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Introductory Biochemistry > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

1
Q

What are some functions of nucleic acids?

A

Information storage, information transmission, catalysis, regulation

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2
Q

What 3 components make up a nucleotide?

A

Nitrogenous base, pentose sugar, phosphates

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3
Q

What are the bases of nucleic acids made of? Are they acidic or basic?

A

Aromatic heterocyclic rings that are planar and rigid, and have hydrophobic faces with polar edges. They are weakly basic

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4
Q

What is the difference between a purine and pyrimidine?

A

Purines are A and G and are a five membered ring fused to a six membered ring. Pyrimidines are C, T and U and are a 6 membered ring

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5
Q

What is a nucleoside?

A

The base and the sugar ring, but no phosphates

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6
Q

What is attached to each of the carbons in the 5 membered sugar ring?

A

The base is attached to the 1’ carbon. The 2’ carbon has an OH attached if the sugar is ribose, and an H if the sugar is deoxyribose. The 3’ carbon has an OH. The 4’ carbon is attached to the 5’ carbon. The 5’ carbon is attached to the phosphate

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7
Q

What type of bonds join phosphates together in a nucleotide?

A

Phosphoanhydride bonds

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8
Q

What type of bonds join nucleotides together?

A

Phosphodiester bonds

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9
Q

Why do nucleic acid strands have directionality?

A

One end has a free 5’ phosphate and the other end has a free 3’ OH

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10
Q

What are the Watson-Crick base pairs?

A

G-C and A-T

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11
Q

Which direction does the DNA double helix turn?

A

Right handed

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12
Q

Why is it important that the helix is held together by non-covalent interactions?

A

The helix needs to be disrupted for the information to be read and transcripted

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13
Q

What is base stacking?

A

The hydrophobic faces of the bases stack up really close together and form hydrophobic interactions to get away from the water

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14
Q

What is the difference between the major groove and the minor groove in DNA?

A

The major groove is deeper and wider than the minor groove

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15
Q

How do DNA binding proteins tell the difference between the major and minor groove of DNA?

A

In the major groove, the edge that faces out looks different for each base pairing. An AT looks different from a TA and a CG looks different than a GC. In the minor groove, AT and TA look the same, and so does CG and GC

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16
Q

Why is the ability to recognize the differences in the bases in the major groove important?

A

It allows proteins to read the sequence of the DNA without opening the helix, so they can bind in the right place

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17
Q

How is DNA compacted into cells?

A

Supercoiling and looping (in prokaryotes) and binding to histones in eukaryotes

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18
Q

What causes DNA to denature?

A

Heat, it disrupts the hydrogen bonds and the base stacking

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19
Q

What happens to DNA when it is denatured?

A

Separates into single strands

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20
Q

Why is it critical that DNA denaturation is reversible?

A

The helix needs to be melted and unwound for the information to be read, but that information still needs to be stored so it needs to go back to the more stable double helix once the information has been read

21
Q

What is hyperchromicity?

A

Monitoring the melting of DNA

22
Q

What is the transition temperature?

A

The temperature where half of the DNA is melted and half is still in the double helix

23
Q

How can we tell if a strand of DNA is denatured?

A

Double stranded DNA absorbs less UV light at 260 nm than single stranded DNA

24
Q

How can the sequence of DNA affect its transition temperature?

A

A sequence with more GC will have a higher melting point

25
Q

Why is RNA unable to form a double helix like DNA?

A

The 2’ OH on the sugar ring

26
Q

What is RNA with enzymatic activity called?

A

Ribozymes

27
Q

How does RNA fold into hairpin structures?

A

Short regions with complementary base pairing within inverted repeat sequences

28
Q

Can RNA only use Watson-Crick base pairs?

A

No, it has more pairings as long as the hydrogen bonds line up. Can pair up G and U, G and A

29
Q

What bases can be found in RNA?

A

A,C,G, U mainly. Some contain modified bases and some have thymine

30
Q

Why is RNA less stable than DNA?

A

The 2’ OH acts as an internal nucleophile that can assist base-catalyzed hydrolysis of a phosphodiester bond to form cyclic nucleotides that break apart the molecule

31
Q

What feature of nucleic acids allows DNA to be copied and transcribed into RNA?

A

Base complementarity

32
Q

What are the building blocks used in the synthesis of DNA?

A

dNTPs - deoxynucleotide triphosphates

33
Q

What are the building blocks used in the synthesis of RNA?

A

NTPs - nucleotide triphosphates

34
Q

When does a nucleotide become a nucleotide residue?

A

When the NTP has lost two of its phosphates from being attached to the growing nucleic acid chain

35
Q

What 3 things does DNA polymerase require to synthesize DNA?

A

A 3’ OH, dNTPs, and a template strand

36
Q

Why does DNA polymerase require a primer to start synthesizing?

A

Needs a 3’ OH to begin, can’t start the strand without that

37
Q

Which strand of DNA contains the coding information?

A

The coding strand/sense strand

38
Q

What strand of DNA doesn’t contain any coding information?

A

The template strand/anti-sense strand. It has complementary base pairing with the coding strand

39
Q

Which strand of DNA does the RNA transcript resemble?

A

The coding strand. The sequence is the same except that all T are replaced with U

40
Q

Which strand does RNA polymerase read to synthesize the RNA transcript? Which direction does it read it in?

A

The template strand is read in the 3’ to the 5’ direction, and the RNA is synthesized 5’ to 3’

41
Q

What is the adaptor molecule that decodes the mRNA to determine which amino acid to add during translation?

A

tRNA, the one with the right anti-codon sequence is the one that will bind to the mRNA

42
Q

What is a tRNA with an amino acid attached called?

A

Amino-acyl tRNA

43
Q

What does the ribosome attach the growing peptide chain to when another amino acid is brought in?

A

The incoming tRNA with the correct anticodon for the next codon on the mRNA

44
Q

What are 8 possible changes to the structure of DNA that can cause mutations?

A
  • Depurination
  • Deamination
  • Single or double strand breaks
  • Base oxidation
  • Thymine dimers
  • Bulky adduct
  • Base mismatch
  • Base alkylation
45
Q

What damage does UV radiation do to DNA?

A

Thymine dimers that distort the DNA double helix and stall replication

46
Q

What damage does ionizing radiation and free radicals do to DNA?

A

Cleavage of the DNA backbone, which causes strand breaks

47
Q

What damage does nitrous acid do to DNA?

A

Causes oxidative deamination and converts a cytosine to a uracil and an adenine to a hypoxanthine

48
Q

Why does DNA use thymine instead of cytosine?

A

So that DNA repair mechanisms can differentiate between a deaminated cytosine and something that is actually supposed to base pair with adenine

Introductory Biochemistry (16 decks)

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