Protein Structure and Function: Study Notes for General Biology

Organic Molecules

Main Classes of Biological Organic Compounds

Organic compounds are essential molecules built on a framework of carbon atoms. In biological systems, four main classes of organic compounds are found:

• Proteins

• Nucleic acids

• Carbohydrates

• Lipids

All biological organic compounds contain carbon (C) and hydrogen (H). They may also include other elements such as oxygen (O), nitrogen (N), phosphorus (P), and sulfur (S). Their properties differ in terms of charge, pH, polarity, size, and shape.

Proteins

Amino Acids: The Building Blocks

Proteins are long chains of amino acid monomers. There are 20 different kinds of amino acids, each sharing a fundamental structure:

• Amino group (-NH2)

• Carboxyl (acid) group (-COOH)

• R group (side chain): variable group that determines the properties of each amino acid

The general structure of an amino acid can be represented as:

• Central carbon atom (C)

• Attached hydrogen atom (H)

• Amino group

• Carboxyl group

• R group (side chain)

Example: The R group is what makes each amino acid unique and gives it specific chemical properties.

Properties of Amino Acids

Each amino acid has specific properties based on its structure, which is determined by the R group. The structures of amino acids differ only due to the R group (also called the "side chain").

Amino Acid	Structure	Property
Leucine (Leu)	CH2-CH(CH3)2	Hydrophobic
Serine (Ser)	CH2-OH	Hydrophilic
Aspartic acid (Asp)	CH2-COOH	Hydrophilic (acidic)

Peptide Bonds

Formation and Types of Peptides

Peptide bonds are covalent bonds that link amino acids together to form peptides and proteins. These bonds are formed through a dehydration reaction between the carboxyl group of one amino acid and the amine group of another.

• Dipeptide: two amino acids joined by a peptide bond

• Tripeptide: three amino acids joined

• Oligopeptide: short chain of amino acids

• Polypeptide: long chain of amino acids

The general reaction for peptide bond formation is:

$\text{Amino acid}_1 + \text{Amino acid}_2 \rightarrow \text{Dipeptide} + H_2O$

Example: The peptide bond forms the backbone of protein structure.

Polypeptide Chains

Orientation and Properties

Polypeptide chains have a backbone formed by peptide bonds, with side chains (R groups) extending outward. These side chains can interact with each other or with water, influencing the protein's properties and function.

• Directionality: The N-terminus is the end with the free amino group; the C-terminus is the end with the free carboxyl group.

• Flexibility: Single bonds on both sides of the peptide bond allow the chain to flex and rotate.

Example: The orientation and flexibility of polypeptide chains are crucial for protein folding and function.

Levels of Protein Structure

Primary Structure

The primary structure of a protein is the unique sequence of amino acids in its polypeptide chain. This sequence is determined by the genetic code (DNA) and is critical for the protein's final shape and function.

• Order of amino acids is essential; even a single change can affect function (e.g., sickle cell anemia).

Secondary Structure

The secondary structure refers to local folding patterns within the polypeptide chain, stabilized by hydrogen bonds between backbone atoms. The two main types are:

• Alpha helix (α-helix): A coiled structure

• Beta pleated sheet (β-sheet): A folded, sheet-like structure

Tertiary Structure

The tertiary structure is the overall three-dimensional shape of a single polypeptide chain, determined by interactions among R groups. These interactions include ionic bonds, hydrogen bonds, covalent bonds (disulfide bridges), and hydrophobic interactions.

• Folding creates functional regions such as grooves or pockets.

Quaternary Structure

Quaternary structure arises when two or more polypeptide chains (subunits) associate to form a functional protein. These subunits are held together by hydrogen bonds, disulfide bridges, ionic interactions, and hydrophobic forces.

• Example: Hemoglobin is composed of multiple polypeptide chains.

Protein Function and Denaturation

Relationship Between Structure and Function

The function of a protein is directly related to its structure. Changes in the amino acid sequence or folding can radically alter protein function.

• Denaturation: The process by which a protein loses its higher-level structure (secondary, tertiary, quaternary) due to factors such as heat, salt, or pH changes, resulting in loss of function.

Example: Ribonuclease loses its activity when denatured.

Diversity and Functions of Proteins

Biological Functions of Proteins

Proteins have unparalleled diversity in size, shape, and chemical properties, allowing them to serve a wide range of functions in cells:

Type of Protein	Function	Example
Enzymatic proteins	Accelerate specific chemical reactions	Digestive enzymes
Defensive proteins	Protect against pathogens and disease	Antibodies
Storage proteins	Store amino acids	Ovalbumin in egg white
Transport proteins	Transport other molecules	Hemoglobin
Receptor proteins	Cause cell to respond to chemical stimuli	Insulin receptor
Contractile and motor proteins	Cause movement of organelles, cells, or organisms	Actin, myosin
Structural proteins	Support organelles, cells, or organisms	Collagen, connective tissue

Review Questions

• What is the structure of an amino acid?

• What is a peptide bond and how does it influence peptide structure?

• Describe the four levels of protein structure.

• Give examples of biological functions of proteins.

• What is denaturation and what can cause it?