Lecture 1

Question 1

What are examples of biomolecules that can be synthesised

Answer 1

1. Taxol
2. Epibatidine
3. Eptifibatide
4. synthetic heparin derivatives

Question 2

What functional groups do amino acids contain

Answer 2

1. Amine and carboxylic acid

Question 3

What is a secondary amino acid

Answer 3

1. Secondary amino acids are amino acids which do not contain the amino group -RNH2
2. but is rather a secondary amine. R2NH

Question 4

What is a peptide

Answer 4

1. A compounds with amino acids linked together by amide bonds
2. Named by number of amino acids e.g. dipeptide, tripeptide
3. generally<50 amino acids

Question 5

Draw amide bond resonance

Answer 5

1. N- lone pair can delocalise
2. slide 6

Question 6

Describe amide bond

Answer 6

1. Has some = character- typically planar - due to resonance
2. But can be non-planar

Question 7

When can an amide bond be non-planar

Answer 7

1. Steric restrictions
2. Steric repulsions
3. Conformational effects
4. Electronic effects- EDG and EWG

Question 8

What are the different types of amino acid

Answer 8

1. Non-polar hydrophobic - prefer greasy environments
2. Polar hydrophilic - amines+alcohols
3. Charged - enhances solubility

Question 9

Describe the Strecker amino acid synthesis

Answer 9

1. Aldehyde + NaCN, NH4Cl –> Cyano
2. Cyano triple bond is hydrolysed to form COOH
3. Cyano + H3O+ –> amino acid
4. Racemic synthesis

Question 10

Describe the Gabriel Malonic ester synthesis

Answer 10

1. EtOCOCBrCOOEt + Nucleophile with N-
2. Br is substituted with amide nucleophile
3. NaOEt + R-X is added - R group attaches
4. H3O+ removes amide
5. Forms racemic amino acid

Question 11

What direction are peptides written from

Answer 11

1. N-terminus to C-terminus

Question 12

Define a protein

Answer 12

1. Macromolecule of one or more polypeptide chains
2. 50% of dry weight of a cell
3. Have primary, secondary, tertiary and quaternary structure

Question 13

What are 8 types of proteins

Answer 13

1. Enzymes
2. Regulatory proteins
3. Transport proteins
4. Storage proteins
5. Contractile and motile proteins
6. structural proteins
7. Protective proteins
8. Exotic proteins

Question 14

What are conjugated proteins

Answer 14

1. Have additional gorups present (may or may not be covalently bound)
2. e.g. glycoproteins, lipoproteins and nucleoprotein, phosphoproteins, metalloproteins

Question 15

What is the primary structure

Answer 15

1. Order of amino acid sequence
2. Written from amino group to carboxyl group

Question 16

How many combinations is possible for an n-peptide

Answer 16

1. 23^n

Question 17

What is the secondary structure

Answer 17

1. How the amino acids in a chain interact with each other and create specific features

Question 18

What are the different types of secondary structure

Answer 18

1. alpha-helix (3.6 residues/turn)
2. beta-sheet
3. beta-turn
4. omega-loop
5. the nature of the ammide bond

Question 19

Describe the amide bond

Answer 19

1. Very rigid- lots of sp2 character
2. trans is preferred due to sterics
3. Rotation is still allowed about the C-N and C-C=O bonds (alpha carbon) which gives rise to the different structural motifs
4. Rotation is referred to as phi and psi

Question 20

What is a Ramachandran Plot

Answer 20

1. Examines which possible conformations are most likely for a given amino acid sequence using sterics
2. Areas of lowest energy equated to a right handed alpha-helix and a beta-sheet
3. Left-handed alpha-helix was less prevelant

Question 21

Why is there nothing in the bottom right quadrant of a Ramachandran plot

Answer 21

1. The carbonyl and R-group are opposite- sterics hinderance

Question 22

What is an alpha-helix

Answer 22

1. Hydrogen-bonding interactiosn between the carbonyl of one amino acid and the amine on another amino acid four units along

Question 23

Which amino acids is the alpha-helix disfavoured by

Answer 23

1. Valine, threonine, isoleucine - too bulky
2. Serine, aspartate and asparagine - too bulky
3. Glycine- too flexible

Question 24

What can an alpha-helix be broken by

Answer 24

1. Proline

Question 25

What is a beta-sheet

Answer 25

1. In the beta-pleated sheet the amino acids hydrogen bond through space 2. These may be termed parallel or antiparallel depending on the N-C direction of the chains

Question 26

Which of the beta-sheets are more stable

Answer 26

1. Anti-parallel tend to be more stable as have more H-bonds

Question 27

What is the Beta-turn

Answer 27

1. The term for a number of short turns that cause beta-sheets to form by folding amino-acid chains back on themselves - usually 3 amino acids

Question 28

What is an omega-loop

Answer 28

1. Much longer than beta-turn 2. Have less structure 3. Not predictable

Question 29

What is the tertiary structure

Answer 29

1. Describes how the polypeptide chains fold together 2. Combines all the motifs: alpha helices etc 3. Often see hiding of non-polar regions within core

Question 30

What other interactions are seen in the tertiary structure

Answer 30

1. Coordination of metals 2. Disulfide bridges- from oxidation of cysteine 3. Hydrophobic interactions - leucine zipper 4. Ionic interactions - salt bridge

Question 31

What is the quaternary structure

Answer 31

1. Bringing together multiple subunits that are not held together by covalent bonds 2. Some are dimers, trimers etc

Question 32

What is a metamorphic protein

Answer 32

1. A single amino acid sequence that adopts multiple folded conformations under native conditions and interconverts reversibly between states. 2. e.g. Lymphotactin- structures are in equilibrium but have different functions