Amino Acids, Protein Structure, and Function

Protein Structure and Function

3.1: Amino Acids and Their Polymerization

Amino acids are the building blocks of proteins. Understanding their structure and how they polymerize is essential for grasping protein function in biological systems.

• Amino Acid: A small organic molecule with a central carbon atom (the α-carbon) bonded to four different groups: an amino group (–NH2), a carboxyl group (–COOH), a hydrogen atom, and a variable side chain (R group).

• When amino acids are linked together by peptide bonds, they form proteins (also called polypeptides).

The Structure of Amino Acids

All amino acids share a common core structure, but differ in their R groups, which determine their properties and functions.

• The α-carbon forms covalent bonds with four different groups:

  1. H — a hydrogen atom

  2. NH2 — an amino functional group

  3. COOH — a carboxyl functional group

  4. R group — a distinctive side chain

• R group (side chain): The variable part of an amino acid, responsible for the diversity in amino acid structure and function.

Figure: Core Structure of Amino Acids

Form	Structure
Non-ionized	Central C bonded to H, NH2, COOH, and R group
Ionized	Central C bonded to H, NH3+, COO–, and R group

Classification of Amino Acids by R Group

The 20 standard amino acids found in organisms are classified based on the properties of their R groups, which affect solubility and reactivity.

• Polarity and Charge: R groups can be charged (acidic or basic), polar (uncharged), or nonpolar.

• Hydrophilic R groups: Charged or highly electronegative atoms; interact well with water.

• Hydrophobic R groups: Nonpolar; do not interact with water, tend to cluster in the interior of proteins.

Table: Amino Acid R Group Classification

Type	Properties	Examples
Charged (Acidic/Basic)	Hydrophilic, form ionic bonds	Lysine, Aspartic acid
Polar (Uncharged)	Hydrophilic, form hydrogen bonds	Serine, Threonine
Nonpolar	Hydrophobic, avoid water	Valine, Leucine

Determining Amino Acid Type:

• If the R group has a positive charge, it is basic (e.g., lysine).

• If the R group has a negative charge, it is acidic (e.g., aspartic acid).

• If the R group is uncharged but contains an oxygen atom, it is likely polar uncharged (e.g., serine).

• If the R group is uncharged and lacks oxygen, it is likely nonpolar (e.g., valine).

Peptide Bond Formation

Amino acids are joined by peptide bonds through a condensation (dehydration) reaction between the carboxyl group of one amino acid and the amino group of another.

• Peptide bond: Covalent bond linking amino acids in a protein.

• Polypeptide: A chain of amino acids linked by peptide bonds.

• Oligopeptide: A short peptide, usually fewer than 50 amino acids.

• Protein: A functional molecule consisting of one or more polypeptides.

3.2: What Do Proteins Look Like?

Proteins have complex structures, organized into four levels: primary, secondary, tertiary, and quaternary.

• Primary Structure: The unique sequence of amino acids in a polypeptide chain.

• Secondary Structure: Local folding patterns stabilized by hydrogen bonds, such as α-helices and β-pleated sheets.

• Tertiary Structure: The overall three-dimensional shape of a single polypeptide, determined by interactions among R groups and the peptide backbone.

• Quaternary Structure: The arrangement of multiple polypeptide subunits in a protein.

Types of Interactions Stabilizing Protein Structure:

• Hydrogen bonds: Between polar side chains and backbone or other R groups.

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

• Van der Waals interactions: Weak attractions between nonpolar molecules.

• Covalent bonds (disulfide bridges): Between cysteine side chains.

• Ionic bonds: Between charged side chains.

Disulfide Bond: A covalent bond between two sulfur atoms, often stabilizing tertiary and quaternary structure (e.g., in cysteine).

3.3: Folding and Function

Protein folding is crucial for function. The final three-dimensional shape determines the protein's activity.

• Molecular Chaperones: Proteins that assist in the folding or refolding of other proteins.

• Protein denaturation: Loss of structure and function due to unfolding, often caused by heat, pH changes, or chemicals.

• Prions: Infectious proteins that cause disease by inducing misfolding in normal proteins.

3.4: Protein Functions as Diverse as Protein Structures

Proteins perform a wide variety of functions in cells and organisms.

• Catalysis: Enzymes accelerate chemical reactions.

• Defense: Antibodies and other proteins protect against disease.

• Transport: Proteins move molecules across membranes or within the body (e.g., hemoglobin).

• Signaling: Proteins transmit signals within and between cells.

• Structure: Proteins provide support and shape to cells and tissues (e.g., collagen, keratin).

• Movement: Proteins enable movement of cells and organisms (e.g., actin, myosin).

Enzyme Active Site: The region of an enzyme where substrate molecules bind and undergo a chemical reaction.

Chapter 3 Review

• Amino acids have a central carbon bonded to an amino group, a hydrogen atom, a carboxyl group, and an R group.

• The structure of the R group affects the chemical reactivity and solubility of the amino acid.

• In proteins, amino acids are joined by peptide bonds between the carboxyl group of one amino acid and the amino group of another amino acid.

• A protein’s primary structure, or sequence of amino acids, is responsible for most of its chemical properties.

• Interactions that take place between C=O and N-H groups in the same polypeptide backbone create secondary structures, which are stabilized by hydrogen bonding.

• Tertiary structure results from interactions between R-groups or R-groups and the peptide-bonded backbone, stabilizing the overall three-dimensional shape.