Difference Between Prokaryotic and Eukaryotic Transcription

Difference Between Prokaryotic and Eukaryotic TranscriptionSUMMARYBiosynthesis of proteins is under direct control of DNA in just or so cases or else under the control of familial ribonucleic acid where DNA is absent. In stochastic variableation for expression of a polypeptide is stored in a polynucleotide twine (Gupta, 2007). Sequences of bases in a fussy segment of a polypeptide chain will determine the order of amino acids in a particular polypeptide (Gupta, 2007). The relationship popularly cognize as underlying dogma explains how protein synthesis is controlled by nucleic acids. There be twain major steps involve in protein synthesis (1) recording and (2) Translation. Transcription involves transfer of genetic study from DNA to mribonucleic acid and Translation involves translation of language of nucleic acids in to that of proteins (Gupta, 2007). Transcription will be discussed in detail in the present topic. textual matterTranscription is the synthesis of ribonuc leic acid which carries the genetic information present in DNA (Fig. 1). The DNA is double drawing stringed and hatful theoretically code for ii separate ribonucleic acid corpuscles (Jain, 2000). However, it has been found that only one of the 2 strands of the gene is transcribed (Jain, 2000). Only in a few exceptional cases both strands are transcribed. This is possible be front the promoter is asymmetrical and uni perpetrational (Jain, 2000). The DNA strand which have a age homology with the ribonucleic acid is know as the coding strand. The second strand which is complementary to ribonucleic acid and serves as the guide for ribonucleic acid synthesis is known as the non-coding strand. It is therefore, a misnomenclature, as it is the non-coding strand which is in fact transcribed to form the primary transcript (Jain, 2000).Transcription in prokaryotesThe principal enzyme involved in placement is the DNA dep break offent RNA polymerase (commonly called as RNA pol). To und erstand the transcription, it is undeniable to learn more than about the RNA polymerase. The bacterial RNA polymerase consists of five polypeptide chains including two chains of (alpha) polypeptide and one chain each of (beta) and (beta dash) and (sigma) polypeptides (Fig.). The RNA polymerase molecule thus ignore be represented as 2, in which the attachment of sigma () factor is non very firm, so that the core enzyme (2) can be easily isolated. The size and function of the prokaryotic RNA polymerase is given in table 1.The active sites of core enzyme are shown in fig. (). formerly RNA synthesis is initiated, dissociates after RNA is 8-9 bases long and then the core enzyme brings about elongation of mRNA. The dissociated sigma factor may again combine with core enzyme to form RNA polymerase holoenzyme (Fig,..).Events in transcriptionThe entire serve up of transcription can be divided in to following steps(1) guidebook recognition(2) fundament(3) prolongation and(4) Ter minationTemplate recognitionThe promoter directs the RNA polymerase to recognize the correct area of the gene and to hold up at this site. The -35 region serves this function and is recognized by the enzyme. The size of the RNA polymerase is such that about 60 nucleotides in the gene are involved in attach of the enzyme to the template. Sigma factor plays an important role in special(prenominal) binding of the enzyme with the template (Jain, 2000). The core enzyme without the sigma factor can bind to DNA but the binding is not promoter specific. The sigma factor is thus requirement for the formation of promoter-enzyme complex. The binding of RNA polymerase to a site other than the promoter is generally referred as loose binding. In presence of sigma factor, the affinity for loose binding is reduced while the affinity for specific binding is increased (Jain, 2000). Thus the chances of only the specific binding taking place are enhanced m all fold in presence of sigma factor (Jai n, 2000).Initiation and elongation of RNA synthesis in prokaryotesRNA synthesis by RNA polymerase proceeds in four steps (i) the holoenzyme first binds at the promoter site, forming the closed promoter complex in which DNA remains double helicle, (ii) the closed complex isomerizes and causes unwinding and detachment of DNA strands to form open (binary) promoter complex, (iii) after unwinding only one of the two strands is copied this is achieved by internalisation of nucleotides, initially without movement of enzyme lede to the formation of RNA chain, up to 9 bases in length. During the incorporation of these 9 bases, at every step, there is a possibility for the release of this small RNA chain, a process described as abortive initiation (Gupta, 2007). A cycle of abortive initiation ordinarily occurs generating a series of short (2-9 base) oligonucleotides, before initiation is usually successful. (iv) Once initiation succeeds, the sigma factor of RNA polymerase dissociates. (v) the disassociation of sigma factor marks the entry of NusA protein, which helps elongation, and promotes pausing and result at specific sites. Core enzyme now undergoes a major conformational rearrangement and a stable ternary elongation complex is formed. This complex moves along DNA, synthesizing RNA all along its path at a rate of about 40 bases per second at 370C (Gupta, 2007). Elongation of RNA transcript continues till an unstable death complex is formed (Gupta, 2007).TerminationThe termination of mRNA chain in prokaryotes is brought about by certain termination signals on DNA. These DNA episodes providing termination signals are called terminators (Gupta, 2007). Once the enzyme hits the terminator, it falls off the template and the transcription stops. The termination signals whenever found on DNA can be of two references (i) Rho () dependent termination and (ii) Rho () independent termination.(i) Rho () dependent terminationThe termination factor () participates in this type of termination (Jain, 2000). Rho () is a 46 KD protein and its active form is a hexamer, having a total mass of 275 KD. It binds to growing RNA chain and moves along the RNA. Once rho catches the RNA polymerase, it results in chain termination. The question arises how?. It has been found that once RNA polymerase hits the terminator sequences, it pauses for a short time. During this period the rho factor reaches the RNA polymerase and causes it to fall off the template. Once RNA polymerase is detached, the RNA chain also comes off and the transcription terminates (Fig).(i) Rho () independent terminationIn some genes, there is a definite region of congenital sequences which causes the termination of RNA chain. This includes two GC rich stretches at the end of RNA transcript which are complementary to each other. These form a 7-20 bp intra-molecular hairpin structure. Further this region is followed by a small stretch of U residues which form relatively weak interaction with dA residues of the gene (Fig..). such a structure is highly unstable thermodynamically and causes the displacement of newly synthesized RNA from the DNA template. Once the RNA is detached, the RNA polymerase falls off and the termination of transcription occurs. This type of termination provides an interesting example where the structure of RNA itself can cause its own termination from the DNA chain.Transcription in EukaryotesThe eukaryotes have more than one type of RNA polymerase. Based on the exertion to -aminitin, an antibiotic which inhibits mRNA synthesis, three classes of RNA polymerases have been identified which are involved in the transcription of diametric class of eukaryotic genes. There properties are given in table 2.The eukaryotic RNA polymerases are large molecules of 500KD in size. It has two large subunits of -200KD and -140KD, respectively. The 200 KD subunit is similar to subunit of E. coli of RNA polymerase and have similar function (the template binding). Besid es these two proteins it also has upto 10 distinct small subunits. A subunit of pol II, which has similarity with one of the subunits present in Pol I and also in Pol triplet, is similar to the -subunit of E. coli enzyme and helps in the enzyme assembly. Besides the RNA polymerase, a number of other transcription factors are also needed for the transcription.Promoter sites for Initiation of transcriptionPromoters for RNA polymerase I could not be initially studied since all genes for rRNA were similar. Promoters for RNA polymerase III, on the other hand, had some unusual downstream promoters. However for RNA polymerase II, several hundred eukaryotic genes have now been sequenced and their promoters studied revealing some general features in three regions located at start point, centred at sited lying between -25 bp and -100 bp. The least effective of these three regions is the TATA or Hogness box (7 bp long) located 20bp upstream to the start point.The TATA box is surrounded by G -C rich sequences and is comparable to pribnow box of prokaryotes. Further upstream is another sequence called CAAT box, which being necessary for initiation, is conserved in some promoters ( globin gene), but is not necessary in some other genes. This sequence lies between -70 and -80 bp. Another sequence called GC box (GGGC GG) is found in one or more copies at -60 or -100 bp upstream in any orientation in several genes. It has been shown that CAAT and GC boxes determine the efficiency of transcription, while TATA box aligns RNA polymerase at proper site, with the help of TFIID and other transcription factors (Gupta, 2007).InitiationIn eukaryotes the initiation is more complex. It involves a number of specific transcription factors. The process has been followed for the Pol II action resulting in the synthesis of mRNA. The process is basically similar for Pol I and Pol III. For initiation, it requires, a number of trans acting factors along with the RNA polymerase. The trans acti ng factors, which are the product of various regulatory genes, bind to either DNA or to each other or to RNA polymerase. They can also bind in various combinations. All the transcription factors involved with Pol II are called TF II. First the factor TF IID binds to TATA box (-15 to -21 region) covering about 25 nucleotides within the -17 to -42 region. Now factor TF IIA associates itself to the complex, further extending the protected region towards upstream, upto the -55 to -80 region. On the other hand TF IIB associates itself protecting the region at -10 to +10. It binds to two strands in a non-symmetrical manner. This complex prepares the stage for binding of RNA polymerase II which covers up to +15 region on template strand and 5 extra nucleotides (up to +20) on the non-template strand. Finally TF IIE joins, extending the protection upto +30 region. Once the entire complex has been assembled, the incorporation of first nucleotide takes place.Transcription factors and elongatio n of RNA chains in eukaryotesCertain accessory proteins of transcription, called the elongation factors enhance the overall activity of RNA polymerase II, leading to increase in elongation rate. Atleast two such proteins (transcription factors) are known (i) the transcription factor TFIIF accelerates RNA chain growth relatively uniformly, in project with RNA polymerase II or pol II, (ii) transcription factor TFIIS (also called SII) helps elongation of RNA chain, by relieving the obstructions in the path of such elongation. TFIIS is known to function by first causing hydrolytic cleavage at 3 end of RNA chain, which are stuck and can not elongate. Thus RNA polymerase moves backwards (hydrolytic cleavage) under the direction of TFIIS before it moves forwards through the block to elongation (fig.) (Gupta, 2007).Termination of RNA synthesis in eukaryotesIn eukaryotes, the actual termination of RNA polymerase II activity during termination may take place through termination sites similar to those found in prokaryotes (the nature of individual termination sites is not known). But these termination sites are believed to be present away (sometimes up to one kilobase away) from the site of 3 end of mRNA. Obviously 3 end of mRNA will be generated due to post-transcriptional cleavage. This cleavage, at the end, is believed to be achieved by what is popularly called snurp (small nucleur RNA-protein complex). Snurp used for post-transcription cleavage has not been identified so far but is believed to be certainly different than the U1 snurp, which is believed to be involved in intron splicing in split genes. Moreover, a sequence 5 AAUAAA 3 has been found just on the 5 side of poly(A) addition site in several eukaryotic mRNAs. The poly(A) tail is added to 3 end of eukaryotic mRNA after processing of precursor mRNA. The sequence 5 AAUAAA 3 in mRNA 3 end seems to be common in eukaryotic mRNA and mutation in this sequence cause elongation of mRNA. This will suggest that this s equence contains the signal for endonucleolytic post-transcriptional cleavage. This sequence therefore, is not involved in the termination of the synthesis of mRNA, but helps in generating 3 end later through endonuclease cleavage, in which snurp helps in an unknown manner.FAQsQ. What is transcription?autonomic nervous system synthesis of RNA which carries the genetic information present in DNA.Q. What is the composition of RNA polymerase in prokaryotes?autonomic nervous system RNA polymerase consists of five polypeptide chains including two chains of (alpha) polypeptide and one chain each of (beta) and (beta dash) and (sigma) polypeptides.Q. What is the function of sigma factor of RNA polymerase in prokaryotes?Ans The function of sigma factor in prokaryotes is Promoter recognition and initiation of transcription.Q. What are the steps in transcription?Ans The entire process of transcription can be divided in to following steps (1) Template recognition, (2) Initiation, (3) Elonga tion and (4) Termination.Q. What is a Promoter?Ans Promoter is defined as a sequence of DNA having the signal which directs the proper binding of RNA polymerase to DNA and activates it to a form which is capable of initiating the transcription.Q. What is the role of NusA protein?Ans NusA protein, helps in elongation, and promotes pausing and termination at specific sites in prokaryotic transcription.Q. How termination of transcription occurs in prokaryotes?Ans The termination of mRNA chain in prokaryotes is brought about by certain termination signals on DNA. These DNA sequences providing termination signals are called terminators (Gupta, 2007). Once the enzyme hits the terminator, it falls off the template and the transcription stops. The termination signals whenever found on DNA can be of two types (i) Rho () dependent termination and (ii) Rho () independent termination.Q. How many RNA polymerases are involved in eukaryotic transcription?Ans three classes of RNA polymerases (Pol I , Pol II and Pol III) have been identified which are involved in the transcription of different class of eukaryotic genes.Q. What the functions of Pol I, Pol II and Pol III?Ans The functions of Pol I is Ribosomal RNA synthesis, Pol II is mRNA synthesis and Pol III is tRNA synthesis, 5S and other small RNA synthesis.Q. What are transcription factors?Ans transcription factors are proteins which are needed for initiation of transcription, but are not a part of RNA polymerase.Q. What is Hogness box?Ans The second region of eukaryotic promoter which is similar to -10 region of prokaryotes. is called the TATA box or Hogness box.Q. What is the role of transcription factor TFIIF and TFIIS?Ans the transcription factor TFIIF accelerates RNA chain growth relatively uniformly, in concert with RNA polymerase II or pol II while transcription factor TFIIS helps elongation of RNA chain, by relieving the obstructions in the path of such elongation.Q. How TFIIS helps in elongation of RNA?Ans TFIIS is known to function by first causing hydrolytic cleavage at 3 end of RNA chain, which are stuck and can not elongate.Q. what is the role of small nucleur RNA-protein complex?Ans Termination takes place at termination sites which are present away from the site of 3 end of mRNA. The 3 end of mRNA will be generated due to post-transcriptional cleavage. This cleavage, at the end, is believed to be achieved by snurp (small nucleur RNA-protein complex).Q. How does Rho () helps in termination of transcription?Ans When RNA polymerase hits the terminator sequences, it pauses for a short time. During this period the rho factor reaches the RNA polymerase and causes it to fall off the template.MCQs1. Transfer of genetic information from DNA to mRNA?a. translation b. transcriptionc. transformation d. All of the to a higher place2. During transcription the DNA strand which have a sequence homology with the RNA is known asa. coding strand b. non-coding strandc. Both a and b d. None of the above3. During transcription the strand which is complementary to RNA and serves as the template for RNA synthesis is known as?a. coding strand b. non-coding strandc. Both a and b d. None of the above4. The principal enzyme involved in transcription isa. RNA polymerase b. DNA polymerasec. transcription factor d. a and b only5. RNA polymerase isa. RNA dependent b. DNA dependentc. protein dependent d. endocrine gland dependent6. The RNA polymerase molecule thus can be represented asa. 2 b. 2c. 2 d. 27. The function of subunit isa. Template binding b. Nucleotide bindingc. Both a and b d. Enzyme assembly8. Sequence of DNA having the signal which directs the proper binding of RNA polymerase to DNA is known asa. Hogness box b. promoterc. CAAT box d. None of the above9. The sigma factor is necessary for the formation ofa. promoter-enzyme complex b. Enzyme assemblyc. CAAT box d. All of the above10. The dissociation of sigma factor marks the entry of NusA proteina. TF IIB b. TF IIEc.TF IIS d. Nus A protein11. Termination of transcription in prokaryotes isa. Rho () dependent b. Rho () independentc. both a and b d. a only12. Hairpin structure for termination of transcription is found ina. Rho () dependent b. Rho () independentc. both a and b d. a only13. which RNA polymerase is found in Eukaryotesa. Pol I b. Pol IIc. Pol III d. All of the above14. TATA box of eukaryotes is comparable to which sequence of prokaryotesa. pribnow box b. CAAT boxc. Hogness box d. All of the above15. Transcription factors helps ina. initiation b. elongationc. termination d. a and b only16. At what region of DNA does RNA polymerase first bind to a genea. Initiation site b. Transcribed regionc. Promoter d. Intron17. RNA polymerase adds new nucleotides to the growing RNAs at what end?a. 3 end b. 5 endc. both a and b d. none of the aboveKey 1-b, 2-a, 3-b, 4-a, 5-b, 6-c, 7-d, 8-b, 9-a, 10-d, 11-c, 12-b,13-d, 14-a, 15-d, 16-c, 17-a.ASSIGNMENTS/TUTORIALSQ. 1 Difference between prokaryotic and eukaryotic tra nscription initiation.Q. 2 rationalise the role of RNA polymerase in prokaryotes.Q. 3 Eukaryotes contain multiple RNA polymerases explain their role?Q. 4 Explain Rho dependent and Rho independent termination of transcription in prokaryotes.Q. 5 What are transcription factors? discuss the role.