Biochemistry Foundations: Elements, Biomolecules, and Molecular Principles

Course Overview

Introduction to Biochemistry

Biochemistry is the study of the molecular nature, chemical properties, and activities of major biological macromolecules, including nucleic acids, amino acids, enzymes, carbohydrates, and lipids. This field uses the principles and language of chemistry to understand and explain biological phenomena.

• Lecturer: Dr. Shawn MacLellan

• Textbook: Biochemistry: Concepts and Connections (2nd Edition, Appling, Anthony-Cahill, Mathews)

• Grading: Midterm 1 (30%), Midterm 2 (30%), Final Exam (40%)

• Letter Grade Scale: A+ (90-100), A (85-89), A- (80-84), B+ (75-79), B (70-74), C+ (60-64), C (55-59), D (40-54), F (0-39)

Chemical Nature of Life

Molecular Basis of Living Systems

All aspects of life are engineered at the molecular level. Understanding molecules is essential for a complete understanding of biology. Living things obey the standard laws of physics and chemistry; no special 'vitalistic' forces are needed to explain life at the molecular level.

• Key Principle: "Anything found to be true of E. coli must also be true of elephants." – Jacques Monod

• Emergent Properties: Biological phenotypes arise from biochemical and molecular genetic processes.

Elements of Life

Major and Minor Elements

Life is composed primarily of a few key elements, with the majority of mass coming from six main elements: carbon (C), hydrogen (H), nitrogen (N), oxygen (O), phosphorus (P), and sulfur (S)—collectively known as CHNOPS. These elements account for about 97% of the mass of living organisms.

• Major Elements: C, H, N, O, P, S

• Essential Ions: Na+, K+, Mg2+, Cl-

• Trace Elements: Fe, Zn, Cu, Se, etc.

Why these elements? Their ability to form strong covalent bonds and their light atomic weights allow for the formation of complex molecules necessary for life.

Carbon: The Backbone of Biomolecules

Properties and Versatility

Carbon is a light element that forms strong covalent bonds and is tetravalent, allowing it to create large, complex, and diverse molecules. Most biological molecules, including proteins, DNA, carbohydrates, and lipids, are carbon-based.

• Covalency: Carbon can form four bonds, enabling complex structures.

• Hydrocarbons: Simple organic molecules made of carbon and hydrogen (alkanes, alkenes, alkynes).

Functional Groups in Organic Molecules

Definition and Importance

Functional groups are specific groups of atoms within molecules that are responsible for characteristic chemical reactions. They are attachments that replace one or more hydrogen atoms bonded to the carbon skeleton of hydrocarbons.

• Common Functional Groups:

Group	Structure	Example
Hydroxyl	-OH	Ethanol
Carboxyl	-COOH	Acetic acid
Amino	-NH2	Amino acids
Phosphate	-PO4	ATP
Carbonyl	-C=O	Ketones, Aldehydes

Additional info: Functional groups determine the reactivity and interactions of biomolecules.

Major Classes of Biomolecules

Monomers and Polymers

Biological macromolecules are formed from smaller units (monomers) that polymerize to form larger structures (polymers).

Monomer	Polymer
Nucleotides	Nucleic acids (DNA, RNA)
Amino acids	Proteins/Enzymes
Monosaccharides	Carbohydrates
Fatty acids	Lipids

Amino Acids and Proteins

Structure and Properties

Amino acids are the building blocks of proteins. All amino acids share a common structure: a central (alpha) carbon bonded to an amino group, a carboxyl group, a hydrogen atom, and a unique side chain (R group).

• Zwitterion Form: At physiological pH (6.8–7.4), amino acids exist as zwitterions, with a positively charged amino group and a negatively charged carboxyl group.

• Polymerization: Amino acids link via peptide bonds to form polypeptides, which fold into secondary (alpha helices, beta sheets) and tertiary structures, forming functional proteins.

• Enzymes: Proteins that catalyze chemical reactions.

Additional info: There are 20 common amino acids, each with unique side chains that determine their chemical properties and roles in proteins.

Carbohydrates

Monosaccharides to Polysaccharides

Carbohydrates are composed of sugar monomers (monosaccharides) that can be linked to form complex polysaccharides such as cellulose and starch.

• Function: Energy storage, structural support, cell recognition.

Lipids

Fatty Acids and Complex Lipids

Lipids are hydrophobic molecules that include fatty acids, phospholipids, and sterols. They are essential for membrane structure and energy storage.

• Fatty Acids: Long hydrocarbon chains with a carboxylic acid group.

• Phospholipids: Major component of cell membranes.

Nucleic Acids

Nucleotides and Genetic Information

Nucleic acids (DNA and RNA) are polymers of nucleotides. Each nucleotide consists of a nitrogenous base, a sugar, and a phosphate group. They store and transmit genetic information.

• DNA: Deoxyribonucleic acid, genetic blueprint.

• RNA: Ribonucleic acid, involved in protein synthesis.

Dimension Prefixes and Molecular Scale

Understanding Biological Scales

Biochemistry operates at scales ranging from nanometers (nm) to angstroms (Å), which are much smaller than everyday experience. Familiarity with dimension prefixes is essential for understanding molecular sizes.

Prefix	Multiplier	Exponential
nano (n)	0.000000001	10-9
micro (μ)	0.000001	10-6
milli (m)	0.001	10-3
centi (c)	0.01	10-2
Angstrom (Å)	0.0000000001	10-10

Additional info: 1 Å = 0.1 nm

Summary

• Biochemistry explores the molecular basis of life, focusing on the structure, synthesis, and function of biological macromolecules.

• Understanding the properties of elements, functional groups, and biomolecules is foundational for further study in biochemistry.

• Familiarity with molecular scale and dimension prefixes is essential for interpreting biochemical data.