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M2M Biochemistry and molecular biology > DNA/RNA LO > Flashcards

DNA/RNA LO Flashcards

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1
Q

What are the purines?

A

adenine, guanine (PURe As Gold)

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2
Q

what are the pyrimidines?

A

cytosine, thymine, and uracil

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3
Q

what is ribose?

A

5 carbon sugar that is the primary building block of ribonucleic acids

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4
Q

how is deoxyribose different than ribose?

A

deoxyribose has been dehydroxylated at the 2’ position

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5
Q

what is a nucleoside?

A

central ribose sugar and a base attached to it at the 1’ position

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6
Q

what is a nucleotide?

A

a nucleoside with at least one phosphate group attached to the 5’ position of the ribose

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7
Q

what is the universal energy currency in the body?

A

ATP

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8
Q

what is the solubility relationship between pyrimidines and purines?

A

pyrimidine > purine

in regards to solubility

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9
Q

what is the solubility relationship between nucleosides, bases, and nucleotides?

A

nucleotide > nucleoside > bases

in regards to solubility

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10
Q

between bases and nucleosides, which is less soluble?

A

base is less soluble than nucleoside

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11
Q

Gout is caused by the build up of ________ which is a precipitant of _______

A

uric acid, purines

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12
Q

The low solubility of purines and their accumulation leads to which 2 diseases covered in lecture?

A

Lesch-Nyhan disease and gout

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13
Q

in regards to the deoxyribose, why is the direction 5’ to 3’ polarity?

A

5’ end has phosphate and 3’ end has hydroxyl group. phosphate at the 5’ end will bind with the hydroxyl group at the 3’ end

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14
Q

What did the Avery, McCloud, and McCarty experiment find?

A

established DNA as the genetic material with their pneumococcus experiments. (smooth strain killed mice, rough strain did not. DNA from heat killed S cultured with R then killed mice BAM!)

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15
Q

what did the Franklin and Wilkins find and how?

A

helical structure of DNA through x-ray diffraction

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16
Q

what are Watson and Crick known for?

A

definitive double-helical structure

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17
Q

What are Chargaff’s rules?

A
  1. Molar ratios of total purines and total pyrimidines are roughly equal (G+A = C+T)
  2. the molar ratios of adenine to thymine, and guanine to cytosine are roughly equal (G=C, A=T)
  3. G+C / A+T ratio is different for different organisms
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18
Q

Describe the Watson-Crick model for DNA structure

A

2 strands in right handed helix
sugar/phosphate groups on the outside of helix (hydrophilic)
bases paired and stacked on the inside (hydrophobic)
major groove and minor groove
10 bp per turn of helix
horizontal distance covered by A-T is almost identical to G-C

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19
Q

what 3 factors within the double helix help stabilize the electrostatic repulsion of the phosphate groups?

A
  1. neutralized by positively charged species in cell (magnesium)
  2. base pair linkages provide stability
  3. base pairs stack on top of one another which allows for delocalization of electrons
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20
Q

what does increasing the salt concentration do to the stability of the DNA?

A

increases the stability of DNA

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21
Q

what do extreme pH do to the stability of the DNA?

A

decreases the stability through altering the ionization of the bases which form H-bonds

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22
Q

what does increasing the length of the DNA strand do to the stability?

A

increases stability

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23
Q

what does a higher GC content do to the stability of the DNA?

A

increases stability

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24
Q

where is circular DNA found?

A

prokaryotes and mitochondra

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25
Q

What occurs during methylation of base pairs?

A

methyl group is added to cytosine or adenine DNA nucleotides

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26
Q

what are the consequences of DNA methylation?

A

decreases gene activity and there is abnormal gene regulation

27
Q

what is the major covalent modifcation of human DNA?

A

methylation of C at CpG sequences

28
Q

when does methylation of cytosine mostly occur?

A

when cytosine is adjacent to a guanine

29
Q

what does deamination of methylcytosine yield?

A

thymine

30
Q

why is deamination of methylcytosine a serious problem?

A

because turns into thymine, then on replication, an adenine will be added instead of a guanine

31
Q

what compound can increase the speed of deamination and where is it mostly found?

A

nitrous acid, cigarette smoke

32
Q

what becomes sensitive to breakage after depurination?

A

phosphate backbone

33
Q

what happens during depurination?

A

breaking off purine base from ribose and leaving a hydroxyl group

34
Q

what can happen if you have a few depurinations right next to each other on DNA?

A

breakage of the phosphate backbone

35
Q

what is usually created as a result of UV radiation in DNA?

A

thymine dimers

36
Q

how are thymine dimers usually repaired?

A

nucleotide excision repair

37
Q

what type of agents are considered carcinogens?

A

alkylating agents (mustard gas, dimethylsulfate, dimethylnitrosamine, CISPLATIN (cancer drug))

38
Q

through what process does actinomycin D work?

A

intercalation. Molecule intercalates into the DNA and then replication cannot continue

39
Q

why can intercalation cause cancer cells to enter apoptosis?

A

causes kink in DNA and replication cannot occur, therefore cell recognizes that it is not functioning properly

40
Q

what does topoisomerase do?

A

removes knots of DNA by removing supercoils

41
Q

what is underwound DNA?

A

produces negative supercoils and decreased twist

42
Q

what is overwound DNA?

A

produces positive supercoils and increased twist

43
Q

what are the 4 methods of attacking DNA metabolism?

A
  1. syntehsis of precursors (dNTP)
  2. intercalation (getting in the middle)
  3. covalently binding bps
  4. disrupting topoisomerases
44
Q

what are the 3 main types of RNA in a human cell?

A
  1. structural
  2. regulatory
  3. information-containing
45
Q

what is the function of rRNA?

A

(ribosomal RNA) make up functional units of ribosomes and translate mRNA

46
Q

what is the function of tRNA?

A

(transfer RNA) brings amino acid specified by codon to ribosome

47
Q

what is the function of snRNA and siRNA?

A

(small nuclear RNA and small interfering RNA) function with in-cell modifications such as splicing

48
Q

what is the function of miRNA and siRNA?

A

(micro RNA and small interfering RNA) downregulate gene expression

49
Q

which is more easily hydrolyzed when comparing RNA and DNA?

A

RNA

50
Q

why is RNA more easily hydrolyzed than DNA?

A

there can be a nucleophilic attack by 2’ OH on the phosphodiester bond

51
Q

what is the ease of hydrolyzing RNA important for?

A

changes in gene expression

52
Q

what is the usually the final form of RNA in humans after it is produced?

A

single strand RNA

53
Q

why can RNA produce many different conformations?

A

there is rotation around the bonds, not hindered by hydrogen bonds from another strand like in DNA

54
Q

How does puromycin work?

A

nucleotide analogue that mimics tRNA acceptor region. therefore allows peptide transfer and termination of translation

55
Q

where do most bacteria get their antibiotic resistance from?

A

environmental DNA such as plasmids

56
Q

how does RNA form hairpin loops?

A

AU, GC, and GU base pairs

57
Q

what does E site of ribosomes hold?

A

holds RNA that will exit

58
Q

what does the P site of ribosomes hold?

A

holds tRNA with growing polypeptide attached

59
Q

what does the A site of ribosomes hold?

A

holds the aminoacyl tRNA

60
Q

what happens at the active site of a ribosome?

A

location where polypeptide chain is formed

61
Q

what are the 4 types of structural RNA?

A
  1. rRNA
  2. tRNA
  3. snRNA
  4. snoRNA
62
Q

what are the 2 types of regulatory RNA’s?

A
  1. miRNA

2. siRNA

63
Q

which RNA is information containing?

A

mRNA

64
Q

how is nucleic acid melting and annealing used to detect one specific DNA sequence in total cellular DNA?

A

you break the hydrogen bonds between the 2 strands of DNA thus pulling the 2 strands apart. After the DNA is in single strand form it wants to re-anneal with it’s complement. If you have a primer in the solution, you can measure if a certain patient has DNA specific to the primer or specific target that you are interested in.

M2M Biochemistry and molecular biology (19 decks)

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