Syllabus and Core Concepts for Biochemistry of the Cell (BIOL 4545)

Course Overview

Introduction to Biochemistry of the Cell

The course Bioquímica de la Célula (BIOL 4545) at Universidad de Puerto Rico, Recinto de Río Piedras, provides a comprehensive exploration of the molecular foundations of cellular biochemistry. It covers the structure, function, and interactions of biological macromolecules, as well as the metabolic pathways and regulatory mechanisms essential for cellular homeostasis.

• Course Code: BIOL 4545

• Credits: 3

• Prerequisites: BIOL 3349, QUIM 3031

• Textbook: Lehninger Principles of Biochemistry, 8th Edition (Nelson & Cox)

Course Description and Objectives

Holistic Approach to Cellular Biochemistry

This course aims to develop a holistic understanding of the fundamental concepts related to the molecules and interactions required to maintain cellular equilibrium. Students will analyze established concepts and recent studies focused on proteins, lipids, carbohydrates, and nucleic acids, emphasizing the relationship between structure and function, dynamic networks, information flow, and energy transformations.

• Macromolecular Structure and Function: Proteins, lipids, carbohydrates, and nucleic acids

• Dynamic Networks: Interactions and regulation within cellular systems

• Energy Transformations: Metabolic pathways and cellular homeostasis

• Evolutionary Perspective: Conservation and change of biological molecules and processes

• Experimental Techniques: Methods for studying and analyzing macromolecules

General Course Objectives

Key Learning Outcomes

• Metabolic Regulation: Describe, compare, and contrast energy transformation processes (e.g., glycolysis, gluconeogenesis, citric acid cycle, electron transport, oxidative phosphorylation).

• Enzyme Mechanisms: Understand and apply principles of enzyme kinetics and regulation.

• Macromolecular Properties: Demonstrate knowledge of nomenclature, chemical and physical composition, structure, and function of proteins, lipids, nucleic acids, and carbohydrates.

• Molecular Forces: Explain intramolecular and intermolecular forces determining macromolecular shape and function.

• Membrane Organization: Understand general concepts and properties of cellular membranes.

• Experimental Methods: Evaluate isolation, purification, and synthesis techniques for macromolecules.

Course Structure and Evaluation

Assessment Methods

• Short quizzes, assignments, participation: 15%

• Partial exams (5): 85%

• Total: 100%

Class Schedule and Topics

Biological Molecules: Structure, Function, and Characterization

• Introduction to Biochemistry, Water: Chapter 1

• pH and Buffers: Chapter 2

• Amino Acids, Peptides, Proteins: Chapter 3

• Primary and Secondary Structure: Chapters 3 & 4

• Tertiary, Quaternary Structure, Protein Folding: Chapter 4

• Protein Techniques: Chapter 5

• Protein Function: Chapter 5

• Enzymology: Chapter 6

• Carbohydrates: Chapter 7

• Nucleotides and Nucleic Acids: Chapter 8

• Lipids: Chapter 10

• Membranes: Chapter 11

Bioenergetics and Metabolism

• Bioenergetics and Biochemical Reactions: Chapter 13

• Carbohydrate Metabolism (Glycolysis, Fermentation, Gluconeogenesis): Chapter 14

• Citric Acid Cycle: Chapter 16

• Fatty Acid Catabolism: Chapter 17

• ATP Synthesis (Oxidative Phosphorylation): Chapter 19

• Amino Acid Catabolism, Urea Cycle: Chapter 18

• Metabolic Regulation and Integration: Chapters 15 & 23

Key Biochemistry Concepts

Macromolecules and Their Functions

• Proteins: Polymers of amino acids; function as enzymes, structural components, signaling molecules.

• Carbohydrates: Energy storage, structural roles, cell recognition.

• Lipids: Membrane structure, energy storage, signaling.

• Nucleic Acids: DNA and RNA; information storage and transfer.

Metabolic Pathways

• Glycolysis: Breakdown of glucose to pyruvate, generating ATP.

• Gluconeogenesis: Synthesis of glucose from non-carbohydrate precursors.

• Citric Acid Cycle: Central metabolic pathway for energy production.

• Oxidative Phosphorylation: ATP synthesis via electron transport chain.

• Fatty Acid Oxidation: Breakdown of fatty acids for energy.

• Amino Acid Catabolism: Degradation of amino acids, urea cycle for nitrogen disposal.

Enzyme Kinetics and Regulation

• Enzyme Mechanisms: Catalysis, substrate specificity, active site function.

• Kinetics: Michaelis-Menten equation: $v = \frac{V_{max}[S]}{K_m + [S]}$

• Regulation: Allosteric control, covalent modification, feedback inhibition.

Cellular Membranes and Transport

• Membrane Structure: Lipid bilayer, embedded proteins.

• Transport Mechanisms: Passive diffusion, facilitated diffusion, active transport.

• Biosignaling: Signal transduction pathways, receptor-ligand interactions.

Course Policies and Academic Integrity

Attendance, Evaluation, and Conduct

• Attendance: Mandatory; affects final grade.

• Exams: In-person only; alternative assessments possible in emergencies.

• Academic Integrity: Strict policy against cheating, plagiarism, and unauthorized use of AI tools.

• Inclusivity: Commitment to diversity, equity, and reasonable accommodations for students with disabilities.

Instructor Information

Contact and Office Hours

• Dr. Carlos I. González Vargas: Office NCN-325, Email: [e-mail], Tues/Thurs 8:30–11:30am

• Dr. Juan S. Ramírez Lugo: Office NCN-317, Email: [e-mail], Tues/Thurs 2:30–4:00pm

Grading System

Grade	Percentage
A	100–90%
B	89–80%
C	79–70%
D	69–60%
F	59–0%

Additional Information

• Learning Platforms: Moodle and Achieve (Macmillan Learning) for course materials and grades.

• Contingency Plans: Emergency procedures for class interruptions.

• Reasonable Accommodations: Procedures for students with disabilities and athletes.

• AI Policy: Permitted use of course assistant; restricted use of other AI tools unless specified.