Ch. 6 DNA and RNA Structure Flashcards

1
Q

What are the roles of nucleotides in cells (3)?

A

Nucleotides form nucleic acids, are in energy related molecules (ATP, GTP, NAD⁺, NADP⁺, FAD), and are in signaling molecules (cAMP, cGMP).

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2
Q

Why is the presence of an OH group on the 2’ carbon of ribose of note?

A

It makes ribonucleotides more reactive and therefore less stable.

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3
Q

What effect does the sugar identity have on the backbone of nucleic acids?

A

The slightly different ring conformation of ribose vs deoxyribose affects DNA and RNA backbones.

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4
Q

What are nucleotides linked by and what does this linkage produce?

A

Nucleotides are linked by phosphodiester bonds to form nucleic acids. This linkage produces a 5’ → 3’ direction.

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5
Q

What should you assume the direction of an unlabeled nucleotide sequence is?

A

Assume the left is 5’ and the right is 3’.

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6
Q

Is the phosphate-sugar backbone hydrophobic or hydrophilic, and what does this allow for?

A

The phosphate-sugar backbone is hydrophilic and H-bonds to water.

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7
Q

What does the 2’ OH of RNA do that DNA does not?

A

The 2’ OH of RNA allows it to rapidly hydrolyze in certain conditions; DNA does not.

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8
Q

What does the presence of RNA’s 2’OH mean for storage?

A

RNA is “temporary” while DNA is more “permanent”.

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9
Q

Are bases hydrophobic or hydrophilic, and what does this allow them to do?

A

Bases are hydrophobic and associate more closely with each other putting them in the same plane. This is called hydrophobic stacking.

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10
Q

How do bases interact with each other?

A

Bases of one nucleic acid can interact with the bases of another nucleic acid through base pairing. Base pairing is via H-bonds (A=T and C≡G).

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11
Q

How does DNA usually exist in the cell?

A

It is usually a right-handed double helix with consistent featues.

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12
Q

What are the consistent features of the DNA right-handed double helix in cells (4)?

A
  1. Major and minor groove present in helix
  2. Antiparallel and complementary strands that allow for replication
  3. ~10 bases per turn
  4. Hydrophobic stacking of bases and various noncovalent forces make the double helix very stable
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13
Q

Why is the DNA helix flexible (4)?

A

The helix is flexible due to bond rotation, thermal fluctuation, localized unpairing of strands, and other factors.

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14
Q

What is the Watson and Crick form of the DNA helix?

A

The B-form. It is the most stable under physiological conditions.

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15
Q

What are the two variant forms of DNA?

A

A form DNA and Z form DNA.

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16
Q

How to these variant forms of DNA differ from B form (broadly and 4)?

A

They very in helix diameter, bases per turn, base tilt, sugar structure, and more.

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17
Q

What is the structure of A form DNA (4)?

A

It is a right-handed helix, a wider helix than B form, the base pairs are more tilted, and the major grooves are deeper while the minor grooves are shallower?

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18
Q

When and where does A form DNA occur?

A

A form DNA occurs in dehydration conditions, but is NOT known to occur in cells.

19
Q

What is the structure of Z form DNA (3)?

A

It is a left handed helix, has a zig-zag backbone pattern, and has more bases per turn.

20
Q

What causes Z form DNA?

A

It is caused by certain base pairs.

21
Q

Where does Z form DNA occur?

A

It is normally found in certain parts of a chromosome, but the function is unclear.

22
Q

What are A tracts?

A

A base sequence pattern in DNA that cause DNA bending.

23
Q

What are DNA palindromes?

A

A base sequence pattern that are the same forwards and backwards. They serve as protein recognition sites.

24
Q

What are inverted repeats?

A

A base sequence pattern that has inverted repeats that are complementary and lead to secondary structure.

25
Q

Where are inverted repeats normally found?

A

They are more common in RNA, but can occur in both RNA and DNA.

26
Q

What can the secondary structure formed by these base sequence patterns do?

A

They can inhibit transcription, translation, etc.

27
Q

What is the structure of RNA and what can it lead to?

A

RNA is single stranded, but regions of the strand can base pair to form secondary structure.

28
Q

What orientation will base paired regions of RNA have?

A

Base paired regions of RNA will be antiparallel.

29
Q

If RNA secondary structure produces a helix, what form will it be?

A

RNA will usually be an A form helical structure because of the ribose ring structure and OH group.

30
Q

What odd base pairing can occur in RNA due to ribose’s properties?

A

RNA can have A=A pairing and G=U pairing.

31
Q

What does the structure of RNA (odd base pairing and secondary structure, etc.) result in?

A

As a result, there is greater structural variety of RNA, which allows for the many functions of RNA.

32
Q

How can double stranded nucleic acids be denatured? Renatured?

A

Double strands can be denatured (melted) by heat or pH. They can renature (anneal) when returned to physiological conditions.

33
Q

What does higher GC DNA mean?

A

Higher GC DNA denatures at higher temperatures because there are more H-bonds.

34
Q

What kinds of duplexes can form upon renaturation (annealing)?

A

RNA duplexes and RNA:DNA duplexes can form.

35
Q

List the melting temperatures of the following from lowest to highest… dsRNA, dsDNA, and RNA:DNA hybrids.

A

Lowest… dsDNA
Intermediate… RNA:DNA hybrids
Highest… dsRNA

36
Q

How can nucleic acids of different species hybridize?

A

The nucleic acids of different species can hybridize IF they are complementary, and will indicate that similar sequences are present.

37
Q

What does hybridization allow for research wise?

A

Hybridization allows for the detection of a gene’s DNA or RNA in a species using a labeled probe.

38
Q

How does hybridization work in a lab?

A

It utilizes gel electrophoresis to separate fragments, transfers the nucleic acid to a membrane, and allows the labeled probe to base pair to a nucleic acid in the membrane.

39
Q

What is southern blotting?

A

A hybridization technique that is used to detect DNA.

40
Q

What is northern blotting?

A

A hybridization technique that is used to detect RNA.

41
Q

What do spontaneous changes in nucleotides lead to?

A

Nucleotides can undergo spontaneous changes that lead to mutations.

42
Q

How does deamination of cytosine effect cells?

A

The deamination of cytosine produces uracil. This might occur ~100 times a day in a cell. This is likely why DNA evolved to use thymine, because the presence of uracil indicates an error.

43
Q

What is base methylation?

A

It is the addition of a methyl group to a base. It is common and related to regulating gene expression.