2O --> ADP + Pi + H+

DG = -7.3kcal/mol

ATP-Involved Reactions

1. Transport

   1. Active transport of mineral in and out of cell

2. Mechanical activity

   1. Muscle contraction

3. Chemical reaction

   1. Production of molecules

10.3 Redox Reactions

Reaction involving the transfer of electrons from an electron donor (reduced) to an electron acceptor (oxidized)

Electron Transport Chain (ETC)

Electron carriers are membrane bound and organized into a system called the ETC

• Electron carriers/donors

  • NAD

  • FAD

• ATP is the final product

Electron Carriers

• Located in PM and intracytoplasmic membranes of bacterial and archaeal cells

• Localized in the internal membranes of mitochondria and chloroplasts in eukaryotic cells

• Nicotinamide adenine dinucleotide (NAD)

• Nicotinamide adenine dinucleotide phosphate (NADP)

• Flavin adenine dinucleotide (FAD)

• Flavin mononucleotide (FMN)

• Coenzyme Q (CoQ)

• Cytochromes

• Nonheme iron proteins

• Ferredoxin

Biochemical Pathway Forms

• Linear

• Cyclic

• Branching

Biochemical Pathways form Complex Networks

Pathways often overlap/feed into each other

• Intermediates of a pathway may be diverted from one pathway to another pathway

Enzyme Terminology

Enzyme

• Proteins that act as biological catalysts

• Accelerate chemical reactions

Catalyst

• Substance that increases the rate of a chemical reaction without changing itself

Substrates

• Reactant which is consumed during enzymatic reaction

Products

• Substances formed by reaction

E + S --> ES complex --> E + P

Structure of Enzymes

• Apoenzyme

  • Inactive, protein component of an enzyme

• Cofactor

  • Inorganic component of an enzyme (ions)

• Coenzyme

  • Organic molecule (NAD, biotin..)

• Holoenzyme

  • Functional, apoenzyme and cofactor

Classification of Enzymes

Six general classes with names based on the substrate

1. Oxidoreductase

   1. Oxidation-reduction reactions

2. Transferase

   1. Reactions involving the transfer of chemical groups between molecules

3. Hydrolase

   1. Hydrolysis (break down) of molecules

4. Lyase

   1. Breaking of C-C, C-O, C-N, and other bonds by a means other than hydrolysis

5. Isomerase

   1. Rearranges molecules to isomer form

6. Ligase

   1. Joining of two molecules using ATP or the energy of other nucleoside triphosphates

Mechanism of Enzyme Reactions

A + B --> AB --> C + D

Enzymes increase reaction rate, but don't alter their equilibrium constants

• Activation energy Ea

  • Energy required to form transition-state complex

  • Enzyme lowers activation energy

Environmental Effects on Enzyme Activity

Enzyme activity may be influenced by

1. pH

2. Temperature

3. Substrate concentration

4. Enzyme concentration

Enzyme Activity and Environmental Conditions

• Each enzyme has optimal temperature and pH

• When temperatures increase, enzyme activity drops quickly

• Reaction rate increases as substrate or enzyme concentration increases

• No further increase occurs after all enzyme molecules are saturated with substrate

Enzyme inhibition

Competitive inhibitor

• Directly competes with substrate to the active/catalytic site

Noncompetitive inhibitor

• Binds enzyme at site other than active site (allosteric site) causing enzyme's conformational change

Ribozymes

• Thomas Cech discovered that some RNA molecules also can work as an enzyme

• Examples

  • Catalyze peptide bond formation

  • Self-splicing

  • Involved in self-replication

Regulation of Metabolism

• For conservation of energy and materials

• To maintain metabolic balance

• Three regulating mechanisms

  1. Metabolic channeling

  2. Regulation of enzyme production

  3. Control enzyme's enzymatic activity (posttranslational regulation)

Metabolic Channeling

• Localizes enzymes and metabolites to specific parts of a cell

Compartmentation

• Distribute/store enzymes and metabolites to certain cell structures or organelles

• Controls availability of enzyme and substrates

Posttranslational Regulation of enzyme activity

• Allosteric regulation

  • Allosteric effector binds reversibly and noncovalently at a regulatory/allosteric site

  • Changes shape of enzyme and alters activity of catalytic site

• Covalent modification

  • Reversible formation of a covalent bond between a small molecule and a specific amino acid side chain (s) on an enzyme that affects its activity

Feedback Inhibition

Also called end product inhibition

• Inhibition of one or more critical enzymes in a pathway regulates entire pathway

• Each end product regulates its own branch of the pathway

Isoenzymes

• Different forms of an enzyme that catalyze the same reaction