7 - PROTEIN STRUCTURE & FUNCTION I

Question 1

Primary Structure

Answer 1

the sequence of amino acids, N-terminal to C-terminal

Question 2

Secondary Structure

Answer 2

the folding of parts of the primary sequence into particular structures
• There are two important types of secondary structure – the α helix and the β sheet

Question 3

PROTEIN FOLDING

Answer 3

The main driving force in protein folding is to attain an energetically stable structure.
For water soluble proteins it is essential to pack hydrophobic side chains into the interior of the protein to ‘hide’ them from the surrounding water molecules.
This forms a hydrophobic core (oil droplets effect).

Question 4

The α helix I

Answer 4

α helices are usually formed from stretches of 5-40 amino acids
The main chain N-H and C=O groups are hydrogen bonded to one another along the axis of the helix
The a helix is very stable

Question 5

The α helix II

Answer 5

There are 3.6 amino acids per turn.
Each amino acid turns the helix through 100°
The vertical distance from 1 amino acid to the next is 0.15nm so the pitch of the helix (turn length) is 0.54nm
The C=O group of amino acid n is hydrogen bonded to the N-H group of amino acid n+4

Question 6

The α helix III

Answer 6

The amino acid side chains project out from the edge of the helix
The sequence of amino acids in an a helix can be plotted on a helical wheel diagram.
Each residue is plotted 100° around a circle or spiral

Question 7

The β sheet

Answer 7

β sheets are formed from non-continuous regions of the polypeptide chain = β strands
The β strands line up and form hydrogen bonds between the C=O groups of one strand and the N-H groups of another

Question 8

The parallel β sheet

Answer 8

H bonds are evenly space within the sheet
The β strands are in an almost fully extended conformation
The β strands all run in the same direction (N => C)

Question 9

The anti-parallel β sheet

Answer 9

narrowly spaced H bond pairs separated by a larger gap.
The β strands are in an almost fully extended conformation.
The β strands run in opposite directions

Question 10

Pleated structure of the β sheet

Answer 10

Cα carbons lie successively above and below the plane of the sheet

Question 11

Loop regions

Answer 11

Secondary structures (a helices, b sheets) are linked by loop regions
Loops vary in length. 
Long loops are called random coils and are highly flexible parts of proteins. 
Short loop regions which connect anti-parallel b strands are called hairpin loops or b turns

Question 12

PROLINE

Answer 12

often found in loop regions because its locked ring structure introduces a ‘kink’ into the polypeptide chain.

Question 13

GLYCINE

Answer 13

often found in loops because its small side chain enables it to form turns when other amino acids could not.

Question 14

β-α-β motif

Answer 14

Although anti-parallel b strands are usually connected by hairpin loops, parallel b strands are usually connected by an a helix
The helix crosses the b sheet from one edge to another
This is called a b-a-b motif

Question 15

Post-translational modifications

Answer 15

• Alterations to some produce the “rare” amino acids – hydroxyproline, hydroxylysine
• Sugars/carbohydrates/glycans can be added to some amino acids (asparagine, threonine, serine) this is called glycosylation – glycoproteins (N-linked, O-linked)
• Lipids can also be added – lipoproteins
• These various post-translational modifications can contribute to secondary structure

Question 16

Tertiary structure

Answer 16

For most proteins, the final three-dimensional structure of a protein is produced by the association of the secondary structures into compact domains