Protein Structure And Function Flashcards
What groups surround the alpha carbon in an amino acid?
Variable side chain
Amino group
H atom
Carboxyl group
How are amino acids classified?
R groups
Define AA residue.
Remnants of AA after it has been joined by a peptide bond to form a protein
What angle is better the alpha carbon and C
Psi
Name the angle between the alpha carbon and N
Phi
Give features of peptide bond.
Partial double bond character Planar Rigidity- no rotation Resonance Stereoisomerism
What is the primary structure?
AA sequence
What is the secondary structure?
Locals spatial arrangement of polypeptide backbone
Alpha helix and beta sheet
What is tertiary structure?
Overall 3D configuration of the protein
What is the quaternary structure?
Association between different polypeptides to form multi subunit protein
Define motif
Folding pattern of 1+ elements of secondary structure
Domain
Polypeptide folded to distinct shape with functional role
Define pI
The pH at which a protein has no overall net charge
Exists as a zwitterion
Define pKA. What does pKa tell you about the side chain?
PKa is the pH at which there is 50% dissociation. Provides information about how strong an acid is.
High pKa = positively charged R group
Low pKa = negatively charged R group
What happens if pH is smaller than the pKa of a amino acid?
Protonated
What happens if pKa is greater than the pH ?
Deprotonated
What does an Isoelectic point greater than 7 mean about the amino acids?
Basic protein
Increasing number of positive amino acids
What happens if the isoelectric point is smaller than 7?
Acidic protein
Increasing number of negatively charged amino acids
What plot is used to predict the secondary structures of a protein from it primary sequence?
Ramachandran
What forces stabilise an alpha helix?
H bonds between N-H and C=O 4 amino acids apart
What happens to the H bonds in a parallel beta sheet compared with a anti parallel beta sheet?
Same location however increased bio due angle and therefore weaker
What is the Henderson - Hasselbach equation?
Henderson- Hasselbach = pH= pKa + log [A-]
[HA]
How can you identify an acidic amino acid?
Side chain negatively charged- indicated H+ has been lost
How can you identify a basic amino acid?
Side chain has positive charge indicating it has gained a proton
What makes an amino acid polar or non-polar
Difference in electronegativity between atoms on side chain
What makes an amino acid hydrophilic or hydrophobic?
Polar= hydrophilic Non-polar= hydrophobic
What is an aliphatic amino acid?
Straight side chain with H and C
What is an aromatic side chain?
Side chain with structure similar to that of benzene
What is the hydrophobic effect?
Internalisation of hydrophobic aa’s leaving hydrophilic aa’s on the surface
Not true from PM proteins
What forces stabilise the primary structure?
Covalent peptide bonds
What forces stabilise the secondary structure?
H bonds
What forces stabilise the tertiary and quaternary structures?
Covalent disulphide bonds Ionic H bonds Vdw Hydrophobic effect
Where do ionic interactions occur?
Between charged side chains form salt bridge
Where do disulphide bonds form? Which proteins are they most commonly found in?
Between cysteine residues
Found in secreted proteins as extracellular environment is harsher
Where do h bonds form?
Between electronegative atom and a H bound to another electronegative atom
NOF
What are vdw forces?
Dipole-dipole interactions that result form the transient localisation of electrons at any given moment.
Intrinsic to any bond type
What is the native conformation of a protein?
Folded protein that is functional
How to detergents and organic solvents cause desaturation of a protein?
Disrupt hydrophobic interactions
How does a change in pH alter protein structure?
Change in ionisation state of amino acids
Outline how proteins fold
Ordered process as would take too long other wise
Localised folding whereby stable conformations maintained
Process driven by need to find most stable conformation
Why does protein misfolding cause disease?
Misfolded proteins non functional therefore unable to work
Can cause other proteins to misfold
Accumulate in cells
