1
Q
What are examples of biomolecules that can be synthesised
A
- Taxol
- Epibatidine
- Eptifibatide
- synthetic heparin derivatives
2
Q
What functional groups do amino acids contain
A
- Amine and carboxylic acid
3
Q
What is a secondary amino acid
A
- Secondary amino acids are amino acids which do not contain the amino group -RNH2
- but is rather a secondary amine. R2NH
4
Q
What is a peptide
A
- A compounds with amino acids linked together by amide bonds
- Named by number of amino acids e.g. dipeptide, tripeptide
- generally<50 amino acids
5
Q
Draw amide bond resonance
A
- N- lone pair can delocalise
- slide 6
6
Q
Describe amide bond
A
- Has some = character- typically planar - due to resonance
- But can be non-planar
7
Q
When can an amide bond be non-planar
A
- Steric restrictions
- Steric repulsions
- Conformational effects
- Electronic effects- EDG and EWG
8
Q
What are the different types of amino acid
A
- Non-polar hydrophobic - prefer greasy environments
- Polar hydrophilic - amines+alcohols
- Charged - enhances solubility
9
Q
Describe the Strecker amino acid synthesis
A
- Aldehyde + NaCN, NH4Cl –> Cyano
- Cyano triple bond is hydrolysed to form COOH
- Cyano + H3O+ –> amino acid
- Racemic synthesis
10
Q
Describe the Gabriel Malonic ester synthesis
A
- EtOCOCBrCOOEt + Nucleophile with N-
- Br is substituted with amide nucleophile
- NaOEt + R-X is added - R group attaches
- H3O+ removes amide
- Forms racemic amino acid
11
Q
What direction are peptides written from
A
- N-terminus to C-terminus
12
Q
Define a protein
A
- Macromolecule of one or more polypeptide chains
- 50% of dry weight of a cell
- Have primary, secondary, tertiary and quaternary structure
13
Q
What are 8 types of proteins
A
- Enzymes
- Regulatory proteins
- Transport proteins
- Storage proteins
- Contractile and motile proteins
- structural proteins
- Protective proteins
- Exotic proteins
14
Q
What are conjugated proteins
A
- Have additional gorups present (may or may not be covalently bound)
- e.g. glycoproteins, lipoproteins and nucleoprotein, phosphoproteins, metalloproteins
15
Q
What is the primary structure
A
- Order of amino acid sequence
- Written from amino group to carboxyl group
16
Q
How many combinations is possible for an n-peptide
A
- 23^n
17
Q
What is the secondary structure
A
- How the amino acids in a chain interact with each other and create specific features
18
Q
What are the different types of secondary structure
A
- alpha-helix (3.6 residues/turn)
- beta-sheet
- beta-turn
- omega-loop
- the nature of the ammide bond
19
Q
Describe the amide bond
A
- Very rigid- lots of sp2 character
- trans is preferred due to sterics
- Rotation is still allowed about the C-N and C-C=O bonds (alpha carbon) which gives rise to the different structural motifs
- Rotation is referred to as phi and psi
20
Q
What is a Ramachandran Plot
A
- Examines which possible conformations are most likely for a given amino acid sequence using sterics
- Areas of lowest energy equated to a right handed alpha-helix and a beta-sheet
- Left-handed alpha-helix was less prevelant
21
Q
Why is there nothing in the bottom right quadrant of a Ramachandran plot
A
- The carbonyl and R-group are opposite- sterics hinderance
22
Q
What is an alpha-helix
A
- Hydrogen-bonding interactiosn between the carbonyl of one amino acid and the amine on another amino acid four units along
23
Q
Which amino acids is the alpha-helix disfavoured by
A
- Valine, threonine, isoleucine - too bulky
- Serine, aspartate and asparagine - too bulky
- Glycine- too flexible
24
Q
What can an alpha-helix be broken by
A
- Proline
25
What is a beta-sheet
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
26
Which of the beta-sheets are more stable
1. Anti-parallel tend to be more stable as have more H-bonds
27
What is the Beta-turn
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
28
What is an omega-loop
1. Much longer than beta-turn
2. Have less structure
3. Not predictable
29
What is the tertiary structure
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
30
What other interactions are seen in the tertiary structure
1. Coordination of metals
2. Disulfide bridges- from oxidation of cysteine
3. Hydrophobic interactions - leucine zipper
4. Ionic interactions - salt bridge
31
What is the quaternary structure
1. Bringing together multiple subunits that are not held together by covalent bonds
2. Some are dimers, trimers etc
32
What is a metamorphic protein
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
