MCB 208 (Introductory microbial physiology)

Structure, functions and synthesis of Proteins

 The term protein originated from the greek word proteios meaning first or prime. It is one
of the major classes of biologically important macromolecules and generally believed to
be the most predominant organic molecules in living systems. Proteins possess the
greatest structural diversity as reflected in their wide range of biological functions. It is
however essential to examine the general structure of proteins inorder to understand their
properties and functions. Proteins can be very large molecules, with molecular weights of
tens or even hundreds of thousands and the five elements found in most naturally
occurring proteins are carbon, hydrogen, oxygen, nitrogen and sulphur. However, other
elements may be essential components of certain specialised proteins such as
haemoglobin (iron) and casein (phosphorus). whatever the size, and in spite of their
diversity, all proteins are made up of a collection of ‘building blocks or monomers called
amino acids which are joined together. These amino acids are thought to have been
among the first organic molecules formed in the early history of the Earth, and many
different types exist in nature. Amino acids are organic molecules that, when linked
together with other amino acids, form a protein. Amino acids are essential to life because
the proteins they form are involved in virtually all cell functions. Some
proteins function as enzymes, some as antibodies, while others provide structural support.
Amino acids exist in 20 different naturally occurring forms and various combinations of
these amino acids account for the nearly infinite variety of proteins. Typically, amino
acids have a basic skeleton consisting of a central carbon atom (called the α carbon)
which is covalently bonded to an amino group (NH 2), a carboxyl group (COOH), a
hydrogen atom (H), and a variable R group. The variations among the amino acids occur
at the R group, which is different in each amino acid and in large part determines the
unique characteristics of the molecule and finally the proteins that contain it. Based on
the variable group, amino acids can be classified into four categories: nonpolar, polar,
negatively charged, and positively charged.
The 20 amino acids found in proteins can be conveniently divided into three or sometimes five
groups, on the basis of the chemical nature of their ‘R’-group, i. e. on the basis of a
polar/nonpolar nature and on the presence or absence of an ionisable ‘R’-group (In solution, the
amino and carboxyl groups become ionised, giving rise to a zwitterion, a molecule with spatially
separated positive and negative charges). Amino acids, when grouped into 3, consist of : the non
polar, polar and electrically charged amino acids. When grouped into 5, there are: Simple,
aliphatic, Polar uncharged, Charged and Aromatic - Sulphur containing amino acids.

In solution,the amino and carboxyl groups become

Figure 1: Back bone of a typical amino acid molecule

Fig. 3: The 2nd and 3rd group of polar and electrically charged ones.
 Positive Negative

Fig 4 : The amino acids as grouped into 5 categories

Proteins, are made up of amino acids joined together by means of peptide bonds, between the –
NH2 group of one amino acid and the –COOH group of another. The formation of a peptide
bond is a form of condensation reaction in which water is lost. The resulting structure of two
linked amino acids is called a dipeptide, having an amino group (–NH2) at one end and a
carboxyl group (–COOH) at the other, referred to as the N terminus and the C terminus. This is
called a dipeptide. Short chains of amino acids which are called peptides and can be dipeptide,
tripeptide and tetrapeptide. A polypeptide contains an unspecified number of amino acids but
usually has more than 20. A protein is the largest of this class of compounds and usually contains
a minimum of 50 amino acids. . Note that usually peptides are known to be compounds
containing peptide bonds, although, the terms polypeptide and protein are often used
interchangeably, though not all polypeptides are large enough to be considered proteins. During
the formation of a peptide bond, Since a water molecule is lost , we refer to the chain so formed
as being composed of amino acid residues, rather than amino acids. This process involved in the
formation of proteins with the loss of water molecule is termed a dehydration synthesis.
Peptide bond formation through a dehydration synthesis

Levels of organization of proteins (levels of protein stucture)

Proteins are so varied and diverse and this is due to the fact that they do not function only as
straight chains like their formation suggest, rather they possess a natural tendency to assume
complex structures and organizational pattern. On this account, proteins have been classified to
have : Primary, secondary, tertiary and quartenary structures. These organizational structures
helps in the understanding of how proteins assume their final shapes. In turn, the shape of a
protein is very vital to its function.

Primary structure
The primary structure of a protein is the fundamental chain of the amino acid residues which is
determined by the order, type and number of the linking amino acids. The primary structure is
the simplest level of protein structure and the basis for the other levels of structure. ultimately it
determines the properties of a particular protein. It is this quality that gives rise to the unlimited
diversity in protein forms and functions. Simply put, the primary structure is the sequence of
amino acids in a particular polypeptide chain.
A tetrapeptide chain formation

Secondary structure
A polypeptide does not remain in its primary state, but instead, it spontaneously arranges itself
into higher levels of complexity. The structure of proteins is more complicated than just a linear
chain of amino acids. Usually a long thin chain would be a very fragile structure, hence proteins
that have undergone folding are more stable and compact. The results of this folding are the
higher levels of protein structures. The secondary structure arises from hydrogen bonding
occurring between a carbonyl (–CO) group and an amido (–NH) group of amino acid residues on
the peptide backbone, which may be on the same or different chains. However, the ‘R’-group
plays no part in secondary protein structure. Two regular patterns of folding result from this
bonding; the α-helix and the β-pleated sheet. The α-helix occurs when hydrogen bonding takes
place between amino acids close together in the primary structure. A stable helix is formed by
the –NH group of an amino acid bonding to the –CO group of the amino acid four residues
further along the chain. This pattern of bonding causes the polypeptide chain to twist into a
characteristic helical shape that resembles a curled ribbon. In the β-pleated sheet the hydrogen
bonding occurs between amino acids usually on one or more separate polypeptide chains lined
up next to each other. This results in a sheet-like structure held together by hydrogen bonds
between the carbonyl group of one amino acid residue and the amido group of another on the
backbone of the chains without involving the R groups. Many proteins contain both types of
structure i.e. α-helix and the β-pleated sheet, although some contain just one type of secondary
structure.
Tertiary structure
This is the overall three dimensional structure of a polypeptide. This structure is primarily due to
interactions between the R groups of amino acid residues that make up a protein. This is due to
interactions between side chains i.e R-groups of amino acid residues, resulting in the folding of
the molecule into a 3-Dimensional protein called the native state. Such bonds in the tertiary
structure are a variety of weak, non-covalent bonds such as hydrogen bonds, ionic bonding,
hydrophobic interactions. For instance in the ionic bonding, R groups with like charges repel one
another while those with opposite charges can form an ionic bond. Similarly, amino acids with
nonpolar hydrophobic R groups cluster together on the inside of the protein leaving hydrophilic
amino acids on the outside to interact with surrounding water molecules. These various bonds
occur between the alpha helix and the beta pleated sheets. However, in addition to these bonds
are covalent disulphide bonds which occur between the –SH groups (sulphur-containing side
chains) on separate cysteine residues to form a strong covalent –S-S linkage (i.e. Disulphide
bonds). This is known as a disulphide bridge and may bring together two cysteine residues that
are far apart. These bonds confer a high degree of stability on the overall protein structure. This
level of structure determines the arrangement of the –R groups in terms of their polarities. Non-
polar residues occur on the inside away from the aqueous phase while charged polar residues are
located on the outside in contact with water. Two types of shapes can be attained in this level of
structure; globular and fibrous. In many cases, this level of structure completes the functional
state of a protein.

Quaternary structure

Many proteins are made up of a single polypeptide chain and thus assume only three levels of
structure. However, some proteins are made up of multiple polypeptide chains which come
together to form its quaternary structure. Examples of such types of protein are, hemoglobin and
DNA. In this level two or more polypeptides interact based on weak forces like those of the
tertiary structure to form a large multiunit protein. The polypeptides in this structure can be the
same or different. The interactions formed in this level are the result of weak bonds between the
R- groups of amino acid residues on separate chains. The most important outcome of this
bonding is that each different type of protein develops its own unique shape which in turn
determines its interaction with other molecules that complement or fits its particular surface
feature. Such degree of specificity provide the functional activity required for different cellular
activities. These proteins are the basis of enzymes which serve as catalysts for all chemical
reactions in the cell, of which nearly every reaction requires a different enzyme. In this level of
structure, some complex proteins may have additional non amino acid components, such as
sugars in the case of glycoproteins, lipids in lipoproteins, or some may contain inorganic
components such as: phosphoproteins, metalloproteins. These components which form an
integral part of the protein structure are known as prosthetic group.

Functions of Proteins

Proteins constitute more than 50% of the dry weight of cells and a typical bacterial cell contains
enormous kinds of proteins at any one time. Of all the cellular macromolecules, they are the most
versatile. Some of their functions include the following:

Protein is termed the building block of living systems. It is called this because it is vital in the
development, maintenance and repair of several cellular organelles and organs. Energy Protein is
a major source of energy. When there is excess protein than needed in the cell, it is converted for
use in the form of energy. If it is not needed due to sufficient intake of other energy sources such
as carbohydrates, the protein will be used to create fat and becomes part of fat cells.

Hormones
Protein is involved in the creation of some hormones. These substances act as chemical
messengers which aid communication between cells, tissues and organs thus helping to control
body functions. Insulin, a small protein, is an example of a hormone that regulates blood sugar. It
involves the interaction of organs such as the pancreas and the liver. Secretin, is another example
of a protein hormone. This substance assists in the digestive process by stimulating the pancreas
and the intestine to create necessary digestive juices.
Enzymes
Enzymes are proteins that increase the rate of chemical reactions in the cell. In fact, most of the
necessary chemical reactions in a cell would not efficiently proceed without enzymes. For
example, some type of enzymes function in aiding digestion of large protein, carbohydrate and
fat molecules into smaller ones, while some assists in the synthesis of DNA. Protein is a major
element in transportation of certain molecules. For example, hemoglobin is a protein that
transports oxygen throughout the body. Protein is also sometimes used to store certain
molecules. Ferritin is an example of a protein that combines with iron for storage in the liver.

Antibodies
Protein forms antibodies which are complex glycoproteins that help prevent infections, illnesses
and diseases. These proteins have specific regions (surface) which identify bacteria, viruses and
other microorganisms and hence attach to them, thereby destroying these antigens. They often
work in conjunction with the other immune systems in cells for instance they surround antigens
in order to keep them contained until they can be destroyed by white blood cells.

Structure: Some Proteins are fibrous and provide cells and tissues with rigidity. For instance,
collagen is the most abundant protein in the human body forming the structural protein of bones,
tendons, ligaments and skin.
Transport and storage: proteins are involved in the transport of molecules across cell
membranes and within the bloodstream. Haemoglobin which carries oxygen in the blood and
ferritin which stores iron are examples of transport and stprage proteins respectively.
Movement: motor proteins such as actin and myosin are involved in musle contraction and
cellular movement.
Regulation of gene expression: some proteins bind to DNA and regulate the transcription of
genes. Transcription factors are key examples of such regulatory proteins.
Virulence proteins: Some pathogenic organisms such as bacteria, fungi, viruses and parasites
produce virulence proteins which play various roles in their ability to invade, survive and
multiply within the host. Examples inCludes adhesin, a surface protein that allows bacteria to
stick to host. Invasin is another example which helps bacteria penetrate host cell membrane.
Some pathogenic organisms also produce virulence proteins which functions as toxins, examples
are the diphthteria, butulism and cholera toxins that interfare with cellular processes and cause
diseases.
Proteins are necessary for growth and maintenance of body tissues
Proteins are in membranes where they act as receptors to receive stimuli from the environment,
they also participate in membrane transport.
Proteins maintain proper pH by regulating the concentration of acids and bases in the blood and
other bodily fluids.

NUCLEIC ACIDS
Nucleic acids are the molecules that store and transmit information in cells. Originally they were
isolated from the cell nucleus and there after found in some other parts of nucleated cells, in cells
without nuclei as well as in viruses. There are two types of nucleic acids: deoxyribonucleic acid
(DNA) and ribonucleic acid (RNA). These two nucleic acids are polymers of repeating subunits
called nucleotides, each of which comprises of three smaller units (A nitrogen base, Ribose sugar
and a Phosphate molecule). Nucleotides play a crucial role in cells as they are the precursors of
Nucleic acid. Biosynthesis simply is that part of metabolism called anabolism i.e. building up.

One of the parts that make up a nucleotide is the nitrogen bases which can either be purine or
pyrimidines. These bases are first synthesized before their addition to the other parts of the
nucleotide.
To form nucleic acid chains, the nucleotide subunits are joined by a covalent bond called a
phosphodiester bond between the phosphate of one nucleotide and the sugar of the adjacent
nucleotide. Thus, the phosphate is a bridge that joins the number 3 carbon atom (termed 3 prime
and written 3’) of one sugar to the number 5 carbon atom (termed 5 prime and written 5’) of the
other. This results in a molecule with a backbone of alternating sugar and phosphate molecules,
with two different ends. The 5’end has a phosphate molecule attached to the sugar; the 3’end has
a hydroxyl group. The formation of these bonds in long chains of several nucleotides produces
nucleic acids.

DNA
A DNA molecule consists of two long strands of nucleotides wrapped around each other to form
a double helix. The double helix looks like a twisted ladder, and each strand is composed of
many nucleotides. Every strand of DNA composing the double helix has a “backbone” consisting
of alternating deoxyribose sugar and phosphate groups. The deoxyribose of one nucleotide is
joined to the phosphate group of the next. The nitrogen-containing bases make up the steps of the
ladder. Note that the purine A is always paired with the pyrimidine T and that the purine G is
always paired with the pyrimidine C. The bases are held together by hydrogen bonds; A and T
are held by two hydrogen bonds, and G and C by three. DNA does not contain uracil (U). The
order in which the nitrogen base pairs occur along the backbone is extremely specific and in fact
contains the genetic instructions for the organism. Nucleotides form genes, and a single DNA
molecule may contain thousands of genes. Genes determine all hereditary traits, and they control
all the activities that take place within cells. One very important consequence of nitrogen-
containing base pairing is that if the sequence of bases of one strand is known, then the sequence
of the other strand is also known. For example, if one strand has the sequence . . . ATGC . . . ,
then the other strand has the sequence . . . TACG . . . . Because the sequence of bases of one
strand is determined by the sequence of bases of the other, the bases are said to be
complementary.

RNA
RNA, the second principal kind of nucleic acid, which is synthesized in the nucleus but mainly
found in the cytoplasm and nucleolus. RNA is involved in decoding the information in the DNA
into a sequence of amino acids in proteins. It differs from DNA in several respects. Whereas
DNA is double-stranded, RNA is usually single-stranded, considerably shorter and exists as a
single chain of nucleotides. Thus there is lack of base equivalence in RNA. Although single-
stranded, it may form short, double-stranded stretches only when parts of the polynucleotide
chain have anti parallel complementary segments and can fold back upon themselves. The five-
carbon sugar in the RNA nucleotide is ribose, which has one more oxygen atom than
deoxyribose. Also, one of RNA’s bases is uracil (U) instead of thymine. The other three bases
(A, G, C) are the same as DNA. Three major kinds of RNA have been identified in cells. They
are messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). Each type
of RNA has a specific role in protein synthesis.