B1.2 Proteins

COMPLETE

What do all amino acids contain?

- Amino group (NH3)
- A carboxylic acid (COOH)
- A hydrogen ( H )
- An R group

How many universal amino acids are there ?

20

Dipeptide

Two amino acids bonded together through a peptide bond

How are dipeptides formed?

condensation of 2 amino acids

Where in a cell does polypeptide formation occur ?

Catalysed in cells by ribosomes

Oligopeptide

Peptide sequences of 2-20 amino acids

Polypeptide

A polymer (chain) of many amino acids linked together by peptide bonds

- main component of proteins

Where does polypeptide formation occur ?

Polypeptides are made on ribosomes

How do plants and animals gain amino acids ?

Plants make amino acids through photosynthesis
Animals obtain amino acids through their foods

What's an essential amino acid ?

one that cannot be synthesised in sufficient quantities by animals so must be obtained from diets

What's a non-essential amino acid?

one that can be synthesised by an animal using metabolic pathways that transform one amino acid into another

Why do vegans require attention to ensure essential amino acids are consumed ?

Animal based food such as fish and meat have a balance of amino acids that are similar to that of a human diet whereas plant based foods have a different balance and some are deficient in certain amino acids

Why is there a limitless diversity of DNA base sequences?

There are 20 amino acids but there is no limit on the number of amino acid sequences in polypeptides so the combinations can continue forever.

Denaturation

A process in which a protein unravels, losing its specific structure and hence function can be caused by changes in pH or salt concentration or by high temperature

How do high temperatures cause denaturation ?

High temperatures disrupt the hydrogen bonds that hold a protein together. Once these bonds are broken the protein will begin to unfold and therefore it's function will be lost

How does pH cause denaturation?

Changing the pH will alter the charge of the protein, which in turn will alter protein solubility and overall shape

What determines chemical characteristics in amino acids ?

The R- group

How do some proteins contain amino acids that aren't in the basic 20 ?

Due to modifications after a polypeptide has been synthesised

Primary structure

Linear sequence of amino acids in a polypeptide

What is the backbone of a polypeptide ?

A repeating sequence of atoms linked by covalent bonds

What allows polypeptides to fold into nearly any 3D shape ?

The bond angles are all tetrahedral and there can be rotation around bonds between the alpha carbons and the adjacent nitrogen and carbons

What is conformation?

protein's unique shape/arrangement that determines its function

What are the 2 commonly occurring secondary structures ?

Alpha helix and Beta pleated

What does the Alpha helix structure look like ?

The polypeptide is wound into a helical shape with hydrogen bonds between the turns

What does the Beta pleated structure look like ?

Two or more sections of polypeptide are arranged parallel with hydrogen bonds between them.
Polypeptide sections run in opposite directions which forms a sheet that is pleated due to the tetrahedral bond angles

Describe the secondary structure of a protein

Secondary structure results from hydrogen bonding. The hydrogen bond causes the amino acids to form pleated sheets or helices

Hydrogen bonds form between the C=O groups and the N-H groups.

Describe the tertiary structure of a protein

Folding of the whole polypeptide chain into a 3D structure that is stabilized by R- group interactions.

What are the 4 main types of R-Group interactions ?

Ionic bonds, Hydrogen bonds, Disulfide bonds, Hydrophobic interactions

Where do ionic bonds form?

Between positively and negatively charged R groups
Amine groups become positive by accepting a proton.
Carboxyl groups become positive by donating a proton.

Why are ionic bonds sensitive to pH changes ?

Due to involvement of protons ( hydrogen ions )

Where do hydrogen bonds form?

Between polar R- groups
A hydrogen atom forms a link between two electronegative atoms such as O or N.

- It is covalently bonded which results in H having a slight positive charge whilst the other has a slight negative.

Where do disulfide bonds form?

Between adjacent cysteine pairs
- strongest interaction
- covalent bonds

Where do hydrophobic interactions occur?

between non-polar R groups

When do tertiary structures develop ?

as a polypeptide is synthesized by ribosomes

- sometimes a chaperone protein will help with this process

What broad categories can all amino acids be divided into ?

Hydrophobic and Hydrophilic

What is the arrangements of amino acids in soluble globular proteins ?

Hydrophilic amino acids will be present on their surface whilst the hydrophobic amino acids will be clustered in the centre of the protein.

Why do globular proteins need to be soluble in water ?

because they carry out their function in the cytoplasm or aqueous solutions outside the cell

Why does arrangement of amino acids in soluble globular proteins stabilise the tertiary structure ?

Because it maximises the hydrophobic interactions between amino acids in the centre and the hydrogen bonding between amino acids on the surface and the water surrounding.

What is the arrangements of amino acids in integral membrane bound proteins ?

The proteins have hydrophobic amino acids on their surface where they contact the non-polar ( hydrophobic ) hydrocarbon core of the membrane.

Why does arrangement of amino acids in integral proteins stabilise the tertiary structure ?

Ensures that it remains positioned correctly in the membrane where its function can be performed.

What do channel proteins do?

Provide passageway through membrane for hydrophilic substances (polar and charged)

What is the arrangements of amino acids in channel proteins ?

Hydrophilic regions with a Hydrophobic region between which holds the transmembrane in position.
- Tunnel lined with hydrophilic amino acids through protein centre

What is the quaternary structure of a protein?

The 3D arrangement of subunits in proteins that consist of more than one polypeptide

What's a non conjugated protein ?

A protein that only has 1 polypeptide subunit

How do non conjugated proteins form a quaternary structure ?

The polypeptides are linked by the same types of interactions as in their tertiary structures.

What's a conjugated protein ?

A protein that has one or more non polypeptide subunits as well as their polypeptides.

What do inclusion of conjugated proteins increase ?

- chemical and functional diversity of proteins

Examples of conjugated and non-conjugated proteins

conjugated: haemoglobin molecule
non conjugated: collagen., insulin

Describe the structure of fibrous proteins

They consist of elongated polypeptides that lack the folding of the typical tertiary structure.

- do not develop secondary structures

The quaternary structure is developed by linking polypeptide chains into filaments/fibres through hydrogen bonding

Describe the structure of collagen

Primary: repeating sequence of 3 amino acids ( P-G-X )
- P prevents formation of alpha helix sheet

Quaternary: 3 polypeptides wound together in a triple helix ( would be impossible if there were alpha helices )

What is the form of globular proteins ?

They have a rounded shape that is formed by the folding of polypeptides
- stabilised by bonds between the R groups of amino acids

How are globular proteins specific ?
- in relation to insulin

Their conformation allows them to bond to specific sites on the receptors which allows a signal to be sent to body signals

When blood sugar concentration is too high signals get sent to body cells through the active site of enzymes and ligand binding