Chapter 5, part A

Microbial Metabolism

• Life fundamental feature:– growth (metabolism)

– reproduction (heritable genetic information)

• Organic compounds in life organisms• Carbohydrates – sugars• Lipids – fatty acids • Proteins – amino acids • Nucleic acids - nucleotides• Vitamins

• Chemical reactions involve the making or breaking of bonds between atoms.– A change in chemical energy occurs during a chemical reaction.

• Endergonic reactions absorb energy.– Synthesis reaction

• Exergonic reactions release energy.– Decomposition Reactions

Carbon

Energy

What do all organisms need?

• Metabolism is the sum of all chemical reactions that occur in living organisms to maintain life. – Catabolism is breakdown and the energy-releasing processes.

• Provides energy and building blocks for anabolism.

– Anabolism is biosynthesis and the energy-using processes• Uses energy and building blocks to build large molecules

• Role of ATP in Coupling Reactions

Nutritional ( metabolic) types of organisms – Trophe = nutrition

• Sources of energy – Chemotrophs: Bond energy is released from a chemical compound

– Phototrophs: Light is absorbed in photo receptors and transformed into chemical energy.

• Sources of carbon– Autotrophs: Carbon dioxide (CO2) is used as source of carbon

Heterotrophs: Organic compounds are metabolized to get carbon for growth and development.

• The collision theory states that chemical reactions can occur when atoms, ions, and molecules collide.

• Reaction rate:– Activation energy - needed to disrupt electronic configurations.

– Frequency of collisions – depends on concentration of the atoms and molecules

• Reaction rate can be increased by:– Increasing temperature or pressure.

– Lowering the activation energy - Catalysts

• Enzymes - biological catalysts

Chemical reactions - Collision theory

Enzymes• Like all catalysts, enzymes work by lowering the activation energy for a reaction,

thus dramatically increasing the rate of the reaction

• Enzymatic reactions –– Substrates - The material or substance

on which an enzyme acts

(The molecules at the

beginning of the process)

– Enzyme– Products - The molecules at the

end the reaction

Reactionwithout enzyme

Reactionwith enzyme

Reactant (Substrate)

Initial energy level

Final energy level Products

Activationenergywithout enzyme

Activationenergywithenzyme

AB A + BEnzyme

Substrate Products

Enzymes• Enzymes are biomolecules that catalyze ( increase the rates of)

chemical reactions.– Almost all enzymes are proteins.

– RNA molecules called ribozymes are capable of performing specific biochemical reactions

• Peptidyl transferase is catalysed by the rRNA component of the large

ribosomal subunit.

• Although most ribozymes are quite rare in the cell,

their roles are sometimes essential to life

Enzymes• Like all proteins, enzymes are made as long, linear chains of amino

acids – Each unique amino acid sequence (peptide) produces a specific structure (a

three-dimensional product) , which has unique properties.

– Active site

• The structure and chemical properties of the active site allow the recognition and binding of the substrate

Figure 5.2

Enzymes

• Enzyme-substrate complex - Substrates bind to the active site of the enzyme

• Bind through hydrogen bonds, hydrophobic interactions, temporary covalent bonds (van der waals) or a combination of all of these

• The active site modifies the reaction mechanism in order to decrease the activation energy of the reaction.

• The product is usually unstable in the active site, it is released and returns the enzyme to its initial unbound state.

• The turnover number is generally 1-10,000 molecules per second.

Enzymes are not used up in that reaction

E + S ES → EP E + P ⇌ ⇌

Enzymes

Figure 5.3

Apoenzyme: protein

Inactive

Cofactor: Nonprotein component

NAD+, (NADH)

NADP+, (NADPH)

FAD

Coenzyme: Organic cofactorVitamins

Coenzyme A

Holoenzyme: Apoenzyme + cofactorActive

Factors Influencing Enzyme Activity

1. Effect of Substrate Concentration on Enzyme Activity

Substrate Product1 + Product2

[E][S]

[P1][P2]

* Point of saturation

Figure 5.5b

Factors Influencing Enzyme Activity

3. Effect of pH on Enzyme Activity2. Effect of Temperature on Enzyme Activity

• Enzymes can be denatured by temperature and pH

* Optimal temperature * Optimal pH

Inhibitors of Enzyme Activity

1. Competitive inhibition – competition for the active site

Figure 5.7a, b

Inhibitors of Enzyme Activity

2. Noncompetitive inhibition

Figure 5.7a, c

Feedback inhibition of biochemical pathways

• The term feedback inhibition refers to a situation in which the substances at the end of a long series of reactions inhibits a reaction at the begining of the series of reactions.

Figure 5.8

• A metabolic pathway is a sequence of chemical reactions occurring within a cell – In each pathway, a principal chemical is modified by chemical reactions.

– Enzymes catalyze these reactions often require dietary minerals, vitamins, and other cofactors in order to function proper

• Metabolic pathways are determined by enzymes.

• Enzymes are encoded by genes.

Metabolic Pathways

Starting molecule

E1 E2 E3

intermediate B end productintermediate A

Enzymes

• Enzymes are usually very specific as to which reactions they catalyze and the substrates that are involved in these reactions

• Enzyme Classification

– Oxidoreductase: Oxidation-reduction reactions

– Transferase: Transfer functional groups

– Hydrolase: Hydrolysis

– Lyase: Removal of atoms without hydrolysis

– Isomerase: Rearrangement of atoms

– Ligase: Joining of molecules, uses ATP

• Oxidation is the removal of electrons.

• Reduction is the gain of electrons.

• Redox reaction is an oxidation reaction paired with a reduction reaction.

Oxidation-Reduction

Figure 5.9

• In biological systems, the electrons are often associated with hydrogen atoms.

– Transfer of electrons or hydrogen atoms from one molecule (hydrogen or electron donor) to another (the acceptor)

• Biological oxidations are often dehydrogenations.

Oxidation-Reduction

Figure 5.10

Energy production - Catabolism

• Cells use biological oxidation-reduction reactions in catabolism to breakdown organic compounds– Release energy associated with the electrons that form bonds between their

atoms

(substrate) (products)

• Energy released during certain metabolic reactions can be trapped to form ATP– Addition of PO4

- a to a molecule is called phosphorylation – ATP is generated by the phosphorylation of ADP.

( C6H12O6) CO2 + H2O + energyhighly reduced compounds (with many hydrogen atoms)

highly oxidized compounds

• Generate ATP – serves as a convenient energy carrier

• During substrate-level phosphorylation, a high-energy from an intermediate in catabolism is added to ADP.

• During oxidative phosphorylation, energy is released as electrons are passed to a series of electron acceptors (an electron transport chain) and finally to O2 or another inorganic compound.

• During photophosphorylation, energy from light is trapped by chlorophyll, and electrons are passed through a series of electron acceptors.

• The electron transfer releases energy used for the synthesis of ATP.

The Generation of ATP

Catabolism Metabolic Pathways

+ATP

+ATP

+ATP

1

2

3

• Most of a cell’s energy is produced from the oxidation of carbohydrates.

• Glycolysis - the most common pathway for the oxidation of glucose. – Glucose is the most commonly used carbohydrate.

• One glucose molecule.• End-product - Pyruvic acid • 2 ATP and 2 NADH moleculesare produced

• Alternatives to Glycolysis– The pentose phosphate pathway

• Used to metabolize five-carbon sugars;• One ATP and 12 NADPH molecules are produced from one glucose

molecule.

– The Entner-Doudoroff pathway • One ATP and two NADPH molecules from one glucose molecule.• Does not involve glycolysis• Pseudomonas, Rhizobium, Agrobacterium

Carbohydrate Catabolism

GlycolysisPreparatory stage Energy-Conserving Stage

• 2 Glucose-3-phosphate oxidized to 2 Pyruvic acid

– 4 ATP produced

– 2 NADH produced

Figure 5.12.2

1,3-diphosphoglyceric acid

3-phosphoglyceric acid

2-phosphoglyceric acid

Phosphoenolpyruvic acid(PEP)

6

7

8

9

10

2 molecules Pyruvic acid

• 2 ATPs are used

• Glucose is split to form 2 Glucose-3-phosphate

1 molecule Glucose

• 1 Glucose + 2 ATP + 2 ADP + 2 PO4– + 2 NAD+

2 pyruvic acid + 4 ATP + 2 NADH + 2H+

substrate-level phosphorylation,

• The two major types of glucose catabolism are:

– Respiration, in which glucose is completely broken down

• To CO2 and H2O - aerobic respiration

• To NO2–, N2 , H2S, CH4 and H2O

– anaerobic respiration

– Fermentation, in which glucose is partially broken down (organic molecule)

Carbohydrate Catabolism

• Pyruvic acid (from glycolysis) is oxidized and decarboyxlated

Respiration - Intermediate Step

Figure 5.13.1

2 Pyruvic acid

2 NADH

Respiration - Krebs Cycle

Figure 5.13.2

• Oxidation of acetyl CoA produces NADH and FADH2

2 Acetyl CoA

6 NADH2 FADH2

Respiration - The Electron Transport Chain• A series of carrier molecules that are, in turn, oxidized and

reduced as electrons are passed down the chain.

• Energy released can be used to produce ATP by chemiosmosis

10 NADH2 FADH2

Chemiosmosis• Protons being pumped across the membrane generate a proton motive force

as electrons move through a series of acceptors or carriers.• Energy produced from movement of the protons back across the membrane

is used by ATP synthase to make ATP from ADP .• Electron carriers are located: • In eukaryotes

– in the inner mitochondrial membrane;

• In prokaryotes– in the plasma membrane.

• oxidative phosphorylation

Figure 5.17

• ATP produced from complete oxidation of 1 glucose using aerobic respiration

• 36 ATPs are produced in eukaryotes.

PathwayBy substrate-

level phosphorylation

By oxidative phosphorylation

From NADH

From FADH

Glycolysis 2 6 0Intermediate step 0 6

Krebs cycle 2 18 4Total 4 30 4

Respiration

Electron acceptor Products

NO3– (nitrate ion ) NO2

– (nitrite ion) , N2 O or N2 + H2O

SO42– (sulfate ion) H2S + H2O

CO32 – (carbonate ion) CH4 + H2O

• Aerobic respiration– The final electron acceptor in the electron transport chain is

molecular oxygen (O2).• Product - H2O

• Anaerobic respiration– The final electron acceptor in the electron transport chain is

not O2. .

Pathway Eukaryote Prokaryote

Glycolysis Cytoplasm Cytoplasm

Intermediate step Cytoplasm Cytoplasm

Krebs cycle Mitochondrial matrix Cytoplasm

ETC Mitochondrial inner membrane

Plasma membrane

Respiration

Learning objectives• Define metabolism, and describe the fundamental differences between anabolism

and catabolism.• Identify the role of ATP as an intermediate between catabolism and anabolism.• Identify the components of an enzyme.• Describe the mechanism of enzymatic action.• List the factors that influence enzymatic activity.• Explain what is meant by oxidation–reduction.• List and provide examples of three types of phosphorylation reactions that generate

ATP.• Explain the overall function of biochemical pathways.• Describe the chemical reactions of glycolysis.• Explain the products of the Krebs cycle.• Describe the chemiosmosis model for ATP generation.• Compare and contrast aerobic and anaerobic respiration.