Chapter 8

Microbial Metabolism

Metabolism is

•         Collection of ALL biochemical reactions that take place within cells of an organism

•         The ultimate function of metabolism is to reproduce the organism

Two classes of chemical reactions:

•         ANABOLISM

–        Building of complex molecules from simpler ones

–        Process by which a cell is built up

–        Energy requiring process (endergonic)

•         CATABOLISM

–        Process by which complex molecules are broken down into simpler ones - energy released (exergonic)

Metabolism includes the following processes:

•         Nutrient uptake

•         Conversion of nutrients into cell components

•         Conversion of nutrients into energy

•         Excretion of waste products

Chemical reactions within the cell are directed by ENZYMES

•         Proteins that catalyze (accelerate) chemical reactions

•         They are specific; they catalyze a single type of chemical reaction

•         After the reaction, they can be reused

•         The enzyme molecule is bigger than a substrate molecule and serves as physical site for reaction

 Enzymes Structure

Apoenzyme (protein) + Cofactor - nonprotein (metal ion) or

Coenzyme - organic molecule = Holoenzyme

 Active site of the Enzyme

•         Tertiary and quaternary structure of a protein molecule provide the active site – the site where the substrate binds (groove)

Enzyme-Substrate Interaction

•         Substrate and enzyme make a temporary union

•         Substrate is inserted into the active site

•         The process is reversible

Role of Coenzymes

•         Removes or donates atoms from or to a substrate

•         Electron carriers (remove electrons from the substrate; transfer them to other molecules)

•         Many coenzymes are vitamins

•         Most important coenzymes:

–        Nicotinamid adenin dinucleotide (NAD+)- catabolic reaction

–        Nicotinamid adenin dinucleotide phosphate (NADP+) anabolic reactions

–        Derivatives of B vitamin

The Mechanism of Enzymatic Action

•         Enzyme attaches to the substrate at the active site

•         Enzyme-substrate complex is formed

•         Substrate molecule is transformed

            -products of the reaction are released

•         The unchanged enzyme can start a new reaction

Synthesis and Hydrolysis Reactions

•         Synthesis

–        Anabolic reactions in which two molecules are united into a new bigger molecule

–        This is dehydration reaction (ATP used and H2O molecule released

•         Hydrolysis

–        Digestion of macromolecules

–        Breaking the bonds require an input of H2O

Transfer Reactions: Oxidation-Reduction Reactions

•         Oxidation - removal of electrons (+energy)

•         Reduction - gain of electrons

•         These reactions are always coupled

The Sensitivity of Enzymes to Their Environment

•         Environmental factors affect the activity of the enzymes

•         The enzymes are unstable in extreme conditions (high temperatures, extreme pH, osmotic pressure)

•         These conditions cause – Denaturation – the shape of the enzyme molecule is changed

Ribozymes- Unconventional Enzymes

•         A form of RNA that can act as catalyst

•         Their only substrate is RNA

•         Removes sections of RNA and joining together the remaining pieces

Types of Enzyme Control

There are two types of enzymes:

•         Constitutive - Present in constant amounts

•         Regulated -Their concentration is regulated

–        Direct Control

•         Competitive inhibition

•         Noncompetitive inhibition

–        Control of Enzyme Synthesis

•         Enzyme repression

•         Enzyme induction

Competitive inhibitors

•         Substances with similar structure as the real substrate

Noncompetitive inhibitors

•         Interact with another part of the enzyme – Allosteric site

•         Causes changing the shape of the active site

Control of Enzyme Synthesis

•         Repression

–        The excess of the end product suppresses the synthesis of the enzyme

•         Induction

–        Presence of a particular substrate induces the synthesis of the relevant enzyme

Energy in Cells

Two types of energy transaction processes

•         Exergonic – release of energy

            X + Y          Z + Energy

•         Endergonic – consumption of energy

            Energy + A + B            C

Generation of ATP (adenosine triphosphate):

Phosphorilation – addition of P to a compound (ADP + P = ATP)

 Catabolism: Getting Materials and Energy

•         Glucose is the most frequent nutrient used for obtaining energy

•         There are three metabolic pathways in which glucose is transformed:

•          Aerobic respiration

•         Anaerobic respiration

•         Fermentation

Respiration of glucose occurs in three stages:

•         Glycolysis

•         The Krebs Cycle

•         Electron transport chain system

Glycolysis (splitting of glucose)

•         Occurs in cytoplasm of most cells

•         Involves splitting of a six-carbon glucose into two three-carbon sugar molecules

•         Direct transfer of phosphate between two substrates– substrate level phosphorylation

•         Net gain:

–        2 ATP molecules,

–        2 molecules of NADH

–        pyruvic acid

Substrate Level Phosphorylation

•         high-energy P directly transferred from a substrate to  ADP

Glycolysis

•         Three-carbon molecules are oxidized  to

–        2 molecules of pyruvic acid

–        2 NAD 2 NADH+

–        4 ATP formed

•         Energy balance of Glycolysis = 2 ATP

Aerobic respiration

Krebs cycle (Tricarboxylic Acid Cycle)

•         A series of biochemical reactions in which chemical energy is released step by step

•         Starting compound is pyruvic acid (from glycolysis) which is transformed into Acetyl CoA

•         Acetyl CoA is decarboxilated (loss of CO2 molecule) and entered into tricarboxylic acid cycle

•         The reduced coenzymes are formed NADH⁺ and FADH₂ (energy stored) – enter the Respiratory Chain

•         In this cycle ATP, NADH and FADH are formed

•         NADH and FADH enter the electron transport chain

•         Total (Glycolysis + Krebs cycle + electron transport chain) =  38 ATP/glucose

Electron transport chain

•         Sequence of carrier molecules that can be oxidized and reduced

•         Located in plasma membrane of prokaryotic cells or in mitochondria in eukaryotic cells

•         Energy is released by transfer of electrons from high-energy to lower energy compounds

•         Protons (H+) are actively pumped out

ATP synthesis – Chemiosmosis

•         Accumulated protons (H+) from outer compartment diffuse through the ATP synthase to inner compartment

•         Rotation of the ATP synthase causes bonding of ADP + P_i         ATP

Anaerobic Respiration

·         Final electron acceptor is an inorganic molecule, other than O2

o   NO₃^-  +  NADH       NO₂^-   +   H₂O   +   NAD⁺ (process called denitrification)

Fermentation

•         Further oxidation of Pyruvic acid (obtained in glycolysis) without the presence of O2

•         Partial oxidation without the presence of O2

•         Final product is organic molecule (not H2O)

•         Only small amounts of ATP is recovered

•         Different bacteria perform different types of fermentation

•         Final product: lactic acid, ethanol, propionic acid, CO2, H2, acetic acid, etc.

Photosynthesis

•         Present in plants and photosynthetic bacteria and algae – Photoautotrophs

•         Conversion of light energy into chemical energy

•         Chemical energy used for conversion of CO2 into reduced carbon compounds (sugars).