1. Intro to protein structure Flashcards
How many amino acids are there?
20
Name 2 Hydrophobic amino acids
Glycine
Proline
Name 5 Hydrophilic amino acids
Asparagine Cysteine Serine Threonine Tyrosine
Amino acids with charged side chains
Always protonated- basic
2 examples:
Arginine
Lysine
Amino acids with charged side chains
Always negatively charged due to proton donation
2 examples:
Glutamate
Aspartate
Why can’t AAs tolerate wide changes in pH?
Ionisation state provides vital biological properties
What gives AAs buffering capacity to resist changes in pH?
Ability to take up/ release protons
Electrophoresis separates proteins on the basis of their charge
Use to distinguish between normal/ mutant forms of proteins which have gained/ lost charge
Chirality of AAs
Alpha Carbon = Chiral centre
Optical isomers
All AAs in proteins are of the L-form
Which is the only non-chiral AA?
Glycine
How is a peptide bond formed?
Condensation reaction
Releases 1 molecule water
Functionality of a protein requires
Definite 3D structure to make them specific
Characteristics of the peptide bond
No free rotation around bond
C=O and N-H are in the same plane
Other 2 bonds in backbone can rotate
Only conformation in which side chains don’t clash with main chain are allowed (Steric Hindrance)
Covalent bonds in a protein
STRONGEST bond
In Primary structure
Can exist as disulphide bridges (Cysteine)
Hydrogen bonds in a protein
When 2 atoms bearing a delta- share a delta+ Hydrogen
Can occur between water molecules or different atoms on different side chains and backbone
Ionic interactions in a protein
Arise from electrostatic attraction between charged side chains
Relatively strong bonds
Majority of charged groups at surface of folded protein
Van der Waals Forces in a protein
Transient, weak electrostatic attractions between 2 atoms due to fluctuating electron cloud
If atoms are close, transient dipole can induce a dipole
Sheer No. means they are influential in overall conformation
Hydrophobic interactions in a protein
Hydrophobic side chains are packed into interior of protein
Hydrophobic core and Hydrophilic surface
Hydrogen bonds between C=O and N-H stabilise…
Helices
Beta pleated sheets
Proline is a KINKY AA
When joined to a peptide chain, NH group is lost
- Prevents side chain from H bonding with C=O from another residue
- Distorts helical conformation
Parallel B pleated sheets
Alternate B strands run in same direction
Antiparallel B pleated sheets
Alternate B strands run in opposite direction
Folding of proteins
Fold into single conformation of lowest energy
Chaperones may be involved to ensure folding occurs in most energetically favourable way
By breaking bonds that hold the protein together, we can denature the proteins into their original flexible polypeptide. Common denaturants:
Urea (breaks H-bonds)
2- Mercaptoethanol (breaks disulphide bonds)
Primary structure of a protein
Linear sequence of AAs that make up protein
Write sequence from Amino terminus to Carboxyl terminus
Secondary structure of a protein
Alpha helices and Beta pleated sheets
Existence dictated by sequence of AAs in primary structure
Tertiary structure of a protein
Arrangement of secondary structure motifs into compact globular structures (Domains)
Quaternary structure of a protein
3D structure of a multimeric protein composed of several subunits
e.g. Oxyhaemoglobin
Post translational modification of proteins
Starting set of 20 AAs can be modified to create novel AAs
Enhances capabilities of protein
Post translational modifications of proteins
Mutation…
Can be identified by electrophoresis as a reduction in molecular weight
