Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Experimental Procedure No growth on minimal medium Prokaryotes Growth on minimal medium plus arginine Wild-type Neurospora crassa Mutagenize with X-rays Grow on rich medium arg mutants 5´ Results Mutation in Enzyme Plus Ornithine Eukaryotes Plus Plus Plus Citruline Arginosuccinate Arginine C E T C T DN A template strand A Transcription 3´ G F G U G mRNA 3´ A C H A G Translation Conclusion Glutamate Enzymes encoded by arg genes arg genes Ornithine Citruline Arginosuccinate 5´ Arginine E F G H arg E arg F arg G arg H Protein 1 2 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Sentence with Spaces Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. WHY DID THE RED BAT EAT THE FAT RAT Delete one letter Replication WHY DID HE RED BAT EAT THE FAT RAT DNA Transcription Only one word changed Reverse transcription RNA Translation Sentence with No Spaces WHYDIDTHEREDBATEATTHEFATRAT Protein Delete one letter WHYDIDHEREDBATEATTHEFATRAT All words after deletion changed 3 4 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. SCIENTIFIC THINKING SCIENTIFIC THINKING Hypothesis: The genetic code is read in groups of three bases. Prediction: If the genetic code is read in groups of three, then a deletion of one or two bases would cause drastic changes to the encoded protein. Deletion of three bases, however, could produce a protein close to the “normal” sequence. Test: Single-base deletion mutants are collected, each of which exhibits a mutant phenotype. Three of these deletions in a single region are combined to assess the effect of deletion of three bases. one Bases Deleted Met Pro Thr His Arg Asp Ala Ser Amino acids AUGCCUACGCACCGCGACGCAUCA Delete one bases AUGCCUAGCACCGCGACGCAUCA All amino acids changed after deletion Met Pro Ser Thr Ala Thr His Three Bases Deleted Met Pro Thr His Arg Asp Ala Ser Amino acids AUGCCUACGCACCGCGACGCAUCA Delete three bases AUGCCUCACCGCGACGCAUCA Met Pro His Arg Asp Ala Ser Amino acids do not change after third deletion Result: The combination of three deletions does not have the same drastic effect as the loss of one or two bases. Conclusion: The genetic code is read in groups of three. Further Experiments: If you also had mutants with one base additions, what would be the effect of combining a deletion and an addition? 5 6 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. SCIENTIFIC THINKING RNA polymerase DNA Start site Unwinding Coding strand Rewinding ׳3 ׳3 ׳5 ׳5 Downstream ׳3 Upstream Template strand mRNA Transcription bubble ׳5 7 8 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. RNA polymerase DNA and RNA polymerase dissociates DNA mRNA dissociates from DNA ׳3 0.25µm ׳5 RNA polymerase ׳5 ׳3 DNA Four, or more U ribonucleotides mRNA hairpin causes RNA polymerase to pause Polyribosome mRNA Cytosine Guanine Adenine Uracil Polypeptide chains Ribosomes ׳5 © Dr. Oscar Miller 9 10 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 5´ cap Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Other transcription factors HO RNA polymerase II OH P CH2 Eukaryotic DNA Transcription factor N+ CH3 TATA box + 3´ G 5´ A lypo l tai A AA Methyl group Initiation complex 11 P P P P P AA 3´ AA mRNA CH3 12 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. E1 I1 E2 I2 E3 I3 E4 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. I4 snRNA Exon 1 snRNPs Intron Exon 2 A 5´ DNA template Exons Introns Transcription c 1. snRNA forms base-pairs with 5´ end of intron, and at branch site. ׳5 poly-A tail ׳3 Spliceosome Primary RNA transcript Introns are removed p c ׳5 a. 3´ Branch point A A 5´ ׳3 3´ 2. snRNPs associate with other factors to form spliceosome. Mature mRNA Lariat A Intron 5´ 1 mRNA 3 2 4 DNA 7 5 6 Exon 1 Exon b. 5´ c. Acceptor end ׳3 3D Ribbon-like Model 3D Space-filled Model Acceptor end Acceptor end 14 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Amino group Icon NH3+ Acceptor end ATP Pi Pi Carboxyl group Trp C Charged tRNA travels to ribosome NH O 3 O– Accepting site Amino acid site Anticodon loop NH + 3 Trp C AM + O Trp AM P P O OH C NH O O 3 + NH3+ Trp C AMP OH Trp C O O O O tRNA tRNA site Anticodon loop 3´ 13 ׳5 Anticodon loop Excised intron Exon 2 Mature mRNA 4. Exons are joined; spliceosome disassembles. b: Courtesy of Dr. Bert O’Malley, Baylor College of Medicine Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 2D “Cloverleaf” Model 3´ 3. 5´ end of intron is removed and forms bond at branch site, forming a lariat. The 3´ end of the intron is then cut. Charged tRNA dissociates Aminoacyl-tRNA Anticodon synthetase specific to tryptophan Anticodon end c: Created by John Beaver using ProteinWorkshop, a product of the RCSB PDB, and built using the Molecular Biology Toolkit developed by John Moreland and Apostol Gramada (mbt.sdsc.edu). The MBT is fi nanced by grant GM63208 15 16 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Large subunit Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 3´ 90° fMet Small subunit Large subunit Small subunit Large subunit 0° E site AUG U A C tRNA in P site U A C A U G Large subunit 3´ Initiation factor mRNA A site 3´ 3´ 3´ Initiation factor 5´ Small subunit 5´ GTP GDP + 5´ 5´ Pi Initiation complex Complete ribosome mRNA Small subunit 5´ 17 18 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 3´ Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. GDP NH3+ O O C C O O Peptide bond formation GTP Amino acid 4 Amino acid 5 P E A E A P 5´ Sectioned ribosome GTP GTP Next round Elongation factor 3´ 3´ Carboxyl end (C terminus) E P Elongation factor GDP + Pi Growing polypeptide “Ejected” tRNA Amino acid 7 COO– A site P site 3´ 5´ Amino acid 6 5´ A P 5´ 3´ Amino acid 3 O O OH E Elongation factor Amino acid 2 Amino acid 2 “Empty” tRNA Elongation factor Amino acid 1 Peptide bond C O Pi NH2 C N Amino acid 2 Amino acid 1 3´ Polypeptide chain NH3+ NH3+ Amino end (N terminus) Amino group Amino acid 1 + A E P A 5´ 5´ 19 20 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Rough endoplasmic reticulum (RER) Polypeptide chain releases Cytoplasm Lumen of the RER Dissociation Protein channel 3´ Release factor SRP binds to signal Docking peptide, arresting elongation Signal recognition particle (SRP) 5´ 3´ NH22 NH Polypeptide elongation continues Signal Exit tunnel Ribosome synthesizing peptide 5´ Sectioned ribosome C A C G U G A U A A P E 21 22 23 24 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. RNA RNA polymerase polymerase IIII 1. RNA polymerase II in the nucleus copies one strand of the DNA to produce the primary transcript. 3´ 5´ Primary Primary RNA RNA transcript transcript 2. The primary transcript is processed by addition of a 5´ methyl-G cap, cleavage and polyadenylation of the 3´ end, and removal of introns. The mature mRNA is then exported through nuclear pores to the cytoplasm. Primary RNA transcript Poly-A tail Cut intron 3. The 5´ cap of the mRNA associates with the small subunit of the ribosome. The initiator tRNA and large subunit are added to form an initiation complex. Cytoplasm Amino acids tRNA arrivesin A site 3´ Large subunit 5´ cap mRNA Small subunit Cytoplasm Empty tRNA moves into E site and is ejected Lengthening polypeptide chain Emptyt RNA Mature mRNA 5´ cap 3´ 3´ mRNA 5´ A site P site E site 4. The ribosome cycle begins with the growing peptide attached to the tRNA in the P site. The next charged tRNA binds to the A site with its anticodon complementary to the codon in the mRNA in this site. 5´ 5. Peptide bonds form between the amino terminus of the next amino acid and the carboxyl terminus of the growing peptide. This transfers the growing peptide to the tRNA in the A site, leaving the tRNA in the P site empty. 5´ 6. Ribosome translocation moves the ribosome relative to the mRNA and its bound tRNAs. This moves the growing chain into the P site, leaving the empty tRNA in the E site and the A site ready to bind the next charged tRNA. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. C G 5´–ATGCCTTATCGCTGA–3´ Template 3´–TACGGAATAGCGACT–5´ mRNA 5´–AUGCCUUAUCGCUGA–3´ Protein Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Polar Leu C T Thr G A C Pro T C C Glu T G A Glu G A A Lys G A A Ser G T C Amino acids T Nucleotides Met Pro Thr Arg Stop a. Normal Deoxygenated Tetramer Normal HBB Sequence A A T T Coding α1 α2 β1 β2 Abnormal Deoxygenated Tetramer Silent Mutation C G α1 α2 Coding 5´–ATGCCCTATCGCTGA–3´ Template 3´–TACGGGATAGCGACT–5´ β1 β2 mRNA 5´–AUGCCCUAUCGCUGA–3´ Protein Hemoglobin tetramer "Sticky" nonpolar sites Met Pro Thr Arg Stop b. Abormal HBB Sequence Missense Mutation Nonpolar (hydrophobic) Leu C T Thr G A C val Pro T C C T G T Glu G A A Lys G A A A T Ser G T C Amino acids T Nucleotides Tetramers form long chains when deoxygenated. This distorts the normal red blood cell shape into a sickle shape. Coding 5´–ATGCCCTATCACTGA–3´ Template 3´–TACGGGATAGTGACT–5´ mRNA 5´–AUGCCCUAUCACUGA–3´ Protein Met Pro Thr His Stop c. Nonsense Mutation A T Coding 5´–ATGCCCTAACGCTGA–3´ Template 3´–TACGGGATTGCGACT–5´ mRNA 5´–AUGCCCUAACGCUGA–3´ Protein 25 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Deletion Deleted AB C D E F G H I J AE F G H I J a. Duplication Duplicated A B C D E F G H I J A B C D B C D E F G H I J b. Inversion Inverted AB C D E F G H I J AD C B E F G H I J c. Reciprocal Translocation d. AB C D E F G H I J K L M D E F G H I J KL M N O P Q R A B C N OP Q R 27 d. Met Pro Stop 26