Nucleic Acids

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1

stores, expresses, transmits hereditary information

DNA/RNA purpose

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ATP-universally used, GTP-protein syntesis, UTP-glycoprotein synthesis, CTP-phospholipid synthesis.

regulators of biosynthesis

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Second messengers in hormone transduction are cAMP, and cGMP (cyclic=c)

secondary messengers

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phosphate group PO4 attached to a methyl group via an ester bond (r-o-r) off of the 5 carbon of the pentose sugar which is then attached at the 1 carbon to the base.

single nucleotide

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The backbone consistes of ester bonds between the phosphate group and 4 carbon. Production byproduct is water.

backbone

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Ribose vs. deoxyribose: deoxyribose is missing a hydroxyl group at carbon 2. this lack of OH makes it more stable.

sugar component of Nucleic acids

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The structure of ATP is basically the same as the DNA except DNA is a monophosphate. So AMP would look like it could belong in a DNA. ADP/ATP would have more phosphates attached.

ATP structure

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Purines: adenine guanine. Imidazole, meaning hexagon and pentagon with 4 nitrogens. Guanine has a double bond O off of C6 and a NH2 off of C2. if atom# 1 is the N on the hexene making the bond between the hexene and pentene atom #4/5 going counter clockwise. adenine has an NH2 off of the 6 carbon. Attachment to the sugar is with one of the N in the pentose region. The bottom one.

purine

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pyrimidines: Uracil, thymine, cytosine. Hexagonal back bone with #1 being the N that is not between the two ketones (c=o). Uracil is just that, hexagon with N at 1,3 with ketones at 2 and 4. thymine is Uracil but at 5 carbon, there is a methyl attachment. Cytosine is a bit different. It has one ketone at C2 and ammonia at C4. The atom at the first postion=N=attachment to the sugar.

pyrimidine

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Once the sugar has been attached, it is now a nucleoside. dA(deoxyadenosine), dG, dC, dT > without the acid of the DNA. Or A(adenosine),G(gunosine),U(uridine),C(cytidine) > without the acid of the RNA

nucleoside

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after phosphate has been added, you have nucleotides. you get your dAMP, dCMP, dGMP, dTMP d=deoxy. There is no d in RNA nucleotides

nucleotide

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now you get to attach them to each other. And like a said before it is a bond between the O of the phosphate and C3 of the sugar(the only C that has a hydroxyl I nDNA). This ester bond is formed by ligase (condensation reaction because you lose a H2O molecule in the process) and catalyzed by DNA/RNA polymerases.

DNA chain

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Face of the ring is hydrophobic- the bases, and the backbone is hydrophillic and leads to a stacked structure A-T(two bonds) C-G(three bonds). There are 10 bases per turn of the helix. The strands run anti-parallel.

DNA strand properties

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normal DNA is B-dna=right handed. Z-dna=left handed and pyrimidines and purines alternate. Maybe for gene regulation. A-dna -dehydrated b-DNA- no significance.

different DNA

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single stranded, linear(not circular). Carries codon information about translation. Used and degraded within days. In bacteria this happens within minutes.

RNA

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Trna: brings amino acid to the ribosome during translation. Looks like a plus sign with three ends having round-abouts on them and the forth end has the 5' and 33' end . Opposite of the fourth end is where you have your anticodon. But invivo its a little different. More realistic looking.

tRNA

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Rrna: responisible for structure of the ribosome and for catalytic activity

rRNA

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snRNA: small nuclear RNA. Integral part of splicing, regulate transcription factors, RNApoIII, and telomeres.

snRNA

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MiRNA: micro-RNA. Used post transcriptionally to silence genes. Binds to the mRNA so translation doesn't happen.

miRNA

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used anti-virally.
nucleosides that are able to integrate into viral DNA and stop transcription by working on viral DNA pol. Also affect mitochondrial DNA which can lead to bone marrow suppression.

nucleoside analogs

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AZT(zidovudine/azidothymidine): made from deoxythymidine-replacement of the 3' OH with an an azide (N=N=N )used for aids as it is a nucleoside specific to reverse transcriptase. Prolong life, reduce dementia for HIV, reduce mother to baby transmission.

AZT

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Didanosie: formed from deoxyadenosine-lose the OH at the 3' position so no ester bond can occur. another reverse transcriptase nucleoside. High affinity for reverse transcriptase. Good for HIV

Didanose

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Acyclovir: made from deoxyguanosise: lose the 3' and 2' carbon on the pentose. Gets phosphorolated faster than a normal dG(that is the next step for all nucleosides to become a nucleotide) specific to viral cells because viral kinase phosphoralates it and that is only present in infected cells. After the first phosphorylation however, it is active and can infect host cells-but usually doesn't. Effective for herpes and varicella zoster

Acyclovir

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Tenofovir: dAMP: after phophoralation of dA, the 3' C with the OH is cleaved. It is then phosphoralated to get dADP-gets incorporated into DNA and terminates ring. Effective for HIV

Tenofovir

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cytosine arabinoside(araC)-cytosine attached to ribose sugar except Oh is trans on the 2' C. so analog of nucleoside. Gets phosphoralated to triphosphate and incorporated in the DNA. Although the 3' OH is present, the position of the 2' OH leads to termination due to steric hinderance and instability. Used in leukemia therapy

AraC

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AraA: same thing as AraC except with an adenine. Used as an antineoplastic agent (inhibit growth of cancer cells) in leukemia and herpes.

AraA

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Cytidine analogs: variation of the the cytodine base aded to the deoxy sugar. One of the C is converted into N. once incorporated in DNA cause problems because the extra N can't be methylated and methylation in euk's is used as transcriptional regulation. Methylation is used to supress a gene

cytidine analogs

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Decitabine: results in the hypomethalation of CDKN2B which leads to the transcription of P15 tumor suppresant gene. Methylation othewise of CDKN2B results in silencing of the p15 gene. prevent tumor formation. Helps in Myelodysplastic sundrome and myeloid leukemia.

Decitibine