Course Overview

Introduction

This course, Biochemistry 545/645, is designed for advanced undergraduate and graduate students to explore the chemical principles and molecular mechanisms underlying protein structure, nutrition, and metabolism. The course integrates foundational biochemistry concepts with applications to human health and disease.

Course Structure and Logistics

Meeting Times and Location

• Term: August 19, 2025 – December 3, 2025

• Sessions: Tuesdays and Thursdays, 9:00–10:15 AM; Fridays, 9:00–9:50 AM (Bioc 645 only)

• Location: Room 302, B Building Health Sciences Campus

Instructor and Communication

• Instructor: Steven R. Ellis, Ph.D.

• Email: steven.ellis@louisville.edu

• Course Platform: Blackboard (for materials, announcements, assignments)

Textbook

• Required: Fundamentals of Biochemistry: Life at the Molecular Level by Donald Voet, Judith Voet, and Charlotte Pratt, 5th edition or newer.

Course Description

Scope and Sequence

The course is the first of a two-semester sequence, beginning with the chemical and physical principles of biochemistry and progressing to the molecular basis of nutrition and metabolism. Emphasis is placed on the structure and function of proteins, metabolic pathways, and the integration of biochemical processes in health and disease.

Course Objectives

Part 1: Protein Structure and Function

• Thermodynamics and Water: Introduce chemical and thermodynamic foundations; illustrate how water and environments impact living systems.

• pH and Buffers: Explain pH changes and buffer control in biological systems.

• Amino Acids: Describe the 20 common amino acids and their properties.

• Protein Synthesis: Analyze techniques and processes involved in protein synthesis.

• Protein Structure: Investigate elements of protein structure and how structure relates to function.

• Protein Function and Disease: Provide examples of protein function in physiological contexts and relate defects to disease.

Part 2: Nutrition and Metabolism

• Bioenergetics: Introduce principles that fuel biological systems.

• Macronutrients and Micronutrients: Differentiate their roles in metabolism.

• Carbohydrate Metabolism: Investigate glucose homeostasis and carbohydrate metabolism.

• Lipid Metabolism: Explore unique aspects and roles of lipids in biological systems.

• Hormonal Regulation: Illustrate the role of hormones in metabolic control.

• Integration of Metabolism: Integrate carbohydrate, lipid, and amino acid metabolism as part of fed/fast cycles.

• Human Nutrition and Disease: Illustrate how protein function in nutrition relates to disease.

Learning Outcomes

• Acquire new skills and abilities in biochemistry.

• Recognize the fundamental sameness of living entities.

• Develop problem-solving skills for complex biochemical problems.

• Prepare for advanced study in biochemical processes.

• Develop decision-making skills based on scientific information.

• Become aware of strengths and weaknesses in scientific reasoning.

• Accept accountability for choices and actions in scientific contexts.

Major Topics and Schedule

Protein Structure (Weeks 1–7)

• Thermodynamics and Bonding Forces

• Aqueous Solutions, Acid/Base Chemistry, Buffers

• Amino Acids and Protein Purification

• Protein Structure and Evolution

• Secondary and Tertiary Structure

• Protein Folding and Disease

• Protein Sequence Analysis

• Collagen, Myoglobin, Hemoglobin

• Hemoglobin Function and Allosteric Regulation

Nutrition and Metabolism (Weeks 8–15)

• Macronutrients and Micronutrients

• Bioenergetics and Photosynthesis

• Anaerobic Glycolysis and Pentose Phosphate Pathway

• Respiration and Electron Transport

• Glycogen Synthesis and Degradation

• Gluconeogenesis and Glucose Homeostasis

• Lipid Metabolism

• Amino Acid Metabolism

• Metabolic Integration and Diabetes

Key Terms and Definitions

• Thermodynamics: The study of energy transformations in biochemical systems.

• Buffer: A solution that resists changes in pH upon addition of acid or base.

• Amino Acid: Organic molecules that serve as the building blocks of proteins.

• Protein Structure: The three-dimensional arrangement of amino acids in a protein, including primary, secondary, tertiary, and quaternary levels.

• Bioenergetics: The study of energy flow and transformation in living organisms.

• Metabolism: The sum of all chemical reactions that occur in living organisms to maintain life.

• Glycolysis: The metabolic pathway that converts glucose into pyruvate, generating ATP.

• Electron Transport Chain: A series of protein complexes that transfer electrons and produce ATP in mitochondria.

Important Equations

• Gibbs Free Energy:

• Henderson-Hasselbalch Equation:

• Michaelis-Menten Equation (Enzyme Kinetics):

Sample Table: Grading Breakdown

Course Policies

• Attendance: Active participation is expected; lectures may be attended in person or asynchronously.

• Academic Honesty: Adherence to university policies regarding plagiarism and academic integrity is required.

• Disabilities: Reasonable accommodations are available through the Disabilities Resource Center.

• Title IX: Sexual misconduct and discrimination are prohibited; resources are available for support.

• Covid-19: Masking and distancing policies may be updated as needed.

Additional info:

• Some lecture topics (e.g., "Thalidomide", "Monoclonal antibodies as drugs") indicate integration of biochemistry with pharmacology and disease relevance.

• Course includes both theoretical foundations and practical applications in human health.