Biochem-L2- Secondary Structure/structure and Folds

what are the single bonds that rotate on the backbone? what does this determine?

• phi N- C alpha bond

• psi Ca-C’ carbonyl carbon bond

determines the SHAPE of the protein

what are chi angles?

these describe the side chains of a protein that have rotatable single bonds

why cant the peptide bone rotate? what characteristics are made due to this?

• due to the partial double bond- the omega angle

• carbonyl carbon-N

• due to the strong electronegtaivitity of the oxygen- causes the C’(carbonyl carbon) to the Nitrogen to act as double bonds

• planar- TRANS

name the dihedral angles in proteins

phi- N- alpha carbon

psi- alpha carbon and carbonyl carbon

chi - rotations in the side chains

primary vs secondary structure

• primary: linear sequence of amino acids linked by peptide bonds

• secondary- local folding of the backbone defined by the repeating psi and phi angles, repeating psi and phi

explain the alpha helix angles

phi- -60 degrees

psi- -40 degree

configuration vs conformation in proteins- differences

• configuration- fixed positions of atoms around the non rotatable bonds- around the omega

• conformation- shape of the polypeptide due to the totable single bonds- ie dihedral angles- psi, phi and chi 

how is protein folding done? and what does folding avoid?

• proteins fold to reach the most stable, energetically stable structure

• bulky atoms that are too close repel each and determines folding

how do steric effects influence the secondary structure?

bulky side chains like valine, isoleucine can clash with the backbone and destabilise the helices- NOT GOOD FOR ALPHA HELICES!

non covalent interactions that stabilise proteins

• hydrogen bonds

• salt bridges/ionic

• hydrophobic interactions

• van der Waals

explain hydrogen bonds- what can form them

• non covalent

• backbone NH and C=O can form hydrogen bonds

• H bonds are weak alone but stronger in huge numbers and stabilise the proteins

explain salt bridges and ionic interactions

• done between oppositely charged side chains like positive lysine and negative aspartate

• strength depends on the distance and environment

explain hydrophobic interactions

non polar side chains cluster together and exclude water which drives compact folding SUCH AS 2 LEUCINES

explain van Der Waals forces

weak interactions between uncharged atoms in large numbers stabilise proteins

describe the covalent interactions in a protein

• disulphide bonds made by Cysteine-cysteine interactions and stabilise the tertiary structure

hoe do proteins fold in general?

side chains project outwards and the backbone hydrogen bonds form internally

what is the tertiary structure of a protein?

the 3D shape of the protein- done by interactions in the SIDE chains- hydrophobic interactions, H bonds, ionic bonds and van der Waals forces along with disulphide bridges