RNA polymerase is an enzyme that produces RNA in cells. It was discovered in 1960 and is essential for all organisms. In prokaryotes, a single RNA polymerase synthesizes different RNA types, while eukaryotic RNA polymerase is a multi-subunit enzyme. RNA polymerase I synthesizes rRNA for ribosomes, polymerase II synthesizes pre-mRNA and most snRNA/miRNA, and polymerase III synthesizes tRNA and other small RNAs. The transcription process involves initiation, elongation, and termination stages.
The tryptophan operon regulates the biosynthesis of tryptophan in E. coli through transcriptional attenuation and repression. It contains five genes encoding the enzymes needed to synthesize tryptophan. When tryptophan levels are high, the tryptophan repressor binds to the operator site, preventing transcription. Additionally, a regulatory region can form a terminator stem-loop structure to halt transcription if tryptophan tRNA levels are high during translation of the leader mRNA sequence. However, if tryptophan levels are low, the terminator structure does not form and transcription of the operon proceeds.
Anjali Krishnan from the Department of Botany discusses polyadenylation. Polyadenylation is the addition of a poly(A) tail to messenger RNA. This is part of processing eukaryotic mRNA before translation. The poly(A) tail is important for nuclear export, translation, and stability of mRNA. It is also involved in degrading mRNA when shortened to a certain length. While polyadenylation degrades prokaryotic RNA, it can also store eukaryotic mRNA for later activation.
The document discusses transcription in prokaryotes and eukaryotes. In prokaryotes, RNA polymerase binds to promoter sequences and transcribes DNA into RNA through initiation, elongation, and termination. Transcription requires RNA polymerase and proceeds similarly in eukaryotes but involves multiple RNA polymerases and occurs in the nucleus. Eukaryotic transcription is more complex, utilizing regulatory sequences, transcription factors, and RNA processing to modify pre-mRNA into mature mRNA through splicing, capping, polyadenylation, and other modifications. Mutations can affect splicing and cause genetic disorders like beta-thalassemia.
Transcription in prokaryotes involves RNA polymerase producing messenger RNA transcripts of genetic material in the cytoplasm. Unlike in eukaryotes, transcription and translation can occur simultaneously. Transcription is controlled by transcription factors and involves three main steps: initiation, elongation, and termination. Initiation requires RNA polymerase binding to promoter regions with sigma factors. Elongation adds complementary bases to the DNA template. Termination can occur via intrinsic terminator sequences forming stem-loop structures or with rho-dependent termination using a rho factor protein.
Post-transcriptional modifications are important processes that convert primary transcript RNA into mature RNA. These modifications include 5' capping, 3' polyadenylation, and splicing of introns in eukaryotes. The modifications help make RNA molecules recognizable for translation and increase protein synthesis efficiency by removing non-coding regions. Different types of RNA undergo specific processing pathways involving nucleases, snoRNAs and other protein complexes.
RNA polymerase is an enzyme that produces RNA in cells. It was discovered in 1960 and is essential for all organisms. In prokaryotes, a single RNA polymerase synthesizes different RNA types, while eukaryotic RNA polymerase is a multi-subunit enzyme. RNA polymerase I synthesizes rRNA for ribosomes, polymerase II synthesizes pre-mRNA and most snRNA/miRNA, and polymerase III synthesizes tRNA and other small RNAs. The transcription process involves initiation, elongation, and termination stages.
The tryptophan operon regulates the biosynthesis of tryptophan in E. coli through transcriptional attenuation and repression. It contains five genes encoding the enzymes needed to synthesize tryptophan. When tryptophan levels are high, the tryptophan repressor binds to the operator site, preventing transcription. Additionally, a regulatory region can form a terminator stem-loop structure to halt transcription if tryptophan tRNA levels are high during translation of the leader mRNA sequence. However, if tryptophan levels are low, the terminator structure does not form and transcription of the operon proceeds.
Anjali Krishnan from the Department of Botany discusses polyadenylation. Polyadenylation is the addition of a poly(A) tail to messenger RNA. This is part of processing eukaryotic mRNA before translation. The poly(A) tail is important for nuclear export, translation, and stability of mRNA. It is also involved in degrading mRNA when shortened to a certain length. While polyadenylation degrades prokaryotic RNA, it can also store eukaryotic mRNA for later activation.
The document discusses transcription in prokaryotes and eukaryotes. In prokaryotes, RNA polymerase binds to promoter sequences and transcribes DNA into RNA through initiation, elongation, and termination. Transcription requires RNA polymerase and proceeds similarly in eukaryotes but involves multiple RNA polymerases and occurs in the nucleus. Eukaryotic transcription is more complex, utilizing regulatory sequences, transcription factors, and RNA processing to modify pre-mRNA into mature mRNA through splicing, capping, polyadenylation, and other modifications. Mutations can affect splicing and cause genetic disorders like beta-thalassemia.
Transcription in prokaryotes involves RNA polymerase producing messenger RNA transcripts of genetic material in the cytoplasm. Unlike in eukaryotes, transcription and translation can occur simultaneously. Transcription is controlled by transcription factors and involves three main steps: initiation, elongation, and termination. Initiation requires RNA polymerase binding to promoter regions with sigma factors. Elongation adds complementary bases to the DNA template. Termination can occur via intrinsic terminator sequences forming stem-loop structures or with rho-dependent termination using a rho factor protein.
Post-transcriptional modifications are important processes that convert primary transcript RNA into mature RNA. These modifications include 5' capping, 3' polyadenylation, and splicing of introns in eukaryotes. The modifications help make RNA molecules recognizable for translation and increase protein synthesis efficiency by removing non-coding regions. Different types of RNA undergo specific processing pathways involving nucleases, snoRNAs and other protein complexes.
Transcription in eukaryotes: A brief view
Transcription is the process by which single stranded RNA is synthesized by double stranded DNA. Transcription in eukaryotes and prokaryotes has many similarities while at the same time both showing their individual characteristics due to the differences in organization. RNA Polymerase (RNAP or RNA Pol) is different in prokaryotes and eukaryotes. Coupled transcription is seen in prokaryotes but not in Eukaryotes. In eukaryotes the pre-RNA should be spliced first to be translated.
In Eukaryotic transcription, synthesis of RNA occurs in the 3’→5’ direction. The 3’ end is more reactive due to the hydroxide group. 5’ end containing phosphate groups meanwhile, is not very reactive when it comes to adding new nucleotides. In Eukaryotes, the whole genome is not transcribed at once. Only a part of the genome is transcribed which also acts as the first, principle stage of genetic regulation.
Eukaryotes have five nuclear polymerases:
• RNA Polymerase I: This produces rRNA (23S, 5.8S, and 18S) which are the major components in a ribosome. This also produces pre-rRNA in yeasts.
• RNA Polymerase II: Helps in the production of mRNA (messenger RNA), snRNA (small, nuclear RNA), miRNA. This is the most studied type and requires several transcription factors for its binding
• RNA Polymerase III: This synthesizes tRNA (transfer RNA), 5S rRNA and other small RNAs required in the cytosol and nucleus.
• RNA Polymerase IV: Synthesizes siRNA (small interfering RNA) in plants.
• RNA Polymerase V: This is the least studied polymerase and synthesizes siRNA-directed heterochromatin in plants.
Eukaryotic transcription can be broadly divided into 4 stages:
• Pre-Initiation
• Initiation
• Elongation
• Termination
Transcription is an elaborate process which cells use to copy the genetic information stored in DNA into RNA. This pre-RNA is modified into mRNA before being transcribed to proteins. Transcription is the first step to utilizing the genetic information in a cell. Both Eukaryotes and Prokaryotes employ this process with the basic phases remaining the same. However eukaryotic transcription is more complex indicating the changes transcription has undergone towards perfection during evolution.
RNA splicing is a process where introns are removed from precursor messenger RNA (pre-mRNA) and exons are joined together to produce mature mRNA. It occurs in the nucleus and is essential for eukaryotes to produce proteins. The spliceosome, a large complex of RNA and proteins, facilitates two transesterification reactions that remove introns and ligate exons. RNA splicing generates protein diversity through alternative splicing and is important for cellular functions and disease processes.
Rifampicin binds to the beta subunit of prokaryotic RNA polymerase, inhibiting prokaryotic transcription initiation. It selectively binds bacterial RNA polymerase without affecting eukaryotic polymerases. This allows rifampicin to be an effective treatment for bacterial infections like tuberculosis and leprosy. Alpha amanitin from death cap mushrooms potently inhibits RNA polymerase II during both transcription initiation and elongation, potentially causing death in 10 days from just one mushroom due to failure of gene expression.
Transcription in prokaryotes and eukaryotesMicrobiology
Transcription is the process of synthesizing RNA from DNA and involves four main stages - initiation, elongation, termination, and post-transcription processing. It occurs differently in prokaryotes and eukaryotes. In prokaryotes, transcription and translation are coupled and occur in the cytoplasm, while in eukaryotes transcription occurs separately in the nucleus. The document provides details on the mechanisms and factors involved in each stage of transcription for both prokaryotes and eukaryotes.
Dna supercoiling and role of topoisomerasesYashwanth B S
supercoiling is one of the important process to condenses the huge amount of DNA to fit inside the histone and its also plays a role during the replication ,transcription etc..,these activities is carried out by an enzyme called topoisomerases.
This document summarizes the process of nuclear export of messenger RNA (mRNA). It begins with an introduction describing how mRNA must be exported from the nucleus to the cytoplasm to be translated into protein. It then discusses the importance of nuclear export and describes the nuclear pore complex that facilitates transport. The document outlines the roles of Ran GTPase and transport receptors in nuclear export. It provides details on the adaptor-receptor system and multistep process of mRNA export, including recruitment of export factors, translocation through the nuclear pore, and release into the cytoplasm. The summary concludes with sections on regulation and quality control of mRNA export.
RNA polymerase is an essential enzyme that copies DNA to produce different types of RNA in prokaryotes and eukaryotes. In prokaryotes, a single type of RNA polymerase synthesizes mRNA, tRNA, and rRNA. Transcription in prokaryotes involves initiation at promoter sequences, elongation as the RNA polymerase moves along DNA, and termination at specific sequences. Initiation requires the RNA polymerase binding to the promoter, unwinding the DNA, and beginning RNA synthesis. Elongation continues RNA synthesis as the DNA unwinds. Termination occurs at specific sequences like palindromes that allow RNA secondary structure formation and polymerase release.
This document provides an outline on RNA editing with 8 sections. It defines RNA editing as any process other than splicing that changes an RNA transcript sequence. It describes the main mechanisms of substitution and insertion/deletion editing, giving examples of A-to-I and C-to-U editing. It discusses the significance of RNA editing in regulating gene expression and increasing protein diversity. It also covers how RNA editing is important in the nervous system, immune system, and its role in cancers and potential for therapeutic intervention.
This document discusses the central dogma of biology and the process of transcription. It describes the three main steps of transcription - initiation, elongation, and termination. Initiation involves the RNA polymerase binding to the promoter sequence on DNA and separating the DNA strands to form an open complex. Elongation is the addition of nucleotides to synthesize RNA. Termination can occur via either Rho-independent or Rho-dependent mechanisms, with the former utilizing a terminator sequence and hairpin structure in the RNA and the latter involving the Rho protein.
Messenger RNA carries genetic code from DNA and is translated by the ribosome into proteins. This involves transfer RNA molecules that associate amino acids with their codons. Translation begins with initiation factors recruiting the small ribosomal subunit to the start codon. Elongation then occurs through peptide bond formation catalyzed by the ribosome and translocation of transfer RNAs. Termination occurs when a stop codon is reached. Translation is highly conserved and essential for protein synthesis in all organisms.
1. DNA replication is the process where parental DNA is used as a template to produce identical copies of DNA or daughter DNA. It ensures faithful transmission of genetic material to offspring.
2. Replication starts at specific origins of replication and involves initiation, elongation, and termination phases. Enzymes involved include DNA polymerases, helicases, primases, ligases and more.
3. Eukaryotic replication is more complex, with multiple polymerases and regulated initiation. Telomerase is required for end-replication and chromosome integrity.
4. DNA repair mechanisms include base excision, nucleotide excision, mismatch and double-strand break repair to fix errors and damage via pathways like non-homologous
DNA replication involves the synthesis of new DNA strands through a semi-conservative process whereby each new molecule contains one old strand and one new strand synthesized using the old strand as a template. Key enzymes involved include helicase, which unwinds the DNA double helix, primase, which initiates DNA synthesis, and DNA polymerase, which catalyzes phosphodiester bond formation to elongate the new strands. Fidelity is maintained through proofreading mechanisms that remove incorrectly incorporated nucleotides and DNA repair pathways that correct errors made during replication.
This document summarizes eukaryotic transcription by RNA polymerases. It discusses the three types of RNA polymerases (I, II, and III) found in eukaryotic cells, what genes each polymerase transcribes, and the basic stages and mechanisms of transcription (initiation, elongation, termination). It also describes the promoters, processing, and other regulatory elements involved in eukaryotic transcription.
It is the process of synthesis of protein by encoding information on mRNA.
Protein synthesis requires mRNA, tRNA, aminoacids, ribosome and enzyme aminoacyl tRNA synthase
CBCS 4TH SEM ,
CHARGING, STRUCTURE AND FUNCTION OF tRNA,
AMINOACYL RNA SYNTHETASE(ASR) PROOFREADING AND EDITING
https://www.youtube.com/watch?v=YzOVMWYLiCE
RNA splicing is the process by which introns, or non-coding sequences, are removed from pre-messenger RNA (pre-mRNA) to produce mature mRNA that can be translated into protein. Most genes contain introns that are removed by a spliceosome, a complex of RNA and proteins, leaving just the coding exons to form mRNA. Alternative splicing allows one gene to encode multiple proteins by selecting different combinations of exons. Errors in splicing can cause diseases if they result in truncated or abnormal proteins.
Eukaryotic transcription is carried out in the nucleus of the cell and proceeds in three sequential stages: initiation, elongation, and termination. Eukaryotes require transcription factors to first bind to the promoter region and then help recruit the appropriate polymerase.
The document discusses three models of DNA replication:
1) Asymmetric replication - the leading and lagging strands are replicated differently due to the 5' to 3' directionality of DNA polymerase. The leading strand replicates continuously while the lagging strand replicates discontinuously in short Okazaki fragments.
2) D-loop model - replication in mitochondria where one strand is displaced to form a D-loop and replicates first before the other strand.
3) Rolling circle model - used by plasmids and viruses where one strand is nicked and displaced to be used as a template, forming multiple copies linked together in a concatemer.
mRNA processing involves several key steps after transcription. These include 5' capping, which protects mRNA from degradation and aids in translation. Polyadenylation adds a poly-A tail to the 3' end, increasing stability and translation efficiency. Splicing removes non-coding introns and joins exons, which can produce different mRNAs and proteins from the same initial transcript. These processing steps are carried out by cellular enzymes for most eukaryotic mRNAs, but some viruses encode their own enzymes or acquire cellular mRNA caps to modify their own transcripts.
Eukaryotic transcription is carried out by three nuclear RNA polymerases that transcribe different genes. RNA polymerase II transcribes protein-coding genes in the nucleus. During transcription initiation, transcription factors help recruit RNA polymerase II to the promoter. Elongation occurs as RNA polymerase synthesizes RNA in a transcription bubble. Termination of RNA polymerase II transcription occurs via cleavage of the nascent RNA transcript followed by RNA degradation. The other polymerases terminate via sequence-specific signals in DNA or the synthesized RNA.
How cells read the genome from DNA to protein NotesYi Fan Chen
The document summarizes the process of transcription and translation in cells. It describes:
1) Transcription of DNA to RNA which is catalyzed by RNA polymerase and involves the formation of RNA through the addition of ribonucleotides.
2) Processing of eukaryotic pre-mRNA which involves capping, splicing, and polyadenylation to form mature mRNA.
3) Translation of mRNA to protein which occurs on ribosomes and involves tRNAs carrying amino acids that are linked together through peptide bond formation catalyzed by the ribosome. Accuracy is ensured by induced fit binding and kinetic proofreading.
Transcription in eukaryotes: A brief view
Transcription is the process by which single stranded RNA is synthesized by double stranded DNA. Transcription in eukaryotes and prokaryotes has many similarities while at the same time both showing their individual characteristics due to the differences in organization. RNA Polymerase (RNAP or RNA Pol) is different in prokaryotes and eukaryotes. Coupled transcription is seen in prokaryotes but not in Eukaryotes. In eukaryotes the pre-RNA should be spliced first to be translated.
In Eukaryotic transcription, synthesis of RNA occurs in the 3’→5’ direction. The 3’ end is more reactive due to the hydroxide group. 5’ end containing phosphate groups meanwhile, is not very reactive when it comes to adding new nucleotides. In Eukaryotes, the whole genome is not transcribed at once. Only a part of the genome is transcribed which also acts as the first, principle stage of genetic regulation.
Eukaryotes have five nuclear polymerases:
• RNA Polymerase I: This produces rRNA (23S, 5.8S, and 18S) which are the major components in a ribosome. This also produces pre-rRNA in yeasts.
• RNA Polymerase II: Helps in the production of mRNA (messenger RNA), snRNA (small, nuclear RNA), miRNA. This is the most studied type and requires several transcription factors for its binding
• RNA Polymerase III: This synthesizes tRNA (transfer RNA), 5S rRNA and other small RNAs required in the cytosol and nucleus.
• RNA Polymerase IV: Synthesizes siRNA (small interfering RNA) in plants.
• RNA Polymerase V: This is the least studied polymerase and synthesizes siRNA-directed heterochromatin in plants.
Eukaryotic transcription can be broadly divided into 4 stages:
• Pre-Initiation
• Initiation
• Elongation
• Termination
Transcription is an elaborate process which cells use to copy the genetic information stored in DNA into RNA. This pre-RNA is modified into mRNA before being transcribed to proteins. Transcription is the first step to utilizing the genetic information in a cell. Both Eukaryotes and Prokaryotes employ this process with the basic phases remaining the same. However eukaryotic transcription is more complex indicating the changes transcription has undergone towards perfection during evolution.
RNA splicing is a process where introns are removed from precursor messenger RNA (pre-mRNA) and exons are joined together to produce mature mRNA. It occurs in the nucleus and is essential for eukaryotes to produce proteins. The spliceosome, a large complex of RNA and proteins, facilitates two transesterification reactions that remove introns and ligate exons. RNA splicing generates protein diversity through alternative splicing and is important for cellular functions and disease processes.
Rifampicin binds to the beta subunit of prokaryotic RNA polymerase, inhibiting prokaryotic transcription initiation. It selectively binds bacterial RNA polymerase without affecting eukaryotic polymerases. This allows rifampicin to be an effective treatment for bacterial infections like tuberculosis and leprosy. Alpha amanitin from death cap mushrooms potently inhibits RNA polymerase II during both transcription initiation and elongation, potentially causing death in 10 days from just one mushroom due to failure of gene expression.
Transcription in prokaryotes and eukaryotesMicrobiology
Transcription is the process of synthesizing RNA from DNA and involves four main stages - initiation, elongation, termination, and post-transcription processing. It occurs differently in prokaryotes and eukaryotes. In prokaryotes, transcription and translation are coupled and occur in the cytoplasm, while in eukaryotes transcription occurs separately in the nucleus. The document provides details on the mechanisms and factors involved in each stage of transcription for both prokaryotes and eukaryotes.
Dna supercoiling and role of topoisomerasesYashwanth B S
supercoiling is one of the important process to condenses the huge amount of DNA to fit inside the histone and its also plays a role during the replication ,transcription etc..,these activities is carried out by an enzyme called topoisomerases.
This document summarizes the process of nuclear export of messenger RNA (mRNA). It begins with an introduction describing how mRNA must be exported from the nucleus to the cytoplasm to be translated into protein. It then discusses the importance of nuclear export and describes the nuclear pore complex that facilitates transport. The document outlines the roles of Ran GTPase and transport receptors in nuclear export. It provides details on the adaptor-receptor system and multistep process of mRNA export, including recruitment of export factors, translocation through the nuclear pore, and release into the cytoplasm. The summary concludes with sections on regulation and quality control of mRNA export.
RNA polymerase is an essential enzyme that copies DNA to produce different types of RNA in prokaryotes and eukaryotes. In prokaryotes, a single type of RNA polymerase synthesizes mRNA, tRNA, and rRNA. Transcription in prokaryotes involves initiation at promoter sequences, elongation as the RNA polymerase moves along DNA, and termination at specific sequences. Initiation requires the RNA polymerase binding to the promoter, unwinding the DNA, and beginning RNA synthesis. Elongation continues RNA synthesis as the DNA unwinds. Termination occurs at specific sequences like palindromes that allow RNA secondary structure formation and polymerase release.
This document provides an outline on RNA editing with 8 sections. It defines RNA editing as any process other than splicing that changes an RNA transcript sequence. It describes the main mechanisms of substitution and insertion/deletion editing, giving examples of A-to-I and C-to-U editing. It discusses the significance of RNA editing in regulating gene expression and increasing protein diversity. It also covers how RNA editing is important in the nervous system, immune system, and its role in cancers and potential for therapeutic intervention.
This document discusses the central dogma of biology and the process of transcription. It describes the three main steps of transcription - initiation, elongation, and termination. Initiation involves the RNA polymerase binding to the promoter sequence on DNA and separating the DNA strands to form an open complex. Elongation is the addition of nucleotides to synthesize RNA. Termination can occur via either Rho-independent or Rho-dependent mechanisms, with the former utilizing a terminator sequence and hairpin structure in the RNA and the latter involving the Rho protein.
Messenger RNA carries genetic code from DNA and is translated by the ribosome into proteins. This involves transfer RNA molecules that associate amino acids with their codons. Translation begins with initiation factors recruiting the small ribosomal subunit to the start codon. Elongation then occurs through peptide bond formation catalyzed by the ribosome and translocation of transfer RNAs. Termination occurs when a stop codon is reached. Translation is highly conserved and essential for protein synthesis in all organisms.
1. DNA replication is the process where parental DNA is used as a template to produce identical copies of DNA or daughter DNA. It ensures faithful transmission of genetic material to offspring.
2. Replication starts at specific origins of replication and involves initiation, elongation, and termination phases. Enzymes involved include DNA polymerases, helicases, primases, ligases and more.
3. Eukaryotic replication is more complex, with multiple polymerases and regulated initiation. Telomerase is required for end-replication and chromosome integrity.
4. DNA repair mechanisms include base excision, nucleotide excision, mismatch and double-strand break repair to fix errors and damage via pathways like non-homologous
DNA replication involves the synthesis of new DNA strands through a semi-conservative process whereby each new molecule contains one old strand and one new strand synthesized using the old strand as a template. Key enzymes involved include helicase, which unwinds the DNA double helix, primase, which initiates DNA synthesis, and DNA polymerase, which catalyzes phosphodiester bond formation to elongate the new strands. Fidelity is maintained through proofreading mechanisms that remove incorrectly incorporated nucleotides and DNA repair pathways that correct errors made during replication.
This document summarizes eukaryotic transcription by RNA polymerases. It discusses the three types of RNA polymerases (I, II, and III) found in eukaryotic cells, what genes each polymerase transcribes, and the basic stages and mechanisms of transcription (initiation, elongation, termination). It also describes the promoters, processing, and other regulatory elements involved in eukaryotic transcription.
It is the process of synthesis of protein by encoding information on mRNA.
Protein synthesis requires mRNA, tRNA, aminoacids, ribosome and enzyme aminoacyl tRNA synthase
CBCS 4TH SEM ,
CHARGING, STRUCTURE AND FUNCTION OF tRNA,
AMINOACYL RNA SYNTHETASE(ASR) PROOFREADING AND EDITING
https://www.youtube.com/watch?v=YzOVMWYLiCE
RNA splicing is the process by which introns, or non-coding sequences, are removed from pre-messenger RNA (pre-mRNA) to produce mature mRNA that can be translated into protein. Most genes contain introns that are removed by a spliceosome, a complex of RNA and proteins, leaving just the coding exons to form mRNA. Alternative splicing allows one gene to encode multiple proteins by selecting different combinations of exons. Errors in splicing can cause diseases if they result in truncated or abnormal proteins.
Eukaryotic transcription is carried out in the nucleus of the cell and proceeds in three sequential stages: initiation, elongation, and termination. Eukaryotes require transcription factors to first bind to the promoter region and then help recruit the appropriate polymerase.
The document discusses three models of DNA replication:
1) Asymmetric replication - the leading and lagging strands are replicated differently due to the 5' to 3' directionality of DNA polymerase. The leading strand replicates continuously while the lagging strand replicates discontinuously in short Okazaki fragments.
2) D-loop model - replication in mitochondria where one strand is displaced to form a D-loop and replicates first before the other strand.
3) Rolling circle model - used by plasmids and viruses where one strand is nicked and displaced to be used as a template, forming multiple copies linked together in a concatemer.
mRNA processing involves several key steps after transcription. These include 5' capping, which protects mRNA from degradation and aids in translation. Polyadenylation adds a poly-A tail to the 3' end, increasing stability and translation efficiency. Splicing removes non-coding introns and joins exons, which can produce different mRNAs and proteins from the same initial transcript. These processing steps are carried out by cellular enzymes for most eukaryotic mRNAs, but some viruses encode their own enzymes or acquire cellular mRNA caps to modify their own transcripts.
Eukaryotic transcription is carried out by three nuclear RNA polymerases that transcribe different genes. RNA polymerase II transcribes protein-coding genes in the nucleus. During transcription initiation, transcription factors help recruit RNA polymerase II to the promoter. Elongation occurs as RNA polymerase synthesizes RNA in a transcription bubble. Termination of RNA polymerase II transcription occurs via cleavage of the nascent RNA transcript followed by RNA degradation. The other polymerases terminate via sequence-specific signals in DNA or the synthesized RNA.
How cells read the genome from DNA to protein NotesYi Fan Chen
The document summarizes the process of transcription and translation in cells. It describes:
1) Transcription of DNA to RNA which is catalyzed by RNA polymerase and involves the formation of RNA through the addition of ribonucleotides.
2) Processing of eukaryotic pre-mRNA which involves capping, splicing, and polyadenylation to form mature mRNA.
3) Translation of mRNA to protein which occurs on ribosomes and involves tRNAs carrying amino acids that are linked together through peptide bond formation catalyzed by the ribosome. Accuracy is ensured by induced fit binding and kinetic proofreading.
The document summarizes key concepts about gene expression and analysis. It describes the central dogma of biology where DNA is transcribed into RNA which is then translated into protein. Gene structure is explained, noting that eukaryotic genes contain introns and exons. The roles of DNA, RNA and proteins in gene expression are outlined. The processes of transcription, including initiation, elongation and termination are summarized. Post-transcriptional processing of RNA including capping, splicing and polyadenylation is covered. Translation including initiation, elongation and termination is also summarized concisely. Control of gene expression occurs at transcriptional, post-transcriptional, translational and post-translational levels.
This document summarizes key aspects of gene transcription including:
1. Transcription is important for regulating cellular function and aberrant control can cause disease.
2. In eukaryotes, transcription and translation are separated in space and time, and primary RNA transcripts undergo extensive processing.
3. Prokaryotic transcription involves RNA polymerase recognizing promoters and transcribing DNA into RNA with sigma factors providing specificity. Eukaryotic transcription involves three RNA polymerases and more complex promoters.
This document discusses the relationship between genotype and phenotype. It provides examples of how gene expression in E. coli and Serratia marcescens is dependent on environmental conditions. It also summarizes the key steps in transcription, including initiation at the promoter, elongation as RNA polymerase copies DNA into mRNA, and termination. Transcription differs between prokaryotes and eukaryotes, with eukaryotic mRNA undergoing additional processing before translation.
Basics of Undergraduate/university fellows
Transcription is more complicated in eukaryotes than in prokaryotes because
eukaryotes possess three different classes of RNA polymerases and because of the
way in which transcripts are processed to their functional forms.
More proteins and transcription factors are involved in eukaryotic transcription.
Transcription is the process of synthesizing RNA using a DNA template. It involves three main steps - initiation, elongation, and termination. In initiation, RNA polymerase binds to promoter sequences on DNA and unwinds the double helix. In elongation, RNA polymerase moves along the DNA strand and adds complementary RNA nucleotides. Termination occurs when the polymerase reaches a terminator sequence and stops adding nucleotides. Prokaryotes and eukaryotes have similar transcription mechanisms but eukaryotes have three RNA polymerases and require additional transcription factors.
Transcription and synthesis of different RNAs
Processing of RNA transcript
Catalytic RNA
RNA splicing and Spliceosome
Transport of RNA through nuclear pore
Translation and polypeptide synthesis
Posttranslational modification
Protein trafficking and degradation
Antibiotics and inhibition of protein synthesis.
RNA is synthesized from DNA in a process called transcription. There are both similarities and differences between prokaryotic and eukaryotic transcription. In prokaryotes, transcription occurs in the cytoplasm, is carried out by a single type of RNA polymerase, and mRNA is transcribed directly from DNA. In eukaryotes, transcription occurs in the nucleus, utilizes three types of RNA polymerases, and produces hnRNA which is processed into mRNA. The key stages of transcription, initiation, elongation, and termination, occur through different mechanisms in prokaryotes and eukaryotes.
Biochem synthesis of rna(june.23.2010)MBBS IMS MSU
The document summarizes key aspects of RNA synthesis and processing. It discusses that RNA is synthesized from a DNA template in a process called transcription, which is carried out by RNA polymerases. It also describes that in eukaryotes, primary RNA transcripts undergo processing including capping, polyadenylation, and splicing to remove introns and join exons, producing mature mRNA that can then undergo translation to synthesize proteins.
The document summarizes RNA synthesis and post-transcriptional modifications. It discusses how RNA is synthesized from a DNA template in the 5' to 3' direction by RNA polymerases. It also describes the differences between prokaryotic and eukaryotic transcription, such as eukaryotes having multiple RNA polymerases and transcription occurring separately from translation. Specific transcription factors that regulate gene expression by binding to regulatory DNA sequences are also mentioned.
RNA synthesis, processing and modification.pptxArifulkarim4
The presentation discusses RNA synthesis, processing, and modification, explaining that RNA is synthesized from DNA through transcription by RNA polymerase. It describes the post-transcriptional modification of primary transcripts, including splicing of introns from mRNA, addition of a 5' cap and 3' poly-A tail, and modification of tRNA. The presentation also covers regulatory sequences that control transcription and the role of reverse transcription in retroviruses like HIV.
Gene expression & protein synthesisssuserc4adda
Gene expression involves the transcription of DNA into mRNA and the translation of mRNA into proteins. There are four main stages of protein synthesis: activation, initiation, elongation, and termination. Transcription is regulated by promoters, enhancers, and response elements that control the rate of transcription and influence which genes are expressed. Translation includes quality control mechanisms to ensure accuracy, such as ensuring amino acids are bound to the proper tRNAs and that termination occurs at stop codons. Mutations can occur during DNA replication or transcription and may be caused by mutagens, though cells have repair mechanisms. Recombinant DNA techniques allow genes to be spliced from one organism into a plasmid or virus for protein production in other cells.
• Define transcription• Define translation• What are the 3 steps.pdfarihantelehyb
• Define transcription
• Define translation
• What are the 3 steps of translation?
• Define the “genetic dogma”
• What is the function of Transfer RNA?
• What is the function of RNA polymerase?
• What is the function of DNA polymerase?
• Define “splicing of RNA”
• What is an exon?
• What component of the cell does the translation?
• What molecule in the cell does transcription?
• What are the functions of: operon, promotor?
• What is the difference between inducible operon and repressible operon?
Solution
• Define transcription
Transcription is the process of making an RNA copy of a gene sequence. This copy, called a
messenger RNA (mRNA) molecule, leaves the cell nucleus and enters the cytoplasm, where it
directs the synthesis of the protein, which it encodes. Here is a more complete definition of
transcription.
• Define translation
Translation is the process of translating the sequence of a messenger RNA (mRNA) molecule to
a sequence of amino acids during protein synthesis. The genetic code describes the relationship
between the sequence of base pairs in a gene and the corresponding amino acid sequence that it
encodes. In the cell cytoplasm, the ribosome reads the sequence of the mRNA in groups of three
bases to assemble the protein. Here is a more complete definition of translation:
• What are the 3 steps of translation?
Step # 1. Initiation:
Initiation of translation in E .coli involves the small ribosome subunit, a mRNA molecule, a
specific charge initiator tRNA, GTP, Mg++ and number of proteinaceous initiation factors (IFs).
These are initially part of the small subunit and are required to enhance binding affinity of the
various translational components (Table 8.1). Unlike ribosomal proteins, IFs are released from
the ribosome once initiation is completed.
Step # 2. Elongation:
Once both subunits of the ribosome are assembled with the mRNA, binding site for two charged
tRNA molecules are formed. These are designated as the ‘P’ or peptidyl and the ‘A’ or
aminoacyl sites. The charged initiator tRNA binds to the P site, provided that the AUG triplet of
mRNA is in the corresponding position of the small subunit. The increase of the growing
polypeptide chain by one amino acid is called elongation.
Step # 3. Termination:
Termination of protein synthesis is carried out by triplet codes (UAG, UAA, UGA; stop codons)
present at site A. These codons do not specify an amino acid, nor do they call for a tRNA in the
A site. These codons are called stop codons, termination codons or nonsense codons. The
finished polypeptide is still attached to the terminal tRNA at the P site, and the A site is empty.
• Define the “genetic dogma”
A theory in genetics and molecular biology subject to several exceptions that genetic information
is coded in self-replicating DNA and undergoes unidirectional transfer to messenger RNAs in
transcription which act as templates for protein synthesis in translation
• What is the function of Transfer RNA?
The tRNA molecule, or tr.
DNA- Transcription and Tranlation, RNA, Ribosomes and membrane proteins.pptxLaibaSaher
Detailed presentation on the topic of DNA, transcription and translation, RNA, Ribosomes and Membrane proteins. Along with their structure and functions. Detailed Diagram and complete description of the processes. Along with references and Gifs that makes the presentation look more creative.
Transcription is the process of creating messenger RNA (mRNA) from DNA. In eukaryotes, RNA polymerase binds to promoter regions and transcribes DNA into pre-mRNA, which undergoes processing including capping, polyadenylation, and splicing to remove introns. The mature mRNA is exported from the nucleus to the cytoplasm for protein synthesis. Prokaryotic transcription involves RNA polymerase binding to promoter regions and transcribing DNA into mRNA. Transcription is regulated by factors that influence RNA polymerase binding and activity.
BIOTRANSFORMATION OF NON-STEROID COMPOUNDS.pptxdrpvczback
BIOTRANSFORMATION OF NON-STEROID COMPOUNDS
BIOTRANSFORMATION
Oxidation
Reduction
Hydrolysis
Isomerization
Condensation
Formation of new carbon bond
Introduction of functional group
Agarose Gel Electrophoresis
Estimate the size of molecules
Agarose in AGE
Gel Loading Buffer
Nucleic Acid Stain
Factor affecting mobility of DNA
Factor affecting Resolution
Smearing
Atomic absorption spectrometry is a technique used to determine the concentration of chemical elements in solution. It works by vaporizing the elements in a flame or graphite furnace and measuring how much light of a specific wavelength is absorbed, which indicates the concentration. Key components of an atomic absorption spectrometer include a light source, atomizer such as a flame or furnace, monochromator, detector, and display. Flame atomic absorption is used for higher concentrations while graphite furnace atomic absorption can detect trace levels. Potential interferences must also be considered and addressed.
Spectrofluorometry
what cause fluorescence
Quantification
Instrumentation
Effect of Solvent, Temperature and pH
Application
Energy change of excited molecules Molecular Spectra
Fate of Excited State
LASER
Colorimeter and Spectrophotometer
Electromagnetic Radiation
EMR
THE ELECTROMAGNETIC SPECTRUM
Interaction of e.m.r. with Matter
Molecular Spectra
Spectrophotometry
Principles OF Spectrophotometry
Introduction
Types of Transcription
factors involves in different Polymerase initiation complex
Structure of transcription factor
Role of transcription factor
Significance
RNA transport
Multiple classes of RNA are exported from the nucleus
Transportation through nuclear pore complex.
Ribosomal subunits are assembled in the nucleolus and exported by exportin 1
tRNAs are exported by a dedicated exportin
Messenger RNAs are exported from the nucleus as RNA-protein complexes
Messenger RNAs are exported from the nucleus as RNA-protein complexes
hnRNPs move from sites of processing to NPCs
Precursors to microRNAs are exported from the nucleus and processed in the cytoplasm
RNA Editing
Discovery of RNA Editing in Trypanosome Mitochondria
real functional genes
RNA EDITING IN KINETOPLAST OF TRYPANOSOMES.
Guide RNA (gRNA)
Guide RNAs Direct Editing in Trypanosomes
Editing is catalyzed by a multiprotein complex
Other Systems with RNA Editing
RECOMBINATION MECHANISM
PROKARYOTIC AND EUKARYOTIC CELLS
RECOMBINATION
MITOTIC AND MEIOTIC RECOMBINATION
CLASSES OF RECOMBINATION
HOMOLOGOUS RECOMBINATION
DOUBLE-STRAND BREAK MODEL
DNA RECOMBINATION
Recombination
Breaking and rejoining of two parental DNA molecules to produce new DNA molecules
Types of recombination
Definition of recombination
Gene Conversion – Characteristics
Holliday model
Holliday junction cleavage
This document discusses protein targeting in eukaryotic cells. It explains that each organelle has a distinct set of proteins that allow it to perform specific functions. There is a complex system that moves newly synthesized proteins from the site of synthesis to their proper destination. Proteins contain targeting sequences that direct them to the correct organelle, such as receptors to the plasma membrane or DNA polymerase to the nucleus. Targeting can occur co-translationally as the protein is synthesized on ER-bound ribosomes or post-translationally after cytosolic synthesis. The targeting sequences help distinguish the destination but are sometimes cleaved off later.
This document discusses protein targeting in eukaryotic cells. It explains that each organelle has a distinct set of proteins that allow it to perform specific functions. There is a complex system that moves newly synthesized proteins from the site of synthesis to their proper destination. Proteins contain targeting sequences that direct them to the correct organelle, such as receptors to the plasma membrane or DNA polymerase to the nucleus. Targeting can occur co-translationally as the protein is synthesized on ER-bound ribosomes or post-translationally after cytosolic synthesis. The targeting sequences help distinguish the destination but are sometimes cleaved off later.
The document provides information about protein synthesis and processing. It begins with an overview of the topics to be covered, including ribosome formation, initiation and elongation factors, termination, the genetic code, tRNA aminoacylation, aminoacyl-tRNA synthetases, translational proofreading, inhibitors, and post-translational modifications. It then discusses the machinery of protein synthesis, including transcription, the genetic code, RNA, tRNA identity, aminoacyl-tRNA synthetases, aminoacylation of tRNA, and the ribosome. The mechanisms of initiation, elongation, and termination are explained in detail.
BIOSYNTHESIS OF PYRIMIDINES
SALVAGE PATHWAY
DE NOVO PATHWAY
SYNTHESIS OF OTHER PYRIMIDINE NUCLEOTIDES
IMPORTANCE
Essential building blocks of nucleic acids
Biologically very important heterocycles
Used in anti-biotics, used as anti-bacterial and anti-fungal also
Derivatives of pyrimidine also possess good anti-viral properties
MECHANISM OF TRANSCRIPTION prashant.pptxdrpvczback
MECHANISM OF TRANSCRIPTION
Transcription is the first step of gene expression, in which a particular segment of DNA is copied into RNA by the enzyme RNA polymerase. During transcription, a DNA sequence is read by RNA polymerase, which produces a complementary RNA strand.
The debris of the ‘last major merger’ is dynamically youngSérgio Sacani
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
BREEDING METHODS FOR DISEASE RESISTANCE.pptxRASHMI M G
Plant breeding for disease resistance is a strategy to reduce crop losses caused by disease. Plants have an innate immune system that allows them to recognize pathogens and provide resistance. However, breeding for long-lasting resistance often involves combining multiple resistance genes
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
The binding of cosmological structures by massless topological defectsSérgio Sacani
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
DERIVATION OF MODIFIED BERNOULLI EQUATION WITH VISCOUS EFFECTS AND TERMINAL V...Wasswaderrick3
In this book, we use conservation of energy techniques on a fluid element to derive the Modified Bernoulli equation of flow with viscous or friction effects. We derive the general equation of flow/ velocity and then from this we derive the Pouiselle flow equation, the transition flow equation and the turbulent flow equation. In the situations where there are no viscous effects , the equation reduces to the Bernoulli equation. From experimental results, we are able to include other terms in the Bernoulli equation. We also look at cases where pressure gradients exist. We use the Modified Bernoulli equation to derive equations of flow rate for pipes of different cross sectional areas connected together. We also extend our techniques of energy conservation to a sphere falling in a viscous medium under the effect of gravity. We demonstrate Stokes equation of terminal velocity and turbulent flow equation. We look at a way of calculating the time taken for a body to fall in a viscous medium. We also look at the general equation of terminal velocity.
2. CONTENTS
• INTRODUCTION
• TYPES OF RNA
• A STRUCTURAL GENE
• EUKARYOTIC RNA POLYMERASES
• MECHANISM OF TRANSCRIPTION IN EUKARYOTES:
- INITIATION
- ELONGATION
- TERMINATION
• TRANSCRIPTION FACTORS
• ACTIVATORS, MEDIATORS & CHROMATIN
MODIFYING PROTEINS
• RNA SPLICING
• DIFFERENCE BETWEEN PROKARYOTIC &
EUKARYOTIC TRANSCRIPTION
2
3. INTRODUCTION
Transcription, or RNA synthesis, is the process of
creating RNA , copy of a sequence of DNA.
Both RNA and DNA are nucleic acids, which
use base pairs of nucleotides as a complementary
language that can be converted from DNA to RNA in
the presence of the correct enzymes.
During transcription, a DNA sequence is read by RNA
polymerase, which produces a complementary RNA
strand.
3
5. 5
Types of RNAs Produced in Cells
Types of RNAs Functions
mRNAs (messenger) code for proteins
rRNAs (ribosomal) comprise ribosomes
tRNAs (transfer) adaptors between mRNA and
amino acids in protein synthesis
hnRNAs (heterogeneous nuclear) precursors & intermediates of mature
mRNAs & other RNAs
snRNAs (small nuclear) splicing of pre-mRNAs
snoRNAs (small nucleolar) rRNA processing/maturation/
methylation
scRNAs (small cytoplasmic) signal recognition particle (SRP) /
tRNA processing
miRNAs (Micro) regulatory RNAs (regulation of
transcription and translation, other??)
siRNAs (small interfering) regulatory RNAs (regulation of
transcription and translation, other??)
Other non-coding RNAs telomere synthesis, X-chromosome
inactivation, protein transport
6. The Central Dogma
▪ The central dogma of molecular biology describes the two-step
process, transcription and translation, by which the information
in genes flows into proteins.
▪ Conventional concept (pre-bioinformatics era) of central dogma
of life:
It is an over simplification of molecular biology.
DNA → RNA → Protein
▪ Current concept (Bioinformatics era) of central dogma of life:
With the advances in cell biology and rapid developments
in bioinformatics, the term Genome, Transcriptome and
Proteome are in current use to represent the central dogma of
molecular biology.
Genome → Transcriptome → Proteome
11. Basic Structure of a Protein-Coding Gene
▪A protein-coding gene consists of a promoter followed by the coding
sequence for the protein and then a terminator.
▪The promoter is a base-pair sequence that specifies where
transcription begins.
▪The coding sequence is a base-pair sequence that includes coding
information for the polypeptide chain specified by the gene.
▪The terminator is a sequence that specifies the end of the mRNA
transcript.
12. DNA and RNA: Nucleotides, Bases and Polynucleotide's
13. • Exons: Exons code for amino acids and
acid sequence of the protein product. It is
these portions of the gene that are
represented in final mature mRNA
molecule.
• Introns: Introns are portions of the gene
that do not code for amino acids, and are
removed (spliced) from the mRNA
molecule before translation.
14. Control regions
• Start site:- A start site for transcription.
• Promoter:- A region a few hundred
nucleotides 'upstream' of the gene (toward
the 5' end). It is not transcribed into mRNA,
but plays a role in controlling the
transcription of the gene. Transcription
factors bind to specific nucleotide
sequences in the promoter region and assist
in the binding of RNA polymerases.
15. • Enhancers: Some transcription factors
(called activators) bind to regions called
'enhancers' that increase the rate of
transcription. Some enhancers are
conditional and only work in the presence of
other factors as well as transcription
factors.
• Silencers: Some transcription factors
(called repressors) bind to regions called
'silencers' that depress the rate of
transcription.
16. Eukaryotic RNA Polymerases (RNAPs)
In bacteria (prokaryote), all mRNA is made from the
same RNA polymerase (single RNAP). However, in
eukaryotes, there are three different RNA polymerases
in animals and four in plants.
1. RNA Polymerase I: synthesizes rRNA
2. RNA Polymerase II: synthesizes all Protein
coding genes & mostly mRNA.
3. RNA polymerase III: synthesizes tRNAs and
also snRNAs (small nuclear RNAs) and
scRNAs (small cellular RNAs).
16
17. 17
Four RNA Polymerases of Eukaryotic Cells
Type of Polymerase Genes Transcribed
RNA pol I rRNA genes (5.8S, 18S, and 28S)
RNA pol II mRNA genes (protein coding genes),
snoRNA genes, some snRNA genes,
microRNAs genes
RNA pol III tRNA genes, 5S rRNA genes
some snRNA genes, genes
for other small RNAs
RNA pol IV plants only; small interfering
RNAs (siRNAs)
18. Eukaryotic Transcription
Initiation:
• In eukaryotes, the initiation of transcription,
requires the presence of a
core promoter sequence in the DNA. Promoters
are regions of DNA which promote transcription
and are found around -10 to -35 base pairs
upstream from the start site of transcription. Core
promoters are sequences within the promoter
which are essential for transcription initiation.
RNA polymerase is able to bind to core promoters
in the presence of various specific transcription
factors.
19. • The most common type of core promoter in eukaryotes is a
short DNA sequence known as a TATA box (Hogness box). The
TATA box, as a core promoter, is the binding site for a
transcription factor known as TATA binding protein (TBP),
which is itself a subunit of another transcription factor, called
Transcription Factor II D (TFIID).
• One transcription factor, DNA helicase, has helicase activity
and so is involved in the separating of opposing strands of
double-stranded DNA to provide access to a single-stranded
DNA template.
19
20. Eukaryotic transcription
ELONGATION:
• In eukaryotes, the RNA is processed at both ends
before it is spliced.
• At the 5‘ end, a cap is added consisting of a
modified GTP (guanosine triphosphate). This occurs
at the beginning of transcription. The 5' cap is used
as a recognition signal for ribosomes to bind to the
mRNA.
• At the 3' end, a poly(A) tail of 150 or more adenine
nucleotides is added. The tail plays a role in the
stability of the mRNA.
20
21. • The Transcription Process
▪ RNA synthesis involves separation of the DNA strands and
synthesis of RNA molecule in the 5' to 3' direction by RNA
polymerase, using one of the DNA strands as a template.
▪ In complementary base pairing, A, T, G, and C on the template DNA
strand specify U, A, C, and G, respectively, on the RNA strand being
synthesized.
22. EUKARYOTIC TRANSCRIPTION
TERMINATION:
• Transcription termination in eukaryotes is less
understood but involves cleavage of the new
transcript followed by template-independent
addition of As at its new 3' end, in a process
called polyadenylation.
23. Termination of transcription in eukaryotes:
addition of poly(A) tails
• In eukaryotes, termination of transcription occurs
by different processes, depending upon the exact
polymerase utilized. For pol I genes, transcription
is stopped using a termination factor, through a
mechanism similar to rho-dependent termination
in bacteria. Transcription of pol III genes ends
after transcribing a termination sequence that
includes a polyuracil stretch, by a mechanism
resembling rho-independent prokaryotic
termination. Termination of pol II transcripts,
however, is more complex.
24. Termination of transcription in eukaryotes:
addition of poly(A) tails
• Transcription of pol II genes can continue for hundreds or
even thousands of nucleotides beyond the end of a coding
sequence. The RNA strand is then cleaved by a complex
that appears to associate with the polymerase. Cleavage
seems to be coupled with termination of transcription and
occurs at a consensus sequence (TTATTT on coding
region of template strand of DNA and consequently
AAUAAA sequence on pre-mRNA). The pre-mRNA,
carrying this signal as AAUAAA, is then cleaved by a
special endonuclease that recognizes the signal and cuts
at a site 11 to 30 residues to its 3' side. Mature pol II
mRNAs are polyadenylated at the 3′-end, resulting in a poly
(A) tail (Template-independent); this process follows
cleavage and is also coordinated with termination.
27. Transcription factors
• Transcriptional control is orchestrated by a large number of
protein ,called “transcription factor”.
• About 10% gene in the human genome encodes
transcription factors.
• RNA-pol does not bind the promoter directly.
• RNA-pol II associates with six transcription factors- TFII A,
TFIIB, TFIID, TFIIE, TFIIF, TFII H.
• These factors, position polymerase molecules at
transcription start sites and help to melt the DNA strands so
that the template strand can enter the active site of the
enzyme.
28. Types
• The general factors : Required for the initiation of RNA synthesis at
all promoters. They determine the site of initiation ; this complex
constitute the basal transcription apparatus.
• The upstream factors : DNA-binding proteins that recognize specific
short consensus elements located upstream the transcription start
point (e.g. Sp1, which binds the GC box). They increase the
efficiency of initiation.
• The inducible factors : Function in the same general way as the
upstream factors, but have a regulatory role. They are synthesized or
activated at specific times and in specific tissues.
29. Structure of transcription factors
• IT HAS 2 DOMAINS :
1.DNA binding domain. 2.Activation
domain.
• GAL4 and GCN4 are yeast
transcription activators.
• The glucocorticoid receptor (GR)
promotes transcription of target
genes.
• SP1 binds to GC-rich promoter
elements in a large number of
mammalian genes.
30. Factor Mass ( kD) Function
TFIIA 69 Stabilize TBP & TAF binding
TFIIB 35 Stabilize TBP binding,
recognize BRE element
TFIID TBP 38 Recognizes TATA box
TAF >960 Regulates DNA binding by
TBP
TFIIE 165 Regulates helicase activity of
TFIIH
TFIIF 87 Binding of TFIIE & TFIIH
TFIIH 470 Unwinds DNA at the
transcription start point
32. • TBP and TFII D binds TATA
• TFII A and TFII B bind TFII D
• TFII F-RNA-pol complex binds TFII B
• TFII F and TFII E open the dsDNA (helicase and
ATPase)
• TFII H: completion of PIC
Pre-initiation complex (PIC)
34. • TF II H is of protein kinase activity to
phosphorylate CTD of RNA-pol. (CTD is the
C-terminal domain of RNA-pol)
• Only the P-RNA-pol can move toward the
downstream, starting the elongation phase.
• Most of the TFs fall off from PIC during the
elongation phase.
Phosphorylation of RNA-polymerase
P-RNA-pol
39. Definition
“ An activator is a DNA- binding protein that
regulates one or more genes by increasing the
rate of transcription.”
They stimulate transcription by two
mechanism:
They interact with mediators proteins and
general transcription factors to facilitate the
assembly of a transcription complex and
stimulate transcription.
They interact with co- activators that facilitate
transcription by modifying chromatin structure.
41. Role In Transcriptional Regulation
How does an activator stimulate transcription?
• The recruitment model argues that its sole effect is to increase the
binding of RNA polymerase to the promoter.
• An alternate model is to suppose that it induces some change in the
conformation of the enzyme.
46. Structure
Mediator is a large
complex of 21
polypeptides with a
combined weight of
1MDa.
Single particle
electron microscopy
images reveals that it
had an elongated,
roughly conical
shape,400 Ao in
length.
47. Role In Transcriptional Regulation
• Assist in the
assembly of Pol II
pre initiation
complexes.
• Also some
mediators have
histone acetylase
activity.
50. Definition
The general process of
inducing changes in the
chromatin structure is called
chromatin remodeling or
chromatin modification.
And hence the proteins
involved in the modification
of the chromatin structure
so that the transcription
factor and the RNA
Polymerase can get an
access to the promoter
DNA and make the gene
transcribable.
51. Chromatin Remodeling Enzymes
These includes
acetylases,
deacetylases,
methylases, etc.
Changes in the
chromatin structure
are initiated by
modifying the N-
terminus tail of the
histones, especially
H3 & H4.
52. Histone acetyl transferases
• Enzymes that can acetylate
histones are called Histone
acetyl transferases.
• Acetylate conserved lysine
amino acids on histone
protein by transferring an
acetyl group from acetyl CoA
to form e- N- acetyl lysine.
• Histone acetylation
neutralizes the positive charge
which renders DNA
accessible to transcription
factor & hence linked with
transcriptional activation.
53. Histone deacetylases
These are a class of
enzymes that remove
acetyl group from e- N-
acetyl lysine on a histone.
Its action is opposite to the
histone acetyl transferases.
They remove those acetyl
groups increasing the
positive charge of histones
and encouraging high-
affinity binding between the
histones and the DNA
backbone.
Increased DNA binding
condenses DNA structure,
preventing transcription.
54. Histone methylases
Histones methylases are
enzymes that catalyze the
transfer of one to three
methyl groups from the
cofactor S- Adenosyl
methionine to lysine and
arginine residues of
histone.
Methylated histones bind
more tightly, which inhibits
transcription.
Deacetylation allows
methylation to occur,
which causes formation of
a heterochromatic
complex.
55. • Transcription factors bind
to specific sequences.
• Remodeling complex binds
via factor.
• Factor is released.
• Remodeling changes the
nucleosomal organization.
• Acetylase complex binds
via remodeling complex.
• Histones are modified.
57. DEFINATIONOF RNA SPLICING
• The process of cutting the pre-RNA to
remove the introns and joining together of the
exons is called splicing.
• This process is done on RNA strands so it
is known as RNA SPLICING.
• In Eukaryotes it takes place in the nucleus
before the mature RNA can be exported to the
cytoplasm.
58. The intron is also present in the RNA copy of the gene and
must be removed by a process called “RNA splicing”
protein
translation
mRNA
RNA splicing
pre-mRNA
intron
59. RNA SPLICING
• Most introns start from the sequence GU and end with
the sequence AG (in the 5' to 3' direction). They are
referred to as the splice donor and splice
acceptor site, respectively. However, the sequences
at the two sites are not sufficient to signal the presence
of an intron. Another important sequence is called
the branch site located 20 - 50 bases upstream of the
acceptor site. The consensus sequence of the branch
site is "CU(A/G)A(C/U)", where A is conserved in all
genes.
• In over 60% of cases, the exon sequence is (A/C)AG at
the donor site, and G at the acceptor site.
59
61. MECHANISM OF SPLICING
RNA splicing mechanism by Spliceosomes
1. Self or Cis- splicing mechanism
- Splicing in single RNA
- Lariat shape
- Common
2. Trans- splicing mechanism
- Splicing in two different RNAs
- Y- shape
- Rare (e.g. C. elegance and higher
eukaryotes
62. Spliceosome Complex Formation
A spliceosome is a complex of specialized
RNA and PROTEIN subunits.
Composed of five snRNPs (U1, U2, U4, U5
and U6), other splicing factors and the pre-
mRNA being assembled.
U1 binds to the 5’ splice site, and U2 to the
branch point, after that the tri-snRNP
complex of U4, U5 and U6.
As a result, the intron is looped out and the
5’ and 3’ exon are brought into close
proximity.
U2 and U6 snRNP are able to catalyze the
splicing reaction.
65. Self-Splicing mechanism-
Group-I intron sequences
1. Guanine in introns
initiate attack on 5’
splice sites.
2. 3’OH of upstream
exons reacts with
downstream exons.
3. Exons are joined and
lariat is released.
66. “hand”
Self-Splicing mechanism-
Group-II intron sequences
1. Adenine in introns
initiates attack on
5’splice sites.
2. 3’-OH of upstream
exons reacts with
downstream exons.
3. Exons is joined and
lariat is released.
74. DIFFERENCE BETWEEN PROKARYOTIC & EUKARYOTIC TRANSCRIPTION
PROKARYOTES
1. Single core DNA dependent
RNA Polymerase
2. RNA Polymerase do not require
additional protein (i.e.
Transcription factor) for
initiation and regulation of
transcription.
3. Transcription takes place on
free DNA
4. Promoter sequences-
TATpuATpu (Pribnow box)
located -10 bp of upstream.&
TTGACA Located -35 bp
upstream
EUKARYOTES
1. Multiple different DNA
dependent RNA Polymerases-
I, II, III
2.. RNA Polymerase requires a
variety of additional proteins
(i.e. Transcription factors) for
initiation and regulation of
transcription.
3. Transcription takes place on
chromatin rather than on free
DNA (so chromatin structure
is an important factor).
4. Promoter sequences-TATAbox
(Hogness box) Located -30bp
upstream & CAATbox Located
-70 to -80bp upstream
74