PROTEIN STRUCTURE AND FUNCTION

300,000 - 400,000 proteins in the genome
Function is directly dependent upon their 3D structure
Linear polymers derived from 20 different amino acids
Versatile structures performing a vast array of different functions

They contain many different functional groups: acids; bases; alcohols; thiols. These may take part in enzyme catalysed reactions

Can interact with other molecules to form complexes.

Primary (sequence)
 Secondary (folding)
 Tertiary (long range folding)
Quatenary (multimeric organisation)
 Supramolecular (large scale assemblies).

• SIGNALING
  e.g Dopamine receptors and insulin receptors
• TRANSPORT
  eg channel proteins and ion channel proteins
• CATALYSIS
  eg pepsin in the stomach digests protein into small amino acids
• MOVEMENT
  e.g actin and myosin in muscle contraction
• STRUCTURE
  e.g structural proteins: keratin strengthens protective coverings (hair) and collagens/elastin provide support for connective tissues.
• REGULATION
  e.g transcription factor amplify/repress gene expression or turns off genes.  

-Substance binds to a protein and may change the structure of a protein which may change the way it reacts with other proteins and molecules.

EG: Lactorferrin changes shape on binding irons allowing other proteins to distingish between the two forms.

-Amino acids exist as stereo isomers
-Isomeric molecules have the same formula and sequence of bonded atoms, but differ only in the 3D orientation of their atoms in space. IE Same molecular formular but differ in spatial arrangement of their atoms.

R = the functional group on different amino acids
Ca = the asymmetric carbon attoms (with 4 different groups attached) gives rise to stereo isomer. None superimposable mirror images.

Only L - isomers are used in protein structures 

-Amino acids are zwitterionic (a neutral molecule with a +ve and -ve electric charge from dipoles at different locations in the molecule) composed of weak acid functional groups.
-Low pH = overall charge is positive
-High pH = overal charge is negative 
-At physiological = both +ve and -ve charge.
-At a certain pH the positive and negative charges are balanced so overall charge = 0
-This is called the ISOLECTRIC POINT.

• Amino acids with charged sides:
  Present on the surface of proteins interacting with water to hold the protein in solution
  EG Aspartic acid, Gluatmic acid, Lysine, Arginine. 
• Polar amino acids:
  Possess groups which can interact with water to form H-bonds. 
  EG Serine, Threonine, Tyrosine, Histidine, Cysteine
• Amino acids with hydrophobic groups:
  Groups which have to avoid water, tend to be buried in the core of a proteins structure or hidden by other amino acids
  Glycine with a hydrogen is the 20th amino acid. 
  EG Alanine, Valine, Phenylanine, Proline. 

Different amino acids varing in range of pKa number (acid dissociation constant). 
The value of pKA can alter depending on surroundings. Usually given at room temp.  

-Join amino acids together
-Condensation reaction (remove H2O)
-Virtually all peptide bonds occur in TRANS conformation ( a form of steroisomerism describing the relative orientation of functional groups)

The carbonyl oxygen has a partial -ve charge, The amide nitrogen has a partial +ve charge, setting up a small electric dipole. (TRANS CONFORMATION)

• A pure double bond between C and O would permit free notation around the C-N bond
• The other extreme would prohibit C-N bond notation but would place too great a charge on the O and N. 

-Have a constant backbone and functional groups pointing away from the backbone
-Most polypeptide chains which make up a protein vary between 50-2000 amino acids. 

AMINO ACIDS -> PEPTIDES -> POLYPEPTIDES 
Polypeptides: have a direction starting at the amino end and finishing at the carboxyl end.
 
AMINO TERMINAL RESIDUE ------------------------------------------> CARBOXYL TERMINAL RESIDUE
N TERMINUS                                                                                           C TERMINUS
                                Plasma membrane, hydrophobic in the middle 

• Peptide bond remains planar (stays straight to a certain extent) but twisting movements are allowed on the a-carbon with the functional group attached.
• Amount of twisting depends on the 2 functional groups bound together.
• Important in the structure of the protein and how it relates to function 

• Stabalise a protein structure
• Mainly in proteins exported from the cell eg insulin. 
• Formed in secondary and tertiary structure stage
• Bond betwen sulphur atoms
• Link polypeptides
• Formed by an oxidation reaction
• Undone by a reduction reaction

• Phi
  -The angle of rotation about the the N-C bond
   
• Psi
  -The angle of rotation about the C-C bond

• Most commonly seen as a right handed helix (twists clockwise) 
• Most stable because of the particular formation of peptide bonds etc.
• Its content of proteins vary from alot to none. 
• EG - keratin has 2 a-helical coils wound around eachother to form a supercoil 
  This is the most stable way that this protein can exist 

• extended structures which are stabilised by interchain H-bonding (relatively weak bond).
• structure due to peptide bonds
• in this strucuture because this is the most stable for this particular molecule (thermodynamically stable) -> lowest energy state.
• Some amino acids do not fit in B-stand structures e.g larger ones. 
• sequences are still varied in the proteins that do fit. 

ALL DETERMINED BY HYDROPHOBIC COLLAPSE

1) initial folding after ribosome is rapid

2) Folding of B - hairpin takes longer tha  a-helix

3) Formation of the secondary and teritary structure can take 15 secs (alot longer) 

4) Requiring chaperone proteins to help the proteins to achieve its final tertiary structure. 
Chaperone: get proteins to where they should be and usher them into final shapes.

5)Protein disulphide isomerase (PDI) ensures correct alignment of disulpide bonds,

6) Prolylisomerase ensures that proline exists in either the CIS or TRANS form to ensure correct location of B-hairpin turns 

WATER SOLUBLE proteins fold into compact structures with non-polar (hydrophobic) core. 
Plar and nonpolar residues are on the surface. 
Many a-helices and B strands have a polar and non polar face. The non polar face will point towards the core of the protein and the polar face will point towards the water. 

N(+) ---------------------------------------------> C (-)
 Charged functional groups
 

The greater the amount of denaturant the greater the rise in unfolding which may cause it to denature further as it is thermodynamically unstable.