Microbiology
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Microbiology. Chapter 8. Part I. Enzymes. Enzymes Catalyze Chemical Reactions of Life. Increase reaction rates without being consumed by the reaction Lower the activation energy Active site is where the substrate binds Active site is where chemistry happens

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Microbiology

Microbiology

Chapter 8


Part i

Part I

Enzymes


Enzymes catalyze chemical reactions of life

Enzymes Catalyze Chemical Reactions of Life

  • Increase reaction rates without being consumed by the reaction

  • Lower the activation energy

  • Active site is where the substrate binds

  • Active site is where chemistry happens

    • Chemistry is performed by side chains of amino acids

    • Cofactors or coenzymes

  • Active site has specificity


Reaction coordinate

Reaction Coordinate

  • Description of energy changes during the reaction

  • Horizontal axis is charts the progessive chemical changes (bond breakage/bond formation) as S is converted into P

  • Vertical axis represents Energy

  • Transition state – not a reaction intermediate

    • Fleeting molecular moment in which bond breakage, bond formation are happening


Reaction coordinate1

Reaction Coordinate

∆G’º = -RTlnK’eq

Just because delta G is favorable

does not mean that the reaction is

fast


Enzyme terminology

Enzyme Terminology

  • Holoenzyme

    • Is a combination of protein (apoenzyme) and one or more cofactors

  • Cofactors

    • Coenzyme – complex organic molecules

    • Metal ions


Enzyme structure

Enzyme Structure

  • Holoenzyme

    • Apoenzyme – protein

    • Cofactors – complex organic molecules

    • Coenzyme – metal ions

  • Active site usually contains the cofactors and coenzymes because they are crucial for the chemistry


Cofactors

Cofactors


Enzyme substrate interactions

Enzyme Substrate Interactions

  • Specificity of active site – induced fit

  • Bonds between substrate and enzyme are weak and reversible

  • Once the enzyme substrate complex has formed chemical reactions occur on the substrate and the product is released

  • Most enzyme reactions are reversible with the exception of enzymes which regulate metabolic pathways


Lysozyme reaction

Lysozyme Reaction


Lysozyme reaction1

Lysozyme Reaction


Types of enzyme inhibition

Types of Enzyme Inhibition


Enzyme location

Enzyme Location


Synthesis and hydrolysis reactions

Synthesis and Hydrolysis Reactions


Enzymes in disease

Enzymes in Disease

  • Virulence Factors

  • Enzymes that are excreted from microorganisms that contribute to the pathogenicity of diseases


Virulence factors

Virulence Factors

  • Streptococcus pyogenes – throat and skin infections

    • Streptokinase – digests blood clots and assists in wound invasion

  • Pseudomonas aeruginose – respiratory and skin pathogen

    • Elastase and collagenase digestive enzymes

  • Clostridium perfringens – gas gangrene

    • Lecithinase C lipase damages cell membranes; therefore massive tissue death


Virulence factors1

Virulence Factors

  • Not all virulence factors secrete enzymes which digest tissues

  • Can protect microbes from effects of drug therapy

  • Penicillinase

    • Inactivates penicillin


Enzymes and their environment

Enzymes and Their Environment

  • Why do you think enzymes only function properly under established conditions of pH, temperature

  • Why do you think agents such as heavy metals and alcohol also have the ability to denature enzymes

  • Take a look at enzyme structure


Part ii

Part II

Metabolism


Metabolism in microbes

Metabolism In Microbes

  • All chemical reactions of a cell

  • Two general classes

    • Anabolism or biosynthesis

    • Catabolism or degradative reactions


Simplified model of metabolism

Simplified Model of Metabolism


Metabolic pathways

Metabolic Pathways

  • The product of one reaction is often the substrate for the next

  • Every pathway has one or more regulatory enzymes

  • All other enzymes in the pathway usually are not regulated

    • They operate whenever the substrate is available


Cell energetics

Cell Energetics

  • Not all cellular reactions are equal with respect to energy

  • Exergonic – Energy Released

  • Endergonic – Energy Requiring


Energy conversions

Energy Conversions


Three stages of metabolism

Three Stages of Metabolism


Glycolysis part i

Glycolysis – Part I


Glycolysis part ii

Glycolysis – Part II


Gap to 1 3 bpg

GAP to 1,3 BPG


Pyruvate dehydrogenase complex

Pyruvate Dehydrogenase Complex


Tca cycle

TCA Cycle


Structure of fad and nad

Structure of FAD and NAD+

  • Both are electron carriers in the ETC


What is the purpose of nadh

What is the purpose of NADH

  • The electron transport chain transfers electrons from NADH to other electron carriers

  • The electrons end up on various molecules

  • However, electron movement is associated with making a proton gradient

  • Proton gradient is responsible for ATP production


Microbiology

NAD


Electron transport chain

Electron Transport Chain


Electron transport chain1

Electron Transport Chain


Electron transport chain2

Electron Transport Chain


Etc in humans

ETC in Humans


Atp synthase

ATP Synthase


Is respiration coupled to atp synthase

Is Respiration Coupled to ATP Synthase?


Coupling

Coupling

  • How could you uncouple the ETC from the production of ATP

  • What if you treated a cell with a weak hydophobic acid such as FCCP or DNP


Dnp caused uncoupling

DNP Caused Uncoupling


Aerobic respiration

Aerobic Respiration

  • Characteristic of many bacteria, fungi, protozoa, and animals

  • Electrons and hydrogen are taken from highly reduced, high energy compounds

  • Electrons and hydrogen end up on O2 to form H20

  • Much ATP is made


Nutrient processing

Nutrient Processing

  • Extremely varied in bacteria

  • Remember Microbes are classified according to their O2 requirements

    • Aerobic respiration

    • Anaerobic respiration

    • Fermentation


Anaerobic respiration

Anaerobic Respiration

  • System involves the same three pathways as aerobic respiration

  • Final electron acceptor is not 02 but instead NO3-, SO4-, CO3-


Final electron acceptors

Final Electron Acceptors


Electron transport in plants

Electron Transport In Plants


Comparison of etc and atp synthesis

Comparison of ETC and ATP Synthesis


Other fates of pyruvate

Other Fates of Pyruvate

  • Fermentation products can be grouped into two general categories

  • Alcoholic fermentation

  • Acidic fermentation


Other fates of pyruvate1

Other Fates of Pyruvate


Anaerobic metabolism

Anaerobic Metabolism


Fermentation

Fermentation

Alcoholic fermentation

Homolactic acid fermentation


Many fermentation pathways

Many Fermentation Pathways


Other energy sources

Other Energy Sources

  • Glucose is a major source of energy

  • However, for any other organic substance usually there exists a microorganism that can degrade that substance for energy

  • Fats

  • Proteins

  • Any other organic molecule


Fat metabolism

Fat Metabolism


Protein metabolism

Protein Metabolism


Metabolism of the major classes of biomolecules

Metabolism of the Major Classes of Biomolecules


Final electron acceptors1

Final Electron Acceptors


Energy accounting

Energy Accounting


A comparison of metabolic processes

A Comparison of Metabolic Processes


Metabolism crossroads

Metabolism Crossroads


Interconnecting pathways

Interconnecting Pathways


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