Metabolism:Fueling Cell Growth

Chapter 6

Metabolism

Cells must accomplish two fundamental tasks to grow Synthesize new components

Biosynthesis Harvest energy

The sum total of chemical reactions of biosynthesis and energy-harvesting is termed metabolism

Principles of Metabolism Metabolism is broken down into two

components Anabolism Catabolism

Catabolism Degradative reactions Reactions produce energy from

the break down of larger molecules

Anabolism Reactions involved in the

synthesis of cell components Anabolic reactions require energy

Anabolic reactions utilize the energy produced from catabolic reactions

Harvesting energy Energy defined as capacity to do work Exists as

Potential energy Stored energy

Kinetic energy Energy in motion

Doing work Energy can be converted from one form to

another Potential kinetic Kinetic potential

Principles of Metabolism

Principles of Metabolism

Harvesting energy Amount of energy available

released from bonds is free energy

Energy available to do work If reactants have more free

energy than products, energy is released

Exergonic reaction If products have more

energy that reactants, energy is consumed

Endergonic reaction

Components of metabolic pathways Process occurs in sequence of chemical reactions

Starting compound is converted to intermediate molecules and end products

Intermediates and end products can be used as precursor metabolites

Metabolic pathways employ critical components to complete processes

Enzymes ATP Chemical energy source Electron carriers Precursor metabolites

Principles of Metabolism

Principles of Metabolism

Role of enzymes Enzymes facilitate each step of metabolic pathway They are proteins acting as chemical catalysts

Accelerate conversion of substrate to product Catalyze reactions by lowering activation energy

Energy required to initiate a chemical reaction

Role of ATP Adenosine triphosphate (ATP)

Energy currency of cell Negatively charged phosphate groups attached to adenosine

molecule Negative charges of phosphate repel

Create unstable bond that is easily broken releasing energy

ATP created by three mechanism Substrate phosphorylation Oxidative phosphorylation Photophosphorylation

Principles of Metabolism

Principles of Metabolism

Substrate phosphorylation Uses chemical energy to

add phosphate ion to molecule of ADP

Oxidative phosphorylation Uses energy from proton

motive force to add phosphate ion to ADP

Photophosphorylation Utilizes radiant energy

from sun the phosphorylate ADP to ATP

Role of chemical energy source Energy source

Compound broken down to release energy Variety of compounds available

Glucose most common organic molecule

Harvesting energy requires series of coupled reactions

Oxidation-reduction reactions

Principles of Metabolism

Principles of Metabolism

Oxidation-reduction reactions Reactions in which one or more electrons is transferred

from one substance to another Compounds that LOSE electrons are oxidized

Termed electron donor Compounds that GAIN electrons are reduced

Termed electron carrier In reactions electrons are removed

Protons often follow generally in the form of H+ ion H+ ion has one proton and no electron

Role of electron carriers Three different types of electron carriers

Nicotinamide adenine dinucleotide NAD+

Flavin adenine dinucleotide FAD

Nicotinamide adenine dinucleotide phosphate NADP+

Reduced forms represent reducing power Due to usable energy in bonds Reduced forms

NADH FADH2

NADPH

Principles of Metabolism

Precursor metabolites Intermediate products produced in catabolic

pathways Used in anabolic pathways

Serve as raw materials for construction of macromolecules

Principles of Metabolism

Principles of Metabolism

Scheme of metabolism Three key pathways

Central metabolic pathways Glycolysis Pentose phosphate pathway Tricarboxcylic acid cycle

Central pathways are catabolic and provide

Energy Reducing power Precursor metabolites

Glycolysis Oxidizes glucose to two molecules of pyruvate

Pentose phosphate pathway (PPP) Breaks down glucose Produces molecules for biosynthesis Works in conjunction with glucose degrading pathways

Tricarboxylic acid cycle (TCA) Krebs Cycle Before entering cycle pyruvate enters transition step

Pyruvate formed in glycolysis and PPP Cycle turns twice to complete oxidation of one glucose

molecule

Principles of Metabolism

Respiration vs. fermentation Respiration uses reducing power to generate ATP

NADH and FADH2 transfer electrons to produce proton motive force

Allows for recycling of electron carriers Electrons join with terminal electron acceptor

Oxygen in aerobic respiration Anaerobic respiration uses another inorganic molecule

Fermentation is partial oxidation of glucose Produces very little ATP Uses pyruvate or derivative as terminal electron acceptor

Other organisms may use other organic molecules as terminal electron acceptor

Principles of Metabolism

Enzymes

Act as biological catalysts Very specific

A particular enzyme will only act with one or a limited number of substrates

Enzymes do not alter the reactants or products of a chemical reaction

Enzymes are not altered by the chemical reaction they catalyze

Enzymes are usually named for the substrate they act on and end in the suffix –ase

Protease

Enzymes Enzyme action

Enzymes act in two steps

Substrate binds to the active site of the enzyme to form an enzyme/substrate complex

A substrate is the specific substance on which the enzyme acts

Products are formed

E + S ES E + P Enzyme is released to bind

new substrate Enzymes are regulated

to prevent over production of product

Enzymes

Cofactors and coenzymes Cofactors

Non-protein component reacting with enzyme

Coenzymes Organic cofactors

Act as carriers for molecules or electrons

NAD+, FAD and NADP+ are coenzymes

Not as specific as enzymes May act with numerous

enzymes

Enzymes

Environmental factors of enzyme activity Enzymes function in narrow range of

environmental factors Factors affecting enzyme activity are

Temperature Increases temperature increases speed of reaction

Extremely high temperature makes enzyme non functional

pH Enzymes function best at pH just above 7

Salt concentration Low salt concentration are most desired

Enzymes

Allosteric regulation Regulation regulates production of

product Regulatory molecule binds to

allosteric site of enzyme Alters affinity of enzyme to

substrate Allosteric enzymes initiates activity

of give pathway Regulation controls metabolic

activity Feedback inhibition

End product of pathway acts on allotter site of enzyme

Shuts pathway down

Enzymes

Enzyme inhibition Non-competitive inhibition

Inhibitor and substrate act on different enzyme sites Allosteric inhibition Feedback inhibition

Competitive inhibition Inhibitor competes for active site with substrate Inhibitor structurally similar to substrate

Sulfa drugs compete with PABA for active site on enzyme that produces folic acid

Central Metabolic Pathways

Pathways modify organic molecules to form High energy intermediates to synthesize ATP Intermediates to generate reducing power Intermediate and end products as precursor

metabolites Pathways

Glycolysis Pentose Phosphate Pathway Tricarboxylic Acid Cycle

Central Metabolic Pathways

Glycolysis Primary pathway to convert one glucose to two

pyruvate 10 step process

Pathway generates Two 3-C pyruvate molecules Net gain of two ATP

2 ATP expended to break glucose 4 ATP harvested

Two molecules reducing power NADH

Six different precursor metabolites 5 intermediates and pyruvate

Glycolysis

Pentose phosphate pathway Generates 5 and 7 carbon sugars

Also produces glyceraldehyde 3-phosphate Can go into glycolysis for further breakdown

Pathway major contributor to biosynthesis Produces reducing power in NADPH Two vital precursor metabolites

Central Metabolic Pathways

Transition step Links glycolysis to Tricarboxylic Acid Cycle Modifies 3-C pyruvate from glycolysis to 2-C acetyl CoA

CO2 is removed through decarboxylation Remaining 2-C acetyl group joined to coenzyme A

Forms Acetyl CoA NAD+ is reduced to NADH

Each pyruvate enters transition step Reaction occurs twice for one glucose

Yield from transition step Reducing power

NADH Precursor metabolites

Acetyl CoA

Central Metabolic Pathways

Tricarboxylic acid cycle Completes the oxidation of glucose Incorporates acetyl CoA from transition step

Releases CO2 in net reaction

Cycle turns once for each acetyl CoA Two turns for each glucose molecule

Cycle produces 2 ATP 6 NADH 2 FADH2

2 precursor metabolites

Central Metabolic Pathways

Tricarboxylic Acid Cycle

Respiration

Uses NADH and FADH2 to synthesize ATP Oxidative phosphorylation

Occurs in electron transport chain Generates proton motive force

Combined with ATP synthase Uses energy in proton motive force to synthesize

ATP

Respiration

Electron transport chain Group of membrane-embedded electron

carriers Arrangement of carriers aids in production of

proton motive force Four types of electron carriers

Flavoproteins Iron-sulfur proteins Quinones Cytochromes

Mechanism of proton motive force Certain carriers accept protons and electrons,

some accept only electrons Pump protons across membrane

Creates a proton gradient (proton motive force Arrangement of carriers causes protons to be

shuttled across membrane

Respiration

Respiration

Electron transport chain of mitochondria Chain consists of following components

Complex I A.k.a NADH dehydrogenase complex

Complex II A.k.a succinate dehydrogenase complex

Coenzyme Q A.k.a cyrochiome bc, complex

Complex III Cytochrome C

A.k.a. Cyrochiome c oxidate complex Complex IV

Each carrier accepts electrons from previous carrier In process protons are pumped across membrane

Electron Transport Chainof Mitochondria

Respiration

Electron transport chain of prokaryotes Respiration is either aerobic or anaerobic In aerobic respiration some prokaryotes have

enzymes equivalent to complex I and II of mitochondria

Do not have enzyme equivalents of complex III or cytochrome c

Use quinones instead (ubiquinone) Shuttles electrons directly to terminal electron

acceptor Oxygen acts as acceptor when available

Electron Transport Chainof Prokaryotes (Aerobic)

Respiration

Electron transport chain in prokaryotes Anaerobic respiration is less efficient Alternative electron carriers used Oxygen does not act as terminal electron acceptor

Some bacteria use nitrate Nitrate converted to nitrite

Nitrite converted to ammonia Sulfur-reduce bacteria use sulfate as terminal electron

acceptor Quinone carrier (menaquinone) produces vitamin K

Respiration

ATP synthase Harvest energy from proton motive force to

synthesize ATP Permits protons to flow back into cell

Produces enough energy to phosphorylate ADP ATP

1 ATP is formed from entry of 3 protons 10 protons pumped out per NADH

One NADH produces 3 molecules ATP 6 protons pumped out per FADH

One FADH2 produces 2 molecules of ATP

Respiration

ATP from oxidative phosphorylation ATP produced through re-oxidation of NADH and

FADH2

Maximum theoretical yield From glycolysis

2 NADH 6 ATP From transition step

2 NADH 6 ATP From TCA

6 NADH 18 ATP 2 FADH2 4 ATP

Respiration Total ATP yield from prokaryotic aerobic respiration

Substrate phosphorylation 4 ATP

Net 2 from glycolysis 2 ATP from TCA

Oxidative phosphorylation 34 ATP

6 ATP from glycolysis Re-oxidation of 2 NADH

6 from transition step Re-oxidation of NADH

22 from TCA cycle Re-oxidation of NADH and FADH2

Total yield 4 + 34 = 38 (theoretical maximum)

Eukaryotic cells have theoretical maximum of 36 2 ATP spent crossing mitochondrial membrane

Fermentation

Used by organisms that cannot respire Due to lack of suitable inorganic electron

acceptor or lack of electron transport chain ATP produced only in glycolysis

Other steps for consuming excess reducing power

Recycles NADH Fermentation pathways use pyruvate or

derivative as terminal electron acceptor

Fermentation

End products of fermentation include Lactic acid Ethanol Butyric acid Propionic acid 2,3-Butanediol Mixed acids

All are produced in a series of reaction to produce appropriate terminal electron acceptors

Catabolism of Other Organic Compounds Cells use variety of organic molecules as

energy sources Use hydrolytic enzymes to break bonds

Hydrolytic reactions add water to break bonds

Catabolism of Other Organic Compounds

Polysaccharides and disaccharides Starch and cellulose polymers of glucose

Amylases breaks down starch to glucose subunits Cellulases breaks down cellulose to glucose subunits

Glucose enters glycolysis for metabolism

Disaccharides are hydrolyzed by specific disaccharidases

Disaccharides are formed between glucose and other monosaccharides

Glucose liberated through hydrolysis enters glycolysis Other monosaccharide modified before metabolism

Lipids Simple lipids are combination of fatty acids

and glycerol Hydrolyzed by lipases

Glycerol is converted to dihydroxyacetone phosphate

Molecule enters glycolysis Fatty acids degraded by β-oxidation

Transfers 2-C fatty acid units to coenzyme A Forms acetyl CoA that enters TCA cycle

Catabolism of Other Organic Compounds

Proteins Hydrolyzed by proteases

Amino group removed through deamination Remaining carbon skeleton converted to

precursor metabolite

Catabolism of Other Organic Compounds

Chemolithotrophs

Chemolithotrophs able to reduce inorganic chemicals as source of energy

Organisms fall into four groups Hydrogen bacteria

Oxidize hydrogen gas Sulfur bacteria

Oxidize hydrogen sulfide Iron bacteria

Oxidized reduced iron Nitrifying bacteria

Two groups One oxidizes ammonia to nitrite One oxidizes nitrite to nitrate

Chemolithotrophs generate ATP through oxidative phosphorylation Amount of energy gained depends on energy source

and terminal electron acceptor Organisms thrive in specific environments

Particularly where reduced inorganic compounds are found

Do not require external carbon source Produce organic carbon from inorganic source through

carbon fixation

Chemolithotrophs

Photosynthesis

Photosynthetic organisms harvest energy from sunlight Use energy to power synthesis of organic compounds

from CO2

Photosynthesis has two distinct stages Light dependent reactions

A.k.a light reactions Converts light energy to chemical energy

Light independent reactions a.k.a dark reactions Uses energy from light reactions to produce organic

compounds

Capturing radiant energy Photosynthetic organisms highly visible due to light

capturing pigments Pigments include

Chlorophyll Found in plants, algae and cyanobacteria

Bacteriochlorophylls Found in purple and green photosynthetic bacteria

Accessory pigments Includes carotenoids and phycobilins

Carotenoids found in eukaryotes and prokaryotes Phycobilins found only in cyanobacteria

Reaction center pigments Function as electron donors

Antennae pigments Funnels light energy to reaction center pigments

Photosynthesis

Photosynthesis

Converting radiant energy to chemical energy Light reactions accomplish two tasks

Synthesize ATP through photophosphorylation Generate reducing power to fix carbon dioxide

Reducing power may be NADH or NADPH

Light Dependant Reactions

Carbon Fixation

Carbon dioxide converted to organic carbon through carbon fixation Occurs in dark reactions in photosynthesis Consumes great deal of energy Calvin cycle most common pathway of carbon

fixation

Carbon fixation

Calvin Cycle A.k.a Calvin-Benson cycle Has three essential stages

Incorporation of CO2 into organic compound

Reduction of resulting molecules

Regeneration of starting compound

One molecule of fructose produces from 6 turns of cycle

6 turns consumes 18 ATP and 12 NADPH

Process has three sages

Anabolic Pathways

Synthesis of subunits from precursor metabolites Pathways consume ATP, reducing power and

precursor metabolites Macromolecules produces once subunits are

synthesized

Lipid synthesis Synthesis begins with transfer of acetyl group

from acetyl CoA to acyl carrier protein Carrier hold fatty acid during elongation

Fatty acid released when reaches required length 14, 16 or 18 carbons long

Glycerol is synthesized from dihydroxyacetone phosphate

Anabolic Pathways

Amino acid synthesis Some precursors are formed in glycolysis

other in TCA cycle Glutamate synthesis essential for formation of

other amino acids Synthesis incorporates ammonia with α-

ketoglutarate produce in TCA cycle Amino group from glutamate can be transferred to

produced other amino acids Precursors for aromatic amino acids produced

in pentose phosphate pathway and glycolysis

Anabolic Pathways

Nucleotide synthesis Nucleotides synthesized as ribonucleotides

and modified to deoxribonucleotides Replace OH group on 2’ carbon of ribose and

replace with hydrogen atom Remove oxygen

Anabolic Pathways