18 - Nucleic Acids I

Question 1

What are some biological roles of nucleic acids?

Answer 1

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

Question 2

How did Watson and Crick propose the DNA structure?

Answer 2

1. Franklin’s X-rays predicted a double helix
2. Chargaff’s rules (A=T, C=G)
3. Chemical structure of each nucleotide

Question 3

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

Answer 3

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

Question 4

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

Answer 4

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

Question 5

What were the implications of the Watson and Crick model?

Answer 5

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

Question 6

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

Answer 6

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

Question 7

What is A DNA?

Answer 7

Dehydrated DNA

Question 8

What is B DNA?

Answer 8

“Standard” DNA

Question 9

What is Z DNA?

Answer 9

A special DNA with high GC and high ionic salt concentrations

Question 10

What is the difference between A DNA and B DNA?

Answer 10

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

Question 11

What is the difference between Z DNA and B DNA?

Answer 11

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

Question 12

What is the significance of the Dickerson dodecamer?

Answer 12

It proved the Watson and Crick model in 1981

Question 13

What is the sequence of the Dickerson dodecamer?

Answer 13

CGCGAATTCGCG

Question 14

What were the results of the Dickerson dodecamer?

Answer 14

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

Question 15

How come the Dickerson dodecamer was good for crystallization?

Answer 15

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

Question 16

What is a nucleoside?

Answer 16

A nitrogenous base plus a sugar

Question 17

What are the names of the nitrogenous bases?

Answer 17

Adenine, cytosine, thymine, guanine, and uracil

Question 18

What is a pyrimidine?

Answer 18

1 ring

Question 19

Which nitrogenous bases are pyrimidines?

Answer 19

Cytosine, thymine, and uracil

Question 20

What is a purine?

Answer 20

2 rings

Question 21

Which nitrogenous bases are purines?

Answer 21

Adenine and guanine

Question 22

What links the nitrogenous base to the sugar?

Answer 22

A glycosidic bond

Question 23

What are the nucleosides in DNA?

Answer 23

Deoxyadenosine, deoxyguanosine, deoxycytidine, and thymidine

Question 24

What are the nucleosides in RNA?

Answer 24

Adenosine, guanosine, cytidine, and uridine

Question 25

Where is the glycosidic bond in a purine?

Answer 25

1'C to 9N

Question 26

Where is the glycosidic bond in a pyrimidine?

Answer 26

1'C to 1N

Question 27

What is a nucleotide?

Answer 27

A nucleoside + phosphate

Question 28

What bond connects the phosphate to a nucleoside?

Answer 28

A phosphoester bond

Question 29

What are some examples of nucleotides?

Answer 29

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

Question 30

What bond connects two nucleotides together?

Answer 30

A phosphodiester bond

Question 31

How is the length of a DNA polymer named?

Answer 31

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

Question 32

What are the properties of the phosphate backbone in DNA?

Answer 32

Phosphate pKa < 1, acid sensitive, base stable

Question 33

What is an exocyclic amine?

Answer 33

An amine not in the ring

Question 34

How is the numbering distinguished in a nucleotide?

Answer 34

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

Question 35

What can be at the termini of a DNA strand?

Answer 35

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

Question 36

What is a lot of nucleic acid chemistry based on?

Answer 36

Hydrogen bonds

Question 37

What are the requirements for an H-bond?

Answer 37

1. Hydrogen with partial positive charge | 2. Source of electron density (lone pair, usually carbonyl or amine)

Question 38

What is a sugar pucker?

Answer 38

Point glycosidic bond/base in a different direction

Question 39

What is the normal sugar pucker in DNA?

Answer 39

51.5 degrees

Question 40

What sugar pucker occurs in A DNA?

Answer 40

C3' endo N pucker

Question 41

What sugar pucker occurs in B DNA?

Answer 41

C2' endo S pucker

Question 42

What is an anti glycosidic bond angle?

Answer 42

Oxygens in pyrimidine is anti

Question 43

What is a syn glycosidic bond angle?

Answer 43

Group is pointed in a different direction

Question 44

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

Answer 44

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

Question 45

What happens when G is Br-ated?

Answer 45

It goes from anti to syn

Question 46

What are most glycosidic bonds in DNA?

Answer 46

Anti (a sin to be syn)

Question 47

What state are the nitrogenous bases at pH = 7?

Answer 47

Deprotonated

Question 48

What higher order structures are seen in DNA?

Answer 48

DNA supercoils

Question 49

What is a supercoil?

Answer 49

A wrapping of a coil

Question 50

When does DNA supercoil?

Answer 50

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

Question 51

What is the packing of DNA?

Answer 51

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

Question 52

What is the significance of DNA supercoiling?

Answer 52

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

Question 53

What secondary structures are present in mRNA?

Answer 53

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

Question 54

What is the stability of RNA?

Answer 54

Phosphate pKa < 1, acid sensitive, base sensitive

Question 55

What does tRNA do?

Answer 55

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

Question 56

Where is the active site of a ribozyme found?

Answer 56

In the hammerhead

Question 57

What are the parts of a tRNA molecule?

Answer 57

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

Question 58

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

Answer 58

The nucleic acids

Question 59

Is DNA acidic or basic and why?

Answer 59

Acidic (hydrophilic) due to the phosphate groups

Question 60

How does DNA and RNA look like?

Answer 60

DNA is a white fiber, RNA is a white power

Question 61

How can DNA be precipitated?

Answer 61

By ethanol (insoluble in organic solvent)

Question 62

How come DNA has UV absorption?

Answer 62

Due to aromatic groups

Question 63

What absorbances are used for nucleic acids and proteins?

Answer 63

Nucleic acids: A260; Proteins: A280

Question 64

Is DNA hypochromic or hyperchromic?

Answer 64

Hypochromic (dsDNA breaks into ssDNA when heated)

Question 65

What is the hyperchromic shift?

Answer 65

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

Question 66

What is the significance of a hyperchromic shift?

Answer 66

It can quantity stability of DNA helix and disruption

Question 67

What is Tm?

Answer 67

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

Question 68

What forces (4) stabilize dsDNA?

Answer 68

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+)