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CHEM 472 Biochem > Final: Chapter 10 - DNA and RNA > Flashcards

Final: Chapter 10 - DNA and RNA Flashcards

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1
Q

What are nitrogenous bases?

A

aromatic nitrogen containing heterocycles

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2
Q

What is a nuceloside?

A

a nitrogenous base linked to a pentose sugar

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3
Q

What are two examples of nucelosides?

A

D-ribose and 2-Deoxy-D-ribose

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4
Q

What is a nucleotide?

A

A phosphate ester of a nucleoside

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5
Q

What is a nucleic acid?

A

linear polynucleotides linked by phosphodiester bridge

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6
Q

What are pyrimidines? Which?

A

smaller nitrogenous bases; cytosine, uracil, and thymine

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7
Q

What are purines? Which?

A

larger nitrogenous bases; adenine guanine

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8
Q

What are three properties of nitrogenous bases?

A

1) electron rich because aromatic with N and O
2) strong UV absorption
3) water insoluble b/c aromatic

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9
Q

What is the difference between uracil and thymine?

A

one methyl group on carbon 5

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10
Q

Which bases are pyrimidines? are they smaller or larger?

A

cytosine, uracil, and thymine; smaller

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11
Q

Which bases are purines? Are they smaller or larger

A

Adenine and Guanine; larger

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12
Q

What kind of bond connects nitrogenous bases and sugars?

A

glycosidic bond

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13
Q

What are the two possible confirmations of a glycosidic bond?

A

beta and alpha

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14
Q

Does a beta glycosidic bond point up or down?

A

up

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15
Q

What configuration are nucleoside glycosidic bonds typically found in?

A

beta

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16
Q

What does anti and syn rotation describe

A

Rotation around a glycosidic bond?

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17
Q

Does syn confirmation mean that nitrogenous base and sugar are stacked or staggered?

A

stacked

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18
Q

Does anti confirmation mean that nitrogenous base and sugar are stacked or staggered?

A

staggered

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19
Q

What is the function of nucleosides?

A

Typically no function besides adenosine

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20
Q

What is the function of adenosine?

A

Produced as a byproduct of ATP usage for energy, accumulates and promotes sleepiness

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21
Q

How does caffeine prevent feeling tired?

A

Blocks adenosine receptors because it has a similar structure

22
Q

What is a nucelotides?

A

nucleoside with a phosphate attached at carbon 5

23
Q

What is the name of a nucleoside containing cytosine?

A

cytidine

24
Q

What is the name of nucleoside containing adenine?

A

adenosine

25
Q

What is the name of a nucleoside containing uracil?

A

uridine

26
Q

What is the name of a nucleoside containing guanine?

A

guanosine

27
Q

Do nucleosides typically reside in anti or syn conformation and why?

A

anti because there is less steric strain

28
Q

Why do nucleotides link to 5’ hydroxyl rather than 2’ or 3’ hydroxyls?

A

Because 5’ is a primary alcohol which is more accessible than a secondary alcohol

29
Q

What are cyclic nucleotides used for?

A

signaling pathways

30
Q

How are cyclic nucleotides formed?

A

Oxygen on phosphate forms ring with 3’ hydroxyl on sugar

31
Q

What are three types of nucleotide reactions?

A

1) hydrolysis
2) functional group transfer
3) nucleic acid synthesis

32
Q

What is a phosphoryl group transfer?

A

transfer of a phosphate group

33
Q

What is a pyrophosphoryl group transfer?

A

transfer of two phosphate groups

34
Q

What is a nucleotide group transfer?

A

transfer of a sugar, phosphate, and nitrogenous base

35
Q

What are three characteristics of nucleic acids?

A

1) Always linked 3’ to 5’ by phosphodiester bonds between phosphates and sugars
2) Highly repetitive sugar phosphate backbone
3) Nitrogenous bases give unique identify to nucleic acids

36
Q

What are Chargaff’s rules?

A

1) cytosine amount should be equal to guanine amount
2) adenine amount should be equal to thymine amount
3) purines amount should be equal to pyrimidine amount

37
Q

What is the Watson and Crick model?

A

Describes DNA as two stranded complementary DNA helix with antiparallel strand that have H-bonding between base pairs

38
Q

How many H-bonds d guanine and cytosine have between them?

A

3

39
Q

How many H-bonds to adenine and thymine have between them?

A

2

40
Q

Why do guanine and cytosine form more H-bonds than adenine and thymine?

A

guanine has a carbonyl that provides an extra H-bond acceptor; adenine does not

41
Q

What is rRNA?

A

A complex secondary structure of RNA that is the primary component of a ribosome

42
Q

How is rRNA characterized?

A

sedimentation coefficients; measure sedimentation velocity in response to centrifugation

43
Q

What is tRNA

A

clover leaf shaped RNA that carries AAs to the ribosome during protein synthesis

44
Q

Why is rRNA structure complex?

A

there is typically base pairing within the strand

45
Q

What is siRNA?

A

short interfering RNA that is complimentary to known RNA and creates double stranded RNA to silence translation

46
Q

Why doesn’t DNA contain uracil?

A

cytosine is likely to deaminate to uracil; if uracil was part of DNA code it would be more difficult to proofread

47
Q

What is the benefit of DNA contain 2-deoxy-D-ribose instead of D-ribose?

A

it is more resistant to alkaline hydrolysis

48
Q

Why does RNA hydrolysis occur? (3 steps)

A

1) in basic conditions the 3’ is deprotonated making it a good nucleophile
2) nucleophilic O attacks electrophilic phosphorus of phosphate
3) phosphate cleaved from 5’ carbon

49
Q

What are two enzymes that perform enzymatic hydrolysis of nucleic acids?

A

1) nucleases
2) restriction endonucleases

50
Q

How can nuclease cleavage vary?

A

Either hydrolyzes 3’ or 5’ side of phosphodiester bond

51
Q

How do endonucleases cleave DNA?

A

identifies specific sequences of DNA and cleaves bond and specific site

CHEM 472 Biochem (12 decks)

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