gene

1. GENES IN PROKARYOTES
Presented by:
Ayesha Javaid
PHD Biotechnology
Course: RDT

2. Contents
• History of Genes
• Prokaryotic Genes
• Number of genes in Prokaryotes
• Structure of Prokaryotic Gene
• Gene Expression in Prokaryotes
• Transcription in prokaryotes
• Translation in prokaryotes
• Gene Regulation in Prokaryotes
• The Trp operon
• Lac operon
• References

3. History of GENE
• The classical concept of gene was deduced by Gergor Mendel
on breeding of experiments in 1865
• The term “Gene” was coined by W Johansen to describe
Mendelian units of hereditary in 1909.
• Gene theory was proposed by T.H Morgan in 1911 (Genes as
basic hereditary units)
• The fine structure of gene was proposed by Seymour Benzere
in 1962
Ref-(Genes IX by Benjamin Lewin)

4. Definition of Gene
• Gene is the unit of genetic information that controls a specific
trait or phenotype.
• The basic unit of heredity passed from parent to offspring.
• Genes are part or fractions of DNA molecule, which is
regarded as genetic material.

5. Prokaryotic Gene
Prokaryotes are single celled organisms that lack membrane
bound organelles
Prokaryotes have single circular chromosome , present in
cytoplasm

6. Number of Genes in Prokaryotes
• Number of genes in prokaryotes vary, depend upon the
organism
• Parasitic bacteria have 500–1200 genes as they depend on the
host cells for information processing systems (translation)
• Free-living bacteria have 1500–7500 genes because of a high
level of gene importation. They also have a large number of
rRNA operons.
• Archaea have 1500–2700 genes found in a symbiont that
derives nutrients from a host, and the small size of this
genome reflects the loss of unnecessary genes.
• The E. coli chromosome is represented by 4,401 genes

7. Structure of Prokaryotic Gene
• Prokaryotic gene is composed of three regions
Promoter region
RNA coding sequence
Termination region
• Prokaryotic gene is uninterrupted as there are no introns present
• The region 5' of promoter sequence is called upstream region
• The region 3' of terminator sequence is called downstream region
Ref-(The Cell (fifth edition) by Geoffrey M. Cooper and Robert E.
Hausman).

8. Prokaryotic Gene structure

9. Promoter Region
• This is situated on upstream of the sequence that codes for
RNA.
• This is the site that interact RNA polymerase before RNA
synthesis
• Promoter region provides the location and direction to initiate
transcription
• At -10 there is a sequence TATAAT or PRIBNOW BOX.
• At -35 another consensus sequence TTGACA
• These two are the most important promoter elements
recognized bytranscription factors.

11. RNA Coding Sequence
• The DNA sequence that will become copied into an RNA
molecule (RNA transcript).
• Starts with an initiator codon and ends with termination
codon
• No introns (uninterrupted).
• Collinear to its mRNA.
• Any nucleotide present on the left is denoted by (-)symbol
and the region is called upstream element. E.g. -10,-20,-35
etc. Any sequence to the right of the start is downstream
elements and numbered as +10,+35 etc.).

12. Terminator Region
• Signals the RNA polymerase to stop transcription from DNA
template.
• Transcription termination occur by Rho dependent or Rho
independent manner

14. Gene Expression in Prokaryotes
• The process by which the information encoded in a gene is
used to either make RNA or protein
• Prokaryotic gene expression (both transcription and
translation) occurs within the cytoplasm of a cell due to the
lack of a defined nucleus; thus, the DNA is freely located
within the cytoplasm.

15. The steps of transcription
• Transcription is an enzymatic process. The mechanism of
transcription completes in three major steps
• 1. Initiation:
• Closed complex formation
• Open complex formation
• Tertiary complex formation
• 2. Elongation
• 3. Termination
• Rho- dependent
• Rho-independent

16. . Initiation:
• The transcription is initiated by RNA polymerase
holoenzyme from a specific point called promotor sequence.
• Bacterial RNA polymerase is the principle enzyme involved
in transcription.
• Single RNA polymerase is found in a bacteria which is called
core polymerase and it consists of α, β, β’ and ω sub units.
• The core enzyme bind to specific sequence on template DNA
strand called promotor. The binding of core polymerase to
promotor is facilitates and specified by sigma (σ) factor. (σ70
in case of E. coli).

18. i. Closed complex:
Binding of RNA polymerase holoenzyme to the promotor
sequence form closed complex
ii. Open complex:
• After formation of closed complex, the RNA polymerase
holoenzyme separates 10-14 bases extending from -11 to +3
called melting. So that open complex is formed. This
changing from closed complex to open complex is
called isomerization.

20. Elongation:
• After synthesis of RNA more than 10 bp long, the σ-factor is
ejected and the enzyme move along 5’-3’ direction
continuously synthesizing RNA.
• The synthesized RNA exit from RNA exit channel.
• The synthesized RNA is proof reads by Hydrolytic editing.
For this the polymerase back track by one or more nucleotide
and cleave the RNA removing the error and synthesize the
correct one.

21. 3. Termination:
There are two mechanism of termination.
i. Rho independent:

22. Continued…
• In this mechanism, transcription is terminated due to specific
sequence in terminator DNA.
• The terminator DNA contains invert repeat which cause
complimentary pairing as transcript RNA form hair pin
structure.
Ref-(CHAMPE, Pamela C – HARVEY, Richard A –
FERRIER, Dennis R. Lippincott's Illustrated Reviews)

23. ii. Rho dependent:
• In this mechanism, transcription is terminated by rho (ρ)
protein.
• It is ring shaped single strand binding ATpase protein.
• The rho protein bind the single stranded RNA as it exit from
polymerase enzyme complex and hydrolyse the RNA from
enzyme complex.
• The rho protein does not bind to those RNA whose protein is
being translated. Rather it bind to RNA after translation.
• In bacteria transcription and translation occur simultaneously
so the rho protein bind the RNA after translation has
completed but transcription is still ON.

25. Translation in Prokaryotes
• As with mRNA synthesis, protein synthesis can be divided
into three phases: initiation, elongation, and termination.
• Translation in bacteria begins with the formation of the
initiation complex, which includes the small ribosomal
subunit, the mRNA, the initiator tRNA carrying N-formyl-
methionine, and initiation factors. Then the 50S subunit
binds, forming an intact ribosome.

27. Operons
• Bacterial genes are often found in operons. An operon is a
cluster of genes that are transcribed together to give a single
messenger RNA (mRNA) molecule, which therefore encodes
multiple proteins.
• Genes of an operon are transcribed together under the control
of single promoter into a single mRNA molecule: –
polycistronic mRNA.

28. Gene Expression of Operon

29. Gene Regulation in Prokaryotes
Two types of genes present in prokaryotes
1-constitutive genes (always turn on)
2-Inducible genes (turned on/ off depending on the environment)
There are three types of regulatory molecules that can affect the expression
of operons
• Repressor
• Activator
• Inducer
Repressors and Activators regulate gene expression by binding to specific
DNA sites adjacent to the genes they control.
Ref-https://pressbooksdev.oer.hawaii.edu/biology/chapter/prokaryotic-
gene-regulation

30. Continued…
• Transcription factors influence the binding of RNA
polymerase to the promoter and allow its progression to
transcribe structural genes
• Activators bind to the promoter site, while repressors bind to
operator regions.
• A repressor is a transcription factor that suppresses
transcription of a gene in response to an external stimulus
• Activator is a transcription factor that increases the
transcription of a gene in response to an external stimulus by
facilitating RNA polymerase binding to the promoter
• An Inducer either activates or represses transcription by
interacting with a repressor or an activator

32. The trp operon: A Repressible Operon
• The trp operon includes five genes that encode enzymes
needed for tryptophan biosynthesis, along with a promoter
(RNA polymerase binding site) and an operator (binding site
for a repressor protein).
• The genes of the trp operon are transcribed as a single mRNA

34. Turning the operon "on" and "off"
• The trp repressor does not always bind to DNA. Instead, it
binds and blocks transcription only when tryptophan is
present. When tryptophan is around, it attaches to the
repressor molecules and changes their shape so they become
active
• When there is little tryptophan in the cell, on the other hand,
the trp repressor is inactive (because no tryptophan is
available to bind to and activate it). It does not attach to the
DNA or block transcription, and this allows the trp operon to
be transcribed by RNA polymerase

36. Inducible genes: The lac Operon
• Gene regulation in prokaryotic cells can also occur through
inducible operons, which have proteins that bind to activate
or repress transcription depending on the local environment
• E. Coli normally carbon source is usually glucose.
• The enzymes required for glucose utilization are
constitutively expressed.
• If the nutrient medium contains lactose instead of glucose as
the carbon source – the bacteria make enzymes that allow them
to utilize lactose
• These genes are therefore inducible, and lactose is the
inducer. – These genes form the lac Operon.

37. • Lac Operon consists of two types of genes; structural
genes and regulatory genes.
• Structural genes of Lac Operon are lac Z, Lac Y and Lac A
• lac Z: It encodes the enzyme β-galactosidase which hydrolyzes
lactose to form glucose and galactose and also converts lactose into its
isomeric form, allolactose.
• lac Y: It encodes the enzyme β-galactoside permease which is a
transporter protein and facilitates the entry of lactose into the cell.
• lac A: It encodes the enzyme β-galactoside transacetylase. This
enzyme transfers an acetyl group from acetyl-CoA to toxic β-galactosides,
glucosides and lactosides and removes them out of the cell.

38. Regulatory genes include a repressor gene (Lac I) along with
Promoter (P) and Operator (O) genes.

39. RNA polymerase must bind to promoter gene in order to transcribe
structural genes.
• Repressor gene (lac I) encodes repressor protein that binds to
operator gene.
• When repressor protein binds to operator, RNA polymerase
cannot bind to promoter.
• No binding of RNA polymerase to promoter, stops the
transcription of structural genes. This occurs in the absence of
lactose in the cell.
• When lactose is present in the cell, it binds to repressor
protein causing its conformational change. This change
dissociates repressor protein form the operator.
• Lactose appears to serve as an inducer here but actually it is
its isomeric form, allolactose, which acts as a real inducer.

42. References
• The Cell (fifth edition) by Geoffrey M. Cooper and Robert E. Hausman.
• Genes IX by Benjamin Lewin.
• CHAMPE, Pamela C – HARVEY, Richard A – FERRIER, Dennis R. Lippincott's Illustrated Reviews :
Biochemistry. 4th edition. Philadelphia : Lippincott Williams & Wilkins, 2008. 520 pp. ISBN 978-1-6083-
1521-5.
• https://pressbooks-dev.oer.hawaii.edu/biology/chapter/prokaryotic-gene-regulation