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MCB 102 > Lecture 1 - Nucleic Acids > Flashcards

Lecture 1 - Nucleic Acids Flashcards

1
Q

What are the functions of nucleotides? (think about the molecules that have them in their structure)

A

Energy for metabolism, Enzyme Cofactors, Signaling pathways

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2
Q

What are the functions of Nucleic Acids?

A

storage of genetic info, transmission of genetic info (mRNA), processing of genetic info (ribozymes), protein synthesis (mRNA and tRNA), regulation (miRNA)

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3
Q

What are nucleotides? structure? draw?

A

has a phosphate group, nitrogenous base, and a ribose sugar

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4
Q

what are nucleosides?

A

has only the nitrogenous base and pentose sugar

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5
Q

what is the nucleobase?

A

has only the nitrogenous base

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6
Q

Describe Pyrimidine bases

A

PyCUT = Pyrimidines, Cytosine, Uracil, Thymine

C is found in both RNA and DNA. U is only found in RNA and T is found only in DNA. Good H-bond acceptors and donors. Neutral at pH7. Almost planar structures that absorb UV light 250-270nm.

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7
Q

Describe Purine bases

A

Pure As Gold = PAG = Purines, Adenine, Guanine

Both are found in DNA and RNA. Both neutral at pH7, planar structures and absorb UV light at 250-270nm.

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8
Q

Nitrogenous bases can often undergo tautomerization. What can this cause? What is the bias towards?

A

Error in DNA synthesis. B-DNA.

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9
Q

What is the difference between deoxyribose and ribose?

A

Ribose has an OH group at the 2nd position while deoxyribose has an H group at the 2nd position.

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10
Q

How many conformations are there in the ribose ring?

A

4

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11
Q

what bond holds the pentose and the nitrogenous base together?

A

beta-N-glycosidic bond

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12
Q

Where is the beta-N-glycosidic bond formed on the nucleotide?

A

N1 for pyrimidines and N9 for purines

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13
Q

What position is the phosphate group attached to the pentose?

A

C5

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14
Q

What position is the nitrogenous base attached to on the ribose?

A

C1

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15
Q

How is the beta-N-glycosidic bond formed? How is it broken?

A

It is formed from the anomeric carbon. It can be broken using acid.

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16
Q

What does Syn and Anti mean?

A

Syn on the same side; Anti on opposite sides

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17
Q

What conformation around the beta-N-glycosidic bond is found most in B-DNA?

A

Anti

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18
Q

Are there any rotations around the beta-N-glycosidic bond?

A

Yes, it’s relatively free rotation. Free rotations around 6 bonds and only around bond 4 there are restrictions.

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19
Q

What are nucleic acids made using?

A

pentose 5’ phosphates like ATP

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20
Q

What is the charge on phosphate groups?

A

negative

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21
Q

Name the nucleoside, and nucleotide for the base (Adenine) and whether they are RNA or DNA. Include shorthand

A

Adenosine and adenylate (RNA), deoxyadenosine and deoxyadenylate (DNA); DNA (A, dA, dAMP - deoxyadenosine-5’-monophosphate), RNA (A, AMP - adenosine-5’-monophosphate)

22
Q

Name the nucleoside, and nucleotide for the base (Guanine) and whether they are RNA or DNA.

A

Guanosine and Guanylate (RNA), deoxyguanosine and deoxyguanylate (DNA); DNA (G, dG, dGMP - deoxyguanosine-5’-monophosphate), RNA (G, GMP - deoxyguanosine-5’-monophosphate)

23
Q

Name the nucleoside, and nucleotide for the base (Thymine and Uracil) and whether they are RNA or DNA.

A

Thymine or deoxythymidine and Thymidylate (RNA) or deoxythymidylate (DNA), Uridine and Uridylate (RNA); DNA (T, dT, dTMP - deoxythymidine-5’-monophosphate), RNA (U, UMP - uridine-5’-monophosphate)

24
Q

Name the nucleoside, and nucleotide for the base (Cytosine) and whether they are RNA or DNA.

A

Cytidine and cytidylate (RNA) deoxycytidine and deoxycytidylate (DNA); DNA (C, dC, dCMP - cytidine-5’-monophosphate), RNA (C, CMP - cytidine-5’-monophosphate)

25
Q

What are minor nucleosides? Examples?

A

Modification of nucleosides after DNA synthesis. 5-methylcytosine is common in eukary and prokary. N6-methyladenosine is common in prokary but not eukary. Their purpose is for epigenetic markering. prokary - marking foreign DNA; eukary - marking active genes.

26
Q

How is Inosine made and what are its functions?

A

A nucleoside created through the deamination of adenosine. It is found on the wobble position of tRNA to help create a richer genetic code.

27
Q

What is pseudouridine? Where is it found and what does it do?

A

It is a nucleoside that is made from the isomerization of uridine during RNA synthesis. It is common in eukary and bacteria. It may stabilize structure of tRNA and help the folding of rRNA in ribosomes.

28
Q

What bonds hold together nucleotides in polynucleotides?

A

covalent bonds called phosphodiester linkages b/w 5’- phosphate and 3’- hydroxyl groups.

29
Q

why is the phosphate-pentose backbone negatively charged?

A

It is negatively charged because of the phosphate groups.

30
Q

why is the phosphate pentose backbone hydrophillic?

A

it’s hydrophillic because the pentose residues can form hydrogen bonds with water

31
Q

Why are the phosphate groups on the backbone ionized at pH7?

A

They have a pKa near 0 they end up with a negative charge.

32
Q

How can the negative charges on the backbone be neutralized?

A

they can be neutralized using ions, polyamines, and positive charges from various sources like proteins.

33
Q

why is RNA more unstable compared to DNA?

A

RNA has an extra OH group at 2’ that can be hydrolyzed in akaline conditions.

34
Q

Do polynucleotides form side chains or branching?

A

No

35
Q

In which direction do we read the polynucleotides?

A

sequence is from 5’ to 3’

36
Q

what base pairs exist in the watson crick model?

A

Purines and Pyrimidines can form hydrogen bonds with each other.

A and T can make 2 H bonds whereas C and G can make 3 H bonds.

37
Q

What are some properties of the watson and crick model?

A

strands have different sequences, they run antiparallel, they are complementary, they have stability due to stacking of the bases.

38
Q

why is water not found inside the helix?

A

packing of DNA doesn’t allow for anything to be inside the helix.

39
Q

what is the min. amount of base pairs for the duplex DNA to be held together?

A

12

40
Q

what is P-electron bonding?

A

it is when atoms share electrons just like in metallic bonds in a sea of electrons

41
Q

why don’t the bases swivel around?

A

Pi-stacking is vertical stacking of bases which prevents them from moving from the base pair. The vertical sharing of electrons allow sharing of the p-electrons from aromatic rings of the bases to create stacking bonds called Zusman slide.

42
Q

What is the evidence that there is pi-stacking?

A

Resulting fluorescence is evidence for vertical bonding due to shared electrons. aromatic dyes that get in b/w the bases shows that there is bonding.

43
Q

Why do aromatic dyes generate a photon in UV light?

A

The dyes can release energy in a photon or heat, but since there is little room in b/w the bases when they are all stacked, which makes a photon release more likely.

44
Q

What is base flipping and what is its purpose?

A

Base flipping is when a base flips out of the helix and can assist the cell in DNA repair and methylation.

45
Q

What are grooves in the backbone?

A

geometry of the base pairs. the edges of each base pair expose hydrogen acceptors and donors that can be recognized through van der vaals forces.

46
Q

what are minor grooves?

A

Minor grooves have similar H bonding patterns

47
Q

what are major grooves?

A

major grooves are sensitive to the identity of base pairs that make it up

48
Q

What properties do all conformations (A,B,Z) of DNA have?

A

strand complementarity, antiparallel strands, AT and CG base pairs

49
Q

What form of DNA is favorable for DNA-RNA or RNA-RNA duplex strands?

A

A form

50
Q

Describe B DNA: helical sense, diameter, base pairs per turn, helix rise per turn, complete turn

A

right handed, 20 angstroms, 10.5 angstroms, 3.4 angstroms, 36 angstroms

MCB 102 (10 decks)

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