Amino Acids & Chemical Evolution of Proteins

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Amino Acids
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Transcript of Amino Acids & Chemical Evolution of Proteins

Amino Acids & Chemical Evolution of ProteinsIntroduction, Cont.
• Optical Activity
d. Chirality and Biochemistry
Introduction, Cont.
• Chemical Evolution
Natural Selection
Proteins: The Effect of Neutral Drift
c. Evolution Through Gene Duplication
Amino Acids of Proteins General Properties
• pK Values of the 20 Standard
- pK1 refer to the α – Carboxylic Acid
- pK2 refer to the α – Amino Groups
- pKR refer to the Side Groups with Acid-Base
Properties
• In chemistry and Biochemistry, a
Dissociation Constant or an Ionization
Constant is a Specific Type of Equilibrium
Constant Used for Reversible Reactions or
Processes
pK = - log Kd
range 2.2
Entirely in Their Carboxylate Forms
• α – Amino Groups All Have pK Values
Near 9.4
Entirely in Their Ammonium Ion Forms
Amino Acids of Proteins General Properties, Cont
In the physiological pH Range, Both
the Carboxylic Acid and the Amino
Groups of α – Amino Acids are
Completely Ionized
The Amino Acids Plays a Role as a Buffer
Amino Acids of Proteins General Properties, Cont
• Substances with this Property are Said to
be “Amphoteric” or “Ampholytes”
Substances?!
• Amphoteric Substances are any Substance
reacting as acid and base: able to react
chemically as either an acid or a base
• The Zwitterionic Character of the α – Amino
Acids Has Been Established by Several
Methods
Amino Acids of Proteins General Properties, Cont
• The Physical Properties of Amino Acids are Characteristic of Ionic Compounds
• Most α – Amino Acids Have Melting Points Nearby 300C
• Nonionic Amino Acids Derivatives Usually Melt Around 100C
• More Soluble in Polar Solvents
• Most α – Amino Acids are Very Soluble in Water
Amino Acids of Proteins
Amino Acids of Proteins
Elimination of Water Molecule
Amino Acids of Proteins
as a Peptide Bond
Amino Acids of Proteins
More Polypeptide Chains
Over 4000 A.A. Residue
• Therefore the molecular Masses of
Polypeptides Range From ~ 4 to over 440
KD
Molecules Can Exist
Consists of a Single Polypeptide Chain of
100 Residue of A.A. Can Form 20 100
Possible Unique Polypeptide Chain of This
Length
Collectively Synthesize an Enormous
Number of Different Protein
Physicochemical Characteristics Stem
the 20 “Standard” Amino Acids
Amino Acids of Proteins
Amino Acids of Proteins
Standard A.A.
from Contact with Water and to Solvate
Hydrophilic Side Chain
there are Three Major Types of A.A.
Amino Acids of Proteins
• Glycine: Was the First A.A. to be Identified
& has the Smallest Possible Side Chain, an
H Atom.
Amino Acids of Proteins
Chain
Conformational Constraints Imposed by
Group
Characterized as Nonpolar Group
Amino Acids of Proteins
Characterized as Nonpolar Group
Amino Acids of Proteins
• Serine & Threonine: Bear Hydroxylic R
Group of Different Sizes
Amino Acids of Proteins
Amino Acids of Proteins
together with Aromatic Groups of
Phenylalanine & Tryptophan Accounts for
Fluorescence Exhibited by Proteins
Amino Acids of Proteins
Make Disulfide Bond with other Cysteine
Molecule, it means that it can Join
Separate Polypeptide Chains or Cross-Link
Two Cysteine in the Same Chain
Amino Acids of Proteins
• Lysine: Has a Butylammonium Side Chain
• Arginine: Has Guanidino Group
Amino Acids of Proteins
= 6.0 Ionizes within the Physiological pH
• As a Consequence, Histidine Side Chain often Participate in the Catalytic Reaction of Enzyme
Amino Acids of Proteins
Chains
Amino Acids of Proteins
Amino Acids of Proteins
Amino Acids of Proteins
• The Three Letter Abbreviation
• The One Letter Symbol
• Often Used when Comparing the A.A. Sequences of Several Similar Proteins
• A.A. in Polypeptides are Named by Dropping the Suffix -ine and Replacing it by -yl
• For example: Alanine Alanyl
Amino Acids of Proteins
Optical Activity
d. Chirality and Biochemistry
• Optically Active Molecules Have an
Asymmetry Such that they are not
Superimposable on their mirror Image
• The Central Atom is Known as Chiral Center
• Molecules that are Nonsupeimposable Mirror
Image are Known as Enantiomers
Optical Activity
• Molecules are Classified as Dextrorotary (Greek: Dextro, right) or Levorotary (Greek: Levo, left)
• This Can be Determined by an Instrument Known as a Polarimeter
• The Quantitative measure of the Optical Activity of the Molecule is Known as it’s Specific Rotation
Observed Rotation
[α] 25
)
d. Chirality and Biochemistry
Glyceraldehyde
The Fisher Convention
• Fischer Projections are Abbreviated Structural Forms that Allow One to Convey Valuable Stereochemical Information to a Chemist without them Having to Draw a 3D Structural Representation of a Molecule
• Horizontal Lines Represent Bonds Coming Out of the Plane of the Paper and Vertical Lines Represent Bonds Going Behind the Plane of the Paper.
Optical Activity
d. Chirality and Biochemistry
The Cahn – Ingold – Prelog System
• Fischer Scheme is Awkward for Molecules with More than One Asymmetric Center
• The Four Groups Surrounding a Chiral Center are Ranked According to a Specific Scheme:
Atoms of Higher Atomic Number Bonded
to a Chiral Center are Ranked Above
those of Lower Atomic Number
Optical Activity
• For Example: the Oxygen of OH Group
Takes Precedence Over the Carbon Atom
of a CH3 Group that is Bonded to the Same
Chiral Center
Functional Groups is:
SH > OH > NH2 > COOH > CHO > CH2OH > C6H5 > CH3 > 2H > 1H
Optical Activity
The Cahn – Ingold – Prelog System
• The Prioritized Groups are Assigned the Letters : W, X, Y, Z
• The Order of Priority Rating is:
W > X > Y > Z
• If the Order of the Groups W X Y is Clockwise, then the Configuration of Asymmetric Center is Designated (S)
• If the Order of the Groups W X Y is Counterclockwise, then the Configuration of Asymmetric Center is Designated (R)
Optical Activity
d. Chirality and Biochemistry
Possessing Asymmetric Centers Almost
• The L Configuration of A.A. is One Example
of this Phenomenon
d. Chirality and Biochemistry
Nonstandard Amino Acids
that Occur in Biological Systems
• Nonstandard A.A. Residue are Often
Important Constituents of Proteins and
Biologically Active Polypeptides
of Proteins
Amino Acid Derivatives in Proteins
• In All Known Cases But One (Section 30- 2D-P: 923), However, These Unusual A.A. Result From The Specific Modification of an A.A. Residue After the Polypeptide Chain Has Been Synthesized
• Famous Modified A.A.:
Nonstandard Amino Acids
Nonstandard Amino Acids. Specialized Roles of Amino Acids
• Nature Tends to Adapt Materials and
Processes that are Already Present to a New
Functions
Mediator of Allergic Reaction:
Histamine (Histidine Decarboxylation Product)
Ornithine
Homocysteine