Chapter 6 Flashcards
Who proposed the correct structure of DNA first?
James Watson & Francis Crick
Who provided the experimental data to prove the structure of DNA?
Rosaland Franklin’s X-ray diffraction suggested that DNA has a helical structure, which helped Watson and Crick develop the DNA model
What are purines and pyrimidines?
Purines (two rings)
- Guanine
- Adenine
Pyrimidines (one ring)
- Cytosine
- Uracil
- Thymine
Nucleic acids are synthesized in which direction?
5’ -> 3’
- POLYMERASE CAN ONLY ADD TO 3’ END
What does deoxyribose mean?
Deoxyribose = Ribose sugar without O on 2’ Carbon (just H instead of OH, as in RNA)
What are Tautomers?
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.
How do tautomers relate to DNA?
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
What is the result of atypical base pairing? (tautomeric shifts)
MUTATIONS as DNA is replicated
How does Base Stacking play a role in the structure of DNA?
Base Stacking in nucleic acids is favored due to hydrophobic, van der Waals, and electrostatic interactions within a polynucleotide chain.
Why is base stacking more favorable than no base stacking?
Base stacking is more stable and reduces energy required to keep DNA together, whereas
How did Erwin Chargaff’s contributions play a role in Watson and Crick’s model?
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.
Why is DNA the primary information molecule?
Because it’s much more stable than RNA, easy to replicate, and its coding system allows it to code for many amino acids.
Besides structure of DNA, what else did Watson and Crick’s model help us understand?
DNA REPLICATION!
What are Palindromes? How do they affect the structure of DNA and RNA?
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
What are Cruciforms in DNA?
Both DNA strands forming a hairpin structure, due to indirect sequence repeats
What forces hold the DNA strands together?
Hydrogen bonds between bases
How can we denature (separate) DNA strands? What is the opposite of denaturation?
Increase temperature or change Ph! Opposite of denaturation is “Annealing”
Which denaturation methods are reversible?
- increasing temperature
- changing Ph (NOT FOR RNA)
What is the “melting point” (Tm) of DNA?
The temperature at which half of the DNA is denatured.
What leads to variations in the melting point?
Will G-C base pairs or A-T base pairs be denatured first?
The amount of H bonds:
* A-T base pairs have 2 H bonds
* G-C base pairs have 3 H bonds
How do we perform cross-species hybridization?
By denaturing DNA with increased temperature then allowing complementary strands (from different DNA) to form duplexes (red + blue)
What are Southern and Northern blots? What is the procedure to perform one?
- Run the nucleic acid sample on an agarose gel to separate by size
- Transfer to nitrocellulose membrane
- Hybridize with labeled nucleic acid probe
- Use autoradiogram or other detection method to see the bands (shows which fragments annealed with probe)
What are southern blots used for?
Detecting specific DNA sequences if our sample is unknown USING DNA PROBE (ex: diagnose diseases, forensic testing, paternity testing)
What are northern blots used for?
Detecting specific RNA sequences if our sample is unknown USING DNA PROBE (ex: for studying gene expression)
