BIOCHEMISTRY (week 1)

Biochemistry Overview

  • Instructor: Prof. Bob Jimenez, PTRP, MBA

Course Schedule (Biochemistry) 2nd Semester, SY 2024-2025

  • Week 1: Course Orientation, Intro to General Chemistry and Biochemistry.

  • Week 2: Digestive system and metabolism.

  • Week 3: Carbohydrate metabolism.

  • Week 4: Glycolysis.

  • Week 5: Tricarboxylic acid cycle.

  • Week 6: Preliminary Examination.

  • Weeks 7-18: Various topics including gluconeogenesis, lipid metabolism, metabolism integration, diabetes, and final examinations.

Chemistry and Biochemistry Basics

  • Definition of Matter: Anything with mass and occupies space.

  • States of Matter:

    • Solids: Definite shape and volume.

    • Liquids: Indefinite shape and definite volume.

    • Gases: Indefinite shape and volume.

Pure Substances and Mixtures

  • Pure Substance: Cannot be separated by physical means. Examples include elements and compounds.

  • Mixtures: Physical combinations of pure substances retaining their identities.

    • Types of mixtures:

      • Homogeneous: Uniform composition.

      • Heterogeneous: Visible differences among components.

Classification of Matter

  • Matter Classes:

    • Pure Substances:

      • Elements: Cannot be broken down.

      • Compounds: Can be broken down into elements.

    • Mixtures:

      • Homogeneous Mixtures: One visible phase.

      • Heterogeneous Mixtures: Two or more visible phases.

Atomic Structure

  • Atoms: Consist of a nucleus (protons + neutrons) and electrons in the outer region.

  • Isotopes: Atoms of the same element with differing neutron counts.

  • Atomic Mass: Average mass of an element's isotopes.

Chemical Bonds

  • Ionic Bonds: Formed from the transfer of electrons between atoms, resulting in charged ions. Foundation of compounds with distinct ionic structures.

  • Covalent Bonds: Atoms share electrons, can be single, double, or triple bonds based on the number of shared electron pairs.

Chemical Reactions and Energy

  • Definition of Reaction: New bonds forming or old bonds breaking.

  • Forms of Energy:

    • Kinetic: Energy in motion.

    • Potential: Stored energy based on position.

    • Chemical energy: Energy stored in bonds.

    • Exergonic and Endergonic: Energy released vs. absorbed, respectively.

Types of Chemical Reactions

  • Synthesis: Combining atoms or molecules to form new substances.

  • Decomposition: Breaking down compounds into simpler substances.

  • Reversible Reactions: Products can revert back to reactants under certain conditions.

Importance of Functional Groups in Organic Chemistry

  • Functional Groups: Atoms or groups of atoms that give distinctive chemical properties to organic compounds.

  • Key Functional Groups: Hydroxyl, carboxyl, amino, phosphate, which define the reactivity and characteristics of various biological molecules.

Amino Acids and Proteins

  • Amino Acids: Building blocks with varying side chains that determine function and structure of proteins. 20 standard amino acids.

  • Protein Structures:

    • Primary: Sequence of amino acids.

    • Secondary: Alpha helices and beta sheets

    • Tertiary and Quaternary: Overall three-dimensional structure and function arrangements.

Key Takeaways for the Course

  • Preparation: Understand the foundational concepts in chemistry for future topics in biochemistry.

  • Application: Recognize the relationship between chemical structures and biological functions.

  • Engagement: Consistent participation and active engagement in class activities and study sessions.