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**Molecular Set 2
Exam 1
| Question | Answer |
|---|---|
| What are nitroogenous bases? | they are the purines and pyrimidines |
| list the purines | adenine and guanine |
| list the pyrimidines | cytosine and thymine |
| can nucleic acids can contain one of two types of sugars | yes |
| where is ribose found | in RIBOnucleic acid (RNA) |
| where is deoxyribose found | DEOXYRIBOnucleic acid (DNA) |
| what is the difference between RNA and DNA | The hydroxyl group as C-2 in ribose is absent in deoxyribose |
| the nucleoside (RNA) name for the base of Adenine | Adensoine |
| the nucleoside (RNA) name for the base of Guanine | Guanosine |
| the nucleoside (RNA) name for the base of Cytosine | Cytidine |
| the nucleoside (RNA) name for the base of Uracil | Uridine |
| the nucleoside (RNA) name for the base of Thymine | no usually found |
| the deoxynuceoside (DNA) name for the base Adenine | deoxyadenosine |
| the deoxynuceoside (DNA) name for the base Guanine | deoxyguanosine |
| the deoxynuceoside (DNA) name for the base Cytosine | deoxycytidine |
| the deoxynuceoside (DNA) name for the base Uracil | not usually found |
| the deoxynuceoside (DNA) name for the base Thymine | deoxythymidine |
| dAMP | Deoxyadenosine-5’-monophosphate |
| dADP | Deoxyadenosine-5’-diphosphate |
| dATP | Deoxyadenosine-5’-triphosphate |
| what is the difference in the ends of DNA | there is a free phosphate group on the 5' end there is a free hydroxyl group on the 3' end |
| composition of DNA in moles | base per mole of phosphate |
| what happens when you link phosphodiester bonds together | you get dinucleotides or trinucleotides |
| what are the complement base pairs and how many hydrogen bonds do each pair have | A-T base pairs have 2 hydrogen bonds G-C base pairs have 3 hydrogen bonds |
| what is the DNA structure represented in the Watson and Crick structure | the B form of DNA |
| what conditions is the sodium salt of DNA under to give B form of DNA | relatively high humidity (92%) |
| what is the common form of DNA in most cells | B form |
| in the B form, how are the base pairs formed | perpendicular to the helical axis |
| how many BP per helical turn in the B form | 10BP |
| what is the pitch of the B form of DNA | 34 A. |
| what is a pitch | 1 turn of the helix |
| what happens when the humidity of surrounding DNA is reduced to 75% | the sodium salt of DNA is in the A form |
| how many degrees are teh BP tilted in the A form | 20 degrees from horizontal |
| how many BP per helical turn is in the A form | 11 BP |
| what is the pitch of the A form | 28A |
| what is the DNA form in the DNA-RNA hybrid | A form |
| what is the difference of Z form of DNA | it is left handed and composed of alternating purines and pyimidines. |
| is the function of Z form of DNA known | no |
| what is the pitch in the Z form | 46A |
| how many residues per helical turn in the Z form | 12 |
| what is the inclination of the Z form | 9 degrees |
| how does denaturing of DNA occur? | by heating, the presence of organic solvents or by high pH |
| what happens when DNA is denatured | the conditions disrupt the hydrogen bonds between DNA strands |
| what happens when salt concentration in the solution is lowered in DNA | it aids in denaturing because the cations are removed that shield the the negative charge on the DNA strands from each other. |
| protein denaturing | fully unfolded protein is forced to unfold and usually then it could never be able to fold back. |
| Can DNA renature | yes |
| denaturing of repulsive forces of the negative charges on the DNA can denature during | low temperatures |
| what is another name for DNA denaturing | DNA melting |
| DNA melting | occurs when the two strands come apart |
| Melting Temperature | the temp at which the DNA strands are HALF denatured |
| how is strand separation measured | by the absorbance of the DNA solution at 260nm. The nucleic acid absorbs light at the wavelength due to the structural properties on the bases. |
| when two DNA strands come together what happens to the absorbency? | the proximity of the bases reduces some of the absorbance properties |
| what is the phenomenon known for the absorbency of bases due to the structural properties of bases at certain temperatures? | Hyperchromic Shift |
| what particular content of DNA has significant effect on DNA stability, Tm and density? | the GC content of DNA |
| what is the relationship between Tm and density with respect with GC content and why? | a lineal relationship. As GC content increase then Tm and density increases. this is due to the Hydrogens |
| how much naturally occurring GC content is there in DNA? | 22%-73% |
| which hydrogen in particular has effect on Tm | the 3rd hydrogen bond that exits between G and C |
| what is the term for renaturing of DNA strands? | Annealing |
| what are the three major factors that contribute to Renaturing efficiency? | Temperature, DNA concentration, Time |
| what is the best temperature for renaturing to occur? | -25 degrees C |
| what is -25 degrees C good for renaturing? | It is low enough that is doesn't promote melting but high enough to allow rapid diffusional movement of DNA and weaken transient bonding between sequence mismatches. |
| what does RAPID COOLING do? | aids in denaturing which prevent DNA to renature |
| what is quenching | the process of rapid cooling of DNA to prevent renaturing. |
| what is the relationship between DNA concentration and renaturing? | the higher the DNA concentration the faster for renaturing. |
| why does high concentration of DNA allow for faster renaturing? | has a greater likelihood of its complementary strands encountering each other within a given mount of time. |
| what is the relationship between time and annealing? | the more time the more annealing occurs |
| what is a fourth factor? | DNA complexity |
| what is the relationship between DNA complexity and annealing? | the more complex the DNA, the slower or less efficient the renaturing is. |
| What does the term Cot use in reference to? | combines the variable of DNA concentration and time in DNA renaturation studies. |
| how is the DNA concentration expressed | Co is the symbol is expressed in moles of nucleotides per liter. |
| how is time expressed? | t is the symbol expressed in seconds |
| What is Cot? | is the product of concentration multiplied by the time. |
| how is Cot typically expressed? | Cot 1/2 or "half Cot" - represents the Cot at which a DNA sample is half annealed. |
| what is the relationship between DNA complexity and Cot Value | DNA complexity increases as the Cot value increases. |
| Hybridization | DNA strand anneals with a complementary RNA strand and creates a hybrid duplex |
| what is the size range of DNA | a few kilobases to hundreds of megabases. |
| what is a convenient way to estimate the size of small DNAs | by TEM or electrophoresis (where the DNA migrates in the gel) |
| what other things does TEM show? | if the DNA is linear, circular or super coiled |
Created by:
kort
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