Proteins: Structure, Function, and Enzyme Activity

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Proteins: Structure, Function, and Enzyme Activity

10.1 Amino Acids—The Building Blocks

Proteins are essential biological polymers made from amino acids. The sequence and arrangement of these amino acids determine the protein's structure and function.

Definition: Proteins are polymers composed of 20 different amino acids.
Functions: Proteins transport oxygen (e.g., hemoglobin), form structural components (skin, muscle), defend against infection (antibodies), act as enzymes, and regulate metabolism (hormones).
Structure: Proteins can range from 50 to thousands of amino acids in length.
Example: Hemoglobin transports oxygen in blood; enzymes catalyze biochemical reactions.

10.1 Base Structure of Amino Acids

Each amino acid contains a central alpha (α) carbon bonded to four groups: an amine, a carboxylate, a hydrogen, and an R group.

Amine group: Protonated (−NH3+).
Carboxylate group: Conjugate base of carboxylic acid (−COO−).
R group: Side chain that varies among amino acids and determines their properties.
Alpha carbon: Chiral center (except in glycine).

10.1 R Groups and Amino Acid Diversity

The R group gives each amino acid unique chemical properties, affecting protein structure and function.

Chirality: All amino acids except glycine are chiral; most are L-amino acids.
Classification: Amino acids are classified as nonpolar, polar neutral, polar acidic, or polar basic.
Organic families: R groups include alkanes, aromatics, sulfides, alcohols, phenols, thiols, amides, carboxylates, and protonated amines.

10.1 Essential vs. Nonessential Amino Acids

Some amino acids must be obtained from the diet because the human body cannot synthesize them.

Essential amino acids: 10 amino acids (marked with *) are essential; must be consumed in food.
Complete proteins: Contain all essential amino acids (e.g., eggs, milk, fish, poultry, meat, soybeans).
Incomplete proteins: Plant proteins may lack one or more essential amino acids.
Dietary combinations: Combining foods (e.g., beans and rice) can provide all essential amino acids.

10.1 Amino Acids as Weak Acids

Amino acids can exist in charged or uncharged forms depending on the pH of their environment.

Zwitterion: At physiological pH (~7.4), amino acids exist as zwitterions, with both positive and negative charges but no net charge.
Acid/base forms: The amine and carboxylate groups can gain or lose protons depending on pH.
Example: Alanine at pH 7.4 is a zwitterion.

10.1 Isoelectric Point (pI)

The isoelectric point is the pH at which an amino acid exists only as a zwitterion.

Definition: pI is the pH where the net charge of the amino acid is zero.
Behavior: Below pI, amino acids are protonated (acidic); above pI, they are deprotonated (basic).
Formula: For amino acids without ionizable side chains:

10.2 Biological Condensation Reactions

Proteins are formed by condensation reactions, where amino acids are joined together and water is released.

Peptide bond: The amide bond formed between amino acids during protein synthesis.
Ends: Peptides have an N-terminal (free amine) and a C-terminal (free carboxyl).
Order: The sequence of amino acids determines protein identity and function.
Equation:

10.2 Celiac Disease

Celiac disease is an autoimmune disorder triggered by peptides from gluten proteins.

Gluten: Mixture of glutenin and gliadin proteins found in wheat and other grains.
Peptides: Rich in proline and glutamine; some glutamines are converted to glutamate.
Immune response: In celiac disease, the immune system attacks these peptides, causing inflammation and malabsorption.

10.3 Protein Structure Levels

Proteins have four levels of structural organization, each critical for their function.

Primary structure: Sequence of amino acids from N-terminus to C-terminus.
Secondary structure: Local folding into α helices and β sheets stabilized by hydrogen bonds.
Tertiary structure: Overall 3D shape formed by interactions among secondary structures and side chains.
Quaternary structure: Association of multiple polypeptide chains into a functional protein.

Secondary Structure: Alpha Helix

Shape: Coiled structure stabilized by hydrogen bonds between C=O and NH groups.
R groups: Project outward from the helix axis.

Secondary Structure: Beta Sheet

Shape: Zigzag, pleated sheet held together by hydrogen bonds between backbone strands.
R groups: Alternate above and below the sheet.

Secondary Structure and Alzheimer’s Disease

Beta-amyloid: Protein fragment forms plaques in the brain.
Structural change: In Alzheimer’s, beta-amyloid shifts from alpha-helical to beta-strand structure, contributing to disease pathology.

Tertiary Structure

Interactions: Nonpolar (hydrophobic), polar (hydrogen bonds), salt bridges (ionic), and disulfide bonds (covalent).
Stabilization: Determines the protein’s 3D shape and function.

Quaternary Structure

Definition: Interaction of two or more polypeptide chains (subunits).
Stabilization: Same forces as tertiary structure.
Example: Hemoglobin has four subunits; some proteins have only one chain and lack quaternary structure.

10.4 Protein Denaturation

Denaturation is the loss of protein structure (secondary, tertiary, or quaternary) without breaking peptide bonds, often resulting in loss of function.

Causes: Heat, pH changes, chemicals, or mechanical agitation.
Effect: Denatured proteins lose their biological activity.

10.5 Protein Functions

Proteins perform a wide range of functions in living organisms.

Enzymes: Catalyze biochemical reactions.
Transport: Move substances (e.g., hemoglobin, albumin).
Structural: Provide support (e.g., collagen, keratin).
Defense: Antibodies protect against pathogens.
Regulation: Hormones control physiological processes.

10.6 Enzymes and Protein Structure

Enzymes are proteins that accelerate chemical reactions by lowering activation energy. Their activity depends on the structure of their active site.

Active site: Region where substrate binds and catalysis occurs.
Substrate: Reactant molecule acted upon by the enzyme.
Cofactors: Inorganic substances assisting catalysis (e.g., metal ions).
Coenzymes: Small organic molecules assisting catalysis (e.g., NAD+).
Specificity: Enzyme active sites are specific for their substrates (e.g., hexokinase fits D-glucose).

10.6 Enzyme-Substrate Models

Two main models explain how enzymes interact with substrates.

Lock-and-key model: Active site is rigid and exactly complementary to the substrate.
Induced-fit model: Active site is flexible and adapts to fit the substrate upon binding.

10.6 Rates of Reaction

Enzymes increase reaction rates by lowering activation energy and facilitating substrate interactions.

Catalysis: Formation of enzyme-substrate (ES) complex lowers activation energy.
Key factors: Proximity, orientation, bond energy, substrate concentration.
Equation:

10.7 Factors Affecting Enzyme Activity

Enzyme activity is influenced by environmental conditions and the presence of inhibitors.

pH optimum: Each enzyme has a pH at which it works best; varies by location in the body.
Temperature optimum: Most human enzymes function best at 37°C.
Inhibitors: Molecules that decrease enzyme activity; can be reversible or irreversible, competitive or noncompetitive.

10.7 Competitive Inhibitors

Competitive inhibitors resemble the substrate and compete for the active site.

Mechanism: Inhibitor binds to active site, preventing substrate binding.
Reversibility: Inhibition can be overcome by increasing substrate concentration.

10.7 Noncompetitive Inhibitors

Noncompetitive inhibitors bind to a site other than the active site, altering enzyme shape and function.

Mechanism: Inhibitor binds remotely, distorting the active site.
Effect: Substrate cannot bind effectively; inhibition cannot be reversed by adding substrate.

10.7 Irreversible Inhibitors

Irreversible inhibitors permanently inactivate enzymes by forming covalent bonds with amino acid side chains.

Mechanism: Covalent modification excludes substrate or blocks catalysis.
Example: Penicillin irreversibly inhibits bacterial cell wall synthesis enzymes.

Table: Essential vs. Nonessential Amino Acids

Amino Acid	Essential?	Notes
Arginine	Essential*	Essential for children
Histidine	Essential*	Essential for children
Isoleucine	Essential*
Leucine	Essential*
Lysine	Essential*
Methionine	Essential*
Phenylalanine	Essential*
Threonine	Essential*
Tryptophan	Essential*
Valine	Essential*
Other amino acids	Nonessential	Can be synthesized by the body

Additional info: Table inferred from context; full list of amino acids not provided in original notes.