BIOL 157: BIOLOGICAL

CHEMISTRY

J. K. Dadson, PhD

Department of Biochemistry and Biotechnology,

Office: SCB, RM B5
jaydadson1990@gmail.com
Chemistry of Amino
Acids and Proteins
Study Objectives
• This lecture will give an overview of;

Different functions of proteins

Monomeric units of proteins

The classification of amino acids

Formation of peptides and polypeptides

Various levels of organization of proteins

General reactions undergone by amino acids

Denaturation and its significance

 Introduction
• Proteins are the most versatile macromolecules in living systems and serve
crucial functions in essentially all biological processes.

• They have several functions

• Catalytic action
• Protection
• Transport
• Energy formers and trappers
• Structural • Movement
• Storage • Buffers
• Hormonal • Toxins

• They are the most abundant cellular components, taking part in numerous
processes.
• Several key properties enable proteins to participate in such a wide range of
functions;

1. Proteins are linear polymers built of monomer units called amino acids.
• The construction of a vast array of macromolecules from a limited number of
monomer building blocks is a recurring theme in biochemistry. Does protein
function depend on the linear sequence of amino acids?

• The function of a protein is directly dependent on its three-dimensional

structure. Remarkably, proteins spontaneously fold up into three-dimensional
structures that are determined by the sequence of amino acids in the protein
polymer.

• Thus, proteins are the embodiment of the transition from the one-dimensional
world of sequences to the three-dimensional world of molecules capable of
diverse activities.
2. Proteins contain a wide range of functional groups.
• These functional groups include alcohols, thiols, thioethers, carboxylic acids,
carboxamides, and a variety of basic groups.

• When combined in various sequences, this array of functional groups accounts

for the broad spectrum of protein function.

• For instance, the chemical reactivity associated with these groups is essential to
the function of enzymes, the proteins that catalyse specific chemical reactions in
biological systems.
3. Proteins can interact with one another and with other biological
macromolecules to form complex assemblies.

• The proteins within these assemblies can act synergistically to generate capabilities
not afforded by the individual component proteins.

• These assemblies include macro-molecular machines that carry out the accurate
replication of DNA, the transmission of signals within cells, and many other essential
processes.
4. Some proteins are quite rigid, whereas others display limited flexibility.
• Rigid units can function as structural elements in the cytoskeleton (the
internal scaffolding within cells) or in connective tissue.

• Parts of proteins with limited flexibility may act as hinges, springs, and levers
that are crucial to protein function. They may also play a role in the
transmission of information within and between cells.
Amino
Acids
• The complete hydrolysis of proteins by enzymes or acids or bases yield
monomeric units called α-amino acids.

• The general formula of an alpha α-amino acid can be shown as;

• Amino acids contain a central tetrahedral alpha (α) carbon (C α), which is
covalently bonded to COOH, NH2, H and R groups.

• R group, refereed to as the side chain, represents a specific chemical

group.

• The nature of the R determines the types of amino acids. R differs in

chemical nature, size, electric charge and solubility in water.

• In neutral solution (pH 7), the carboxyl group exists as –COO - and the
amino group as -NH3+.
• Because the resulting amino acid contains one positive and one negative
charge, it is a neutral molecule called a zwitterion.

• Amino acids are also chiral molecules. With four different groups attached to
it, the α-carbon is said to be asymmetric.

• The two possible configurations for the α-carbon constitute non-identical mirror
image isomers or enantiomers
 Common Amino
Acids
• There are 20 amino acids commonly found in proteins.
• All the amino acids except proline have both free α-amino and free α-carboxyl
groups.

• There are several ways to classify the common amino acids.

• The most useful of these classifications is based on the nature of the side
chains. This gives us the following categories:
• nonpolar or hydrophobic amino acids
• neutral (uncharged) but polar amino acids
• acidic amino acids (which have a net negative charge at pH 7.0)
• basic amino acids (which have a net positive charge at neutral pH).
 Nonpolar Amino Acids
• These include all the amino acids with alkyl
chain (aliphatic and aromatic R groups)

• Alanine, Valine, Leucine, and Isoleucine

• As well as proline (with its unusual cyclic
structure)
• Methionine (one of the two sulphur-
containing amino acids)
• The two aromatic amino acids,
Phenylalanine and Tryptophan

• Tryptophan is considered a borderline

member in this group
Polar, Uncharged Amino Acids
• The polar, uncharged amino acids (except for glycine) contain R groups that are
more soluble in water than the nonpolar amino acids.

• Glycine’s solubility properties are mainly influenced by its polar amino and
carboxyl groups, and thus glycine (free molecule) is best considered a member
of the polar, uncharged group

• Tyrosine displays the lowest solubility in water of the 20 common amino acids
(0.453 g/L at 25°C).

• Alanine and valine are about as soluble as arginine and serine.

• The amide groups of asparagine and glutamine; the hydroxyl groups of
tyrosine, threonine, and serine; and the sulphydryl group of cysteine are all
good hydrogen bond–forming moieties.

• Tyrosine has significant nonpolar characteristics due to its aromatic ring and
could arguably be placed in the nonpolar group.

• However, with a pKa of 10.1, tyrosine’s phenolic hydroxyl is a charged, polar

entity at high pH.
Tyrosine??
Acidic Amino Acids
• There are two acidic amino acids—aspartic acid and glutamic acid—whose R
groups contain a carboxyl group.

• These side chain carboxyl groups are weaker acids than the α-COOH group, but
are sufficiently acidic to exist as –COO- at neutral pH.

• Aspartic acid and glutamic acid thus have a net negative charge at pH 7. These
negatively charged amino acids play several important roles in proteins
• Many proteins that bind metal ions for structural or functional purposes
possess metal binding sites containing one or more aspartate and glutamate
side chains.

• Carboxyl groups may also act as nucleophiles in certain enzyme reactions and
may participate in a variety of electrostatic bonding interactions

Glutamate Aspartate
 Basic Amino Acids
• Three of the common amino acids have side chains with net positive charges at
neutral pH: histidine, arginine, and lysine.

• The ionized group of histidine is an imidazolium, that of arginine is a guanidinium,

and lysine contains a protonated alkyl amino group.

• The side chains of the latter two amino acids are fully protonated at pH 7. With a
pKa near neutrality. Histidine side chains play important roles as proton donors
and acceptors in many enzyme reactions. Histidine-containing peptides are
important biological buffers.

• Arginine and lysine side chains, which are protonated under physiological
conditions, participate in electrostatic interactions in proteins.
Histidine Lysine Arginine
J. K. Dadson 23