Amino acids, peptides and proteins

Question 1

Amino acid

Answer 1

A class of organic compound with at least one amino group and one carboxyl group

Question 2

Peptide

Answer 2

An organic compound formed from the linking of <= 50 amino acids

Question 3

Peptides are written from their…

Answer 3

…N to C terminus.

Question 4

Protein

Answer 4

Macromolecules consisting of one of more polypeptide chains linked via non-covalent or dithiane interactions

Question 5

Functions of proteins

Answer 5

Enzymes
Transporters
Regulatory proteins

Question 6

Conjugated proteins

Answer 6

Have additional groups that may or may not be covalently bound
e.g. glycoproteins, lipoproteins, nucleoproteins, metalloproteins

Question 7

Secondary structure

Answer 7

Interactions between amino acids in the same polypeptide chain

Question 8

Alpha-helix

Answer 8

H bond interactions between the carbonyl of one amino acid (i) and the amine of another amino acid (i+4)

Question 9

Which amino acids disfavour alpha-helix formation?

Answer 9

Amino acids with bulky R groups e.g. V T I
Charged amino acids e.g. S D N
Glycine (flexible)
** Alpha-helices are broken by proline due to its locked structure **

Question 10

Beta-sheet

Answer 10

H bonding of amino acids through space

Can be parallel or anti-parallel depending on the N–>C direction of the chains

Question 11

Beta-turn

Answer 11

A number of short turns that cause beta-sheets to form through folding of peptide chains back on themselves
Usually involve 3 amino acids (i) and (i+3)

Question 12

Tertiary structure

Answer 12

How all the polypeptide chains fold together to form the protein

Question 13

Examples of tertiary structures

Answer 13

Coordination of metals
Disulfide bridges
Ionic interactions
Hydrophobic interactions e.g. Leucine zipper

Question 14

Leucine zipper

Answer 14

= coiled-coil

The vdW interaction between a pair of amphipathic alpha-helices through their hydrophobic faces

Question 15

Amphipathic

Answer 15

Having both hydrophilic and hydrophobic parts

Question 16

Quaternary structure

Answer 16

Bringing together multiple subunits

Not held together by covalent bonds

Question 17

Why are acid chlorides not often used in peptide synthesis?

Answer 17

Due to potential racemisation via ketene formation

Question 18

DCC

Answer 18

Poorly soluble

Removed from reactions by filtration

Question 19

DIC

Answer 19

DCM-soluble
Removed by DCM-washes
Used in solid-phase chemistry

Question 20

EDC / ECI / WSC.HCl

Answer 20

Water-soluble

Removed by water washes

Question 21

Problems associated with solution-phase synthesis

Answer 21

Increasing the concentration of the reaction can increase the probability of side reactions
Adding excess reagent can lead to a mixture of products

Question 22

SPPS works…

Answer 22

…C–>N.

Question 23

Advantages of SPPS

Answer 23

The polymer is so large that it is less likely to self-react

Can be purified by filtration

Question 24

Main problem associated with SPPS

Answer 24

Cleavage of the peptide from the polymer

Question 25

Types of resin support

Answer 25

Polystyrene Polyacrylamide PEG-polystyrene

Question 26

Disadvantage of polystyrene

Answer 26

Hydrophobic - so is incompatible with polar solvents

Question 27

Example of a drug made by SPPS.

Answer 27

Enfuvitide (anti-HIV drug) | 36 amino acids long