Amino acids and Protein structure Flashcards
Why is the primary structure of the a protein important ?
It defines the structure of a protein which is influential in determining the function of the protein- ie. globular protein or fibrous protein
Name 11 functions of proteins.
Structural, Movement, Enzymes & Catalysts , Transport, Membrane Transport, Hormones, Receptors, Defence, Gene Regulation, Chromosome Sorting
Comment on direction of polypeptide sequence .
1st aa - NH3 +
last aa - COO- group
There is alternation of R groups up and down the plane with each residue in the polypeptide chain
What is meant by a peptide bond?
The C — N bonds between the carboxyl group of one amino acid and amino group of another amino acid.
It is shorter than expected:
Rigid
No rotation
Nearly always has trans arrangements of groups
Name other covenant linkages between polypeptides
Disulfide Bridges
Glycosylation
Phosphorylation
Methylation
Describe what is meant by Disulifide bridges
Covelant bonds derived by two thiol groups ( in Cys subunits)
Can be intramolecular and intermolecular
Describe what is meant by Glycosylation
Adding a sugar element to a protein- can either be O linked ( OH of thr and ser) OR N linked ( NH2 of asn)
Describe what is meant by Methylation?
Adding on of a methyl group via the NH2 group of lys or arg eg. histones affecting gene expression
Explain what is meant by primary structure?
The specific sequence of amino acid in a polypeptide chain
Explain what is meant by secondary structure?
The folding of polypeptide chain- eg. alpha helix and beta pleated sheet
Explain what is meant by tertiary structure?
Relating to the 3D structure of the protein
How the whole polypeptide folds upon itself
Explain what is meant by quaternary structure?
How the folded polypeptides chains interact and join together- hoe the whole functional protein is formed in 3D
Describe the structure alpha helix
Formed due to H bonds forming between the peptide bond carbonyl O and the H of the N - H of every 4th peptide bond- INTRAMOLECULAR
Said to be the max stabilisation energy due to 3-6 turns
Has rigid cylindrical shape- is said to act as a support for the protein.
R groups are on the outside and Right handed helix
Describe the structure of beta pleated sheet
H bonds hold strands together in a Beta sheet
R groups can be up/down the plane
Proteins with high % of beta sheet are fibrillar proteins
and high tensile strength.
What are the two types of beta pleated sheet?
antiparalel or paralel
Describe the collagen triple structure
Ideal for structural proteins-
three chains- with hydrogen bonds every 3 residues which form intermolecularly between the chains-
optimal state- Gly - X - Y - Gly - X - Y
X= proline mainly
Y=mainly hydroxyproline
What is a super-secondary structure?
when alpha helix and beta pleated sheets form common domains found in domains.
e.g. Beta barrel
Beta sandwich
Rossman fold
What is meant by phosphorylation?
The adding of phosphate ( big negative group) to a molecule. The structure of the molecule changes which means that the function changes.
e.g cell signal transduction- phosphorylation of Tyr in insulin receptor
changes activity of enzyme - phosphorylation of GP in response to glucagon- activating the enzyme- increasing production of glucose. - glycogenolysis
What are the forces that stabilise protein structure?
Covalent (DBS) and Non covalent ( H bonds, electrostatic interactions, VdW forces and hydrophobic interactions)
Explain what is meant by Hydrogen Bonding?
2 d- atoms compete for the same H atom- A hydrogen bond is a partially electrostatic attraction between a hydrogen (H) which is bound to a more electronegative atom such as nitrogen (N), oxygen (O), or fluorine (F), and another adjacent atom bearing a lone pair of electrons.
H-Bond Donators:
O eg O-H
N eg N-H
H-Bond Acceptor”
O eg carbonyl c=O
Explain what is meant by Electrostatic interactions
The interactions present between charged side chains
eg. physiological pH
Asp, Glu COOH —> COO- (ionised)
Lys, Arg NH2 —> NH3+ (ionised)
Explain what is meant by VdW forces?
The sum of attractive forces between molecules
This is due to the fact there is dipole effect from the momentary unequal distribution of electrons
Explain what is meant by Hydrophobic effect
when proteins are in aqueous environment- hydrophobic regions of the protein fold in such a way that they minimise contact with aqueous environment- these regions do not form H bonds
What conditions are proteins sensitive to?
pH- due to fact that electrostatic and H bonding is affected- changing the structure.
Temperature- breaks the non-covenant bonds which changes the structure
Ionic strength
