Genetica per Scienze Naturali a.a. 03-04 prof S. Presciuttini 1. Genes and RNA The initial products...

Genetica per Scienze Naturalia.a. 03-04 prof S. Presciuttini

1. Genes and RNA TThe initial products of all genes he initial products of all genes is a sequence of is a sequence of ribonucleic acid ribonucleic acid

(RNA).(RNA). RNA is produced by a process that copies the nucleotide sequence in RNA is produced by a process that copies the nucleotide sequence in

DNA. Since this process is reminiscent of transcribing (copying) DNA. Since this process is reminiscent of transcribing (copying) written words, the synthesis of RNA is called written words, the synthesis of RNA is called transcriptiontranscription..

The DNA is said to be transcribed into RNA, and the RNA is called The DNA is said to be transcribed into RNA, and the RNA is called a a transcripttranscript..

One way to think about the different biological roles of DNA and One way to think about the different biological roles of DNA and RNA is to consider that the DNA (that is, the genome) is the RNA is to consider that the DNA (that is, the genome) is the instruction manual for producing all the RNAs that the cell needs, instruction manual for producing all the RNAs that the cell needs, whereas RNA is the erasable readout of those parts of the manual whereas RNA is the erasable readout of those parts of the manual relevant to any given task. relevant to any given task.


2. Properties of RNA Although RNA and DNA are both nucleic acids, RNA Although RNA and DNA are both nucleic acids, RNA

differs in several important ways:differs in several important ways:1. RNA is a single-stranded nucleotide chain, 1. RNA is a single-stranded nucleotide chain, not a double helixnot a double helix. One . One

consequence of this is that RNA can form a much greater variety of consequence of this is that RNA can form a much greater variety of complex three-dimensional molecular shapes than can double-stranded complex three-dimensional molecular shapes than can double-stranded DNA. DNA.

2. RNA has 2. RNA has riboseribose sugar in its nucleotides, rather than deoxyribose. As the sugar in its nucleotides, rather than deoxyribose. As the names suggest, the two sugars differ in the presence or absence of just one names suggest, the two sugars differ in the presence or absence of just one oxygen atom. Analogous to the individual strands of DNA, there is a oxygen atom. Analogous to the individual strands of DNA, there is a phosphate-ribose backbone to RNA, with a base covalently linked to the 1 phosphate-ribose backbone to RNA, with a base covalently linked to the 1 position on each ribose.position on each ribose.


3. Uracil instead of thymine The The nucleotides nucleotides of of RNA carry the bases RNA carry the bases

adenine, guanine, and cytosine, but the adenine, guanine, and cytosine, but the pyrimidine base pyrimidine base uraciluracil (abbreviated U) (abbreviated U) is found in place of thymineis found in place of thymine::

However, uracil forms However, uracil forms hydrogen bonds with hydrogen bonds with adenineadenine just as thymine does. just as thymine does.


4. Classes of RNA RNAs can be grouped into two general classesRNAs can be grouped into two general classes::

Some RNAs are intermediaries in the process of decoding genes Some RNAs are intermediaries in the process of decoding genes into polypeptide chains; these molecules are calledinto polypeptide chains; these molecules are called ""informationalinformational" RNAs." RNAs.

In the other class, the RNA itself is the final, functional product. In the other class, the RNA itself is the final, functional product. TThese RNAs hese RNAs are calledare called " "functionalfunctional" RNAs" RNAs


5. Informational RNAs For the For the vast majority of genesvast majority of genes, the RNA is only an , the RNA is only an intermediateintermediate in in

the synthesis of the ultimate functional product, which is a protein. the synthesis of the ultimate functional product, which is a protein. The informational RNA of this vast majority of genes is always The informational RNA of this vast majority of genes is always messenger RNA (messenger RNA (mRNAmRNA).). In prokaryotes, In prokaryotes, the transcriptthe transcript, as it is synthesized directly from the DNA (the , as it is synthesized directly from the DNA (the

primary transcript), primary transcript), is the mRNAis the mRNA. In eukaryotes, however, the . In eukaryotes, however, the primary primary transcripttranscript is processed through modification of the 5 is processed through modification of the 5’’ and 3 and 3’’ ends and removal ends and removal of pieces of the primary transcript (introns). At the end of this pre-mRNA of pieces of the primary transcript (introns). At the end of this pre-mRNA processing, an mRNA is produced. processing, an mRNA is produced.

The sequence of nucleotides in mRNA is converted into the sequence The sequence of nucleotides in mRNA is converted into the sequence of amino acids in a polypeptide chain by a process called of amino acids in a polypeptide chain by a process called translationtranslation. . In this connection the word translation is used in much the same way In this connection the word translation is used in much the same way as we use it in translating a foreign language: the cell has a way of as we use it in translating a foreign language: the cell has a way of translating the language of RNA into the language of polypeptides. translating the language of RNA into the language of polypeptides. Proteins are made up of one or more polypeptide chains.Proteins are made up of one or more polypeptide chains.


6. Functional RNAs FFunctional RNAs action is purely at the level of the RNA; they are unctional RNAs action is purely at the level of the RNA; they are

never translated into polypeptides. Each class of functional RNA is never translated into polypeptides. Each class of functional RNA is encoded by a relatively small number of genes (a few tens to a few encoded by a relatively small number of genes (a few tens to a few hundred).hundred). The main classes of functional RNAs contribute to various The main classes of functional RNAs contribute to various steps in the informational processing of DNA to protein. Two classes steps in the informational processing of DNA to protein. Two classes of functional RNAs are found in all organisms:of functional RNAs are found in all organisms: Transfer RNA (Transfer RNA (tRNAtRNA) molecules act as transporters that ) molecules act as transporters that bring amino acids to bring amino acids to

the mRNAthe mRNA during the process of translation (protein synthesis). The tRNAs are during the process of translation (protein synthesis). The tRNAs are general components of the translation machinery; they can bring amino acids to general components of the translation machinery; they can bring amino acids to the mRNA of any protein-coding gene.the mRNA of any protein-coding gene.

Ribosomal RNAs (Ribosomal RNAs (rRNAsrRNAs) are components of ) are components of ribosomesribosomes, which are large , which are large macromolecular assemblies that act as guides to coordinate the assembly of the macromolecular assemblies that act as guides to coordinate the assembly of the amino acid chain of a protein. Ribosomes are composed of several types of amino acid chain of a protein. Ribosomes are composed of several types of rRNA and about 100 different proteins. As in the case of tRNA, the rRNAs are rRNA and about 100 different proteins. As in the case of tRNA, the rRNAs are general translational components that can be used to translate the mRNA of any general translational components that can be used to translate the mRNA of any protein-coding gene.protein-coding gene.


7. One DNA strand is the template Transcription relies on the complementary pairing of bases. The two Transcription relies on the complementary pairing of bases. The two

strands of the DNA double helix separate locally, and one of the strands of the DNA double helix separate locally, and one of the separated strands acts as a separated strands acts as a templatetemplate (alignment guide) for RNA (alignment guide) for RNA synthesis. In the chromosome overall, both DNA strands are used as synthesis. In the chromosome overall, both DNA strands are used as templates, but in any one gene templates, but in any one gene only one strandonly one strand is used, and in that is used, and in that gene it is always the same strand.gene it is always the same strand.

One or the other DNA strand is used as transcriptional template.


8. 5’3’RNA growth is always in the 5RNA growth is always in the 5’’33’’ direction; in other words, direction; in other words, nucleotides are always nucleotides are always added at a 3added at a 3’’ growing tip growing tip::

RNA polymerase moves RNA polymerase moves always always from the 3from the 3’’ end of the template strand, creating an end of the template strand, creating an RNA strand that grows in a 5RNA strand that grows in a 5’’33’’ direction (since it must be direction (since it must be antiparallelantiparallel to the to the template strand). template strand). SSome genes are transcribed from one strand of the DNA double helix; ome genes are transcribed from one strand of the DNA double helix; other genes use the other strand as the templateother genes use the other strand as the template


9. Transcription in actionEukaryotes have Eukaryotes have several hundred several hundred identical genes encoding identical genes encoding ribosomal RNAribosomal RNA. The long . The long filaments are DNA molecules filaments are DNA molecules coated with proteins. The fibers coated with proteins. The fibers extending in clusters from the main extending in clusters from the main axes are molecules of ribosomal axes are molecules of ribosomal RNA which will be used in the RNA which will be used in the construction of the cell's ribosomes. construction of the cell's ribosomes. TTranscription begins at one end of ranscription begins at one end of each gene, with the RNA molecules each gene, with the RNA molecules getting longer as they proceed getting longer as they proceed toward completion. Note the large toward completion. Note the large number (up to 100) of RNA number (up to 100) of RNA molecules that are transcribed molecules that are transcribed simultaneously from each gene.simultaneously from each gene.

TTranscription of ranscription of ribosomal RNA (rRNA) genesribosomal RNA (rRNA) genes in in the developing egg cell of the spotted newtthe developing egg cell of the spotted newt


10. RNA Polymerases In most prokaryotes, a single RNA polymerase does the job of In most prokaryotes, a single RNA polymerase does the job of

transcribing all types of RNA.transcribing all types of RNA. EEukaryotes have three different RNA polymerases, which specialize ukaryotes have three different RNA polymerases, which specialize

as follows:as follows:1. RNA polymerase I (Pol I) transcribes 1. RNA polymerase I (Pol I) transcribes rRNA genesrRNA genes..2. RNA polymerase II (Pol II) transcribes 2. RNA polymerase II (Pol II) transcribes protein-coding genesprotein-coding genes..3. RNA polymerase III (Pol III) transcribes 3. RNA polymerase III (Pol III) transcribes other functional RNA genesother functional RNA genes (for (for

example, tRNA genes).example, tRNA genes). IIn eukaryotesn eukaryotes,, transcription of nuclear chromosomes takes place transcription of nuclear chromosomes takes place

entirely entirely within the nucleuswithin the nucleus, and the transcripts then move through , and the transcripts then move through nuclear poresnuclear pores out into the cytoplasm, where out into the cytoplasm, where translationtranslation occurs. occurs. Since prokaryotes have no nucleus, there is no comparable movement Since prokaryotes have no nucleus, there is no comparable movement of transcripts, and translation can take place immediately, right on the of transcripts, and translation can take place immediately, right on the growing transcript.growing transcript.


11. Three stages of transcription TTranscription ranscription is usually described in terms of is usually described in terms of three three

distinct stages:distinct stages:InitiationInitiationElongationElongationTTerminationermination


12. INITIATIONA DNA sequence to which RNA polymerase binds to initiate A DNA sequence to which RNA polymerase binds to initiate transcription is termed a transcription is termed a promoterpromoter..

A promoter is part of the A promoter is part of the regulatory regionregulatory region adjacent to the coding region of a adjacent to the coding region of a gene. gene. SSince an RNA transcript is made in the 5ince an RNA transcript is made in the 5’’33’’ direction, the convention is direction, the convention is to view the gene in the 5to view the gene in the 5’’33’’ orientation, too (the orientation of the orientation, too (the orientation of the nontemplate strand), even though transcription actually starts at the 3nontemplate strand), even though transcription actually starts at the 3’’ end of end of the template strand. By convention the first-transcribed end of the gene is called the template strand. By convention the first-transcribed end of the gene is called the 5the 5’’ end. Using this view, the promoter is at the beginning of the gene and, so, end. Using this view, the promoter is at the beginning of the gene and, so, is said to be at the 5is said to be at the 5’’ end of the gene, and the regulatory region is called the 5 end of the gene, and the regulatory region is called the 5’’ regulatory regionregulatory region


13. The promoter

Promoter sites have regions of similar sequences, as indicated by the yellow region in the 13 different promoter sequences in E. coli. Spaces (dots) included to maximize homology at consensus sequences. The gene governed by each promoter sequence is indicated on the left. Numbering is given in terms of the number of bases before () or after (+) the RNA synthesis initiation point.


14. The TATA boxTwo regions of partial similarity appear in virtually Two regions of partial similarity appear in virtually all promotersall promoters..

These regions have been termed the These regions have been termed the --35 (minus 35) and 35 (minus 35) and --10 regions 10 regions because of their locations relative to the transcription initiation point.because of their locations relative to the transcription initiation point.

RNA polymerase scans the DNA for a promoter sequence, binds to the RNA polymerase scans the DNA for a promoter sequence, binds to the DNA at that point, then unwinds it and begins the synthesis of an RNA DNA at that point, then unwinds it and begins the synthesis of an RNA molecule at the transcriptional initiation site. Hence, we see that the molecule at the transcriptional initiation site. Hence, we see that the principle of DNA binding is a result of interactions between the principle of DNA binding is a result of interactions between the protein (here, the RNA polymerase) and a specific base sequence in protein (here, the RNA polymerase) and a specific base sequence in the DNAthe DNA..


15. RNA polymerase in bacteria

Schematic diagram of prokaryotic RNA polymerase. The core enzyme contains two polypeptides, one polypeptide, and one ’ polypeptide. The addition of the subunit allows initiation at promoter sites.


16. The factor In order to recognize their promoters, bacterial RNA polymerase enzymes require a In order to recognize their promoters, bacterial RNA polymerase enzymes require a

specialized subunit called the sigma factor (σ), which specialized subunit called the sigma factor (σ), which directly contacts the directly contacts the promoter sequencepromoter sequence. The complex formed by the sigma subunit with the remaining . The complex formed by the sigma subunit with the remaining polymerase core subunits constitutes the bacterial polymerase core subunits constitutes the bacterial holoenzymeholoenzyme..

Bacteria contain a variety of sigma factors that specifically recognize different Bacteria contain a variety of sigma factors that specifically recognize different promoter sequences. It is therefore the sigma factor that determines which genes are promoter sequences. It is therefore the sigma factor that determines which genes are transcribed.transcribed.

All cells have a All cells have a primary sigma factorprimary sigma factor, which , which directs transcription from the promoters of directs transcription from the promoters of essential housekeeping genes, and a variable essential housekeeping genes, and a variable number of alternative sigma factors whose number of alternative sigma factors whose levels or activities are increased levels or activities are increased in response in response to specific signalsto specific signals. E. coli, a symbiotic . E. coli, a symbiotic bacterium leading a relatively sheltered life in bacterium leading a relatively sheltered life in the gut of other organisms, has only the gut of other organisms, has only 77 sigma sigma factors.factors.


17. Structure of a bacterial RNA polymerase

The structure of the T. aquaticus holoenzyme shows how three structural domains of the sigma subunit bind to the core enzyme in a position to recognize the promoter elements. The DNA is numbered relative to the transcription start site at +1. The σ2 domain recognizes the -10 region (red), while the σ3 domain binds to the flanking base pairs of the extended -10 region. The σ4 domain, which binds to the -35 element (red), is anchored to a flexible flap of the β subunit that may allow movement of the σ4 subunit to allow for different spacings between the -35 and -10 regions.


18. ELONGATIONShortly after initiating transcription, Shortly after initiating transcription, the sigma factor dissociatesthe sigma factor dissociates from the RNA from the RNA polymerasepolymerase, which, which moves along the DNA, maintaining a transcription " moves along the DNA, maintaining a transcription "bubblebubble" to " to expose the template strand, and catalyzes the 3expose the template strand, and catalyzes the 3’’ elongation of the RNA strand. The elongation of the RNA strand. The polymerase compares free ribonucleotide triphosphates with the next exposed base on polymerase compares free ribonucleotide triphosphates with the next exposed base on the DNA template and, if there is a complementary match, adds it to the chain.the DNA template and, if there is a complementary match, adds it to the chain.


19. TERMINATIONSSpecific nucleotide sequences in the DNA act as pecific nucleotide sequences in the DNA act as signals for signals for RNA RNA chain terminationchain termination. In . In the mechanism the mechanism called called directdirect terminationtermination, the termination signal , the termination signal consist of about 40 bpconsist of about 40 bp containing a GC-rich containing a GC-rich palindromepalindrome, followed by an oligo A region, which , followed by an oligo A region, which forms a local stem-loop structure in the RNA.forms a local stem-loop structure in the RNA. The The resulting double-stranded RNA section is called a resulting double-stranded RNA section is called a hairpin loop. It is followed by the hairpin loop. It is followed by the terminal run of terminal run of U'sU's that correspond to the A residues on the DNA that correspond to the A residues on the DNA template. This sequence disrupts the base pairing of template. This sequence disrupts the base pairing of newly synthesized RNA with the DNA template, newly synthesized RNA with the DNA template, forcing the RNA and the polymerase to fall off.forcing the RNA and the polymerase to fall off.


20. RNA Processing in Eukaryotes Transcription works in much the same way in eukaryotes as in Transcription works in much the same way in eukaryotes as in

prokaryotes; that is, there are specific promoter sequences to which prokaryotes; that is, there are specific promoter sequences to which the RNA polymerase binds, and the polymerase moves along the gene the RNA polymerase binds, and the polymerase moves along the gene synthesizing RNA in the 5synthesizing RNA in the 5’’33’ ’ direction.direction.


21. The RNA polymerase II holoenzyme

Model of RNA Polymerase II Model of RNA Polymerase II Transcription Initiation Transcription Initiation MachineryMachinery.The machinery .The machinery depicted here encompasses depicted here encompasses over over 85 polypeptides in 85 polypeptides in 1010 (sub) complexes: core RNA (sub) complexes: core RNA polymerase II (RNAPII) polymerase II (RNAPII) consists of 12 subunits; TFIIH, consists of 12 subunits; TFIIH, 9 subunits; TFIIE, 2 subunits; 9 subunits; TFIIE, 2 subunits; TFIIF, 3 subunits; TFIIB, 1 TFIIF, 3 subunits; TFIIB, 1 subunit, TFIID, 14 subunits; subunit, TFIID, 14 subunits; core SRB/mediator, more than core SRB/mediator, more than 16 subunits; Swi/Snf complex, 16 subunits; Swi/Snf complex, 11 subunits; Srb10 kinase 11 subunits; Srb10 kinase complex, 4 subunits; and complex, 4 subunits; and SAGA, 13 subunitsSAGA, 13 subunits..


22. mRNA maturation IIn eukaryotesn eukaryotes,, the initial product of transcription, the primary RNA the initial product of transcription, the primary RNA

transcript, is processed in several ways before its transport to the transcript, is processed in several ways before its transport to the cytosol. These processing steps are all performed by specific proteins cytosol. These processing steps are all performed by specific proteins that bind to the RNA. Until it reaches its final, mature form, the that bind to the RNA. Until it reaches its final, mature form, the primary transcript is sometimes called primary transcript is sometimes called pre-mRNApre-mRNA. .

First, during transcription, a First, during transcription, a capcap consisting of a consisting of a 7-methylguanosine7-methylguanosine residue is added to the 5residue is added to the 5’’ end of the transcript, linked by a end of the transcript, linked by a triphosphate bond.triphosphate bond.

Then an Then an AAUAAAAAUAAA sequence near the 3 sequence near the 3’’ end is recognized by an end is recognized by an enzyme that enzyme that cuts off the end of the RNAcuts off the end of the RNA approximately 20 bases approximately 20 bases farther down. At this time a stretch of 150 to 200 adenine nucleotides farther down. At this time a stretch of 150 to 200 adenine nucleotides called a called a poly(A) tailpoly(A) tail is added at the cut 3 is added at the cut 3’’ end. end.

Next, a crucial splicing step removes any introns from the RNA Next, a crucial splicing step removes any introns from the RNA transcript, converting pre-mRNA into transcript, converting pre-mRNA into mature mRNAmature mRNA..


23. Mechanism of exon splicing For many eukaryotic genes the For many eukaryotic genes the capped and tailed transcriptscapped and tailed transcripts are shortened by the are shortened by the

elimination of internal introns elimination of internal introns before transport into the cytoplasmbefore transport into the cytoplasm.. Exon-intron junctions of mRNAs show specific sequences that are highly Exon-intron junctions of mRNAs show specific sequences that are highly

conservedconserved, i.e.,, i.e., they are the same in most introns in most species. they are the same in most introns in most species. TThere is a here is a GUGU at at the 5the 5’’ splice site of the intron and an splice site of the intron and an AG AG at the 3 at the 3’’ splice site in virtually all cases splice site in virtually all cases examined ("the GU-AG rule")examined ("the GU-AG rule")

Consensus sequences of 5Consensus sequences of 5’’ and 3 and 3’’ splice splice junctions in eukaryotic mRNAs. Almost junctions in eukaryotic mRNAs. Almost all introns begin with GU and end with all introns begin with GU and end with AG. From the analysis of many exonAG. From the analysis of many exon intron boundaries, intron boundaries, extended consensus extended consensus sequences of preferred nucleotides at sequences of preferred nucleotides at the 5the 5’’ and 3 and 3’’ ends have been ends have been establishedestablished. In addition to AG, other . In addition to AG, other nucleotides just upstream of the 3 splice nucleotides just upstream of the 3 splice junction also are important for precise junction also are important for precise splicing.splicing.


24. The spliceosome Other less well conserved sequences are found flanking these. These Other less well conserved sequences are found flanking these. These

common configurations of the pre-mRNA are recognized by common configurations of the pre-mRNA are recognized by small small nuclear ribonucleoprotein particlesnuclear ribonucleoprotein particles, or snRNPs, which catalyze the , or snRNPs, which catalyze the cutting and splicing reactions. cutting and splicing reactions.

During the process of splicing, During the process of splicing, the snRNPs, the primary the snRNPs, the primary transcript, and associated transcript, and associated factors all come together to factors all come together to form a high-molecular-weight form a high-molecular-weight (60S) (60S) ribonucleoprotein ribonucleoprotein complexcomplex, called a , called a spliceosomespliceosome, which catalyzes , which catalyzes the splicing reactions.the splicing reactions.


25. The translationAt At INITIATIONINITIATION, the , the ribosomeribosome recognizes the starting point in a recognizes the starting point in a segment of mRNA and binds a segment of mRNA and binds a molecule of molecule of tRNAtRNA bearing a bearing a single amino acid. In all bacterial single amino acid. In all bacterial proteins, this first amino acid is N-proteins, this first amino acid is N-formylmethionine.formylmethionine.In In ELONGATIONELONGATION, a second , a second amino acid is linked to the first amino acid is linked to the first one. The one. The ribosome then shifts its ribosome then shifts its positionposition on the mRNA molecule, on the mRNA molecule, and the elongation cycle is and the elongation cycle is repeated.repeated.At At TERMINATIONTERMINATION, w, when the hen the stop codon is reached, stop codon is reached, the chain the chain of amino acids folds of amino acids folds spontaneously to form a proteinspontaneously to form a protein. . Subsequently, the ribosome splits Subsequently, the ribosome splits into its two subunits, which rejoin into its two subunits, which rejoin before a new segment of mRNA is before a new segment of mRNA is translated. translated.


26. Ribosomes are protein factories The meeting place for amino acidThe meeting place for amino acid bound tRNAs and mRNA is the ribosome. bound tRNAs and mRNA is the ribosome.

Ribosomes are large macromolecular assemblies acting like complex subcellular Ribosomes are large macromolecular assemblies acting like complex subcellular machines. Each ribosome consists of a large and a small subunitmachines. Each ribosome consists of a large and a small subunit, which shows , which shows slight differences between prokaryotes and eukaryotesslight differences between prokaryotes and eukaryotes. Each subunit in turn is . Each subunit in turn is composed of several rRNA types and as many as 50 proteins.composed of several rRNA types and as many as 50 proteins.

Ribosomes contain specific sites that enable them to bind to the mRNA, the tRNAs, Ribosomes contain specific sites that enable them to bind to the mRNA, the tRNAs, and other specific protein factors, all required for protein synthesis.and other specific protein factors, all required for protein synthesis.

The addition of a single The addition of a single amino acid to the amino acid to the growing polypeptide growing polypeptide chain in the course of chain in the course of translation of mRNAtranslation of mRNA


27. The tRNAs The basis for the specificity between codon and The basis for the specificity between codon and

amino acid lies in the structure of transfer RNA amino acid lies in the structure of transfer RNA (tRNA) molecules.(tRNA) molecules.

A molecule of tRNA has a clover-leaf shape A molecule of tRNA has a clover-leaf shape consisting of four double-helical stems and three consisting of four double-helical stems and three single-stranded loopssingle-stranded loops..

The middle loop carries a nucleotide triplet called The middle loop carries a nucleotide triplet called the anticodon, whose job it is to bind with a the anticodon, whose job it is to bind with a specific codon in the mRNA by specific RNA-to-specific codon in the mRNA by specific RNA-to-RNA base pairing. Since codons in mRNA are RNA base pairing. Since codons in mRNA are read in the 5 3direction, anticodons are oriented in read in the 5 3direction, anticodons are oriented in the 3 5 direction.the 3 5 direction.

Each tRNA is specific for only one amino acid Each tRNA is specific for only one amino acid and carries that amino acid attached at its free 3 and carries that amino acid attached at its free 3 end. Amino acids are added to the tRNA by end. Amino acids are added to the tRNA by enzymes called aminoacyl-tRNA synthetases. enzymes called aminoacyl-tRNA synthetases. Each amino acid has a specific synthetase that Each amino acid has a specific synthetase that links it to only those tRNAs that recognize the links it to only those tRNAs that recognize the codons for that amino acid.codons for that amino acid.

The structure of an alanine tRNA, The structure of an alanine tRNA, showing the aminoacyl-tRNA showing the aminoacyl-tRNA binding to its correct codon in binding to its correct codon in mRNA. mRNA. Some nuclotides carry Some nuclotides carry rarerare modified bases modified bases


28. Chain termination ThreeThree codons codons of the genetic code, of the genetic code, UAG, UGA, and UAA, do not UAG, UGA, and UAA, do not

specify an amino acid. These are called specify an amino acid. These are called stop codonsstop codons or termination or termination codons. They can be regarded as punctuation marks ending the codons. They can be regarded as punctuation marks ending the message encoded in the mRNA. Stop codons often are called message encoded in the mRNA. Stop codons often are called nonsense codons.nonsense codons.

TThe three stop codons are not recognized by a tRNA, but instead by he three stop codons are not recognized by a tRNA, but instead by protein factors called protein factors called release factorsrelease factors. When the peptidyl-tRNA is in . When the peptidyl-tRNA is in the P site, the release factors bind to the A site in response to the chainthe P site, the release factors bind to the A site in response to the chain terminating codons. The polypeptide is then released from the P site, terminating codons. The polypeptide is then released from the P site, and the ribosomes dissociate into two subunits, ending translation.and the ribosomes dissociate into two subunits, ending translation.

In one way of analyzing DNA sequences to look for potential genes, In one way of analyzing DNA sequences to look for potential genes, computers are programmed to look for open reading frames (ORFs), computers are programmed to look for open reading frames (ORFs), which are long DNA sequences beginning with an initiation codon which are long DNA sequences beginning with an initiation codon (for example 5-ATG-3) and ending with one of the three stop codons.(for example 5-ATG-3) and ending with one of the three stop codons.

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Genetica per Scienze Naturali a.a. 03-04 prof S. Presciuttini 1. Genes and RNA The initial products...

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