Chapter 6

Question 1

Who proposed the correct structure of DNA first?

Answer 1

James Watson & Francis Crick

Question 2

Who provided the experimental data to prove the structure of DNA?

Answer 2

Rosaland Franklin’s X-ray diffraction suggested that DNA has a helical structure, which helped Watson and Crick develop the DNA model

Question 3

What are purines and pyrimidines?

Answer 3

Purines (two rings)
- Guanine
- Adenine

Pyrimidines (one ring)
- Cytosine
- Uracil
- Thymine

Question 4

Nucleic acids are synthesized in which direction?

Answer 4

5’ -> 3’

• POLYMERASE CAN ONLY ADD TO 3’ END

Question 5

What does deoxyribose mean?

Answer 5

Deoxyribose = Ribose sugar without O on 2’ Carbon (just H instead of OH, as in RNA)

Question 6

What are Tautomers?

Answer 6

Structural (constitutional) isomers that can interconvert in a rapid equilibrium. They occur when an isomer differs in the placement of a hydrogen due to protons and bonds shifting on a molecule.

-> One form
is predominant at physiological
pH.

Question 7

How do tautomers relate to DNA?

Answer 7

Tautomers can form among each of the DNA bases (A, T, G, C), resulting in different H bonds between pairs of bases

examples (BASE* = tautomer)
C-A
T-G
A-C
G-T

Question 8

What is the result of atypical base pairing? (tautomeric shifts)

Answer 8

MUTATIONS as DNA is replicated

Question 9

How does Base Stacking play a role in the structure of DNA?

Answer 9

Base Stacking in nucleic acids is favored due to hydrophobic, van der Waals, and electrostatic interactions within a polynucleotide chain.

Question 10

Why is base stacking more favorable than no base stacking?

Answer 10

Base stacking is more stable and reduces energy required to keep DNA together, whereas

Question 11

How did Erwin Chargaff’s contributions play a role in Watson and Crick’s model?

Answer 11

1:1 RATIOS between G-C and A-T: The base composition of DNA generally varies from one species to another (G+C content remains same within a species) but does not change with age, nutritional state, or environment.

Question 12

Why is DNA the primary information molecule?

Answer 12

Because it’s much more stable than RNA, easy to replicate, and its coding system allows it to code for many amino acids.

Question 13

Besides structure of DNA, what else did Watson and Crick’s model help us understand?

Answer 13

DNA REPLICATION!

Question 14

What are Palindromes? How do they affect the structure of DNA and RNA?

Answer 14

Sequences that are mirrored (the same backwards and forwards)

Short palindromes, under 50 bp, prevent DNA degradation, while palindromes longer than 50 bp result in mutations and DNA instability.

• A long palindrome has the unique ability to fold back onto itself to form a secondary structure called a cruciform or hairpin

Question 15

What are Cruciforms in DNA?

Answer 15

Both DNA strands forming a hairpin structure, due to indirect sequence repeats

Question 16

What forces hold the DNA strands together?

Answer 16

Hydrogen bonds between bases

Question 17

How can we denature (separate) DNA strands? What is the opposite of denaturation?

Answer 17

Increase temperature or change Ph! Opposite of denaturation is “Annealing”

Question 18

Which denaturation methods are reversible?

Answer 18

• increasing temperature
• changing Ph (NOT FOR RNA)

Question 19

What is the “melting point” (Tm) of DNA?

Answer 19

The temperature at which half of the DNA is denatured.

Question 20

What leads to variations in the melting point?
Will G-C base pairs or A-T base pairs be denatured first?

Answer 20

The amount of H bonds:
* A-T base pairs have 2 H bonds
* G-C base pairs have 3 H bonds

Question 21

How do we perform cross-species hybridization?

Answer 21

By denaturing DNA with increased temperature then allowing complementary strands (from different DNA) to form duplexes (red + blue)

Question 22

What are Southern and Northern blots? What is the procedure to perform one?

Answer 22

1. Run the nucleic acid sample on an agarose gel to separate by size
2. Transfer to nitrocellulose membrane
3. Hybridize with labeled nucleic acid probe
4. Use autoradiogram or other detection method to see the bands (shows which fragments annealed with probe)

Question 23

What are southern blots used for?

Answer 23

Detecting specific DNA sequences if our sample is unknown USING DNA PROBE (ex: diagnose diseases, forensic testing, paternity testing)

Question 24

What are northern blots used for?

Answer 24

Detecting specific RNA sequences if our sample is unknown USING DNA PROBE (ex: for studying gene expression)

Question 25

What are western blots used for?

Answer 25

Detecting specific PROTEINS USING ANTIBODIES as probes

Question 26

What is the difference between DNA and RNA nucleotides? Which is more susceptible to high pH levels, DNA or RNA?

Answer 26

RNA is more susceptible to hydrolysis than DNA since the 2′OH group, present only in RNAs, can interact with the phosphate group, which results in breaking up of the bonds through transesterification.

Question 27

What kind of macromolecule is ATP made out of? (Hint: what does ATP stand for?)

Answer 27

Adenosine (nucleoside) Triphosphate

(nucleotide base + 5-carbon sugar = nucleoside) + 3 phosphate groups

Question 28

How do Mg^2+ (magnesium) or K^+ (potassium) ions stabilize RNA structure at specific sites?

Answer 28

RNA backbone is negative, so these positive ions help to stabilize the charge.

Question 29

What are the different consequences between DNA and RNA base pair modifications?

Answer 29

If a DNA base is changed, it will have much many more long-term consequences, whereas abnormal changes in RNA bases doesn’t have long-term or permanent affects