BIOL 3020: Biochemistry and Molecular Biology

Lecture 3

Properties of Amino Acids

 What is an Amino Acid?

The side chain

Side differentiates
R Chain one amino acid
from another

a
H2N C COOH

a-amino group a-carboxyl group

H

Amino derivatives of carboxylic acids

Ionic States of amino acids at physiological pH

Ampholyte
R

+
H23N C COOH

pKa: ~10 pKa: ~2.5

H

Most amino acids exist as zwitterions at

physiological pH
Nearly all amino acids are chiral molecules

Chiral Carbon
R

+ a
H32N C COOH

H
When a carbon atom has four different substituents
attached to it, the carbon is said to be chiral, or a
stereocenter, or an asymmetric carbon.
 The L- or D- form of amino acids

COO- NH3+

Enantiomers

CO R N

Glycine L-alanine
 The L- or D- form of amino acids

COO- NH3+

With hydrogen atom points away from the viewer, if the tracing from the
carboxyl group (COO-) to R group to the amino group (NH3+) is counter-
clockwise (CO R N), the amino acid is in L-form; if it is clockwise, the amino
acid is in D-form

With hydrogen atom points towards the viewer, if the tracing from the
carboxyl group (COO-) to R group to the amino group (NH3+) is counter-
clockwise (CO R N), the amino acid is in D-form; if it is clockwise, the amino
acid is in L-form

L- and D-forms of amino acids are non-superimposable mirror images

 The L/D-form of amino acids in Fischer Projections
Fischer Projections W
A method of depicting structures with tetrahedral carbon
centers
Z X
The bonds to the central carbon are represented by
horizontal and vertical lines from the substituent atoms
to the carbon atom, which is at the center of the cross
Y
Horizontal bonds: project out of the page toward the viewer
Vertical bonds: project behind the page away from the viewer

R COO-

+ +
H3N COO- H NH3

L-amino acid H R D-amino acid

 The L/D-form of amino acids in Fischer Projections
Horizontal bonds: project out of the page toward the viewer
Vertical bonds: project behind the page away from the viewer

R COO-

+ +
H3N COO- H NH3

H R
With H on vertical line (projecting away With H on horizontal line (projecting
from the viewer), if the tracing from COO- toward the viewer), if the tracing from
to R to NH3+ is counter-clockwise, it is in COO- to R to NH3+ is counter-clockwise,
L-form; if the tracing from COO- to R to it is in D-form; if the tracing from COO-
NH3+ is clockwise, it is in D-form to R to NH3+ is clockwise, it is in L-form
R/S-system (aka The Cahn-Ingold-Prelog System)

The four groups surrounding a chiral center are assigned

a priority, based on atomic number
Atoms of higher atomic number bonded to a chiral center are
ranked above those of lower atomic number;
If any of the first substituent atoms are of the same element, the
priority of these groups is established from the atomic numbers
of the second, third, etc., atoms outward from the asymmetric
center.
The lowest-priority substituent, often hydrogen, is
pointed away from the viewer.
S: if the progression from the highest to the lowest
priority is counter-clockwise;
R: if the progress from the highest to the lowest priority is
clockwise.
For almost all amino acids, the L isomer has S
absolute configuration

L-Alanine L-Valine L-Cysteine

S S R
 Types of amino acids in living cells
There are 20 standard amino acids found in
proteins; only L-amino acids are constituents of
proteins.
Over the next few days, learn one for each of
the 20 amino acids!

There are other L-amino acids in living cells

Some as biochemical intermediates
Some with modified R-groups after synthesis
There are also D-amino acids in living cells

Overall, about 300 amino acids occur in living

organisms
 Names of Amino Acids
Alanine Ala A
Only 1 Aa begins with a certain letter Some are phonetically suggestive
C Cys Cysteine F Phe Phenylalanine (Fenylalanine)
H His Histidine R Arg Arginine (aRginine)
I Ile Isoleucine Y Tyr Tyrosine (tYrosine)
M Met Methionine W Trp Tryptophan (double ring in the
S Ser Serine molecule)
V Val Valine
A letter close to the initial is used
More than 1 Aa begins with a certain D Asp Aspatic acid (near A)
letter, that letter is assigned to the
most commonly occurring Aa E Glu Glutamic acid (near G)

A Ala Alanine K Lys Lysine (near L)

G Gly Glycine
Amides
L Leu Leucine
N Asn Asparagine (contains N)
P Pro Proline
Q Gln Glutamine (Q-tamine)
T Thr Threonine Clicker Users: Ready? Set, GO!!
Which of the following amino acids has
NO chiral carbon?

A. Glycine
B. Alanine
C. Proline
D. Serine
Ways of grouping amino acids
Our Textbook splits them into four groups

The hydrophobic (non-polar) ones (9);

The polar ones (6);

The positively charged at physiological pH (3);

The negatively charged at physiological pH (2).

 The non-polar amino acids
g
g
b b g d b
a a a

(imino acid)

Indole

Phenyl
d
g d
b
a
The polar amino acids

Carboxamide
The positively charged amino acids
(at physiological pH)
guanidinium

e
d Imidazole

g
b
a
Histidine can bind or release protons near
physiological pH

Acid Base

pKa 6.5

+
H
 The positively charged amino acids
(at physiological pH)
pKa 10 pKa 12.5

These three are also known as Basic Amino Acids

 The negatively charged amino acids
(at physiological pH)
pKa 4.07
pKa 3.9 g-
carboxyl
b- group
carboxyl
COOH group g
b b
a a

Aspartic acid

These two are also known as Acidic Amino Acids

Polar versus Non-Polar Amino Acids

FAMIL VW PG
Clicker Users: Ready? Set, GO!!
Which of the following are basic amino acids and
carry positive charges at physiological pH?

A. Valine and Leucine

B. Glutamate and Aspartate

C. Cysteine and Methionine

D. Lysine and Arginine

Other notes: there are two amino
acids that contain sulfur
Disulfide bond formed between
two cysteines

Reduction

Oxidation
 Other notes: The Three Aromatics

Phenylketonuria
The side chains of Trp and Tyr absorb lights at 280 nm, which
allows the measurement of protein concentrations using
spectrophotometer

A = elLc

el: the extinction coefficient (or molar absorptivity) at

wavelength for the particular substance being studied.
L is the path length of the cell holder.
c is the concentration of the solution.
Related but Distinct amino acids
 Which of the following is true regarding the
molecule shown here?

A. This molecule is L-aspartate and

its absolute configuration is S
B. This molecule is L-glutamate and
its absolute configuration is S
C. This molecule is L-asparagine and
its absolute configuration is R
D. This molecule is D-aspartate and
its absolute configuration is R
 Specifics for Lecture 3
Identification of chiral centers in amino acids and be able to distinguish L- & D-
form of amino acids; which form is used in the ribosomal synthesis of protein?
A basic understanding of R/S system in determining the absolute configuration
of a chiral center. Are all L-amino acids have S-configuration? If not, why?
Abbreviations (three letter and one letter) of all 20 standard amino acids;
The chemical structures of all 20 standard amino acids: given the structure of
an amino acid, you should be able to recall its name;
Be able to classify an amino acid as non-polar, polar, acidic, or basic;
What are in common among Val, Leu, Ile, and Thr? What are in common
among Ser, Thr, and Tyr? What are in common among Phe, Tyr, and Trp?
Why is it possible to use spectrophotometer to estimate the concentration of
proteins in a solution? What could be a limitation of this method?
The side chains of proline and glycine are classified as non-polar but why are
they often found on the surface of a globular protein?
Better know most of the materials on the slides and on the assigned readings.