Exam 3 Study Guide

Enzymes and Metabolic Regulation

Enzyme Function and Mechanisms

Enzymes are biological catalysts essential for cellular metabolism. They accelerate chemical reactions by lowering the activation energy required for the reaction to proceed, without being consumed in the process.

• Specificity: Each enzyme acts on a specific substrate due to the unique shape of its active site.

• Mechanism: Enzymes bind substrates, orient them correctly, and stabilize the transition state, making reactions more efficient.

How Enzymes Lower Activation Energy

• Binding substrates at the active site

• Correctly orienting molecules for reaction

• Stabilizing the transition state

Enzyme Inhibition

• Competitive Inhibition: Inhibitor binds to the active site, competing with the substrate. Can be overcome by increasing substrate concentration.

• Noncompetitive Inhibition: Inhibitor binds to an allosteric site, altering the enzyme's shape and function. Cannot be overcome by adding more substrate.

• Feedback Inhibition: The end product of a metabolic pathway inhibits the first enzyme in the pathway, preventing overproduction.

Key Terms

• Allosteric Site: A regulatory region on the enzyme where molecules can bind and change enzyme activity.

• Exoenzymes: Enzymes secreted outside the cell to break down large molecules (e.g., amylase digests starch).

Energy Coupling and ATP

ATP (adenosine triphosphate) is the primary energy currency of the cell, storing energy in its phosphate bonds. Energy coupling links energy-releasing (catabolic) reactions to energy-requiring (anabolic) reactions.

• ATP Hydrolysis: $\mathrm{ATP} \rightarrow \mathrm{ADP} + \mathrm{P_i}$ releases energy for cellular processes.

• Energy Coupling: Catabolic reactions generate ATP, which is then used to drive anabolic reactions.

Oxidation and Reduction (Redox Reactions)

Redox reactions involve the transfer of electrons between molecules, fundamental to energy production in cells.

• Oxidation: Loss of electrons

• Reduction: Gain of electrons

• Mnemonic: OIL RIG (Oxidation Is Loss, Reduction Is Gain)

NAD+ / NADH

• NAD+: Electron carrier that accepts electrons during metabolic reactions, becoming NADH.

• NADH: Reduced form, donates electrons to the electron transport chain (ETC) for ATP production.

Major Metabolic Pathways

Glycolysis

Glycolysis is the breakdown of glucose into pyruvate, generating ATP and NADH. It occurs in the cytoplasm and does not require oxygen.

• Outputs: 2 pyruvate, 2 ATP (net), 2 NADH

• Oxygen Required? No

Transition Step

• Pyruvate is converted to acetyl-CoA, producing CO2 and NADH.

Krebs Cycle (Citric Acid Cycle)

The Krebs cycle oxidizes acetyl-CoA, generating electron carriers and ATP.

• Outputs: CO2, NADH, FADH2, ATP

Electron Transport Chain (ETC)

• Location: Cytoplasmic membrane in bacteria

• Process: NADH donates electrons, creating a proton gradient used by ATP synthase to produce ATP

• Final Electron Acceptor: O2 (in aerobic respiration)

Fermentation

• Purpose: Regenerate NAD+ for glycolysis

• Common Product: Lactic acid

• ATP Produced: 2 ATP per glucose

Comparing Metabolic Pathways

Pathway	O2 Required?	ETC?	ATP Produced
Aerobic Respiration	Yes	Yes	~38
Anaerobic Respiration	No	Yes	<38
Fermentation	No	No	2

Example:

In Escherichia coli, the presence or absence of oxygen and glucose determines whether the cell uses aerobic respiration, anaerobic respiration, or fermentation.

Photosynthesis

Light Reactions and Calvin Cycle

• Light Reactions: Use light energy to produce ATP and NADPH, releasing O2.

• Calvin Cycle: Uses ATP and NADPH to fix CO2 into sugars (carbon fixation).

Relationship to Respiration

• Photosynthesis stores energy in sugars; respiration releases energy from sugars.

Microbial Growth and Nutrition

Elements Needed for Growth

• Carbon: Cell structure

• Hydrogen: Organic molecules

• Nitrogen: Proteins and DNA

• Sulfur: Amino acids

• Phosphorus: ATP, DNA

• Oxygen: Respiration

Oxygen Requirements and Groups

Group	O2 Requirement
Obligate aerobe	Requires O2
Facultative anaerobe	Grows with or without O2
Microaerophile	Requires low O2
Aerotolerant anaerobe	Tolerates but does not use O2
Obligate anaerobe	O2 is toxic

Enzymes for Oxygen Detoxification

• Superoxide Dismutase (SOD): Converts superoxide radicals to hydrogen peroxide

• Catalase: Converts hydrogen peroxide to water and oxygen

• Peroxidase: Also breaks down hydrogen peroxide

Biofilms

Biofilms are surface-attached microbial communities embedded in a protective slime matrix (extracellular polymeric substances).

• Contain channels for nutrient and water flow

• Cells communicate via quorum sensing

• Resistant to antibiotics and immune responses

• Cause chronic infections (e.g., dental plaque, catheter infections)

• Can be used in bioremediation

Microbial Growth: Binary Fission and Growth Curve

• Binary Fission Steps:

  1. DNA replication

  2. Cell elongation

  3. Septum formation

  4. Cell division

• Growth Curve Phases:

  • Lag: Adaptation to environment

  • Log: Rapid cell division

  • Stationary: Nutrient limitation; cell division equals cell death

  • Death: Cell death exceeds division

Measuring Microbial Growth

Method	Advantages	Disadvantages
Plate Count	Counts only living cells	Slow, requires incubation
Turbidity	Fast, measures growth quickly	Counts live and dead cells

Control of Microbial Growth

Definitions

• Sterilization: Removal of all microbes

• Disinfection: Removal of pathogens from inanimate objects

• Antisepsis: Removal of pathogens from living tissue

• Degerming: Physical removal of microbes (e.g., washing)

• Sanitization: Reducing microbes on food utensils

• Biocide/Germicide: Kills microbes

• Bacteriostasis: Inhibits growth without killing

Microbial Resistance to Control Methods

Microbe Type	Relative Resistance
Prions	Most resistant
Endospores	Highly resistant
Mycobacteria	Resistant
Gram-negative bacteria	Moderately resistant
Gram-positive bacteria	Less resistant
Viruses	Variable
Enveloped viruses	Least resistant

Physical Control Methods

• Autoclave: Uses steam at 121°C under pressure to sterilize and destroy endospores

• Pasteurization: Reduces pathogens in food and beverages

• Filtration: Physically removes microbes from liquids or air

• Radiation: Damages microbial DNA

• Soap: Degerming agent that emulsifies oils and washes microbes away

Metabolism of Other Molecules

• Lipids: Broken into fatty acids and glycerol; fatty acids undergo beta-oxidation and enter the Krebs cycle

• Proteins: Broken into amino acids, which are converted into intermediates of glycolysis or the Krebs cycle

Adaptations and Special Microbial Groups

• Halophiles: Microbes that tolerate or require high salt concentrations

• Thermophiles: Microbes adapted to high temperatures with heat-stable enzymes and special membrane lipids

Sample Exam-Style Questions and Key Concepts

• Catabolic reactions: Products have less potential energy than reactants

• Allosteric site: Binding here changes enzyme shape and activity

• Noncompetitive inhibition: Cannot be overcome by adding substrate

• After glycolysis: Most energy from glucose is in pyruvic acid

• After Krebs cycle: Most energy is in NADH

• Beta-oxidation: Fatty acids are catabolized in the Krebs cycle

• Obligate anaerobes: Lack both SOD and catalase

• Facultative anaerobe: Grows with or without oxygen, but better with oxygen

• Biofilms: Polysaccharide-covered communities, cause disease, and are resistant to treatment

• Autoclaving: Most effective for destroying endospores

Summary Table: Metabolic Pathways and ATP Yield

Pathway	O2 Required?	ETC?	ATP Produced
Aerobic Respiration	Yes	Yes	~38
Anaerobic Respiration	No	Yes	<38
Fermentation	No	No	2

Key Equations

• ATP Hydrolysis: $\mathrm{ATP} \rightarrow \mathrm{ADP} + \mathrm{P_i} + \text{energy}$

• Glycolysis (overall): $\mathrm{Glucose} + 2\,\mathrm{NAD}^+ + 2\,\mathrm{ADP} + 2\,\mathrm{P_i} \rightarrow 2\,\mathrm{Pyruvate} + 2\,\mathrm{NADH} + 2\,\mathrm{ATP} + 2\,\mathrm{H}_2\mathrm{O}$

• Krebs Cycle (per glucose): $2\,\mathrm{Acetyl{-}CoA} + 6\,\mathrm{NAD}^+ + 2\,\mathrm{FAD} + 2\,\mathrm{ADP} + 2\,\mathrm{P_i} \rightarrow 4\,\mathrm{CO}_2 + 6\,\mathrm{NADH} + 2\,\mathrm{FADH}_2 + 2\,\mathrm{ATP}$

Additional info: Some explanations and tables were expanded for clarity and completeness based on standard microbiology curriculum.