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Topic 11 (ch8) Microbial Metabolism

Topics

– Metabolism

– Energy

– Pathways

– Biosynthesis

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Metabolism

• Catabolism

• Anabolism

• Enzymes

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Catabolism

Enzymes involved in breakdown of complex organic molecules to extract energy and form simpler end products

Anabolism

Enzymes involved in the use of energy from catabolism to synthesize macromolecules and cell structures from precursors (simpler products)

Metabolic balancing act

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Catabolism and anabolism – simple model

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Enzymes – what are they?

• Function

• Structure

• Enzyme-substrate interaction

• Cofactors

• Action

• Regulation

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Function

• Catalysts for chemical reactions

• Lower the energy of activation

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What Affects Enzymes?

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Unfolding Kills Enzymes

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Enzymes Inhibited by Competition (more later…)

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Enzyme are Made of…

– Many protein enzymes are complete without additions

– Apoenzymes are inactive if not bound to non-protein cofactors (inorganic ions or coenzymes)

– Binding of apoenzyme and its cofactor(s) yields holoenzyme

– Some are RNA molecules called ribozymes

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Types of Enzyme(Based on Structure)

• Simple enzyme

– protein alone

• Conjugated enzyme

– protein and nonprotein

• Three-dimensional features

– Enable specificity

• Active site or catalytic site

A Conjugated Protein Enzyme

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Another Example of Conjugated Enzymes

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Enzymes in 3D

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Enzyme-substrate interactions

• Substrates specifically bind to the active sites on the enzyme

– “lock-and-key”

– Induced fit

• Once the reaction is complete, the product is released and the enzyme reused

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Substrate Fit

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Lock-and-key model, and induced fit

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Cofactors

• Bind to and activate the enzyme

• Ex. Metallic cofactors

– Iron, copper, magnesium

• Coenzymes

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Coenzyme

• Transient carrier - alter a substrate by removing a chemical group from one substrate and adding it to another substrate

• Ex. vitamins

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Example: coenzyme transfers chemical groups between substrates

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Action

• Exoenzymes

• Endoenzymes

• Constitutive

• Induction or repression

• Types of reactions

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Exoenzymes vs. Endoenzymes

•Exoenzymes -inactive inside the cell, active after release.•Endoenzymesremain in the cell and are active

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Constitiutive and Regulated enzymes

Constitutive enzymes-present in constant amountsRegulated enzymes are either induced or repressed.

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Reaction types

• Condensation (associated with anabolic reactions)

• Hydrolysis (associated with catabolic reactions)

• Transfer reactions

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enzyme-catalyzed synthesisand hydrolysis reactions

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Transfer reactions

• Transfer of electrons from one substrate to another– Oxidation

(add O2 to a compound with a loss of electrons, increase charge)

– Reduction (add e- to a compound, decrease charge)

• Oxidoreductase

• Transfer of functional groups from one molecule to another– Transferases

• Aminotransferases

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How to remember re-dox?

• LEO goes GER

• Losing Electrons is Oxidation

• Gaining Electrons is Reduction

Image from http://library.thinkquest.org

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Examples of oxidoreductase, transferase, and hydrolytic enzymes

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Enzyme Regulation

• Metabolic pathways

• Direct control

• Genetic control

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Patterns of metabolism

Different metabolic pathways are regulated by the enzymes that catalyze the reactions.

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Two common direct control mechanisms-Competitive and Noncompetitive inhibitions

Another Control -Feedback Inhibition

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Genetic control

• Repression

• Induction

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Energy

• Cell energetics

– Exergonic

– Endergonic

• Redox reaction (change in oxidation number)

• Electron carrier

• Adenosine Triphosphate (ATP)

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Cell energy model (simplified)

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Redox Reaction (again)

• Reduction and oxidation reaction (LEO goes GER):– Oxidation: loss of electrons, or gain of oxygen, gives

increase in oxidation number.

– Reduction: gain of electrons, or loss of oxygen, gives decrease in oxidation number.

• Electron carriers transfer electrons and hydrogens– Electron donor

– Electron acceptor

• Energy is also transferred and captured by the phosphate in form of ATP

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Electron carriers

• Coenzymes

– Nicotinamide adenine dinucleotide (NAD)

• Respiratory chain carriers

– Cytochromes (protein)

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NAD reduction

simple annotated

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Adenosine Triphosphate(ATP - $$!)

• Temporary energy repository - energy storage!

• Break phosphates bonds to release free energy

• Three part molecule:– Nitrogen base

– 5-carbon sugar (ribose)

– Chain of phosphates

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AMP grows to ATP, each stage higher in energy

Carbohydrates – Most Important

• Many organisms oxidize carbohydrates as primary energy source for anabolic reactions

• Glucose most common carbohydrate used

• Glucose catabolized by two processes:

– Cellular respiration

– Fermentation

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Phosphorylation of glucose by ATP

ATP can phosphorylate an organic molecule like glucose during catabolism

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ATP can be synthesized by substrate-level phosphorylation.

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Various Pathways

• Catabolism– Embden-Meyerhof-Parnas (EMP) pathway

or glycolysis

– Tricarboxylic acid cycle (TCA)

– Respiratory chain• Aerobic

• Anaerobic

– Alternate pathways

– Fermentation

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Metabolism Summary of Glucose and Energy

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Aerobic respiration (O2)

Three stages:

• Glycolysis

• Tricarboxylic acid (TCA)

• Electron transport

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Basics of Glycolysis

• In cytoplasm for most cells

– Divided into three stages involving 10 total steps

• Energy-investment stage

• Lysis stage

• Energy-conserving stage

(cont. next slide)

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Basics of Glycolysis

• In cytoplasm for most cells

• Oxidation of glucose

• Phosphorylation of some intermediates (Uses two ATPs)

• Splits a 6 carbon sugar into two 3 carbon molecules

• Coenzyme NAD is reduced to NADH

• Substrate-level-phosphorylation (Four ATPs are synthesized)

(cont. next slide)

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Basic of Glycolysis (continued)

• Water is generated

• Net yield of 2 ATPs

• Final intermediates are two Pyruvic acid molecules (notice that it require 2 different, parallel pathways to finally generate both pyruvic acid molecules…)

Overview

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Glycolytic Steps:Metabolism of Glucose

to 2 Pyruvic Acid molecules (pyruvate)

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TCA cycle• Each pyruvic acid is processed to enter the

TCA cycle (two complete cycles)

• CO2 is generated

• Coenzymes NAD and FAD are reduced to NADH and FADH2

• Net yield of two ATPs

• Critical intermediates are synthesized

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TCA Cycle Steps

Each cycle handles one 3 carbon molecule.

This means it takes two cycles to burn up one 6 carbon glucose molecule.

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Electron transport

• NADH and FADH2 donate electrons to the electron carriers

• Membrane bound carriers transfer electrons (redox reactions)

• The final electron acceptor completes the terminal step (ex. Oxygen)

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Electron Transport (continued)

Driven by:

• Chemiosmosis

• Proton motive force (PMF)

e- Transport

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Chemiosmosis and the electron transport system, with oxidative

phosphorylation e- transport and formation of a proton gradient

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Electron Transport Chain Locations

• Eukaryotes

– mitochondria

• Prokaryotes

– Cytoplasmic membrane

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ATP Yield:One glucose molecule, aerobic respiration

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Anaerobic respiration (No O2)

• Similar to aerobic respiration, except nitrate or nitrite is the final electron acceptor

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Fermentation

• Glycolysis only

• NADH from glycolysis is used to reduce the organic products

• Organic compounds as the final electron acceptors

• ATP yields are small (per glucose molecule), compared to respiration

• Must metabolize large amounts of glucose to produce equivalent respiratory ATPs

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Types of fermenters

• Facultative anaerobes

– Fermentation in the absence of oxygen

– Respiration in the presence of oxygen

– Ex. Escherichia coli

• Strict fermenters

– No respiration

– Ex. yeast

Why Fermentation?

– Sometimes cells cannot completely oxidize glucose by cellular respiration

– Cells require constant source of NAD+

• Cannot be obtained simply using glycolysis and Krebs cycle

– Fermentation pathways provide cells with alternate source of NAD+

• Partial oxidation of sugar (or other metabolites) to release energy using an organic molecule from within the cell as final electron acceptor

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Products of fermentation

• Alcoholic fermentation

• Acidic fermentation

• Mixed acid fermentation

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Fermentation of ethyl alcohol and lactic acid

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Pyruvate mixed acid fermentation diverse products

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Fermentation Products

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Respiration comparison

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Biosynthesis

• Anabolism– Amphibolic ( )

– Gluconeogenesis

– Beta oxidation

– Amination

– Transamination

– Deamination

– Macromolecules

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Amphibolic

• Integration of the catabolic and anabolic pathways

• Intermediates serve multiple purposes

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Overview of anabolic and catabolic relationships

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Gluconeogenesis

• Pyruvate (intermediate) converts to glucose

• Occurs when the glucose supply is low

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Gluconeogenesis

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Beta oxidation

• Metabolism of fatty acids into acetyl-CoA Krebs (TCA cycle)

• 4 steps:

– Oxidation by FAD

– Hydation of C2=C3 bond

– Oxidation by NAD+

– Thiol cleavage at C2-C3 Acetyl-CoA

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Production and Conversion of Amino Acids:amination, transamination, deamination

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Fitting Cellular Together

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The Big Picture

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Macromolecules

• Cellular building blocks

– Monosaccharides

– Amino acids

– Fatty acids

– Nitrogen bases

– Vitamins

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Photosynthesis – free power!

2 independent reactions in the chloroplast

6H2O + 6CO2 C6H12O6+ 6O2

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Photosynthesis (cont.)