Lecture 1 Flashcards
What are examples of biomolecules that can be synthesised
- Taxol
- Epibatidine
- Eptifibatide
- synthetic heparin derivatives
What functional groups do amino acids contain
- Amine and carboxylic acid
What is a secondary amino acid
- Secondary amino acids are amino acids which do not contain the amino group -RNH2
- but is rather a secondary amine. R2NH
What is a peptide
- A compounds with amino acids linked together by amide bonds
- Named by number of amino acids e.g. dipeptide, tripeptide
- generally<50 amino acids
Draw amide bond resonance
- N- lone pair can delocalise
- slide 6
Describe amide bond
- Has some = character- typically planar - due to resonance
- But can be non-planar
When can an amide bond be non-planar
- Steric restrictions
- Steric repulsions
- Conformational effects
- Electronic effects- EDG and EWG
What are the different types of amino acid
- Non-polar hydrophobic - prefer greasy environments
- Polar hydrophilic - amines+alcohols
- Charged - enhances solubility
Describe the Strecker amino acid synthesis
- Aldehyde + NaCN, NH4Cl –> Cyano
- Cyano triple bond is hydrolysed to form COOH
- Cyano + H3O+ –> amino acid
- Racemic synthesis
Describe the Gabriel Malonic ester synthesis
- 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
What direction are peptides written from
- N-terminus to C-terminus
Define a protein
- Macromolecule of one or more polypeptide chains
- 50% of dry weight of a cell
- Have primary, secondary, tertiary and quaternary structure
What are 8 types of proteins
- Enzymes
- Regulatory proteins
- Transport proteins
- Storage proteins
- Contractile and motile proteins
- structural proteins
- Protective proteins
- Exotic proteins
What are conjugated proteins
- Have additional gorups present (may or may not be covalently bound)
- e.g. glycoproteins, lipoproteins and nucleoprotein, phosphoproteins, metalloproteins
What is the primary structure
- Order of amino acid sequence
- Written from amino group to carboxyl group
How many combinations is possible for an n-peptide
- 23^n
What is the secondary structure
- How the amino acids in a chain interact with each other and create specific features
What are the different types of secondary structure
- alpha-helix (3.6 residues/turn)
- beta-sheet
- beta-turn
- omega-loop
- the nature of the ammide bond
Describe the amide bond
- 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
What is a Ramachandran Plot
- 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
Why is there nothing in the bottom right quadrant of a Ramachandran plot
- The carbonyl and R-group are opposite- sterics hinderance
What is an alpha-helix
- Hydrogen-bonding interactiosn between the carbonyl of one amino acid and the amine on another amino acid four units along
Which amino acids is the alpha-helix disfavoured by
- Valine, threonine, isoleucine - too bulky
- Serine, aspartate and asparagine - too bulky
- Glycine- too flexible
What can an alpha-helix be broken by
- Proline
What is a beta-sheet
- In the beta-pleated sheet the amino acids hydrogen bond through space
- These may be termed parallel or antiparallel depending on the N-C direction of the chains
Which of the beta-sheets are more stable
- Anti-parallel tend to be more stable as have more H-bonds
What is the Beta-turn
- 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
What is an omega-loop
- Much longer than beta-turn
- Have less structure
- Not predictable
What is the tertiary structure
- Describes how the polypeptide chains fold together
- Combines all the motifs: alpha helices etc
- Often see hiding of non-polar regions within core
What other interactions are seen in the tertiary structure
- Coordination of metals
- Disulfide bridges- from oxidation of cysteine
- Hydrophobic interactions - leucine zipper
- Ionic interactions - salt bridge
What is the quaternary structure
- Bringing together multiple subunits that are not held together by covalent bonds
- Some are dimers, trimers etc
What is a metamorphic protein
- A single amino acid sequence that adopts multiple folded conformations under native conditions and interconverts reversibly between states.
- e.g. Lymphotactin- structures are in equilibrium but have different functions
