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Metabolism: The Generation of Energy

I.Energy and work

A.Energy:

Capacity to do work

Three types of work occur in living organisms:

Chemical work:

Biosynthesis

Transport work:

Movement of molecules against a concentration gradient

Mechanical work:

Movement

Sunlight:

Ultimate source of all biological energy:

Converted to complex organic molecules by photoautotrophs:

Complex organic molecules serve as carbon and energy sources for heterotrophs

Cells obtain energy by carrying out chemical reactions:

2000 chemical reactions can occur in a single cell:

Each reaction (with a few exceptions) mediated by a different enzyme:

Cell must synthesize at least 2000 enzymes

B.Enzymes:

Protein catalysts:

Increase the rate of reactions but do not alter their equilibrium constant

Specific for:

Reaction catalyzed  Molecules acted upon

Bring substrates together at the active site (catabolic site):

Enzyme-substrate complex

Speed up reactions hundreds of thousands of times

Active at temperatures ranging between 0o- 37oC

During a chemical reaction energy available for the performance of work is either released or absorbed:

G = energy available for work

 = change in

G = Free Energy Change:

Amount of usable energy liberated or absorbed during a chemical reaction:

Expressed in calories

G chemical energy:

Exergonic reactions have negative G (-8000 calories):

Release energy

Occur spontaneously

Endergonic reactions have positive G (+8000 calories):

Absorb energy

Do not occur spontaneously:

Energy must be supplied before the reaction can occur

Cells use energy released by exergonic reactions to drive endergonic reactions:

Couple an exergonic with an endergonic reaction by means of a common reactant:

1.Exergonic reaction:

A  B

G = -10,000 calories

2.Endergonic reaction:

C  D

G = +5,000 calories

3.Coupled reaction:

A + X  B + Y

G = -2,000 calories

Know:

A  B has a G of -10,000 calories

Calculate that:

Y has absorbed 8000 calories in going from X to Y

Add:

Y to C  D:

4.Coupled reaction C + Y  D + X

G = -3000 calories

Y (common reactant):

Releases 8000 calories in going from Y to X

Uses 5000 calories in going from C to D:

Leaving a G of -3000 calories

C.Reactions involved in production of cellular energy are oxidation reactions:

Oxidation:

Loss of electrons & a gain in positive valance

Electron donor:

Oxidized substance gives up electrons

Oxidation reactions always accompanied by reduction reactions:

Reduction:

Gain of electrons & a loss of positive valance

Requires an:

Electron acceptor:

Reduced substance

Accepts electrons

Examples of a coupled oxidation/reduction reaction:

H2 2H+ + 2e-(electron donating)

O + 2e-  O2-(electron accepting)

2H+ + O2- H2O (water formation)

Hydrogen is oxidized (loses electrons)

Oxygen is reduced (gains electrons)

Glucose is the primary energy source of most microorganisms:

Complete oxidation of glucose:

Glucose (C6H12O6) + 6O2 6CO2 + 6H2O

Oxidation of glucose releases electrons:

Glucose  6CO2 + 12 electrons + 12H+

Reduction of oxygen consumes electrons:

6O2 + 12 electrons + 12H+  6H2O

Electrons never exist as free electrons:

Must be part of a molecule

D.Electron carriers:

Carry electrons between reactions:

Able to:

Accept & donate electrons readily:

Undergo reversible oxidation & reduction

Two most important electron carriers:

Nicotinamide Adenine Dinucleotide (NAD):

Electron carrier involved in catabolic processes

Nicotinamide Adenine Dinucleotide Phosphate (NADP):

Electron carrier involved in biosynthetic processes

Electrons carriers:

Transfer electrons from one redox pair to another:

Act as common reactants

E.Energy transfer compounds:

Energy released by oxidation must be saved for use by the cell:

Much energy released during oxidation is transferred to a phosphate compound via a high energy phosphate bond ~P (squiggle P)

Several types of energy transfer compounds in cells:

Able to transfer large amounts of free energy:

Energy which is not stored or transferred is usually released as heat:

Lost to the cell for useful work

Most common high energy phosphate compound in the cell

ATP (Adenosine Triphosphate):

Other high energy compounds in cells:

GTP (Guanidine Triphosphate)

UTP (Uridine Triphosphate)

II.Metabolism:

A.Total of all the organized chemical activity of the cell:

Made possible by:

1.Flow of energy through cell:

Release of energy from reduced organic compounds

Use of energy in:

The synthesis of macromolecules

Movement

2.The activities of enzymes

B.Metabolism has two major parts:

1.Catabolism:

Reactions by which energy producing molecules are degraded:

Reactions which liberate energy

2.Anabolism:

Reactions leading to the synthesis of biopolymeres:

Making large molecules from smaller molecules:

Requires energy

Albert Lehninger:

Catabolism may be divided into three stages:

Stage one:

Proteins

Carbohydrates

Lipids

Large nutrient molecules are hydrolyzed to their component parts:

Amino acids

Monosaccharides

Fatty acids

Glycerol

Hydrolysis does not release much energy

Stage two:

Products of Stage one are degraded to a few simpler molecules:

Acetyl coenzyme A

Pyruvate

Tricarboxylic acid cycle intermediates

Stage two reactions may occur under aerobic or anaerobic conditions:

Produces small amounts of:

ATP

NADH

Stage three:

Nutrient carbon fed into Tricarboxylic acid cycle:

Oxidized completely to CO2:

Generates much energy:

Produces:

ATP

NADH

FADH2

C.Catabolism begins with wide variety of molecules:

Number and complexity reduced at each step:

Nutrient molecules  smaller and smaller number of metabolic intermediates:

Finally fed into the TCA cycle

Nutrients serve two functions in heterotrophic metabolism:

Oxidized to provide energy

Supply carbon or building blocks for synthesis of new cell constituents

D.Amphibolic pathways function both:

Catabolically and anabolically

Glycolysis - Most important

TCA cycle

Most reactions in these two pathways are reversible:

Can be used to synthesize and degrade molecules

E.The break down of Glucose to pyruvate:

Three Major pathways:

1.Glycolytic (Embden-Myrerhof) Pathway

2.Pentose Phosphate Pathway (hexose monophosphate pathway)

3.Entner-Doudoroff:

Converts glucose to pyruvate and glyceraldhyde 3-phosphate by producing 6-phosphoglyconate and then dehydrating it

Found primarily in some Gram-negative bacteria:

Pseudomonas

Rhizobium

Agrobacterium

III.Glycolysis:

A.Most common biochemical pathway to pyruvate

Found in all major groups of microorganisms

Occurs in the cytoplasm in the presence or absence of oxygen

Two major parts:

Six-carbon stage

Three-carbon stage

B.Six-carbon stage:

Glucose phosphorylated twice  fructose 1,6 bisphosphate:

Uses 2 ATP molecules:

Does not release energy

C.Three-carbon stage:

Fructose 1,6 bisphosphate cleaved:

Two 3-carbon molecules result:

Glyceralaldehyde-3-P

Dihydroxyacetone-P

(converted to Glyceralaldehyde-3-P)

These three carbon molecules:

Converted to Pyruvate in five steps:

Glyceralaldehyde-3-P is oxidized:

NAD+ is electron acceptor

Inorganic phosphate incorporated at the same time  1,3 bisphosphoglycerate (high energy molecule)

~P on carbon 1 transferred to ADP  ATP:

D.Substrate level phosphorylation:

ATP synthesized by direct transfer of a ~P to ADP from an intermediate of a catabolic pathway

E.GLYCOLYTIC PATHWAY

F.SUMMARY OF GLYCOLYSIS:

4 ATP molecules are synthesized:

2 from each 3 carbon fragment

2 ATP used to phosphorylate glucose subtracted from the total of 4:

 net gain of 2 ATP molecules

Net energy yield from glycolysis small:

Not efficient in retaining energy for cell use:

26% of the energy released is retained:

Rest lost as heat

The two pyruvate molecules still have most of the energy stored in glucose

IV.The Tricarboxylic Acid (TCA) Cycle:

  1. Generalities

In eukaryotic cells:

Occurs in the mitochondria

In prokaryotic cells:

Occurs in the cell membrane

Degrades pyruvate to CO2

B.Pyruvate Dehydrogenase Complex

Oxidizes pyruvate to CO2 and Acetyl Coenzyme A (acetyl-CoA)

Acetyl-CoA produced by the catabolism of:

Carbohydrates

Lipids

Amino acids

Acetyl-CoA is the substrate of the TCA cycle

  1. TCA Cycle

C.Summary of the TCA Cycle

Two complete cycles are needed to oxidize the two pyruvate molecules produced by glycolysis

During each cycle 8 e- & 8 H atoms are removed from the substrate:

For each glucose molecule the TCA cycle removes 16 e- & 16 H atoms

12 of the e- are transferred to NADH (each NAD accepts 2 e-)

4 e- are transferred to FADH2

(each FAD accepts 2 e-)

6 NADH & 2 FADH2 are produced for each molecule of glucose that is oxidized during the TCA cycle

Other NADH Production:

2 NADH are produced during the conversion of pyruvate to acetate

2 NADH are produced during glycolysis

D.Total production of reduced electron carriers:

NADH:

6 from TCA cycle

2 from oxidation of pyruvate to acetyl-CoA

2 from glycolysis

FADH2:

2 from TCA cycle

V.Electron Transport and Oxidative Phosphorylation:

A.Electron Transport Chain:

Composed of a series of e- carriers

Transfer e- from NADH and FADH2 to terminal e- acceptor (O2)

Allows electrons to flow down a chain of electron carrier enzymes of successively lower energy levels

B.Electron transport chain carriers located in:

Membranes of mitochondrial cristae in eukaryotic cells

Plasma membrane of prokaryotic cells

Arranged in 4 complexes of carriers:

Each complex capable of transporting e- part of way to O2

Complexes connected by:

Coenzyme Q

Cytochrome C

As electrons pass from one carrier to next:

Lose energy:

Some saved in ATP (OXIDATIVE PHOSPHORYLATION)

VI.ATP Yield from the Aerobic Oxidation of Glucose:

A.Glycolysis:

Substrate-level phosphorylation:

2 ATP

Oxidative Phosphorylation with 2 NADH:

6 ATP

B.Two pyruvate molecules converted to 2 Acetyl-Co A molecules:

Oxidative Phosphorylation with 2 NADH

6 ATP

C.Tricarboxylic Acid Cycle

Substrate-level phosphorylation

2GTP  2 ATP

Oxidative Phosphorylation with 6 NADH

18 ATP

Oxidative Phosphorylation with 2 FADH2

4 ATP

Total Aerobic Yield 38 ATP

VII.FERMENTATION:

A.Energy yielding process in which organic molecules serve as both electron donors and acceptors.

During Fermentation:

NADH oxidized to NAD

Pyruvate or a pyruvate derivative acts as the terminal e- acceptor:

End product of the reaction acts as electron acceptor

B.Alcoholic fermentation:

Many fungi (yeast), some bacteria, algae and protozoa ferment sugars to CO2 & ethyl alcohol

Ethyl alcohol is terminal electron acceptor

No ATP molecules generated from NADH

Fermentation occurs in the presence or absence of oxygen

Oxygen is not the terminal electron acceptor

Only 2 ATP molecules for each molecule of glucose fermented.

Produced during glycolysis by substrate level phosphorylation

C.Many different types of Fermentations:

Often characteristic of particular microbial groups

Organisms with different enzymes convert pyruvate to other organic compounds:

Acetic acid Lactic acid

Succinic acidIsopropanol

Formic acidButanol

PropionateButyrate

D.Lactic fermentation:

Lactobacillus, Bacillus, Chorella (alga) convert pyruvate to lactic acid:

Lactobacillus:

Responsible for the souring of milk & the production of fermented milk products

VII.Anaerobic Respiration:

A.Some bacteria use terminal electron acceptors other than oxygen:

Nitrate

Nitrite

Sulfate

Carbonate

B.Oxidation with a terminal electron acceptor other than O2 is anaerobic respiration

Less efficient than aerobic respiration:

Only 2 NADH molecules produced (during glycolysis)

TCA cycle does not occur

C.Biochemistry not well understood:

Many variations:

Actual steps depend on species

D.Electron transport system functions in anaerobic respiration:

But electrons are handed to the terminal electron acceptor earlier than in aerobic respiration:

The third ATP molecule is not made:

Two ATP molecules produced for each NADH

VIII.Comparison of fermentation, anaerobic respiration, & aerobic respiration:

A.Fermentation produces 2 ATP molecules

B.Anaerobic respiration produces about 6 ATP molecules

C.Aerobic respiration produces 38 ATP molecules

IXBiosynthetic Pathways:

A.Catabolic pathways produce:

Reduced electron carriers

ATP

B.Biosynthesis uses:

Energy saved in ATP to synthesize cell components

Biosynthesis = Anabolism

C.Extra Cellular Digestion:

Nutrients are not supplied to cells as small easily used molecules:

Usually supplied as macromolecules:

Bacteria cannot ingest solid materials:

Nutrients must be in a soluble form:

Large molecules must be broken down outside the cell

Extra cellular digestion:

Extra cellular enzymes:

Produced in the cell:

Secreted from the cell

Act outside of the cell

Hydrolyze macromolecules outside the cell:

H2O added to complex molecule: Breaks it into its simpler components:

Small enough to enter the cell:

Polysaccharides  6 Carbon Sugars

Proteins  Amino Acids

Lipids  Fatty Acids

Inside the cell smaller molecules enter various metabolic pathways

D.Carbohydrate anabolism:

For many microorganisms:

Hexose sugars serve as the:

Primary energy source

Primary carbon source

Glucose most important 6 carbon sugar that enter the cell:

Other 6 C sugars:

Often converted to glucose before being metabolized

Hexose sugars often complexed as polysaccharides:

Starch Glycogen

Pectin Cellulose

Agar

Must be broken down outside the cell

E.As glucose enters the cell:

Phosphorylated:

Glucose-6-phosphate  glycolysis Pyruvate

Pyruvate feeds into:

Aerobic respiration

or

Anaerobic respiration

or

Fermentation

F.Excess glucose may be converted to polysaccharide:

Stored by the cell

Used to construct cell structures

G.Uridine Diphosphoglucose (UDP-glucose): Key metabolic intermediate in the synthesis of:

Polysaccharides within the cell

Heteropolysaccharides:

Make up:

Cell wall

Capsule

Slime layers

  1. Amino Acids

A.Amino Acid Synthesis:

20 found in proteins

B.Essential amino acids:

Cannot be made by the organism:

Must be supplied by the environment:

Escherichia coli:

Makes all 20 from ammonia

Leuconostoc mesenteroids:

Makes 4

C.Ability to synthesize amino acids depends on cell's genetic information:

Enzymes present in cell determined by its genes

Amino acid synthesis requires reduced nitrogen source:

Ammonia Nitrite

Nitrate

Amino group (NH2) is added to intermediates from:

Glycolysis

Krebs cycle

D.Amino acid catabolism:

Amino acids may be:

Used as energy sources:

Amino group removed:

Amino acid converted to organic acid

Organic acid oxidized via:

Glycolysis

Krebs cycle

Carboxyl group removed:

E.Amino acid synthesis and amino acid catabolism:

Closely linked to other metabolic pathways