[Q3(A) Discuss the regulation and expression of gene in prokaryotes with example of the operon models

of gene activity. Illustrate the different levels of gene regulation and control.]

 Gene expression and regulation in prokaryotes

genes are the sequences on the DNA that control all life activity of an Organism
whether prokaryotic or eukaryotic. These genes show their activity by forming
certain products as proteins which interact with the environment and Organism
changes its behaviour accordingly as environment changes by producing different
proteins, through processes like transcription and translation. These systems are
highly regulated systems.
In case of prokaryotic cells like bacteria they undergo sudden environment changes
so they need to control and regulate the expression of genes according to their need
and environment. For example, different food sources. To understand the gene
expression and their regulation in prokaryotes we will discuss operon models of
gene activity.

 operon model
operon system is an integrated system of more genes whose accumulative
expression is dependent on the single promotor operator region of DNA sequence.
This is an on and off switch system. If promoter region is on then the expression of
all genes clustered ahead of promoter region Will occur and if the switch is off that
is promoter region is of, no expression of genes will occur. This is a very
interesting system of gene expression in prokaryotes.

[Lumenlearning.com]
the mechanism of operons was described by Jacob and Monod in Paris. So an
operon system consists of structural genes whose transcription will produce
products and promoter region where polymerase will bind and start transcription
And an operator. We will take example of Lac operon model to understand gene
expression and their regulation In prokaryotes.

 Lac operon system

in Lac operon system the cluster of genes placed under a promoter will produce
enzymes required to break lactose in the cell. Lac operon Is an inducible operon.
The primary source of food for any cell is glucose for energy, same is the case in
prokaryotes. But when there is no or little glucose and high lactose prokaryotes
will take lactose and break it and use energy that is Lac operon system is turned on.
Bacteria need to break this lactose into sugar so they need enzymes and these
enzymes will come from the transcription of genes in Lac operon. So, Lac operon
depends upon the presence of lactose in environment.
 Structure of Lac operon
Lac operon consists of one promoter region, operator region and downstream these
promoter-operator are present 3 genes that is lac z, lac y and lac a. Lac z gene code
for beta galactosidase which perform the catalytic activity. That is breakdown of
lactose into sugar for energy uses. Lac y and lac a produce permease and acetylases
which help in the uptake of lactose from the environment.

[Microbenotes.com]
  Expression of lac operon
There is a mechanism underlying this. First, we consider what if there is no lactose
in environment. Actually upstream that Lac promoter region Is present Lac I gene.
When there is no lactose the Lac I gene code for an inhibitor or repressor protein
which binds to the operator region and does not allow polymerase to transcript the
genes and this is necessary because no lactose means cell does not need beta
galactosidase for breakdown because there is no lactose . so, with inhibitor on the
promoter as default, promoter region will be shut off.
But when lactose is present then this lactose will stimulate the cell for its uptake by
binding to the inhibitor on the Lac promoter. This lactose will convert into its
allosteric from that is L allolactose will bind to the inhibitor and changes its
configuration which caused the inhibitor to be shed off from the promoter region.
The promoter region is now on and it can transcribe genes into Messenger RNA
and finally into its enzymes that is beta galactosidase permease and acetylase
which will uptake the lactose and break it for energy. That's how lactose present
affects Lac operon system and genes are expressed. We can see that the basic
control is at transcriptional level.
 Regulation of Lac operon
regulation of expression of Lac operon means that there are a system of
mechanisms underlying the expression of Lac operon. we will examine this
mechanism by considering the presence of glucose. We know that glucose is the
primary food source for any cell even if other food sources like lectors is present in
the environment. Cell will uptake glucose. In the prokaryotic cells there are present
cAMPs whose concentration depends upon the glucose in the environment. There
is an inverse relation between glucose and cAMPs. There is also a catalytic
activation Protein[cap] Site at the Lac operon region. Actually, when there is no
glucose but lactose then lactose uptake will be preferred. For this simply, the
cAMPs concentration will rise in absence of glucose and it bind to the cap Site and
Lac promoter region And transcription of genes occur that is they will express and
produces beta galactosidase for lactose catabolism. this is a positive control that is
increase in cAMPs will give a positive sign To the Lake operon for the production
of Messenger RNA which will produce enzymes . So when increase in one thing
increase the other thing it is called positive control. but if both glucose and lactose
are present in the environment cell will definitely uptake glucose not the lactose. In
this scenario concentration of cAMPs will decrease , no cAMPs -cap complex is
formed and no promotion of lac promoter and no expression of genes occur even
though lactose is present. That's how glucose concentration controls the expression
of Lac operon.

[Wikipedia.com]

Tryptophan operon
Tryptophan operon contains coding genes involved in the formation of proteins, which are
used to tryptophan metabolism.
 It consist of 5 genes involved in tryptophan synthesis
 These genes expressed as single strand of mRNA template.
 Trp repressor is encoded by another gene
 Trp operator found just behind of the promoter
 If tryptophan present, it will block RNA polymerase hence, no transcription occur.
 In the absence of tryptophan, transcription increases.

Levels of gene regulation and control in prokaryotes

in prokaryotes genetic control is regulated at basic 3 levels that is transcriptional
level, translational level and post translational level.
 Transcriptional level control
this is the most active step of gene regulation because in this part Messenger RNA
will be produced and if Messenger RNA of a gene are produced then there are fair
chances it will be converted to proteins. So, if Messenger RNA are not allowed to
produce at all, no chance of protein Or expression can be greatly controlled here by
selective expression according to the environment and other sources. There are 2
types of regulatory systems that is positive and negative regulatory systems which
makes use of various components to induce or suppress transcription.
for example we just saw in Lac operon system that the presence of repressor or
inhibitor does not allow the transcription . So this is a preferably negative regulated
system. In this lactose is an inducer which will then change the configuration of
repressor and allowed transcription.
 translational level control
in the transcriptional level the rate of protein synthesis is controlled by many
factors. Some of the Messenger RNA are degraded enzymatically according to cell
need. but generally the life span of Messenger RNAs are predetermined
genetically, Messenger RNA life span also depends upon the free ribosome
available for translation.

References
 Varma and Agarwal, cell biology, genetics, molecular biology, S Chand
publishers, 2005
 Gerald Karp, cell and molecular biology, 6th edition 2011
 Snusted and Simmons, principle of genetics,6th edition, 2012
 BENJAMIN A. PIERCE, Genetics a conceptual approach
 https://microbenotes.com/lac-operon/

[Q3(B) Explain the transcription factors in prokaryotes and the mechanism of

prokaryotic transcription in detail.]
  Mechanism of prokaryotic transcription
Transcription is the process through which a particular DNA sequence is converted
into RNA copy with the assistance of RNA polymerase enzyme. This is the main
step of central dogma. The RNA produced is then matured into Messenger RNA
which will be used for protein production . In prokaryotes only one type of RNA
polymerase is required to produce all types of RNA that is ribosomal RNA,
transfer RNA and Messenger RNA.
 This RNA polymerase is composed of 6 Subunits that is 2 Alpha chains, one
beta, one beta dash, one Sigma and one Omega chain.
This is a very efficient enzyme because it performs all activities alone like
separation, production and binding. like DNA polymerase it does not need any
primer it just need a Sigma factor for it's working.
 Transcription occurs only in one strand of DNA called as template or sense
strand the other which is not transcribed is known as non-template and
antisense strand.
 The direction of RNA synthesis is 5’ to 3’.
 The actually transcribing region of DNA sequence is called as coding
region.
Transcription in prokaryotes is divided into 3 steps that is initiation elongation and
termination.
 initiation
Initiation occurs when RNA polymerase binds to the DNA specific sequence. these
are known as binding sites. Binding sites have special regions called promoters ,
20-200 nucleotide sequence where interaction takes place. These are present some
bases, upstream the coding region. One promoter region is at -10 sequence that is
TATAATG. -10 means it is 10 base pairs upstream the coding sequence. It is also
known as pribnow box or Tata box. Another sequence or promoter is present -35
sequence upstream the coding sequence. Here the enzyme will attach. The enzyme
consists of 2 parts that is core enzyme and Sigma factor. Sigma factor is the part
which recognize the binding site. Because for correct transcription Product, correct
initiation is necessary.
 [Karp,2011]
So Sigma factor is responsible for correct initiation. It will bind and form open
promoter complex. After complex formation the Sigma factor is shed off and then
the main enzyme do the synthesis. Actually, in initiation First nucleoside
triphosphate is bonded with DNA by open promoter complex. The first edit
Nucleoside can be ATP or GTPT after that the first triphosphate FORMS hydrogen
bond with DNA then the second will come and will attach to the first one on ability
basis and initiation is completed in this way.
 Elongation
after the Sigma factor is released from the main enzyme the main enzyme will go
on adding the nucleosides to the chain. The rate being almost 40 basis per second
at 37 Celsius.
 termination
termination of a transcriptional unit occur at specific sequence in the DNA. There
are 2 types of terminators one depends upon the presence of protein rho called rho
dependent termination. The other one is rho independent. In rho independent
termination There occurs a sequence in DNA of inverted GC sequences which
causes the newly synthesised Messenger RNA to form a hairpin Which does not
allow RNA polymerase to go on. GC base pairs are followed by AT base pairs
these form week hydrogen Bonds with the uracil of growing Messenger RNA and
helps in the release of newly synthesised RNA.
This RNA produced will be processed to form messenger RNA.
 [Slideshare.net]
 Transcription factors
Transcriptional factors are proteins. Transcriptional factors are involved in the
process of transcription and translation, end product is proteins. Transcriptional
factors include a variety of enzymes, primers, promoters, excluding RNA
polymerase. RNA polymerase is involved in the initiation and regulation of
transcriptional genes.
Prokaryotic transcriptional factors
The initiation of transcription is the most significant and specific control point
for gene expression. Transcription is thus regulated by different number of
biomolecules, and many other factors including DNA sequences, proteins and
small molecules. These are all called transcriptional factor.
 Initiation starts when RNA polymerase moves to a specific upstream of
gene known as promoter.
  Sigma factor, important part of holoenzyme, brings changes in gene
expression state. It is also very important as it identifies the promoter
sites as well as recruit holoenzyme to promoter
 Transcriptional factors initiates or inhibit the process of transcription
 Transcriptional factors regulate transcription process typically in
response to cellular environment.
 Transcriptional factors are either controlled during transcription or
translation modification
Nucleoid associated proteins
In addition to modulating polymerase recruitment to promoters, several global
factors are considered as "nucleoid-associated proteins" that impose structural
constraints on the chromosome by altering the conformation of the bound DNA,
thus influencing other processes involving DNA such as replication and
recombination.

References
 Varma and Agarwal, cell biology, genetics, molecular biology, S Chand
publishers, 2005
 Gerald Karp, cell and molecular biology, 6th edition 2011
 Snusted and Simmons, principle of genetics,6th edition, 2012
 BENJAMIN A. PIERCE, Genetics a conceptual approach
 https://openoregon.pressbooks.pub/mhccmajorsbio/chapter/prokaryotic-transcription