Biochemistry Fundamentals

Study Notes

Metabolic Pathways

Definition: Series of chemical reactions that occur within a cell to convert energy and nutrients into ATP and other molecules
Types:
- Catabolic pathways: Break down molecules to release energy (e.g. glycolysis, citric acid cycle)
- Anabolic pathways: Build molecules to store energy (e.g. gluconeogenesis, fatty acid synthesis)
Key players:
- Substrates: Molecules that undergo chemical changes
- Products: Molecules resulting from chemical changes
- Intermediates: Molecules formed during the pathway
- Coenzymes: Molecules that facilitate chemical reactions
Regulation:
- Feedback inhibition: End products inhibit earlier enzymes in the pathway
- Allosteric regulation: Binding of molecules to enzymes affects their activity
- Post-translational modifications: Chemical changes to enzymes affect their activity

Enzyme Kinetics

Definition: Study of the rates of enzyme-catalyzed reactions
Key concepts:
- Substrate binding: Enzyme binds to substrate, forming an enzyme-substrate complex
- Catalysis: Enzyme facilitates chemical reaction, releasing product and regenerating enzyme
- Michaelis-Menten equation: Describes the kinetics of enzyme-catalyzed reactions
- Km (Michaelis constant): Concentration of substrate at which enzyme is half-saturated
- Vmax (maximum velocity): Maximum rate of reaction at saturating substrate concentrations

Protein Structure

Primary structure: Sequence of amino acids in a protein
Secondary structure: Local arrangements of amino acids (e.g. alpha helices, beta sheets)
Tertiary structure: 3D arrangement of amino acids in a protein
Quaternary structure: Arrangement of multiple polypeptide chains in a protein
Protein folding: Process by which a protein assumes its native structure
Denaturation: Loss of native structure, often due to changes in temperature, pH, or solvent

Lipid Metabolism

Fatty acid synthesis:
- Acetyl-CoA is converted to malonyl-CoA, then to fatty acyl-CoA
- Fatty acyl-CoA is elongated and desaturated to form unsaturated fatty acids
Fatty acid oxidation:
- Beta-oxidation: Fatty acids are broken down into acetyl-CoA, releasing energy
- Alpha-oxidation: Fatty acids are broken down into acetyl-CoA, releasing energy
Cholesterol metabolism:
- Synthesis: Acetyl-CoA is converted to cholesterol through the mevalonate pathway
- Regulation: Feedback inhibition by cholesterol and bile acids

Nucleic Acid Synthesis

DNA replication:
- Unwinding of double helix by helicase
- Binding of primers to template strands
- Synthesis of new strands by DNA polymerase
RNA synthesis (transcription):
- Binding of RNA polymerase to promoter region
- Synthesis of RNA strand from template DNA
DNA repair:
- Base excision repair: Repair of damaged bases
- Nucleotide excision repair: Repair of bulky lesions

Protein Metabolism

Protein synthesis (translation):
- Initiation: Binding of ribosome to mRNA
- Elongation: Addition of amino acids to growing polypeptide chain
- Termination: Release of completed polypeptide chain
Protein degradation:
- Proteasomal degradation: Breakdown of proteins by proteasomes
- Lysosomal degradation: Breakdown of proteins by lysosomal enzymes
- Ubiquitin-proteasome pathway: Targeted degradation of proteins marked with ubiquitin

Description

Test your knowledge of biochemistry with this quiz covering metabolic pathways, enzyme kinetics, protein structure, lipid metabolism, nucleic acid synthesis, and protein metabolism. From glycolysis to protein synthesis, this quiz has it all.