Biochem-L3- Structure and Motifs

what stabilises an alpha helix?

hydrogen bonds between back bone NH and residue C=O

what is a dipole

one side is more positive than the other in a single molecule due to electrons not being shared equally

how are dipoles arranged in an alpha helix?

carbonyl(C=O) point along the helix axis and N-H groups point down.

• N terminus(NH2) is slightly positive and the C terminus(COOH) is slightly negative

what are P loops structured? what is their function?

short, conserved motifs in nucleotide binding proteins like GTPases

have a conserved Glycine XXXX Glycine Lysine

• stabilise nucleotides like GTP and ATP- to release energy

• holds phosphate groups in place for binding- stabilises negative charge by using backbone and positive dipole of the N terminus

what is the arrangement of types of amino acids in a alpha helix? what kind of amino acids?

• hydrophobic interactions are clustered and interacts with hydrophobic surfaces

• polar/positively charged residues cluster on the inner face to interact with DNA/RNA

• polarity of alpha helix sides

what are beta structures? how are they held together?

• extended structures where 2 or more beta strands lie side by side- backbone is almost linear- flat appearance

• held by hydrogen bonds between C=O and N-H from the other strand

types of beta sheets directionality?

• parallel- strands in the same direction

• antiparrelel- strands run in opposite directions

• combination

differences between alpha and beta sheet?

alpha: same polypeptide twists due to psi(40) and phi(60), hydrogen bonding from C=O of residue and NH residue, happens locally. dipole present- P loops for GTPases and DNA binding

beta- linear strands of beta side by side. held together by C=O of one strand to NH of another strand, side chains stick out and in from the sheet, can be local or distance

typical psi and phi angles for beta sheets and alpha sheets?

alpha- phi (60 degrees), psi(40 degrees)

beta- phi(-125 degrees), psi(120 degrees)

what are motifs in proteins

conserved short sequence of SECONDARY structures that have a specific function

types of protein motifs

• helix tur helix

• zinc fingers

• beta-alpha-beta

• EF-hand

what is a super secondary structure? give an example

combination of secondary structures that form a 3D arrangement like EF-hand for calcium binding

• 2 alpha helices connected by a loop

• loop has aspartame to bind calcium ions

• calcium binding stabilises it and helps with muscle contractions

what are alpha and beta sheets- what kind of structure and why?

these are SECONDARY structures

• BACKBONE bending into repeating patterns of psi and phi

• stabilised by hydrogen bonds between backbone C=O and NH groups