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Chapter 13 (Sections 13.1-13.3) Gene Expression

Chapter 13 (Sections 13.1-13.3) Gene Expression. From DNA to Proteins. Most genes specify the structure of proteins DNA affects the phenotype of the organism at the molecular level through the process of gene expression, in which DNA specifies the makeup of a cell’s proteins

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Chapter 13 (Sections 13.1-13.3) Gene Expression

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  1. Chapter 13(Sections 13.1-13.3)Gene Expression

  2. From DNA to Proteins • Most genes specify the structure of proteins • DNA affects the phenotype of the organism at the molecular level through the process of gene expression, in which DNA specifies the makeup of a cell’s proteins • The first major step of gene expression is transcription, the synthesis of RNA molecules complementary to DNA • The second major step is translation, in which RNA becomes a coded template to direct polypeptide synthesis

  3. 13.1 DISCOVERY OF THE GENE–PROTEIN RELATIONSHIP LEARNING OBJECTIVES: • Summarize the early evidence indicating that most genes specify the structure of proteins • Describe Beadle and Tatum’s experiments with Neurospora

  4. Early Evidence • 1908: Archibald Garrod proposed that a rare genetic disease (alkaptonuria) resulted in the absence of an enzyme in the metabolic pathway that breaks down the amino acid tyrosine • 1926: James Sumner was the first to prove that an enzyme, urease, was a protein

  5. Beadle and Tatum • 1940s: George Beadle and Edward Tatum • looked for mutations interfering with known metabolic reactions that produce essential molecules (amino acids and vitamins) • They worked with the bread mold Neurospora, (expresses recessive mutations) • Wild-typeNeurosporamanufactures essential molecules • Mutant strains require an additional nutrient • Showed that each mutant strain had a mutation in only one gene and that each gene affected only one enzyme (the one-gene, one-enzyme hypothesis)

  6. More Evidence • 1949: Linus Pauling showed that a mutation of a single gene alters the structure of the protein hemoglobin • Other scientists showed that many proteins are constructed from two or more polypeptide chains, each under the control of a different locus • The definition of a gene was extended to include that one gene is responsible for one polypeptide chain

  7. KEY CONCEPTS 13.1 • Beadle and Tatum demonstrated the relationship between genes and proteins in the 1940s

  8. 13.2 INFORMATION FLOWFROM DNA TO PROTEIN LEARNING OBJECTIVES: • Outline the flow of genetic information in cells, from DNA to RNA to polypeptide • Compare the structures of DNA and RNA • Explain why the genetic code is said to be redundant and virtually universal, and discuss how these features may reflect its evolutionary history

  9. Ribonucleic Acid (RNA) • When a gene that codes for a protein is expressed, the information in DNA is copied to aribonucleic acid (RNA) • Like DNA, RNA is a polymer of nucleotides, but RNA has some important differences: • RNA is usually single-stranded • The sugar in RNA isribose • The base uracil substitutes for thymine

  10. Nucleotide Structure of RNA • RNA nucleotides form complementary base-pairs with DNA • Uracil base-pairs with adenine

  11. Uracil Ribose Adenine Ribose Cytosine Ribose Guanine Ribose Fig. 13-3, p. 285

  12. Transcription • The process of transcriptioncopies the information in DNA to RNA • The sequence of RNA bases is determined by complementary base pairing with the DNA template strand • Three main kinds of RNA molecules are transcribed: messenger RNA, transfer RNA, and ribosomal RNA

  13. Three Types of RNA • Messenger RNA (mRNA) • Single RNA strand that carries information for making a protein • Transfer RNA (tRNA) • Single RNA strand that folds back on itself to form a specific shape; each kind of tRNA bonds with one kind of amino acid and carries it to the ribosome • Ribosomal RNA (rRNA) • Globular, structural part of ribosomes with catalytic functions needed during protein synthesis

  14. Translation • The process of translation uses the information transcribed in mRNA to specify the amino acid sequence of a polypeptide • A sequence of three consecutive bases in mRNA (codon)specifies one amino acid • The series of codons that specifies the amino acid sequence is a triplet code • Codons for amino acids and for start and stop signals are collectively called the genetic code

  15. Genetic Code

  16. Second letter U C A G UCU U UUU UAU UGU Phe Tyr Cys UCC C UUC UAC UGC Ser U A UUA UCA Stop Stop UAA UGA Leu G UUG UCG Trp Stop UAG UGG U CUU CCU CAU CGU His C CUC CCC CAC CGC C Third letter (3’ end) Leu Pro Arg A CGA CUA CCA CAA Gln G CGG CUG CCG CAG First letter (5’ end) U AUU ACU AAU AGU Asn Ser C Ile AUC ACC AAC AGC A Thr A AUA ACA AAA AGA Lys Arg G AUG Met ACG AAG AGG or start U GUU GCU GAU GGU C Asp G GUC GCC GAC GGC A Val Ala Gly GUA GCA GAA GGA G Glu GUG GCG GAG GGG Fig. 13-5, p. 286

  17. tRNA • Transfer RNAs connect amino acids and nucleic acids • Each tRNA links with a specific amino acid • tRNA recognizes the mRNA codon for that amino acid • Each tRNA has a sequence of three bases (anticodon)that hydrogen-bonds with the mRNA codon by complementary base pairing • The amino acids carried by the tRNAs are linked in the order specified by the sequence of codons in the mRNA

  18. A tRNA Molecule

  19. Loop 3 Hydrogen bonds Loop 1 (a) The 3-D shape of a tRNA molecule is determined by hydrogen bonds formed between complementary bases. Loop 2 Anticodon Fig. 13-6a, p. 287

  20. (b) One loop contains the anticodon; these unpaired bases pair with a complementary mRNA codon. The amino acid attaches to the terminal nucleotide at the hydroxyl (OH) 3′ end. OH 3′ end Amino acid accepting end P 5′ end Hydrogen bonds Loop 3 Loop 1 Modified nucleotides Loop 2 Anticodon Fig. 13-6b, p. 287

  21. Amino acid (phenylalanine) (c) This stylized diagram of an aminoacyl-tRNA shows that the amino acid attaches to tRNA by its carboxyl group, leaving its amino group ex- posed for peptide bond formation. Anticodon Fig. 13-6c, p. 287

  22. Ribosomes • Ribosomesare the site of translation • Composed of two different subunits, each containing protein and rRNA • Attach to the 5′ end of mRNA and travel along it, allowing tRNAs to attach sequentially to the codons of mRNA • Amino acids carried by tRNAs are positioned in the correct order and joined by peptide bonds to form a polypeptide

  23. Overview: Transcription and Translation

  24. How Genetic Code Works • mRNA consists of a linear sequence of four different RNA nucleotides (A, U, G, and C) • Three-letter combinations (triplets) of the four bases form a total of 64 codons representing the 20 amino acids, plus stop and start codons • The code is read, one triplet at a time, from a fixed starting point that establishes the reading frame for the message

  25. Genetic Code is Redundant • More than one codon specifies most amino acids – only methionine and tryptophan are specified by single codons

  26. KEY CONCEPTS 13.2 • The transmission of information in cells is typically from DNA to RNA to polypeptide

  27. 13.3 TRANSCRIPTION LEARNING OBJECTIVES: • Compare the processes of transcription and DNA replication, identifying both similarities and differences • Compare bacterial and eukaryotic mRNAs, and explain the functional significance of their structural differences

  28. RNA Polymerases • In eukaryotic transcription, most RNA synthesis requires one of three RNA polymerases • RNA polymerase I catalyzes synthesis of several kinds of rRNA molecules that are components of ribosomes • RNA polymerase II catalyzes production of protein-coding mRNA • RNA polymerase III catalyzes synthesis of tRNA and one of the RNA molecules

  29. RNA Synthesis • RNA polymerases carry out synthesis in the 5′ → 3′ direction • The template strand of DNA and the complementary RNA strand are antiparallel – the DNA template is read in the 3′ → 5′ direction

  30. Upstream and Downstream

  31. Molecular View of Transcription

  32. Initiation • The nucleotide sequence in DNA to which RNA polymerase and associated proteins initially bind is called the promoter • Once RNA polymerase has recognized the correct promoter, it unwinds the DNA double helix and initiates transcription

  33. Elongation • During the elongation stage, as each nucleotide is added to the 3′ end of the RNA molecule, two phosphates are removed in an exergonic reaction • The remaining phosphate becomes part of the sugar–phosphate backbone • The last nucleotide to be incorporated has an exposed 3′ hydroxyl group

  34. Termination • Termination occurs when RNA polymerase recognizes a termination sequence of bases in the DNA template • RNA polymerase separates from the template DNA and the newly synthesized RNA • In eukaryotic cells, RNA polymerase adds about 10 to 35 nucleotides to the mRNA molecule after it passes the termination sequence

  35. KEY POINT:Initiation, Elongation, and Termination

  36. RNA polymerase binds to promoter region in DNA DNA 1 Promoter region Termination sequence Direction of transcription DNA template strand 2 RNA transcript Rewinding of DNA Unwinding of DNA 3 4 DNA RNA transcript RNA polymerase Stepped Art Fig. 13-9, p. 290

  37. Template and Nontemplate Strands • Only one DNA strand is transcribed for a given gene, but the opposite strand may be transcribed for another gene

  38. mRNA transcript mRNA transcript Promoter region Promoter region Promoter region RNA polymerase Gene 2 Gene 1 Gene 3 mRNA transcript Only one of the two strands is transcribed for a given gene, but the opposite strand may be transcribed for a neighboring gene. Each transcript starts at its own promoter region (orange). The orange arrow associated with each promoter region indicates the direction of transcription. Fig. 13-10, p. 291

  39. Noncoding mRNA Sequences • At the 5′ end, a noncoding leader sequence has recognition sites that bind and position ribosomes for translation • The start codon follows the leader sequence and signals the beginning of the coding sequence for the polypeptide • At the end of each coding sequence, a stop codon(UAA, UGA, UAG)signals the end of the protein • Followed by noncoding 3′ trailing sequences

  40. Bacterial mRNA

  41. Promoter region Transcribed region mRNA termination sequence DNA Upstream leader sequences Protein-coding sequences Translated region Downstream trailing sequences Start codon Stop codon mRNA Polypeptide Fig. 13-11, p. 291

  42. mRNA Modification • In eukaryotes, the original transcript (precursor mRNA, or pre-mRNA) is modified in before it leaves the nucleus • These posttranscriptional modification and processing activities produce mature mRNA for transport and translation • A 5′ cap stabilizes the mRNA and allows ribosomes to bind • Polyadenylationadds a poly-A tail at the 3′ end, which helps export mRNA from the nucleus, stabilizes mRNA, and facilitates initiation of translation

  43. Noncoding and Coding Sequences • Most eukaryotic genes have interrupted coding sequences:long sequences of bases within protein-coding sequences that do not code for amino acids in the final polypeptide • introns • Intervening sequences • exons • Expressed sequences which are parts of the protein-coding sequence

  44. Posttranscriptional Modifications • When a gene is transcribed: • the entire gene is copied as a large pre-mRNA transcript containing both introns and exons • To become a functional message: • the pre-mRNA is capped, a poly-A tail added, introns are removed, and exons spliced together to form a continuous protein-coding message • Following pre-mRNA processing: • mature mRNA is transported through a nuclear pore into the cytosol to be translated by a ribosome

  45. Splicing Exons • Splicing may involve the association of several small nuclear ribonucleoprotein complexes (snRNPs)to form a large ribonucleoprotein complex (spliceosome)which catalyzes reactions that remove introns. • RNA within the intron may act as an RNA catalyst (ribozyme),splicing itself without the use of a spliceosome or protein enzymes

  46. KEY POINT: Eukaryotic Posttranscriptional Modification

  47. Formation of pre-mRNA • 2. Processing of pre-mRNA • 3. Mature mRNA in nucleus • 4. Mature mRNA in cytosol mRNA termination sequence 1st exon 1st intron 2nd intron 3rd exon 2nd exon Promoter Template DNA strand Transcription, capping of 5′ end 7-methylguanosine cap Start codon 1 Stop codon 1st intron 2nd intron Small nuclear ribonucleoprotein complex –AAA... Poly-A tail 3′ end 2 1st exon 2nd exon 3rd exon –AAA... Poly-A tail 3 ′ end 3 Protein-coding region Nuclear envelope Nuclear pore Cytosol Transport through nuclear envelope to cytosol –AAA... Poly-A tail 3 ′ end Start codon 4 Stop codon Protein-coding region Fig. 13-12, p. 292

  48. KEY CONCEPTS 13.3 • A sequence of DNA base triplets is transcribed into mRNA codons

  49. KEY CONCEPTS 13.4 • A sequence of mRNA codons is translated into a sequence of amino acids in a polypeptide

  50. 13.5 VARIATIONS INGENE EXPRESSION LEARNING OBJECTIVES: • Describe a polyribosome in bacterial cells • Briefly discuss RNA interference • Describe retroviruses and the enzyme reverse transcriptase

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