Protein Structure Flashcards
What are proteins used for in the body?
Enzymes Transporters Machines Immune protection Ion channels Receptors Ligands
General structure of an amino acid
H,NH2,COOH,R attached to a central carbon group. R group distinguishes the type of amino acid.
What is a zwitterion
When both the NH2 and COOH group are charged. (NH3+ and COO-)
NH2=base proton acceptor
COOH=acid proton donor
How are amino acids classified?
According to chemical properties of the R groups
Which is the N terminal and C terminal of a protein?
N= NH3+end (amino end) and C=COO- end (carboxyl end)
What is amino acid residue
An amino acid after its bonded. What’s left of it w.g NH-CHR-CO
Categories by which amino acids are categorised
Chemical properties: Hydrophobic hydrophilic Polar Non polar Acidic Basic Neutral
Physical properties:
Aliphatic
Aromatic
If the pH of the solution < the Pk value then the side chain will be…..?
Protonated
Is the pH of a solution> the pK value then…..?
The group will be deprotonated
Are positively charged R groups basic or acidic?
Basic - high pK and NH3 = positive charge. Are protonated as a base accepts a proton
Same fo reverse
How is a polypeptide bond formed
Between COOH and NH3. Cones nation reaction- loss of h2o.
in which plane do peptide bonds (C-N) lie in a polypeptide
all in the same plane, they are planar
why are all peptide bonds(C-N) in the same plane and what advantages does this give?
peptide bonds C-N has partial double bond characteristics meaning they are unable to rotate. This makes the bonds more rigid. The other bonds are free to rotate (N-CHR and C-CO)
What is cis/trans conformation
whether the side chain(Rgroup) is on the same side of the bond(cis) or opposite sides on the peptide bond(trans)
what is the isoelectric point (pI) of proteins
pH at which a protein forms a zwitterion. A molecule with both a positive and negative charge
pI>7 = acidic or basic protein?
basic because contain mainly positively charged proteins. lower pH required to deprotonate the COOH
pI<7 = basic or acidic?
acidic because protein contains mainly negatively charged amino acids and pH needs to be raised considerably to protonate
if proteins pHpI?
pHpI protein is deprotonated
what type of bond are peptide bond and what do they hold together
covalent bonds and they hold together primary sequence
structure of alpha helix?
H bonds stabilise structure and its shaped by the sugar phosphate backbone. Also hydrophobic residues are strong helix formers
structure of beta sheet
R groups alternate, each R group is on opposite side to last R group on chain. they are arranged anitparrallely to form beta sheet. hydrogen bonds form between sheets to stabilise structure. can also line up parallel or a mix of both.
example of beta sheet and alpha helix
beta sheet- fatty acid binding protein
alpha helix- iron storage protein ferritin
structure, role and example of a fibrous protein
long strands/sheets of repaying structures. role is to support and protect shape. e.g collagen
structure, role and example of a globular protein
compact shape and made of mixture of secondary structures. role is in catalysis and regulation. e.g carbonic anhydrase
