PROTEINS Flashcards
R: side chain
determines the specific nature of the amino acid
NONPOLAR SIDE CHAINS
– no side chain (Gly)
– aliphatic side chain (Ala, Val, Leu, Ile)
– alicyclic side chain: „imino acid” (Pro)
– containing sulfur (Met)
aromatic (Phe, Trp)
POLAR SIDE CHAINS
aliphatic
– containing alcoholic hydroxyl group (Ser, Thr)
– containing thiol group (Cys)
– amides (Asn, Gln)
aromatic (containing phenolic hydroxyl Tyr)
AMINO ACIDS WITH NET POSITIVE CHARGE at pH7
aliphatic (Arg, Lys)
aromatic (His)
What stereoisomer are almost all a.a?
L-stereoisomer
What a.a. can absorb UV-Light
tyrosine, tryptophan and phenylalanine,
Tryptophan absorbs 4 times more at 280 nm
phenylalanine very small amount.
How does cysteine form cystine?
By being oxidized and forming covalent bond with other cysteine forming disulfide bond
A.A haveing positive charge at ph 7?
Lysine, arginine, hisitidine
A.A having negatice charge at ph 7?
Aspartate, glutamate
Zwitterion
A.A can act either as acid or base and has a net chare of 0
What kind of reaction forms peptide bond?
Condensation
Chromatography
purification of protein
Electrophoresis
seperates proteins according to their size and charge. Smaller travel faster, larger slower.
Primary structure
Determine how the protein folds and the function of the protein.
proteases
enzyme that hydrolytic cleavage peptide bonds.
Some proteases cleave only peptide bond adjacent to particular a.a
Peptide bond
HAs double bond character
cannot rotate
atoms in the bond are coplanar
A.a interior
hydrophobic
alpha helix
R-gropus protrude outwards 1 helical turn =3,6 a.a residues Stabalized with h-bonds and wander waals L-a.a present Only right handed alpha helix present
A.a residues preventing alpha helix
Glu,Lys,Arg
Proline in alpha helics
Rarely found since it cant participate in h-bonding
H-bonds in beta-sheet
In line in antiparallel
distorted/not in line in parallel
Beta turn
4 a.a residues
1.a.a Carvonyl oxygen form h-bond with 4a.a residue amino-group
Gly and Pro often occur in B-turn
secondary structure
the spatial arrangement
aplha-keratin
alpha helix, cross-linked by disulfide bonds
silk fibroin
b-conformation
collagen
tripple helix
2ndary structure is left handed
3 a.a/turn
Domain
A section of protein structure that perform a particular chemical or physical task, like binding to substrate that gives the overall role of the protein.
selenocysteine
The 21 a.a
not product of PTM, insertded during translation
what a.a occurs naturally
d-a.a
confromation
spatial relationship of every atom in molecule
conformation
the geometric relationship between given set of molecules
d- or L- a.a
Beta sheet
r-groups opposite to each other
Form H-bonds with adjacent segments
Tend to have right-handed twist
Teritary stucture
3-D shape
how 2nd structual feauters assemble to form domains and how they relate to each other.
Quaternary
defines the polypeptide composition of protein
H-bomds
salt bridges
covalent disulfide
sulfhhydryl oxidase
catalyzes oxidation of cysteine residue to form disulfide bonds
Chaperone
participate in the folding of proteins, prevent aggregation,
Prion
Protein conformstion disease
resulting from the deposition od insoluable protein aggregates in neural cells
