MedChem L19

Amino acids contain

amino group and carboxyl group

Ribosomal peptides

Sequence assembly under nucleic acid control

Non-ribosomal peptides

Sequence assembly under control of a single enzyme

Alpha carbon

Carbon carrying the R group, the amino and carboxylic acid group

Acidity of carboxylic acid

React with bases to give carboxylate salts

Basicity of amines

React with acids to give amine salts

Internal salts

Have the charecteristic physical properties of salts

Zwitterion

Exists in a dipolar form

Hydrophobic groups

Tend to arrange themselves in the centre of the protein away from the water phase

Hydrophilic groups

Tend to arrange themselves so that they point out into the surrounding water phase

Acidic side chains

Negatively charged

Basic side chains

Positively charged

Chirality and amino acids

All amino acids are optically active except glycine

Configuration of amino acids

S

Peptides

Ubiquotous in living organisms and involved in all body functions

Polyamide

Backbone consisting of a linear chain of a-amino acids

Residue

Amino acids in a peptide sequence

Side of N terminal

Left

Side of C terminal

Right

Disulfide bonds

Formed between the side groups of 2 cysteines

Roles of proteins

Give strength and elasticity to skin

Make up muscles and tendons

Antibody proteins protect us against disease

Haemoglobin is the protein which transports oxygen

Structural units of proteins

Polymers of high molecular weight called polypeptides

Fibrous proteins

Structural functions

Insoluble in water

Kreatins

Make up protective tissue

Collagen

Make up connective tissue

silks

Fibroin of spider webs

Globular

Almost spherical in shape

Soluble in water

Enzymes

Biological catalysts

Hormones

Chemical messengers that regulate bioprocesses

Transport proteins

Carriers of small molecules

what does the overall structure of a protein influence

Function

Primary structure of a protein

The most fundamental level of protein structure

The sequence of covalently linked amino acids in the polypeptide

Determines the 3D dimensional shape of a protein

Secondary structure

Non covalent forms such as hydrogen bonding and hydrophobic interactions determine how a polypeptide twist into a particular 3-D shape

Hydrophobic interactions drive

The formation of the overall shape and hydrogen bonding stabilises it

Hydrogen bonding

The force of attraction between the partial positive charge on hydrogen and the partial negative charge on the oxygen of the carbonyl

What gives rise to the secondary structure of proteins

Hydrogen bonding

What does the secondary structure refer to

Overall 3D repeating pattern

What stabilises the secondary structure

Hydrogen bonds

a-Helix

Polypeptide backbone coils as a right handed screw

Where do hydrogen bonds extend from in a-Helix

H atoms of the NH units

Where do hydrogen bonds extend to in a-Helix

Oxygen atoms of carbonyl units

Where are the oxygen atoms of the carbonyl units situated in a-Helixs that the H atoms bind to

4 residues further along the polypeptide backbone

Where are the R groups pointed in a-Helix

Outward

What does the R group pointing outward influence

Further folding and the way the protein interacts with other proteins and the environment

How do protein chains lie in the B-pleated sheet

Side by side

How are chains held in place in B-pleated sheet

Hydrogen bonds

What does the tertiary structure of a protein refer to

Interactions between side chains at non adjacent points in secondary structure

How is the tertiary structure of protein stabilised

Non covalent bond interactions

e.g Hydrogen bonding

Salt bridges

Hydrophobic interaction

Covalent bonds - disulphide linkages

Quaternary structure

2+ polypeptide units assemble together to form the final protein structure