Amino Acids & Proteins Flashcards
4 major types of macromolecules
proteins
nucleic acids
lipids
carbohydrates
How do proteins contribute to the cell?
enzymes to catalyse reactions
stuructural proteins in connective tissue
interact with DNA and RNA - control nucleic acids
lipid bound proteins act as transport systems
glycosylated or interact with sugars
Lactofernin & flexibility & function?
binding to iron, lactrofernin undergoes conformational change
allows other molecules to distinguish between iron free and iron bound forms
structure of amino acid
all proteins are linear polymers
simple unit is an amino acid
contain:
variable group, amino group, carboxyl group and a H
Both acid and amine bonded to alpha carbon
how do you define an alpha carbon
the carbon next to the carboxyl group
variation of amino acids
variation in the side chain distinguish them
identity and properties of amino acid dependent on nature of R group
what is chirality
molecules that are distinguishable in their mirror form
have potentially different chemical properties
alpha carbon has 4 different substituents - making it chiral
what amino acids are chiral
all apart from glycine
chiral isomers
L isomer carboxyl group on the Right
D isomer carboxyl group on the L
Amino acids in proteins are always in L form
4 main group of amino acids?
Hydrophobic with non-polar R groups
Polar with neutral R groups, charge not evenly distributed
Positively charged with positive R groups at physiological pH
Negatively charged with negative R groups at physiological pH
Key properties of: Glycine
LOOK UP STRUCTURE
No chirality as R group is H
Flexible
Acts to provide flexibility to proteins when other side chains too bulky
Gly, G
Key properties of: Alanine
LOOK UP STRUCTURE
CH3 R group
Ala, A
Alanine scanning directed mutagenesis
change of functional group to alanine
see if any changes on properties
see if protein driven by structure
Key properties of: Proline
LOOK AT DIAGRAM
Unusual amino acid
side chain bonds to amino group
tight restraints on conformation of protein
peptide bind forms cis & trans conformations
in proteins that need to be rigid
Key properties of: Histidine
LOOK AT DIAGRAM
in active site of many enzymes
only amino acid with pKa of side chain near neutral
side chain can alter charge
His, H
Histidine side chain
LOOK AT DIAGRAM
can alter its charge at physiological pH
modulated by other amino acids surrounding It
often found in active sites of enzymes
imidazole ring can bind to release protons
Key properties of: Cysteine
LOOK AT DIAGRAM
contains free thiol group (SH)
form covalent bonds with another cysteine
disulphide bond formed
only covalent bond found to hold chain in correct fold
pKa of 8.4 so found in active sites
residues form a covalent bond in some proteins to form cystine
Define: zwitterionic
in solution at ph 7
amino acids exist predominantly as zwitterions
Amine group is protonated NH3+
Carboxyl group is deprotonated COO-
pH raised with zwitterions
LOOK AT DIAGRAM
Carboxylic acid first group to give up a proton
pHA of near 2
dipolar persists until pH approaches 9
protonated amine group then loses a proton
titration curve of glycine
LOOK AT DIAGRAM
carboxyl group pKa 2.0
amino group pKa 10.0
R carries no charge the aa has isoelectric point of 6
define: isoelectric point
amino acid electrically neutral
acidic charge neutralised by basic charge
charged r groups
LOOK AT DIAGRAMS
some (Lys) carry a basic charge
some (Glu) carry an acidic charge
due to charge on the R group
A.A with aromatic side chains
LOOK AT DIAGRAMS
Phenylalenine
Tyrosine
Tryptophan
Absorb strongly near 280nm
Rich in aromatic residues = detect for presence of proteins up to 80n m
Bulky side chains
pKa value of: terminal alpha carboxyl group
3.1
pKa value of: aspartic acid and glutamic acid
4.1
pKa value of: histidine
6.0
pKa value of: terminal alpha amino group
8.0
pKa value of: cysteine
8.3
pKa value of: tyrosine
10.9
pKa value of: lysine
10.8
pKa value of: arginine
12.5
pKa values dependent on?
temperature
ionic strength
microenvironment
ionisable group
not exact as biological systems can change
Peptide bond formation
LOOK AT DIAGRAM
aa join together to make peptide bond
loss of a molecule of water
one O- combines with H3- to create peptide bonds
carboxyl and amino groups join
trans peptide bond
peptide chain in proteins in trans formation
R group on different sides of the protein
avoiding steric clashes
cis peptide bond
LOOK AT TYPICAL BOND LENGTHS
R group on same sides of protein
proline found in cis formation
