lec 8 Proteins and Their Amino Acid Building Blocks: Structure and Function

Proteins and Their Amino Acid Building Blocks

Introduction to Biochemistry

Biochemistry is the study of the chemical processes and substances that occur within living organisms. It bridges biology and chemistry, focusing on the molecular mechanisms that underlie life, including the structure and function of biomolecules.

• Biomolecules include proteins, nucleic acids, carbohydrates, and lipids.

• Biochemistry is foundational for fields such as medicine, physiology, pharmacology, and cell biology.

The Four Classes of Biomacromolecules

Living organisms are composed of four major classes of biomacromolecules, each with distinct structures and functions:

• Proteins: Polymers of amino acids, responsible for catalysis, structure, transport, and regulation.

• Carbohydrates: Polysaccharides and simple sugars, providing energy and structural support.

• Lipids: Fatty acids, triglycerides, and phospholipids, forming membranes and storing energy.

• Nucleic Acids: DNA and RNA, storing and transmitting genetic information.

Class	Examples	Main Function
Proteins	Enzymes, antibodies, hemoglobin	Catalysis, structure, transport
Carbohydrates	Glucose, starch, cellulose	Energy, structure
Lipids	Phospholipids, cholesterol	Membranes, energy storage
Nucleic Acids	DNA, RNA	Genetic information

Roles of Proteins in the Body

Proteins are essential macromolecules with diverse functions:

• Enzymes: Catalyze biochemical reactions (e.g., hexokinase, catalase).

• Hormones: Regulate physiological processes (e.g., insulin, growth hormone).

• Storage Proteins: Store essential substances (e.g., ferritin, ovalbumin).

• Transport Proteins: Move molecules across membranes or in blood (e.g., hemoglobin, serum albumin).

• Structural Proteins: Provide support and shape (e.g., collagen, keratin).

• Protective Proteins: Defend against pathogens (e.g., antibodies).

• Contractile Proteins: Enable movement (e.g., actin, myosin).

Protein Structure and Amino Acids

General Structure of Amino Acids

Amino acids are the building blocks of proteins. Each amino acid contains:

• An alpha carbon (Cα)

• A carboxylic acid group (-COOH)

• An amine group (-NH2)

• A unique side chain (R group)

The alpha carbon is typically a chiral center, except in glycine.

Chirality and Isomerism in Amino Acids

A carbon atom is chiral if it is bonded to four different groups. Chirality leads to the existence of stereoisomers:

• Enantiomers: Non-superimposable mirror images (e.g., L- and D-amino acids).

• Diastereoisomers: Stereoisomers that are not mirror images.

• Constitutional isomers: Differ in the connectivity of atoms.

Classification of Amino Acids

Amino acids are classified based on the properties of their side chains:

• Nonpolar: Hydrophobic, side chains are alkanes or aromatic rings.

• Neutral Polar: Hydrophilic, side chains contain hydroxyl, thiol, or amide groups.

• Acidic: Side chains contain carboxylic acid groups (negatively charged at pH 7).

• Basic: Side chains contain amine groups (positively charged at pH 7).

Class	Side Chain Feature	Example Amino Acids
Nonpolar	Alkane/arene	Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline
Neutral Polar	Hydroxyl/thiol/amide	Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine
Acidic	Carboxylic acid	Aspartate, Glutamate
Basic	Amine	Lysine, Arginine, Histidine

Zwitterions and Acid-Base Properties

At physiological pH (~7.4), amino acids exist as zwitterions, molecules with both positive (amino group) and negative (carboxyl group) charges. The side chain may also be charged, depending on the amino acid and the pH.

• Zwitterion: Both the amino group is protonated ($\mathrm{NH_3^+}$) and the carboxyl group is deprotonated ($\mathrm{COO^-}$).

• The isoelectric point (pI) is the pH at which the amino acid has no net charge.

Protein Structure: Levels of Organization

Primary Structure

The primary structure of a protein is the linear sequence of amino acids joined by peptide bonds. The sequence is written from the N-terminus (amino end) to the C-terminus (carboxyl end).

• Peptide bond: Covalent bond formed between the carboxyl group of one amino acid and the amino group of another, releasing water.

• The order of amino acids determines the protein's properties and function.

Secondary Structure

The secondary structure refers to local folding patterns stabilized mainly by hydrogen bonds between backbone atoms. The two most common types are:

• Alpha helix (α-helix): Right-handed coil stabilized by hydrogen bonds every fourth residue.

• Beta sheet (β-sheet): Extended strands connected by hydrogen bonds, can be parallel or antiparallel.

Tertiary Structure

The tertiary structure is the overall three-dimensional shape of a single polypeptide chain, stabilized by interactions among side chains (R groups):

• Hydrophobic interactions: Nonpolar side chains cluster away from water.

• Hydrogen bonds: Between polar side chains or backbone atoms.

• Disulfide bonds: Covalent bonds between cysteine residues.

• Ionic interactions (salt bridges): Between acidic and basic side chains.

• Van der Waals forces: Weak attractions between all atoms.

Quaternary Structure

The quaternary structure describes the arrangement of multiple polypeptide chains (subunits) in a protein complex. Stabilized by the same interactions as tertiary structure, plus interchain disulfide bonds in some cases.

Shape-Determining Amino Acids

Some amino acids play special roles in determining protein shape:

• Glycine: Smallest side chain, provides flexibility, often found in turns.

• Proline: Rigid ring structure, introduces kinks or turns in polypeptide chains.

• Cysteine: Forms disulfide bonds, stabilizing tertiary and quaternary structures.

Summary Table: Protein Structure Levels

Level	Description	Stabilizing Forces
Primary	Sequence of amino acids	Peptide (amide) bonds
Secondary	Local folding (α-helix, β-sheet)	Hydrogen bonds (backbone)
Tertiary	3D folding of a single chain	Hydrophobic effect, H-bonds, ionic bonds, disulfide bonds, van der Waals
Quaternary	Assembly of multiple chains	Same as tertiary, plus interchain disulfide bonds

Key Concepts and Applications

• Protein function is determined by structure: Even small changes in amino acid sequence can alter function.

• Enzyme specificity and antibody recognition depend on precise 3D structure.

• Protein misfolding can lead to diseases (e.g., prion diseases).

Additional info: For further study, refer to Chapter 18, sections 18.1–18.6 in your textbook for more details on protein structure, amino acid properties, and the relationship between structure and function.