Amino Acids & Proteins: Primary Structure Flashcards
What are the four different levels of protein structure?
primary–AA sequence
secondary–ways they fold
tertiary–complete 3D structure
quaternary– spatial arrangement of polypeptides in a multi subunit protein
Common features of amino acids: (6)
- all proteins are linear polymers of alpha amino acids
- amino and carboxyl grps are ionized at physiological pH
- each of the 20 common have a different R group
- alpha carbon is chiral: usually in the L configuration in proteins
- either polar or non-polar
- some have special chemical properties
Which amino acids are considered hydrophobic?
ala, val, leu, ile, met, trp, pro, phe
Facts about hydrophobic AAs (Ala, val, leu, ile): (3)
they have aliphatic side chains
the diversity of the side chain contributes to optimal packing in the protein interior
Which AA is often chosen as replacement to determine amino acid function using site directed mutagenesis?
Ala
Whats special about Met?
contains sulfur which can be oxidized to s double bond o or SO2 which can effect protein function
other than that it is relatively inert
Trp?
largest amino acid
absorbs UV light most at 280 nm and can therefore be used to determine [protein]
Phe?
dullllllllll
Pro?
the only imino acid
the side chain connected to NH group causes kink in polypeptide chain
What are the polar AAs?
gly, asn, gln, his, ser, thr, tyr, cys
Gly?
simplest AA, side chain = H
Asn & Gln?
uncharged amides of the acidic AAs asp and glu
can be H bond donors or acceptors
His?
imidazole side chain which can be positively charged at neutral pH
can be buffer
Ser, Thr, & Tyr?
all have hydroxy group
often nucleophiles in reactions and are proton donors or acceptors
OH can be covalently attached to other groups
Tyr?
derivative of Phe and both are precursors of amino acid neurotransmitters
Cys?
forms disulfide bonds with other cys’!! (sulfhydryl group)
provides covalent crosslinking
inside the cell (reducing) SH form outside the cell oxidized S-S form
Charged amino acids?
asp, glu, lys, arg
Asp & Glu?
negatively charged carboxyl side chains at pH 7
= acidic
Lys & Arg?
positively charged side chains at pH 7
=basic
What configuration are most AA in protein?
L (other config = D, enantiomer)
If multiple chiral centres are present what system is used for configuration? what configuration are most amino acids?
R & S system, S
what is pI?
the isoelectric point on a titration curve, which is a pH value at which the net charge of the molecule is 0
molecules with a lot of acidic AAs will have a low pI and vice versa
What is a peptide bond?
an amide covalent linkage formed through dehydration of alpha carboxyl group
What results when a peptide bond is formed? (7)
an H2O molecule is lost, no charge when bond is formed, very stable, rigid and planar, trans, uncharged but polar, partial double bond character
