B1.2 Proteins

What is the generalized structure of an amino acid

NH₂–CH(R)–COOH

What does the amine group look like

–NH₂

What does the carboxyl group look like

–COOH

What is the alpha carbon

The central carbon atom bonded to the amine group, carboxyl group, hydrogen atom, and R group.

What is the R group

The variable side chain that differs between amino acids and determines their properties.

How many amino acids are used by living organisms to build proteins

20 amino acids.

What is a dipeptide

Two amino acids joined by one peptide bond.

What is an oligopeptide

A short chain of amino acids, typically 3–20 amino acids long.

What is a polypeptide

A long chain of many amino acids joined by peptide bonds.

What is a peptide bond

A covalent bond (–CO–NH–) formed between the carboxyl group of one amino acid and the amine group of another.

What type of reaction forms a peptide bond

A condensation reaction (dehydration synthesis).

What molecule is removed during peptide bond formation

Water (H₂O).

Which parts of the amino acids are removed to form water

An –OH from the carboxyl group and an –H from the amine group.

Where in the cell are polypeptides synthesized

On ribosomes, either free in the cytoplasm or attached to the rough endoplasmic reticulum.

Can plant cells synthesize all amino acids

Yes, plant cells can synthesize all 20 amino acids.

Can animal cells synthesize all amino acids

No, animals can synthesize only some amino acids.

What are essential amino acids

Amino acids that cannot be synthesized by the body in sufficient amounts and must be obtained from the diet.

What are non-essential amino acids

Amino acids that can be synthesized by the body.

Why must vegans pay attention to food combinations

Some plant foods are low in certain essential amino acids, so eating a variety of foods ensures all essential amino acids are obtained.

Give examples of complementary plant protein combinations. Beans and rice; lentils and whole grains; hummus and pita.

Why is there an infinite variety of peptide chains

Proteins can vary in length, and the 20 amino acids can be arranged in any sequence and repeated multiple times.

What is the formula for the number of possible amino acid sequences in a chain of length n

20ⁿ

How many possible dipeptides can be formed

400 (20²).

What is denaturation

The permanent alteration of a protein’s three-dimensional shape, causing loss of function.

Which levels of protein structure are affected by denaturation

Secondary, tertiary, and quaternary structures (but usually not primary structure).

How does high temperature denature proteins

It increases molecular vibrations, breaking hydrogen bonds, ionic bonds, and hydrophobic interactions.

How does pH denature proteins

Changes in pH alter charges on amino acid side chains, disrupting ionic and hydrogen bonds.

How does denaturation affect enzyme activity

The active site changes shape, so the substrate can no longer bind effectively.

Give an example of protein denaturation by heat. Egg white proteins solidify when cooked.

Give an example of a protein affected by pH. Pepsin functions best in the acidic environment of the stomach.

How do R-groups affect the properties of amino acids

The structure of the R-group determines whether an amino acid is hydrophilic or hydrophobic, polar or non-polar, and positively or negatively charged.

What does hydrophilic mean

"Water-loving"; amino acids with polar or charged R-groups that interact readily with water.

What does hydrophobic mean

"Water-fearing"; amino acids with non-polar R-groups that avoid water.

What does polar mean

The R-group has uneven charge distribution, allowing hydrogen bonding with water or other molecules.

What does non-polar mean

The R-group has no significant charge separation and does not interact well with water.

What is a charged R-group

An R-group that carries a positive or negative charge, enabling ionic interactions.

What is the backbone of a polypeptide

The repeating sequence of atoms –N–Cα–C– along the chain, excluding the R-groups.

What is protein conformation

The specific three-dimensional shape of a protein.

What is the primary structure of a protein

The linear sequence of amino acids joined by peptide bonds.

What type of bond forms the primary structure

Peptide bonds (covalent bonds).

How does DNA determine protein conformation

The DNA base sequence determines the amino acid sequence, and the properties of those amino acids cause the protein to fold into a precise and predictable shape.

What is secondary structure

Local folding of the polypeptide backbone into alpha-helices and beta-pleated sheets.

What bonds stabilize secondary structure

Hydrogen bonds between the C=O and N–H groups of the polypeptide backbone.

What is an alpha-helix

A coiled secondary structure stabilized by hydrogen bonds within the same region of the backbone.

What is a beta-pleated sheet

A sheet-like secondary structure formed by hydrogen bonds between adjacent polypeptide strands.

What is tertiary structure

The overall three-dimensional shape of a single polypeptide chain caused by interactions between R-groups.

Which interactions stabilize tertiary structure

Hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide covalent bonds.

How do polar R-groups affect tertiary structure

They form hydrogen bonds with other polar groups or water.

How do non-polar R-groups affect tertiary structure

They cluster together in the interior of soluble proteins to avoid water.

How do charged R-groups affect tertiary structure

Oppositely charged R-groups attract and form ionic bonds (salt bridges).

What is a disulfide bond

A strong covalent bond (–S–S–) formed between two cysteine amino acids.

Can amino acids be hydrophobic or hydrophilic

Yes, depending on the properties of their R-groups.

How are amino acids arranged in soluble globular proteins

Hydrophobic amino acids are usually buried inside, while hydrophilic amino acids are exposed on the surface.

How are amino acids arranged in integral membrane proteins

Hydrophobic amino acids face the lipid bilayer, while hydrophilic regions extend into aqueous environments.

How are amino acids arranged in channel proteins

Hydrophobic amino acids face the membrane, while hydrophilic amino acids line the channel interior.

What is quaternary structure

The association of two or more polypeptide subunits into a functional protein.

What is a non-conjugated protein

A protein made only of amino acids.

What is a conjugated protein

A protein that contains one or more non-protein prosthetic groups.

Give an example of a conjugated protein. Hemoglobin, which contains heme groups.

Give an example of a non-conjugated protein. Collagen or insulin.

What are fibrous proteins

Long, narrow proteins with structural roles.

What is the function of collagen

Provides tensile strength and structural support in connective tissues such as skin, tendons, and bones.

Describe the structure of collagen. Three polypeptide chains are wound together into a strong triple helix.

What are globular proteins

Compact, spherical proteins with diverse functional roles.

What is the function of insulin

A hormone that regulates blood glucose levels.

Describe the structure of insulin. Two polypeptide chains linked by disulfide bonds, folded into a specific globular shape.

Why is insulin considered highly specific

Its precise three-dimensional shape allows it to bind specifically to insulin receptors on target cells.