Biochem week 2

physiological pH

7.4

when pH>pka is the proton on/off?

off

when pH<pka is the proton on/off?

on

where are peptide bonds formed?

between the carboxyl and amino group

why can’t rotation occur at the peptide bond?

because of its double bond character

why is protein structure important?

structure determines function

is trans or cis orientation more preferred?

trans because with cis orientations, clashes can occur

primary structure

sequence of a chain of amino acids

secondary structure

shows arrangement of the backbone

tertiary structure

3D structure of a protein due to side chain interactions

quaternary structure

protein consisting of more than one amino acid chain

what are the different types of the secondary structure?

• α-helix

• β-sheets

• turn

• random coil

is antiparallel or parallel bonding between chains more stable?

antiparallel because they are more aligned and the distances are shorter

what disrupts 2° structure?

urea breaks H-bonds

what are the main functions of proteins?

• structural support

• transport

• signaling/binding

why is side chain ionization important?

• for 3° and 4° structure: making salt bridges

• can act as proton donor or acceptor

how are bonds in proteins broken?

• heat

• acid/base can disrupt ionic bonds

• urea

• detergent can disrupt hydrophobic interactions