From Gene to Protein Transcription & Translation PDF

From Gene to Protein Transcription & Translation Concept 1: Genes specify proteins via transcription and translation Presented by Dr Ghada Kh...

From Gene to Protein Transcription & Translation Concept 1: Genes specify proteins via transcription and translation Presented by Dr Ghada Khawaja Overview: The Flow of Genetic Information The Products of Gene Expression: A Developing Story The information content of DNA is in the form of specific sequences of nucleotides Some proteins aren’t enzymes The DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins Many proteins are composed of several polypeptides, each of which has its own gene Proteins are the links between genotype and phenotype one gene–one polypeptide Gene expression, the process by which DNA directs protein synthesis, includes two stages: transcription and translation Note that it is common to refer to gene products as proteins rather than polypeptides Basic Principles of Transcription and Translation Nuclear envelope RNA is the bridge between genes and the proteins for which they code Transcription is the synthesis of RNA under the direction of DNA DNA Transcription produces messenger RNA (mRNA) TRANSCRIPTION Translation is the synthesis of a polypeptide, using information in the Pre-mRNA RNA PROCESSING mRNA Ribosomes are the sites of translation mRNA DNA TRANSCRIPTION mRNA In prokaryotes, translation of mRNA can begin before transcription has Ribosome TRANSLATION Ribosome TRANSLATION finished In a eukaryotic cell, the nuclear envelope separates transcription from Polypeptide Polypeptide translation Eukaryotic RNA transcripts are modified through RNA processing to (a) Bacterial cell (b) Eukaryotic cell yield finished mRNA A primary transcript is the initial RNA transcript from any gene prior to processing DNA TRANSCRIPTION The central dogma is the concept that cells are governed by a cellular chain of command: DNA RNA protein mRNA DNA RNA Protein (a) Bacterial cell  Nuclear envelope DNA DNA TRANSCRIPTION TRANSCRIPTION Pre-mRNA RNA PROCESSING mRNA Ribosome mRNA TRANSLATION Polypeptide (a) Bacterial cell (b) Eukaryotic cell Nuclear Nuclear envelope envelope DNA DNA TRANSCRIPTION TRANSCRIPTION Pre-mRNA Pre-mRNA RNA PROCESSING mRNA TRANSLATION Ribosome Polypeptide (b) Eukaryotic cell (b) Eukaryotic cell The Genetic Code During transcription, one of the two DNA strands, called the template How are the instructions for assembling amino acids into proteins strand, provides a template for ordering the sequence of encoded into DNA? complementary nucleotides in an RNA transcript There are 20 amino acids, but there are only four nucleotide bases in The template strand is always the same strand for a given gene DNA During translation, the mRNA base triplets, called codons, are read in How many nucleotides correspond to an amino acid? the 5 to 3 direction Codons along an mRNA molecule are read by translation machinery Codons: Triplets of Nucleotides in the 5 to 3 direction Each codon specifies the amino acid (one of 20) to be placed at the The flow of information from gene to protein is based on a triplet corresponding position along a polypeptide code: a series of nonoverlapping, three-nucleotide words The words of a gene are transcribed into complementary nonoverlaping three-nucleotide words of mRNA These words are then translated into a chain of amino acids, forming a polypeptide Cracking the Code DNA template 3 5 DNA strand A C C A A A C C G A G T molecule All 64 codons were deciphered by the mid-1960s Of the 64 triplets, 61 code for amino acids; 3 triplets are “stop” T G G T T T G G C T C A 5 3 Gene 1 signals to end translation The genetic code is redundant (more than one codon may specify a TRANSCRIPTION particular amino acid) but not ambiguous; no codon specifies more Gene 2 than one amino acid U G G U U U G G C U C A mRNA 5 3 Codons must be read in the correct reading frame (correct Codon groupings) in order for the specified polypeptide to be produced TRANSLATION Protein Trp Phe Gly Ser Gene 3 Amino acid  Second mRNA base U C A G UUU UCU UAU UGU U Phe Tyr Cys UUC UCC UAC UGC C U Ser UUA UCA UAA Stop UGA Stop A Leu Third mRNA base (3 end of codon) First mRNA base (5 end of codon) UUG UCG UAG Stop UGG Trp G CUU CCU CAU CGU U His CUC CCC CAC CGC C C Leu Pro Arg CUA CCA CAA Gln CGA A Concept 2: Transcription is the DNA-directed CUG CCG CAG CGG G AUU ACU AAU AGU U synthesis of RNA: a closer look Asn Ser AUC Ile ACC AAC AGC C A AUA ACA Thr AAA AGA A Transcription is the first stage of gene expression Lys Arg Met or AUG start ACG AAG AGG G GUU GCU GAU GGU U Asp GUC GCC GAC GGC C G Val Ala Gly GUA GCA GAA GGA A Glu GUG GCG GAG GGG G Evolution of the Genetic Code Molecular Components of Transcription The genetic code is nearly universal, shared by the simplest bacteria RNA synthesis is catalyzed by RNA polymerase, which pries the DNA to the most complex animals strands apart and hooks together the RNA nucleotides Genes can be transcribed and translated after being transplanted The RNA is complementary to the DNA template strand from one species to another RNA synthesis follows the same base-pairing rules as DNA, except that uracil substitutes for thymine The DNA sequence where RNA polymerase attaches is called the promoter; in bacteria, the sequence signaling the end of transcription is called the terminator The stretch of DNA that is transcribed is called a transcription unit (a) Tobacco plant (b) Pig expressing expressing a firefly gene a jellyfish gene  Promoter Transcription unit Synthesis of an RNA Transcript 5 3 3 5 DNA Start point RNA polymerase The three stages of transcription 1 Initiation – Initiation Nontemplate strand of DNA 5 3 – Elongation 3 5 Template strand of DNA – Termination Unwound RNA transcript DNA Promoter Transcription unit Promoter Transcription unit 5 3 5 3 3 5 3 5 DNA DNA Start point Start point RNA polymerase RNA polymerase 1 Initiation Nontemplate strand of DNA 5 3 3 5 Template strand of DNA RNA Unwound transcript DNA 2 Elongation Rewound DNA 5 3 3 5 3 5 RNA transcript  Promoter Transcription unit 1 A eukaryotic promoter 5 3 Promoter Nontemplate strand 3 5 DNA DNA 5 T A T A A AA 3 Start point 3 A T AT T T T 5 RNA polymerase 1 Initiation TATA box Start point Template strand 2 Several transcription Nontemplate strand of DNA Transcription 5 3 factors bind to DNA 5 factors 3 Template strand of DNA RNA Unwound transcript DNA 5 3 2 Elongation 3 5 Rewound DNA 3 Transcription initiation 5 3 complex forms 3 5 3 5 RNA polymerase II RNA Transcription factors transcript 3 Termination 5 3 5 3 3 3 5 5 3 5 5 3 RNA transcript Completed RNA transcript Direction of transcription (“downstream”) Transcription initiation complex RNA Polymerase Binding and Initiation of Elongation of the RNA Strand Transcription As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at a time Promoters signal the transcriptional start point and usually extend several dozen nucleotide pairs upstream of the start point Transcription progresses at a rate of 40 nucleotides per second in eukaryotes Transcription factors mediate the binding of RNA polymerase and the initiation of transcription A gene can be transcribed simultaneously by several RNA polymerases The completed assembly of transcription factors and RNA polymerase II bound to a promoter is called a transcription initiation complex Nucleotides are added to the 3 end of the growing RNA molecule A promoter called a TATA box is crucial in forming the initiation complex in eukaryotes  Nontemplate strand of DNA RNA nucleotides Concept 3: Eukaryotic cells modify RNA after RNA polymerase transcription Enzymes in the eukaryotic nucleus modify pre-mRNA (RNA A T C C A A 3 5 processing) before the genetic messages are dispatched to the C 3 end cytoplasm During RNA processing, both ends of the primary transcript are usually altered C A U C C A Also, usually some interior parts of the molecule are cut out, and the 5 T 3 other parts spliced together A G G T T 5 Direction of transcription Template strand of DNA Newly made RNA Alteration of mRNA Ends Termination of Transcription Each end of a pre-mRNA molecule is modified in a particular way – The 5 end receives a modified nucleotide 5 cap The mechanisms of termination are different in bacteria and – The 3 end gets a poly-A tail eukaryotes Polyadenylation is the addition of a poly(A) tail to an RNA molecule. In bacteria, the polymerase stops transcription at the end of the The poly(A) tail consists of multiple adenosine monophosphates; in other terminator and the mRNA can be translated without further words, it is a stretch of RNA that has only adenine bases. modification In eukaryotes, RNA polymerase II transcribes the polyadenylation These modifications share several functions signal sequence – They seem to facilitate the export of mRNA – They protect mRNA from hydrolytic enzymes – They help ribosomes attach to the 5 end Protein-coding Polyadenylation segment signal 5 3 G P P P AAUAAA AAA … AAA Start Stop 5 Cap 5 UTR 3 UTR Poly-A tail codon codon (UTR: untranslated region) RNA processing: Addition of the 5 cap and poly-A tail  RNA transcript (pre-mRNA) 5 Split Genes and RNA Splicing Exon 1 Intron Exon 2 Protein Most eukaryotic genes and their RNA transcripts have long noncoding snRNA Other stretches of nucleotides that lie between coding regions proteins These noncoding regions are called intervening sequences, or introns snRNPs The other regions are called exons because they are eventually expressed, In some cases, RNA usually translated into amino acid sequences splicing is carried out by Spliceosome RNA splicing removes introns and joins exons, creating an mRNA molecule spliceosomes with a continuous coding sequence Spliceosomes consist of a 5 variety of proteins and 5 Exon Intron Exon Intron Exon 3 several small nuclear Pre-mRNA 5 Cap Poly-A tail ribonucleoproteins Codon 130 31104 105 numbers 146 (snRNPs) that recognize Introns cut out and the splice sites exons spliced together mRNA 5 Cap Poly-A tail 1146 5 UTR 3 UTR Coding RNA processing: RNA splicing segment RNA transcript (pre-mRNA) RNA transcript (pre-mRNA) 5 5 Exon 1 Intron Exon 2 Exon 1 Intron Exon 2 Protein Protein Other Other snRNA proteins snRNA proteins snRNPs snRNPs In some cases, RNA In some cases, RNA splicing is carried out by splicing is carried out by Spliceosome spliceosomes spliceosomes Spliceosomes consist of a Spliceosomes consist of a 5 variety of proteins and variety of proteins and several small nuclear several small nuclear ribonucleoproteins ribonucleoproteins (snRNPs) that recognize (snRNPs) that recognize the splice sites the splice sites Spliceosome components Cut-out mRNA intron 5 Exon 1 Exon 2 Ribozymes Ribozymes are catalytic RNA molecules that function as enzymes and can splice RNA The discovery of ribozymes made out of date the belief that all biological catalysts were proteins Proteins often have a modular architecture consisting of discrete Three properties of RNA enable it to function as an enzyme regions called domains – It can form a three-dimensional structure because of its ability to In many cases, different base-pair with itself exons code for the different domains in a – Some bases in RNA contain functional groups that may protein participate in catalysis Exon shuffling may result – RNA may hydrogen-bond with other nucleic acid molecules in the evolution of new proteins The Functional and Evolutionary Importance of Introns Some introns contain sequences that may regulate gene expression Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing Concept 4: Translation is the RNA-directed This is called alternative RNA splicing Consequently, the number of different proteins an organism can synthesis of a polypeptide: a closer look produce is much greater than its number of genes Genetic information flows from mRNA to protein through the process of translation Molecular Components of Translation Accurate translation requires two steps Aminoacyl-tRNA synthetase (enzyme) – First: a correct match between a tRNA and an amino acid, done by the enzyme Amino acid A cell translates a mRNA message aminoacyl-tRNA synthetase into protein with the help of transfer – Second: a correct match P P P Adenosine RNA (tRNA) between the tRNA anticodon ATP and an mRNA codon tRNA transfer amino acids to the Flexible pairing at the third base of growing polypeptide in a ribosome a codon is called wobble and Translation is a complex process in allows some tRNAs to bind to terms of its biochemistry and more than one codon mechanics An aminoacyl-tRNA synthetase joining a specific amino acid to a tRNA The Structure and Function of Transfer RNA Accurate translation requires two Aminoacyl-tRNA steps Molecules of tRNA are not identical synthetase (enzyme) – Each carries a specific amino acid on one end – First: a correct match between a tRNA and an amino acid, – Each has an anticodon on the other end; the anticodon base-pairs with a complementary Amino acid codon on mRNA done by the enzyme aminoacyl-tRNA synthetase P Adenosine A tRNA molecule consists of a single RNA strand that is only about 80 nucleotides long Flattened into one plane to reveal its base pairing, a tRNA molecule looks like a cloverleaf – Second: a correct match P P P Adenosine P Pi between the tRNA anticodon ATP Because of hydrogen bonds, tRNA actually twists and folds into a three-dimensional and an mRNA codon Pi Pi molecule Flexible pairing at the third base of tRNA is roughly L-shaped a codon is called wobble and allows some tRNAs to bind to more than one codon The structure of transfer RNA (tRNA) An aminoacyl-tRNA synthetase joining a specific amino acid to a tRNA  Aminoacyl-tRNA synthetase (enzyme) Ribosomes Amino acid Ribosomes facilitate specific coupling of tRNA anticodons with mRNA P Adenosine codons in protein synthesis P P P The two ribosomal subunits (large and small) are made of proteins and Adenosine P Pi ATP Aminoacyl-tRNA Pi Pi tRNA synthetase ribosomal RNA (rRNA) Bacterial and eukaryotic ribosomes are somewhat similar but have tRNA significant differences: some antibiotic drugs specifically target Amino bacterial ribosomes without harming eukaryotic ribosomes acid P Adenosine AMP Computer model An aminoacyl-tRNA synthetase joining a specific amino acid to a tRNA Aminoacyl-tRNA Growing polypeptide Exit tunnel synthetase (enzyme) tRNA molecules Amino acid Large P Adenosine The anatomy of E P subunit A P P P Adenosine P Pi a functioning ribosome ATP Aminoacyl-tRNA Small Pi Pi tRNA synthetase subunit 5 tRNA mRNA 3 (a) Computer model of functioning ribosome Amino Growing polypeptide acid P site (Peptidyl-tRNA Amino end Exit tunnel Next amino binding site) acid to be P Adenosine added to A site (Aminoacyl- polypeptide AMP tRNA binding site) E site chain Computer model (Exit site) E tRNA E P A Large mRNA 3 subunit mRNA binding site Small 5 Codons Aminoacyl tRNA subunit (“charged tRNA”) (b) Schematic model showing binding sites (c) Schematic model with mRNA and tRNA  A ribosome has three binding sites for tRNA Growing Exit tunnel – The P site holds the tRNA that carries the growing polypeptide chain tRNA polypeptide – The A site holds the tRNA that carries the next amino acid to be added to the molecules chain – The E site is the exit site, where discharged tRNAs leave the ribosome Large subunit E P A Small subunit 5 mRNA 3 (a) Computer model of functioning ribosome Building a Polypeptide P site (Peptidyl-tRNA Exit tunnel binding site) The three stages of translation – Initiation A site (Aminoacyl- – Elongation tRNA binding site) E site – Termination (Exit site) All three stages require protein “factors” that aid in the translation E P A Large process subunit mRNA binding site Small subunit (b) Schematic model showing binding sites  Amino end of polypeptide Ribosome Association and Initiation of Translation The initiation stage of translation brings together mRNA, a tRNA with the first amino acid, and E the two ribosomal subunits mRNA 3 First, a small ribosomal subunit binds with mRNA and a special initiator tRNA P A Then the small subunit moves along the mRNA until it reaches the start codon (AUG) 5 site site Proteins called initiation factors bring in the large subunit that completes the translation initiation complex Large ribosomal subunit 3 U A C 5 P site 5 A U G 3 Pi Initiator  tRNA GTP GDP E A mRNA 5 5 3 3 Start codon Small mRNA binding site ribosomal Translation initiation complex subunit Amino end of polypeptide Elongation of the Polypeptide Chain E 3 During the elongation stage, amino acids are added one by one to mRNA P A the preceding amino acid at the C-terminus of the growing chain 5 site site GTP Each addition involves proteins called elongation factors and occurs GDP  P i in three steps: codon recognition, peptide bond formation, and translocation Translation proceeds along the mRNA in a 5′ to 3′ direction E P A  Amino end of polypeptide Termination of Translation E Termination occurs when a stop codon in the mRNA reaches the A site of the mRNA 3 ribosome P A site site GTP The A site accepts a protein called a release factor 5 GDP  P i The release factor causes the addition of a water molecule instead of an amino acid This reaction releases the polypeptide, and the translation assembly then comes apart E P A Release factor 3 E 5 P A Stop codon (UAG, UAA, or UGA) Amino end of polypeptide Termination of Translation E Termination occurs when a stop codon in the mRNA reaches the A site of the mRNA 3 ribosome Ribosome ready for P A The A site accepts a protein called a release factor site site GTP next aminoacyl tRNA 5 GDP  P i The release factor causes the addition of a water molecule instead of an amino acid This reaction releases the polypeptide, and the translation assembly then comes apart E E P A P A Release factor Free GDP  P i polypeptide GTP 3 3 E 5 2 GTP 5 P A 2 GDP  2 P i Stop codon (UAG, UAA, or UGA)  Termination of Translation Completing and Targeting the Functional Protein Termination occurs when a stop codon in the mRNA reaches the A site of the ribosome The A site accepts a protein called a release factor Often translation is not sufficient to make a functional protein The release factor causes the addition of a water molecule instead of an amino acid Polypeptide chains are modified after translation or targeted to This reaction releases the polypeptide, and the translation assembly then comes specific sites in the cell apart Release factor Free polypeptide 5 3 3 2 GTP 3 5 5 2 GDP  2 P i Stop codon (UAG, UAA, or UGA) Completed Polyribosomes Growing polypeptide Protein Folding and Post-Translational Modifications polypeptides A number of ribosomes can Incoming translate a single mRNA ribosomal simultaneously, forming a subunits During and after synthesis, a polypeptide chain spontaneously coils polyribosome (or polysome) and folds into its three-dimensional shape Start of mRNA End of Proteins may also require post-translational modifications before Polyribosomes enable a cell to (5 end) mRNA make many copies of a (a) (3 end) doing their job polypeptide very quickly Some polypeptides are activated by enzymes that cleave them Other polypeptides come together to form the subunits of a protein Ribosomes mRNA (b) 0.1 m Targeting Polypeptides to Specific Locations Concept 5: Mutations of one or a few Two populations of ribosomes are evident in cells: free ribsomes (in nucleotides can affect protein structure and the cytosol) and bound ribosomes (attached to the ER) Free ribosomes mostly synthesize proteins that function in the function cytosol Bound ribosomes make proteins of the endomembrane system and Mutations are changes in the genetic material of a cell or virus proteins that are secreted from the cell Point mutations are chemical changes in just one base pair of a Ribosomes are identical and can switch from free to bound gene The change of a single nucleotide in a DNA template strand can lead to the production of an abnormal protein Targeting Polypeptides to Specific Locations Polypeptide synthesis always begins in the cytosol Synthesis finishes in the cytosol unless the polypeptide signals the ribosome to attach to the ER Wild-type hemoglobin Sickle-cell hemoglobin Polypeptides destined for the ER or for secretion are marked by a signal peptide Wild-type hemoglobin DNA Mutant hemoglobin DNA A signal-recognition particle (SRP) binds to the signal peptide 3 C T T 5 3 C A T 5 The SRP brings the signal peptide and its ribosome to the ER 5 G A A 3 5 G T A 3 1 Ribosome 5 mRNA 4 mRNA mRNA Signal 5 G A A 3 5 G U A 3 ER peptide Signal membrane 3 peptide SRP Protein Normal hemoglobin Sickle-cell hemoglobin removed 6 Glu Val SRP 2 receptor CYTOSOL protein ER LUMEN Translocation complex  Wild type DNA template strand 3 T A C T T C A A A C C G A T T 5 Types of Small-Scale Mutations 5 A T G A A G T T T G G C T A A 3 mRNA5 A U G A A G U U U G G C U A A 3 Protein Met Lys Phe Gly Stop Amino end Carboxyl end Point mutations within a gene can be divided into two general (a) Nucleotide-pair substitution (b) Nucleotide-pair insertion or deletion categories A instead of G Extra A 3 T A C T T C A A A C C A A T T 5 3 T A C A T T C A A A C C G A T T 5 – Nucleotide-pair substitutions 5 A T G A A G T T T G G T T A A 3 U instead of C 5 A T G T A A G T T T G G C T A A 3 Extra U – One or more nucleotide-pair insertions or deletions 5 A U G A A G U U U G G U U A A 3 Met Lys Phe Gly 5 A U G U A A G U U U G G C U A A 3 Met Stop Stop Silent (no effect on amino acid sequence) Frameshift causing immediate nonsense (1 nucleotide-pair insertion) T instead of C A missing 3 T A C T T C A A A T C G A T T 5 3 T A C T T C A A C C G A T T 5T 5 A T G A A G T T T A G C T A A 3  5 A T G A A G T T G G C T A A 3A A instead of G U missing 5 A U G A A G U U U A G C U A A 3 5 A U G A A G U U G G C U A A 3 Met Lys Phe Ser Stop Met Lys Leu Ala Missense Frameshift causing extensive missense (1 nucleotide-pair deletion) A instead of T T T C missing 3 T A C A T C A A A C C G A T T 5 3 T A C A A A C C G A T T 5 5 A T G T A G T T T G G C T A A 3 5 A T G T T T G G C T A A 3 U instead of A A A G missing 5 A U G U A G U U U G G C U A A 3  A A 5 A U G U U U G G C U A A 3U Met Met Phe Gly Stop Stop Nonsense No frameshift, but one amino acid missing (3 nucleotide-pair deletion) Substitutions Wild type DNA template strand 3 T A C T T C A A A C C G A T T 5 A nucleotide-pair substitution replaces one nucleotide and its 5 A T G A A G T T T G G C T A A 3 partner with another pair of nucleotides Silent mutations have no effect on the amino acid produced by a mRNA5 A U G A A G U U U G G C U A A 3 codon because of redundancy in the genetic code Protein Met Lys Phe Gly Stop Missense mutations still code for an amino acid, but not the Amino end Carboxyl end correct amino acid (a) Nucleotide-pair substitution: silent Nonsense mutations change an amino acid codon into a stop A instead of G codon, nearly always leading to a nonfunctional protein 3 T A C T T C A A A C C A A T T 5 5 A T G A A G T T T G G T T A A 3 U instead of C 5 A U G A A G U U U G G U U A A 3 Met Lys Phe Gly Stop  Insertions and Deletions Wild type DNA template strand 3 T A C T T C A A A C C G A T T 5 Insertions and deletions are additions or losses of nucleotide pairs in 5 A T G A A G T T T G G C T A A 3 a gene mRNA5 A U G A A G U U U G G C U A A 3 These mutations have a disastrous effect on the resulting protein Protein Met Lys Phe Gly Stop more often than substitutions do Amino end Carboxyl end Insertion or deletion of nucleotides may alter the reading frame, (a) Nucleotide-pair substitution: missense producing a frameshift mutation T instead of C 3 T A C T T C A A A T C G A T T 5 5 A T G A A G T T T A G C T A A 3 A instead of G 5 A U G A A G U U U A G C U A A 3 Met Lys Phe Ser Stop Wild type Wild type DNA template strand 3 T A C T T C A A A C C G A T T 5 DNA template strand 3 T A C T T C A A A C C G A T T 5 5 A T G A A G T T T G G C T A A 3 5 A T G A A G T T T G G C T A A 3 mRNA5 A U G A A G U U U G G C U A A 3 mRNA5 A U G A A G U U U G G C U A A 3 Protein Met Lys Phe Gly Stop Protein Met Lys Phe Gly Amino end Carboxyl end Stop Amino end Carboxyl end (b) Nucleotide-pair insertion or deletion: frameshift causing (a) Nucleotide-pair substitution: nonsense immediate nonsense A instead of T T instead of C Extra A 3 T A C A T C A A A C C G A T T 5 3 T A C A T T C A A A C G G A T T 5 5 A T G T A G T T T G G C T A A 3 5 A T G T A A G T T T G G C T A A 3 U instead of A Extra U 5 A U G U A G U U U G G C U A A 3 5 A U G U A A G U U U G G C U A A 3 Met Stop Met Stop 1 nucleotide-pair insertion Wild type Mutagens DNA template strand 3 T A C T T C A A A C C G A T T 5 5 A T G A A G T T T G G C T A A 3 Spontaneous mutations can occur during DNA replication, mRNA5 A U G A A G U U U G G C U A A 3 recombination, or repair Protein Met Lys Phe Gly Stop Mutagens are physical or chemical agents that can cause mutations Amino end Carboxyl end (b) Nucleotide-pair insertion or deletion: frameshift causing extensive missense A missing 3 T A C T T C A A C C G A T T 5 5 A T G A A G T T G G C T A A 3 U missing 5 A U G A A G U U G G C U A A 3 Met Lys Leu Ala 1 nucleotide-pair deletion Wild type Concept 6: While gene expression differs DNA template strand 3 T A C T T C A A A C C G A T T 5 5 A T G A A G T T T G G C T A A 3 among the domains of life, the concept of a mRNA5 A U G A A G U U U G G C U A A 3 Protein Met Lys Phe Gly gene is universal Stop Amino end Carboxyl end Archaea are prokaryotes, but share many features of gene (b) Nucleotide-pair insertion or deletion: no frameshift, but one expression with eukaryotes amino acid missing T T C missing 3 T A C A A A C C G A T T 5 5 A T G T T T G G C T A A 3 A A G missing 5 A U G U U U G G C U A A 3 Met Phe Gly Stop 3 nucleotide-pair deletion  DNA TRANSCRIPTION Comparing Gene Expression in Bacteria, Archaea, 3 and Eukarya 5 RNA RNA polymerase transcript Exon RNA RNA transcript Bacteria and eukarya differ in their RNA polymerases, termination PROCESSING (pre-mRNA) Intron Aminoacyl- of transcription, and ribosomes; archaea tend to resemble eukarya In summary, a gene can be defined NUCLEUS tRNA synthetase in these respects as a region of DNA that can be Amino acid Bacteria can simultaneously transcribe and translate the same gene expressed to produce a final functional product, either a CYTOPLASM tRNA AMINO ACID ACTIVATION In eukarya, transcription and translation are separated by the polypeptide or an RNA molecule mRNA Growing polypeptide nuclear envelope 3 In archaea, transcription and translation are likely coupled A P Aminoacyl E (charged) Ribosomal tRNA subunits TRANSLATION E A Anticodon Codon Ribosome RNA polymerase What Is a Gene? Revisiting the Question DNA mRNA The idea of the gene has evolved through the history of genetics Polyribosome We have considered a gene as – A discrete unit of inheritance Direction of 0.25 m – A region of specific nucleotide sequence in a chromosome RNA transcription – A DNA sequence that codes for a specific polypeptide chain polymerase DNA Polyribosome Polypeptide (amino end) Ribosome mRNA (5 end)  Polypeptide tRNA Amino Transcription unit acid Promoter 5 3 3 3 5 5 Template strand RNA polymerase of DNA E A Anti- RNA transcript codon Codon mRNA Ribosome Pre-mRNA 5 Cap Poly-A tail mRNA