1. Intro to protein structure

Question 1

How many amino acids are there?

Answer 1

20

Question 2

Name 2 Hydrophobic amino acids

Answer 2

Glycine

Proline

Question 3

Name 5 Hydrophilic amino acids

Answer 3

Asparagine
Cysteine
Serine
Threonine
Tyrosine

Question 4

Amino acids with charged side chains
Always protonated- basic
2 examples:

Answer 4

Arginine

Lysine

Question 5

Amino acids with charged side chains
Always negatively charged due to proton donation
2 examples:

Answer 5

Glutamate

Aspartate

Question 6

Why can’t AAs tolerate wide changes in pH?

Answer 6

Ionisation state provides vital biological properties

Question 7

What gives AAs buffering capacity to resist changes in pH?

Answer 7

Ability to take up/ release protons

Question 8

Electrophoresis separates proteins on the basis of their charge

Answer 8

Use to distinguish between normal/ mutant forms of proteins which have gained/ lost charge

Question 9

Chirality of AAs

Answer 9

Alpha Carbon = Chiral centre
Optical isomers
All AAs in proteins are of the L-form

Question 10

Which is the only non-chiral AA?

Answer 10

Glycine

Question 11

How is a peptide bond formed?

Answer 11

Condensation reaction

Releases 1 molecule water

Question 12

Functionality of a protein requires

Answer 12

Definite 3D structure to make them specific

Question 13

Characteristics of the peptide bond

Answer 13

No free rotation around bond
C=O and N-H are in the same plane
Other 2 bonds in backbone can rotate
Only conformation in which side chains don’t clash with main chain are allowed (Steric Hindrance)

Question 14

Covalent bonds in a protein

Answer 14

STRONGEST bond
In Primary structure
Can exist as disulphide bridges (Cysteine)

Question 15

Hydrogen bonds in a protein

Answer 15

When 2 atoms bearing a delta- share a delta+ Hydrogen

Can occur between water molecules or different atoms on different side chains and backbone

Question 16

Ionic interactions in a protein

Answer 16

Arise from electrostatic attraction between charged side chains
Relatively strong bonds
Majority of charged groups at surface of folded protein

Question 17

Van der Waals Forces in a protein

Answer 17

Transient, weak electrostatic attractions between 2 atoms due to fluctuating electron cloud
If atoms are close, transient dipole can induce a dipole
Sheer No. means they are influential in overall conformation

Question 18

Hydrophobic interactions in a protein

Answer 18

Hydrophobic side chains are packed into interior of protein

Hydrophobic core and Hydrophilic surface

Question 19

Hydrogen bonds between C=O and N-H stabilise…

Answer 19

Helices

Beta pleated sheets

Question 20

Proline is a KINKY AA

Answer 20

When joined to a peptide chain, NH group is lost

• Prevents side chain from H bonding with C=O from another residue
• Distorts helical conformation

Question 21

Parallel B pleated sheets

Answer 21

Alternate B strands run in same direction

Question 22

Antiparallel B pleated sheets

Answer 22

Alternate B strands run in opposite direction

Question 23

Folding of proteins

Answer 23

Fold into single conformation of lowest energy

Chaperones may be involved to ensure folding occurs in most energetically favourable way

Question 24

By breaking bonds that hold the protein together, we can denature the proteins into their original flexible polypeptide. Common denaturants:

Answer 24

Urea (breaks H-bonds)

2- Mercaptoethanol (breaks disulphide bonds)

Question 25

Primary structure of a protein

Answer 25

Linear sequence of AAs that make up protein

Write sequence from Amino terminus to Carboxyl terminus

Question 26

Secondary structure of a protein

Answer 26

Alpha helices and Beta pleated sheets

Existence dictated by sequence of AAs in primary structure

Question 27

Tertiary structure of a protein

Answer 27

Arrangement of secondary structure motifs into compact globular structures (Domains)

Question 28

Quaternary structure of a protein

Answer 28

3D structure of a multimeric protein composed of several subunits
e.g. Oxyhaemoglobin

Question 29

Post translational modification of proteins

Answer 29

Starting set of 20 AAs can be modified to create novel AAs

Enhances capabilities of protein

Question 30

Post translational modifications of proteins

Mutation…

Answer 30

Can be identified by electrophoresis as a reduction in molecular weight