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Energy Changes in Nuclear Reactions (Section)An analytical

Chemistry: The Central Science | 12th Edition | ISBN: 9780321696724 | Authors: Theodore E. Brown; H. Eugene LeMay; Bruce E. Bursten; Catherine Murphy; Patrick Woodward ISBN: 9780321696724 27

Solution for problem 44E Chapter 21

Chemistry: The Central Science | 12th Edition

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Chemistry: The Central Science | 12th Edition | ISBN: 9780321696724 | Authors: Theodore E. Brown; H. Eugene LeMay; Bruce E. Bursten; Catherine Murphy; Patrick Woodward

Chemistry: The Central Science | 12th Edition

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Problem 44E

Problem 44E

Energy Changes in Nuclear Reactions (Section)

An analytical laboratory balance typically measures mass to the nearest 0.1 mg. What energy change would accompany the loss of 0.1 mg in mass?

Step-by-Step Solution:
Step 1 of 3

April 6, 2016 Chapter 12: Gene Transcription and RNA Modification Prokaryotic Transcription  Overview of Transcription  Central Dogma o DNA  RNA  Proteins o Classes  Components of Transcription o Transcription Sequences o Transcription Steps  I. Initiation  II. Elongation  III. Termination o The Various Roles of RNA Transcripts – This is an important point to consider: RNA has numerous functions it can perform after transcription  1. Structural  2. Standard  3. Atypical (Assessed by the Sedimentation Coefficient)  Steps Detailed o I. Initiation  A. Promoter Sequence  B. RNA Polymerase II (Halo-Enzyme, made of two components)  C. Haloenzyme Binding  D. Short RNA Strand Synthesis o II. Elongation o III. Termination  This is marked by the breaking of the DNA/RNA hybrid  Prokaryotes rely on Rho Pathways, Rho separates them by breaking the H-Bonds Eukaryotic Transcription  Overview o Complications and Differences with Eukaryotic DNA  1) Histone Association  The Histones are attracted because of the charges (Agrinine, Lysin to the Phosphates)  Histone modification is a way of allowing the unwinding of DNA from Histones  2) Cellular Complexity  Polycistronic mRNA is not seen in Eukaryotes  Organelles exist which allow for specific, regional protein construction – no Polycistronic nuclear mRNA  3) Multicellularity  There’s a complex balance in Eukaryotes – some genes are permanently upregulated, some permanently downregulated o RNA Polymerases  Poly I – rRNA except for 5S Subunit  Poly II – mRNA, structural genes, and Small Nuclear RNA of Spliceosomes  Poly III – tRNA and the 5S Ribosomal RNA subunit  A Look at RNA Polymerase o I. Clamp –  The units work like a jaw, having to open up to take the DNA o II. Bridge –  The DNA settles at the Bridge and makes a Right Handed turn  Right turns occur at β’ and β (The catalytic units) o III. Rudder –  Eukaryotes have a rudder that is 9bp ahead that breaks the template in order to dissociate  This is only significant difference between Eukaryotes and Prokaryotes  Steps for Structural Genes o I. INITIATION  A Promotor region initiates the transcription process, similar concept to that of Prokaryotes  1. Start Site (+1)  2. TATA Box Region (Adjacent to -25) o A Core Promoter sequence region exists in Eukaryotes, the TATA Box and Start Site are the Core Promoter o A well-defined TATA Box free of mutations results in definitely having small amounts of transcription (Basal Transcription)  3. Regulatory Elements (Between -50 and -100bp) o There are enhancers and silencers (and they are sequences, not proteins o Present between -50 and -100 o Two Actors: Cis Trans Next to, immediately Opposite, away from, upstream or within the chromosome Different chromosome, factors that diffuse Usually sequences through cytoplasm and nucleus, and bind to trans  Then the Closed Complex must form (All 5 Transcription Factors and RNA II)  I. RNA Polymerase II  II. Transcription Factors of RNA Polymerase II (5 Proteins, General Transcription Factors (GTFs)) o 1] TFIID  Recognizes the TATA Sequence After Promoter Region,  Huge protein complex Need these components  TATA Binding Protein (TBP) to carry out Transcription  TBP-Associated Factors (TAFs)  Binds and moves to read the rest, then A. RNA Polymerase II reverses before “deciding” to bind B. Transcription Factors  Does so after DNA has opened up o 2] TF2B C. Mediator Complex  Brings in the RNA Poly II to bind to the Promoter Sequence  Forms the Bridge o 3] TFIIF  Comes in along with RNA Polymerase II o 4] TFIIE  Initiates and maintains the Open Complex o 5] TFIIH  Acts as Helicase to continue open up o II. ELONGATION  How Does Basal transcription move into Elongation  RNA Polymerase II has a Carboxy-Terminal Domain (CTD)  When it is Phosphorylated, Elongation begins  TFIIH also has ATPase and Protein Kinase Activity (hydrolyzes ATP and transfers Phosphate)  That activity causes separation of TFIIB and RNA Polymerase II  That release causes the release of others as well  III. Mediator Protein Complex o Co-Activator, Large Complex o Appears to regulate the ability of TFIIH to Phosphorylate CTD  Elongation process o III. TERMINATION  Initiation of Termination begins  Two Models  1. Allosteric Model  2. Torpedo Model  RNA Modification o There is Co-Linear Process to Gene Expression in Prokaryotes o Eukaryotes stray from Co-Linearity  They instead splice and remove and modify (the whole process is Trimming) o Types of RNA Trimming  1) rRNA – Occurs in the Nucleolus; ribo-endonucleases  2) mRNA – 5’ Capping and 3’ Poly-A Tails Occur  3) tRNA  Occurs in the Nucleoplasm instead of the Nucleolus  Made of huge precursors, but need to get to 70-90bp to be functional  They have to undergo cleavage at the 5’ and 3’ ends  Acted on by RNase P (made of 375bp RNA and 20kDA Protein) o Forms the acceptor stem, reading as 5’ CCA 3’ o Is a Ribozyme, so RNA does the catalytic action of removing the nucleotides  tRNA Nucleotidyl Transferase ensures that the 5’ CCA sequence is present o This is the acceptor Stem (accepts the AA) RNase P RNase Z RNase D 375bp RNA unit Removes 170bp The only Exonuclease 20kDa Protein Fragment on the Removes about 9bp 3’ End Removes Acts after RNase Z removes the nucleotides on Allows RNase D fragment the 5’ End Action Usually ensures the 5’ CCA 3’ code Ribozyme (RNA does the If 5’CCA3’ is not present, tRNA catalysis) Nucleotidyl Transferase ensures its Endonuclease addition (every tRNA will have this) This is the Acceptor Stem has an amino acid connector Components of Transcription  Discovery of Introns o Were not thought to exist in Eukaryotes because Prokaryotes do not utilize introns o Experiment utilized Hybridization (Double Stranded cDNA of β- Globin and its mature mRNA) o General Concept  1) Denaturing of Globin cDNA  Hydrogen bonds between coding and template strands are broken  2) Measuring the Anneal Rates and Images  Separated mRNA would anneal much more quickly because of the size (it’s smaller)  It anneals with the template (because it would be the RNA version of the Coding Strand)  cDNA is constructed by reverse transcriptase on mRNA to create the template strand o What is cDNA  It is formed through reverse transcriptase so as the have a protein-ready (they have no introns)  This the DNA that can be purchased o Found the existence of Exon Loops (R- Loops, mRNA Displacement Loops) and Intron Loops (Double Stranded DNA)  Introns were not displaced because the complementary sections in the mRNA had been spliced o Procedure  1) mRNA Isolation (Functional β Globin RNA)  2) cDNA (the entire Globin Gene)  3) Separate DNA (70% formamyde to break bonds, 16 hours)  4) Dilute to Anneal (diluting formamyde allows annealing)  5) Stain for Viewing on the slide (heavy metal)  6) Observe R-Loops and Intron Segments (Electron Microscopes)  Splicing – Removing of Introns, Attaching Exons Together (phosphodiester bond); Has Three Types o I. Fall Into Group I and Group II (intrinsic, self-splicing)  Mostly in lower Eukaryotes, Protoplast, Mitochondria  These have intrinsic properties (self-splicing)  In Vitro studies show these splice spontaneously  In Vivo studies show Mutarase increases the rate, but does not induce Splicing Group I Group II Guanosine is the key factor One of the Introns has Adenine, (Guanosine Binding Sites Exist, which makes the process very binding to each other to initiate) – position specific – no outside outside molecule molecule Initial break occurs in the 5’ end after 2ndCarbon Catalyzes the Guanosine binds s(from Guanosine attachment of Adenine with the 5’ Alcohol attacking Exon 1, forming a Enstof the Intron, which causes the loop and free Exon) 1 Exon Break at the 3’ End of Exon (forms a loop within Intron and an open 3’ Hydroxy, like in Group 1) 5’ Break initiates the 3’ Break (because the free alcohol in the open 3’ Exon 1 can now attack Exon 2) Then the 5’ End of Exon 2 Break occurs because of the Catalytic capacity of the free Exon 1 and (This 3’ End of the Exon attacks the 2 ndIntron Structure) Left with two strands, Guanosine capped single strand (Intron) and mature mRNA Leaves an “Intron Ring” with the original Adenine having released the Exon 2 o II. Spliceosomes are the third type  These involve a catalytic complex to act and produce mRNA  Act on pre-mRNA  These produce mRNA which is identical to the Coding Strand  The introns are removed with these massive Complexes  Made of Small Nuclear RNA (snRNA) and Proteins  SNERPS  The snRNAs have specific and important functions  Subunit Functions  1) BIND – Bind to an intron sequence and precisely recognize the intron-exon boundaries  2) HOLD – Hold the pre-mRNA in the correct configuration  3) BOND – Catalyze the chemical reactions that remove introns and covalently link exons  Consensus Sites for Splicing  The intron is defined by particular sequences within the intron and at the boundary  “GU-A-AG”  These sequences are seen consistently, with the central Adenine serving as a branch site (similar to Group II)  SNERPS Types  1) U1 – identifies the Intron, binds to the 5’ Splice Site  2) U2 – comes in after and binds to the Adenine in the Branch Site  3) U4/U6 Dimer – enters as a dimer along with U5 to induce proximity  4) U5 – comes in with U4/U6 (sort of trimer action)  Spliceosome Steps  1) U1 Binds to the 5’ Splice Site  2) U2 Binds to the Adenine in the Branch Site  3) U4/U6 Dimer and U5 Bind and induce a proximity loop  4) 5’ Splicing Occurs (after all SNERPS are present) with the newly exposed 5’ intron segment attaching itself to the Adenine in the Branch Site (so a loop is formed there, called a Lariat, and the open 3’ Segment of Exon 1 is attached to U6)  5) Lariat causes U1 and U4 to be released at this point and U5 and U6 (also attached to the open 3’ segment in Exon 1) come together to cause a positional shift to induce catalysis  6) the 3’ Splice Site is cut, leaving an open 5’ Segment in Exon 2  7) The catalysis at the 3’ Splice Site allows the open end of Exon 1 (a 3’ Segment) and of Exon 2 (5’ Segment) to come together though 3’ Catalytic capacity 1) U1 Binds to the 5’ Splice Site 2) U2 Binds to the Adenine in the 3) U4/U6 Dimer and U5 Bind and Branch Site induce a proximity loop 4) 5’ Splicing Occurs (after all SNERPS 5) Lariat causes U1 and U4 to be are present) with the newly exposed released at this point and U5 and U6 5’ intron segment attaching itself to (also attached to the open 3’ segment the Adenine in the Branch Site (so a in Exon 1) come together to cause a loop is formed there, called a Lariat, positional shift to induce catalysis and the open 3’ Segment of Exon 1 is attached to U6) 6) the 3’ Splice Site is7) The catalysis at the 3’ Splice Site allows the open cut, leaving an open end of Exon 1 (a 3’ Segment) and of Exon 2 (5’ 5’ Segment in Exon 2 Segment) to come together though 3’ Catalytic capacity  What are the advantages of Introns o 1. Alternate Splicing  Introns can be split in different wants and manners  So mRNA combinations can occur, different copies of mRNA can be created  And each codes for small variation polypeptide in a protein  This sort of specific peptide variation is a crucial occurrence in Biological Development is crucial o 2. A Smaller Genome with a large capacity for proteins  Two or More Polypeptides can be coded from the same gene  **Not the same as Polycistronic, these are from the same gene, not mRNA  So the organisms can carry fewer genes and produce more proteins o 3. Allows for an increased structural integrity of the chromosome  Capping o Almost all mature mRNA has to be capped  Done with a 7-Methyl Guanosine Cap  Covalently bonded and attached to the 5’ end  Prevents exonuclease degradation  Occurs when RNA Polymerase II has constructed a transcript 20-25bp long o Does so through Cap Binding Proteins (after 20-25bp)  1) RNA 5’ Tiphosphotase  The first nucleotide that comes into the strand during transcription is a Tri-Phosphate (so that’s what is present on the 5’ end)  So some phosphates need to be removed  This enzyme removes one Phosphate  2) Guanosine Transferase  Guanosine Triphosphate comes in  Has two phosphates removed (pyrophosphate)  This Monophosphate is connected to first nucleotide (with two Phosphates now)  3) Methyl transferase  Adds to the 7 Position in Guanosine  Must be on the 5’ end  Won’t be taken into the cellular areas without the cap April 8, 2016 Chapter 12: Gene Transcription and RNA Modification April 6, 2016 Chapter 12: Gene Transcription and RNA Modification Prokaryotic Transcription  Overview of Transcription  Central Dogma o DNA  RNA  Proteins o Classes  Components of Transcription o Transcription Sequences o Transcription Steps  I. Initiation  II. Elongation  III. Termination o The Various Roles of RNA Transcripts – This is an important point to consider: RNA has numerous functions it can perform after transcription  1. Structural  2. Standard  3. Atypical (Assessed by the Sedimentation Coefficient)  Steps Detailed o I. Initiation  A. Promoter Sequence  B. RNA Polymerase II (Halo-Enzyme, made of two components)  C. Haloenzyme Binding  D. Short RNA Strand Synthesis o II. Elongation o III. Termination  This is marked by the breaking of the DNA/RNA hybrid  Prokaryotes rely on Rho Pathways, Rho separates them by breaking the H-Bonds EUKARYOTIC TRANSCRIPTION Overview  Complications and Differences with Eukaryotic DNA o 1) Histone Association  The Histones are attracted because of the charges (Agrinine, Lysin to the Phosphates)  Histone modification is a way of allowing the unwinding of DNA from Histones o 2) Cellular Complexity  Polycistronic mRNA is not seen in Eukaryotes  Organelles exist which allow for specific, regional protein construction – no Polycistronic nuclear mRNA o 3) Multicellularity  There’s a complex balance in Eukaryotes – some genes are permanently upregulated, some permanently downregulated  RNA Polymerases o Poly I – rRNA except for 5S Subunit o Poly II – mRNA, structural genes, and Small Nuclear RNA of Spliceosomes o Poly III – tRNA and the 5S Ribosomal RNA subunit A Look at RNA Polymerase  I. Clamp – o The units work like a jaw, having to open up to take the DNA  II. Bridge – o The DNA settles at the Bridge and makes a Right Handed turn o Right turns occur at β’ and β (The catalytic units)  III. Rudder – o Eukaryotes have a rudder that is 9bp ahead that breaks the template in order to dissociate o This is only significant difference between Eukaryotes and Prokaryotes Steps for Structural Genes  I. INITIATION o A Promotor region initiates the transcription process, similar concept to that of Prokaryotes  1. Start Site (+1)  2. TATA Box Region (Adjacent to -25)  A Core Promoter sequence region exists in Eukaryotes, the TATA Box and Start Site are the Core Promoter  A well-defined TATA Box free of mutations results in definitely having small amounts of transcription (Basal Transcription)  3. Regulatory Elements (Between -50 and -100bp)  There are enhancers and silencers (and they are sequences, not proteins  Present between -50 and -100  Two Actors: Cis Trans Next to, immediately upstream or within the Opposite, away from, chromosome Different chromosome, factors that diffuse through Usually sequences cytoplasm and nucleus, and bind to trans o Then the Closed Complex must form (All 5 Transcription Factors and RNA II)  I. RNA Polymerase II  II. Transcription Factors of RNA Polymerase II (5 Proteins, General Transcription Factors (GTFs))  1] TFIID o Recognizes the TATA Sequence After Promoter o Huge protein complex Region, Need these  TATA Binding Protein (TBP) components to carry  TBP-Associated Factors (TAFs) out Transcription o Binds and moves to read the rest, then reverses before “deciding” to bind A. RNA Polymerase II o Does so after DNA has opened up B. Transcription  2] TF2B Factors o Brings in the RNA Poly II to bind to the Promoter Sequence C. Mediator Complex o Forms the Bridge  3] TFIIF o Comes in along with RNA Polymerase II  4] TFIIE o Initiates and maintains the Open Complex  5] TFIIH o Acts as Helicase to continue open up  II. ELONGATION o How Does Basal transcription move into Elongation o RNA Polymerase II has a Carboxy-Terminal Domain (CTD)  When it is Phosphorylated, Elongation begins o TFIIH also has ATPase and Protein Kinase Activity (hydrolyzes ATP and transfers Phosphate) o That activity causes separation of TFIIB and RNA Polymerase II  That release causes the release of others as well  III. Mediator Protein Complex  Co-Activator, Large Complex  Appears to regulate the ability of TFIIH to Phosphorylate CTD o Elongation process  III. TERMINATION o Initiation of Termination begins o Two Models  1. Allosteric Model  2. Torpedo Model  RNA Modification  There is Co-Linear Process to Gene Expression in Prokaryotes  Eukaryotes stray from Co-Linearity o They instead splice and remove and modify (the whole process is Trimming)  Types of RNA Trimming o 1) rRNA – Occurs in the Nucleolus; ribo-endonucleases o 2) mRNA – 5’ Capping and 3’ Poly-A Tails Occur o 3) tRNA  Occurs in the Nucleoplasm instead of the Nucleolus  Made of huge precursors, but need to get to 70-90bp to be functional  They have to undergo cleavage at the 5’ and 3’ ends  Acted on by RNase P (made of 375bp RNA and 20kDA Protein)  Forms the acceptor stem, reading as 5’ CCA 3’  Is a Ribozyme, so RNA does the catalytic action of removing the nucleotides  tRNA Nucleotidyl Transferase ensures that the 5’ CCA sequence is present  This is the acceptor Stem (accepts the AA) RNase P RNase Z RNase D 375bp RNA unit Removes 170bp The only Exonuclease 20kDa Protein Fragment on the 3’ Removes about 9bp End Removes nucleotides Acts after RNase Z removes the fragment on the 5’ End Allows RNase D Action Usually ensures the 5’ CCA 3’ code Ribozyme (RNA does the catalysis) If 5’CCA3’ is not present, tRNA Nucleotidyl Endonuclease Transferase ensures its addition (every tRNA will have this) This is the Acceptor Stem has an amino acid connector COMPONENTS OF TRANSCRIPTION Discovery of Introns  Were not thought to exist in Eukaryotes because Prokaryotes do not utilize introns  Experiment utilized Hybridization (Double Stranded cDNA of β-Globin and its mature mRNA)  General Concept o 1) Denaturing of Globin cDNA  Hydrogen bonds between coding and template strands are broken o 2) Measuring the Anneal Rates and Images  Separated mRNA would anneal much more quickly because of the size (it’s smaller)  It anneals with the template (because it would be the RNA version of the Coding Strand)  cDNA is constructed by reverse transcriptase on mRNA to create the template strand  What is cDNA o It is formed through reverse transcriptase so as the have a protein-ready (they have no introns) o This the DNA that can be purchased  Found the existence of Exon Loops (R-Loops, mRNA Displacement Loops) and Intron Loops (Double Stranded DNA) o Introns were not displaced because the complementary sections in the mRNA had been spliced  Procedure o 1) mRNA Isolation (Functional β Globin RNA) o 2) cDNA (the entire Globin Gene) o 3) Separate DNA (70% formamyde to break bonds, 16 hours) o 4) Dilute to Anneal (diluting formamyde allows annealing) o 5) Stain for Viewing on the slide (heavy metal) o 6) Observe R-Loops and Intron Segments (Electron Microscopes) Splicing – Removing of Introns, Attaching Exons Together (phosphodiester bond); Has Three Types  I. Fall Into Group I and Group II (intrinsic, self-splicing) o Mostly in lower Eukaryotes, Protoplast, Mitochondria o These have intrinsic properties (self-splicing) o In Vitro studies show these splice spontaneously o In Vivo studies show Mutarase increases the rate, but does not induce Splicing Group I Group II Guanosine is the key factor (Guanosine Binding One of the Introns has Adenine, which makes the Sites Exist, binding to each other to initiate) – process very position specific – no outside molecule outside molecule 2nd Carbon Catalyzes the attachment of Adenine Initial break occurs in the 5’ end after Guanosine with the 5’ End of the Intron, which causes the binds s(from Guanosine Alcohol attacking Exon 1, 1 Exon Break at the 3’ End of Exon (forms a loop forming a loop and free Exon) within Intron and an open 3’ Hydroxy, like in Group 1) 5’ Break initiates the 3’ Break (because the free alcohol in the open 3’ Exon 1 can now attack Exon 2) Then the 5’ End of Exon 2 Break occurs because of the Catalytic capacity of the free Exon 1 and (This 3’ End of the Exon attacks the 2dIntron Structure) Left with two strands, Guanosine capped single strand (Intron) and mature mRNA Leaves an “Intron Ring” with the original Adenine having released the Exon 2  II. Spliceosomes are the third type o These involve a catalytic complex to act and produce mRNA  Act on pre-mRNA  These produce mRNA which is identical to the Coding Strand o The introns are removed with these massive Complexes  Made of Small Nuclear RNA (snRNA) and Proteins  SNERPS  The snRNAs have specific and important functions o Subunit Functions  1) BIND – Bind to an intron sequence and precisely recognize the intron-exon boundaries  2) HOLD – Hold the pre-mRNA in the correct configuration  3) BOND – Catalyze the chemical reactions that remove introns and covalently link exons o Consensus Sites for Splicing  The intron is defined by particular sequences within the intron and at the boundary  “GU-A-AG”  These sequences are seen consistently, with the central Adenine serving as a branch site (similar to Group II) o SNERPS Types  1) U1 – identifies the Intron, binds to the 5’ Splice Site  2) U2 – comes in after and binds to the Adenine in the Branch Site  3) U4/U6 Dimer – enters as a dimer along with U5 to induce proximity  4) U5 – comes in with U4/U6 (sort of trimer action) o Spliceosome Steps  1) U1 Binds to the 5’ Splice Site  2) U2 Binds to the Adenine in the Branch Site  3) U4/U6 Dimer and U5 Bind and induce a proximity loop  4) 5’ Splicing Occurs (after all SNERPS are present) with the newly exposed 5’ intron segment attaching itself to the Adenine in the Branch Site (so a loop is formed there, called a Lariat, and the open 3’ Segment of Exon 1 is attached to U6)  5) Lariat causes U1 and U4 to be released at this point and U5 and U6 (also attached to the open 3’ segment in Exon 1) come together to cause a positional shift to induce catalysis  6) the 3’ Splice Site is cut, leaving an open 5’ Segment in Exon 2  7) The catalysis at the 3’ Splice Site allows the open end of Exon 1 (a 3’ Segment) and of Exon 2 (5’ Segment) to come together though 3’ Catalytic capacity 1) U1 Binds to the 5’ Splice Site 2) U2 Binds to the Adenine in the Branch Site 3) U4/U6 Dimer and U5 Bind and induce a proximity loop 4) 5’ Splicing Occurs (after all SNERPS are present) 5) Lariat causes U1 and U4 to be released at this with the newly exposed 5’ intron segment point and U5 and U6 (also attached to the open 3’ attaching itself to the Adenine in the Branch segment in Exon 1) come together to cause a Site (so a loop is formed there, called a Lariat, and positional shift to induce catalysis the open 3’ Segment of Exon 1 is attached to U6) 6) the 3’ Splice Site is cut, 7) The catalysis at the 3’ Splice Site allows the open end of Exon 1 (a 3’ leaving an open 5’ Segment Segment) and of Exon 2 (5’ Segment) to come together though 3’ in Exon 2 Catalytic capacity What are the advantages of Introns  1. Alternate Splicing o Introns can be split in different wants and manners o So mRNA combinations can occur, different copies of mRNA can be created  And each codes for small variation polypeptide in a protein o This sort of specific peptide variation is a crucial occurrence in Biological Development is crucial  2. A Smaller Genome with a large capacity for proteins o Two or More Polypeptides can be coded from the same gene o **Not the same as Polycistronic, these are from the same gene, not mRNA o So the organisms can carry fewer genes and produce more proteins  3. Allows for an increased structural integrity of the chromosome Capping o Almost all mature mRNA has to be capped  Done with a 7-Methyl Guanosine Cap  Covalently bonded and attached to the 5’ end  Prevents exonuclease degradation  Occurs when RNA Polymerase II has constructed a transcript 20-25bp long o Does so through Cap Binding Proteins (after 20-25bp)  1) RNA 5’ Tiphosphotase  The first nucleotide that comes into the strand during transcription is a Tri- Phosphate (so that’s what is present on the 5’ end)  So some phosphates need to be removed  This enzyme removes one Phosphate  2) Guanosine Transferase  Guanosine Triphosphate comes in  Has two phosphates removed (pyrophosphate)  This Monophosphate is connected to first nucleotide (with two Phosphates now)  3) Methyl transferase  Adds to the 7 Position in Guanosine  Must be on the 5’ end  Won’t be taken into the cellular areas without the cap  Capping o Almost all mature mRNA has to be capped  Done with a 7-Methyl Guanosine Cap  Covalently bonded and attached to the 5’ end  Prevents exonuclease degradation  Occurs when RNA Polymerase II has constructed a transcript 20-25bp long  Occurs while synthesis is occurring o Does so through Cap Binding Proteins (after 20-25bp)  1) RNA 5’ Tiphosphotate  2) Guanisine Triphosphate  3) Methyl transferase  Adds to the 7 Position in Guanisine  Must be on the 5’ end  Won’t be taken into the cellular areas without the cap o Purposes of Capping  1) Gate keeper proteins in the Nuclear Pores check for the cap to allow passage  2) Protects from Endonucleases – 5’ end is targeted for degradation  3) 5’ Intron Identification on the 5’ End  4) Translation – initiation factors search for the presence of a cap in the mRNA  Tailing o Almost all mature mRNA also has a tail  Added on with the purpose of stabilizing the RNA  Synthesis stops (through allosteric or torpedo models) 500- 2000bp later  Consists of a Poly A Tail  It is not coded in the sequence but is added after transcription o Process  1) Polyadenylation Signal is read in the strand (AAUAAA)  2) Endonuclease cleavage occurs 20bp downstream of that Signal  3) Poly-A Polymerase adds about 200 nucleotides with Adenine on the 3’ end o Purposes of Capping – stabilizes the mature mRNA  RNA Editing o This is different than other types of modifications in that the RNA sequence is actually altered  So in addition to Alternate Splicing, RNA Editing can occur  Only about 25 can undergo this in our cells, but Drosophila have numerous  First discovered in trypanosomes (sleeping sickness) o How does this occur  1) Addition or Deletion  2) Base Conversion (Deaminase)  Results in s truncated protein from a truncated mRNA strand o ApoB Example  Apo is a gene involved with digestion of lipids  There are two types, B 100and B 48  1) B100 Stop o Very long Codons: o Creates a 4563 Amino Acid Protein o Used in the Liver UAA UAG  2) B 48 UGA o Much shorter (truncated) o Creates a 2153 Amino Acid Protein o Used in the Intestines  In this case, a CAA sequence is changed to a UAA sequence, which is a Stop Codon  If Inosine is changed, it is seen as Guanine Chapter 13: Translation  Overview o The mRNA moves to the cytosol o Involves the transferring of information from a nucleotides bp sequence into a sequence of Amino Acids (aa) o Genetic Basis  Looking at structural gene (coding for proteins)  The cell is characterized by a protein and its roles  “Right Cell, Right Concentration, Right Time, Right Protein”  Experiments to Discovery o I. Archibald Garrod  He was studying patients with Alkaptonuria  Similar idea of PKU  Lack of proper Tyrosine digestion (but farther down the metabolic line)  The transformation of Homogentisic Acid to Maleylacetoacetic acid (done by Homogentisic Acid Oxidase)  He proposed that “an inborn error in metabolism existed,” manifested as the dysfunctional enzyme o II. Beadle and Tatum  They heard of Garrod’s proposal and wanted to determine if those enzymes were present in a 1 Gene-1 Enzyme relationship  Experimented on Neurospora  They induced mutation (X-Rays) in the Neurospora to influence the metabolism of Homoserine  The mold had easily observable anabolic pathways  Wanted to specifically view the creation of Methionine, which was the first step needed for translation  Process  Induced mutants and identified the mutated steps in the pathway  Allowed them to divide in Minimal Agar (low nutrients)  What they found was that if an enzyme were missing, the whole pathway was odd BUT if that enzyme was added, the pathway could resume  So from that, they concluded that one enzyme was coded for by one gene o III. Modifications of the Theory  1) Enzymes are Only One Category of Proteins – proteins vary in their functions, so many types exist  2) Some Proteins are Composed of Multiple Polypeptides – so various genes are needed or cut in different ways  Polypeptide = Structure  Protein Name = Function  3) Not All Genes Are Structural  4) One Gene can Code for Various Polypeptides (splicing, editing)  Translation o Overview  This is the process of interpretation  Nucleotide Code/Genetic Code  This is made of codons which are paired to an aa  Theoretically, the four nucleotides would result in 64 possible combinations  But instead, some overlap exists – this is the Degenerate nature of the Genetic Code o AUG (Methionine) is always first (Start Codon) o Degenerate Nature  Glycine has multiple Codons: GGU, GGG, GGC, GGA  So the mRNA sequence has that changing nucleotide on the 3 rd spot (the 3’ End)  So, considering the tRNA, this location would be first (the 5’ end)  So it is said to “presume” when it sees the Wobble Base o Synonymous Codes rd  These generally occur in the 3 location to create synonymous codes (like Glycine)  These codons are also Universally present (eukaryotes and prokaryotes)  Amino Acids o Amino Acids that cannot be synthesized are called Essential Amino Acids o There are 20 amino acids that can be found in polypeptides o Set Up  Types  Nonpolar  Charged  Aromatic  Polar Basic  Polar Acidic  Polar Neutral  Made from an Amino Group (left, 5’ mRNA, positive) and a Carboxylic Group (right, 3’ mRNA, negative) with Peptide Bonds forming  A long string is polypeptide  Locations  Nonpolar – Adjacent to Lipid Core, Inside the Domain  Polar – Inside Cellular Space o Protein Structure  Classes  1. Primary – the basic polypeptide sequence; dictates Tertiary Interactions: ultimate structure and function; never found within the 1. H-Bonds cell 2. Disulfide Bridges  2. Secondary – Hydrogen Bonding occurs 3. Van Der Wals  3. Tertiary – Interactions occur result in 3-Dimensional 4. Hydrophobic Structure Exclusion  4. Quaternary – multiple tertiary structures come 5. Polar and Ionic bonds together; multimeric unit  Dysfunction of the Proteins  Denaturing proteins involves breaking the fundamental bonds, stripping away the function of the protein  Dissociating involves the separation of quaternary structures  Chaperones can help mend large proteins o 1) Heat Shock proteins provide an optimal environment in which large proteins can re- associate o 2) Post translational proteins help import the primary level polypeptide to pass through channels in order to enter cell structures (mitochondria, chloroplasts, peroxisomes, nucleus) April 4, 2016 Chapter 12: Gene Transcription and RNA Modification  Overview of Transcription  Central Dogma o DNA  RNA  Proteins o Classes  1. Eukaryotes  2. Prokaryotes  Polycistronic RNA 3. Outliers  Viruses and Reverse Transcriptase  Components of Transcription o Transcription Sequences DNA RNA  Starting  Starting o Promoter Sequence site o Prokaryotes for RNA Polymerase  Ribosomal Binding Site at the 5’ Binding  Start Codon – specifies the first o Transcription Sequence amino acid in the sequence, also present in the DNA modified AUG in Prokaryotes  Stopping o Eukaryotes o Terminator Sequence  Have 3’ and 5’ Modifications (Cap  Regulatory and Tail), so just a start Codon is o Also has regulatory needed (AUG) (different than sequences that alter and Prokaryotes) influence the rates of  The Ribosome will travel back and transcription forth over the mRNA before it “decides” which start codon  Stopping o Stop Codon exists instead o Transcription Steps  I. Initiation  II. Elongation  III. Termination o The Various Roles of RNA Transcripts – This is an important point to consider: RNA has numerous functions it can perform after transcription  1. Structural  This is mRNA  Codes for proteins, over 90% of genes  2. Standard  tRNA and rRNA are also present in high concentrations  Involved in the Transcribing portion  3. Atypical (Assessed by the Sedimentation Coefficient)  7S is the Signal Recognition Particle (SRP) (7S + 6 Proteins, co-translational recruitment)  Spliceosomes (snRNA and snoRNA)  Nucleolus RNA  Viruses  Steps Detailed o I. Initiation  A. Promoter Sequence  Has TTGACG at -35 (16-18bp long) and TATAAT at - 10 crucial for the +1 location  B. RNA Polymerase II (Halo-Enzyme, made of two Core Enzyme Subunits: compenents)  Has a Motif (super-secondary structure) that binds to β (and Beta Prime) – Catalyzes the bond -35 location on the major groove ω – Assembles the Core  Core Unit Various Subunit Components o β and β’ catalyze ester formation in both Eukaryotes and Prokaryotes o ω – Assembles the Core  σ Factor o Single subunit that allows the Core to function o Induces the opening up of the strands  C. Haloenzyme Binding  It binds loosely and beings to “scan” the DNA for a Promoter Sequence  Then the Closed Complex forms o This occurs when the σ Factor and DNA Poly II bind at the -35 Promoter Region  Shortly afterwards, the Open Complex Forms  D. Short RNA Strand Synthesis  In the Open Complex, a small strand of mRNA is formed (8-10bp)  This synthesis causes the release of the σ Factor and the End of Initiation  The Core Enzyme continues to move and transcribe o II. Elongation  The Transcription Bubble forms as copying occurs, About 17bp long, Codes at a rate of 43 Nucleotides Hz o III. Termination  This is marked by the breaking of the DNA/RNA hybrid  Prokaryotes rely on Rho Pathways  Rho separates them by breaking the H-Bonds Rho Dependent Rho Independent  Rho acts like Helicase  Intrinsically occurs  Has Requirements to Bind: because of the nature of the o I. Rho Utilization Sequence (Rut) mRNA sequence in DNA (allows for Rho Binding)  This form also has a Stem o II. Alternating GC Rich Regions to Loop that interferes with form Stem Loop the Ribosome  Process  Sequences Present o RNA Stem Loop forms downstream o 1. Alternating GC Rich  This occurs because of the GC o 2. 3’ End mRNA Uracil Rich Alternating Regions (so DNA has Adenine)  They have an affinity for each  Adenine of DNA and the other Uracil of RNA are already o The Stem Loop slows down weak, now Poly II slowed polymerase by blocking the Ribosome (touches lightly)  NUS-A has also been found o So Rho can catch up from behind and is known to further slow and stall the transcription process Eukaryotic Transcription  Overview o Complications and Differences with Eukaryotic DNA  1) Histone Association  The Histones are attracted because of the charges (Agrinine, Lysin to the Phosphates)  Histone modification is a way of allowing the unwinding of DNA from Histones o Acetylation essentially neutralizes the positive charges are Histone Tails o So it essentially blocks the DNA binding with the Histone and allows unwinding  2) Cellular Complexity  Polycistronic mRNA is not seen in Eukaryotes  Organelles exist which allow for specific, regional protein construction – no Polycistronic nuclear mRNA  3) Multicellularity  All the sequences in every cell cannot function at all times  There’s a complex balance in Eukaryotes – some genes are permanently upregulated, some permanently downregulated o RNA Polymerases  Poly I – rRNA except for 5S Subunit  Poly II – mRNA, structural genes, and Small Nuclear RNA of Spliceosomes  Poly III – tRNA and the 5S Ribosomal RNA subunit  A Look at RNA Polymerase o I. Clamp –  The units work like a jaw, having to open up to take the DNA o II. Bridge –  The DNA settles at the Bridge and makes a Right Handed turn  Right turns occur at β’ and β (The catalytic units) o III. Rudder –  Eukaryotes have a rudder that is 9bp ahead that breaks the template in order to dissociate  This is only significant difference between Eukaryotes and Prokaryotes  Steps for Structural Genes o I. INITIATION  A Promotor region initiates the transcription process, similar concept to that of Prokaryotes  1. Start Site (+1)  2. TATA Box Region (Adjacent to -25) o A Core Promoter sequence region exists in Eukaryotes, the TATA Box and Start Site are the Core Promoter o A well-defined TATA Box free of mutations results in definitely having small amounts of transcription (Basal Transcription)  3. Regulatory Elements (Between -50 and -100bp) o There are enhancers and silencers (and they are sequences, not proteins o Present between -50 and -100 o Two Actors:  A. Cis  Next to, immediately upstream or within the chromosome  Usually sequences  B. Trans  Opposite, away from,  Different chromosome, factors that diffuse through cytoplasm and nucleus, and bind to trans  Then the Closed Complex must form (All 5Transcription Factors and RNA II)  I. RNA Polymerase II  II. Transcription Factors of RNA Polymerase II (5 Proteins, General Transcription Factors (GTFs)) o 1] TFIID  Recognizes the TATA Sequence After Promoter Region, 3 Components for  Huge protein complex transcription:  TATA Binding Protein (TBP) A. RNA Polymerase II  TBP-Associated Factors (TAFs) B. Transcription Factors  Binds and moves to read the rest, then C. Mediator Complex reverses before “deciding” to bind  Does so after DNA has opened up o 2] TF2B Closed Complex:  Brings in the RNA Poly II to bind to the Promoter Sequence Prokaryotes have the  Forms the Bridge Sigma Complex o 3] TFIIF Eukaryotes have:  Comes in along with RNA Polymerase II 1. All Five TFAs o 4] TFIIE 2. RNA Polymerase II  Binds to RNA Polymerase II  Initiates and maintains the Open Complex o 5] TFIIH  Binds to RNA Polymerase II and Acts as Helicase to continue open up o II. ELONGATION  How Does Basal transcription move into Elongation  RNA Polymerase II has a Carboxy- Terminal Domain (CTD)  When it is Phosphorylated, Elongation begins  TFIIH also has ATPase and Protein Kinase Activity (hydrolyzes ATP and transfers Phosphate)  That activity causes separation of TFIIB and RNA Polymerase II  That release causes the release of others as well  While TFIIH is Phosphorylating, it is still breaking H-Bonds  So TFIIF remains attached to RNA Polymerase II  III. Mediator Protein Complex o Co-Activator, Large Complex o Appears to regulate the ability of TFIIH to Phosphorylate CTD o TFIIH and Mediator have the same function, so they ensure that Phosphorylation and Elongation occurs  Elongation process o III. TERMINATION  Initiation of Termination begins 500-2000bp Downstream of the PolyA sequence  This sequence is the signal to end, coming in at the 3’ End  Once Poly-A is made, Termination Downstream occurs  Two Models  1. Allosteric Model o Factors play a role o Elongation Factors are lost or Termination Factors bind  2. Torpedo Model o And exonuclease binds to the 5’ end of the mRNA o Starts digesting in the 5’ to 3’ direction and eventually catches up to RNA Polymerase II  RNA Modification o There is Co-Linear Process to Gene Expression in Prokaryotes  Similar all the way from DNA to RNA to AA Sequence o Eukaryotes stray from Co-Linearity  They instead splice and remove and modify (the whole process is Trimming)  Pre-RNA or Heterogeneous RNA is the same length as the Template Strand, so essentially the Coding Strand  Then splicing and modification takes place on Pre-RNA to form the mRNA (removing introns) o Type of RNA Processing  1) rRNA  Trimming occurs with rRNA  Formed by RNA Polymerase I (except for 5S)  Occurs in the Nucleolus  Here, done by Endonucleases in the center  2) mRNA  5’ Capping and 3’ Poly-A Tails Occur to stops nucleases from digesting  3) tRNA  Made of huge precursors and various processes o 2 Endo and Exo Nucleases  They have to undergo cleavage at the 5’ and 3’ ends  1. RNaseP o Acted on by RNase P (made of 375bp RNA and 20kDA Protein) o Forms the Acceptor Stem at the 3’ End, reading as 5’ CCA 3’

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Chapter 21, Problem 44E is Solved
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Textbook: Chemistry: The Central Science
Edition: 12
Author: Theodore E. Brown; H. Eugene LeMay; Bruce E. Bursten; Catherine Murphy; Patrick Woodward
ISBN: 9780321696724

This textbook survival guide was created for the textbook: Chemistry: The Central Science, edition: 12. Chemistry: The Central Science was written by and is associated to the ISBN: 9780321696724. The full step-by-step solution to problem: 44E from chapter: 21 was answered by , our top Chemistry solution expert on 04/03/17, 07:58AM. The answer to “Energy Changes in Nuclear Reactions (Section)An analytical laboratory balance typically measures mass to the nearest 0.1 mg. What energy change would accompany the loss of 0.1 mg in mass?” is broken down into a number of easy to follow steps, and 29 words. Since the solution to 44E from 21 chapter was answered, more than 386 students have viewed the full step-by-step answer. This full solution covers the following key subjects: Energy, mass, loss, change, changes. This expansive textbook survival guide covers 49 chapters, and 5471 solutions.

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Energy Changes in Nuclear Reactions (Section)An analytical