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86 Cards in this Set

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1. What is DNA?
-Deoxyribonucleic acid
-Used to store the genetic information (genome)
-Polymerized from deoxyribose
2. What is RNA?
-Ribonucleic acid
-Used to convert the genetic information into protein
-Polymerized from ribonucleotides
3. What forms the genetic code?
The linear sequences of bases in RNA or DNA form the genetic code
4. What is the genetic code?
The instructions to make a specific protein
6. What are the three cellular processes that convert the genetic code into specific proteins?
1. Replication

2. Transcription

3. Translation
5. What is the central dogma for information flow?
DNA -> RNA -> Protein
7. What is replication?
Duplicating the DNA sequence (genome) prior to every cell division
8. What is transcription?
Copying of the DNA sequence information into messenger RNA (mRNA)
9. What is translation?
Conversion of the information in mRNA into a linear amino acid sequence
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)
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
12. Why is RNA unstable compared to DNA?
RNA has a hydroxy (-OH) group on C2 which can act as a nucleophile

*DNA is stable since the OH is a H
13. How are nucleotides joined to from nucleic acids?
Nucleotides are joined by a phosphodiester linkage between the 3' and 5' hydroxyls
14. Do nucleic acids have polarity?
YES!

The chain has polarity because there is a 3' end and a 5' end
15. What is the most important property of nucleic acids?
Complimentary base pairing of A/T and G/C
16. What is base pairing?
Specific purine bases form hydrogen bonds to specific pyrimidine bases
17. What bases pair with each other?
1. G and C form 3 hydrogen bonds (more stable)

2. A and T (or U) form 2 hydrogen bonds (less stable)
18. What does base pairing between complimentary strands generate?
An antiparallel duplex structure
19. What is meant by a an antiparallel duplex structure?
The sequence of one strand defines the sequence of the pairing strand
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)
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
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)
23. What bases are in DNA?
Adenine, cytosine, guanine, and thymine
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
25. What bases are in RNA?
Adenine, cytosine, guanine, and uracil
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)
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
28. What is intrastrand base pairing?
Complimentary regions within the single strand generate intrastrand base pairing
29. What are the four different functional classes of RNA?
1. Messenger RNA (mRNA)

2. Transfer RNA (tRNA)

3. Ribosomal RNA (rRNA)

4. Catalytic RNA
30. What is messenger RNA?
A copy of the information needed to make a protein
31. What does transfer RNA do?
It carries activated amino acids to ribosomes for polypeptide synthesis
32. What is ribosomal RNA?
An integral part of ribosomes, and it accounts for about 80% of RNA in cells
33. What are catalytic RNAs?
They have catalytic activity (example is ribosome)

*complex secondary structures in RNA can serve catalytic functions
34. What causes mutations?
Changes to the bases sequence in DNA causes mutations

*generally mutations are undesirbale
35. What can mutations cause?
Changes in the corresponding amino acid sequence
36. What do repair systems do?
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
37. What is nucleic acid instability caused by?

Four things...
1. Oxidation
2. Base hydrolysis (depurination)
3. Amine hydrolysis (deamination)
4. UV light
38. Is damage to RNA a serious problem?
Damage to RNA rarely causes a biological problem because you can always make more
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
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)
41. What is depurination?
When water reacts with DNA to hydrolyze the base from the sugar

*purines are particularly prone to this reaction
42. Is depurination a frequent reaction?
YES!!

Happens at a high frequency (about 10,000 events/day/cell)
43. What is deamination?
When water removes the amine groups from bases

*can alter the genetic code
44. How can deamination alter the genetic code?
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
45. How do nucleic acids react with UV light?
It causes dimerization of adjacent pyrimidines
46. What is dimerization?
When adjacent pyrimidines form either cyclobutane dimers or 6,4 photoproducts

*both products block biological function
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
48. What are the DNA damage repair systems called?
Base excision repair

Nucleotide excision repair
49. What are three common enzymes that make or degrade nucleic acids?
1. Polymerases

2. Ligase

3. Nucleases
50. What do polymerases do?
They make DNA or RNA from precursor dNTPs or NTPs in a template dependent manner
51. What is DNA polymerase used for?

Two things...
1. Replicating DNA (makes complimentary DNA strands)

2. Repairing DNA
52. What do ligases do?
They join DNA or RNA fragments together in an energy dependent manner
53. What do nucleases do?
They degrade DNA or RNA by hydrolytic cleavage of phosphodiester bonds
51. What is RNA polymerase use for?
Making RNA from DNA for transcription
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
55. What is the one way in which DNA and RNA polymerase differ?
DNA polymerase requires a primer whereas RNA polymerase starts from scratch
56. What does the primer used by DNA polymerase do?
The primer binds to the complimentary template region and provides a 3' OH which is the nucleophile
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
58. What does a proofreading nuclease do?
It removes incorrect bases from the growing 3' end
59. How does influenza replicate?
-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
60. What are the main types of nucleases?
1. Exonucleases

2. Endonucleases
61. What do exonucleases do?
They hydrolyze nucleic acids from an end
62. What do endonucleases do?
They hydrolyze nucleic acids without needing a free end
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
64. What are restriction endonucleases?
They are enzymes that bind to specific DNA sequences and cut both strands of DNA at the binding site
65. What are restriction endonucleases especially important for?
Recombinant DNA
66. What type of sequence do most restriction endonucleases recognize?
Palindromic Sequence (read the same in either direction)
67. What are the breaks like that restriction endonuclease make?
They make complimentary "sticky end" breaks so that ends can base pair again
68. What four things is isolating specific DNA fragments useful for?
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)
69. What are four approaches to making nucleic acids in the lab?
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)
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
71. How does gel electrophoresis separate DNA?
It separates DNA based on size

Smallest fragments move the farthest (closer to positive end)
72. What does Polymerase Chain Reaction (PCR) do?
Make nearly unlimited copies of DNA sequence from as little as a single target molecule in a complicated mixture of other DNA sequences
73. What three things is PCR useful for?
1. Isolation of genes

2. Detecting a specific DNA sequence

3. Genetic engineering (change sequence)
74. What is key to PCR?
Short opposing oligonucleotide (primers) that hybridize to DNA of interest
75. How does the target sequence increase?
Exponential increase
76. In short how does PCR work?
Reiterative cycles of DNA synthesis exponentially amplify a specific DNA sequence
77. How are radioactive nucleotides made?
dNTPs containing radioactive phosphorus (32P) are used to make radioactive nucleic acids using either DNA or RNA polymerase
78. What is radioactive DNA or RNA called?
A probe
79. How are radioactive nucleic acids detected?
Very sensitive detection methods (i.e. autoradiography) exist to detect radioactive nucleic acids
80. What is an example of a technique that uses a probe?
Souther blot analysis
81. What is the purpose of a southern blot analysis?
TO identify a specific sequence in a large mixture of unrelated sequences
82. How is the DNA of interest identified in a southern blot analysis?
It is identified by hybridization with a specific radiolabeled probe
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
84. What is the solid that the DNA from the gel is added to?
Nitrocellulose
85. What is the key to southern blotting?
Hybridization

*hybrid molecule (1 strand radioactive other nonradioactive) allows for identification of specific DNA fragments in a mixture