Chapter 17: Nucleic Acids & Protein Synthesis

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kfindley
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Chapter 17: Nucleic Acids & Protein Synthesis
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2014-04-28 13:52:17
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Nucleic Acids & Protein Synthesis
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  1. Nucleic Acids
    • - Molecules that store information for cellular growth and reproduction-DNA & RNA-Large molecules consisting of long chains of monomers called nucleotides found in the cell nucleus
    • - Polymers of nucleotides or polynucleotides
    • (nucleosides with a phosphate group bonded to -OH on C5')
    • - Have a unique sequence of bases in RNA, which is called its primary structure
    • - Carry information from one cell to the next
  2. DNA & RNA consist of:
    • Monomers called nucleotides that consist of:
    • -pentose sugar
    • -base
    • -phosphate
  3. Purines:
    • - Adenine (A) *DNA & RNA
    • - Guanine (G) *DNA & RNA
  4. Pyrimidines:
    • - Cytosine (C) *DNA & RNA
    • - Thymine (T) *DNA ONLY
    • - Uracil (U) *RNA ONLY
  5. The bases in DNA & RNA are:
    • - Pyrimidines C, T, and U
    • - Purines A and G
  6. DNA contains the bases:
    • - Cytosine (C)
    • - Guanine (G)
    • - Adenine (A)
    • - Thymine (T) * different in DNA than in RNA
  7. RNA contains the bases:
    • - Cytosine (C)
    • - Guanine (G)
    • - Adenine (A)
    • - Uracil (U) * different in RNA than in DNA
  8. The pentose (5 carbon) sugar in RNA is:
    - Ribose
  9. The pentose (5 carbon) sugar in DNA is:
    • Deoxyribose with no O atom on carbon 2'
    • - ' means prime
  10. A nucleoside is:
    • - A combination of a sugar and a 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
  11. 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
    • - Named using the name of the nucleoside, followed by 5'-monophosphate
  12. The nucleotides of RNA are identical to those of DNA except for:
    In DNA the sugar is deoxyribose and deoxythymidine which replaces uridine.
  13. Components of DNA:
    • - Bases: A,G,C and T
    • - Sugar: Deoxyribose
    • - Nucleoside: Base + deoxyribose sugar
    • - Nucleotide: Base + deoxyribose sugar + phosphate
    • - Nucleic Acid: Polymer of deoxyribose nucleotides
  14. Components of RNA:
    • - Bases: A,G,C and U
    • - Sugar: Ribose
    • - Nucleoside: Base + ribose sugar
    • - Nucleotide: Base + ribose sugar + phosphate
    • - Nucleic Acid: Polymer of ribose nucleotides
  15. Nucleosides that contain a purine end with:
    Nucleosides that contain a pyrimidine end with:
    Nucleosides of DNA add:
    • 1. -osine (Ex: adenosine/guanosine)
    • 2. -idine (Ex: cytidine/thymidine)
    • 3. deoxy to the beginning of their name
  16. Nucleic Acid Primary Structure:
    • - Nucleotides are joined by a 3'-5' phosphodiester bond
    • - The 3'-OH group of the sugar in one nucleotide forms an ester bond to the phosphate group on the 5'-carbon of the sugar of the next nucleotide
  17. Primary Structure of Nucleic Acids in DNA and RNA chains:
    • - Each sugar in a sugar-phosphate backbone is attached to a base
    • - The bases extend out from the nucleic acid backbone
    • - Are labeled starting with the free 5' end to the 3' end
  18. DNA contains complementary base pairs, equal amounts of A and T and equal amounts of G and C bases in which:
    • - Adenine is always linked by two hydrogen bonds with thymine (A-T)
    • - Guanine is always linked by three hydrogen bonds with cytosine (G-C)
  19. Double Helix:
    • - has two strands of nucleotides that wind together
    • - is held in place by two hydrogen bonds that form between the base pairs A-T
    • - is held in place by three hydrogen bonds that form between the base pairs G-C
  20. In the double helix of DNA:
    • - the two chains are held together by hydrogen bonds that link bases A-T and G-C
    • - the bases along one strand complement the bases along the other
  21. Write the complementary base sequence for the matching strand in the following DNA section:
    -A-G-T-C-C-A-A-T-C-
    -T-C-A-G-G-T-T-A-G-
  22. In DNA replication:
    • - genetic information is maintained each time a cell divides 
    • - the DNA strands unwind
    • - each parent strand bonds with new complementary bases
    • - two new DNA strands form that are EXACT copies of the parent DNA
    • - the separate strands of the parent DNA are the templates for the synthesis of complementary strands, which produces two exact copies (daughter DNAs)
  23. How many hydrogen bonds link each of the following base pairs?

    1. A-T
    2. G-C
    • 1. Bases are linked by two hydrogen bonds
    • 2. Bases are linked by three hydrogen bonds
  24. In DNA fingerprinting:
    • - enzymes are used to cut DNA chains into smaller sections
    • - the resulting fragments are separated by size and treated with a radioactive isotope that adheres to specific base sequences
    • - the resulting pattern of bands are known as a DNA fingerprint

    *One application of DNA fingerprinting is in forensic science, where DNA from samples such as blood, hair, or semen is used to connect a suspect with a crime
  25. RNA:
    • - makes up most of the nucleic acid found in the cell
    • - transmits the genetic information needed for cell operation
    • - transmits information from DNA to make proteins
    • - molecules are polymers of nucleotides and differ from DNA in four ways
  26. 4 ways RNA differs from DNA:
    • 1. The sugar in RNA is ribose rather than deoxyribose found in DNA
    • 2. The base uracil replaces thymine
    • 3. RNA molecules are single stranded; DNA is double stranded
    • 4. RNA molecules are much smaller than DNA molecules
  27. Types of RNA:
    • - Messenger RNA (mRNA)
    • - Transfer RNA (tRNA)
    • - Ribosomal RNA (rRNA)
  28. Messenger RNA:
    • - rRNA
    • - 5% of total RNA
    • - Carries information for protein synthesis from the DNA in the nucleus to the ribosomes
  29. Transfer RNA:
    • - tRNA
    • - 15% of total RNA
    • - Brings amino acids to the ribosomes for protein synthesis
    • - smallest RNA, only type that can translate genetic information into amino acids for proteins
    • - cloverleaf shape when hydrogen bonds form between its complementary bases
    • - the acceptor stem attaches to an amino acid and its anticodon bonds with a condon on mRNA
  30. Ribosomal RNA:
    • - rRNA
    • - 80% of total RNA
    • - Major component of the ribosomes; protein synthesis
  31. Protein Synthesis involves:
    • - Transcription
    • - Translation

    *The genetic information in DNA is replicated in cell division and used to produce mRNAs that code for the amino acids needed for protein synthesis
  32. Transcription:
    • - mRNA is formed from a gene on a DNA strand
    • - begins when a section of DNA containing the gene unwinds
    • - within the unwound DNA, RNA polymerase enzymes uses one of the strands as a template to synthesize mRNA
    • - the mRNA is released at the termination point
    • -mRNA is synthesized using complementary base pairing, with uracil (U) and thymine (T)
    • - the newly formed mRNA moves out of the nucleus to ribosomes in the cytoplasm
  33. Translation:
    tRNA molecules bring amino acids to mRNA to build a protein
  34. RNA Polymerase:
    • -G-A-A-C-T-
    •  ↓  ↓  ↓  ↓ ↓

    -C-U-U-G-A-
  35. What is the sequence of bases in mRNA produced from a section of the template strand of DNA that has the sequence of bases:

    -C-T-A-A-G-G-
    -G-A-U-U-C-C-
  36. Genetic Code:
    • - a series of three nucleotides in mRNA called codons that determine the amino acid order for the protein
    • - has different codon for all 20 amino acids needed to build a protein
    • - contains certain codons that signal the "start" and "end" of a polypeptide chain

    *Ex: -UUU-UUU-UUU- codes for three phenylalanine amino acids:

    • Codons in mRNA       -UUU-UUU-UUU-
    • Translation                 ↓      ↓      ↓
    • Amino acid sequence  -Phe-Phe-Phe-
  37. From Table 17.4, write the order of amino acids coded for by a section of mRNA with the base sequence:

    -GCC-GUA-GAC-
    • GCC = alanine
    • GUA = valine
    • GAC = aspartic acid

    • -GCC-GUA-GAC-
    •    ↓     ↓      ↓
    •   Ala-Val-Asp
  38. 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
    • - once the peptide bond is formed, the initial tRNA detaches from the ribosome, which shifts to the next available codon; this process is called translocation
  39. Chain Elongation:
    - the ribosome moves along the mRNA from codon to codon, attaching new amino acids to the growing polypeptide chain
  40. 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
  41. Termination Step:
    • - all 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
    • - 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 alpha helices, beta 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
  42. Which codons in mRNA act as stop signals rather than amino acids and code for the termination of protein synthesis?
    UGA, UAA, and UAG
  43. When does this happen:

    Ribosomes move along mRNA, adding amino acids to a growing peptide chain.
    Translocation
  44. When does this happen:

    A completed peptide chain is released.
    Termination
  45. When does this happen:

    A tRNA attaches to its specific amino acid.
    Activation
  46. When does this happen:

    A tRNA binds to the AUG codon of the mRNA on the ribosome.
    Initiation
  47. Steps in Protein Synthesis:

    1. DNA Transcription
    • Site: Nucleus, nucleotides, RNA polymerase
    • Process: A DNA template is used to produce mRNA
  48. Steps in Protein Synthesis:

    2. Activation of tRNA
    • Site: Cytoplasm, amino acids, tRNAs, aminoacyl tRNA sythetase
    • Process: Molecules of tRNA pick up specific amino acids according to their anticodons
  49. Steps in Protein Synthesis:

    3. Initiation and Chain Elongation
    • Site: Ribosome, Met-tRNA, mRNA, amino acyl tRNAs
    • Process: A start codon binds the first tRNA carrying amino acid methionine to the mRNA. Successive tRNAs bind to and detach from the ribosome as each amino acid adds to the polypeptide
  50. Steps in Protein Synthesis:

    4. Chain Termination
    • Site: Ribosome, stop codon on mRNA
    • Process: A polypeptide is released from ribosome
  51. Complementary Sequences in DNA, mRNA, tRNA, and Peptides
    • Nucleus:
    • DNA coding strand:     -GCG-AGT-GGA-TAC-
    • DNA template strand: -CGC-TCA-CCT-ATG-

    • Ribosome (cytoplasm):
    • mRNA:                        -GCG-AGU-GGA-UAC-
    • tRNA anticodons:          -CGC-UCA-CCU-AUG-
    • Polypeptide amino acids: -Ala-Ser-Gly-Tyr-
  52. The following section of DNA is used to build mRNA for a protein:

    -GAA-CCC-TTT-

    1. What is the corresponding mRNA sequence?
    2. What are the anticodons on the tRNAs?
    3. What is the amino acid order in the peptide?
    1. -CUU-GGG-AAA-

    2. GAA for CUU; CCC for GGG; UUU for AAA

    3. Leu-Gly-Lys
  53. 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.
    • 1) E. DNA produces mRNA.
    • 2) A. mRNA attaches to a ribosome.
    • 3) D. A tRNA brings an amino acid to its codon on mRNA.
    • 4) B. The ribosome moves along mRNA to add amino acids to the growing peptide chain.
    • 5) C. A completed polypeptide is released.
  54. Mutation:
    • - change in the nucleotide sequence of DNA;
    • - 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
  55. Substitution or Point Mutation
    • - replacement of one base in the template strand of DNA with another
    • - If this changes the nucleotide, a different amino acid may be inserted into the polypeptide
    • - if a base in DNA changes a codon in the mRNA
  56. Silent Mutation
    - if a substitution or point mutation produces no change in the amino acid sequence
  57. Frameshift Mutation
    • - insertion of a single nucleotide into the sequence resulting in a change to all subsequent codons, leading to a new amino acid sequence
    • - 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
  58. Genetic Disease
    • - Hereditary 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
  59. Examples of Genetic Diseases
    • - Galactosemia
    • - Cystic fibrosis
    • - Down syndrome
    • - Muscular dystrophy
    • - Huntington's disease
    • - Sickle cell anemia
    • - Hemophilia
    • - Tay Sachs disease
  60. 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.
    • A. Frameshift
    • B. Frameshift
    • C. Substitution
  61. Viruses
    • - 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
  62. Stages of a Virus
    • - 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 infect other cells.
  63. 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
  64. HIV-1 Virus
    • - 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
    • - 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
  65. AZT
    - similar to thymidine, mimics the structure of the nucleosides used for DNA synthesis, which inhibit the reverse transcriptase enzyme
  66. Lexiva
    - protease inhibitor that prevents protein synthesis used by viruses to make more copies
  67. 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
    • A. retrovirus
    • B. virus
    • C. protease inhibitor
    • D. reverse transcription
  68. Nucleic Acids are ? and ?
    DNA and RNA
  69. DNA contains ? arranged as a ? with ? with an order called?
    Deoxynucleotides A,T,G,C arranged as a double helix with complementary base pairs A-T, G-C with an order called Genetic Code.
  70. RNA contains ? with three types ? and ? and ?
    Nucleotides A,U,G,C with three types mRNA and tRNA and rRNA.
  71. Protein Synthesis uses ? specific for ? produce a ?
    Codons specific for Amino Acids produce a Protein.

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