protein structure

structure of an amino acid

carboxylic group

amino group

r group

how do two aa’s form a dipeptide ?

they condense tg

two aa ‘s line up losing a water molecule to form a peptide bond (first aa loses OH from COOH grp while second loses H frm NH2 grp )

polypeptide

single molecule, made up of a long chain of aas covalently linked by peptide bonds

each pp is encoded for by a single gene

protein

fully folded functional molecule

contains all subunits, prosthetic groups, cofactors/coenzymes

e.g. haemoglobin protein contains 2 α and 2 β subunits each with a haem prosthetic group

how many haemoglobin genes must there be ?

2 
haemoglobin A codes for alpha polypeptide while B codes for beta polypeptide 

what makes amino acids soluble 

many OH or NH groups in their R groups as they can form H bonds or r groups that can be ionised 

primary structure

order of aa’s in a polypeptide chain

secondary structure

folding of pp chain due to formation of h bonds into two specific 3D shapes:

alpha helix- each aa forms h bonds w/ the aa 4 units along 

beta pleated sheet - 2 parts of the pp chain lay side by side and h bonds form between them 

polypeptide bond

covalent bond linking two aas

what 4 bonds form between aas in the tertiary structure 

h bonds
ionic 
disulphide bridge 
hydrophobic interactions
as these form the pp chain folds into a complex 3d shape 

ionic bonds 

can form between ionised amino and carboxylic grps 

disulfide bridges

covalent bonds that form between the sulfur atoms of 2 cysteines

hydrophobic interactions

form between non polar R grps

Quaternary structure 

final, 3D shape of the proteins formed from more than one polypeptide chain

conjugated protein

contain non protein prosthetic grps 

prosthetic grp 

molecule/ ion that is tightly bound to proteins and required for biological function can be organic or inorganic but never another aa 

haemoglobin

globular protein so it folds into a spherical shape
soluble
haem prosthetic grp which O2 binds to also has iron 
4 pps ( 1 haem for each )
2 alpha 2 beta subunits 

quaternary 

haemoglobin function

transport 02 +CO2 in blood

globular proteins

spherical proteins

soluble bcs hydrophilic R groups found on outside of protein/ hydrophobic R groups cluster in the centre

denature easily/sensitive to temperature/ pH because shape is critical to function

may be conjugated or require cofactor/ coenzymes

fibrous proteins

INSULIN

hormone (peptide)

synthesised by b-cells of pancreas

reduces blood glucose - stimulates uptake of glucose & conversion into glycogen

globular protein

carbonic anhydrase

enzyme

CO2 transport

reacts CO2 + H2O to form carbonic acid (CO2 transported as hydrogencarbonate ions in plasma )

globular protein 

(salivary a) amylase

enzyme
hydrolyses starch into maltose/ dextrins
globular protein

insulin structure

synthesised as single polypeptide from one gene (Tertiary structure)

contains 3 disulphide bonds

post-translation modification

- hydrolysed into 2 chains by peptidases & stored in secretory vesicles

carbonic anhydrase structure

Zn2+ ion = prosthetic group

forms part of active site – takes part in reaction

held in position by 3 histidines

synthesised as single polypeptide from one gene (Tertiary structure)

salivary amylase structure 

synthesised as single polypeptide from one gene (Tertiary structure)

metalloenzyme – requires 2 ions:

Cl- needed as cofactor to help starch bind to active site

Ca2+ stabilises enzyme

Fibrous proteins

form structures, e.g. connective tissues: bone, cartilage….

fibrous proteins properties

linear unbranched and insoluble - primary structure contains repeated sequence of hydrophobic amino acids

so insufficient OH groups to form intramolecular H bonds, so do not coil into helix

high tensile strength - extensive cross-links (between pps)

collagen – structure:

3 collagen polypeptides form intermolecular H bonds causing them to form a rope-like triple helix

covalent bonds form between triple helices to form microfibrils

Extracellular matrix (ECM) proteins

form a complex scaffold around cells, providing structural support – they include collagen (for tensile strength), elastin (for elasticity)

tendons

transmit pulling force of muscle to bone

they require high tensile strength

consist mainly of collagen

ligaments 

connect bones/ stabilise joints

they require tensile strength and some elasticity

consist of collagen and elastin

denaturation

process of disrupting protein structure by breaking bonds

always causes loss of function and is irreversible