Replication, transcription, translation2012

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  • Figure 16.5 The structure of a DNA strand.
  • Figure 16.6 Rosalind Franklin and her X-ray diffraction photo of DNA.
  • Figure 16.7 The double helix.
  • Figure 16.UN01 In-text figure, p. 310
  • Figure 16.8 Base pairing in DNA.
  • Figure 16.9 A model for DNA replication: the basic concept.
  • Figure 16.10 Three alternative models of DNA replication.
  • Figure 16.UN03 Summary figure, Concept 16.1 2
  • Figure 17.UN01 In-text figure, p. 328
  • Figure 17.3 Overview: the roles of transcription and translation in the flow of genetic information.
  • Figure 17.4 The triplet code.
  • Figure 17.5 The codon table for mRNA.
  • Figure 17.7 The stages of transcription: initiation, elongation, and termination.
  • Figure 17.13 Correspondence between exons and protein domains.
  • Figure 17.14 Translation: the basic concept.
  • Figure 17.17 The anatomy of a functioning ribosome.
  • Figure 17.17 The anatomy of a functioning ribosome.
  • Figure 17.24 Types of small-scale mutations that affect mRNA sequence.
  • Figure 17.26 A summary of transcription and translation in a eukaryotic cell.
  • Replication, transcription, translation2012

    1. 1. Replication, Transcription, Translation
    2. 2. Make up of DNA • DNA is a polymer of nucleotides, each consisting of a nitrogenous base, a sugar, and a phosphate group • Sugar: deoxyribose • Nitrogenous base: Adenine, Thymine, Cytosine, Guanine
    3. 3. Figure 16.5 Sugar–phosphate backbone Nitrogenous bases Thymine (T) Adenine (A) Cytosine (C) Guanine (G) Nitrogenous base Phosphate DNA nucleotide Sugar (deoxyribose) 3′ end 5′ end
    4. 4. Figure 16.6b (b) Franklin’s X-ray diffraction photograph of DNA
    5. 5. 3.4 nm 1 nm 0.34 nm Hydrogen bond (a) Key features of DNA structure (b) Partial chemical structure 3′ end 5′ end 3′ end 5′ end T T A A G G C C C C C C C C C C C G G G G G G G G G T T T T T T A A A A A A Figure 16.7a
    6. 6. Figure 16.UN01 Purine + purine: too wide Pyrimidine + pyrimidine: too narrow Purine + pyrimidine: width consistent with X-ray data
    7. 7. Chargaff’s rule • A = T, and the amount of G = C
    8. 8. Figure 16.8 Sugar Sugar Sugar Sugar Adenine (A) Thymine (T) Guanine (G) Cytosine (C)
    9. 9. DNA replication • Ensures that new cells will have a complete set of DNA • During replication the DNA molecule separates into 2 strands, then produces 2 new complementary strands • Each original strand serves as a template for the new strands to form from • Each new DNA is composed of an old strand and a new complementary strand
    10. 10. Figure 16.9-3 (a) Parent molecule (b) Separation of strands (c) “Daughter” DNA molecules, each consisting of one parental strand and one new strand A A A A A A A A A A A A T T T T T T T T T T T T C C C C C C C C G G G G G G G G
    11. 11. Semiconservative Model of Replication • When DNA replicates, each daughter molecule will have one old strand (derived or “conserved” from the parent molecule) and one newly made strand • Competing models were the conservative model (the two parent strands rejoin) and the dispersive model (each strand is a mix of old and new)
    12. 12. Figure 16.10 (a) Conservative model (b) Semiconservative model (c) Dispersive model Parent cell First replication Second replication
    13. 13. DNA replication • The copying of DNA is remarkable in its speed and accuracy • More than a dozen enzymes and other proteins participate in DNA replication
    14. 14. DNA replication speed • In prokaryotes DNA replication begins at one point then spreads in 2 directions until the entire chromosome is replicated • In eukaryotes DNA replication occurs at hundreds of places at once and proceeds in both directions until the entire chromosome is copied. • Replication forks- sites where separation (of the double helix) and replication are occurring
    15. 15. The players • Helicases are enzymes that untwist the double helix at the replication forks • Single-strand binding proteins bind to and stabilize single-stranded DNA • Topoisomerase corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands • DNA polymerases: add nucleotides to the 3′ end of DNA • The initial nucleotide strand is a short RNA primer
    16. 16. • Primase: enzyme that makes the RNA primer; (uses the parental DNA as a template) • The primer is short (5–10 nucleotides long), and the 3′ end serves as the starting point for the new DNA strand
    17. 17. Antiparallel elongation • The antiparallel structure of the double helix affects replication • DNA polymerases add nucleotides only to the free 3′ end of a growing strand; therefore, a new DNA strand can elongate only in the 5′ to 3′ direction
    18. 18. • Along one template strand of DNA, the DNA polymerase synthesizes a leading strand continuously, moving toward the replication fork • To elongate the other new strand, called the lagging strand, DNA polymerase must work in the direction away from the replication fork • The lagging strand is synthesized as a series of segments called Okazaki fragments, which are joined together by DNA ligase
    19. 19. Proofreading and repairing DNA • DNA polymerases proofread newly made DNA, replacing any incorrect nucleotides • In mismatch repair of DNA, repair enzymes correct errors in base pairing • DNA can be damaged by exposure to harmful chemical or physical agents such as cigarette smoke and X-rays; it can also undergo spontaneous changes • In nucleotide excision repair, a nuclease cuts out and replaces damaged stretches of DNA
    20. 20. Figure 16.UN03 DNA pol III synthesizes leading strand continuously Parental DNA DNA pol III starts DNA synthesis at 3′ end of primer, continues in 5′ → 3′ direction Origin of replication Helicase Primase synthesizes a short RNA primer DNA pol I replaces the RNA primer with DNA nucleotides 3′ 3′ 3′ 5′ 5′ 5′ 5′ Lagging strand synthesized in short Okazaki fragments, later joined by DNA ligase
    21. 21. Basic Principles of Transcription and Translation • RNA is the bridge between genes and the proteins for which they code • Transcription is the synthesis of RNA under the direction of DNA • Transcription produces messenger RNA (mRNA) • Translation is the synthesis of a polypeptide, using information in the mRNA • Ribosomes are the sites of translation
    22. 22. • In prokaryotes, translation of mRNA can begin before transcription has finished • In a eukaryotic cell, the nuclear envelope separates transcription from translation • Eukaryotic RNA transcripts are modified through RNA processing to yield finished mRNA
    23. 23. Figure 17.UN01 DNA RNA Protein
    24. 24. Figure 17.3 DNA mRNA Ribosome Polypeptide TRANSCRIPTION TRANSLATION TRANSCRIPTION TRANSLATION Polypeptide Ribosome DNA mRNA Pre-mRNA RNA PROCESSING (a) Bacterial cell (b) Eukaryotic cell Nuclear envelope
    25. 25. How do nucleotide bases code for amino acids? • 4 nucleotide bases • 20 amino acids • 3 bases= 1 codon= 1 amino acid
    26. 26. Figure 17.4 DNA template strand TRANSCRIPTION mRNA TRANSLATION Protein Amino acid Codon Trp Phe Gly 5′ 5′ Ser U U U U U 3′ 3′ 5′3′ G G G G C C T C A A AAAAA T T T T T G G G G C C C G G DNA molecule Gene 1 Gene 2 Gene 3 C C
    27. 27. • During transcription, one of the two DNA strands, called the template strand, provides a template for ordering the sequence of complementary nucleotides in an RNA transcript • The template strand is always the same strand for a given gene • During translation, the mRNA base triplets, called codons, are read in the 5′ to 3′ direction
    28. 28. Cracking the code • All 64 codons were deciphered by the mid-1960s • Of the 64 triplets, 61 code for amino acids; 3 triplets are “stop” signals to end translation • The genetic code is redundant (more than one codon may specify a particular amino acid) but not ambiguous; no codon specifies more than one amino acid • Codons must be read in the correct reading frame (correct groupings) in order for the specified polypeptide to be produced
    29. 29. Figure 17.5 Second mRNA base FirstmRNAbase(5′endofcodon) ThirdmRNAbase(3′endofcodon) UUU UUC UUA CUU CUC CUA CUG Phe Leu Leu Ile UCU UCC UCA UCG Ser CCU CCC CCA CCG UAU UAC Tyr Pro Thr UAA Stop UAG Stop UGA Stop UGU UGC Cys UGG Trp GC U U C A U U C C C A U A A A G G His Gln Asn Lys Asp CAU CGU CAC CAA CAG CGC CGA CGG G AUU AUC AUA ACU ACC ACA AAU AAC AAA AGU AGC AGA Arg Ser Arg Gly ACGAUG AAG AGG GUU GUC GUA GUG GCU GCC GCA GCG GAU GAC GAA GAG Val Ala GGU GGC GGA GGG Glu Gly G U C A Met or start UUG G
    30. 30. Transcription • Making mRNA starts with RNA polymerase, which pries the DNA strands apart and hooks together the RNA nucleotides • The RNA is complementary to the DNA template strand • RNA synthesis follows the same base-pairing rules as DNA, except that uracil substitutes for thymine
    31. 31. • The DNA sequence where RNA polymerase attaches is called the promoter; in bacteria, the sequence signaling the end of transcription is called the terminator
    32. 32. Figure 17.7-4 Promoter RNA polymerase Start point DNA 5′ 3′ Transcription unit 3′ 5′ Elongation 5′ 3′ 3′ 5′ Nontemplate strand of DNA Template strand of DNA RNA transcript Unwound DNA 2 3′ 5′3′ 5′ 3′ Rewound DNA RNA transcript 5′ Termination3 3′ 5′ 5′ Completed RNA transcript Direction of transcription (“downstream”) 5′ 3′ 3′ Initiation1
    33. 33. mRNA editing • Enzymes in the eukaryotic nucleus modify pre- mRNA (RNA processing) before mRNA leave the cytoplasm • During RNA processing, both ends of the primary transcript are usually edited • Also, usually some interior parts of the molecule are cut out, and the other parts spliced together
    34. 34. • Each end of a pre-mRNA molecule is modified in a particular way – The 5′ end receives a modified nucleotide 5′ cap – The 3′ end gets a poly-A tail • These modifications share several functions – They seem help mRNA leave the nucleus – They protect mRNA from hydrolytic enzymes – They help ribosomes attach to the 5′ end
    35. 35. RNA splicing • Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides that lie between coding regions • These noncoding regions are called intervening sequences, or introns • The other regions are called exons because they are eventually expressed, usually translated into amino acid sequences • RNA splicing removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence
    36. 36. Gene DNA Exon 1 Exon 2 Exon 3Intron Intron Transcription RNA processing Translation Domain 3 Domain 2 Domain 1 Polypeptide Figure 17.13
    37. 37. The Basis of Translation • A cell translates an mRNA message into protein with the help of transfer RNA (tRNA) • tRNA transfer amino acids to the growing polypeptide in a ribosome
    38. 38. Figure 17.14 Polypeptide Ribosome Trp Phe Gly tRNA with amino acid attached Amino acids tRNA Anticodon Codons U U U UG G G G C A C C C C G A A A C G C G 5′ 3′ mRNA
    39. 39. tRNA • Molecules of tRNA are not identical – Each carries a specific amino acid on one end – Each has an anticodon on the other end; the anticodon base-pairs with a complementary codon on mRNA
    40. 40. Ribosomes • Ribosomes help join tRNA anticodons with mRNA codons in protein synthesis • The two ribosomal subunits (large and small) are made of proteins and ribosomal RNA (rRNA)
    41. 41. Figure 17.17b Exit tunnel A site (Aminoacyl- tRNA binding site) Small subunit Large subunit P A P site (Peptidyl-tRNA binding site) mRNA binding site (b) Schematic model showing binding sites E site (Exit site) E
    42. 42. Ribosome binding sites • A ribosome has three binding sites for tRNA – The P site holds the tRNA that carries the growing polypeptide chain – The A site holds the tRNA that carries the next amino acid to be added to the chain – The E site is the exit site, where discharged tRNAs leave the ribosome
    43. 43. Figure 17.17c Amino end mRNA E (c) Schematic model with mRNA and tRNA 5′ Codons 3′ tRNA Growing polypeptide Next amino acid to be added to polypeptide chain
    44. 44. Termination of polypeptide • 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 • 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
    45. 45. Mutations • changes in the genetic material of a cell or virus • Point mutations are chemical changes in just one base pair of a gene • The change of a single nucleotide in a DNA template strand can lead to the production of an abnormal protein
    46. 46. Types of Substitution Mutations • Silent mutations have no effect on the amino acid produced by a codon because of redundancy in the genetic code • Missense mutations still code for an amino acid, but not the correct amino acid • Nonsense mutations change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein
    47. 47. Frameshift mutations • Insertions and deletions are additions or losses of nucleotide pairs in a gene • may alter the reading frame
    48. 48. Figure 17.24e DNA template strand mRNA5′ 5′ Protein Amino end Stop Carboxyl end 3′ 3′ 3′ 5′ Met Lys Phe Gly A A A A A A A A A AT T T T T T T T TT C C C C C C G G G G G G A A A A AG GGU U U U U (b) Nucleotide-pair insertion or deletion: frameshift causing extensive missense Wild type missing missing A U A A AT T TC C A T TC C G A AT T TG GA A ATCG G A G A A GU U U C A AG G U 3′ 5′ 3′ 3′ 5′ Met Lys Leu Ala 1 nucleotide-pair deletion 5′
    49. 49. Figure 17.26 TRANSCRIPTION DNA RNA polymerase Exon RNA transcript RNA PROCESSING NUCLEUS Intron RNA transcript (pre-mRNA) Poly-A Poly-A Aminoacyl- tRNA synthetase AMINO ACID ACTIVATION Amino acid tRNA 5′Cap Poly-A 3′ Growing polypeptidemRNA Aminoacyl (charged) tRNA Anticodon Ribosomal subunits A AE TRANSLATION 5′ Cap CYTOPLASM P E Codon Ribosome 5′ 3′

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