Protein Structure and Folding Flashcards
How man amino acids are there in the human body?
20
How can you differentiate AA?
Properties: charge, ability of H bonding, acidic/basic, neutral, hydrophobic, hydrophilic, aliphatic, aromatic. Non-polar = side chain: alkyl. Polar = side chain: neutral, acidic, basic
What is the structure of an AA?
Central C, a H, a carboxyl group COOH, an amino group NH2, an R group
What is an AA residue?
what remains of AA after it has been joined by peptide bond
Describe a protein in a primary structure
linear chain of AA joined by petide bond (condensation reaction) between –> amino + carboxyl
What is the bond present in a primary structure?
Peptide/covalent
What are the bonds in a secondary structure?
helices, H bonds between N-H and C=O
Describe a tertiary structure and the bond present
3-D, folding into globular shape. Hydrophobic on inside. Covalent, ionic, H bonds, van der waals, hydrophobic. Disulphide: bonds of 2 sulphides, 2 cys residues
What bonds are in a quaternary structure?
multi-subunit protein. Covalent, ionic, H bonds, van der waals, hydrophobic. Disulphide: bonds of 2 sulphides
How does pH affect a protein in terms of pK?
If the pH of the solution < the pK value then the group will be protonated. If the pH of the solution > the pK value then the group will be deprotonated
What are amyloid fibres?
Misfolded, insoluble form of a normal soluble protein. Highly ordered, high degree of β-sheet
What is a peptide bond?
Type of covalent bond, joins AA, between N-C terminus via condensation reaction. Planar, trans conformation, C-N bond has partial double bond characteristics = unable to rotate
What is pI?
pI = isoelectric point = pH at which there is no overall net charge of the protein. pH < pI is protonated, pH > pI is deprotonated
What is a base?
Proton acceptor, NH2 amino group
What is an acid?
Proton donor, carboxyl group COOH
what is pKa?
tells you the strength of the acid = how likely the groups are to loose/gain protons
pH at which the weak acid or base exists in 50% ionised and 50% unionised form
if an AA has a high pKa what does that indicate?
its a basic AA
what is a zwitter ion?
AA usually present in this state. Molecule or ion having separate positively and negatively charged groups
what happens when pKa is equal to pH?
there will be equal amounts of protonated and deprotonated forms
what is the henderson-hasselbach equation?
pH = pKa+log(base/acid)
