Proteins (DP IB Biology)

The genetic code, meaning the DNA base sequence, determines the number and order of amino acids in a polypeptide.

False.

Polypeptides can vary in length from a few to thousands of amino acids.

Examples of polypeptides include:

• Rubisco

• Insulin

• Rhodopsin

• Collagen

• Spider silk

or any other valid answer.

Denaturation is the irreversible change of protein conformation caused by temperature and pH extremes that interfere with the bonds maintaining protein structure.

False.

The bonds that form between different R groups are relatively weak compared to the peptide bonds that hold the amino acids in sequence.

The optimum pH for a protein is the pH at which the protein's 3D structure is not denatured.

Certain protein drugs need to be delivered by injection because they would be denatured by stomach acid if taken orally.

An extremophile is an organism that has evolved to have proteins that are stable even at extreme pH or temperature.

False.

Denaturation is almost always irreversible, meaning the protein cannot be re-formed in its original conformation by reversing the change in conditions.

Pepsin, a protein-digesting enzyme, has an optimum pH of 2 because it works in the stomach where the low pH causes proteins in the diet to become denatured.

Denaturation of enzymes can be used in experiments to measure enzyme activity, such as establishing the optimum pH or temperature of an enzyme like pepsin or lipase.

Conformation refers to the three-dimensional shape or structure of a protein, which can be altered by the breaking of bonds between different R groups.

Twenty amino acids are commonly found in proteins.

All amino acids share a carboxyl group and an amine group, bonded by a central carbon atom.

An R-group, or variable group, is the part of an amino acid that makes it unique and determines its properties, such as whether it is acidic or basic, or polar or non-polar.

False.

Humans can naturally synthesise only eleven amino acids within their cells, while nine are essential and must come from the diet.

R-groups can be either hydrophobic (non-polar) or hydrophilic (polar).

True.

The properties of the R groups of the amino acids in the protein determine the way the protein folds into a 3D shape.

Hydrophilic R-groups are polar or charged, acidic or basic.

The primary structure is the sequence of amino acids bonded by covalent peptide bonds, which is determined by the cell's DNA and is specific for each protein.

Secondary structure is caused by weak hydrogen bonds between carboxyl (C=O) and amino (N-H) groups. The two main forms are alpha-helix (α-helix) and beta-pleated sheet (β-pleated sheet).

The four types of bonds/interactions that contribute to tertiary structure are:

1. Hydrogen bonds between polar R-groups

2. Hydrophobic interactions between non-polar amino acids

3. Covalent disulfide bridges between cysteine amino acids

4. Ionic bonds between charged R-groups

Quaternary structure refers to the arrangement of multiple polypeptide chains (subunits) and any non-polypeptide components. Only proteins with multiple polypeptide chains have quaternary structure.

In secondary structure, hydrogen bonds form between amino and carboxyl groups, while in tertiary structure, hydrogen bonds form between R groups as well as amino and carboxyl groups.

Haemoglobin has four subunits (two α-globins and two β-globins), each with a prosthetic haem group containing an iron ion (Fe²⁺).

Proteins with more non-polar amino acids are less soluble in aqueous solutions and are generally used for structural purposes, often found in the centre of proteins or in contact with cell membranes.

Polar amino acids make proteins soluble and are found:

• on membrane surfaces to interact with water

• lining interior pores for transport

• on enzyme surfaces for aqueous solubility

Insulin consists of two chains (21 and 30 amino acids long) joined by disulfide bridges, and can form two different quaternary structures called dimers and hexamers that act as storage molecules.

Cryo-EM (cryogenic electron microscopy) involves rapid freezing of protein solutions and using electrons to produce microscopic images. Unlike X-ray crystallography, it doesn't require protein crystallization and can show proteins in their cellular context.

Globular proteins are compact, roughly spherical (circular) in shape and soluble in water.

Globular proteins form a spherical shape when folding into their tertiary structure because their non-polar hydrophobic R-groups are oriented towards the centre of the protein away from the aqueous surroundings, while their polar hydrophilic R-groups are oriented on the outside.

The orientation with polar hydrophilic R-groups on the outside enables globular proteins to be soluble in water, as the water molecules can surround these polar groups.

The solubility of globular proteins in water means they can be easily transported around organisms and be involved in metabolic reactions, playing important physiological roles.

The folding of the protein due to R-group interactions results in globular proteins having specific shapes, allowing them to play roles like catalysing reactions (enzymes) or responding to specific antigens (immunoglobulins).

Some globular proteins are conjugated, containing a prosthetic group. For example, haemoglobin contains the prosthetic group haem.

Fibrous proteins have a large number of hydrophobic R-groups, which makes them insoluble in water.

Fibrous proteins have a highly repetitive amino acid sequence that creates very organised, strong structures. Their insolubility also makes them suitable for structural roles.

Collagen molecules are formed from three polypeptide chains held together by hydrogen bonds to form a triple helix structure.

Covalent cross-links form between R-groups of amino acids in the parallel triple helices, further reinforcing the structure.

Collagen is found in a wide variety of connective tissues including tendons, cartilage, ligaments, bones, teeth, skin, walls of blood vessels, and the cornea of the eye.