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56 Cards in this Set
- Front
- Back
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Who was Friedrich Mischer?
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Swiss biochemist.
*Noticed septic patients had a lot more of a compound with high phosphate content. *Discovered the "nuclein" (DNA) in WBCs |
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What did Griffith contribute to the study of DNA?
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In 1928, Griffith discovered that genetic information could be passed from one bacteria to another; "transforming" principle
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What did Avery and MacLeod and McCarty contribute?
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Transforming material was pure DNA, not protein, lipid or carbs
*Worked with Drosophilia |
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What did Watson and Crick contribute to the study of DNA?
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It's structure!
*No actual experiments, looked at other people's data |
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What are the components of DNA?
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DNA is a polymer of nucleotides
*Pentose sugar *Purine or pyrimidine (nitrogenous base) attached to 1C * Phosphate (attached to 5C) |
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What type of bond forms between phosphate and pentose?
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Phosphoester
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What is a nitrogenous base + pentose sugar called?
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Nucleoside
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What is the bond between pentose and base called?
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N-beta-glycosyl bond
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What are the components of nitrogenous bases?
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* Ring structure
*Heterocyclic (2N, 4C) *Hydrophobic *Planar *Exists in 2 tautomeric forms *Strongly absorbs in UV range *Purine or pyrimidine |
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How can you tell the difference between purine and pyrimidine?
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Small name= big structure (2 rings)
Big name= small structure (1 ring= pyrimidine) |
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What are the 5 nitrogenous bases?
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Adenine, Guanine; Cytosine, Thymine, Uracil (RNA)
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What are the characteristics of a pentose sugar?
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*Heterocyclic
*Furanose (closed, 5C ring) *Hydrophillic *Non-planar |
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Why is a pentose sugar NON-PLANAR, but a base is planar?
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No double bonds in pentose sugar, so it is slightly puckered
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What are the 3 conformations of pentose sugar?
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2,2 endo
3,3 exo 2 endo, 3 exo |
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What are the 2 conformations of base and sugar?
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Anti (opposite) and syn (same side)
Syn conformation only happens in certain conditions |
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What links nucleotides?
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Phosphodiester bond
Deprotonated hydroxyl on pentose ring attacks alpha phosphoryl group (DNA polymerase facilitates) This is a type of metal-ion and acid-base catalysis (Asp residues and Mg2+ are in the active site) *Diphosphate is released |
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Where are phosphodiester bonds formed?
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3' end
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What constitutes the backbone?
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Phosphate+ Sugar
The backbone is hydrophillic |
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True or False: Nucleotides are planar
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TRUE. They roject out of plane on axis of backbone.
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Who discovered the structure of DNA?
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Rosalind Franklin via X-ray diffraction analysis.
*She noticed that 2 chains crossed each other |
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What is the Watson Crick model of DNA?
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*Each DNA molecule has 2 helical polynucleotides
*R-handed double helix *Hydrophillic backbone of alternating deoxyribose and phosphate *C-2 endo deoxyribose *Bases are hydrophobic and stacked away from water *Bases are perpendicular to the helical axis *Major and minor groove *Antiparallel *Complementary *3.4A minor periodicity (between two adjacent bp), 34A major periodicity, one complete turn with 10 bases |
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Why the helical conformation?
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It minimizes the exposure of the bases to water
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How many bases are there per turn?
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10.5 /turn
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What is the translational rise?
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3.4A
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What is the pitch?
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36A
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What is Chargraff's Rule?
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A pairs with T, C pairs with G
DNA from different tissues of the same species have the same base composition DNA base composition does not change with age, nutritional state, or change altered environment |
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True or False: Bases are directly in the center of DNA?
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FALSE. Bases lie more to one side. This is due to major and minor groove
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How many H bonds do G-C have? A-T?
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3 for GC, 2 for AT
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What type of DNA is found in cells?
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B-form DNA (10.5 bp/turn)
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What is the distance between a purine and pyrmidine bonded?
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20A
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What forces affect the stability of the DNA double helix?
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Hydrophobic interactions- stabilize inside
Stacking Interactions- these are VDW forces H-bond: facilitates stacking |
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What destabilizes DNA?
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Electrostatic interactions (due to the negative phosphate). These can be neutralized by positive charged Na+ or proteins
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What are the 3 forms of DNA?
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A-form (R-handed, in ethanol, 2.6A between bp)
B-form (R-handed, in cells) Z-form (L-handed, more elongated, less diameter |
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What is the purpose of minor types of DNA structure?
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Z-like structure observed where transcription starts
Runs of multiple G are A-like Structural variations play a role in DNA-protein interactions |
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What is a palindrome? What is a mirror repeat?
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Palindrome= 2 fold symmetry on different strands
Mirror repeat= 2 fold symmetry on same strand. |
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What is a hairpin? What is a cruciform?
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A bend in the DNA causes complementary bp to bind.
A cruciform is 2 hairpins. |
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What is a triple helix? What type of bonding occurs? Why does it occur?
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2 polypeptides are bound. The third is bound to the helix by a Hoogstein base pair.
It occurs to regulate transcription (prevent it) |
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When does a tetraplex occur?
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When there are a series of guanine residues, which make the DNA twist and it gets stabilized.
It is found at the end of the chromosome by telomers |
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What does monocistronic mean? Where are these found? What does polycistronic mean?
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Monocistronic= 1 gene encoding for polypeptide. Mostly in eukaryotes.
Polycistronic= multiple genes encoding for a protein. These are mostly in prokaryotes. |
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What are hte classes of RNA?
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1. mRNA
2. tRNA 3. rRNA 4. siRNA 5. miRNA 6. Ribozymes |
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What is the secondary structure of RNA?
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Single Strand
*Can fold onto self to form a double helix (if it does, it forms A-form, R-handed) |
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Which bp denature first?
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A-T (because only 2 H bonds).
*Unwinding is cooperative |
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What is hyperchromisity?
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denatured DNA absorbs more UV
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What is hypochromisity?
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A decrease in absorbance due to renaturation of DNA
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How many steps are in renaturation?
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2. The first is the RDS, which is second order of finding complementary sequence to nucleate base pairing.
The second is faster, zippering reaction to form long molecules |
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What can mutgens do to bp?
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Thymine dimers! Mutation
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What level of structure is supercoiling?
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Tertiary
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When does supercoiling occur?
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When two strands are constrained in any way
2 ends of the DNA need to be anchored or fixed (either to a scaffold or to eachother) |
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What is the difference between R and L-handed supercoiling?
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Right-handed= + Supercoiling (OVERWOUND)
Left-handed= - Supercoiling (UNDERWOUND) |
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What is the linking number?
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Lk= Tw+ Wr
Tw= number of times two strands pass each other in a double helix Wr= number of times the double helix pass each other in supercoiled DNA |
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What does a negative supercoil mean for writhe?
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NEGATIVE WRITHE
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If a relaxed DNA had Lk=200 and delta Lk=2, what type of supercoil?
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POSITIVE. It would be 200+2=202
If delta Lk was -2, Lk= 198, and would be a negative supercoil. |
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How can you tell the difference between + and - supercoil experimentally?
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Run in a 2-D gel electrophoresis.
Increase the number of supercoils, the DNA moves faster |
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What is the purpose of supercoiling during transcription
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Helps determine transcription direction
+ Supercoils occur ahead of RNA polymerase. Topoisomerase remove these supercoils |
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What are DNA topoisomerases?
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Enzymes that remove supercoils from DNa and control the degree of supercoiling in the cell
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What are the two types of topoisomerases?
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I. Type 1
-breaks one of the strands, pass unbroken through it, rejoins strand. It changes Lk by 1 No ATP required II. Type 2 ATP required Both strands are broken. Changes Lk by 2 |
