Proteins

Give the general structure of an amino acid and what each respresents

NH₂ - Amine

COOH- Carboxyl

R - Side chain

What are proteins?

They are polymers made up of amino acid monomers

How many amino acids are common in all organisms and how do they differ?

• 20 amino acids

• They differ only in their side group

What is a peptide bond?

A bond formed between 2 amino acids through a condensation reaction, where water is removed

How are dipeptides formed?

• A condensation reaction between 2 amino acids

How are polypeptides formed?

Through the condensation of three or more amino acids

How many polypeptides are needed for a functional protein?

One or more polypeptides

Draw a peptide bond

What happens during hydrolysis of a protein? (3)

• Addition of water

• Breaks the peptide bonds

• Resulting in polypeptides being broken down into amino acids

Which levels of protein structure relate to a single polypeptide chain?

The primary, secondary and tertiary stages

Describe the primary structure of all proteins and what is the name given to this structure?

• It is a sequence of amino acids linked together by peptide bonds through condensation reactions

• (always mention these when asked about primary structure in any form)

• A polypeptide.

How is the primary structure of a protein determined?

It is determined by DNA. 

• By instructing the cell to add certain amino acids in specific quantities in a certain sequence, during translation.

• This affects the shape and, therefore, the function of the protein

Describe the secondary structure of a protein

The local coiling or folding of the polypeptide chain occurring as a result of the hydrogen bonding between amino acids in the peptide backbone which does not involve r groups

What bonding is the secondary structure of a protein held by, which groups form this bond and what are the charges?

• Hydrogen bonding.

• This hydrogen bond forms between the H in the -NH- region and the oxygen in  the -C=O region of another amino acid

• The hydrogen in the -NH- region has a partially positive charge while the oxygen in the -C=O- group has a partially negative charge

Which 2 factors can easily break this secondary structure and why?

• High Temperature and high pH

• This is because of the hydrogen bonds which hold the secondary structure together which are easily broken by high heat and pH changes

Which 2 types of shape can be formed due to these hydrogen bonds?

• α-helix

• β-pleated sheet

When does the alpha helix shape occur?

The α-helix shape occurs when the hydrogen bonds form between every fourth peptide bond.

When does the beta sheet shape occur?

• The β-pleated sheet shape forms when the protein folds so that two parts of the polypeptide chain are parallel to each other

• This enables hydrogen bonds to form between the folded layers

For which type of proteins is the secondary structure the highest folding level for?

• Fibrous proteins

What is the tertiary structure of a protein?

• Unique 3D structure where bonds which form between the side chains (r-group) of the protein due to the twisting and folding of the secondary structure.

What are the 4 types of additional bonds which can form in the tertiary structure of proteins?

• Hydrogen bonds

• Disulfide bridges

• Ionic bonds

• Hydrophobic interactions

List the the additional bonds in order of strongest to weakest

Disulfide bonds

Ionic Bonds

Hydrogen bonds

Hydrophobic interactions

Features of disulfide bonds (3)

• Forms between 2 cysteine R groups and helps to stabilise proteins

• Broken by reduction

• Common in proteins secreted from cells (eg insulin)

Features of ionic bonds (3)

• Forms between positively charged amine group and negatively charged COO^- groups

• Stronger than hydrogen bonds but not common

• Broken by pH changes

Features of hydrogen bonding(2)

• Forms between strongly polar r groups

• Weakest bonds that form

Define quaternary structure of a protein

When there is more than 1 polypeptide chain working together as a functional macromolecule

List 6 functions of protein (THEACS)

• Enzymes: biological catalysts to speed up metabolic reactions

• Transport proteins (eg. Channel and carrier proteins/haemoglobin)

• Structural proteins: provide support (collagen in connective tissue, keratin in hair and nails)

• Hormones: Regulate processes (eg insulin)

• Antibodies: Part of the immune response

• Contractile proteins: Enable movement (actin and myosin in muscle)

Biochemical test for protein

• Biuret reagent

Colour change for biochemical test for protein

Blue to purple

What must be present for the biochemical test to work?

There must be at least 2 peptide bonds present

• There will be a negative result if there is only amino acids or dipeptides

What are prosthetic groups?

Non-protein structure that is permanently integrated into an enzyme or protein's structure

What is an example of a prosthetic group?

Heme

What are conjugated proteins?

A complex protein consisting of a simple amino acid shell bound to a non-protein chemical component.

What are examples of conjugate proteins? (3)

• Glycoproteins

• Lipoproteins

• Haemoglobin

What is a globular protein?

A protein that folds into a compact, roughly spherical 3D shape, which is soluble in water

What are features of a globular protein? (3)

• Compact and spherical (describes the 3D tertiary structure).

• Hydrophilic R-groups on the outside (to form hydrogen bonds with water).

• Globular proteins carry out functional or metabolic roles due to highly specific shapes

Examples of globular proteins

• Haemoglobin

• Enzymes

• Antibodies

What are fibrous proteins?

Proteins which are in long, parallel strands and insoluble in water

What are features of a fibrous protein? (3)

• No tertiary folding

• Insoluble in Water: Because hydrophobic R-groups face outwards, they are completely insoluble.

• Structural Role: They provide mechanical strength, elasticity, and protection to structural tissues.

Examples of fibrous proteins and where they are found(3)

• Collagen: Found in tendons, bones, cartilage, and walls of blood vessels.

• Keratin: Found in hair, nails, and the outer layer of skin.

• Elastin: Found in elastic connective tissue (like the lungs, large arteries like the aorta, and skin