Basic Structure of an Amino

Acid
All amino acids found in proteins have this basic structure
(exception of proline) differing only in the structure of the R-group
or the side chain.

The simplest, and smallest, amino acid found in proteins is glycine

for which the R-group is a hydrogen (H).

The carbon atom next to the carbonyl group is called the α–carbon
and amino acids with a side chain bonded to this carbon are
referred to as alpha amino acids.

Amino acids are building blocks of proteins and are intermediates

in metabolism.

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It is important to keep in mind that one of the more important
reasons to understand amino acid structure and properties is to be
able to understand protein structure and properties - because the
chemical properties of the amino acids of proteins determine the
biological activity of the protein. The sequence of amino acid
provides the necessary information to determine how proteins will
fold into three-dimensional structures and the stability of the
resulting structure.

And proteins have important biological functions including:

 Catalyze all (or most) of the reactions in living cells
 Control virtually all-cellular process.

BACK TO AMINO ACIDS

Humans can produce 10 of the 20 amino acids. The others must be

supplied in the food. Failure to obtain enough of even 1 of the 10
essential amino acids, those that we cannot make, results in
degradation of the body's proteins—muscle and so forth—to obtain
the one amino acid that is needed. Unlike fat and starch, the
human body does not store excess amino acids for later use—
the amino acids must be in the food every day.

The 10 non-essential amino acids:

alanine, asparagine, aspartic acid, cysteine, glutamic acid,
glutamine, glycine, proline, serine and tyrosine. Tyrosine is
produced from phenylalanine, so if the diet is deficient in
phenylalanine, tyrosine will be required as well.

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The essential amino acids are arginine (required for the young, but
not for adults), histidine, isoleucine, leucine, lysine, methionine,
phenylalanine, threonine, tryptophan, and valine. These amino
acids are required in the diet. Plants, of course, must be able to
make all the amino acids (although- two of the essential amino
acids, lysine and tryptophan, are poorly represented in most plant
proteins). Thus strict vegetarians should ensure that their diet
contains sufficient amounts of these two amino acids. Humans, on
the other hand, do not have all the enzymes required for the
biosynthesis of all of the amino acids.

Representation of amino acids: Amino acids are

represented by symbols
Name Three-letter symbols and One-letter symbols of amino acids
The Amino Acids
(For each amino acid, both the three-letter and single-letter codes are given. CLICK the
NAME to see the structural formula)
Alanine Ala A hydrophobic
Arginine Arg R free amino group makes it basic and hydrophilic
Asparagine Asn N carbohydrate can be covalently linked ("N-linked) to its -NH
Aspartic acid Asp D free carboxyl group makes it acidic and hydrophilic
Cysteine Cys C oxidation of their sulfhydryl (-SH) groups link 2 Cys (S-S)
Glutamic acid Glu E free carboxyl group makes it acidic and hydrophilic
Glutamine Gln Q moderately hydrophilic
Glycine Gly G so small it is amphiphilic (can exist in any surroundings)
Histidine His H basic and hydrophilic
Isoleucine Ile I hydrophobic
Leucine Leu L hydrophobic
Lysine Lys K strongly basic and hydrophilic
Methionine Met M hydrophobic
Phenylalanine Phe F very hydrophobic
Proline Pro P causes kinks in the chain

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 carbohydrate can be covalently linked ("O-linked") to its
Serine Ser S
-OH
carbohydrate can be covalently linked ("O-linked") to its
Threonine Thr T
-OH
Tryptophan Trp W scarce in most plant proteins
a phosphate or sulfate group can be covalently attached to its
Tyrosine Tyr Y
-OH
Valine Val V hydrophobic

Classification of Amino Acids: according

to side chains
There are a total of 20 amino acids. amino acid can be divided into
4 categories depending on the side chain side chain.

Acidic side chain Asp, Glu

Basic side chain Lys, Arg, His
Ser, Thr, Tyr
Polar, uncharged side chain
Cys, Asn, Gln
Gly, Ala, Val
Non polar side chain Leu, Ile, Phe
Trp, Pro, Met

Assignment: Draw these amino acids

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To form peptides or proteins,the carbonyl (-COOH) group of one
amino-acid reacts with the amino group (-NH2) of a second amino
acid to create an amide group with the liberation of water (H2O)
the following animation illustrate the creation of a dipeptide

Table of α -Amino Acids Found in Proteins

pK1 pK2 pK R
Amino Symb
Structure* (COO (NH2 Grou
Acid ol
H) ) p
Amino Acids with Aliphatic R-Groups

Gly -
Glycine 2.4 9.8
G

Alanine Ala - A 2.4 9.9

Valine Val - V 2.2 9.7

Leu -
Leucine 2.3 9.7
L

Isoleucine Ile - I 2.3 9.8

Non-Aromatic Amino Acids with Hydroxyl R-Groups

Ser -
Serine 2.2 9.2 ~13
S

Threonine Thr - T 2.1 9.1 ~13

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Amino Acids with Sulfur-Containing R-Groups

Cys -
Cysteine 1.9 10.8 8.3
C

Methionine Met-M 2.1 9.3

Acidic Amino Acids and their Amides

Aspartic Asp -
2.0 9.9 3.9
Acid D

Asn -
Asparagine 2.1 8.8
N

Glutamic Glu -
2.1 9.5 4.1
Acid E

Gln -
Glutamine 2.2 9.1
Q

Basic Amino Acids

Arg -
Arginine 1.8 9.0 12.5
R

Lys -
Lysine 2.2 9.2 10.8
K

His -
Histidine 1.8 9.2 6.0
H

Amino Acids with Aromatic Rings

Phenylalan Phe -
2.2 9.2
ine F

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Tyrosine Tyr - Y 2.2 9.1 10.1

Tryptophan Trp-W 2.4 9.4

Imino Acids

Pro -
Proline 2.0 10.6
P

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Protein Structure: Various Levels of Complexity
The molecular structure of a protein is quite complex. However, its
study can be simplified by defining the various levels of structural
organization.

Primary-Secondary-Tertiary-Quaternary Structure

There are four different levels of structures: primary, secondary,

tertiary and quaternary structure.

Primary Structure: The amino acid sequence is the primary

structure. With 20 amino acids and the ability to vary the length of
the polymer means that the possibilities are endless, hence the
great variety of cellular proteins that exist.

Secondary Structure: The polypeptide chain can arrange itself

through interaction among amino acids R chains and hydrogen
bonds. Here, proteins can assume two conformational structures
known as alpha-helix and beta-sheets. These conformations are
possible because of constraints that the amino acid backbone
imposes on the structure.

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Structural features of the Alpha-Helix:
- There are 3.6 amino acids per turn of the helix.
- Each peptide bond is trans and planar
- N-H groups of all peptide bonds point in the same direction,
which is roughly parallel to the axis of the helix
- C=O groups of all peptide bonds point in the opposite direction,
and also parallel to the axis of the helix
- The C=O group of each peptide bond is hydrogen bonded to the
N-H group of the peptide bond four amino acid units away from it
- All R- groups point outward from the helix

Alpha-helix stability is affected by different factors, which include:

Assignment: Describe, with the use of appropriate diagrams,
factors that affect the stability of alpha helix- for next class.

About 1/4th of all amino acid residues in polypeptides are found in

alpha-helices, the exact fraction varying greatly from one protein
to the next

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Beta pleated sheet

This secondary structure has been defined as the secondary level of protein
organization in which the backbone of the peptide chain (Beta-strands) is
extended into a zigzag arrangement resembling a series of pleats, with the
peptide bonds organized in planes of alternating slopes (alternating ascending
and descending direction). The Beta pleated sheet can be formed between two
peptide chains or between different segments of the same peptide chain.

Characteristics of the Beta-pleated sheet include;

1. – Each peptide bond is planar and has the trans conformation

2.- The C=O and N-H groups of peptide bonds from adjacent chains point toward
each other and are in the same plane so that hydrogen bonding is possible
between them
3.- All R- groups on any one chain alternate, first above, then below the plane of
the sheet, etc.

There are two kinds of Beta pleated sheets:

Antiparallel: when the adjacent polypeptide chains run in opposite direction

Parallel: Adjacent polypeptide chains running in the

same direction

Usually the segment of polypeptides that shows a

Beta conformation are called individually beta-
strands, and they are represented by an arrow

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pointing in the direction in which the strand runs
(from the amino to the carboxyl group)

Both models are found in proteins, but the

antiparallel structure is more stable than the parallel
beta-sheet.
Betas conformation content in proteins is very
variable: myoglobin, for example, does not show
this kind of secondary structure, while 45 percent of
the amino acids in chymotrypsin are part of a beta
conformation.

It is important to note that not all the polypeptide

chain is part of an alpha-helix or a beta
conformation. There are also bends, segments
irregularly coiled or forming extended stretches:
Carboxypeptidase, for example, shows 38 % of the
amino acids forming alpha-helix and 27 % forming
beta structures, consequently around 35 % of the
residues are not included in these secondary
structures.

Beta turn
It’s the secondary level of protein organization which
permits the change of direction of the peptide chain
to get a folded structure.

Tertiary Structure: A protein bends and folds according to the

main amino acid chain. These bends and folds determine a three-

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dimensional shape or structure known as the tertiary structure. The
tertiary structure determines the biological function of the
protein(in multi polymeric protein ---see next level of structure---,
it is the quaternary structure that determines function). A protein
must fold into a three dimensional structure for it to function
correctly.

Quaternary Structure: There is one more level of complexity

within the conformation of proteins. Many proteins are formed by
more than one polypeptide chain joined together by covalent
bonds. In this case each polypeptide chain is referred to as a
subunit. The structure formed by the interaction of different
subunits is called the quaternary structure of proteins. In proteins
with more than one subunit it is the quaternary structure that
determines biological function.

The Importance of the Primary Structure

All the structural levels of a protein (secondary, tertiary and

quaternary) are ultimately determined by the primary structure
because all the information needed for the molecule to achieve its
conformation is imprinted within the primary structure. It is this
polypeptide chain (and its components) that determines where the
proteins bend, fold, and where they can link to another polymer
chain.

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