ASPECTS OF MOLECULAR BIOLOGY & BIOINFORMATICS RELEVANCE IN INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
In recent times giant strides have been taken in harnessing our knowledge of the
molecular basis of many biological phenomena. Many new techniques such as the
polymerase chain reaction (PCR) and DNA sequencing have arrived on the scene. In
addition major projects involving many countries such as the human genome project
have taken place. Coupled with all these exciting technological developments, new
vocabulary such as genomics has arisen. All this has transformed the approaches used
in industrial microbiology. New approaches anchored on developments in molecular
biology have been followed in many industrial microbiology processes and products
such as vaccines, the search for new antibiotics, and the physiology of microorganisms.
It therefore now appears imperative that any discussion of industrial microbiology and
biotechnology must take these developments into account. This section will discuss only
selected aspects of molecular biology in order to provide a background for understanding
some of the newer directions of industrial microbiology and biotechnology. The
discussion will be kept as simplified and as brief as possible, just enough in complexity
and length needed to achieve the purpose of this content. The student is encouraged to
look at many excellent texts in this field.
Protein Synthesis:
Proteins are very important in the metabolism of living things. They are in hormones for
transporting messages around the body; they are used as storage such as in the whites of
eggs of birds and reptiles and in seeds; they transport oxygen in the form of hemoglobin;
they are involved in contractile arrangements which enable movement of various body
parts, in contractile proteins in muscles; they protect the animal body in the form of
antibodies; they are in membranes where they act as receptors, participate in membrane
transport and antigens and they form toxins such as diphtheria and botulism. The most
important function if it can be so termed is that form the basis of enzymes which catalyze
all the metabolic activities of living things; in short proteins and the enzymes formed from
them are the major engines of life.
In spite of the incredible diversity of living things, varying from bacteria to protozoa to
algae to maize to man, the same 20 amino acids are found in all living things. On account
of this, the principles affecting proteins and their structure and synthesis are same in all
living things.
The genetic macromolecules (i.e. the macromolecules intimately linked to heredity) are
deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The genetic information
which determines the potential properties of a living thing is carried in the DNA present
in the nucleus, except in some viruses where it is carried in RNA. DNA is also present in
the organelles mitochondria and chloroplasts. (Just an interesting fact about mitochondrial
DNA. Individuals inherit the other kinds of genes and DNA from both parents jointly.
However, eggs destroy the mitochondria of the sperm that fertilize them. On account of
this, the mitochondrial DNA of an individual comes exclusively from the mother. Due to
the unique matrilineal transmission of mitochondrial DNA, data from mitochondrial
DNA sequences is used in the study of genelogy and sometimes for forensic purposes).
DNA consists of four nucleotides, adenine, cytosine, guanine and thymine. RNA is
very similar except that uracil replaces thymine . RNA occurs in the nucleus and in the cytoplasm as well as in the ribosomes.
The processes of protein synthesis will be summarized briefly below. In protein
synthesis, information flow is from DNA to RNA via the process of transcription, and
thence to protein via translation. Transcription is the making of an RNA molecule from a
DNA template. Translation is the construction of a polypeptide from an amino acid sequence of RNA
molecule(for more details on molecular biology search on main page of this blog). The only exception to this is in retroviruses where reverse transcription occurs and where a single-stranded DNA is transcribed from
a single-stranded RNA (the reverse of transcription); it is used by retroviruses, which
includes the HIV/AIDS virus, as well as in biotechnology.
Transcription
An enzyme, RNA polymerase, opens the part of the DNA to be transcribed. Only one
strand of DNA, the template or sense strand, is transcribed into RNA. The other strand,the anti-sense strand is not transcribed. The anti-sense strand is used in making ripe
tomatoes to remain hard. The RNA transcribed from the DNA is the messenger or mRNA.
As some students appear to be confused by the various types of RNA, it is
important that we mention at this stage that there are two other types of RNA besides
mRNA. These are ribosomal or rRNA and transfer or tRNA; they will be discussed later
in this chapter. At this stage it is suffice to mention that in the analogy of a building,
messenger RNA, mRNA is the blueprint or plan for construction of a protein (building);
ribosomal RNA rRNA the construction site (plot of land) where the protein is made,
while transfer RNA, tRNA, is the vehicle delivering the proper amino acid (building
blocks) to the (building) site at the right time. When mRNA is formed, it leaves the nucleus in eukaryotes (there is no nucleus in prokaryotes!) and moves to the ribosomes.
Translation
In all cells, ribosomes are the organelles where proteins are synthesized. They consist of
two-thirds of ribosomal RNA, rRNA, and one-third protein. Ribosomes consist of two
sub-units, a smaller sub-unit and a larger sub-unit. In prokaryotes, typified by E. coli, the
smaller unit is 30S and larger 50S. Sis Svedberg units, the unit of weights determined
from ultra centrifuge readings. The 30S unit has 16S rRNA and 21 different proteins. The
50S sub-unit consists of 5S and 23S rRNA and 34 different proteins. The smaller sub-unit
has a binding site for the mRNA. The larger sub-unit has two binding sites for tRNA.
The messenger RNA (mRNA) is the‘blueprint’ for protein synthesis and is transcribed
from one strand of the DNA of the gene; it is translated at the ribosome into a polypeptide
sequence. Translation is the synthesis of protein from amino acids on a template of
messenger RNA in association with a ribosome. The bases on mRNA code for amino
acids in triplets or codons; that is three bases code for an amino acid. Sometimes different
triplet bases may code for the same amino acid. Thus the amino acid glycine is coded for
by four different codons: GGU, GGC, GGA, and GGG. However, a codon usually codes
for one amino acid. There are 64 different codons; three of these UAA, UAG, and UGA are
stop codons and stop the process of translation. The remaining 61 code for the amino
acids in proteins. (Table 3.1). Translation of the message generally begins at AUG, which
also codes for methionine. For AUG to act as a start codon it must be preceded by a
ribosome binding site. If that is not the case it simply codes for methionine.
Promoters are sequences of DNA that are the start signals for the transcription of
mRNA. Terminators are the stop signals. mRNA molecules are long (500-10,000 nucleotides).
Ribosomes are the sites of translation. The ribosomes move along the mRNA and bring
together the amino acids for joining into proteins by enzymes.
Transfer RNAs (tRNAs) carry amino acids to mRNA for linking and elongation into
proteins. Transfer RNA is basically cloverleaf-shaped. (see Fig. 3.2) tRNA carries the
proper amino acid to the ribosome when the codons call for them. At the top of the large
loop are three bases, the anticodon, which is the complement of the codon. There are 61
different tRNAs, each having a different binding site for the amino acid and a different
anticodon. For the codon UUU, the complementary anticodon is AAA. Amino acid
linkage to the proper tRNA is controlled by the aminoacyl-tRNA synthetases. Energy for
binding the amino acid to tRNA comes from ATP conversion to adenosine
monophosphate (AMP).
Elongation terminates when the ribosome reaches a stop codon, which does not code
for an amino acid and hence not recognized by tRNA.
After protein has been synthesized, the primary protein chain undergoes folding:
secondary, tertiary and quadruple folding occurs. The folding exposes chemical groups
which confer their peculiar properties to the protein.
Protein folding(to give a three-dimensional structure) is the process by which a protein
assumes its functional shape or conformation. All protein molecules are simple
unbranched chains of amino acids, but it is by coiling into a specific three-dimensional
shape that they are able to perform their biological function. The three-dimensional
shape (3D) conformation of a protein is of utmost importance in determining the
properties and functions of the protein. Depending on how a protein is folded different
functional groups may be exposed and these exposed group influence its properties.
The reverse of the folding process is protein denaturation, whereby a native protein is
caused to lose its functional conformation, and become an amorphous, and nonfunctional amino acid chain. Denatured proteins may lose their solubility, and
precipitate, becoming insoluble solids. In some cases, denaturation is reversible, and
proteins may refold. In many other cases, however, denaturation is irreversible.
Denaturation occurs when a protein is subjected to unfavorable conditions, such as
unfavorable temperature or pH. Many proteins fold spontaneously during or after their
synthesis inside cells, but the folding depends on the characteristics of their surrounding
solution, including the identity of the primary solvent (either water or lipid inside the
cells), the concentration of salts, the temperature, and molecular chaperones. Incorrect
folding sometimes occurs and is responsible for prion related illness such as Creutzfeldt Jakob disease and Bovine spongiform encephalopathy (mad cow disease), and amyloid
related illnesses such as Alzheimer’s Disease. When enzyme molecules are misfolded
they will not function.
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Cited By Kamal Singh Khadka
Msc Microbiology, TU
Assistant Professor in Pokhara University, Pokhara Bigyan Tatha Prabidhi Campus, NA, PNC, LA.
Pokhara, Nepal.
Suggested Readings:
molecular basis of many biological phenomena. Many new techniques such as the
polymerase chain reaction (PCR) and DNA sequencing have arrived on the scene. In
addition major projects involving many countries such as the human genome project
have taken place. Coupled with all these exciting technological developments, new
vocabulary such as genomics has arisen. All this has transformed the approaches used
in industrial microbiology. New approaches anchored on developments in molecular
biology have been followed in many industrial microbiology processes and products
such as vaccines, the search for new antibiotics, and the physiology of microorganisms.
It therefore now appears imperative that any discussion of industrial microbiology and
biotechnology must take these developments into account. This section will discuss only
selected aspects of molecular biology in order to provide a background for understanding
some of the newer directions of industrial microbiology and biotechnology. The
discussion will be kept as simplified and as brief as possible, just enough in complexity
and length needed to achieve the purpose of this content. The student is encouraged to
look at many excellent texts in this field.
Protein Synthesis:
Proteins are very important in the metabolism of living things. They are in hormones for
transporting messages around the body; they are used as storage such as in the whites of
eggs of birds and reptiles and in seeds; they transport oxygen in the form of hemoglobin;
they are involved in contractile arrangements which enable movement of various body
parts, in contractile proteins in muscles; they protect the animal body in the form of
antibodies; they are in membranes where they act as receptors, participate in membrane
transport and antigens and they form toxins such as diphtheria and botulism. The most
important function if it can be so termed is that form the basis of enzymes which catalyze
all the metabolic activities of living things; in short proteins and the enzymes formed from
them are the major engines of life.
In spite of the incredible diversity of living things, varying from bacteria to protozoa to
algae to maize to man, the same 20 amino acids are found in all living things. On account
of this, the principles affecting proteins and their structure and synthesis are same in all
living things.
The genetic macromolecules (i.e. the macromolecules intimately linked to heredity) are
deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The genetic information
which determines the potential properties of a living thing is carried in the DNA present
in the nucleus, except in some viruses where it is carried in RNA. DNA is also present in
the organelles mitochondria and chloroplasts. (Just an interesting fact about mitochondrial
DNA. Individuals inherit the other kinds of genes and DNA from both parents jointly.
However, eggs destroy the mitochondria of the sperm that fertilize them. On account of
this, the mitochondrial DNA of an individual comes exclusively from the mother. Due to
the unique matrilineal transmission of mitochondrial DNA, data from mitochondrial
DNA sequences is used in the study of genelogy and sometimes for forensic purposes).
DNA consists of four nucleotides, adenine, cytosine, guanine and thymine. RNA is
very similar except that uracil replaces thymine . RNA occurs in the nucleus and in the cytoplasm as well as in the ribosomes.
The processes of protein synthesis will be summarized briefly below. In protein
synthesis, information flow is from DNA to RNA via the process of transcription, and
thence to protein via translation. Transcription is the making of an RNA molecule from a
DNA template. Translation is the construction of a polypeptide from an amino acid sequence of RNA
molecule(for more details on molecular biology search on main page of this blog). The only exception to this is in retroviruses where reverse transcription occurs and where a single-stranded DNA is transcribed from
a single-stranded RNA (the reverse of transcription); it is used by retroviruses, which
includes the HIV/AIDS virus, as well as in biotechnology.
Transcription
An enzyme, RNA polymerase, opens the part of the DNA to be transcribed. Only one
strand of DNA, the template or sense strand, is transcribed into RNA. The other strand,the anti-sense strand is not transcribed. The anti-sense strand is used in making ripe
tomatoes to remain hard. The RNA transcribed from the DNA is the messenger or mRNA.
As some students appear to be confused by the various types of RNA, it is
important that we mention at this stage that there are two other types of RNA besides
mRNA. These are ribosomal or rRNA and transfer or tRNA; they will be discussed later
in this chapter. At this stage it is suffice to mention that in the analogy of a building,
messenger RNA, mRNA is the blueprint or plan for construction of a protein (building);
ribosomal RNA rRNA the construction site (plot of land) where the protein is made,
while transfer RNA, tRNA, is the vehicle delivering the proper amino acid (building
blocks) to the (building) site at the right time. When mRNA is formed, it leaves the nucleus in eukaryotes (there is no nucleus in prokaryotes!) and moves to the ribosomes.
Translation
In all cells, ribosomes are the organelles where proteins are synthesized. They consist of
two-thirds of ribosomal RNA, rRNA, and one-third protein. Ribosomes consist of two
sub-units, a smaller sub-unit and a larger sub-unit. In prokaryotes, typified by E. coli, the
smaller unit is 30S and larger 50S. Sis Svedberg units, the unit of weights determined
from ultra centrifuge readings. The 30S unit has 16S rRNA and 21 different proteins. The
50S sub-unit consists of 5S and 23S rRNA and 34 different proteins. The smaller sub-unit
has a binding site for the mRNA. The larger sub-unit has two binding sites for tRNA.
The messenger RNA (mRNA) is the‘blueprint’ for protein synthesis and is transcribed
from one strand of the DNA of the gene; it is translated at the ribosome into a polypeptide
sequence. Translation is the synthesis of protein from amino acids on a template of
messenger RNA in association with a ribosome. The bases on mRNA code for amino
acids in triplets or codons; that is three bases code for an amino acid. Sometimes different
triplet bases may code for the same amino acid. Thus the amino acid glycine is coded for
by four different codons: GGU, GGC, GGA, and GGG. However, a codon usually codes
for one amino acid. There are 64 different codons; three of these UAA, UAG, and UGA are
stop codons and stop the process of translation. The remaining 61 code for the amino
acids in proteins. (Table 3.1). Translation of the message generally begins at AUG, which
also codes for methionine. For AUG to act as a start codon it must be preceded by a
ribosome binding site. If that is not the case it simply codes for methionine.
Promoters are sequences of DNA that are the start signals for the transcription of
mRNA. Terminators are the stop signals. mRNA molecules are long (500-10,000 nucleotides).
Ribosomes are the sites of translation. The ribosomes move along the mRNA and bring
together the amino acids for joining into proteins by enzymes.
Transfer RNAs (tRNAs) carry amino acids to mRNA for linking and elongation into
proteins. Transfer RNA is basically cloverleaf-shaped. (see Fig. 3.2) tRNA carries the
proper amino acid to the ribosome when the codons call for them. At the top of the large
loop are three bases, the anticodon, which is the complement of the codon. There are 61
different tRNAs, each having a different binding site for the amino acid and a different
anticodon. For the codon UUU, the complementary anticodon is AAA. Amino acid
linkage to the proper tRNA is controlled by the aminoacyl-tRNA synthetases. Energy for
binding the amino acid to tRNA comes from ATP conversion to adenosine
monophosphate (AMP).
Elongation terminates when the ribosome reaches a stop codon, which does not code
for an amino acid and hence not recognized by tRNA.
After protein has been synthesized, the primary protein chain undergoes folding:
secondary, tertiary and quadruple folding occurs. The folding exposes chemical groups
which confer their peculiar properties to the protein.
Protein folding(to give a three-dimensional structure) is the process by which a protein
assumes its functional shape or conformation. All protein molecules are simple
unbranched chains of amino acids, but it is by coiling into a specific three-dimensional
shape that they are able to perform their biological function. The three-dimensional
shape (3D) conformation of a protein is of utmost importance in determining the
properties and functions of the protein. Depending on how a protein is folded different
functional groups may be exposed and these exposed group influence its properties.
The reverse of the folding process is protein denaturation, whereby a native protein is
caused to lose its functional conformation, and become an amorphous, and nonfunctional amino acid chain. Denatured proteins may lose their solubility, and
precipitate, becoming insoluble solids. In some cases, denaturation is reversible, and
proteins may refold. In many other cases, however, denaturation is irreversible.
Denaturation occurs when a protein is subjected to unfavorable conditions, such as
unfavorable temperature or pH. Many proteins fold spontaneously during or after their
synthesis inside cells, but the folding depends on the characteristics of their surrounding
solution, including the identity of the primary solvent (either water or lipid inside the
cells), the concentration of salts, the temperature, and molecular chaperones. Incorrect
folding sometimes occurs and is responsible for prion related illness such as Creutzfeldt Jakob disease and Bovine spongiform encephalopathy (mad cow disease), and amyloid
related illnesses such as Alzheimer’s Disease. When enzyme molecules are misfolded
they will not function.
Cited By Kamal Singh Khadka
Msc Microbiology, TU
Assistant Professor in Pokhara University, Pokhara Bigyan Tatha Prabidhi Campus, NA, PNC, LA.
Pokhara, Nepal.
Suggested Readings:
www.cenicana.org/investigacion/seica/imagenes.../modern_indutrial.pdf
www.crcpress.com › Life Science › Developmental Biology
www.microbiology-journal.com/
do.rulitru.ru/docs/4/3296/conv_1/file1.pdf
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