Chemistry Flashcards
Define 5 types of non- covalent bonds and draw structures
1) hydrogen bonds
2) van der waals
3) phi-phi overlap
4) ionic bonds
5) hydrophobic interactions
Define “isoelectric point of a protein” and describe its impact on the physiochemical properties of a protein using an acidic protein as an example
The pH at which a molecule or surface carries no electrical charge. At the isoelectric point the protein is least soluble. An acidic protein in basic conditions will be neutral and therefore at its least soluble.
Name the 20 standard amino acids (BAPAN)
Basic- lysine histidine arginine
Acidic- aspartic acid glutamic acid
Polar- serine threonine cysteine tyrosine glutamine asparagine
Aromatic- phenylalanine, tyrosine, tryptophan
Non- polar- proline, leucine, alanine, valine, glycine, methionine, isoleucine
What is somatostatin
Growth inhibiting hormone
Hypothalamic releasing factors pathway
Thyotropin releasing hormone (TRH) makes thyroid stimulating hormone (TSH) which controls T3 and T4 release in the thyroid.
If TSH is high then lots of T3/4 results in under active thyroid/ hypothyroidism
Name anterior pituitary hormones
TSH
ACTH
LH
Name posterior pituitary hormones
Oxytocin, arginine, vasopressin (anti-diuretic hormone)
Describe the lab synthesis of peptides
React 2 amino acids to form an amide bond and a peptide. Side chains of amino acids may react and give unwanted products. Eg) lysine has NH2 side chain and glutamic acid has (COOH) side chain. We add “protecting groups” to ensure only functional groups we want to react will react.
How do we ensure an amino acid is formed and not a salt?
There must be chemical activation of the carboxyl component to ensure it attacks the amino component.
This activation involves the addition of a good “leaving group” (conjugate base of a sting acid eg) Cl).
Also called “coupling”
Describe an amide bond and it’s properties.
Main properties are due to conjugation of the N lone pair of electrons with carbonyl group.
Resulting in a partial double bond character.
Amide bond is PLANAR.
Chemically inert and unlikely to react.
What is a torsion/dihedral angle?
The angle between two intersecting planes.
Peptide bond has partial double bond character so is planar.
What are the angles called:
(1) between N-Calpha
(2) between Calpha-C
(1) Phi
(2) Psi
What are steric factors?
They are factors that act through side chains and influence the confirmation of a peptide chain.
Steric factors repel eachother in cis conformation (unfavourable) but do not in trans conformation (favourable). Preferred torsion angle is when steric factors aren’t too close. However bond angles are limited to just phi and psi being able to rotate and only by 180 degrees.
Describe alpha helix
Each H bond is week in isolation but the sum of them makes helix stable.
Side chains point outwards and towards the N terminus.
Right handed helix.
Describe the beta sheet.
Side chain point alternatively in opposite strands.
Much more extended than alpha helix.
May be parallel or anti parallel.
