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Biochem II > 3/4 Structure of Nucleic Acids and synthesis of DNA > Flashcards

3/4 Structure of Nucleic Acids and synthesis of DNA Flashcards

1
Q

What is the quaternary structure for proteins vs Nucleic acids?

A

for proteins it is a complex, for nucleic acids it is an association with histones

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2
Q

which tautomer form is used for base pairing of pyrimidines and purines?

A

keto form is used

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3
Q

what bases are purines and what are pyrimidines?

A

GA are purines, CUT are pyrimidines

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4
Q

What types of bond is between the base and sugar in nucleic acids?

A

glycosidic bond

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5
Q

what type of bond is between the sugar and phosphate backbone in genetic material?

A

phosphodiester bonds

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6
Q

reduction of which carbon on ribose will convert to deoxyribose?

A

2’ C

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7
Q

which carbons of deoxy/ribose takes part in creating the backbone for genetic material?

A

3’ and 5’

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8
Q

which carbon of the sugar is the base added to in nucleic acid?

A

1’

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9
Q

which conformation is the base in relation to the sugar for nucleic acids usually and why?

A

anti due to steric hinderance

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10
Q

what is the difference between nucleotides and nucleosides?

A

nucleosides are only base and sugar while nucleotides are base, sugar and any number of phosphate groups

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11
Q

what ratio does chargaffs rule outline?

A

ratio is [A=T x G=C] = 100% of bases

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12
Q

what is different about GC bonds vs AT bonds?

A

GC bonds are triple and thus closer harder to break while AT bonds are double

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13
Q

Describe the double helix structure of DNA

A

It is a helix with two antiparallel strands that form helixes that result in a major groove and minor groove

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14
Q

What are the forms that the double helix can be in and how are they named

A

Standard is B form with a clockwise(right) direction, A form is usually a DNA-RNA hybrid which is wider and is right handed, Z form is transient left handed form with extremely tight turns with almost no differences in groove size

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15
Q

what is the differences in purpose between RNA and DNA

A

RNA expresses information while DNA retains and passes on information to future generations

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16
Q

What two factors make RNA more unstable than DNA and why

A

2’ OH on ribose and Uracil instead of T, these features can be fixed as in DNA but requires energy so is only done for DNA since its accuracy is more important

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17
Q

How does RNA instability in pH compare to DNA?

A

DNA will only denature by strands but RNA will denature into individual bases in the presence of high pH

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18
Q

How does the subunits of ribosomes between prokaryotes and eukaryotes compare?

A 
prokaryotes= 50S + 30S = 70S
eukaryotes= 60S + 40S = 80S
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19
Q

what ribosomes are the same in both euks and proks

A

5S

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20
Q

What extra ribosome does eukaryotes have that has different genetic information than the nuclear DNA?

A

mitoRNA 55S

21
Q

What are tRNA?

A

they are small RNA forms with a cloverleaf pattern with a CCA sequence that attaches to amino acids and have an anticodon for recognizing translated sequences on mRNA

22
Q

what is the “melting temperature” and how is it calculated?

A

Tm= 69.3+0.41(%G+C)

23
Q

Why does RNA denature into bases while DNA does not for high pH?

A

2’ ribose OH loses an -H in high pH and the oxidized O- breaks the phosphodiester bonds of the backbone

24
Q

what is reannealing

A

AKA hybridizing, is when temp are taken back down below melting and strands of DNA and sometimes RNA can come together and bind at their complementary sequences.

25
Q

How are DNA organized

A

that coil around a core of 8 histones from H2-4 and is linked from histone to another by H1 histone. These strands of chromatin can coil into a larger chromatid which then is paired with a centrosome to form a chromosome

26
Q

how many chromosomes do we have?

A

normal is 23 pairs including a possible mismatched a pair of sex chromosomes

27
Q

How does AZT/cipro work?

A

azt is a antibiotic that binds to bacterial 50S and inhibs protein synth (warning mito DNA is similar), cipro target DNA gyrase

28
Q

how does chemo agents work?

A

ie 5FU are analogues that interferes with the cell replication process and thus slows down tumors more than healthy cells (although high amt of side fx)

29
Q

what are the constituent components of prok DNA replication?

A

DNA pol I-III, helicase, gyrase(topoII), topoisomerase, SSRB, RNAse H, Ligase, RNA primase

30
Q

What are the characteristics of DNA replication?

A

semiconservative and read 3-5 but synthed 5-3, leading and lagging strands with different mechanisms, higher fidelity vs transcription, lagging strands fragments are joined by exonuclease, polymerase and ligase

31
Q

what shape is prok DNA? euk DNA? implications?

A

prok are circular, euks are linear. linear DNA leads to 3’ overhang which requires noncoding telomeres to support them

32
Q

what is DNA pol alpha?

A

primase

33
Q

what is DNA pol beta

A

repair, primer excision

34
Q

What is DNA pol gamma

A

mito DNA synth

35
Q

what is DNA pol delta

A

replication, 3-5 exonuclease, proofreading

36
Q

what is DNA pol epsilon

A

replication, 3-5 exonuclease, proofreading, DNA repair

37
Q

What is DNA pol I

A

replication, repair, primer excision

38
Q

What is DNA pol II

A

DNA repair

39
Q

What is DNA pol III

A

major replicative poly, 3-5 exonuclease for proofreading

40
Q

Which polymerase in euks are responsible for leading and lagging strands?

A

leading strand: pol epsilon

lagging strand: pol gamma

41
Q

What is the significance of the degree of DNA methylation

A

biological marker of strand age

42
Q

What are the two important sources of DNA dmg

A

UV light causing thymine dimers
benz[a]pyrene from smoking causing guanine adducts

both fixed by nucleotide excision repair

43
Q

what enzyme removes the initial base in base excision repair?

A

glycosylase removes the glycosidic bond

44
Q

how do the pol nucleases differ in BER from NER

A

BER- APexo/endo NER-Endo

45
Q

how is the correct template chosen for mismatch repair?

A

mechanism chooses higher methylated strand as correct

46
Q

What are the three genetic recombinations?

A

homologous recombination, nonhomologous translocation (balanced or not), random transposition

47
Q

why is DNA have T and RNA have U when T requires more energy to create?

A

T is more stable than U against deamination

48
Q

why is primase necessary in DNA repair?

A

3’OH is already present

Biochem II (18 decks)

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