Overview
This textbook provides a comprehensive overview of biochemistry, exploring the chemical processes underlying life, with emphasis on biomolecules, cellular structures, metabolism, genetic information, and the integration of biological systems.
Basic Chemistry Review
- Matter is composed of elements, which are made of atoms with protons, neutrons, and electrons.
- Chemical bonds include ionic (electron transfer) and covalent (electron sharing); molecular structure determines properties.
- Functional groups (e.g., hydroxyl, amino, carboxyl, carbonyl, phosphate) dictate biomolecule behavior.
- Key reaction types: substitution, elimination, addition, redox, hydrolysis, and acid-base reactions.
- pH measures hydrogen ion concentration; buffers maintain stable pH for biological systems.
Biomolecules & Cells
- Major classes: amino acids, sugars, fatty acids, and nucleotides; these build proteins, carbohydrates, lipids, and nucleic acids.
- Proteins are polymers of amino acids with diverse roles (catalytic, structural, regulatory) and hierarchical structure (primary–quaternary).
- Carbohydrates serve as energy sources and structural elements; lipids form membranes and store energy.
- Nucleic acids (DNA, RNA) store and transmit genetic information.
- Cells are either prokaryotic (no nucleus) or eukaryotic (nucleus, organelles); all use membranes to compartmentalize and regulate activities.
Water & Thermodynamics
- Water’s polarity enables hydrogen bonding, making it an excellent solvent and vital for structure, metabolism, and homeostasis.
- Thermodynamic laws: energy is conserved; spontaneous processes increase disorder (entropy).
- Free energy (ΔG) predicts reaction spontaneity; ATP hydrolysis powers cellular work.
Enzymes & Catalysis
- Enzymes are biological catalysts that lower activation energy, thus increasing reaction rates.
- Enzyme kinetics are described by Michaelis-Menten parameters (Km and Vmax); enzymes are regulated by genetic, covalent, and allosteric mechanisms.
- Inhibitors may compete with substrates or act allosterically.
Metabolic Pathways
- Major pathways: glycolysis (glucose breakdown), citric acid cycle (energy extraction), oxidative phosphorylation (ATP synthesis), gluconeogenesis (glucose synthesis).
- Anabolism builds complex molecules; catabolism degrades them.
- Metabolism is integrated and highly regulated by hormones (e.g., insulin, glucagon) and signaling pathways.
Genetic Information
- DNA is a double helix of nucleotide bases (A-T, G-C); genetic information is replicated semiconservatively.
- Transcription converts DNA to RNA; translation converts mRNA to protein using the genetic code (triplet codons).
- Gene expression is controlled at transcriptional and translational levels, involving promoters, enhancers, transcription factors, and epigenetic modifications.
Cell Regulation & Integration
- Cells communicate via hormones, neurotransmitters, and second messengers (cAMP, IP3, Ca2+).
- Signal transduction involves cell-surface and nuclear receptors; cascades amplify and diversify responses.
- Metabolism is coordinated across tissues (e.g., liver, muscle, adipose) according to feeding or fasting state.
Protein Quality Control & Disease
- Protein structure is maintained by chaperones; misfolded or damaged proteins are degraded by the ubiquitin-proteasome system or autophagy.
- Proteostasis is key to cellular health; its failure is linked to diseases (e.g., Alzheimer's, diabetes).
Key Terms & Definitions
- Enzyme — protein catalyst that accelerates biochemical reactions.
- Metabolism — sum of all chemical reactions in a living organism.
- ATP — energy currency molecule, powers cellular processes.
- Gene — DNA sequence encoding a functional product.
- Buffer — substance that resists changes in pH.
- Oxidation-Reduction (Redox) Reaction — electron transfer between molecules.
- Transcription — synthesis of RNA from a DNA template.
- Translation — synthesis of protein from an mRNA template.
- Allosteric Regulation — enzyme activity modulation by binding of effectors at specific sites.
- Proteostasis — processes maintaining protein structure and function.
Action Items / Next Steps
- Review chapter summaries and end-of-chapter questions for active recall.
- Practice biochemical calculations (e.g., pH, free energy, enzyme kinetics).
- Complete recommended online quizzes and animations (see companion website).
- Focus on diagrams and models of pathways, protein structures, and signaling cascades.
- Prepare for exams by working through practice problems on metabolism, enzyme regulation, and genetic information flow.