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Chapter 17 From Gene to Protein Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Overview: The Flow of Genetic Information • The information content of DNA – Is in the form of specific sequences of along the DNA strands Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings • The DNA inherited by an organism – Leads to specific traits by dictating the synthesis of proteins • The process by which DNA directs protein synthesis, gene expression – Includes two stages, called Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 17.1: • Genes: – specify proteins via transcription and translation – Specify different types of RNA via transcription Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Basic Principles of Transcription and Translation • Transcription – Is the synthesis of RNA under the direction of DNA. It produces: • messenger RNA (mRNA) • ribosomal RNA (rRNA) • Transfer RNA (tRNA) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings • Translation – Is the actual synthesis of a polypeptide, which occurs under the direction of – Occurs on Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings In prokaryotes • Transcription and translation occur simultaneously TRANSCRIPTION DNA mRNA Ribosome TRANSLATION Polypeptide (a) Prokaryotic cell. In a cell lacking a nucleus, mRNA produced by transcription is immediately translated without additional processing. Figure 17.3a Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings In eukaryotes • Transcription and translation occur at different times • RNA transcripts are modified before becoming true mRNA Nuclear envelope DNA TRANSCRIPTION Pre-mRNA RNA PROCESSING mRNA Ribosome TRANSLATION Polypeptide Figure 17.3b Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings (b) Eukaryotic cell. The nucleus provides a separate compartment for transcription. The original RNA transcript, called pre-mRNA, is processed in various ways before leaving the nucleus as mRNA. • Cells are governed by a cellular chain of command – DNA mRNA protein Or – DNA rRNA Or DNA tRNA Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Genetic Code Genetic information – Is encoded as a sequence of base triplets, called Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings During transcription • The DNA base sequence of a gene determines the sequence of bases of an mRNA molecule Gene 2 DNA molecule Gene 1 Gene 3 DNA strand 3 5 A C C A A A C C G A G T (template) TRANSCRIPTION mRNA 5 U G G U U U G G C U C A Codon TRANSLATION Protein Trp Amino acid Phe Gly Ser Figure 17.4 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 3 The Genetic Code • A codon in messenger RNA Figure 17.5 Second mRNA base U C A UAU UUU UCU Tyr Phe UAC UUC UCC U UUA UCA Ser UAA Stop UAG Stop UUG Leu UCG CUU CUC C CUA CUG CCU CCC Leu CCA CCG Pro AUU AUC A AUA AUG ACU ACC ACA ACG Thr GUU G GUC GUA GUG lle Met or start GCU GCC Val GCA GCG Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Ala G U UGU Cys UGC C UGA Stop A UGG Trp G U CAU CGU His CAC CGC C Arg CAA CGA A Gln CAG CGG G U AAU AGU Asn AAC AGC Ser C A AAA AGA Lys Arg G AAG AGG U GAU GGU C GAC Asp GGC Gly GAA GGA A Glu GAG GGG G Third mRNA base (3 end) First mRNA base (5 end) – Is either translated into an amino acid or serves as a translational stop signal Evolution of the Genetic Code • The genetic code is nearly universal – Shared by organisms from the simplest bacteria to the most complex animals Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 17.2: Transcription • RNA synthesis – Is catalyzed by which opens the DNA strands and connects the RNA nucleotides – Follows the same rules as DNA, except that in RNA, uracil substitutes for thymine Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Synthesis of an RNA Transcript • The stages of transcription are Promoter – Initiation Transcription unit 5 3 3 5 Start point RNA polymerase – Elongation – Termination DNA Initiation. After RNA polymerase binds to the promoter, the DNA strands unwind, and the polymerase initiates RNA synthesis at the start point on the template strand. 1 5 3 Unwound DNA 3 5 Template strand of DNA transcript 2 Elongation. The polymerase moves downstream, unwinding the DNA and elongating the RNA transcript 5 3 . In the wake of transcription, the DNA strands re-form a double helix. Rewound RNA RNA 5 3 3 5 3 5 RNA transcript 3 Termination. Eventually, the RNA transcript is released, and the polymerase detaches from the DNA. 5 3 3 5 5 Figure 17.7 Completed RNA transcript Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 3 RNA Polymerase Binding and Initiation of Transcription • signal the initiation site for transcription • – Help eukaryotic RNA polymerase recognize promoter sequences 1 Eukaryotic promoters TRANSCRIPTION DNA RNA PROCESSING Pre-mRNA mRNA TRANSLATION Ribosome Polypeptide Promoter 5 3 3 5 T A T A A AA AT A T T T T TATA box Start point Template DNA strand Several transcription factors 2 Transcription factors 5 3 3 Additional transcription 3 5 factors RNA polymerase II 5 3 Figure 17.8 Transcription factors 3 5 5 RNA transcript Transcription initiation complex Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Elongation of the RNA Strand • As RNA polymerase moves along the DNA – It continues to untwist the double helix, adding successive complementary nucleotides, and extending the RNA molecule Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Elongation Non-template strand of DNA RNA nucleotides RNA polymerase A T C C A A 3 3 end U 5 A U C C A T A G G T T Direction of transcription (“downstream”) 5 Newly made RNA Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Template strand of DNA Concept 17.3: • Enzymes in the eukaryotic nucleus – Modify in specific ways before the genetic messages are dispatched to the cytoplasm Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Alteration of mRNA Ends • Each end of a pre-mRNA molecule is modified in a particular way A modified guanine nucleotide added to the 5 end TRANSCRIPTION 50 to 250 adenine nucleotides added to the 3 end DNA Pre-mRNA RNA PROCESSING 5 mRNA Protein-coding segment Polyadenylation signal 3 G P P P AAUAAA AAA…AAA Ribosome TRANSLATION 5 Cap 5 UTR Start codon Stop codon Polypeptide Figure 17.9 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 3 UTR Poly-A tail Split Genes and RNA Splicing • RNA splicing – Removes introns and joins exons TRANSCRIPTION RNA PROCESSING DNA Pre-mRNA 5 Exon Intron Pre-mRNA 5 Cap 30 31 1 Coding segment mRNA Ribosome Intron Exon Exon 3 Poly-A tail 104 105 146 Introns cut out and exons spliced together TRANSLATION Polypeptide mRNA 5 Cap 1 3 UTR Figure 17.10 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Poly-A tail 146 3 UTR The Functional Importance of Introns • The presence of introns – Allows for alternative RNA splicing Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings • Proteins often consist of discrete structural and functional regions called domains • In many cases different the different domains in a protein Gene DNA Exon 1 Intron Exon 2 Transcription RNA processing Intron Exon 3 Translation Domain 3 Domain 2 Domain 1 Polypeptide Figure 17.12 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings code for Concept 17.4: • Translation is the mRNA-directed synthesis of a polypeptide • A cell translates an mRNA message into protein – With the help of Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Translation TRANSCRIPTION DNA mRNA Ribosome TRANSLATION Polypeptide Amino acids Polypeptide tRNA with amino acid Ribosome attached Gly tRNA Anticodon A A A U G G U U U G G C Codons 5 mRNA Figure 17.13 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 3 • Molecules of tRNA are not all identical – Each carries a specific one end – Each has an end Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings on on the other The Structure and Function of Transfer RNA • A tRNA molecule 3 A C C A 5 C G G C C G U G U A A U A U U C UA C A C AG * G * G U G U * C C * * U C * * G AG C G C U A * G A A* C U * A G A A C C Amino acid attachment site C U C G A G A G * * G A G G Hydrogen bonds Anticodon Figure 17.14a Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Ribosomes • Facilitate the specific coupling of tRNA anticodons with mRNA codons during protein synthesis Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The ribosomal subunits • Are constructed of proteins and RNA molecules named ribosomal RNA (rRNA) DNA TRANSCRIPTION mRNA Ribosome TRANSLATION Polypeptide Exit tunnel Growing polypeptide tRNA molecules Large subunit E P A Small subunit 5 mRNA 3 (a) Figure 17.16a Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The ribosome has three binding sites for tRNA • The P site P site (Peptidyl-tRNA binding site) • The A site A site (AminoacyltRNA binding site) E site (Exit site) Large subunit E P A • The E site mRNA binding site Figure 17.16b Small subunit (b) Schematic model showing binding sites. A ribosome has an mRNA binding site and three tRNA binding sites, known as the A, P, and E sites. This schematic ribosome will appear in later diagrams. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Amino end Growing polypeptide Next amino acid to be added to polypeptide chain tRNA 3 mRNA 5 Codons (c) Schematic model with mRNA and tRNA. A tRNA fits into a binding site when its anticodon base-pairs with an mRNA codon. The P site holds the tRNA attached to the growing polypeptide. The A site holds the tRNA carrying the next amino acid to be added to the polypeptide chain. Discharged tRNA leaves via the E site. Figure 17.16c Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Building a Polypeptide • We can divide translation into three stages – Initiation – Elongation – Termination Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Ribosome Association and Initiation of Translation • The initiation stage of translation – Brings together mRNA, tRNA bearing the first amino acid of the polypeptide, and two subunits of a ribosome P site 3 U A C 5 5 A U G 3 Initiator tRNA Large ribosomal subunit GTP GDP E A mRNA 5 Start codon mRNA binding site 5 3 Small ribosomal subunit 3 Translation initiation complex 2 Figure 17.17 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Elongation of the Polypeptide Chain • In the elongation stage of translation – Amino acids are added one by one to the preceding amino acid 1 TRANSCRIPTION Amino end of polypeptide DNA mRNA Ribosome Codon recognition. The anticodon of an incoming tRNA base-pairs with the complementary mRNA codon in the A site. TRANSLATION Polypeptide mRNA Ribosome ready for next aminoacyl tRNA E 3 P A site site 5 2 GTP 2 GDP E E P P A 2 GDP Figure 17.18 3 Translocation. The ribosome translocates the tRNA in the A site to the P site. The empty tRNA in the P site is moved to the E site, where it is released. The mRNA moves along with its bound tRNAs, bringing the next codon to be translated into the A site. A GTP Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Peptide bond formation. This step attaches the polypeptide to the tRNA in the A site. E P A Termination of Translation • The final stage of translation is termination when the ribosome reaches a in the mRNA Release factor Free polypeptide 5 3 3 5 5 3 Stop codon (UAG, UAA, or UGA) 1 When a ribosome reaches a stop 2 The release factor hydrolyzes 3 The two ribosomal subunits codon on mRNA, the A site of the the bond between the tRNA in and the other components of ribosome accepts a protein called the P site and the last amino the assembly dissociate. a release factor instead of tRNA. acid of the polypeptide chain. The polypeptide is thus freed from the ribosome. Figure 17.19 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Completing and Targeting the Functional Protein • Polypeptide chains – Undergo modifications after the translation process • Proteins may be modified in ways that affect their three-dimensional shape • Other molecules may be attached to proteins, such as sugars, lipids, phosphates Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Targeting Polypeptides to Specific Locations • Two populations of ribosomes are evident in cells – Free in the cytosol, and bound to ER • Free ribosomes in the cytosol – Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings • Proteins destined for the endomembrane system or for secretion – Must be transported into the ER – Have signal peptides to which a signalrecognition particle (SRP) binds, enabling the translation ribosome to bind to the ER Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The signal mechanism for targeting proteins to the ER 2 1 Polypeptide An SRP binds synthesis begins to the signal on a free peptide. ribosome in the cytosol. 3 The SRP binds to a receptor protein in the ER membrane. 4 5 A signalcleaving The polypeptide begins enzyme translocating across the cuts off the membrane. signal peptide. 6 The rest of the completed polypeptide leaves the ribosome and folds into its final conformation. Ribosome mRNA Signal peptide Signalrecognition particle (SRP) SRP receptor CYTOSOL protein ERLUMEN Translocation complex Figure 17.21 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Signal peptide removed ER membrane Protein What is a gene? • A gene – Is a region of DNA whose final product is either a or an Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings • A summary of transcription and translation in a eukaryotic cell DNA TRANSCRIPTION 1 RNA is transcribed from a DNA template. 3 5 RNA transcript RNA polymerase RNA PROCESSING Exon 2 In eukaryotes, the RNA transcript (premRNA) is spliced and modified to produce mRNA, which moves from the nucleus to the cytoplasm. RNA transcript (pre-mRNA) Intron Aminoacyl-tRNA synthetase NUCLEUS Amino acid tRNA FORMATION OF INITIATION COMPLEX CYTOPLASM 3 After leaving the nucleus, mRNA attaches to the ribosome. mRNA AMINO ACID ACTIVATION 4 Each amino acid attaches to its proper tRNA with the help of a specific enzyme and ATP. Growing polypeptide Activated amino acid Ribosomal subunits 5 TRANSLATION A succession of tRNAs add their amino acids to the polypeptide chain Anticodon as the mRNA is moved through the ribosome one codon at a time. (When completed, the polypeptide is released from the ribosome.) 5 E A AAA UG GU U U A U G Codon Figure 17.26 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Ribosome