Ch 4: Cellular Metabolism, Part 1Ch 4: Cellular Metabolism, Part 1Ch 4: Cellular Metabolism, Part 1Ch 4: Cellular Metabolism, Part 1

EnergyEnergy as it relates to Biology as it relates to Biology Energy for synthesis and movement Energy transformation

EnzymesEnzymes and how they speed reactions

MetabolismMetabolism and metabolic pathways and metabolic pathways Catabolism (ATP production)Catabolism (ATP production) Anabolism (Anabolism (Synthesis of biologically

important molecules))

Energy in Biol. Systems:Energy in Biol. Systems: General definition of energy: General definition of energy:

Capacity to do workCapacity to do work Chemical, transport, movementChemical, transport, movement

First Law of Thermodynamics: First Law of Thermodynamics: Energy can neither be created Energy can neither be created nor destroyednor destroyed

Ultimate source of energy: Sun!Ultimate source of energy: Sun!

Fig 4-2

2 types of energy:2 types of energy:

Kinetic energyKinetic energy = motion = motionexamples ?

Potential energyPotential energy = stored energy = stored energyexamples ?

Energy (E) Transfer OverviewEnergy (E) Transfer Overview

Figure 4-1

Potential Energy

Kinetic Energy

WORK

heatheat (~ 70% of energyused in physical exercise)

Bioenergetics =Bioenergetics = study of energy flow

through biol. systems

Chemical reactions transfer energyChemical reactions transfer energy

A + B A + B C + DC + D

Substratesor reactants

Products

Speed of reaction = Reaction rateInitial force = Activation Energy

Potential Energy Stored in Chemical Potential Energy Stored in Chemical Bonds of Substrate can be . . .Bonds of Substrate can be . . .

1.1. transferred to the chemical bonds of transferred to the chemical bonds of the productthe product

2.2. released as heat (usually waste)released as heat (usually waste)

3.3. used to do work (used to do work (= = free energy)free energy)

Chemical Reactions Chemical Reactions p 93p 93

Activation energy

Endergonic vs. exergonic reactions reactions

Coupled reactionsCoupled reactionsDirect coupling vs. indirect couplingDirect coupling vs. indirect coupling

Reversible vs. irreversible reactionsReversible vs. irreversible reactions

Activation EnergyActivation Energy

Fig 4-3

Endo- and Exergonic ReactionsEndo- and Exergonic Reactions

Which is which??

ATP + H2O ADP + Pi + H+ + Energy

Enzyme (= Biol. Catalyst)Enzyme (= Biol. Catalyst)

1.1. Enzymes are proteinsEnzymes are proteins

2.2. rate of chemical reaction by lowering activation rate of chemical reaction by lowering activation energyenergy

3.3. is is not changed itself itself

1.1. It may change DURING the reactionIt may change DURING the reaction

4.4. does not change the nature of the reaction nor the does not change the nature of the reaction nor the resultresult

5.5. is specificis specific

Some important characteristics of an enzyme:

Fig 4-6

Enzymes lower activation energy:Enzymes lower activation energy:All chemical reactions in body must be conducted at body temp.!!

How do enzymes lower activation energy ?

Some more characteristics of Some more characteristics of enzymes:enzymes:

Usually end in –aseUsually end in –ase Inactive form: -ogenInactive form: -ogen in few cases RNA has enzymatic in few cases RNA has enzymatic

activity activity (eg: rRNA (eg: rRNA peptide bond) peptide bond) Isoenzymes may be produced in different Isoenzymes may be produced in different

areas of the bodyareas of the body E.g., LDHE.g., LDH

Small region of the complex Small region of the complex 3D structure is active (or 3D structure is active (or

binding) site.binding) site.

Enzymes bind to substrateEnzymes bind to substrate

Active Site:Active Site:

Old: Lock-and-key model / New: Induced-fit model

Enzyme-substrate interaction: Enzyme-substrate interaction: The old and the new modelThe old and the new model

Lock and Key:

Induced fit:

Naming of EnzymesNaming of Enzymes

KinaseKinase

PhosphatasePhosphatase

PeptidasePeptidase

DehydrogenaseDehydrogenase

mostly suffix mostly suffix -ase-asefirst part gives info on functionfirst part gives info on function

examples

Isoenzymes = Isoenzymes = different models of same different models of same

enzyme (differ in 1 or few aa)enzyme (differ in 1 or few aa)

Examples:Examples:

1.1. AmylaseAmylase

2.2. LDH → LDH → importance in diagnostics

Catalyze same reaction but under different Catalyze same reaction but under different conditions and in different tissues/organsconditions and in different tissues/organs

Enzyme Activity Enzyme Activity depends on depends on

1. Proteolytic activation (for some)(for some)

2.2. Cofactors & coenzymes Cofactors & coenzymes (for some)(for some)

3.3. TemperatureTemperature

4.4. pHpH

5.5. Other molecules interacting with enzymeOther molecules interacting with enzyme

1.1. Competitive inhibitorsCompetitive inhibitors

2.2. Allosteric modulatorsAllosteric modulators

1) Proteolytic 1) Proteolytic Activation Activation

Also 1. Pepsinogen Pepsin2. Trypsinogen Trypsin

2) Cofactors & Coenzymes2) Cofactors & Coenzymes

structure:Inorganic molecules (?)

function:conformational change of active site

structure:Organic molecules (vitamin derivatives, FADH2 ....)

function:act as receptors & carriers for atoms or functional groups that are removed from substrate

3)

4) Molecules interacting with enzyme4) Molecules interacting with enzyme

Competitive inhibitorsCompetitive inhibitors: : bind to active sitebind to active site

block active siteblock active site

E.g.: Penicillin binds covalently (= irreversiblyto important bacterial enzyme active site)

Fig 4-13

4)4) Molecules interacting with enzyme, cont’dMolecules interacting with enzyme, cont’d

Allosteric modulatorsAllosteric modulators (fig 4-14)(fig 4-14):: bind to enzyme bind to enzyme away from active siteaway from active site change shape change shape of active site (for better or for worse)of active site (for better or for worse)

= end product inhibitionSpecial case:

Allosteric Modulation

Reaction Rate Depends on Enzyme Reaction Rate Depends on Enzyme & Substrate Concentration& Substrate Concentration

Reversible Reactions follow the Reversible Reactions follow the Law of Mass ActionLaw of Mass Action

Three Major Types of Enzymatic Three Major Types of Enzymatic Reactions:Reactions:

1.1. Oxydation - Reduction reactionsOxydation - Reduction reactions(transfer of electrons or protons (H(transfer of electrons or protons (H++))))

2.2. Hydrolysis - Dehydration reactionsHydrolysis - Dehydration reactions(breakdown & synthesis of water)(breakdown & synthesis of water)

3.3. Addition-Subtraction-Exchange (of a Addition-Subtraction-Exchange (of a functional group) reactionsfunctional group) reactions

?

MetabolismMetabolism

Catabolism Anabolism