Enzymes in Biology

Enzymes

• Definition: Biological molecules, typically proteins, that speed up chemical reactions in living organisms
• Characteristics:
  • Highly specific to a particular reaction or substrate
  • Increase reaction rates without being consumed by the reaction
  • Optimal pH and temperature for activity
  • Inhibited or activated by various molecules
• Types:
  • Oxidoreductases (catalyze oxidation-reduction reactions)
  • Transferases (catalyze transfer of groups between molecules)
  • Hydrolases (catalyze hydrolysis reactions)
  • Ligases (catalyze formation of new bonds)
  • Isomerases (catalyze isomerization reactions)
• Regulation:
  • Allosteric regulation (conformational change in response to binding of inhibitor or activator)
  • Feedback inhibition (end product of a pathway inhibits an enzyme earlier in the pathway)
  • Covalent modification (phosphorylation, ubiquitination, etc.)

Metabolic Pathways

• Definition: Series of enzyme-catalyzed reactions that convert a starting molecule into a product
• Types:
  • Catabolic pathways (break down molecules to release energy)
  • Anabolic pathways (build molecules using energy)
  • Amphibolic pathways (involved in both catabolism and anabolism)
• Key pathways:
  • Glycolysis (breakdown of glucose to pyruvate)
  • Citric acid cycle (breakdown of acetyl-CoA to produce ATP, NADH, and FADH2)
  • Pentose phosphate pathway (generate NADPH and pentoses)
  • Fatty acid synthesis (build fatty acids from acetyl-CoA)
• Regulation:
  • Substrate inhibition (high concentrations of substrate inhibit enzyme activity)
  • Product inhibition (high concentrations of product inhibit enzyme activity)
  • Hormonal regulation (insulin, glucagon, etc.)

Protein Structure

• Primary structure: Sequence of amino acids in a protein
• Secondary structure: Local folded structures, such as alpha helices and beta sheets
• Tertiary structure: Overall 3D shape of a protein
• Quaternary structure: Interaction between multiple polypeptide chains
• Types of bonds:
  • Hydrogen bonds (between amino acids and water)
  • Ionic bonds (between charged amino acids)
  • Disulfide bonds (between cysteine residues)
  • Peptide bonds (between amino acids)

DNA Replication

• Semiconservative replication: Each new DNA molecule contains one old strand (template) and one new strand
• Steps:
  1. Initiation: Binding of helicase to origin of replication, unwinding of DNA
  2. Unwinding: Separation of DNA strands, binding of primers
  3. Synthesis: Addition of nucleotides to template strands, proofreading and editing
  4. Elongation: Continuous synthesis of new DNA strands
  5. Termination: Completion of DNA replication, ligation of Okazaki fragments
• Enzymes involved:
  • Helicase (unwinds DNA)
  • Primase (synthesizes primers)
  • Polymerase (synthesizes new DNA strands)
  • Ligase (joins Okazaki fragments)

Cell Signaling

• Definition: Process by which cells respond to stimuli, such as hormones, growth factors, or neurotransmitters
• Types of signaling:
  • Autocrine signaling: Signaling within a cell
  • Paracrine signaling: Signaling between nearby cells
  • Endocrine signaling: Signaling between distant cells
• Signal transduction pathways:
  • Receptor tyrosine kinases: Activate downstream signaling pathways
  • G-protein coupled receptors: Activate G-proteins, which activate downstream signaling pathways
  • Ligand-gated ion channels: Directly open or close ion channels
• Second messengers:
  • Cyclic AMP (cAMP): Activates protein kinase A
  • Inositol triphosphate (IP3): Releases calcium from intracellular stores
  • Diacylglycerol (DAG): Activates protein kinase C

Enzymes

• Enzymes are biological molecules, typically proteins, that speed up chemical reactions in living organisms
• They are highly specific to a particular reaction or substrate
• Enzymes increase reaction rates without being consumed by the reaction
• They have an optimal pH and temperature for activity
• Enzymes can be inhibited or activated by various molecules

Types of Enzymes

• Oxidoreductases catalyze oxidation-reduction reactions
• Transferases catalyze the transfer of groups between molecules
• Hydrolases catalyze hydrolysis reactions
• Ligases catalyze the formation of new bonds
• Isomerases catalyze isomerization reactions

Enzyme Regulation

• Allosteric regulation involves a conformational change in response to binding of an inhibitor or activator
• Feedback inhibition occurs when the end product of a pathway inhibits an enzyme earlier in the pathway
• Covalent modification involves phosphorylation, ubiquitination, etc.

Metabolic Pathways

• Metabolic pathways are series of enzyme-catalyzed reactions that convert a starting molecule into a product
• Catabolic pathways break down molecules to release energy
• Anabolic pathways build molecules using energy
• Amphibolic pathways are involved in both catabolism and anabolism

Key Metabolic Pathways

• Glycolysis breaks down glucose to pyruvate
• The citric acid cycle breaks down acetyl-CoA to produce ATP, NADH, and FADH2
• The pentose phosphate pathway generates NADPH and pentoses
• Fatty acid synthesis builds fatty acids from acetyl-CoA

Regulation of Metabolic Pathways

• Substrate inhibition occurs when high concentrations of substrate inhibit enzyme activity
• Product inhibition occurs when high concentrations of product inhibit enzyme activity
• Hormonal regulation involves insulin, glucagon, etc.

Protein Structure

• The primary structure is the sequence of amino acids in a protein
• The secondary structure consists of local folded structures, such as alpha helices and beta sheets
• The tertiary structure is the overall 3D shape of a protein
• The quaternary structure is the interaction between multiple polypeptide chains
• Types of bonds include hydrogen bonds, ionic bonds, disulfide bonds, and peptide bonds

DNA Replication

• DNA replication is semiconservative, meaning each new DNA molecule contains one old strand and one new strand
• The process involves initiation, unwinding, synthesis, elongation, and termination
• Enzymes involved in DNA replication include helicase, primase, polymerase, and ligase

Cell Signaling

• Cell signaling is the process by which cells respond to stimuli, such as hormones, growth factors, or neurotransmitters
• Types of signaling include autocrine, paracrine, and endocrine signaling
• Signal transduction pathways involve receptor tyrosine kinases, G-protein coupled receptors, and ligand-gated ion channels
• Second messengers include cAMP, IP3, and DAG