[FMS] CBS - protein structure + function

Question 1

At physiological pH what is ionised?

Answer 1

• Asp and Glu carboxyl groups are ionised – COO-
• Lys and Arg amino groups are ionised – NH3+

Question 2

5 features of a peptide bond

Answer 2

Question 3

What are 2 clinical conditions that are a result of defects in metabolism?

Answer 3

Phenylketonuria (PKU), defective
phenylalanine hydroxylase (phe→tyr) resulting in reduced tyr production and hormones that are
derived from it

Albinism (many forms) one form due to defective tyrosinase
(tyr →melanin)

Question 4

what molecule does the first amino acid have and which end is it found?

Answer 4

First aa has NH3⁺ group
N-terminal end

NH3+ = N terminus
COO- = C terminus

Question 5

what molecule does the last amino acid have and which end is it found?

Answer 5

Last aa has COO⁻ group
C-terminal end

Question 6

what are the 2 Post translational covalent modifications?

Answer 6

1. Disulphide (S-S) bridges between two cys
   Joining subunits together e.g. insulin
2. Glycosylation
   O-linked -OH of thr and ser
   N-linked -NH2 of asn

^ remember:
diSulphide= S-S

glycosylatiON =O/N linked

O=OH
N= AsparagiNe

Question 7

what are the 4 levels of 3D structure

Answer 7

Primary – sequence of aa in peptide chain
Secondary – folding/coiling of peptide chain (usually into a α-helix or β-pleated sheet)
Tertiary – peptide chain folds upon itself
Quaternary – folded peptide chains join together

Question 8

what bonds is the alpha helix formed by in the same polypeptide chain?

Answer 8

formed by H-bonds in same polypeptide chain (backbone not side chains)

Question 9

where do the h-bonds in alpha helixes form?

Answer 9

H-bonds formed between the amino and carbonyl groups of every fourth peptide bond.

Question 10

is the alpha helix regular or irregular, and is it right or left-handed?

Answer 10

regular, right-handed helix

remember alpha helix is RR = regular righthanded

Question 11

whats the residue number for an alpha helix and how are the turns stabilised?

Answer 11

3.6 residues/turn stabilised by H-bonds

Question 12

are the r groups on the inside or outside of an alpha helix?

Answer 12

R groups on the outside

Question 13

what kind of shape does an alpha helix have and why?

Answer 13

rigid cylinder shape, acts as ‘architectural’ support for protein

Question 14

what kind of peptide chains are b-pleated sheets made from?

Answer 14

Linear peptide chains

Question 15

what kind of bonds hold the sheets together in b-pleated sheets?

Answer 15

H-bonding between peptide chains holds strands together in a β-sheet

Question 16

where do the side chains lie in a b-pleated sheet?

Answer 16

Side chains in each strand alternately lie above and below the plane of the sheet

Question 17

what 2 forces stabilise protein structure?

Answer 17

covalent
non covalent

Question 18

give an example of a specific covalent force that stabilizes protein structure?

Answer 18

Covalent:
Disulphide bridges (not all proteins have them)

Question 19

give examples of 4 specific non-covalent forces that stabilizes protein structure?

Answer 19

Non–covalent:
Hydrophobic effect
Hydrogen bonds
Electrostatic interactions
Van der Waals forces

REMEMBER: HHEV

Question 20

what are the 2 types of b-sheet structures?

Answer 20

Question 21

how many chains is a collagen helix made up of?

Answer 21

3

Question 22

what kind of bonds are between collagen triple helix

Answer 22

h bonds

Question 23

how many residues are there in collagen triple helix

Answer 23

3

Question 24

is a collagen triple helix right or left handed?

Answer 24

left handed helix

Question 25

which protein has a high % of b sheets

Answer 25

Fibrillar proteins silk fibres (fibroin) properties of high tensile strength, but no elasticity

Question 26

why are there hydrophobic regions in a protein?

Answer 26

Hydrophobic regions of a protein fold in such a way to minimise the contact with aqueous environment. Hydrophobic regions are unable to form hydrogen bonds

Question 27

what 3 things can proteins be denatured by?

Answer 27

heat, detergents, pH

Question 28

what disease arises from the mutation of a protein?

Answer 28

mutation = misfolding e.g SICKLE CELL DISEASE GLUTAMIC ACID to VALINE at position 6 on globin surface. Glu is hydrophilic and negatively charged, Val is hydrophobic. Stabilises polymerization of HbS.

Question 29

what 2 diseases arise from stable aggregation of proteins

Answer 29

Amyloid proteins forming plaques in **Alzheimer’s Disease** (aggregation of misfiled proteins) Prion protein polymerisation in **Creuzfeldt-Jakob Disease** REMEMBER: Amyloid = Alzheimers Prion = CJD

Question 30

whats the disease called when theres defects in metabolism that result in reduced tyrosine production and hormones derived from it?

Answer 30

**Phenylketonuria (PKU)**, defective phenylalanine hydroxylase (phe→tyr) resulting in reduced tyr production and hormones that are derived from it

Question 31

whats the disease called when theres defects in metabolism that result in defective tyrosinase

Answer 31

**Albinism (many forms)** form due to defective tyrosinase (tyr →melanin)

Question 32

what are the 4 structural features of lysozymes

Answer 32

Question 33

What is X and Y in this sequence: - Gly - X - Y - Gly - X - Y - ?

Answer 33

X = mainly proline Y = mainly hydroxy-proline

Question 34

Where are electrostatic interactions found?

Answer 34

Between **charged side chains**

Question 35

what is the structure of a protein determined by?

Answer 35

**sum of multiple low energy bonds** - The amount of **stablization energy** in a protein is quite **small**

Question 36

What do amino acids encode in addition to the final protein structure

Answer 36

Amino acid sequence encodes the final structure but also the **pathway that leads to that structure**