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49 Cards in this Set
- Front
- Back
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DNA components; base, sugar, phosphate
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A, G, C, T
deoxyribose mono phosphate |
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RNA components: base, sugar, phosphate
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A, G, U, C
ribose mono phosphate |
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precursors of DNA and RNA synthesis
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nucleotide triphosphtaes
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Nucleotide monophosphates - leaving group
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PPi is leaving group
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3 parts to nucleotide
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- Phosphate
- Purine or pyrimidine - Pentose |
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NItrogenous bases
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- Pyrimidine
- Purine |
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Purines
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- Adenine
- Guanine |
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Pyramidine
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- Cytosine
- Thymine (DNA) - Uracil (RNA) |
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RNA nucleic acids
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Adenine
Guanosine Cytosine Uracil |
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DNA nucleic acids
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Deoxyadenosine
Deoxyguanosine Deoxycytidine Thymidine or deoxythymidine |
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2 conformations of ribose
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aldehyde
B-furanose |
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Deoxyadenylate
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5'-monophosphate
symbols: A, dA, dAMP nucleoside: deoxyadenosine |
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Deoxyguanylate
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symbols: G, dG, dGMP
nucleoside: deoxyguanosine |
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Deoxythymidylate
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symbols: T, dT, dTMP
nucleoside: deoxythmidine |
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Deoxycytidylate
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symbols: C, dC, dCMP
nucleoside: deoxycytidine |
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Ribonucleotide: adenylate
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Symbols: A, AMP
Nucleoside: Adenosine |
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Ribonucleotide:guanylate
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Symbols: G, GMP
Nucleoside: guanosne |
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Ribonculeotide: uridylate
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Symbols: U, UMP
Nucleoside: Uridine |
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Ribonucleotide: cytidylate
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Symbols: C, CMP
Nucleoside: Cytidine |
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Minor purine and pyrimidyne bases
* RIBOSE SUGAR |
5-methylcytidine
N6-methyladenosine N2-methylguanosine 5-hydroxymethylcytidine Inosine Pseudouridine 7-methylguanosine 4-thiouridine |
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Adenosine MONOphosphates
*Adenine group attached |
Adenosine 5-monophosphate
Adenosine 2-monophosphate Adenosine 3-monophosphate Adenosine 2,3-cyclic monophosphate |
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The alpha, beta, gamma nucleotides
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Deoxyadenosine-5-monophosphate (dAMP)
Deoxyadenosine-5-diphosphate (dADP) Deoxyadenosine-5-triphosphate (dATP) |
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Adenine- ribonucleoside 5-phosphate
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mono- AMP
di- ADP tri- ATP |
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Guanine- ribonucleoside 5-phosphate
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mono-GMP
di-GDP tri-GTP |
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Cytosine- ribonucleoside 5-phosphate
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mono- CMP
di- CDP tri- CTP |
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Uracil ribonucleoside 5-phosphate
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mono- UMP
di- UDP tri- UTP |
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Adenine deoxyribonucleoside 5-phosphates
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mono- dAMP
di- dADP tri- dATP |
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Guanine deoxyribonucleoside 5-phosphates
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mono- dGMP
di- dGDP tri- dGTP |
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Cytosine deoxyribonucleoside 5-phosphates
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mono- dCMP
di- dCDP tri- dCTP |
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Thymine deoxyribonucleoside 5-phosphates
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mono- dTMP
di- dTDP tri- dTTP |
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Two common cyclic nucleotides
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Adenosine 3', 5' -cyclic monophosphate (cyclic AMP)
Guanosine 3',5'- cyclic monophosphate (cyclic GMP) |
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Absorption spectra - molar extincition coefficient at 260nm
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AMP: 15, 400
GMP: 11,700 UMP: 9,900 dTMP:9,200 CMP: 7,500 |
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Characteristics of DNA: characteristics of deoxynucleotides, how are they linked
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- deoxynucleotides (lack 2-OH) are building blocks
- linked through phosphodiester bonds |
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Sturcture of DNA
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- double stranded
- antiparallel |
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Bases of DNA
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C=G
A=T complimentary bases - # C's equals # of G's - A=T |
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What is the direction of the DNA?
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5'-3' direction
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Direction of the helices
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Right handed (except Z-DNA)
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What creates the major and minor grooves?
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- Strands are not diametrically opposed in the helix
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Stabilizing features
1. types of bonds 2. hydrophilic vs. hydrophobic parts 3. how do bases stack 4. function of cations |
- H-bonds
- Hydrophilic sugar-phosphate backbone is external - Hydrophobic bases are internal due to water environment - Base stacking (bases on same strand) - Cations neutralize the negatively charged phosphates |
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Length + strength correlation of H bonds
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longer DNA = more stable
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Thymine angstrom distance
Cytosine angstrom distance |
T- 11.1 A
C- 10.8 A |
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Importance of grooves
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- Most interaction occurs here
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What happens when 2 strands of DNA separate/ replicate
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2 daughter strands helices are identical when they are built
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Model of replication- how are daughter helices are built
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One is 5', the other is 3'
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Type A helix
- Composition - # base pairs - Direction of helix |
- RNA/RNA + DNA/RNA
- 11 bp/ turn - Right handed helix |
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Type B helix
- Composition - # base pairs - Direction |
- DNA/DNA in solution
- 10.4 bp/turn - right handed helix |
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Type Z helix
- Composition - # bp - Direction |
- Double stranded DNA, alternating purine-pyrimidine sequences
- 12 bp/ turn - Major groove becomes convex surface and may be protein binding site, because LEFT HANDED HELIX |
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Syn vs. Anti
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- Syn: purine/pyr is directly on top of sugar
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What bond allows for rotation?
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B- glycosidic
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