Amino Acid Theory

Question 0

What is the primary structure of a protein?

Answer 0

The linear sequence of amino acids in a polypeptide chain joined by peptide bonds.

Question 1

What is a peptide bond?

Answer 1

Peptide bonds line amino acids and are formed by condensation of the α-carboxyl group of Anne amino acid with the α-amino group of another amino acid

Question 2

Define the term torsion angle.

Answer 2

• sometimes called dihedral angles

- a measure of rotation about a bond typically taken to lie between -180 and +180 degrees

Question 3

What is the phi φ angle?

Answer 3

The angle of rotation about the bond between the nitrogen and the α-carbon atom.

Question 4

What is the psi (ψ) angle?

Answer 4

The angle of rotation about the bond between the α-carbon and the carbonyl carbon atoms.

Question 5

What is the meaning of the φ and ψ angles?

Answer 5

They determine the path of the polypeptide chain.

Question 6

What does the Ramachandran plot show?

Answer 6

The 2-D plot shows the allowed combinations of φ and ψ angles when steric clashes between the atoms are absent or minimised.

Question 7

What is the secondary structure of a protein?

Answer 7

Regions of regularly repeating conformations of the peptide chains I.e. α-helices and β-sheets.

Question 8

What is the screw sense?

Answer 8

The direction in which a helical structure rotates with respect to its axis.

• if viewed down the axis of a helix, the chain turns in a clockwise direction - right handed screw sense
• if the turning is anticlockwise the screw sense is left-handed

Question 9

What is the secondary structure of a protein?

Answer 9

The regular folding of regions of the polypeptide

• formed by a regular pattern of hydrogen bonds between the peptide N-H and C=O groups of amino acids near one another in a linear sequence
• common types are: α-helix, β-pleated sheets, turns and loops

Question 10

Describe the α-helix.

Answer 10

• rod-like coiled structure stabilised by interchain hydrogen bonds
• a tightly coiled backbone forms inner rod.
• R groups extend outward, helically
• each of the residues are related by a translation of 1.5 Å - this results in 3.6 amino acids per turn

Question 11

How is the α-helix schematically represented?

Answer 11

As twisted ribbons or rods.

Question 12

Which amino acid residues are unlikely to be utilised in α-helix and why?

Answer 12

• valine, threonine, isoleucine- destabilise α-helices because of steric clashes
• serine, aspartate, asparagine- tend to disrupt α-helices because their R groups contain H-bond donors or acceptors in close proximity
• proline- α-helix breaker because it lacks NH group and because it’s ring structure prevents it from assuming the φ value that fits the helix

Question 13

Describe the β-sheets.

Answer 13

• stabilised by hydrogen bonding between polypeptide strands
• β-pleated sheet consists of two or more polypeptide chains-β-strands
• the distance between adjacent aas along a β-strand is 3.5 Å
• chains can run parallel or antiparallel
• the R groups project alternately above and below the plane of the strands

Question 14

What are β-strands?

Answer 14

Polypeptide chains that are almost fully extended.

Question 15

What are β-sheets?

Answer 15

Multiple β strands arranged side-by-side.

Question 16

How are β strands stabilised?

Answer 16

By hydrogen bonds between C=O and -NH on adjacent strands.

Question 17

What are parallel β sheets?

Answer 17

Strands that run in the same N- to C- terminal direction.

Question 18

Describe the antiparallel β sheet?

Answer 18

• strands run in opposite N- to C- terminal directions
• the H-bonds are nearly perpendicular to the chains
• they are more stable than parallel chains with distorted H-bonds

Question 19

What roles do loops and turns play in protein structure?

Answer 19

They connect α-helices and β-strands and allow a peptide chain to fold back on itself to make a compact structure.

Question 20

What are loops?

Answer 20

Containing hydrophilic residues I.e. Methionine

-found on the protein surfaces.

Question 21

What are turns?

Answer 21

These are loops containing 5 residues or less

-often containing Gly

Question 22

How are β-strands schematically represented?

Answer 22

-broad arrows pointing in the direction of the carbonyl-terminal end to indicate the type of β-sheet formed- i.e. Parallel or antiparallel

Question 23

What is a motif?

Answer 23

Recurring protein structure that crop up in different proteins

Question 24

What are some of the Supersecondary structure motifs?

Answer 24

• helix-loop-helix: two helices connected by a turn
• Coiled-coil: two amphipatic α-helices that interact parallely via their hydrophobic edges
• βαβ unit: two parallel β strands connected to an intervening α-helix by two loops

Question 25

What is a hairpin motif?

Answer 25

Two adjacent antiparallel β strands connected by a β turn

Question 26

What is a β meander?

Answer 26

An antiparallel composed of sequential β strands connected by loops or turns

Question 27

What is a Greek key motif?

Answer 27

4 antiparallel strands -strands 1,2 in the middle, 3 and 4 on the outer edges

Question 28

What is a β sandwich motif?

Answer 28

Stacked β strands or sheets

Question 29

What is the tertiary structure of proteins?

Answer 29

Results from the folding of a polypeptide chain into a closely packed 3 dimensional structure.
-i.e. Myoglobin

Question 30

Describe globular proteins?

Answer 30

• usually water soluble, compact, roughly spherical
• hydrophobic interior, hydrophilic surface
• they include enzymes, carrier and regulatory protein

Question 31

What are the three molecular representations of Ribonuclease A?

Answer 31

• space-filling model- bound substrate analog black
• cartoon ribbon model- shows secondary structure
• substrate binding site view

Question 32

Describe fibrous proteins.

Answer 32

• proteins that provide structural support for cells and tissues
  i. e. α-keratin and collagen

Question 33

Describe α-keratin.

Answer 33

• primary competent of wool, hair, nails,
• forms coiled coils
• consists of two right-handed α helices intertwined
• the two helices are cross-linked by weak interactions i.e. van der Waals forces and ionic interactions

Question 34

Describe Collagen.

Answer 34

• major component of skin, bones, tendon, cartilage and teeth
• an extracellular protein, rod-shaped molecule
• contains 3 helical polypeptide chains each nearly 1000 residues
• glycine appears at every third residue in the amino acid sequence

Question 35

What is a fold?

Answer 35

• a combination of secondary structures that form the core of a domain
• simple domains have simple folds, others have more complex folds
• domains can be classified by characteristic folds

Question 36

What are domains?

Answer 36

• independently folded, compact units in proteins
• domain size: ~25 to ~300 amino acid residues
• domains are connected to other domains by loops
• they illustrate the evolutionary conversation of protein structure