BCHM-3050 Lecture Notes - Lecture 8: Enzyme, Methionine, Threonine
8 Jun 2018
School
Department
Course
Professor
Alpha Amino Acid structure
Alpha acids: monomers that make up proteins
Amino group is attached to alpha carbon (N-terminus)
Side chain ( R ) and hydrogen atom are also attached to alpha
carbon
§
Different amino acids distinguished by the side chain
§
○
Carboxylic group attached to beta carbon (C-terminus)
○
•
Residue that isn't a hydrogen atom
Amino acid will be chiral
○
This is the case for most amino acids
○
•
Residue which is the 2nd hydrogen atom for the alpha carbon
Amino acid is not chiral
○
Glycine
○
•
Charges on N and C terminus cancel each other out
Carboxylic acid = deprotonated (-)
○
Amino group = protonated (+)
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Zwitterion: compound with both charges
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BUT residue can add to the compound making it overall negative
or positive
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•
Alpha amino acid stereochemistry
Central alpha carbon = Sp3 hybridized
Aka planar
○
•
For all AA except glycine the alpha carbon is asymmetrical
Aka chiral
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•
Stereoisomers = L and D
Can be enantiomers or diastereomers
○
L isomer is used in polypeptide chain under normal circumstance
Cell viability depends on proper protein function
Depends on the ability of a protein to adopt a well
defined active structure
□
§
○
D also has a role in physiology
Ex. Antibiotics and bacterial cell walls
§
○
Preference for L amino acids has two consequences:
Surface of any protein is asymmetric
Basis of molec recognition of binding targets by
proteins
□
§
Stereochem of amino acids promote formation of secondary
structure in proteins
§
○
•
For L: amino group is to the left
•
For D: amino group is to the right
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Rest of the groups:
Carbonyl group = top
○
R group = bottom
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•
UV absorption of Amino acid
Nucleic acid = 260 nm
Absorb light more strongly
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•
Protein = 280 nm
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20 Common amino acids and classification
Amino acids are grouped based on chemical/ physical properties
4 different classes:
Aliphatic or aromatic character
§
Polarity of side chain
Note: variety of side chains allow proteins enormous
versatility in structure and function
□
§
Presence or absence of ionizable groups
§
○
•
Nonpolar
Aromatic Aliphatic (side chain) Strange
Phenylalanine
(Phe F)- most
hydrophobic
amino acids
Tryptophan
(Trp w)
Tyrosine (Tyr
y)- along with
tryptophan they
have
hydrophobic
character but the
polar group in
side chain
tempers it.
Aromatic
amino
acids
absorb light
in near UV
region of
electromag
netic
spectrum
•
Glycine (Gly G)- side chains found
on surface of protein b/c it cant form
tight turns
Valine (Val V)
Alanine (Ala A)- neutral
Leucine (Leu L) - greater tendency
to transfer from water to
hydrocarbon solvent than alanine
Isoleucine (ile I)- two chiral carbons
Proline (Pro P)-
only amino acid in
which the side
chain forms a
covalent bond w
the alpha amino
grp. Has ring.
methionine (Met
M)-not technically
an aliphatic amino
acid. Hydrophobic
chain
Polar
Acidic Charge (-) Neutral Basic Charge
(+)
Aspartate(Asp P)
Glutamate (Glu E)
Share steric similarites w
aparagine and glutamine.
Asparagine and glutamine
have nonionizable, uncharged
polar side chains
Serine (Ser S)
Cysteine (Cys C)- the side
chain can ionize at high pH
and then the oxidation of
the two chains yield
disulfide bond
Product = cystine
Threonine (Thr T)
Aspargine (Asn N)
Glutamine (Gln Q)
Found on surface of
proteins. Have polar side
chains and can form
multiple H bonds
Histidine (His
H)- least basic.
Has 50/50
positive ionized
Lysine(Lys K)-
Arginine (Arg
R)-
Selenocysteine and pyrrolysine
•
Titration curve of Histidine
At first the histidine loses its proton at pH6
When incorporated into proteins the pka ranges from 6.5-7.4
Ionizable side chain depends on electrostatic environment
§
○
•
When in proximity of other charged groups the side chains are altered
significantly
•
Amino acid post translation modification
Function of post translation modification:
Signal pathway
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Calcium binding sites
Required for clot formation
§
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Stabilization/folding
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Enzyme activity
Activation, inactivation or suppression
§
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Gene expression or suppression
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•
Acetylation or methylation in histone tails
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Chapter 5: Introduction to proteins (P1)
Wednesday, May 30, 2018
10:35 PM
Document Summary
Amino group is attached to alpha carbon (n-terminus) Side chain ( r ) and hydrogen atom are also attached to alpha carbon. Different amino acids distinguished by the side chain. This is the case for most amino acids. Residue which is the 2nd hydrogen atom for the alpha carbon. Charges on n and c terminus cancel each other out. But residue can add to the compound making it overall negative or positive. For all aa except glycine the alpha carbon is asymmetrical. L isomer is used in polypeptide chain under normal circumstance. Depends on the ability of a protein to adopt a well defined active structure. Preference for l amino acids has two consequences: Basis of molec recognition of binding targets by proteins. Stereochem of amino acids promote formation of secondary structure in proteins. For l: amino group is to the left. For d: amino group is to the right. Amino acids are grouped based on chemical/ physical properties.
