Proteins: Structure, Properties, and Functions (Concept 5.4)

Proteins

Monomer/Subunit of Proteins

Proteins are essential macromolecules in all living organisms, composed of long chains of amino acids. The monomer or basic subunit of a protein is the amino acid.

• Amino acids are organic molecules with a central carbon atom (the alpha carbon), an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and a unique side chain (R group).

• There are 20 standard amino acids found in proteins.

• Proteins are also called polypeptides when referring to their unstructured, linear form.

Elements and Functional Groups Present

Proteins are primarily composed of the elements carbon (C), hydrogen (H), oxygen (O), nitrogen (N), and sometimes sulfur (S).

• Amino group: -NH2

• Carboxyl group: -COOH

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

Peptide Bonds

A peptide bond is a covalent bond that links amino acids together in a protein chain.

• Formed by a dehydration synthesis (condensation) reaction between the carboxyl group of one amino acid and the amino group of another.

• The resulting bond is called a peptide bond and has the following structure:

$\text{Peptide bond:} \quad -CO-NH-$

• The chain of amino acids is called a polypeptide.

Recognizing Amino Acids by Formula or Shape

Amino acids share a common structure but differ in their side chains (R groups). The general formula is:

$\mathrm{H_2N{-}CHR{-}COOH}$

• The alpha carbon is bonded to four groups: an amino group, a carboxyl group, a hydrogen atom, and an R group.

• The R group is unique for each amino acid and determines its properties.

What Distinguishes Each of the 20 Different Amino Acids?

The side chain (R group) attached to the alpha carbon distinguishes each amino acid.

• R groups can be nonpolar, polar, acidic (negatively charged), or basic (positively charged).

• This diversity in R groups leads to a wide range of chemical behaviors and functions.

Example: Glycine has a hydrogen atom as its R group, while tryptophan has a large, aromatic R group.

Polarity of Side Chains and Protein Structure

The polarity and chemical nature of the side chain (R group) influence where an amino acid is found in a protein's 3D structure.

• Hydrophobic (nonpolar) amino acids tend to be buried inside the protein, away from water.

• Hydrophilic (polar or charged) amino acids are usually found on the surface, interacting with the aqueous environment.

• This distribution helps proteins fold into their functional shapes.

Example: In globular proteins, leucine (nonpolar) is often found in the core, while lysine (positively charged) is on the surface.

Levels of Protein Structure

Proteins have four levels of structure, each contributing to their final shape and function.

• Primary structure: The linear sequence of amino acids in a polypeptide chain.

• Secondary structure: Local folding patterns such as alpha helices and beta pleated sheets, stabilized by hydrogen bonds.

• Tertiary structure: The overall 3D shape of a single polypeptide, formed by interactions among R groups (hydrophobic interactions, hydrogen bonds, ionic bonds, disulfide bridges).

• Quaternary structure: The association of two or more polypeptide chains (subunits) into a functional protein complex.

Example: Hemoglobin has quaternary structure, consisting of four polypeptide subunits.

Major Functions of Proteins in Living Things

Proteins perform a vast array of functions essential for life.

• Enzymes: Catalyze biochemical reactions (e.g., amylase, DNA polymerase).

• Structural proteins: Provide support and shape (e.g., collagen, keratin).

• Transport proteins: Carry substances (e.g., hemoglobin transports oxygen).

• Defense proteins: Protect against disease (e.g., antibodies).

• Signaling proteins: Coordinate cellular activities (e.g., insulin, growth hormone).

• Movement proteins: Enable movement (e.g., actin, myosin in muscles).

• Storage proteins: Store amino acids or other substances (e.g., casein in milk).

Summary Table: Types of Amino Acid Side Chains

The following table classifies amino acids based on the properties of their side chains:

Type	Properties	Example Amino Acids
Nonpolar (hydrophobic)	Do not interact with water; found in protein interiors	Leucine, Valine, Alanine
Polar (uncharged)	Form hydrogen bonds; often on protein surfaces	Serine, Threonine, Asparagine
Acidic (negatively charged)	Carry a negative charge at physiological pH	Aspartic acid, Glutamic acid
Basic (positively charged)	Carry a positive charge at physiological pH	Lysine, Arginine, Histidine

Additional info: The table and some examples are inferred from standard biology textbooks to provide a complete overview for study purposes.