Organic Molecules: Proteins – Structure, Function, and Diversity

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Organic Molecules: Proteins

Introduction to Proteins

Proteins are essential organic molecules that play a wide variety of roles in living organisms. They are highly diverse in both structure and function, making them crucial for biological processes. Proteins are polymers composed of amino acids, which are the building blocks of these macromolecules.

Definition: Proteins are biologically functional molecules consisting of one or more polypeptides folded into a specific three-dimensional structure.
Importance: Proteins perform structural, enzymatic, transport, defensive, hormonal, receptor, contractile, and motor functions.
Example: Hemoglobin, an oxygen-transport protein in blood, and antibodies, which defend against pathogens.

Protein Functions

Major Types of Protein Functions

Proteins serve a variety of functions in cells and organisms, each determined by their unique structure.

Enzymatic Proteins: Accelerate chemical reactions (e.g., digestive enzymes).
Defensive Proteins: Protect against disease (e.g., antibodies).
Transport Proteins: Move substances across membranes or within the body (e.g., hemoglobin).
Hormonal Proteins: Coordinate organismal activities (e.g., insulin regulates blood sugar).
Receptor Proteins: Respond to chemical stimuli (e.g., nerve cell receptors).
Contractile and Motor Proteins: Enable movement (e.g., actin and myosin in muscles).
Structural Proteins: Provide support (e.g., keratin in hair, collagen in connective tissue).

Protein Type	Function	Example
Enzymatic	Catalyze chemical reactions	Digestive enzymes
Defensive	Protection against disease	Antibodies
Transport	Transport substances	Hemoglobin
Hormonal	Coordination of activities	Insulin
Receptor	Response to stimuli	Nerve cell receptors
Contractile/Motor	Movement	Actin, myosin
Structural	Support	Keratin, collagen

Amino Acids: Building Blocks of Proteins

Structure of Amino Acids

Amino acids are the monomers that make up proteins. Each amino acid has a central carbon atom (α-carbon) bonded to four groups: an amino group, a carboxyl group, a hydrogen atom, and a variable side chain (R group).

Amino Group: , can be positively charged at neutral pH.
Carboxyl Group: , can be negatively charged at neutral pH.
Side Chain (R group): Determines the properties and identity of the amino acid.
α-Carbon: Central carbon to which all groups are attached.

General formula:

Classification of Amino Acids

There are 20 common amino acids, each with a unique R group. Amino acids are classified based on the properties of their side chains:

Nonpolar (hydrophobic): Side chains are mostly hydrocarbons.
Polar (uncharged hydrophilic): Side chains contain electronegative atoms (e.g., oxygen, nitrogen).
Polar (charged hydrophilic): Side chains are either acidic (negatively charged) or basic (positively charged).

Type	Examples	Properties
Nonpolar	Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline, Phenylalanine, Tryptophan	Hydrophobic
Polar (Uncharged)	Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine	Hydrophilic
Polar (Acidic)	Aspartic acid, Glutamic acid	Negatively charged
Polar (Basic)	Lysine, Arginine, Histidine	Positively charged

Determining Amino Acid Properties

The nature of the R group determines the chemical behavior of each amino acid. To classify an amino acid:

Does the side chain have a negative charge? If yes, it is acidic.
Does the side chain have a positive charge? If yes, it is basic.
If uncharged, does it have an oxygen atom? If yes, it is polar uncharged.
If none of the above, it is nonpolar.

Polypeptides and Peptide Bonds

Formation of Polypeptides

Amino acids are linked together by peptide bonds through dehydration synthesis (condensation) reactions, forming polypeptide chains.

Peptide Bond: Covalent bond between the carboxyl group of one amino acid and the amino group of another.
Directionality: Polypeptides have an N-terminus (free amino group) and a C-terminus (free carboxyl group).
Flexibility: Single bonds adjacent to the peptide bond allow rotation, contributing to protein folding.

Equation for peptide bond formation:

Hydrolysis and Digestion

Proteins are broken down into amino acids by hydrolysis reactions, especially during digestion.

Hydrolysis: Addition of water breaks peptide bonds, releasing amino acids.
Enzymes: Pancreatic enzymes catalyze hydrolysis in the small intestine.

Equation for hydrolysis:

Levels of Protein Structure

Primary Structure

The primary structure of a protein is its unique sequence of amino acids, determined by genetic information.

Linear sequence: The order of amino acids from N-terminus to C-terminus.
Genetic control: DNA encodes the sequence.

Secondary Structure

Secondary structure refers to local folding patterns stabilized by hydrogen bonds between backbone atoms.

α-Helix: Spiral structure stabilized by hydrogen bonds.
β-Pleated Sheet: Sheet-like structure formed by hydrogen bonding between parallel strands.
Stabilization: Hydrogen bonds between carbonyl and amino groups in the backbone.

Tertiary Structure

Tertiary structure is the overall three-dimensional shape of a polypeptide, determined by interactions among R groups.

Interactions: Hydrogen bonds, ionic bonds, hydrophobic interactions, van der Waals forces, and disulfide bridges.
Functional groups: Outer surfaces present functional groups for interaction with other molecules.

Quaternary Structure

Quaternary structure arises when a protein consists of two or more polypeptide chains, forming a functional unit.

Subunit interactions: Multiple polypeptides associate via non-covalent interactions.
Example: Hemoglobin, composed of four polypeptide subunits.

Protein Domains and Interactions

Domains

Domains are distinct functional regions within a protein, often responsible for specific activities.

Multiple domains: Most proteins have several domains, each contributing to the protein's overall function.

Protein-Protein Interactions

Proteins often interact with other proteins to carry out cellular processes.

Binding mechanisms: Hydrogen bonds, ionic bonds, hydrophobic effects, van der Waals forces.

Protein Folding and Denaturation

Folding

Proper folding is essential for protein function. Folding is often spontaneous due to favorable interactions, but molecular chaperones may assist in cells.

Stability: Folded proteins are more energetically stable.
Molecular chaperones: Proteins that help other proteins fold correctly.

Denaturation

Proteins can lose their structure and function due to changes in environmental conditions.

Causes: pH, temperature, ionic concentration changes.
Effects: Loss of secondary, tertiary, and quaternary structure; loss of biological function.

Protein Shape and Regulation

Shape Flexibility

Protein shape is crucial for function. Some proteins are disordered when inactive and fold into active shapes when needed.

Regulation: Proteins may be regulated by controlling folding and activation.

Hemoglobin and Sickle Cell Disease

Hemoglobin Structure

Hemoglobin is a protein with quaternary structure, responsible for oxygen transport in blood.

Subunits: Four polypeptide chains.
Mutation: A single amino acid change can cause sickle cell anemia, altering hemoglobin's shape and function.

Summary Table: Levels of Protein Structure

Level	Description	Stabilizing Forces
Primary	Sequence of amino acids	Peptide bonds
Secondary	Local folding (α-helix, β-sheet)	Hydrogen bonds
Tertiary	Overall 3D shape	R group interactions
Quaternary	Association of multiple polypeptides	Non-covalent interactions

Additional info: Protein structure and function are central topics in General Biology, and understanding the relationship between amino acid sequence, folding, and biological activity is essential for further study in biochemistry and molecular biology.