Chemistry of Amino
Acids and Proteins
© 2013 Pearson Education, Inc.
Learning Objectives
At the end of this class, learners are expected to;
Identifythe structure and naming of amino acids
Explain the classification & properties of amino acids
Describe the process of peptide formation
Enumerate the functions of proteins
Highlight the reactions of amino acids and proteins
What are proteins?
What are the common sources of proteins?
Why are they structurally diverse?
Functions of Proteins
Proteins perform many different functions in the body.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 4
Amino Acids
Amino acids
are the building blocks of proteins.
contain a carboxylic acid group and an amino group on the
alpha () carbon.
are ionized in solution.
There are 20 common amino acids found in human proteins.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 5
Ionization of Amino Acids
At the pH of most bodily fluids, amino acids are ionized.
The carboxylic acid group (−COOH) donates an H+ to the
amino group (−NH2) to give a carboxylate (−COO−) and an
ammonium ions (−NH3+).
The ionized form of amino acids is called a zwitterion.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 6
Classification of Amino Acids
7
© 2013 Pearson Education, Inc. Chapter 19, Section 1 7
1. Amino acids are classified according to their R
groups
© 2013 Pearson Education, Inc. Chapter 19, Section 1 8
Classification of Amino Acids continued…
Nonpolar Polar (neutral)
Amino acids are classified as
nonpolar with hydrocarbon
side chains (hydrophobic).
polar (neutral) with polar side
chains (hydrophilic). Acidic Basic
polar with charged R groups
acidic side chains (negatively
charged) while basic chains
are positively charged.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 9
Nonpolar Amino Acids
A nonpolar amino acid has an R group that is H, an alkyl
group, or aromatic. The R group is always neutral.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 10
Polar (Neutral) Amino Acids
A polar amino acid has an R group that is either an
alcohol, thiol, or amide.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 11
Polar (Acidic) and Polar (Basic)
An amino acid is
acidic with a carboxyl R group (COO–).
basic with an amino R group (NH3+).
© 2013 Pearson Education, Inc. Chapter 19, Section 1 12
2. Classification based on Nutritional
requirement
Essential amino acids Non-Essential amino acids
Arginine Alanine (from pyruvic acid)
Histidine Asparagine (from aspartic acid)
Isoleucine Aspartic Acid (from oxaloacetic acid)
Leucine Cysteine
Lysine Glutamic Acid (from oxoglutaric acid)
Methionine Glutamine (from glutamic acid)
Phenylalanine Glycine (from serine and threonine)
Threonine Proline (from glutamic acid)
Tryptophan Serine (from glucose)
Valine Tyrosine (from phenylalanine)
© 2013 Pearson Education, Inc. Chapter 19, Section 1 13
Amino Acid Stereoisomers:
Fischer Projections of Amino Acids
Amino acids
are chiral except glycine,
which has two H atoms
attached to the alpha carbon
atom.
have Fischer projections that
are stereoisomers.
that are L isomers are used in
proteins.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 14
Amino Acids as Zwitterions
A zwitterion has an equal number of —NH3+ and COO–
groups.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 15
Isoelectric Point (pI)
The isoelectric points (pI)
are the pH at which zwitterions have an overall zero
charge.
of nonpolar and polar (neutral) amino acids exist at pH
values from 5.1 to 6.3.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 16
Zwitterions in Acidic Solutions
In solutions that are more acidic than the pI,
the COO– in the zwitterion accepts a proton.
the amino acid has a positive charge.
Alanine, with a pI of 6.0, has a 1+ charge in solutions
that have a pH below pH 6.0.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 17
Zwitterions in Basic Solutions
In solutions that are more basic than the pI,
the NH3+ in the zwitterion loses a proton.
the amino acid has a negative charge.
Glycine, with a pI of 6.0, has a 1– charge in solutions
that have a pH above pH 6.0.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 18
Summary of pH, pI, and Ionization
© 2013 Pearson Education, Inc. Chapter 19, Section 1 19
Ionized Forms of Polar (Acidic) and
Polar (Basic) Amino Acids
Polar (acidic) and polar (basic) amino acids also ionize the
COO and NH3+ in their polar R groups.
Zwitterions of polar (acidic) amino acids exist at pH values
from 2.8 to 3.2.
Zwitterions of polar (basic) amino acids exist at pH values
from 7.6 to 10.8.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 20
Zwitterions of Aspartic Acid
Aspartic acid, a polar (acidic) amino acid,
has a pI of 2.8.
forms a zwitterion at pH 2.8.
forms negative ions with charges 1– and 2– at pH
values greater than pH 2.8.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 21
Electrophoresis: Separation of
Amino Acids
In electrophoresis, an electric current is used to separate
a mixture of amino acids, and
the positively charged amino acids move toward the
negative electrode.
the negatively charged amino acids move toward the
positive electrode.
an amino acid at its pI does not migrate.
the amino acids are identified as separate bands on the
filter paper or thin layer plate.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 22
Electrophoresis
With an electric current, a mixture of lysine, aspartate,
and valine are separated.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 23
The Peptide Bond
A peptide bond
is an amide bond.
forms between the carboxyl group of one amino acid
and the amino group of the next amino acid.
contains an N (free H3N+) terminal written on the left.
contains a C (free COO–) terminal written on the right.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 24
Formation of a Dipeptide
© 2013 Pearson Education, Inc. Chapter 19, Section 1 25
Naming Dipeptides
A dipeptide is named with
a -yl ending for the N-terminal (free H3N+) amino acid.
the full amino acid name of the free carboxyl group
(COO–) at the C-terminal end.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 26
Guide to Drawing a Peptide
© 2013 Pearson Education, Inc. Chapter 19, Section 1 27
Sample Problem- Drawing a Peptide
Draw the condensed structural formula for the tripeptide Gly-Ser-Met, GSM.
Solution
Analyze the Problem
The name Gly-Ser-Met gives the order of the amino acids. The N-terminal amino acid drawn on the
left is glycine, the middle amino acid is serine, and the C-terminal amino acid drawn on the right is
methionine.
Step 1 Draw the structures for each amino acid in the peptide, starting with the N-terminal amino acid on the left.
© 2013 Pearson Education, Inc. Chapter 19 Section 1 28
Sample Problem- Drawing a Peptide
Continued
Step 2 Remove the O atom from the carboxylate group of the N-terminal amino acid and two
H atoms from the adjacent amino acid. Repeat this process until the
C-terminal amino acid is reached.
© 2013 Pearson Education, Inc. Chapter 19 Section 1 29
Sample Problem- Drawing a Peptide
Continued
Step 3 Connect the remaining parts of the amino acids by forming amide
(peptide) bonds.
Study Guide
Draw the condensed structural formula for the dipeptide Phe-Thr, part of the peptide
glucagon, which increases blood glucose levels.
© 2013 Pearson Education, Inc. Chapter 19 Section 1 30
Primary Structure of Proteins
The primary structure of a protein is
the particular sequence of amino acids.
the backbone of a peptide chain or protein.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 31
Primary Structure of Insulin
Insulin
was the first protein to have its
primary structure determined.
has a primary structure of two
polypeptide chains linked by
disulfide bonds.
has an A chain with 21 amino
acids and a B chain with 30
amino acids.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 32
Secondary Structure: Alpha Helix
The secondary structures of proteins describes the type of
structure that forms when amino acids form hydrogen bonds
within a single polypeptide chain or between polypeptide chains
An alpha helix (α-helix) has
a coiled shape held in place by hydrogen bonds between the
amide groups and the carbonyl groups of the amino acids
along the chain.
hydrogen bonds between the H of an —NH group and the O of
C═O of the fourth amino acid down the chain.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 33
Secondary Structure: Alpha Helix (continued)
© 2013 Pearson Education, Inc. Chapter 19, Section 1 34
Secondary Structure: Beta-Pleated
Sheet
A beta-pleated sheet (β-pleated sheet) is a
secondary structure that
can form between adjacent polypeptide chains or
within the same polypeptide chain when the rigid
structure of the amino acid proline causes a bend in
the polypeptide chain.
has hydrogen bonds between chains.
has R groups above and below the sheet.
is typical of fibrous proteins, such as silk.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 35
Secondary Structure: Beta-Pleated Sheet (continued)
© 2013 Pearson Education, Inc. Chapter 19, Section 1 36
Secondary Structure: Triple Helix
A triple helix
consists of three alpha helix chains
woven together.
contains large amounts of glycine,
proline, hydroxyproline, and
hydroxylysine that contain
–OH groups for hydrogen bonding.
is found in collagen, connective tissue,
skin, tendons, and cartilage.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 37
Tertiary Structure
The tertiary structure of a protein
gives a specific three-dimensional shape to the polypeptide chain.
involves the attractions and repulsions of the R groups of the
amino acids of the peptide chain.
is stabilized by:
1. hydrophobic and hydrophilic interactions,
2. salt bridges,
3. hydrogen bonds, and
4. disulfide bonds.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 38
Tertiary Structure (continued)
The interactions of the
R groups give a
protein its specific
three-dimensional
tertiary structure.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 39
R Group Interactions in
Tertiary Structures
© 2013 Pearson Education, Inc. Chapter 19, Section 1 40
Globular Proteins
Globular proteins Myoglobin
have compact,
spherical shapes.
carry out synthesis,
transport, and
metabolism in the
cells.
such as myoglobin
store and transport
oxygen in muscle.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 41
Fibrous Proteins
Fibrous proteins
consist of long, fiber-like
shapes.
such as alpha keratins make
up hair, wool, skin, and nails.
such as feathers contain
beta keratins with large
amounts of beta-pleated
sheet structures.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 42
Quaternary Structure
The quaternary structure Hemoglobin
is the combination of two or
more polypeptide chains.
is stabilized by the same
interactions found in tertiary
structures.
of hemoglobin consists of
two alpha chains and two
beta chains with heme
groups in each subunit that
pick up oxygen for transport
in the blood to the tissues.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 43
Summary of Protein Structures
© 2013 Pearson Education, Inc. Chapter 19, Section 1 44
Summary of Protein Structures
(continued)
© 2013 Pearson Education, Inc. Chapter 19, Section 1 45
Protein Hydrolysis
Protein hydrolysis
splits the peptide bonds to give smaller peptides
and amino acids.
occurs in the digestion of proteins.
occurs in cells when amino acids are needed to
synthesize new proteins and repair tissues.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 46
Hydrolysis of a Dipeptide
In the lab, the hydrolysis of a peptide requires acid
or base, water, and heat.
In the body, enzymes catalyze the hydrolysis of
proteins.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 47
Denaturation
Denaturation involves
the disruption of bonds in the secondary, tertiary, and quaternary
protein structures.
heat and organic compounds that break apart H bonds and
disrupt hydrophobic interactions.
acids and bases that break H bonds between polar R groups
and disrupt ionic bonds.
heavy metal ions that react with S—S bonds to form solids.
agitation, such as whipping, that stretches peptide chains until
bonds break.
© 2013 Pearson Education, Inc. Chapter 19, Section 1 48
Applications of Protein
Denaturation
© 2013 Pearson Education, Inc. Chapter 19, Section 1 49
Sickle Cell Anemia
A small change in the
sequence of the
primary structure can
have a significant
impact on protein
structure
In sickle cell anemia a
glutamic acid is
replaced by a valine in
the amino acid
sequence
50 50
© 2013 Pearson Education, Inc. Chapter 19, Section 1 50
Ninhydrin Reaction
Triketohydrindene hydrate, commonly known as ninhydrin, reacts
with amino acids to form a purple colored imino derivative, This
derivative forms a useful test for amino acids, most of which are
colorless.
51 51
© 2013 Pearson Education, Inc. Chapter 19, Section 1 51
Protein Tests: Biuret
Biuret reagent is a light blue solution
containing Cu2+ ion in an alkaline
solution.
Biuret turns purple when mixed with a
solution containing protein.
The purple color is formed when copper
ions in the biuret reagent react with the
peptide bonds of the polypeptide chains
to form a complex.
52 52
© 2013 Pearson Education, Inc. Chapter 19, Section 1 52
Xanthroprotic Test
Concentrated Nitric acid will form a yellow complex
with tryptophan and Tyrosine side chains in proteins
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© 2013 Pearson Education, Inc. Chapter 19, Section 1 53
Disulfide Bridge Test
Disulfide bridges will react with Pb2+ ion from lead acetate in an
acidfied solution. A black precipitate indicates the presence of
disulfide-bonded cysteine in proteins.
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