PRT3402- Agricultural Biochemistry
PJJ UPM / UPMET
UNIT 2
Structure and function of amino acids and proteins
Introduction to Unit
In this unit the chemistry and structure of amino acids as the basic
components will be discussed. Amino acids are the monomers for proteins which are
the polymers. However short chains amino acids, known as polypeptides, are
structurally important prelude to the formation of protein sequences and molecules.
Learning Outcomes
At the end of this unit the students will be able to:
1. Recognise the basic structure of amino acids and how its chemistry
affect its function and the function of proteins.
2. Describe the build-up of amino acids as monomers into peptides and
protein structures and its increasing complexity as polymers.
3. Describe the various structure of protein and how they are build-up
from amino acids and peptides
4. Discuss some examples of biologically important proteins and their
functions
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PRT3402- Agricultural Biochemistry
PJJ UPM / UPMET
TOPIC 1 : STRUCTURE OF AMINO ACIDS, PEPTIDES AND POLYPEPTIDES
Main Points
1.1
Amino acids are the monomeric units or building blocks of proteins. About
twenty or so amino acid occur naturally that are arranged sequentially to form
the primary sequence of protein. Proteins are the molecules that carry out
various functions including enzymes, storage, transport, structural polymers,
hormones, mechanical functions amd many other specialized function such as
antibodies.
1.2
The basic structure of an amino acid will have a primary amino group (-NH3+),
a carboxyl group (-COO-), a hydrogen atom and a variable side chain (R
groups) attached to a central α-carbon.
1.3
The central α-carbon atom is covalently linked to the amino group, carboxyl
group, hydrogen and the variable R group. The resulting molecule will have
one positive charge (-NH3+) and a negative charge (-COO-), thus forming a
zwitterions or neutral molecule. The R group side chains vary in sizes,
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PRT3402- Agricultural Biochemistry
PJJ UPM / UPMET
structure and electric charges thus differentiating one amino acid from the
other.
1.4
All the amino acids can be group in any of the following general R groupings
due to the differences in side chains:
a. Non-polar aliphatic – glycine, alanine, valine leucine, isoleucine, proline
and methionine. This group is hydrophobic nature.
b. Polar uncharged – serine, threonine, cysteine, asparagine and glutamine
Polarity of serine and threonine is due to the hydroxyl group, polarity of
cysteine due to the sulfhydrl group and polarity of asparagines and
glutamine is due to the amide group.
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PRT3402- Agricultural Biochemistry
PJJ UPM / UPMET
c. Positively charged (basic and polar) – lysine, arginine and histidine. Lysine
has a second amino group, arginine has a positive guanidido group whilst
histidine has imidazole group. At neutral pH, the side chain of arginine and
lysine are protonated and thus positively charged. Histidine can be
positively charged or uncharged. Thus this group of basic amino acids is
strongly polar and found mainly at the exterior part of proteins where they
can be hydrated by the surrounding aqueous environment.
d. Negatively charged (acidic and polar) – aspartate (aspartic acid) and
glutamate (glutamic acid). Both molecules contain a second carboxyl
group. At neutral pH, the carboxyl groups on the side chains of aspartate
and glutamate are deprotonated and possess a negative charge.
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PRT3402- Agricultural Biochemistry
PJJ UPM / UPMET
e. Aromatic group – phenylalanine, tyrosine, tryptophan. These contain
aromatic R groups, non-polar and hydrophobic. The presence of aromatic
groups renders these amino acids as a strong absorber of near-ultraviolet
region of the light spectrum. This characteristic can be used for analytical
detection by measuring absorption at 280 nm.
1.5
Polar amino acids in which R contains polar hydrophilic groups can form
hydrogen bond with H2O. Whilst non-polar amino acids are those with R
groups containing alkyl hydrophobic molecules that cannot form hydrogen
bonds
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PRT3402- Agricultural Biochemistry
1.6
PJJ UPM / UPMET
The twenty or so naturally occurring amino acids are commonly found in
proteins. They are linked to each other through peptide bond forming peptides
and eventually into proteins. α-carboxyl group of one amino acid (with side
chain R1) forms a covalent
peptide bond with α-amino group of another
amino acid ( with the side chain R2) by removal of a molecule of water. The
result is a dipeptide (i.e. Two amino acids linked by one peptide bond).
1.7
The dipeptide can then forms a second peptide bond with a third amino acid
(with side chain R3) to give tripeptide. Peptides are short polymers of amino
acids which are classified based on the number of amino acids in the
sequence. The classification used are dipeptides made up of two amino acids
molecule, tripeptides have three amino acids, tetrapeptides have four amino
acids and pentapeptides have five amino acids.
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PRT3402- Agricultural Biochemistry
1.8
PJJ UPM / UPMET
Oligopeptides have chain of10-20 amino acids and polypeptides are those
having several dozens of amino acids in a length. When the polypeptides are
strung in a chain of several polypeptides they make up the protein molecules.
Typically peptides are chain with less than 50 amino acids and any
polypeptides with more than 50 amino acids are proteins.
1.9
The order in which amino acids are linked to make a protein - the primary
structure - will determine the chemical characteristics and shape of the
protein. When the amino acids are linked together in proteins, only the sidechain groups and the terminal -amino and -carboxyl groups are free to
ionize.
1.10
Furthermore, proteins evolve over time by changes in their amino acid
sequences. Some changes are called conservative because they maintain the
nature of the side chain (e.g., Asp replacing Glu). Others are called
nonconservative changes because they alter the nature of the side chain
(e.g., Asp replacing Ala).
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PRT3402- Agricultural Biochemistry
PJJ UPM / UPMET
TOPIC 2: STRUCTURE AND TYPES OF PROTEINS
Main Points
2.1
Protein structure starts with a primary structure leading to a more complex
quartenary structure. The primary level of structure in a protein is the linear
sequence of amino acid as joined together by peptide bonds (e.g. –Ala-GluVal-Thr-Asp-Pro-Gly-). The sequence is determined by the sequence of
nucleotide bases in the gene encoding the protein. The precise primary
structure of a protein is determined by inherited genetic information.
2.2
At one end is an amino acid with a free amino group (the N-terminus) and at
the other is an amino acid with a free carboxyl group (the C-terminus). Every
protein has a defined order of amino acids. The primary structure is the
fundamental level of structure where higher organisations are based.
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PRT3402- Agricultural Biochemistry
2.3
PJJ UPM / UPMET
The term "secondary structure" refers to local folding of the backbone of a
linear polymer to form a regular, repeating structure. For a polypeptide, the
secondary structure is determined by the amino acid sequence (i.e., the
primary structure) and the solvent environment in which it is located. The
polypetide chain can arrange itself into two most common types of protein fold
through hydrogen bonding interactions, ionic attractions and repulsions,
hydrophobic interactions, and others between adjacent amino acids
sequence. As a result, the following secondary structure are identified:
a)
-helix (helical) and
b)
-sheet (Pleated segment)
Both -helix and -sheet make up the protein secondary structure.
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PRT3402- Agricultural Biochemistry
2.4
PJJ UPM / UPMET
α-helix is a spiral structure resulting from hydrogen bonding between one
peptide bond and the fourth one. Polypeptide chain is coiled tightly like a
spring forming an alpha helix,
helical structure is right handed and the
backbone of the peptide forms the inner part of the coil whilst the side chains
extend outward of the coil. The helix is stabilized by intramolecular hydrogen
bonds between the N-H of one amino acid and the C=O of another amino
acid.
2.5
β-sheets is another form of secondary structure in which two or more
polypeptides (or segments of the same peptide chain) are linked together by
hydrogen bond between H- of NH- of one chain and carbonyl oxygen of
adjacent chain (or segment). Individual protein chains are aligned side-byside with other protein chain. The protein chains can be in parallel or
antiparallel position - held together by intermolecular hydrogen bonding
between separate chains.
antiparallel beta sheet
2.6
parallel beta sheet
Tertiary protein structure is the manifestation of three dimensional folding of a
protein. The formation of protein's tertiary structure may due to:
a) Weak interactions - hydrogen bonds
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PRT3402- Agricultural Biochemistry
PJJ UPM / UPMET
b) Ionic bonds involving negatively charged and positively charged
amino acid side-chains
c)
Disulfide bonds, covalent linkages formed from two cysteine
residues.
d) Non-Polar hydrophobic interactions. The non-polar groups repel
water and other polar groups resulting in attraction of the non-polar
groups for each other.
2.7
Tertiary structures are seen to be stabilized by interactions between amino
acids that are often far apart and they have little regularity. Because they arise
from folding of secondary structures, which are dependent on the primary
amino acid sequence, tertiary structures are specific for each protein
sequence.
2.8
Quartenary structure consists of two or more polypeptide chains of tertiary
structure, each referred as subunit of protein. They are held together by noncovalent interaction like H-bonds, ionic, disulphide bonds or hydrophobic
interactions. Examples of protein having quaternary structure include:
•
Insulin - two polypeptide chains (dimeric)
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PRT3402- Agricultural Biochemistry
•
PJJ UPM / UPMET
Collagen - fibrous protein of three polypeptides (trimeric) that are
supercoiled like a rope.
•
2.9
Hemoglobin - globular protein with four polypeptide chains (tetrameric)
The following diagram showed the successive structural complexity of
proteins made up from its basic building block of amino acids.
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PRT3402- Agricultural Biochemistry
2.10
PJJ UPM / UPMET
According to shape and solubility, three classes of protein are identified:
1) Fibrous protein (e.g. Collagen)
- Simple, regular linear structure
- Structural role in cells
- insoluble in water or dilute salt
2) Globular protein (e.g Myoglobin)
- Spherical in shape
- polypeptide chain compactly folded
- Hydrophobic amino acids chain – interior
- Hydrophilic chain – exterior
- Soluble to aqueous solution
3) Membrane protein
- Found in membrane system of cells
- Have hydrophobic amino acids outward
- Insoluble in aqueous solution
2.11
Myoglobin is oxygen binding protein in the muscle tissue. It stores oxygen and
facilitate oxygen diffusion in muscle tissue. Haemoglobin is found in red blood
cells and its role is to transport oxygen from lung to other parts of tissue. It is
clear from the diagram below that both molecules are built on similar motif.
The multiple subunit structure of hemoglobin gives it important oxygen binding
properties that are different than myoglobin's, consistent with hemoglobin's
role in oxygen transport.
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PRT3402- Agricultural Biochemistry
2.12
PJJ UPM / UPMET
High orders of Protein structure. A functional protein is not just a polypeptide
chain, but one or more polypeptides precisely twisted, folded and coiled into a
molecule of unique shape (conformation). This conformation is essential for
some protein function e.g. it enables a protein to recognize and bind
specifically to another molecule e.g. hormone/receptor; enzyme/substrate and
antibody/antigen.
2.13
Notwithstanding the basic structure of Proteins made from amino acids, it can
also joined and can contain other non-acid amino molecules. Some examples
of other chemical groups include
1) Glycoprotein – protein containing carbohydrate, component of extracellular
matrix that surround cells of most tissue in animal
2) Lipoprotein - protein containing lipid- function to transport lipids to the sites
of synthesis
3) Nucleoprotein - protein joined with nucleic acids -storage and transmission
of genetic materials
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