Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

CHE 541 > 18 - Nucleic Acids I > Flashcards

18 - Nucleic Acids I Flashcards

1
Q

What are some biological roles of nucleic acids?

A

Virus infection, nucleic processes (replication, transcription), and translation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

How did Watson and Crick propose the DNA structure?

A
  1. Franklin’s X-rays predicted a double helix
  2. Chargaff’s rules (A=T, C=G)
  3. Chemical structure of each nucleotide
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What were the contributions of Watson and Crick to the DNA model?

A

Crick developed theory for X-ray diffraction of helices, while Watson built models

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What was the “average DNA” model proposed in 1953?

A

Anti-parallel, right handed, double helix with H bonds base pairs on inside and sugar-phosphate backbone on outside

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What were the implications of the Watson and Crick model?

A

Complementary strands suggested mechanisms of replication, heredity, and recognition (3’ to 5’ polarity)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What was Rosalind Franklin’s contribution to the 1953 model?

A

X-ray diffraction, showed helix with symmetry (10 bp/repeat, 3.4 A between base pairs) (photo 51)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is A DNA?

A

Dehydrated DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is B DNA?

A

“Standard” DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is Z DNA?

A

A special DNA with high GC and high ionic salt concentrations

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is the difference between A DNA and B DNA?

A

A DNA has a greater tilt, and the center of the helix is free, and it is shorter and wider

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is the difference between Z DNA and B DNA?

A

Z DNA is a left handed helix, and is more stretched out

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is the significance of the Dickerson dodecamer?

A

It proved the Watson and Crick model in 1981

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is the sequence of the Dickerson dodecamer?

A

CGCGAATTCGCG

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What were the results of the Dickerson dodecamer?

A

B-DNA, not a straight rod, had sequence dependent characteristics, water bound on outside

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

How come the Dickerson dodecamer was good for crystallization?

A

It was self complementary (had same conformation for good crystallization), and has GCs at the end to help prevent fraying (3 H-bonds)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is a nucleoside?

A

A nitrogenous base plus a sugar

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What are the names of the nitrogenous bases?

A

Adenine, cytosine, thymine, guanine, and uracil

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What is a pyrimidine?

A

1 ring

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Which nitrogenous bases are pyrimidines?

A

Cytosine, thymine, and uracil

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What is a purine?

A

2 rings

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Which nitrogenous bases are purines?

A

Adenine and guanine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What links the nitrogenous base to the sugar?

A

A glycosidic bond

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What are the nucleosides in DNA?

A

Deoxyadenosine, deoxyguanosine, deoxycytidine, and thymidine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What are the nucleosides in RNA?

A

Adenosine, guanosine, cytidine, and uridine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Where is the glycosidic bond in a purine?

A

1’C to 9N

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Where is the glycosidic bond in a pyrimidine?

A

1’C to 1N

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What is a nucleotide?

A

A nucleoside + phosphate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What bond connects the phosphate to a nucleoside?

A

A phosphoester bond

29
Q

What are some examples of nucleotides?

A

AMP, dADP, ATP, cAMP, NAD+, etc.

30
Q

What bond connects two nucleotides together?

A

A phosphodiester bond

31
Q

How is the length of a DNA polymer named?

A

As an “n-mer”, where n is the number of nucleotides

32
Q

What are the properties of the phosphate backbone in DNA?

A

Phosphate pKa < 1, acid sensitive, base stable

33
Q

What is an exocyclic amine?

A

An amine not in the ring

34
Q

How is the numbering distinguished in a nucleotide?

A

Regular numbering on the base, prime numbering on the ribose sugar

35
Q

What can be at the termini of a DNA strand?

A

A hydroxyl, a phosphate, or something else (solid surface, sugar, etc.)

36
Q

What is a lot of nucleic acid chemistry based on?

A

Hydrogen bonds

37
Q

What are the requirements for an H-bond?

A
  1. Hydrogen with partial positive charge

2. Source of electron density (lone pair, usually carbonyl or amine)

38
Q

What is a sugar pucker?

A

Point glycosidic bond/base in a different direction

39
Q

What is the normal sugar pucker in DNA?

A

51.5 degrees

40
Q

What sugar pucker occurs in A DNA?

A

C3’ endo N pucker

41
Q

What sugar pucker occurs in B DNA?

A

C2’ endo S pucker

42
Q

What is an anti glycosidic bond angle?

A

Oxygens in pyrimidine is anti

43
Q

What is a syn glycosidic bond angle?

A

Group is pointed in a different direction

44
Q

What is the significance of a syn/anti glycosidic bond?

A

Different orientation relative to ribose structure, so different functionalities for H-bonding and major/minor groove

45
Q

What happens when G is Br-ated?

A

It goes from anti to syn

46
Q

What are most glycosidic bonds in DNA?

A

Anti (a sin to be syn)

47
Q

What state are the nitrogenous bases at pH = 7?

A

Deprotonated

48
Q

What higher order structures are seen in DNA?

A

DNA supercoils

49
Q

What is a supercoil?

A

A wrapping of a coil

50
Q

When does DNA supercoil?

A

When locally unwinding DNA (gene expression), and packaging at nucleosomes

51
Q

What is the packing of DNA?

A

DNA –> beads on a string –> chromatin fiber –> condensed scaffold –> chromosome

52
Q

What is the significance of DNA supercoiling?

A

It was a significant problem to overcome for crystal structure of nucleosomes (get ordered crystal)

53
Q

What secondary structures are present in mRNA?

A

Stem and loop (local helical structure with single strand connections)

54
Q

What is the stability of RNA?

A

Phosphate pKa < 1, acid sensitive, base sensitive

55
Q

What does tRNA do?

A

It recognized both the code (mRNA) and protein (amino acid)

56
Q

Where is the active site of a ribozyme found?

A

In the hammerhead

57
Q

What are the parts of a tRNA molecule?

A

Amino acid attachment site, T-phi-C loop, variable arm, anticodon loop, DHU loop, and phosphorylated 5’ terminus

58
Q

Where do most of the catalytic activity in ribosomes come from?

A

The nucleic acids

59
Q

Is DNA acidic or basic and why?

A

Acidic (hydrophilic) due to the phosphate groups

60
Q

How does DNA and RNA look like?

A

DNA is a white fiber, RNA is a white power

61
Q

How can DNA be precipitated?

A

By ethanol (insoluble in organic solvent)

62
Q

How come DNA has UV absorption?

A

Due to aromatic groups

63
Q

What absorbances are used for nucleic acids and proteins?

A

Nucleic acids: A260; Proteins: A280

64
Q

Is DNA hypochromic or hyperchromic?

A

Hypochromic (dsDNA breaks into ssDNA when heated)

65
Q

What is the hyperchromic shift?

A

When dsDNA –> ssDNA, A260 (extinction coefficient) changes

66
Q

What is the significance of a hyperchromic shift?

A

It can quantity stability of DNA helix and disruption

67
Q

What is Tm?

A

Melting temperature: temperature at which 1/2 of FNA is separated into single strands

68
Q

What forces (4) stabilize dsDNA?

A
  1. Hydrophobic effect (purines and pyrimidines buried in interior)
  2. Stacking (VDW, pi stacking of aromatic rings)
  3. H-bonds (between base pairs)
  4. Electrostatics (negatively charged phosphates and cations like Mg2+)

CHE 541 (20 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions