Botany

4
Class XII : Gene Regulation
Analysis of various PMTs from 2008-2013
12 10 8 12 10 8

12 10 8

2008

6 4 2 AIPMT AIIMS BHU AFMC AMU

2009

6 4 2 AIPMT AIIMS BHU AFMC AMU

2010

6 4 2 AIPMT AIIMS BHU AFMC AMU

12 10 8

12 10 8

12 10 8

2011

6 4 2 AIPMT AIIMS BHU AFMC AMU

2012

6 4 2 AIPMT AIIMS BHU AFMC AMU

2013

6 4 2 NEET AIIMS AMU K.CET K.NEET

DNA is organized into genes which store and express the genetic information that contribute towards the phenotype, and is passed on to successive generations. When we analyze the concentration of different proteins, even in a simple bacteria like E.coli, vast differences can be seen. While some proteins may be synthesized in as 5 to 10 molecules, others may be produced in as many as 100,000 copies per cell. This suggests that gene expression is regulated. Let us consider the most fundamental issues in molecular genetics: How is genetic expression regulated? Bacteria such as Escherichia coli are exposed to a wide variety of environmental conditions. For example E. coli cells may encounter rapidly changing growth conditions as they pass from mammalian intestinal tracts to sewer

gene regulation in prokaryotes

systems to polluted rivers, lakes, ponds, and so on. Each of these ecological niches will provide different organic molecules for use as energy sources. Natural selection preserves, those organisms that have ways of adapting to the wide range of environmental conditions encountered during their evolution. Therefore, the adaptability of bacteria and other prokaryotes depends on their ability to regulate the expression of specific genes in response to environmental signals. The expression of the genes is continually being turned on and turned off in response to changes in the environment. The expression of particular genes is turned on when the products of these genes are needed for growth in a given environment. Their expression is turned off when their products are no longer needed for growth in the existing milieu.
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The synthesis of gene transcripts and translation products requires the expenditure of considerable energy. By turning
Operon turned off (lactose is absent)

off the expression of genes when their products are not needed, an organism can avoid wasting energy. Gene expression can be (and is) regulated at several different
Operon

Regulatory gene
DNA mRNA Protein

Promoter Operator

Lac z

Lactose-utiliza

Lac y

tion genes

Lac a

RNA polymerase cannot attach to the promoter Active repressor

Operon turned on (lactose inactivates the repressor)

DNA mRNA Protein Lactose Inactive repressor

RNA polymerase is bound to the promoter Translation

-galactosidase

Permease

Transacetylase

levels - for example, transcription, mRNA processing, mRNA turnover, translation, and enzyme function. The regulation of transcription is the not important mode of the control of gene expression, at least in prokaryotes. Regulation can occur at both the initiation and the termination of mRNA transcription. Genes that specify products that are continuously being expressed in most cells are called constitutive genes, such as t RNA molecules, r RNA molecules, ribosomal proteins, RNA polymerase, enzymes, etc., that are frequently required to maintain cellular housekeeping functions. In contrast, the expression of certain genes is turned on in response to the changed environment. Such genes are called inducible genes. The substances or molecules responsible for their induction are called inducers. Enzymes that are involved in catabolic (degradative) pathways, such as in lactose, galactose, or arabinose utilization, are characteristically inducible. Induction occurs at the level of transcription. It alters the rate of synthesis of enzymes, not the activity of existing enzyme molecules.

Induction and repression in prokaryotes

Induction should not be confused with enzyme activation, in which the binding of a small molecule to an enzyme increases the activity of the enzyme (but does not affect its rate of synthesis). Bacteria possess the metabolic capacity to synthesize most of the organic molecules (such as amino acids, purines, and vitamins) required for their growth. For example, E. coli has five genes coding for enzymes that are required in the synthesis of tryptophan. These five genes must be expressed in E. coli cells growing in an environment devoid of tryptophan. When E. coli cells are present in an environment containing concentration of tryptophan sufficient to support optimal growth, the synthesis of the tryptophan biosynthetic enzymes is turned off. This process of turning off the expression of sets of genes is called repression. A gene whose expression has been turned off in this way is said to be repressed; when its expression is turned on, a gene of this type is said to be derepressed. Enzymes that are components of anabolic (biosynthetic) pathways are frequently subject to repression (are repressible).

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Repression, like induction, occurs at the level of transcription. Repression should not be confused with feedback inhibition, in which the binding of an end product to the first enzyme in a biosynthetic pathway inhibits the activity of the enzyme (but does not affect its synthesis).
Induction Activity of enzymes involved in lactose utilization (a) Repression Activity of tryptophan biosynthetic enzymes (b)

Lactose added

repressor gene), codes for a protein called the repressor, under the appropriate conditions, the repressor binds to the second element, the operator (or operator sequence). The operator is always located contiguous to the structural gene or genes whose expression it regulates. When the repressor is bound to the operator, transcription of the structural genes cannot occur because the binding of the repressor to the operator sterically prevents RNA polymerase from binding at the promoter site (the RNA polymerase binding site) which is always located contiguous with (or even overlapping) the operator sequence. The complete contiguous unit, including the structural gene or genes, the operator, and the promoter, is called an operon.
Regulator gene
Operon

Promoter for regulator gene

Tryptophan added

Promoter for operon Operator

10 15 Minutes

20

25

Structural genes SG1 SG2 SG3

Transcription Translation Repressor

Effector molecule (inducer or co-repressor)

Fig.: The Operon Model: Components

10 15 25 20 Minutes Fig.: Induction (a) and repression (b) of enzyme synthesis in bacteria.

The Operon Model

Induction and repression of gene expression can be accomplished by essentially the same mechanism. This mechanism was first accurately described in 1961 when Francois Jacob and Jacques Monod, both 1965 Nobel Prize recipients, proposed the operon model to explain the regulation of genes encoding the enzymes required for lactose utilization in E. coli. Jacob and Monod proposed that the transcription of one or a set of contiguous structural genes (genes coding for polypeptides) is regulated by two controlling elements. One of these elements, called the regulator gene (or

The regulator gene need not to be closely linked to the operon; infact, it can be located at any position in the genome. Hence, regulator gene is normally not considered to be part of the operon proper, which consists of the structural genes plus their promoter and operator. Whether the repressor binds to the operator or not depends on the presence or absence of a metabolite called an effector molecule.

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Modes of regulation for an inducible operon

RNA polymerase (Binding to promoter blocked) PR R PO Repressor (active, binds to operator) RNA polymerase PO O SG1 SG2 SG3
PR

Mode of regulation for a repressible operon

RNA polymerase O PO Ribosomes translating mRNA Repressor inducer complex (inactive, cannot bind to operator) mRNA RNA polymerase SG3

SG1

SG2

Repressor bound to operator Inducer added RNA polymerase SG3

PR

SG1

SG2

Polypeptide 1 Polypeptide 2 Polypeptide 3

Ribosomes translating mRNA Repressor inducer complex (inactive, cannot bind to operator) mRNA
PR R PO

Co-repressor added RNA polymerase (Binding to promoter blocked) SG1 SG2 SG3

Repressor bound to operator

Polypeptide 1 Polypeptide 2 Polypeptide 3

Fig.: Operon Model : Induction

The product of the regulator gene (R), the repressor, in the absence of the effector molecule (called an inducer, for inducible operons), binds to the operator, preventing RNA polymerase from binding to the promoter for the operon (PO). Thus, transcription of the structural genes cannot occur. When inducer is added, it binds to the repressor, causing it to be released from the operator (O). This, in turn, allows RNA polymerase to bind to the promoter (PO) and initiate transcription of the structural genes. The resulting multigenic mRNA is rapidly translated by ribosomes producing the three polypeptide products of the structural genes.

Repressor/co-repressor complex (active, binds to operator) Fig.: Operon Model : Repression

In this case, the repressor can only bind to the operator in the presence of the effector molecule (called a co-repressor, for repressible operons). In its absence, the operator is free, permitting RNA polymerase to bind at the adjoining promoter (PO) and to initiate transcription of the structural genes. When co-repressor is added, it forms a complex with the repressor.This repressor-corepressor complex then binds to the operator (O). This, is turn, prevents RNA polymerase from binding at PO and transcribing the three structural genes.

Lac operon : An inducible operon

The lac operon contains a promoter, an operator, and three structural genes, z, y and a, coding for the enzymes b-galactosidase, b-galactoside permease, and b-galactoside transacetylase, respectively. b-galactoside permease pumps lactose into the cell, where b-galactosidase cleaves it into glucose and galactose. The function of the transacetylase is still not clear. The lac regulator gene, designated the i gene, codes for a repressor.

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The active form of the lac repressor, however, is a tetramer that contains four copies of the i gene-product. In the absence of the inducer, (i.e., lactose, actually allolactose) the repressor binds to the lac operator sequence, preventing RNA polymerase from binding to the promoter and transcribing the structural genes. The inducer of the operon, allolactose, is derived from lactose in a reaction that is catalyzed by b-galactosidase. Once formed, allolactose binds to the repressor, causing it to be released from the operator; in so doing, it induces transcription of the z, y, and a structural genes. In the absence of tryptophan (the co-repressor), RNA polymerase binds to the promoter region and transcribes the structural genes of the operon. In the presence of tryptophan, the co-repressor/repressor complex binds to the operator region and prevents the binding of RNA polymerase to the promoter. The operator sequence of the trp operon lies entirely within the promoter region. The trp operon repressor is the product of gene trpR, which is not closely linked to the trp operon.

Trp absent

RNA polymerase mRNA transcript

Transcription proceeds

Inactive repressor Corepressor (tryptophan) Active repressor Active repressor bound to operator; transcription blocked

Trp present

Tryptophan operon : A repressible operon

RNA polymerase cannot bind

Transcription termination

1 2 3

UUUUUUUU

Stop

A - with Trp

2 1
UGG UGG

3 4

UUUUUUUU

mRNA Trp

TrpTrp

Multiple Choice Questions

1. Lac operon in E. coli, is induced by (a) I gene (b) promotor gene (c) b-galactosidase (d) lactose. 2. The lac operon is an example of (a) repressible operon (b) overlapping genes (c) arabinose operon (d) inducible operon. 3. The wild type E.coli cells are growing in normal medium with glucose. They are transferred to a medium containing only lactose as sugar. Which of the following changes take place? (a) The lac operon is induced (b) E.coli cells stop dividing (c) The lac operon is repressed (d) All operons are induced.
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B - without Trp

4. InA. negative operon Fig.: In the presence of tryptophan, a loop required for termination (formed (a) corepressor repressor by segments 3binds and 4)with is formed and leader RNA is made. B. In Trp(b) corepressor does becomes not bindstalled with repressor starvation a ribosome at two consecutive Trp segment 2 base-pairs with segment codons, (c) corepressor binds with inducer3, and transcription of fullmRNA can proceed. lengthTrp (d) camp have negative effect on lac operon. 5. In E. coli, during lactose metabolism repressor binds to (a) regulator gene (b) operator gene (c) structural gene (d) promoter gene. 6. E.coli cells with a mutated gene of the lac operon cannot grow in medium containing only lactose as the source of energy because (a) the lac operon is constitutively active in these cells (b) they cannot synthesize functional beta galactosidase (c) in the presence of glucose, E.coli cells do not utilize lactose (d) they cannot export lactose from the cell to the medium.

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7. In E. coli cell, according to operon theory, an operator gene combines with (a) inducer gene to switch on structural gene transcription (b) repressor protein to switch off structural gene transcription (c) regulator gene to switch on structural gene transcription (d) repressor protein to switch on structural gene transcription. 8. Match the componenets of Lac operon of E. coli given under Column I with their function listed in Column II. Choose the answer with correct combination of alphabets of the two columns. Column I Column II (Components of (Function) Lac operon) i. Structural gene p. Binding site for repressor protein ii. Operator gene q. Codes for repressor protein iii. Promoter gene r. Induces lactose transport from the medium s. Codes for enzyme proteins iv. Regulator gene t. Binding site for RNA polymerase. (i) (ii) (iii) (iv) (a) q t p r (b) r s t p (c) s p t q (d) t s q p 9. In the lac operon model, lactose molecules function as (a) inducers which bind with the operator gene (b) repressors which bind with the operator gene (c) inducers which bind with the repressor protein (d) corepressors which bind with repressor protein. 10. The sequence of structural gene in lac operon concept is (a) lac A, lac Y, lac Z (b) lac A, lac Z, lac Y (c) lac Y, lac Z, lac A (d) lac Z, lac Y, lac A 11. According the lac operon concept, which functional unit of the bacterial genetic material is responsible for suppressing the activity of the operator gene in the absence of lactose? (a) Regulator gene (b) Structural gene (c) Promotor gene (d) Repressor protein. 12. Transcriptionally active chromatin tends to be (a) methylated (b) undermethylated (c) condensed (d) deacetylated 13. Arrange the steps of gene regulation in a chronological order (from start to end) (i) Assemblage of transcription factors.

(ii) Chromatin remodeling. (iii) RNAi interference. (iv) Enhancer stimulation. (a) (iii), (ii), (iv), (i) (b) (ii), (i), (iv) (iii) (c) (ii), (iv), (i), (iii) (d) (i), (ii), (iv), (iii) 14. Statement 1 : Enhancer is responsible for time and tissuespecific gene expression. Statement 2 : Enhancer can be upstream, downstream, or within the gene it regulates. (a) Statement 1 and 2 are true and statement 2 is the correct explanation of statement 1. (b) Statement 1 and 2 are true but statement 2 is not the correct explanation of statement 1. (c) Statement 1 is true and statement 2 is false. (d) Both statement 1 and 2 are false. 15. Small temporal RNAs (stRNAs) are generated by ______ mediated cleavage of longer precusor that fold to create duplex regions. The stRNAs then bind to mRNAs, leading to _______ of mRNA or ______ of translation Select the correct sequence of words to fill up the above given passage. (a) Dicer, repression, stimulation (b) Drosha, splicing, initiation (c) Drosha, translation, initiation (d) Dicer, degradation, inhibition 16. In the Lac operon system, b-galactosidase is coded by (a) a-gene (b) i-gene (c) z-gene (d) y-gene 17. In lac operon, the genes a, i, y and z code respectively for (a) repressor protein, permease, b-galactosidase, transacetylase (b) transacetylase, permease, b-galactosidase, repressor protein (c) permease, transacetylase, repressor protein, b-galactosidase (d) transacetylase, repressor protein, permease, b-galactosidase. 18. Which enzyme will be produced in a cell in if there is a nonsense mutation in the lac Y gene? (a) Transacetylase (b) Lactose permease and transacetylase (c) b-galactosidase (d) Lactose permease

Answer key
1. 6. 11. 16. (d) (c) (a) (c) 2. (d) 7. (b) 12. (b) 17. (d) 3. 8. 13. 18. (a) 4. (a) 5. (b) (c) 9. (c) 10. (d) (b) 14. (b) 15. (d) (c) nn
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