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38 Cards in this Set
- Front
- Back
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DNA |
Deoxyribonucleic acid -sugar -nitrogen base (devoid of an OH on 2 C) -PO4 |
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Nucleosides |
base + sugar |
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Nucleotides |
base+ sugar +PO4 (phosphates) |
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Purine |
-has two rings -A and G |
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Pyrimidine |
-has one ring -T and C |
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Ionic bonds |
relatively weak |
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Hydrogen bonds |
easily made and easily broken |
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Covalent bonds |
strongest bonds |
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How is a DNA sequence read? |
5' to 3' |
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What is the 5' carbon on a DNA strand? |
5 is the #5 carbon in ribose, it is touching phosphates |
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What does a DNA molecule look like? 5' carbon? 3' carbon? |
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what is the 3' carbon in ribose? |
it is the #3 carbon in ribose, it is touching a hydroxyl |
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what is the 2 carbon? |
#2 carbon in ribose. In RNA it has an OH, in DNA it has only an H |
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Which bonds are easier to break: A-T or G-C |
A=T because they only have two bonds rather than three |
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Z-DNA |
-does not exist in nature, only in lab -left handed helix, one strand is going counterclockwise -12 bp/turn |
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B-DNA |
-exists in nature -right handed -10 bp/turn |
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A-DNA |
-right handed -11 bp/turn |
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Condensed form of DNA |
closed circular |
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Positive supercoil |
twisting DNA in opposite direction of helix. BAD! |
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Negative supercoil |
twisting DNA in same direction of helix. GOOD! |
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How does supercoiliing work |
supercoiling creates a lot of potential energy, breaking a bond will release pressure (relaxed form) and create lots of kinetic energy |
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what must happen to DNA so that replication may occur |
Condensed from turning into relaxed form |
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DNA replication is __? |
semiconservative |
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Precursor |
-Kinase: adds PO4 (ADP - ATP) must have deoxy ATP for DNA |
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Ribonucleotide reductase |
removes OH ATP - dNTP |
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DNA polymerase |
•forms phosphodiester bond •removes alpha and beta PO4 •alpha PO4 5C or 3C (5'->3') •needs primer (denovo- cannot come from nothing) |
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DNA pol III |
main polymerizer? •5000 bases per second |
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DNA pol I |
•editing •5' -> 3' exonuclease •removes primer • 10 bases per second • proofreading |
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Klenow fragment |
•large subunit of DNA pol I •no proofreading • has removed proofreading ability, all it can do is synthesize DNA |
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ORI site |
•origin of replication •where DNA replication begins in a chromosome • 245 bp - 5 eq •theta replication eventually becomes replication fork |
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DNA helicase |
•separates DNA •ATP dependent •creates and supercoils •turns DNA left handed to make it single stranded •creates a positive supercoil |
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SSb proteins |
•binds to single stranded DNA, keeps it from coming back together |
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Primase |
•DNA pol I •RNA primer •recognize 3' GTC 5' |
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Whole DNA replication system |
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DNA ligase |
•ATP dependent •joins DNA • creates phosphodiester bond between nucleotides to make on continuous strand of DNA |
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Topoisomerase I |
•cuts one strand, begins to unravel around the other (endonuclease) •converts negatively supercoiled to relaxed •ligase (energy supercoil) •does not use ATP, uses kinetic energy of supercoil |
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Problem: there is a positive supercoil of DNA helicase, topo I cannot help because it only converts negative supercoils? |
Topo I and Topo II cancel each other out and create relaxed DNA |
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Proofreading |
•dcm & dam: methylates DNA and inhibits nuclease • adds an extra carbon onto an old DNA |
