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86 Cards in this Set
- Front
- Back
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1. What is DNA?
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-Deoxyribonucleic acid
-Used to store the genetic information (genome) -Polymerized from deoxyribose |
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2. What is RNA?
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-Ribonucleic acid
-Used to convert the genetic information into protein -Polymerized from ribonucleotides |
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3. What forms the genetic code?
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The linear sequences of bases in RNA or DNA form the genetic code
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4. What is the genetic code?
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The instructions to make a specific protein
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6. What are the three cellular processes that convert the genetic code into specific proteins?
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1. Replication
2. Transcription 3. Translation |
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5. What is the central dogma for information flow?
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DNA -> RNA -> Protein
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7. What is replication?
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Duplicating the DNA sequence (genome) prior to every cell division
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8. What is transcription?
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Copying of the DNA sequence information into messenger RNA (mRNA)
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9. What is translation?
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Conversion of the information in mRNA into a linear amino acid sequence
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10. Describe the genetic code.
Two points... |
1. It is colinear with the polypeptide sequence
2. It consists of nonoverlapping triplets of bases in nucleic acids codes for specific amino acids (3 bases -> 1 amino acid) |
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11. Just a review, but what is the structure of a nucleotide?
Three parts... |
1. Phosphate
2. Sugar (ribose or deoxyribose) 3. Purine or pyrimidine base |
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12. Why is RNA unstable compared to DNA?
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RNA has a hydroxy (-OH) group on C2 which can act as a nucleophile
*DNA is stable since the OH is a H |
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13. How are nucleotides joined to from nucleic acids?
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Nucleotides are joined by a phosphodiester linkage between the 3' and 5' hydroxyls
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14. Do nucleic acids have polarity?
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YES!
The chain has polarity because there is a 3' end and a 5' end |
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15. What is the most important property of nucleic acids?
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Complimentary base pairing of A/T and G/C
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16. What is base pairing?
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Specific purine bases form hydrogen bonds to specific pyrimidine bases
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17. What bases pair with each other?
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1. G and C form 3 hydrogen bonds (more stable)
2. A and T (or U) form 2 hydrogen bonds (less stable) |
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18. What does base pairing between complimentary strands generate?
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An antiparallel duplex structure
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19. What is meant by a an antiparallel duplex structure?
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The sequence of one strand defines the sequence of the pairing strand
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20. How is base pairing reversible?
Two points... |
1. At high temperature or pH, DNA strands dissociate (melting or denaturation)
2. At low temperature or neutral pH, DNA strands will reassociate (annealing) |
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21. How is base pairing key to nucleic acid structure and function?
Three things... |
1. The bases on one strand define the bases on the other
2. One strand can be used to repair or copy the other strand 3. Base pairing allows one strand to serve as a template for synthesis of the other strand |
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22. Describe DNA.
Four points... |
1. Stable source of genetic info
2. Uses deoxyribose nucleotides 3. Usually double-stranded helix 4. Usually present as huge linear molecules called chromosomes (encode thousands of proteins) |
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23. What bases are in DNA?
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Adenine, cytosine, guanine, and thymine
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24. Describe RNA.
Four points... |
1. Unstable copy used for protein synthesis
2. Uses ribose nucleotides 3. Usually a short single-stranded species 4. Usually encodes a single protein |
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25. What bases are in RNA?
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Adenine, cytosine, guanine, and uracil
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26. Describe the structure of DNA?
Four things... |
1. Two continuous strands from a double helix
2. Sugar phosphate backbone is on the outside 3. The bases are on the inside 4. There are two unequal grooves (major and minor) |
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27. Describe the structure of RNA?
Four things... |
1. Usually single-stranded
2. Has diverse structure and thus divers functions 3. Intrastrand base pairing to form complex secondary structures 4. Can contain unusual bases, modifications, or alternative forms of base pairing |
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28. What is intrastrand base pairing?
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Complimentary regions within the single strand generate intrastrand base pairing
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29. What are the four different functional classes of RNA?
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1. Messenger RNA (mRNA)
2. Transfer RNA (tRNA) 3. Ribosomal RNA (rRNA) 4. Catalytic RNA |
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30. What is messenger RNA?
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A copy of the information needed to make a protein
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31. What does transfer RNA do?
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It carries activated amino acids to ribosomes for polypeptide synthesis
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32. What is ribosomal RNA?
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An integral part of ribosomes, and it accounts for about 80% of RNA in cells
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33. What are catalytic RNAs?
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They have catalytic activity (example is ribosome)
*complex secondary structures in RNA can serve catalytic functions |
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34. What causes mutations?
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Changes to the bases sequence in DNA causes mutations
*generally mutations are undesirbale |
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35. What can mutations cause?
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Changes in the corresponding amino acid sequence
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36. What do repair systems do?
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The repair systems recognize and repair DNA damage by using the complimentary strand as a template BUT these repair systems don't always restore the genetic code
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37. What is nucleic acid instability caused by?
Four things... |
1. Oxidation
2. Base hydrolysis (depurination) 3. Amine hydrolysis (deamination) 4. UV light |
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38. Is damage to RNA a serious problem?
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Damage to RNA rarely causes a biological problem because you can always make more
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39. How does oxygen radical formation damage DNA?
Two ways... |
1. The bases can be damaged, altering the genetic code
2. The phosphodiester backbone can be broken causing a break in the continuity of DNA |
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40. What are some common antioxidants that we eat because they are believed to help prevent oxidative damage?
Three things... |
1. Vitamins A, C, and E
2. Carotene 3. Lycopene (red color in tomatoes) |
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41. What is depurination?
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When water reacts with DNA to hydrolyze the base from the sugar
*purines are particularly prone to this reaction |
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42. Is depurination a frequent reaction?
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YES!!
Happens at a high frequency (about 10,000 events/day/cell) |
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43. What is deamination?
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When water removes the amine groups from bases
*can alter the genetic code |
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44. How can deamination alter the genetic code?
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Cytosine deamintates to uracil so there's a change in the code from a C to a U
*part of the reason T is used in DNA |
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45. How do nucleic acids react with UV light?
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It causes dimerization of adjacent pyrimidines
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46. What is dimerization?
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When adjacent pyrimidines form either cyclobutane dimers or 6,4 photoproducts
*both products block biological function |
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47. In general, what do DNA damage repair systems do?
Three things... |
1. Identify the incorrect base
2. Remove entire nucleotide from the chain 3. Install a replacement nucleotide using the intact complimentary strand to determine the correct nucleotide to insert |
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48. What are the DNA damage repair systems called?
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Base excision repair
Nucleotide excision repair |
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49. What are three common enzymes that make or degrade nucleic acids?
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1. Polymerases
2. Ligase 3. Nucleases |
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50. What do polymerases do?
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They make DNA or RNA from precursor dNTPs or NTPs in a template dependent manner
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51. What is DNA polymerase used for?
Two things... |
1. Replicating DNA (makes complimentary DNA strands)
2. Repairing DNA |
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52. What do ligases do?
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They join DNA or RNA fragments together in an energy dependent manner
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53. What do nucleases do?
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They degrade DNA or RNA by hydrolytic cleavage of phosphodiester bonds
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51. What is RNA polymerase use for?
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Making RNA from DNA for transcription
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54. How do both DNA and RNA polymerases work?
Two things... |
1. Use a DNA strand as a template
2. Synthesize new strands in direction of 5' end to 3' end |
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55. What is the one way in which DNA and RNA polymerase differ?
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DNA polymerase requires a primer whereas RNA polymerase starts from scratch
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56. What does the primer used by DNA polymerase do?
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The primer binds to the complimentary template region and provides a 3' OH which is the nucleophile
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57. How does DNA polymerase avoid errors?
Two ways... |
1. Spatial contriants within the active site heavily favor the addition of complimentary bases to the growing 3' end
2. Polymerases have a proofreading nuclease |
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58. What does a proofreading nuclease do?
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It removes incorrect bases from the growing 3' end
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59. How does influenza replicate?
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-It stores genetic info in RNA
-During replication there are high levels of mutations b/c RNA polymerase doesn't have proofreading nucleases -These mutations help virus to adapt to new hosts and cellular defenses |
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60. What are the main types of nucleases?
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1. Exonucleases
2. Endonucleases |
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61. What do exonucleases do?
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They hydrolyze nucleic acids from an end
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62. What do endonucleases do?
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They hydrolyze nucleic acids without needing a free end
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63. How are nucleases diverse?
Two ways... |
1. Some are specific for DNA, some are specific for RNA, and some can degrade either
2. A few DNAases only hydrolyze DNA at a specific sequence |
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64. What are restriction endonucleases?
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They are enzymes that bind to specific DNA sequences and cut both strands of DNA at the binding site
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65. What are restriction endonucleases especially important for?
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Recombinant DNA
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66. What type of sequence do most restriction endonucleases recognize?
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Palindromic Sequence (read the same in either direction)
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67. What are the breaks like that restriction endonuclease make?
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They make complimentary "sticky end" breaks so that ends can base pair again
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68. What four things is isolating specific DNA fragments useful for?
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1. Determining the nucleotide sequence (and hence the protein it makes)
2. Using DNA to make lots of a specific protein 3. Using the DNA sequence to study how the organism regulates the production of a particular protein 4. Identifying particular individual organisms (csi) |
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69. What are four approaches to making nucleic acids in the lab?
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1. Purify it directly from the source (genomic DNA)
2. If DNA has been isolated, use bacteria to make a lot of it (plasmid DNA) 3. Enzymatically make lots of copies of DNA (PCR) 4. Purchase short chemically generated single strand of desired sequence (Oligonucleotides) |
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70. How can one isolate the DNA fragment of interest from the rest of the DNA?
Two parts... |
1. Use a chosen restriction endonuclease and cut off the uninteresting regions of DNA from your fragment
2. Separate DNA fragments by gel electrophoresis and purify fragment of interest |
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71. How does gel electrophoresis separate DNA?
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It separates DNA based on size
Smallest fragments move the farthest (closer to positive end) |
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72. What does Polymerase Chain Reaction (PCR) do?
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Make nearly unlimited copies of DNA sequence from as little as a single target molecule in a complicated mixture of other DNA sequences
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73. What three things is PCR useful for?
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1. Isolation of genes
2. Detecting a specific DNA sequence 3. Genetic engineering (change sequence) |
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74. What is key to PCR?
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Short opposing oligonucleotide (primers) that hybridize to DNA of interest
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75. How does the target sequence increase?
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Exponential increase
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76. In short how does PCR work?
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Reiterative cycles of DNA synthesis exponentially amplify a specific DNA sequence
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77. How are radioactive nucleotides made?
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dNTPs containing radioactive phosphorus (32P) are used to make radioactive nucleic acids using either DNA or RNA polymerase
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78. What is radioactive DNA or RNA called?
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A probe
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79. How are radioactive nucleic acids detected?
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Very sensitive detection methods (i.e. autoradiography) exist to detect radioactive nucleic acids
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80. What is an example of a technique that uses a probe?
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Souther blot analysis
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81. What is the purpose of a southern blot analysis?
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TO identify a specific sequence in a large mixture of unrelated sequences
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82. How is the DNA of interest identified in a southern blot analysis?
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It is identified by hybridization with a specific radiolabeled probe
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83. What is the procedure of a southern blot?
Five parts... |
1. Make radioactive DNA (or RNA) probe using the DNA sequence you want to identify
2. Cleave DNA with restriction endonucleases and separate by gel electrophoresis 3. Transfer DNA in the gel to a solid support 4. Add radioactive probe to nitrocellulose and let probe hybridize to DNA of interest 5. Hybridization allows detection of DNA of interest following exposure to x-ray film |
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84. What is the solid that the DNA from the gel is added to?
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Nitrocellulose
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85. What is the key to southern blotting?
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Hybridization
*hybrid molecule (1 strand radioactive other nonradioactive) allows for identification of specific DNA fragments in a mixture |
