Enzymes, Nucleic Acids, and Metabolism: Study Notes for GOB Chemistry

Chapter 20: Enzymes and Vitamins

Definition and Function of Enzymes

Enzymes are biological catalysts that accelerate chemical reactions in living organisms by lowering the activation energy required. They do not alter the overall free energy change (ΔG) of a reaction.

• Enzyme: A protein that increases the rate of a chemical reaction without being consumed.

• Activation Energy: The minimum energy required for a reaction to proceed.

• Example: Amylase catalyzes the breakdown of starch into sugars in the mouth.

Blood Sugar and Buffering Systems

Blood sugar regulation and buffer systems are essential for maintaining homeostasis in the body.

• Blood Buffer: The bicarbonate buffer system maintains blood pH.

• Example: The reaction $\mathrm{CO_2 + H_2O \leftrightarrow H_2CO_3 \leftrightarrow HCO_3^- + H^+}$ helps regulate blood pH.

Enzyme Structure and Active Site

Enzymes have a specific three-dimensional structure with an active site where substrates bind and reactions occur.

• Active Site: The region on the enzyme where the substrate binds.

• Substrate: The molecule upon which an enzyme acts.

Mechanism of Enzyme Action

Enzyme-catalyzed reactions typically proceed in three steps: substrate binding, conversion to product, and product release.

• Steps: Enzyme (E) + Substrate (S) → ES complex → Enzyme + Product (P)

• Induced Fit Model: The enzyme changes shape to accommodate the substrate.

Enzyme Classification and Types

Enzymes are classified into six main types based on the reactions they catalyze. Each enzyme is specific to its substrate and reaction type.

• Oxidoreductases: Catalyze oxidation-reduction reactions.

• Transferases: Transfer functional groups between molecules.

• Hydrolases: Catalyze hydrolysis reactions.

• Lyases: Add or remove atoms to or from a double bond.

• Isomerases: Rearrange atoms within a molecule.

• Ligases: Join two molecules together.

Enzyme Activity and Regulation

Enzyme activity can be affected by temperature, pH, substrate concentration, and the presence of inhibitors or activators.

• Competitive Inhibition: Inhibitor competes with substrate for the active site.

• Noncompetitive Inhibition: Inhibitor binds elsewhere, changing enzyme shape and function.

• Allosteric Regulation: Regulation by molecules binding to sites other than the active site.

• Feedback Inhibition: End product of a pathway inhibits an earlier step.

Enzyme Kinetics and Substrate Specificity

Enzymes exhibit specificity for their substrates and can be regulated by reversible or irreversible inhibitors.

• Michaelis-Menten Equation:

$V = \frac{V_{max}[S]}{K_m + [S]}$

• Irreversible Inhibition: Inhibitor forms a covalent bond with the enzyme, permanently inactivating it.

Vitamins as Enzyme Cofactors

Many enzymes require non-protein helpers called cofactors, which can be metal ions or organic molecules (coenzymes). Many coenzymes are derived from vitamins.

• Example: NAD+ (from niacin) is a coenzyme in redox reactions.

Chapter 21: Nucleic Acids

Structure of Nucleotides and Nucleic Acids

Nucleic acids are polymers of nucleotides, which consist of a sugar, a phosphate group, and a nitrogenous base.

• DNA: Deoxyribonucleic acid; double helix structure; stores genetic information.

• RNA: Ribonucleic acid; single-stranded; involved in protein synthesis.

• Base Pairing: A-T (2 hydrogen bonds), G-C (3 hydrogen bonds) in DNA.

DNA Replication and RNA Transcription

DNA replication is the process by which DNA makes a copy of itself. Transcription is the synthesis of RNA from a DNA template.

• DNA Replication: Semi-conservative; each new DNA molecule contains one old and one new strand.

• Enzymes: DNA polymerase, helicase, ligase.

• Transcription: RNA polymerase synthesizes mRNA from DNA.

Translation and the Genetic Code

Translation is the process by which mRNA is decoded to synthesize proteins. The genetic code is universal and specifies amino acids using codons (three-base sequences).

• tRNA: Transfers amino acids to the ribosome during protein synthesis.

• rRNA: Structural and catalytic component of ribosomes.

• mRNA: Carries genetic information from DNA to ribosomes.

Gene Regulation and Mutations

Gene expression is regulated at multiple levels, and mutations can alter genetic information.

• Gene Regulation: Promoters, enhancers, repressors, and epigenetic modifications.

• Mutations: Changes in DNA sequence; can be silent, missense, or nonsense.

Biotechnology Applications

Modern biotechnology uses nucleic acids in techniques such as PCR (polymerase chain reaction), cloning, and sequencing.

• PCR: Amplifies specific DNA sequences.

• Restriction Enzymes: Cut DNA at specific sequences.

Chapter 22-24: Metabolism

Overview of Metabolism

Metabolism is the sum of all chemical reactions in the body, divided into catabolism (breakdown of molecules to release energy) and anabolism (synthesis of molecules).

• Three Stages: Digestion, production of acetyl-CoA, and oxidation in the citric acid cycle.

Cell Structure and Function

Cells contain organelles that compartmentalize metabolic processes.

• Mitochondria: Site of the TCA (Krebs) cycle and electron transport chain.

• Cytosol: Site of glycolysis.

• Other Organelles: Nucleus, ribosomes, lysosomes, cell membrane.

ATP: The Energy Currency

ATP (adenosine triphosphate) stores and transfers energy for cellular processes.

• Hydrolysis of ATP: Releases energy for cellular work.

$\mathrm{ATP + H_2O \rightarrow ADP + P_i + energy}$

Electron Carriers and Oxidation-Reduction

NAD+, FAD, and CoA are coenzymes that transfer electrons and acyl groups in metabolic reactions.

• NAD+: Accepts electrons to become NADH.

• FAD: Accepts electrons to become FADH2.

• CoA: Transfers acyl groups.

Glycolysis and Pyruvate Metabolism

Glycolysis is the breakdown of glucose to pyruvate, producing ATP and NADH.

• Net Reaction:

$\mathrm{Glucose + 2NAD^+ + 2ADP + 2P_i \rightarrow 2Pyruvate + 2NADH + 2ATP + 2H_2O}$

• Fate of Pyruvate: Aerobic (to acetyl-CoA), anaerobic (to lactate or ethanol).

Citric Acid Cycle (TCA Cycle)

The citric acid cycle oxidizes acetyl-CoA to CO2, generating NADH and FADH2 for the electron transport chain.

• Key Steps: Citrate formation, decarboxylation, regeneration of oxaloacetate.

• Energy Yield: 3 NADH, 1 FADH2, 1 GTP per acetyl-CoA.

Electron Transport Chain and Oxidative Phosphorylation

Electrons from NADH and FADH2 are transferred through protein complexes to oxygen, producing ATP.

• Oxygen: Final electron acceptor; forms water.

• ATP Yield: Approximately 30-32 ATP per glucose molecule.

Metabolism of Carbohydrates, Lipids, and Proteins

Carbohydrates, lipids, and proteins are metabolized through interconnected pathways to provide energy and building blocks.

• Glycogenesis: Synthesis of glycogen from glucose.

• Glycogenolysis: Breakdown of glycogen to glucose.

• Gluconeogenesis: Synthesis of glucose from non-carbohydrate sources.

• Lipolysis: Breakdown of triglycerides to fatty acids and glycerol.

• Beta-Oxidation: Fatty acid breakdown to acetyl-CoA.

• Ketogenesis: Formation of ketone bodies from acetyl-CoA.

• Transamination and Deamination: Amino acid catabolism.

Summary Table: Key Metabolic Pathways

Pathway	Main Substrate	Main Product	Location
Glycolysis	Glucose	Pyruvate, ATP, NADH	Cytosol
Citric Acid Cycle	Acetyl-CoA	CO2, NADH, FADH2, GTP	Mitochondrial matrix
Electron Transport Chain	NADH, FADH2	ATP, H2O	Inner mitochondrial membrane
Glycogenesis	Glucose	Glycogen	Cytosol (liver, muscle)
Glycogenolysis	Glycogen	Glucose	Cytosol (liver, muscle)
Beta-Oxidation	Fatty acids	Acetyl-CoA	Mitochondrial matrix

Energy Yield from Nutrients

Carbohydrates, fats, and proteins yield different amounts of ATP upon complete oxidation.

• Carbohydrates: ~4 kcal/g

• Fats: ~9 kcal/g

• Proteins: ~4 kcal/g

Additional info: These notes expand on the provided outline with definitions, examples, and key equations to ensure a comprehensive review for GOB Chemistry students.