Biochem Lecture Sept. 4th

Course Details and Contact

• Dr. James Choy, jchoy4@uwo.ca

• Office: MSB 302

• Office hours: Thursdays 3-4:30 pm (Sept 11 – Oct 23), Zoom or in-person

• Course: UNIT A: Proteins

Unit Overview

• UNIT A: Proteins

• Topics listed across the unit (from Page 2):

  • Topic 1: Fundamental concepts of Biochemistry

  • Topic 2: Amino acid and ionization

  • Topic 3: Protein structure and analysis

  • Topic 4: Protein function

  • Topic 5: Enzyme catalysis

• Topic note, Lecture slides, Practice Quiz, Independent Learning

Topic 1 – Fundamental concepts of biochemistry

• Learning Objectives

  • Identify the four major classes of biological molecules

  • Identify the three major types of biological polymers

  • Describe how enthalpy, entropy, and free energy apply to biological systems

  • Describe the central dogma of molecular biology

Readings and Review (Topic 1)

• Readings

  • Chapter 1, Sections 1 - 3

  • Chapter 3, Section 3

• Review references

  • Figure 1.2: Elements found in biological systems

  • Table 1.1: Common functional groups and linkages

  • Box 1.A: Units used in biochemistry

What is Biochemistry?

• Definition (from Figure 1.1): "The scientific discipline that seeks to explain life at the molecular level. A thorough understanding of each molecule’s physical structure and chemical reactivity helps to lead to an understanding of how molecules cooperate and combine to form larger functional units and, ultimately, the intact organism."

Course Map (Course structure across UNIT A–C and other units)

• UNIT A: Proteins

  • 01 Fundamental Concepts of Biochemistry

• UNIT B: Metabolism

• UNIT C: Nucleic Acids

  • 02 Amino Acids and Ionization

  • 03 Protein Structure & Analysis

  • 04 Protein Function

  • 07 Carbohydrate Structure

  • 08 Fundamental Concepts in Metabolism

  • 09 Carbohydrate Metabolism

  • 10 Citric Acid Cycle

  • 11 Oxidative Phosphorylation

  • 12 Lipid Metabolism

  • 13 Summary of Metabolic Pathways

  • 14 Nucleic Acid Structure

  • 15 DNA Replication

  • 16 DNA Repair

  • 17 Molecular Basis of Cancer

  • 18 Bacterial Transcription

  • 19 Eukaryotic Transcription

  • 20 RNA Processing

  • 21 Translation

  • 22 Recombinant DNA Technology

  • 23 Sequencing Genomes

  • 06 Lipids & Biological Membranes

  • 05 Enzyme Catalysis

Major biomolecule classes in cells

• Most of the cell’s small molecules can be divided into four classes:

  • Amino acids

  • Carbohydrates (also called monosaccharides)

  • Nucleotides

  • Lipids

Amino acids – a major biomolecule

• Amino acids contain:

  • An amino group

  • A carboxylate group

  • A side chain (R group)

• Example: Alanine has a methyl group as its side chain

• Identity of an amino acid is determined by its side chain

Monomers, residues, and polymers

• Monomers link sequentially to form polymers

• Key terms:

  • Monomer

  • Residue

  • Polymer

Major biological polymers

• Three major kinds of biological polymers:

  • Proteins (polymers of amino acids)

  • Nucleic acids (polymers of nucleotides)

  • Polysaccharides (polymers of carbohydrates)

Energy and Metabolism – thermodynamics basics

• Cells need energy to carry out functions

• Thermodynamic terms in biochemistry:

  • Enthalpy, H – The heat content of a system; units: \text{J mol}^{-1}

  • Entropy, S – A measure of disorder/randomness; units: \text{J K}^{-1} \text{mol}^{-1}

  • High entropy means more disorder (e.g., gas molecules spread out)

  • Low entropy means more order (e.g., solid crystals with fixed positions)

  • Gibbs free energy, G – The free energy based on H and S; units: \text{J mol}^{-1}

• Relationship (Reading: Section 1.3):
  G = H - T S
  where T is temperature in Kelvin (K)

Enthalpy, Entropy, and Gibbs Free Energy

• \Delta G represents the Gibbs free energy change

• \Delta G = \Delta H - T\Delta S

• Interpretation:

  • If \text{ΔG} < 0 spontaneous (exergonic) process

  • If \text{ΔG} > 0: Non-spontaneous (endergonic) process, requires energy input

  • If \text{ΔG} = 0: System is at equilibrium

• Living systems tend towards states of higher entropy (\Delta S > 0) and lower enthalpy (\Delta H < 0) to achieve spontaneous processes.

Coupled chemical reactions

• Concept: Cells couple energy-releasing reactions with energy-requiring steps to make the net \Delta G negative

• Example transitions (from Page 13):

  • A → B: \text{ΔG} = +15 \text{ kJ/mol}

  • B → C: \text{ΔG} = -20 \text{ kJ/mol}

  • Overall A → C: \text{ΔG}_{\text{overall}} = -5 \text{ kJ/mol}

• Key takeaway: Net negative \Delta G drives cellular processes even when some steps are energetically unfavorable, via coupling with favorable steps

Central dogma of molecular biology

• Transcription = RNA synthesis

• Translation = Protein synthesis

• Storage of genetic information

• Reference: Reading Section 3.3

Topic 02 – Amino Acids (Preview of Amino Acid content)

• Topic 02: Amino Acids

• Pre-class activities:

  • Video: Net charge (watch before class on Wednesday)

• Available resources:

  • Lecture slides

  • AMINO ACID IONIZATION STATES (PPTX, PDF)

  • Lectures: SECTION 1, SECTION 2 (Lecture 1) and SECTION 1, SECTION 2 (Lecture 2)

  • Independent learning and practice quiz