Amino Acids

&
Proteins
Dr. Riris Istighfari Jenie, M.Si., Apt
riris_jenie@ugm.ac.id

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 Outline
•  1: Amino Acids: Building Blocks of Proteins
•  2: Acid-Base Chemistry of Amino Acids
•  3: Optical Activity and Stereochemistry of
Amino Acids
•  4: Spectroscopic Properties of Amino Acids
•  5: Protein Structure

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•  Proteins are linear copolymers built from
monomeric units called amino acids.
•  Twenty amino acids are commonly found in
proteins.
•  These amino acids contain a variety of different
functional groups:
–  Alcohols (R-OH)
–  Phenols (Ph-OH)
–  Carboxylic acids (R-COOH)
–  Thiols (R-SH)
–  Amines (R-NH2)
–  and others…

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•  Protein function depends on both
–  amino acid content, and
–  amino acid sequence.
•  Protein fold into diverse shapes such as
–  spherical
–  elipsoidal
–  long strands, etc.
•  All information for 3-D structure is
contained in the linear sequence of amino
acids.

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Structure of Proteins

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Amino Acids Can Join Via Peptide Bonds

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•  To understand protein function, we must
first understand the nature of amino acids.
•  Amino acids are essentially α-amino acids:
alpha carbon (IUPAC #2 position)

H2N – C – COOH
|
R
•  When R is not H, the alpha carbon
is asymetric, giving rise to isomers.

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Properties of Amino Acids
•  High melting points, over 200°C
•  More soluble in water than in ether.
•  Larger dipole moments than simple
acids or simple amines.
•  Less acidic than most carboxylic acids,
less basic than most amines.
O
+ _
pKa = 10
H3N CH C O pKb = 12
R
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Amino Acid Ionization, pKas
Each of the 20 common α-amino acids has two
pKa values, for the carboxyl group and the
amino group attached to the α-carbon.

+NH -CH -COOH < === > +NH -CH -COO- + H+

3 2 3 2

+NH -CH -COO- < === > NH -CH -COO- + H+

3 2 2 2

Seven of the 20 have an ionizable sidechain

and therefore have a third pKa value.

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 Proton Is Adsorbed or Desorbed

Proton： abundant and small, affects the charge of a

molecule
lone pair High pKa Low
electrons H+

H+
Amino
N H N H
H H

Low pKa High

O H O
Carboxylic
C O
C O
H+

Ampholyte contains both positive and negative groups on its molecule

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 2-Acid Base Amino Acid
Amino Acid Ionization

•  Carboxylic acids are traditional Bronsted-Lowery

acids, donating a proton in aqueous solution.
•  The pKa for carboxylic acids is normally around
2 to 5. That is, the pH at which these acids are
50% ionized:

R-COOH à R-COO- + H+

pH= [less than 2] à [above 5]

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•  Amino groups function as bases,
accepting a proton.
•  The pKa for amino groups is usually
around 9 – 10. Again, at the pKa these
groups are 50% ionized:

R-NH3+ à R-NH2 + H+

pH= [below 9] à [above 10]

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•  Even though both acids and amines are present in the
same molecule, they mostly behave as though they were
separate entities:

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•  Summary:
At low pH, proton concentration [H+]is high.
Therefore, both amines and carboxylic
acids are protonated. (-NH3+ & -COOH)
At high pH, proton concentration is low.
Therefore, both amines and carboxylic
acids are deprotonated. (-NH2 & -COO-)
At neutral pH, amines are protonated(-NH3+)
and carboxylates are deprotonated(-COO-)

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 Zwitterion
•  Amino acid exists as a dipolar ion.
•  -COOH loses H+, -NH2 gains H+.

•  Actual structure depends on pH.

•  “Zwitter” Ions:
•  Ions bearing two charges were named
zwitter ions by German scientists; the
name still applies today, especially for
amino acids at neutral pH:

+H -
3N – CH2 – COO

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Acid-Base Properties of Amino Acids
Draw the following chemical structures for glycine:
(Non-existent form:) H2N – CH2 - COOH

pH=1:

pH=7:

pH=12:

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Acid-Base Properties of Amino Acids
Draw the following chemical structures for glycine:
(Non-existent form:) H2N – CH2 - COOH

pH=1: +H
3N – CH2 - COOH

pH=7:

pH=12:

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Acid-Base Properties of Amino Acids
Draw the following chemical structures for glycine:
(Non-existent form:) H2N – CH2 - COOH

pH=1: +H
3N – CH2 - COOH

pH=7: +H
3 N – CH 2 – COO-

pH=12:

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Acid-Base Properties of Amino Acids
Draw the following chemical structures for glycine:
(Non-existent form:) H2N – CH2 - COOH

pH=1: +H
3N – CH2 - COOH

pH=7: +H
3 N – CH 2 – COO-

pH=12: H2N – CH2 – COO-

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Low pH Neutral pH High pH

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Structure and pH

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 Isoelectric Point

•  pH at which amino acids exist as the

zwitterion (neutral).
•  Depends on structure of the side chain.
•  Acidic amino acids, isoelectric pH ~3.
•  Basic amino acids, isoelectric pH ~9.
•  Neutral amino acids, isoelectric pH is
slightly acidic, 5-6.
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Amino acids: (Aliphatic)

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•  Amino acid Proline
(The only secondary (2°) amino acid or (“imino”
acid.)

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•  Amino acids (Aromatic)

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•  Amino acids (Alcohols)

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•  Amino acids (Sulfur)

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•  Amino acids (Acids and related amides)

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•  Amino acids (Basic)

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•  Histidine (Acid/Base Activity)

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Essential Amino Acids:
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine a
Threonine
Tryptophan a
Valine
Arginine b
Histidine b
a Aromatic b Probably essential

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 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

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 Mirror Images of Amino Acid

α

Mirror
image
α

Same chemical properties

Stereo isomers
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Only L-amino acids are constituents of proteins.

“L” and “D” isomeric nomenclature is similar to

the “R” and “S” utilized in modern organic
chemistry.
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 D, L Assignments
The convention for making D, L assignments is
to draw a Fischer projection with the
carboxyl at the top and the R at the bottom.

+NH to the left = L to the right = D

3

COO H COO H
+
NH3 H H NH 3+
CH 2-OH CH 2-OH

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41
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 Spectroscopic Properties
•  All amino acids absorb in infrared region
•  Only Phe, Tyr, and Trp absorb UV
•  Absorbance at 280 nm is a good
diagnostic device for amino acids
•  NMR spectra are characteristic of each
residue in a protein, and high resolution
NMR measurements can be used to
elucidate three-dimensional structures
of proteins
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 Reaction with Ninhydrin

•  Used to visualize spots or bands of amino

acids separated by chromatography or
electrophoresis.
•  Deep purple color formed with traces of
any amino acid.
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•  Amino acids are polymerized via amide or
“peptide” bonds:

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 Structure of Peptide
•  The peptide bond is an amide bond.
•  Amides are very stable and neutral.

=>
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 Peptide Bond Formation

•  The amino group of one molecule condenses

with the acid group of another.
•  Polypeptides usually have molecular weight
less than 5000.
•  Protein molecular weight 6000-40,000,000.
=>
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 Formation of Peptide Bonds by Dehydration

Amino acids are connected head to tail

NH2
1 COOH NH2
2 COOH

Carbodiimide Dehydration
-H2O
O

NH2
1 C N

H
2 COOH
 Peptide Bond Is Rigid and Planar

C H
C N
O C
 Fig 5.18 Making a polypeptide chain

Ser Phe Cys

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 Fig 5.18 Making a polypeptide chain

R
groups

Ser Phe Cys

linear “chain” or “array” of amino acids

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•  Copolymer of amino acids:
– a “polypeptide”

Definition:
Amino acid polymers of ≤50 amino acids are called
“polypeptides, peptides, oligopeptides, etc.”
Amino acids polymer of >50 amino acids are called “proteins.”
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•  An example of a “dipeptide” is the sweetener
Aspartame.
•  Other names include:
–  NutraSweet
–  Equal
–  Tri-Sweet
–  Sanecta
•  IUPAC Name:
“N-L- α – Aspartyl-L-phenylalanine 1-methyl ester”

Abbreviated Structure:
Asp – Phe - OCH3

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•  Cross links between peptide chains:
–  Disulfide linkages between individual
“cysteines” are called “cystines:”

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•  Insulin is the smallest protein, with 51
amino acids in two chains linked by
cystine (disulfide) cross links:

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•  Peptide bonds have partial double bond
character due to resonance that limits
rotation about this bond:

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59
 Classification
of Proteins
•  Simple: hydrolyze to amino acids only.
•  Conjugated: bonded to a nonprotein
group, such as sugar, nucleic acid, or
lipid.
•  Fibrous: long, stringy filaments, insoluble
in water, function as structure.
•  Globular: folded into spherical shape,
function as enzymes, hormones, or
transport proteins.
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 Levels of Protein Structure

•  Primary: the linear sequence of the amino acids

in the chain and the disulfide links.
•  Secondary: structure formed by hydrogen
bonding. Examples are α-helix and pleated
sheet.
•  Tertiary: complete 3-D conformation, overall
shape of proteins.
•  Quaternary: association of two or more peptide
chains to form protein, interaction between
proteins
Protein Structure:

•  Twisting about various bonds in the

polypeptide backbone gives proteins a
variety of shapes.

•  Bond angles give rise to secondary

structures. Then, localized secondary
structures help drive the peptide folding
that gives rise to tertiary structure.

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•  Overall structure depends upon:
–  number of amino acids (length of protein)
–  specific composition of amino acids
(number of amino acids of each type)

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 Primary Structure (1o)
The sequence of amino acids (N-term to C-term)
in a peptide or protein is its primary structure.

A pentapeptide

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 Primary Structure

•  Unique sequence of amino acids

•  Linear arrangement of amino acids

Met-Lys-Val-Phe-Gly-Arg-Cys-Glu-Leu-Ala...

amino terminus carboxyl terminus

N-terminus C-terminus

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 Primary structure of a
protein: Lysozyme

• 129 amino acids in length

• with 20 amino acids, many

possible proteins with a
length of 129 amino acids

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 Fig 5.21 Normal vs. Sickle-cell Hemoglobin

* *
Glu Val
acidic nonpolar
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 Secondary Structure (2o)
•  Certain segments of amino acid sequence
take on a regular structure or folded
pattern
– Alpha helix
– Beta pleated sheet
Both of these secondary protein structures are
stabilized by hydrogen bonding between the
carbonyl oxygen atoms and the nitrogen atoms of
amino acids in the protein chain.

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 Secondary structure of a protein
Lysozyme
See p82

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Secondary structure: α-helix
 Alpha Helix
Each carbonyl oxygen can hydrogen bond
with an N-H hydrogen on the next turn of the
coil.

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Secondary structure: β-pleated sheet

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 Pleated Sheet
Each carbonyl oxygen hydrogen bonds
with an N-H hydrogen on an adjacent
peptide chain.

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Summary of Structure

=>
 Tertiary Structure (3o)

•  Overall 3-D shape of the entire

polypeptide
–  Held together by various bonds and
interactions
•  Hydrogen bonds
•  Ionic bonds
•  Disulfide bridges (two Cysteines)
•  Hydrophobic interactions (including van
der Walls interactions)
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 Fig 5.22 Examples of bonds/interactions
contributing to the tertiary structure of a protein

two cysteine side chains

See
p83

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Fig 5.19 3D structure of lysozyme

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Tertiary (3°) Structure the Protein Myoglobin
Water-soluble proteins fold into compact structures with non-polar cores.

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•  In the case of myoglobin and many other
proteins, the majority of hydrophobic amino
acids (yellow) are found inside in structure:

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•  The Cro protein of Lambda bacteriophage
is a dimer of identical subunits:

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•  Hemoglobin is a protein tetramer,
containing two identical pairs of subunits:

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 Quarternary Structure (4o)

•  Applies only to proteins consisting of more

than one polypeptide chain (or subunit)
•  Refers to the arrangement of the subunits
relative to each other

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 The four levels of protein structure
see p82-83
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 Quaternary structure of proteins

4 subunits of a
Hemoglobin
tetrameric protein Collagen
triple helix α and β chains
with heme
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