Chapter 17 201 From Gene to Protein In 1909, Archibald Garrod, a British physician, hypothesized that inherited diseases are caused by the patient’s inability to produce certain enzyme. Alkaptonuria patients have dark red urine as they are not able to produce an enzyme to metabolize alkapton, which becomes dark when exposed to air.

201 In 1950s, George Beadle and Edward Tatum exposed the orange red mold Neurospora to X-rays, and then cultivated the mold from the individual ascospores in minimal media containing different amino acid supplements. They discovered that some fungi had undergone mutation which required nutritional suppliments. These mutant strains are known as auxotrophs. The wild-type or normal strains can grow in minimal medium without nutritional supplements. They hypothesized that the mutant strains had defective genes due to radiation, and were not able to synthesize the necessary enzymes. They formulated one-gene-one–enzyme hypothesis which states that the function of a gene is to produce one specific enzyme.

EXPERIMENT RESULTS CONCLUSION Fig. 17-2 Growth: Wild-type cells growing and dividing No growth: Mutant cells cannot grow and divide Minimal medium RESULTS Classes of Neurospora crassa Wild type Class I mutants Class II mutants Class III mutants Minimal medium (MM) (control) MM + ornithine Condition MM + citrulline MM + arginine (control) Figure 17.2 Do individual genes specify the enzymes that function in a biochemical pathway? CONCLUSION Class I mutants (mutation in gene A) Class II mutants (mutation in gene B) Class III mutants (mutation in gene C) Wild type Precursor Precursor Precursor Precursor Gene A Enzyme A Enzyme A Enzyme A Enzyme A Ornithine Ornithine Ornithine Ornithine Gene B Enzyme B Enzyme B Enzyme B Enzyme B Citrulline Citrulline Citrulline Citrulline Gene C Enzyme C Enzyme C Enzyme C Enzyme C Arginine Arginine Arginine Arginine

EXPERIMENT Growth: Wild-type cells growing and dividing No growth: Fig. 17-2a EXPERIMENT Growth: Wild-type cells growing and dividing No growth: Mutant cells cannot grow and divide Figure 17.2 Do individual genes specify the enzymes that function in a biochemical pathway? Minimal medium

RESULTS Classes of Neurospora crassa Wild type Minimal medium (MM) Fig. 17-2b RESULTS Classes of Neurospora crassa Wild type Class I mutants Class II mutants Class III mutants Minimal medium (MM) (control) MM + ornithine Condition MM + citrulline Figure 17.2 Do individual genes specify the enzymes that function in a biochemical pathway? MM + arginine (control)

CONCLUSION Wild type Precursor Precursor Precursor Precursor Gene A Fig. 17-2c CONCLUSION Class I mutants (mutation in gene A) Class II mutants (mutation in gene B) Class III mutants (mutation in gene C) Wild type Precursor Precursor Precursor Precursor Gene A Enzyme A Enzyme A Enzyme A Enzyme A Ornithine Ornithine Ornithine Ornithine Gene B Enzyme B Enzyme B Enzyme B Enzyme B Citrulline Citrulline Citrulline Citrulline Gene C Figure 17.2 Do individual genes specify the enzymes that function in a biochemical pathway? Enzyme C Enzyme C Enzyme C Enzyme C Arginine Arginine Arginine Arginine

201 Protein Synthesis: Transcription Translation DNA RNA Protein Central dogma of molecular biology

Fig. 17-3 DNA TRANSCRIPTION mRNA Ribosome TRANSLATION Polypeptide (a) Bacterial cell Nuclear envelope DNA TRANSCRIPTION Pre-mRNA RNA PROCESSING Figure 17.3 Overview: the roles of transcription and translation in the flow of genetic information mRNA TRANSLATION Ribosome Polypeptide (b) Eukaryotic cell

DNA TRANSCRIPTION mRNA (a) Bacterial cell Fig. 17-3a-1 Figure 17.3 Overview: the roles of transcription and translation in the flow of genetic information (a) Bacterial cell

DNA TRANSCRIPTION mRNA Ribosome TRANSLATION Polypeptide Fig. 17-3a-2 DNA TRANSCRIPTION mRNA Ribosome TRANSLATION Polypeptide Figure 17.3 Overview: the roles of transcription and translation in the flow of genetic information (a) Bacterial cell

Nuclear envelope DNA TRANSCRIPTION Pre-mRNA (b) Eukaryotic cell Fig. 17-3b-1 Nuclear envelope DNA TRANSCRIPTION Pre-mRNA Figure 17.3 Overview: the roles of transcription and translation in the flow of genetic information (b) Eukaryotic cell

Nuclear envelope DNA TRANSCRIPTION Pre-mRNA mRNA (b) Eukaryotic cell Fig. 17-3b-2 Nuclear envelope DNA TRANSCRIPTION Pre-mRNA RNA PROCESSING mRNA Figure 17.3 Overview: the roles of transcription and translation in the flow of genetic information (b) Eukaryotic cell

Animation: Transcription 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 Animation: Transcription Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Completed RNA transcript Fig. 17-7 Promoter Transcription unit 5 3 3 5 DNA Start point RNA polymerase 1 Initiation Elongation Nontemplate strand of DNA RNA nucleotides 5 3 RNA polymerase 3 5 RNA transcript Template strand of DNA Unwound DNA 3 2 Elongation 3 end Rewound DNA 5 5 3 3 3 5 5 Figure 17.7 The stages of transcription: initiation, elongation, and termination 5 Direction of transcription (“downstream”) RNA transcript Template strand of DNA 3 Termination Newly made RNA 5 3 3 5 5 3 Completed RNA transcript

Several transcription factors must bind to the DNA before RNA Fig. 17-8 1 A eukaryotic promoter includes a TATA box Promoter Template 5 3 3 5 TATA box Start point Template DNA strand 2 Several transcription factors must bind to the DNA before RNA polymerase II can do so. Transcription factors 5 3 3 5 3 Additional transcription factors bind to the DNA along with RNA polymerase II, forming the transcription initiation complex. Figure 17.8 The initiation of transcription at a eukaryotic promoter RNA polymerase II Transcription factors 5 3 3 5 5 RNA transcript Transcription initiation complex

Nuclear envelope DNA TRANSCRIPTION Pre-mRNA mRNA TRANSLATION Ribosome Fig. 17-3b-3 Nuclear envelope DNA TRANSCRIPTION Pre-mRNA RNA PROCESSING mRNA Figure 17.3 Overview: the roles of transcription and translation in the flow of genetic information TRANSLATION Ribosome Polypeptide (b) Eukaryotic cell

Gene 2 Gene 1 Gene 3 DNA template strand mRNA Codon TRANSLATION Fig. 17-4 Gene 2 DNA molecule Gene 1 Gene 3 DNA template strand TRANSCRIPTION Figure 17.4 The triplet code mRNA Codon TRANSLATION Protein Amino acid

First mRNA base (5 end of codon) Third mRNA base (3 end of codon) Fig. 17-5 Second mRNA base First mRNA base (5 end of codon) Third mRNA base (3 end of codon) Figure 17.5 The dictionary of the genetic code

203 RNA polymerase: Sigma factor: Aminoacyl synthetase: Peptidyl transferase: Release factor:

Figure 17.14 The structure of transfer RNA (tRNA) 3 Amino acid attachment site 5 Hydrogen bonds Anticodon (a) Two-dimensional structure 5 Amino acid attachment site 3 Figure 17.14 The structure of transfer RNA (tRNA) Hydrogen bonds 3 5 Anticodon Anticodon (c) Symbol used in this book (b) Three-dimensional structure

(a) Two-dimensional structure Fig. 17-14a 3 Amino acid attachment site 5 Hydrogen bonds Figure 17.14 The structure of transfer RNA (tRNA) Anticodon (a) Two-dimensional structure

(b) Three-dimensional structure Fig. 17-14b Amino acid attachment site 5 3 Hydrogen bonds Figure 17.14 The structure of transfer RNA (tRNA) 3 5 Anticodon Anticodon (c) Symbol used in this book (b) Three-dimensional structure

Aminoacyl-tRNA Amino acid synthetase (enzyme) tRNA Aminoacyl-tRNA Fig. 17-15-4 Aminoacyl-tRNA synthetase (enzyme) Amino acid P P P Adenosine ATP P Adenosine tRNA P P i Aminoacyl-tRNA synthetase P i P i tRNA Figure 17.15 An aminoacyl-tRNA synthetase joining a specific amino acid to a tRNA P Adenosine AMP Computer model Aminoacyl-tRNA (“charged tRNA”)

203 In eukaryotes, before a mRNA leaves the nucleus, it is tagged with 7-methylguanosine at the 5’ end (to protect the mRNA from hydrolytic enzymes), and 50 to 250 adenine (A) to the 3’ end to form a poly-A tail. The tail helps prevent degradation of the RNA.

Protein-coding segment Polyadenylation signal 5 3 Fig. 17-9 Protein-coding segment Polyadenylation signal 5 3 G P P P AAUAAA AAA … AAA 5 Cap 5 UTR Start codon Stop codon 3 UTR Poly-A tail Figure 17.9 RNA processing: addition of the 5 cap and poly-A tail

exons spliced together Coding segment Fig. 17-10 5 Exon Intron Exon Intron Exon 3 Pre-mRNA 5 Cap Poly-A tail 1 30 31 104 105 146 Introns cut out and exons spliced together Coding segment mRNA 5 Cap Poly-A tail 1 146 Figure 17.10 RNA processing: RNA splicing 5 UTR 3 UTR

204 Heterogenous nuclear RNA (hnRNA) or primary transcript The small nuclear RNA (snRNA) together with small nuclear ribonucleoproteins (snRNPS) form spliceosome: removes introns and splices the exons.

RNA transcript (pre-mRNA) 5 Exon 1 Intron Exon 2 Fig. 17-11-1 RNA transcript (pre-mRNA) 5 Exon 1 Intron Exon 2 Protein Other proteins snRNA snRNPs Figure 17.11 The roles of snRNPs and spliceosomes in pre-mRNA splicing

RNA transcript (pre-mRNA) 5 Exon 1 Intron Exon 2 Fig. 17-11-2 RNA transcript (pre-mRNA) 5 Exon 1 Intron Exon 2 Protein Other proteins snRNA snRNPs Spliceosome 5 Figure 17.11 The roles of snRNPs and spliceosomes in pre-mRNA splicing

RNA transcript (pre-mRNA) 5 Exon 1 Intron Exon 2 Fig. 17-11-3 RNA transcript (pre-mRNA) 5 Exon 1 Intron Exon 2 Protein Other proteins snRNA snRNPs Spliceosome 5 Figure 17.11 The roles of snRNPs and spliceosomes in pre-mRNA splicing Spliceosome components Cut-out intron mRNA 5 Exon 1 Exon 2

The Functional and Evolutionary Importance of Introns Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during RNA splicing. Such variations are called alternative RNA splicing. Because of alternative splicing, the number of different proteins an organism can produce is much greater than its number of genes. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Exon shuffling may result in the evolution of new proteins. Proteins often have a modular architecture consisting of discrete regions called domains. In many cases, different exons code for the different domains in a protein. Exon shuffling may result in the evolution of new proteins. Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings

Gene DNA Exon 1 Intron Exon 2 Intron Exon 3 Transcription Fig. 17-12 Gene DNA Exon 1 Intron Exon 2 Intron Exon 3 Transcription RNA processing Translation Domain 3 Figure 17.12 Correspondence between exons and protein domains Domain 2 Domain 1 Polypeptide

(b) Schematic model showing binding sites Fig. 17-16b P site (Peptidyl-tRNA binding site) A site (Aminoacyl- tRNA binding site) E site (Exit site) E P A Large subunit mRNA binding site Small subunit (b) Schematic model showing binding sites Growing polypeptide Amino end Next amino acid to be added to polypeptide chain Figure 17.16 The anatomy of a functioning ribosome E tRNA mRNA 3 Codons 5 (c) Schematic model with mRNA and tRNA

Translation initiation complex Fig. 17-17 Large ribosomal subunit 3 U C 5 A P site Met 5 A Met U G 3 Initiator tRNA GTP GDP E A mRNA 5 5 3 3 Start codon Figure 17.17 The initiation of translation Small ribosomal subunit mRNA binding site Translation initiation complex

Amino end of polypeptide E 3 mRNA 5 Fig. 17-18-1 P A site site Figure 17.18 The elongation cycle of translation

GDP Amino end of polypeptide E 3 mRNA 5 E P A Fig. 17-18-2 P A site GTP GDP E P A Figure 17.18 The elongation cycle of translation

GDP Amino end of polypeptide E 3 mRNA 5 E P A E P A Fig. 17-18-3 P A site A site 5 GTP GDP E P A Figure 17.18 The elongation cycle of translation E P A

GDP GDP Amino end of polypeptide E 3 mRNA Ribosome ready for Fig. 17-18-4 Amino end of polypeptide E 3 mRNA Ribosome ready for next aminoacyl tRNA P site A site 5 GTP GDP E E P A P A Figure 17.18 The elongation cycle of translation GDP GTP E P A

Release factor 3 5 Stop codon (UAG, UAA, or UGA) Fig. 17-19-1 Figure 17.19 The termination of translation

Release factor Free polypeptide 3 3 2 5 5 Stop codon Fig. 17-19-2 Release factor Free polypeptide 3 3 2 5 5 GTP Stop codon (UAG, UAA, or UGA) 2 GDP Figure 17.19 The termination of translation

Release factor Free polypeptide 5 3 3 3 2 5 5 Stop codon Fig. 17-19-3 Release factor Free polypeptide 5 3 3 3 2 5 5 GTP Stop codon (UAG, UAA, or UGA) 2 GDP Figure 17.19 The termination of translation

Amino acids tRNA with amino acid attached Ribosome tRNA Anticodon 5 Fig. 17-13 Amino acids Polypeptide tRNA with amino acid attached Ribosome Trp Phe Gly Figure 17.13 Translation: the basic concept tRNA Anticodon 5 Codons 3 mRNA

Completed polypeptide Growing polypeptides Incoming ribosomal subunits Fig. 17-20 Completed polypeptide Growing polypeptides Incoming ribosomal subunits Polyribosome Start of mRNA (5 end) End of mRNA (3 end) (a) Ribosomes Figure 17.20 Polyribosomes mRNA (b) 0.1 µm

Ribosome mRNA Signal peptide ER membrane Signal peptide removed Fig. 17-21 Ribosome mRNA Signal peptide ER membrane Signal peptide removed Signal- recognition particle (SRP) Protein CYTOSOL Translocation complex Figure 17.21 The signal mechanism for targeting proteins to the ER ER LUMEN SRP receptor protein

Fig. 17-25 DNA TRANSCRIPTION 3 Poly-A RNA polymerase 5 RNA transcript RNA PROCESSING Exon RNA transcript (pre-mRNA) Intron Aminoacyl-tRNA synthetase Poly-A NUCLEUS Amino acid AMINO ACID ACTIVATION CYTOPLASM tRNA mRNA Growing polypeptide Cap 3 A Activated amino acid Poly-A P Ribosomal subunits Figure 17.25 A summary of transcription and translation in a eukaryotic cell E Cap 5 TRANSLATION E A Anticodon Codon Ribosome

207 Differences in transcription: Eukaryotes Prokaryotes Only one gene is 1. Several genes are transcribed at a time transcribed together. 2. Splicing of exons 2. No splicing after introns have been removed. 5’ end is tagged with 3. No modification 7-methylguanosine. 4. 3’ end is tagged with 4. No modification 100-200 adenines. Movement of the 5. No ( no nuclear functional RNA membrane) (the final transcript) through the nuclear membrane.

208 Mutation: Point mutation (Base substitution): Silent mutation: Nonsense mutation: Missense mutation: Addition mutation: Deletion mutation: Frame-shift mutation:

208-209 Mutagens: UV light: Nitrous acid (HNO2): changes cytosine to uracil 5-Bromouracil: it pairs with guanine (G) intead of adenine (A) Transposon (jumping gene) can cause addition or deletion of DNA when it jumps from one chromosome to another.

209 Ames Test: It is used to detect the mutagenicity of a chemical. It was developed by Bruce Ames of U.C. Berkeley in 1965. Mutant strain of Salmonella typhimurium together with rat liver extract is mixed with the test chemical. The mutant strain is not able to grow in medium without histidine, which is an amino acid. The mixture is plated onto the histidine-free medium. Rat liver extract is used to simulate the body conditions. It contains enzymes, which may convert a harmless chemical to a carcinogen.

209 3. A control plate is similarly prepared but without the inclusion of the chemical. The culture plates are incubated at 37oC for 2 days. If a significant number of colonies appears on the agar plate with the suspected chemical compared to the control plate. It indicates that a reverse mutation has taken place. It implies that the chemical causes mutation. Any chemical that can cause mutation may also cause cancer.

209 What is a gene? A unit of inheritance that is responsible for a trait. A specific locus on chromosome. A region of specific nucleotide sequence that includes thousands of genes. A DNA sequence that codes for a specific polypeptide. A region of DNA that codes for the production of a RNA molecule.