Proteins

Proteins are polymers of amino acids

They make up more than 50% dry mass of cells

Proteins contain C,H,O, and N. Some contain S

Proteins may form complexes with other substances

Diversity of functions

Proteins are diverse. Dome of their functions include:

Cell membranes

Antibodies

Haemoglobin

Keratin in hair

Collagen in bone and connective tissue

Amino acid structure

This is the amino groupIt contains nitrogen and is basicNitrogen bonds to 2 hydrogen atoms and the central carbon

This is the acid carboxyl group –COOHWhich will lose a H+ into solution

This is the residual groupEach amino acid has a different R groupIt will determine the type of amino acid

Types of amino acidsThe R group gives amino acids different properties

There are 20 essential amino acids used to make proteins

The smallest amino acid is glycine where R = H

Some other R groupsThe amino acid is named according to the R group [in red] Each name has a abbreviation [in blue]

This is the a central carbonIf the R group is not H then this is an asymmetrical carbon

All amino acids can exist as optical isomers but in nature only one form is foundThis is the L -isomer

Remember amino acids are 3-D structuresA large R group will make this more complex

Amino acids form Zwitterions

the proton is lost here making this side negatively charged

Amino acids form Zwitterions

The N picks up a proton and this now has a positive charge

Amino acids form Zwitterions

The molecule has an overall neutral chargeThis only occurs at a particular pHThis is the isoelectric pointThe R group will change the isoelectric point for different amino acids

Or:

If the amino acid is placed in a more acidic (more H+) solution:

Protons are accepted here

Because protons are removed from solution the solution becomes less acidic again

The amino acid has acted as a buffer

If the solution is becomes more basic:

H+ is donated from here so the acidity is restored

To recapAmino acids form zwitterions – with both basic and acidic propertiesAt a certain pH – the isoelectric point - the ions formed are neutralThey are amphotericThey are able to donate or accept hydrogen ions to keep the pH the sameSo they act as buffers

Soluble proteins in cells and in the blood are important as buffers

Dipeptids

2 amino acids can be joined by the removal of water

This is a dipeptide molecule

Held by a peptide bond

This is a dipeptide molecule

Held by a peptide bond

Water is formed this is condensation

A peptide bond can be broken by hydrolysis or addition of water

In this way long chains of amino acids can be formed = polypeptidesNotice that there is still an amino end and a carboxylic end

The order of the amino acids in the chain is determined by the DNA sequence of the gene coding for the protein

This is the Primary Protein structure

The primary sequence is folded into a highly specific 3D structure which is held together by various bonds

Bonds involved in maintaining the shape of proteins

H bonds

Ionic bonds

Disulfide bond/ bridges

Hydrophobic interactions

1. H Bond [hydrogen bonds]

These are weak attractions between an electronegative oxygen in a carboxylic group and an electropositive H on OH or NH groupsThe large number of these bonds make them significant even though they are weak

2. Ionic bonds

These only form at the right pH

An electron is donated or accepted between ionized amine and carboxylic group.

A relatively weak bond broken by a change in pH

Ionic bonds may also form between residual groups

3. Disulfide bridgeThis forms between 2 cysteine amino acids

(R= CH2SH)

It is a covalent bond

4. Hydrophobic interactions

Hydrophobic R groups in the polypeptide chain are shielded by Hydrophilic ones in an aqueous solution

There are 4 levels of Protein structure

Primary SecondaryTertiaryQuaternary

There are 4 levels of Protein structure

Primary SecondaryTertiaryQuaternary

All proteins show this

Seen in most proteins

Seen in globular proteins

Seen in some proteins

Primary structure

This is the sequence of amino acids It is determined by the DNA codeThe amino acids are held together by peptide bonds

All proteins will have primary structure

Secondary structure

The polypeptide chain is twisted into

∝-helixOr a

β- pleated

sheet

Held together by H-bonds

All or only part of a polypeptide chain may coil into an α-helix

β-Pleated sheets are formed by hydrogen

bonds between parallel chains of polypeptides or a single chain folded back on itself

Proteins with just secondary structure form fibrous proteins which are insoluble

Fibrous Proteins

e.g. collagenA tough protein used as connective tissueIt is an insoluble, fibrous proteinsCollagen and has a high tensile strength

Collagen is made from 3 α-helix molecules twisted like

a rope

The most common amino acid is glycine which is small because R=HThis allows the molecule to twist tightly

The collagen triple helices are bundled together into fibrilsThese form Collagen fibres

Notice how the joins of the fibrils are staggered to prevent lines of weakness forming

Fibrils

Fibre

Scanning em of collagen

e.g. KeratinThis is the protein in hair and skin

It is formed from α-Helix polypeptides

e.g. elastinThis protein is found in connective tissue for instance in alveoliIt can be stretched and will recoil to the original shape

Tertiary Structure: globular proteins

This structure may involve any of these :

Hydrogen bonds

Disulfide bridges

Ionic bonds

Hydrophobic interactions

There may be sections with secondary structure

The proteins have an overall 3-D globular shape which is highly specific

because it is determined by the bonds forming between specific amino acids in the primary sequence

Globular proteins have specific shapes and are soluble

Enzymes are globular proteinsThey have a specific active site

The hydrophilic exterior R groups makes the molecule soluble in water

Quarternary Structure

e.g. Haemoglobin: made of 4 polypeptides

These are formed from 2 or more polypeptide chainsHeld together by hydrophobic interactions

Summary of levels of Protein structure

Conjugated proteinsthese contain a non-protein group

For example the haem group in haemoglobinThere is one haem group in each of the 4 polypeptides

myogloin

Myoglobin has only one polypeptide with a haem group in it

Test for protein – the Biuret test

In a basic solution CuSO4 will interact with peptide bondsThe colour will change to lilac