Protein structure and function Flashcards
What are the 2 ends of a polypeptide?
-First amino acid has NH3+ group (N terminal end)
-Last amino acid has COO- group (C terminal end)
Definition of amino acid
-Amino acid has a carboxylic group and amino group attached to the same carbon (alpha carbon)
-When these combine a peptide bond is formed
2 examples of post translational covalent modifications
-Disulphide (S-S) bridges between 2 cysteines
=>join subunits together (e.g. insulin)
-Glycosylation (addition of sugars)
=> O linked -OH of threonine and serine
=> N linked -NH2 of asparagine
Primary structure of proteins
-sequence of amino acids in peptide chain
Secondary structure of proteins
-folding/coiling of peptide chain (alpha helix or beta pleated sheet)
Tertiary structure of proteins
-peptide chain folds upon itself
-how the whole polypeptide subunit is folded in 3D
Quaternary structure of proteins
-folded peptide chains join together
-how the whole functional protein is formed in 3D
Alpha helix features
-Stabilised by hydrogen bonds within the same polypeptide chain (backbone not sidechains)
-H bonds formed between peptide bond carbonyl-O and H of N-H every 4th peptide
-Regular right handed helix
-3.6 residues/turn stabilised by H bonds
-R groups on the outside
-Rigid cylinder shape, acts as ‘architectural’ support for protein
Beta pleated sheets features
-Stabilised by hydrogen bonds between peptide strands
-Linear peptide strands
2 types of beta sheet structures
A) -Antiparallel beta sheet
-Beta hairpin bend
B) -Parallel beta sheet
-(arrow points to C terminus)
What is collagen triple helix?
-3 chains
-Found in collagen
-Hydrogen bonds between chains
-3 residues/turn
-Left handed helix
Proteins with high % of alpha helix and beta pleated sheet
-Hb is made up of 60% alpha helix
-Fibrillar proteins (e.g. silk fibres - fibroin) have high % beta pleated sheet
=> Gives them high tensile strength, but no elasticity
What forces stabilise protein structure?
Covalent
-Disulphide bridges
Non-covalent bonds
-Hydrogen bonds
-Electrostatic interactions
-Van der Waals forces
-Hydrophobic effects
What is a hydrogen bond?
-2 electro negative atoms compete for the same hydrogen atom
H bond donors:
-O e.g. O-H
-N e.g. N-H
H bond acceptors:
-O e.g. C–O
What are electrostatic interactions?
-Exist between charged side chains
At physiological pH:
-Aspartate and Glutamate carboxyl groups (COO-) are ionised
-Lysine and Arginine amino groups (NH3+) are ionised
What are Van der Waals forces?
-The sum of the attractive or repulsive forces between molecules
=>Excluding those due to covalent, hydrogen, electrostatic
-Dependent on dipole effect caused by unequal distribution of electrons
=>Partial negative and partial positive charge across a covalent bond
What are hydrophobic effects?
-Hydrophobic regions of a protein fold in such a way to minimise the contact with aqueous environment
-Hydrophilic outside, hydrophobic inside
-Hydrophobic regions are unable to form hydrogen bonds
Why are proteins sensitive to denaturation?
-Amount of stabilisation energy in a protein is quite small
-Proteins have thousands of possible structures only one of which is functional
-Amino acid sequence encodes the final structure but also the pathway that leads to that structure
What factors can denature protein?
-Temperature
-pH
-Ionic strength
How many amino acids make up the proteins in humans?
20
-Each AA has a different R group attached to the alpha carbon
-R group defines properties and function
What are essential amino acids?
9 of the 20 amino acids cannot be synthesised in the body
-They are supplemented through diet
3 amino acids that are not universally encoded in DNA
Hydroxyproline (hydroxylation of proline) - component of collagen that forms triple helix structure
Selenocysteine -encoded by STOP codons and has reduced pKa
Homocysteine - contains extra methyl group needed to synthesis cysteine
Features of peptide bond
-Forms between alpha amino and alpha carboxylic groups of adjacent AAs.
-Very strong bond which is short, has no rotation, with R groups in the trans configuration
-Partial negative charge on oxygen atom and partial positive charge on nitrogen atom help form H bonds
Defects in AA metabolism leading to disease
-One form of albinism due to defective tyrosinase (tyrosine -> melanin)
-Phenylketonuria (PKU)
-Defective phenylalanine hydroxylase (phenylalanine->tyrosine)
-Causes reduced tyrosine production and hormones which are derived from it (dopamine and melanin)
Recognise structures of 20 amino acids
