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Chapter 17 Nucleic Acids and Protein Synthesis 1 17.1 Components of Nucleic Acids Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Nucleic Acids 2 Nucleic acids are • molecules that store information for cellular growth and reproduction • deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) • large molecules consisting of long chains of monomers called nucleotides found in the cell nucleus Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Nucleic Acids 3 The nucleic acids DNA and RNA consist of monomers called nucleotides that consist of a • pentose sugar • base • phosphate Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition nucleotide Copyright © 2012 by Pearson Education, Inc. Bases 4 The bases in DNA and RNA are • pyrimidines C, T, and U • purines A and G Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Bases in DNA and RNA 5 DNA contains the bases • Cytosine (C) • Guanine (G) same in both DNA and RNA • Adenine (A) • Thymine (T) different in DNA than in RNA RNA contains the bases • Cytosine (C) • Guanine (G) same in both DNA and RNA • Adenine (A) • Uracil (U) different in RNA than in DNA Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Pentose Sugars 6 The pentose (five-carbon) sugar • in RNA is ribose • in DNA is deoxyribose, with no O atom on carbon 2' • has carbon atoms numbered with primes to distinguish them from the atoms in the bases Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Nucleosides 7 A nucleoside • is a combination of a sugar and base • has a base linked by a glycosidic bond to C1′ of a sugar (ribose or deoxyribose) • is named by changing the base ending to -osine for purines and -idine for pyrimidines Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Nucleosides 8 A base forms an N-glycosidic bond with a ribose or deoxyribose sugar to form a nucleoside. Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Nucleotides 9 A nucleotide • is formed when the phosphate group on C5′ in the nucleoside group bonds to −OH on C5′ of a ribose or deoxyribose sugar • is named using the name of the nucleoside, followed by 5′-monophosphate Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Nucleotides 10 The nucleotides of RNA are identical to those of DNA, except in DNA the sugar is deoxyribose and deoxythymidine replaces uridine. Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Components in DNA and RNA 11 Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Naming Nucleosides and Nucleotides 12 Nucleosides • that contain a purine end with osine • that contain a pyrimidine end with idine • of DNA add deoxy to the beginning of their name Corresponding nucleotides in RNA and DNA are named by adding -5'-monophosphate. Abbreviations for bases A, G, C, U, and T are often used in respective nucleosides and nucleotides. Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Nucleosides and Nucleotides in DNA, RNA 13 Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Learning Check 14 Give the name and abbreviation for the following and list its base and sugar. Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Solution 15 Give the name and abbreviation for the following and list its base and sugar. The name of this nucleotide is Guanosine-59-monophosphate (GMP) Deoxyguanosine-59-monophosphate (dGMP) Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Chapter 17 Nucleic Acids and Protein Synthesis 16 17.5 Protein Synthesis Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Initiation of Protein Synthesis 17 For the initiation of protein synthesis, • an mRNA attaches to a ribosome • the start codon (AUG) in mRNA forms hydrogen bonds to methionine on tRNA • the second codon attaches to a tRNA with the next amino acid • a peptide bond forms between the adjacent amino acids at the first and second codons During chain elongation, the ribosome moves along the mRNA from codon to codon, attaching new amino acids to the growing polypeptide chain. Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Initiation of Protein Synthesis 18 An activated tRNA with anticodon AGU bonds to serine at the acceptor stem. Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Translocation 19 Once the peptide bond is formed, the initial tRNA detaches from the ribosome, which shifts to the next available codon, a process called translocation. During translocation, • the first tRNA detaches from the ribosome • the ribosome shifts to the adjacent codon on the mRNA • a new tRNA/amino acid attaches to the open binding site • a peptide bond forms and that tRNA detaches • the ribosome shifts down the mRNA to read the next codon Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Peptide Formation 20 Peptide chain starts to form Met Met Ser Ser Anticodons UAC AGA AGA tRNA • •• AUG • •• • • • UCU CUC Ribosome Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition UCU Leu GAG •• • CUC UUU Ribosome shifts Copyright © 2012 by Pearson Education, Inc. Protein Synthesis: Translation 21 Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Termination 22 In the termination step, • all the amino acids are linked • the ribosome reaches a “stop” codon: UGA, UAA, or UAG • there is no tRNA with an anticodon for the “stop” codons • the polypeptide detaches from the ribosome Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Termination 23 Once the polypeptide is released, • the R groups of the amino acids in the new polypeptide can form hydrogen bonds to give the secondary structures of α helices, β-pleated sheets, or triple helices • chains form cross-links such as salt bridges and disulfide bonds to produce tertiary and quaternary structures, which makes it a biologically active protein Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Learning Check 24 Assign each of the following terms to a definition or concept. activation initiation translocation termination A. B. C. D. Ribosomes move along mRNA, adding amino acids to a growing peptide chain. A completed peptide chain is released. A tRNA attaches to its specific amino acid. A tRNA binds to the AUG codon of the mRNA on the ribosome. Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Solution 25 Assign each of the following terms to a definition or concept. activation initiation translocation termination A. B. C. D. Ribosomes move along mRNA, adding amino acids to a growing peptide chain. translocation A completed peptide chain is released. termination A tRNA attaches to its specific amino acid. activation A tRNA binds to the AUG codon of the mRNA on the ribosome. initiation Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Summary of Protein Synthesis 26 Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Complementary Sequences in DNA, mRNA, tRNA, and Peptides 27 Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Learning Check 28 The following section of DNA is used to build mRNA for a protein. —GAA—CCC—TTT— A. What is the corresponding mRNA sequence? B. What are the anticodons on the tRNAs? C. What is the amino acid order in the peptide? Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Solution 29 A. What is the corresponding mRNA sequence? —CUU—GGG—AAA— B. What are the anticodons for the tRNAs? GAA for CUU; CCC for GGG; UUU for AAA C. What is the amino acid order in the peptide? —CUU—GGG—AAA— Leu — Gly — Lys Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Learning Check 30 Place the following statements in order of their occurrence in protein synthesis. A. mRNA attaches to a ribosome. B. The ribosome moves along mRNA to add amino acids to the growing peptide chain. C. A completed polypeptide is released. D. A tRNA brings an amino acid to its codon on mRNA. E. DNA produces mRNA. Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Solution 31 Place the following statements in order of their occurrence in protein synthesis. E. DNA produces mRNA. A. mRNA attaches to a ribosome. D. A tRNA brings an amino acid to its codon on mRNA. B. The ribosome moves along mRNA to add amino acids to the growing peptide chain. C. A completed polypeptide is released. Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Chapter 17 Nucleic Acids and Protein Synthesis 32 17.6 Genetic Mutations Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Mutations 33 A mutation, or change in the nucleotide sequence of DNA, can • result from mutagens such as radiation and chemicals • produce one or more incorrect codons in mRNA • produce a protein containing one or more incorrect amino acids • produce defective proteins and enzymes • cause genetic diseases Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Types of Mutations 34 • • • • A substitution or point mutation is the replacement of one base in the template strand of DNA with another. If a substitution or point mutation changes the nucleotide, a different amino acid may be inserted into the polypeptide. If this produces no change in the amino acid sequence, it is called a silent mutation. A frameshift mutation is the insertion of a single nucleotide into the sequence resulting in a change to all subsequent codons, leading to a new amino acid sequence. Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Normal DNA and Protein Synthesis 35 The normal DNA sequence produces a mRNA that provides instructions for the correct series of amino acids in a protein. Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Mutation: Substitution 36 Substitution • of a base in DNA changes a codon in the mRNA • of a different codon leads to the placement of an incorrect amino acid in the polypeptide Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Frameshift Mutation 37 In a frameshift mutation, • an extra base adds to or is deleted from the normal DNA sequence • all the codons in mRNA and amino acids are incorrect from the base change Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Effect of Mutations 38 When a mutation causes a change in the amino acid sequence the structure of the resulting protein may be severely altered, causing loss of its biological activity. Altered enzymes cannot catalyze reactions, and possible toxins may accumulate in the body and may be lethal. When this condition is hereditary, it is called a genetic disease. Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Examples of Genetic Diseases 39 Galactosemia Cystic fibrosis Down syndrome Muscular dystrophy Huntington’s disease Sickle-cell anemia Hemophilia Tay-Sachs disease Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Learning Check 40 Identify each type of mutation as a substitution or frameshift. A. Cytosine (C) enters the DNA sequence. B. One adenosine is removed from the DNA sequence. C. A base sequence of TGA in DNA changes to TAA. Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Solution 41 Identify each type of mutation as a substitution or frameshift. A. Cytosine (C) enters the DNA sequence. frameshift B. One adenosine is removed from the DNA sequence. frameshift C. A base sequence of TGA in DNA changes to TAA. substitution Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Chapter 17 Nucleic Acids and Protein Synthesis 42 17.7 Viruses Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Viruses 43 Viruses • are small particles of DNA or RNA that require a host cell to replicate • cause a viral infection when the DNA or RNA enters a host cell • are synthesized in the host cell from the viral RNA produced by viral DNA Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Some Diseases Caused by Viruses 44 Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Viruses 45 FIGURE 17.17 After a virus attaches to the host cell, it injects its viral DNA and uses the host cell’s amino acids to synthesize viral protein. It uses the host cell’s nucleic acids, enzymes, and ribosomes to make viral RNA. When the cell bursts, the new viruses are released to Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition infect other cells. Copyright © 2012 by Pearson Education, Inc. Reverse Transcription 46 In reverse transcription, • a retrovirus, which contains viral RNA but no viral DNA, enters a cell • the viral RNA uses reverse transcriptase to produce a viral DNA strand • the viral DNA strand forms a complementary DNA strand • the new DNA uses the nucleotides and enzymes in the host cell to synthesize new virus particles Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Reverse Transcription 47 FIGURE 17.18 After a retrovirus injects its viral RNA into a cell, it forms a DNA strand by reverse transcription. The DNA forms a doublestranded DNA called a provirus, which joins the host cell DNA. When the cell replicates, the provirus produces the viral RNA Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition needed to produce more Copyright © 2012 by Pearson Education, Inc. HIV Virus and AIDS 48 The HIV-1 virus • is a retrovirus that infects T4 lymphocyte cells • decreases the T4 level and the immune system fails to destroy harmful organisms • causes pneumonia and skin cancer associated with AIDS HIV virus Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. AIDS Treatment 49 Treatment for AIDS is based on attacking HIV-1 at different points in its life cycle, such as prevention of reverse transcription of the viral DNA and protein synthesis. For example, AZT, similar to thymidine, mimics the structures of the nucleosides used for DNA synthesis, which inhibit the reverse transcriptase enzyme. Lexiva is a protease inhibitor that prevents protein synthesis used by viruses to make more copies. Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. AIDS Treatment 50 Azidothymine (AZT) Lexiva Insert structure AZT pg 625. Insert structure Lexiva pg 625. Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Learning Check 51 Match the following terms with the descriptions below: virus retrovirus protease inhibitor reverse transcription A. a virus containing RNA B. small particles requiring host cells to replicate C. a substance that prevents the synthesis of viral proteins D. using viral RNA to synthesize viral DNA Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Solution 52 A. a virus containing RNA retrovirus B. small particles requiring host cells to replicate virus C. a substance that prevents the synthesis of viral proteins protease inhibitor D. using viral RNA to synthesize viral DNA reverse transcriptase Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc. Concept Map: Nucleic Acids and Protein Synthesis 53 Chemistry: An Introduction to General, Organic, and Biological Chemistry, Eleventh Edition Copyright © 2012 by Pearson Education, Inc.