CHAPTER 16 : Amino Acids and Proteins: Structure, Classification, and Biological Functions

Chapter 16: Amino Acids and Proteins

Learning Goals

• Classify proteins by their functions and structural types.

• Identify and draw amino acid structures at physiological pH, including names and abbreviations.

• Describe the formation and naming of peptides and the primary structure of proteins.

• Explain secondary, tertiary, and quaternary protein structures and denaturation.

• Describe enzymes, their mechanisms, and factors affecting enzyme activity.

Proteins and Amino Acids

Functions of Proteins

Proteins are essential polymers in living organisms, composed of 20 different amino acids. Their function depends on the sequence and type of amino acids present.

• Structural: Form components like cartilage, muscles, hair, and nails.

• Enzymatic: Regulate biological reactions (e.g., digestion, metabolism).

• Transport: Hemoglobin and myoglobin transport oxygen in blood.

• Storage: Store nutrients (e.g., casein in milk, ferritin in liver).

• Hormonal: Regulate body metabolism (e.g., insulin, growth hormone).

• Protection: Recognize and destroy foreign substances (e.g., immunoglobulins).

Table: Structural Classification of Proteins

Class of Protein	Function	Examples
Structural	Provide structural components	Collagen, Keratin
Contractile	Make muscles move	Myosin, Actin
Transport	Carry substances	Hemoglobin, Lipoproteins
Storage	Store nutrients	Casein, Ferritin
Hormone	Regulate metabolism	Insulin, Growth hormone
Enzyme	Catalyze reactions	Sucrase, Trypsin
Protection	Immune response	Immunoglobulins

Amino Acids: Structure and Classification

Amino acids are the building blocks of proteins. Each has a central α-carbon bonded to:

• An ammonium group (–NH3+)

• A carboxylate group (–COO–)

• A hydrogen atom

• A unique R group (side chain)

Amino Acid Structure

General formula:

$ext{H}_3 ext{N}^+ - ext{C}( ext{H})( ext{R}) - ext{COO}^-$

Classification of Amino Acids

• Nonpolar (hydrophobic): R group is H, alkyl, or aromatic (e.g., Valine, Glycine).

• Polar (hydrophilic): R group is hydroxyl, thiol, or amide (e.g., Asparagine, Serine).

• Acidic: R group is a carboxylate (e.g., Aspartate, Glutamate).

• Basic: R group is an amine (e.g., Lysine, Arginine, Histidine).

Table: Examples of Amino Acid Types

Type	Example	Structure
Nonpolar	Valine (Val, V)	$ext{H}_3 ext{N}^+ - ext{CH}( ext{CH}_3)_2 - ext{COO}^-$
Polar	Asparagine (Asn, N)	$ext{H}_3 ext{N}^+ - ext{CH}_2 ext{CONH}_2 - ext{COO}^-$
Acidic	Aspartate (Asp, D)	$ext{H}_3 ext{N}^+ - ext{CH}_2 ext{COO}^- - ext{COO}^-$
Basic	Lysine (Lys, K)	$ext{H}_3 ext{N}^+ - ( ext{CH}_2)_4 ext{NH}_3^+ - ext{COO}^-$

Drawing Amino Acids

All amino acids share the same backbone but differ by their R groups. Example structures at physiological pH:

• Aspartic acid (Asp, D): $ext{H}_3 ext{N}^+ - ext{CH}_2 ext{COO}^- - ext{COO}^-$

• Asparagine (Asn, N): $ext{H}_3 ext{N}^+ - ext{CH}_2 ext{CONH}_2 - ext{COO}^-$

Essential Amino Acids

Of the 20 amino acids, 9 are essential and must be obtained from the diet. Complete proteins (e.g., eggs, milk, meat, fish) contain all essential amino acids, while plant proteins may lack one or more.

Table: Essential Amino Acids for Adults

Amino Acid	Abbreviation
Histidine	His, H
Isoleucine	Ile, I
Leucine	Leu, L
Lysine	Lys, K
Methionine	Met, M
Phenylalanine	Phe, F
Threonine	Thr, T
Tryptophan	Trp, W
Valine	Val, V

Protein Structure

Primary Structure

The primary structure of a protein is the specific sequence of amino acids joined by peptide bonds. Peptide bonds are amide bonds formed between the carboxylate group of one amino acid and the ammonium group of the next.

• Dipeptide: Two amino acids

• Tripeptide: Three amino acids

• Tetrapeptide: Four amino acids

Peptide Bond Formation

$ext{Amino Acid}_1 + ext{Amino Acid}_2 ightarrow ext{Dipeptide} + ext{H}_2 ext{O}$

Naming Peptides

Peptides are named from the N-terminus, replacing the ending of each amino acid (except the C-terminus) with yl. Example: Ala-Gly-Ser = Alanylglycylserine.

Secondary, Tertiary, and Quaternary Structures

Secondary Structure

• Alpha helix (α-helix): Coiled structure stabilized by hydrogen bonds between C=O and N–H groups.

• Beta-pleated sheet (β-sheet): Sheet-like structure formed by hydrogen bonds between adjacent polypeptide chains.

• Triple helix: Three polypeptide chains woven together, typical of collagen.

Tertiary Structure

The overall 3D shape of a protein, stabilized by:

• Hydrophobic interactions (nonpolar R groups)

• Hydrophilic interactions (polar R groups)

• Salt bridges (ionic bonds between acidic and basic R groups)

• Hydrogen bonds

• Disulfide bonds (between cysteine residues)

Quaternary Structure

Combination of two or more polypeptide chains (subunits), stabilized by the same interactions as tertiary structure. Example: Hemoglobin has four subunits.

Table: Summary of Protein Structural Levels

Level	Bond/Interaction	Description
Primary	Peptide bonds	Sequence of amino acids
Secondary	Hydrogen bonds	Alpha helix, beta sheet
Tertiary	Hydrophobic, hydrophilic, salt bridges, disulfide	3D folding
Quaternary	Same as tertiary	Multiple polypeptide chains

Denaturation of Proteins

Denaturation is the loss of secondary, tertiary, or quaternary structure due to:

• Heat or organic compounds

• Acids and bases

• Heavy metal ions

• Agitation

Denaturation disrupts protein function, as seen when cooking eggs or treating burns with tannic acid.

Enzymes

Enzyme Structure and Function

Enzymes are proteins that act as biological catalysts, increasing reaction rates by lowering activation energy. The active site is a region where the substrate binds and the reaction occurs.

Enzyme Classification

Class	Type of Reaction
Oxidoreductases	Redox reactions
Transferases	Transfer functional groups
Hydrolases	Hydrolysis reactions
Lyases	Add/remove groups to double bonds
Isomerases	Isomerization
Ligases	Join molecules using ATP

Enzyme-Substrate Binding Models

• Lock-and-key model: Substrate fits exactly into the active site.

• Induced-fit model: Enzyme and substrate adjust shapes for optimal binding.

Factors Affecting Enzyme Activity

• Temperature: Optimum is usually 37°C; activity decreases above or below this due to denaturation.

• pH: Optimum is usually 7.4; extreme pH disrupts enzyme structure.

• Inhibitors:

  • Competitive: Compete with substrate for active site; inhibition reversed by increasing substrate.

  • Noncompetitive: Bind elsewhere, changing enzyme shape; inhibition not reversed by substrate.

  • Irreversible: Covalently bind to enzyme, permanently inactivating it.

Enzyme Kinetics

• Rate of reaction depends on substrate concentration and enzyme saturation.

• First-order: $ext{Rate} = k[ ext{A}]$

• Second-order: $ext{Rate} = k[ ext{A}][ ext{B}]$

• Zero-order: $ext{Rate} = k$ (enzyme saturated)

Practice and Application

• Draw and classify amino acids by polarity and charge.

• Name and draw peptides from given amino acid sequences.

• Identify protein structural levels from descriptions.

• Match enzyme names to their catalyzed reactions.

• Predict effects of temperature, pH, and inhibitors on enzyme activity.

Summary

This chapter covers the structure and classification of amino acids and proteins, the formation and naming of peptides, the four levels of protein structure, the process and consequences of denaturation, and the mechanisms and regulation of enzyme activity. Understanding these concepts is essential for grasping the biochemical processes in living organisms.