2 Protein Structure

_____ bonds between AAs are formed by a ____________ reaction.

Amide bonds between AAs are formed by a condensation reaction.

why is the central C-N bond very strong?

• due to resonance

• the C-N bond has partial double bond character, so only broken by very harsh chemical conditions or enzymes

outline the conformation of AAs.

• Cis (Z) conformation - both substituents on the same side of the C-N bond.

• trans (E) conformation - substituents on opposite sides of the C-N bond.

why are cis conformations rarer than trans conformation?

trans conformation is more stable as there is less steric chain.

describe how bonds in peptides can rotate.

• peptide bonds are rigid & planar, so form a flat, straight line as shown in the diagram

• bonds on either side of the C-N & C-C bonds can rotate, the R groups are alternating away from the polypeptide backbone.

define the primary structure.

the sequence of amino acids

what is the N-terminus & C-terminus?

• N-terminus - the free amino group on the end of the polypeptide.

• C-terminus - the free carboxylic acid at the other end of the polypeptide

in what direction are AAs numbered?

from the N-terminus to the C-terminus (N —> C)

define secondary structure.

Local 3D structure formed by hydrogen bonding between backbone atoms

how are H bonds able to form?

due to partial ionisation of the C=O and N-H bonds.

what is meant by local in the deifnition of secondary structure?

not all the AAs are involved in the secondary structure.

define α helices.

• a single helix in which all C=O & N-H bonds of the peptide backbone are involed in H bonding

• R groups point outside of the helix

define β sheets.

• a secondary structure in which 2 or more peptide strand H bond to each other to form a sheet-liek sructure

• unlike in α helices not every C=O & N-H bond is involved in H bonding

what the diff between parallel & antiparallel sheets?

• parallel - peptide chains which are H bonding to each other run in same direction

• antiparallel - peptde chain run in opposite direction, often linked by a turn (loop of AAs)

define tertiary structure.

• Global 3D structure of a whole polypeptide chain

• formed by non-covalent & covalent interactions

outline the non-covalent & covalent interactions.

non-covalent:

• Ionic bonds

• Hydrogen bonds

• Hydrophobic bonds

• Van der Waal’s forces

covalent:

• Disulfide bonds

how do these covalent and noncovalent interactions result in proteins with diff functions?

• tertary structure can produce pockets to allow entry & bonding of a protein’s substrate. e.g. in enzymes, the active site, in receptors the binding site.

• globular proteins fold so hydrophilic residues are on the outside & hydrophobic residues are on the inside.

define disulfide bond.

how many disulfides are there in human insulin?

there are 3

• the separate polypeptides chains (A & B) are joined by 2 intermolecular disulfides

• the A chain has 1 intramolecular disulfide

define quaternary structure

• 2 or more polypeptides assciated via non-covalent interactions

• each polypeptide is called a subunit

  • together the protein is referred to as oligomeric

do all proteins have quarternary structure?

No