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80 Cards in this Set
- Front
- Back
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What are the exceptions to the central dogma?
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1.Noncoding RNA doesn't get translated into protein.
2. Reverse transcription |
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What is the nitrogenous base attached to the 1' carbon via?
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An N glycosidic bond
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The sugars used in DNA (Deoxyribonucleic acid) and RNA (ribonucleic acid) are different. What are the consequences of this?
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The absence of an Oxygen and instead just a hydrogen on the 2' carbon makes DNA more stable and less reactive compared to RNA
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What are the pyrimidines? the purines?
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Pyr. = cytosine and thymine
Pur= adenine and guanine |
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What is the difference btwn thymine and uracil?
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The presence of a methyl group of thymine.
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How can cytosines next to guanines on the same stand of DNA be modified? What does this modification result in?
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They can be modified by enzymatic addition of a methy group. This modification influences the struc of DNA indirectly, and is involv. in gene exp.
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What is deamination?
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It is the spontaneous removal of an amine group from a nucleotide, a common type of DNA damage
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What deaminations are easy to detect? Which are not? Why?
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The deamination of cytosine = Uracil, and adenine = hypoxanthine are easy to detect because they are not naturally found in DNA. However, the deaminated methyl-cytosine = thymine and is hard to detect b/c thymine is normally in DNA
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What gives the nucleotide its neg charge?
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The phosphate groups. 1 to 3 phosphate groups are attached to the 5' carbon of the sugar via an ester linkage
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Which phosphate is incorporated into the nucleic acids? what are the others used for?
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The alpha *P* is the only actually incorporated. beta and gamma *P* provide energy
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What joins the nucleotides?
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A phosphodiester bond
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Strands of DNA are held together by what?
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They are held together by H bonds btwn nitro bases
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Which pairs have 3 bonds and which have 2 H-bonds? What are the consequences of this?
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A-T = 2 H-bonds
G-C = 3 H-bonds --> this means that these base pairs are stronger |
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Describe 4 characteristics of the alpha-helix
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1. bases lie perpedicular to azis of symmetry
2. there are 10 BP/turn 3. Major groove = btwn turns 4. minor groove = btwn strands *the grooves are where proteins interact with DNA |
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What makes up chromatin?
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DNA and proteins
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Whats the difference btwn euchromatin and heterochromatin?
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Euchromatin is in the minority, less dense and is transcriptionally active. While heterochromatin is more dense and is NOT transcriptionally active.
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What is the site of ribosome synthesis?
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Nucleoli
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What is the compaction ratio of the nucleus?
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10,000 to 1
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What are histones?
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They are small positively charged proteins. DNA wraps 2x around the histone octamer to make nucleosome bead
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What is linker DNA?
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~50 BP that seperate nucleosomes. Histone H1 binds linker DNA
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What are nucleofilaments? What anchors them?
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30 nm fibers of packed nucleosomes. They are anchored via scaffolding proteins to form chromosomes.
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How can you neutralize histones? What happens when you do?
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Acetylation of histones neutralizes the positvie charges and weakens interaction with DNA. This is how proteins involved in replication/transcription can get around histones
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What do HATs and HDACs do?
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HATs = histone acteyl transferases --> they add acetyl
HDACs = histone deacetylase --> they remove acetyl group |
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When deacetylaed the chromatin is more OR less dense?
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It becomes MORE condensed.
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Transcription factors/proteins recruited by transcription factors often have what kind of activity?
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HAT activity --> adding of acetyl
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Histone acetylation favors what? deacetylation?
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Acetylation favors formation of euchromatin while deacetylation favors heterochromatin
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What phase does DNA synthesis occur in?
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The discrete phase or S (synthetic) phase
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What are cycle events controlled by?
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Cyclins and associated Kinases (CDKs)
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What controls checkpoint in the cycle? give examples. What are they checking?
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Tumor suppressors control checkpoints i.e. p53, pRB. They are checking the DNA i.e. after G1 are the chromosomes still intact etc.
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What is licensing?
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It occurs in late G1 and S phase, this process ensures that all regions of DNA are replicated completely, but only once, per cycle
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When are things transcribed in S phase?
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Regions of the genome that are actively transcribed are replicated early in S phase, while untranscribed regions are replicated later in S
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DNA is semi-conservative, what does this mean?
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Semi-conservative replication means that each of the two new daughter helicases contains one strand of parental DNA and one strand of newly synthesized DNA
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Is replication bi-directional?
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Yes, it can begin at many places along chromosome and moves in both directions away from point of origin
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How many times is the origin of replication used?
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only 1x
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What are replication forks?
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Regions of transition btwn the unwound parent duplex and the newly replicated daughter DNA. The unwound region is called a replication bubble
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DNA polymerase goes in what direction?
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5' to 3' only!
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True or false the ORC cannot initiate replication.
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TRUE
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How do you "license" the origin for replication?
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Cdc6 and Cdt1 bind ORC in G1 and then recruit MCM to form the pre-replicative complex.
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What does the origin actually "fire" once its licensed?
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Not until cdc6, mcm and ORC are phosphorylated by S-Cdk. This causes both the disassembly of the pre-RC and initiation of DNA replication
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What is the function of MCM?
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It has helicase activity that forms the replciation bubble and allows the preinitiation complex to form, containing DNA polymerase and associated proteins. It will also migrate with the fork and help to seperate strands
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What does helicase do?
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It is enzymes that moves along one strand of DNA. They change conformation to bind the double strand and use ATP to seperate the 2 strands and return to their orig. conformation
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What prevents the 2 strands from reannealing?
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Single strand binding proteins (RPA) bind to the single strands and prevents parental DNA from reannealing.
*prevents DNA from forming hairpin loops w/ itself |
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What do Tompoisomerases do?
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It makes reversible nickes in the DNA ahead of the replication form, pass the unbroken strands thru the gap and then reseals the gap.
*prevents supercoiling and tangling of DNA ahead of replication fork |
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DNA synthesis occurs which direction? reads it in what direction?
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DNA synthesis occurs in the 5' to 3' direction but it reads the template in the 3' to 5' direction
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What does DNA polymerase need before it can start DNA synthesis?
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Primase (an RNA polymerase) must provide the first 3' OH thru its RNA primer
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DNA polymerase has 3' to 5' exonucleus activity. What does this mean?
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This allows it to proofread by excising the last nucleotide added if it doesnt bp correctly with the template strands
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Where do we find phosphodiester bonds in the strands?
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A phosphodiester bond is created btwn the 5' PO4 of the incoming nucleotide and the 3' OH of the previous nucleotide
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How does DNA polymersase proofread? Name the steps
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Polymerase adds an incorrect nucleotide
1. Mispaired nucleotide is removed by 3' to 5' proofreading 2. Correctly paired 3'end allows the addition of next nucleotide 3. Synthesis continues in the 5' to 3' direction |
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What is the leading strand?
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This strand is copied continuously from the origin of replication, in the same idrection as the replication fork
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What is the lagging strand?
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This strand must be copied discontinuously in small fragments beginning at the replication fork and moving torward the origin. The fragments are called okasaki fragments
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The RNA primers are removed from the okasaki fragments by?
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By RNA hydrolases = RNases
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What does DNA ligase do?
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Uses ATP to make the final phosphodiester bond to seal the nicks and join the fragments together
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Are epigentic signals mitotic or genetic inhertiable?
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Mitotic inhertitable. They are passed along in somatic cells but the pattern is erased in germ cells
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How do epigentic signals influence gene expression?
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They influence by effecting the chromatin structure by regulating accessibility of the DNA to transcription factors
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Epigentic signals include what?
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Histone modification and DNA methylation
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Why is DNA methylation important?
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Its important for normal development, x chromosome inactivation and imprinting. Its necessary to maintain chromosomal stability be keeping repetitive seguences in non-coding regions in a repressed state
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DNA methylation occurs wehre?
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on cytosines in next to guanines on the same strand of DNA (CpG strands)
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What has happened b/c of evolution to the CpG sequences?
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Thru evolution, many of the CpG sequences have mutated to TpG, the remaining CpG's are not evenly distributed in the genome. --> CpG islands
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What are CpG islands?
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Are C-G rich areas often at the 5' end of genes (especially housekeeping genes that are constitutively expressed), which are not normally methylated.
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Since Methylation in the 5' regulatory regions of genes suppresses gene expression this means.....?
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That patterns of DNA methylation represent a type of epigentic info that must be passed on to each of the 2 daughter cells
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What maintains the same patterns of methylation during DNA replication?
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DNA maintaenance methylase. It recognizes hemi-methylated sites and methylates the other newly synthesized strand
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What maintains the histone code?
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DNA replication
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Describe how modified nucleosomes are distributed to the daughter cells during DNA replication?
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The histones are evenly distrubuted among the 2 daughter cells w/ each getting half from the parent and thus having gaps. New histone proteins bind the gaps & are modified by reader-writer remodeling complexes to match the ones already previously bound
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Why cant the 3' end of the lagging strand be replicated completely?
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Due to the removal of the RNA primer from the end of the lagging strand. So some DNA is lonst from ends of chromosome w/ every round of DNA rep.
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What are telomeres?
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They are the end of chromosomes that do not encode proteins. They are many tandem copies of 6 bp DNA sequences, plus the proteins that bind them
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What do telomeres do?
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They provide a 3' overhang that folds back and provides structure for prots to bind. They protects ends of chromosome from degradation & fusion and distinguish ends of intact chromosomes from broken ones
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What is senescence and what triggers it?
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The loss of telomeric DNA triggers cell cycle checkpoint mechanisms and cells stop growing permenantly --> senescence
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What is telomerase?
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It is an enzyme not found in somatic cells, but in germ cells, stem cells and a lot of cancer cells.
-Its expression is associated w/ the immortalization of cell lines -It uses RNA template to extend 3' end of parental strand so its a reverse transcriptase |
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What happens at the "crisis point" of telomere length?
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Cells either enter senescense or become immortal as cancer b/c the checkpoint mech. has failed
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What does leomerase do?
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The length of telomeres is maintained in germ cells & some stem cells. It carries its own RNA template complmentary to the G-rish strand of the telomere.
*Not in somatic cells |
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What happens if you reactivate telomerase?
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You get cells that have a selective growth advantage over normal cells and can keep replicating indefinitely
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True or false: 13 proteins are transcribed and translated in the mito. but most are done in the nucleus & then translated in cytosol before protein goes to mito.
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TRUE
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What is the big advantage to mito DNA vs. nuclear DNA?
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Mito. DNA is more economical because nearly every base pair is used to make a functional product. While nuclear DNA has a lot of repitition
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True or false: Replication mito. DNA is limited to the S phase
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FALSE, it is not limited to just the S phase, it more closely resembles bacterial DNA replication
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How much of genome actually encodes proteins?
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Less than 2%
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What is the biggest disadvantage to mito. DNA vs. nuclear DNA?
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Mito. DNA has a higher mutation rate than nuclear DNA. This is partially due to its close proximity to sites of generation of oxygen radicals but also due to less efficient repair mechs.
*these mutations seem to contribute to the decreased efficiency of oxi metabolism w/ increased age but also the aging process in general. |
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What is pk?
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it is where the drug is 1/2 ionized and 1/2 not
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What is the ratio of the ionized fraction dependent on?
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The ionization constant (pK) of that specific drug and the pH of the body fluid in which drug is present
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If the pH is below pK, what does that mean?
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Acids = nonionic form
Base = ionic form |
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if the pH is above the pK what does that mean?
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Acid = ionic form
Base = nonionic form |
