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BTBC209IU Biochemistry 1: International University

The document outlines key concepts about amino acids and biochemistry. It discusses the 20 common amino acids, including their structures, properties, and 3- and 1- letter codes. It also covers acid-base properties, including pKa values and titration curves. Additional topics include rare amino acids, reactions of amino acids, stereochemistry, and spectroscopic properties. The document is a class outline for biochemistry that provides essential information about amino acid structures and characteristics.

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LinhNguye
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56 views36 pages

BTBC209IU Biochemistry 1: International University

The document outlines key concepts about amino acids and biochemistry. It discusses the 20 common amino acids, including their structures, properties, and 3- and 1- letter codes. It also covers acid-base properties, including pKa values and titration curves. Additional topics include rare amino acids, reactions of amino acids, stereochemistry, and spectroscopic properties. The document is a class outline for biochemistry that provides essential information about amino acid structures and characteristics.

Uploaded by

LinhNguye
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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VIETNAMATIONAL UNIVERSITY HCMC

INTERNATIONAL UNIVERSITY

BTBC209IU
Biochemistry 1

Nguyen Kim Truc (PhD)


Office: A1.705
Email: [email protected]
AY 2019-2020, semester 2
Class outline

• Take attendance by typing full name and ID


• Midterm online: week 20/4/2020 – 25/4/2020
• Lecture
Amino acids _ Protein
Biomolecules
Structures and properties of amino acids

• Amino acids contain a central tetrahedral carbon atom


• There are 20 common amino acids
• Amino acids can join via peptide bonds
• Rarely, several other amino acids occur in proteins
• Some amino acids are not found in proteins
Structures and properties of amino acids

chiral carbon

Anatomy of an amino acid. Except for proline and its derivatives,


all of the amino acids commonly found in proteins possess this
type of structure.

proline
Structures and properties of amino acids

amino group

Two amino acids can carboxylic group

react with loss of a water


molecule to form a
covalent bond. The bond
joining the two amino
acids is called a peptide
bond.
The 20 Common Amino Acids

You should know names, structures, pKa values, 3-letter


and 1-letter codes

• Nonpolar amino acids


• Polar, uncharged amino acids
• Acidic amino acids
• Basic amino acids
The 20 Common Amino Acids

Some of the nonpolar (hydrophobic) amino acids.


The 20 Common Amino Acids

Some of the nonpolar (hydrophobic) amino acids.


The 20 Common Amino Acids

Some of the polar, uncharged amino acids


The 20 Common Amino Acids

Some of the polar, uncharged amino acids


The 20 Common Amino Acids

The acidic amino acids


The 20 Common Amino Acids

The basic amino acids


Several amino acids occur rarely in proteins

• Selenocysteine in many
organisms
• Pyrrolysine in several
archaeal species

Common ancestor of all life


Several amino acids occur rarely in proteins

• Hydroxylysine and hydroxyproline are found in connective-tissue proteins


(collagen)
• Carboxy-glutamate is found in blood-clotting proteins
• Pyroglutamate is found in bacteriorhodopsin
Several amino acids occur rarely in proteins

OH group : ( polar ) provide active site for rxn to occur

Phosphorylated amino acids

• Phosphorylated amino acids – play important and well-


characterized roles in signaling pathways and metabolism
Several Amino Acids Do Not Occur in Proteins,
But Play Other Roles in Nature

behavior

take it, side effect is sleepy

Several amino acid derivatives that act as neurotransmitters and hormones.


Acid-base properties of amino acids

the COOH is deprotonated 1st fully deprotonated


deprotonted : loose H

neutral

protonated : up take H

fully deprotonated

The ionic forms of the amino acids, shown without consideration of any
ionizations on the side chain.
Acid-base properties of amino acids

• Amino Acids are Weak Polyprotic Acids


• The degree of dissociation depends on the pH of the medium
• For amino acids which do not have a dissociable side chain,
the first dissociation is that of the alpha-carboxyl group:
• H2A+ + H2O → HA0 + H3O+
diproton (H2)

[HA 0 ][H 3O + ]
K a1 =
[H 2 A + ]

The ionic forms of the amino acids, shown without consideration


of any ionizations on the side chain.
Acid-base properties of amino acids

For amino acids which do not have a dissociable side chain, the
second dissociation is that of the alpha-amino group:
HA0 + H2O → A− + H3O+

− +
[A ][H3O ]
Ka 2 = 0
[HA ]
pKa Values of the Amino Acids

You should know these numbers and know what they mean

• Alpha carboxyl group: pKa = 2


• Alpha amino group: pKa = 9
• These numbers are approximate, but entirely suitable for our
purposes.
Acid-Base Properties of Amino Acids

the point at which the net charge of molecule is 0


Acid-Base Properties of Amino Acids
pKa Values of the Amino Acids

You should know the pK values for these R groups and what
they mean

Arginine, Arg, R: pKa(guanidino group) = 12.5


Aspartic Acid, Asp, D: pKa (β−carboxyl) = 3.9
Cysteine, Cys, C: pKa (sulfhydryl) = 8.3
Glutamic Acid, Glu, E: pKa (γ−carboxyl) = 4.3
Histidine, His, H: pKa (imidazole) = 6.0
Titrations of polyprotic amino acids
Alpha-carboxyl: has pKa smaller -> more acidic property -> lose proton faster

More acidic due to inductive effect


with N
If increasing the pH -> the
alpha carboxyl tend to
deprotonate first

y-carboxyl: bigger pKa -> less acid

titration curve

Alpha carboxyl: pKa =2


y-carboxyl : pKa= 4.3
Alpha amino: pKa =9

Titration of glutamic acid


Titrations of polyprotic amino acids

Titration of lysine
Reactions of Amino Acids

(a) Edman’s reagent (phenylisothiocyanate) reacts with the N-


terminal amino acid of a peptide or protein to form a cyclic
thiazoline derivative that reacts in weak aqueous acid to yield a
PTH-amino acid.
Reactions of Amino Acids

(b) Cysteine residues react with each other to form disulfides. This
reaction is an oxidation-reduction reaction.
Stereochemistry of Amino Acids

• All but glycine are chiral


• L-amino acids predominate in nature
• D,L-nomenclature is based on D- and L-glyceraldehyde
• R,S-nomenclature system is superior, since amino acids like
isoleucine and threonine (with two chiral centers) can be named
unambiguously
Stereochemistry of Amino Acids
Stereochemistry of Amino Acids
Rules for description of chiral centers in the
(R,S) system

Naming a chiral center in the (R,S) system is accomplished by


viewing the molecule from the chiral center to the atom with the
lowest priority. The priorities of the functional groups are:
SH > OH > NH2 > COOH > CHO > CH2OH > CH3
Spectroscopic Properties

• All amino acids absorb at infrared wavelengths


• Only Phe, Tyr, and Trp absorb UV
• Absorbance at 280 nm is a good diagnostic test for amino acids
• NMR spectra are characteristic for each residue in a protein,
and high resolution NMR measurements can be used to
elucidate three-dimensional structures of proteins
Spectroscopic Properties

The UV spectra
of the aromatic
amino acids at
pH 6
Q&A

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