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Orotic Aciduria

Back 1

defect in orotic acid phosphoribosyltransferease or orotidine 5'- phosphate decarboylate. Autosommal Recessive. Megablastic anemia without hyperammonemia.

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Adenosine deaminase deficency

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excess ATP and dATP imbalances nucleotide pool via feedback inhibition of ribonucleotide reductase-->prevents DNA synthesis decreases lymphocyte count. Causes SCID.

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Lesch-Nyhan Syndrome

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Defective purine salvage owing to asbsence of HGPRT. Hypoxanthine to IMP and guanine to GMP. Results in excess uric acid production.
Clinical: retardation, self-mutalation, aggression, hyperuricemia, gout, choreoathetosis. X-LINKED Recessive.

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Helicase

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unwinds DNA template at replication fork. Bubble, two forks

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Direction of DNA synthesis

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laid down 5" to 3', but read in the 3' to 5' direction, template strand copied in the 3 to 5 direction.

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Single-stranded binding proteins

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prevents newly seperated strands from annealing

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Primase

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makes an RNA primer on which DNA polymerase II can initiate replication

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Fluoroquinolones

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inhibit DNA gyrase (specific prokaryotic topoisomerase)

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DNA pol III

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Prokaroytic only, elongates 3 end in leading strand, and elongates lagging strand until it reaches primer of preceding fragment. Has 3->5 exonuclease activity "proofreads" each nucleotide

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DNA polyermase delta

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eukaryotes ahve DNA polymerase. Delta does the leading strand.

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polymerase alpha

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eukaryotes, okazaki fragments, lagging strands

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polymerase gamma

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is the only one not actually in the nucleus, it replicates mitochondrial DNA

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DNA ligase

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joins okazaki fragments

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DNA topoisomerase II

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creates a nick in the helix to relieve supercoils cuts both strands. Top. I cuts only in one strand

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gyrase

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topoisermase in prokaryotes

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Name the drugs that target the bacterial DNA gyrase

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Fluroquinolones:
nalidixic acid, norfloxacin and ciprofloxacin.

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DNA polyermase I

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degrades RNA primer and fills in the gap with DNA

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xeroderma pigmentosum

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excision endonucleases are mutated cannot repair thymine dimers

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nucleotide excision repair

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,endonucleases release damaged bases, dna polyermase and ligase fill and reseal the gap

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base excision repair

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specific glycosylases recognize and remove damaged bases, AP endonuclease cuts DNA at apyriminic site, empty sugar is removed, and the gap is filled and resealed.

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Mismatch Repair

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unmethylated, newly synthesized string is recognized, mismatched nucleotides are removed, and the gap is filled and sealed.

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Heriditary nonpolyposis colorectal cancer (HNPCC)

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mismatch repair mutation

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mRNA start codons

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Eukaryotes: codes for methionine
Prokaryotes: codes for forml-methionine (f-met)

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mRNA stop codons

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UGA, UAA, UAG

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RNA polymerase I

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makes RNA

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uracil DNA glycosylase

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looks for deamination reactions transforming C to U, implicated in colon cancer by nitrates, base excision repair leaving the backbone intact

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AP endonuclease

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looks for the AP site made by the glycosylase, and then DNA polyermase and ligase come in and the dna is restored.

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deamination

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C to U

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reverse transcriptase

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is an RNA dependent DNA polyermase --it requires a primer

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deoxynucleotide triphosphates

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dATP,dCTP, dTTP, dGTP

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nucleotide phosphates

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substrates for RNA synthesis

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+ 1 base

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the start site of transcription

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Transcription in RNA is made in what direction

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5 to 3

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direction that the template strand is copied

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3 to 5

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what is an operon

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operona set of genes under the control of one promoter are called operons

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Huntington's chorea

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is a CAG expansion, neurodegenerative disorder

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Fragile X syndrome

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CGG expansion, extra large testis, jaw, and ears. X-linked effecting the expression of the FMR1 gene.

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TATA box

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place where the RNA pol. binds inorder to bind to the promoter. sigma portion of RNA polyermase binds the TATA box

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rho-independent termination

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when the stem-loop structure forms and RNA polyermase falls off. stem is composed of C-G

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rho-dependent

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a protein called rho stops termination

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In prokaroyotes where does transcription and translation occur?

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in the cytosol

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Shine-delgarno sequence

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this is where the ribosome binds. The S-D is just upstream, it is how the ribosome finds the start codon.

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poly-A site

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stop site

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TATA box (mamallian cells)

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located at -25

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Transcription factors

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bind TATA box, TF-IID TBP is the part of TF-IID

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RNA polyermase I

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makes rRNA

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RNA Polyermase II

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makes mRNA
--opens DNA at promoter site

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RNA polyermase III

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makes tRNA

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Prokaryote RNA polyermase

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makes all three kinds of RNA

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Pre-mRNA

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when the poly A site comes up, an endonuclease cuts on the 3 side of the mRNA. this all occurs in the nucleus

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hnRNA

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equal pre-mRNA

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capping

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occurs in nucleus
--cap occurs on the 5' end
--the cap is a methy-Guanine cap
--serves as the S-G region for ribosomes.

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tailing

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poly-A-polyermase comes along and puts on the poly-A tail. The substrate is ATP.

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splicesome

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--bind around introns and exons, and removes the introns with snRNA's

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activator protein

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Activator proteins turn on genes
--activator genes bind to activator sites

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repressor proteins

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turn off genes and bind operator sites

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Lac operon

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--remove the repressor protein by the addition of lactose
--put an activator protein by adding cAMP
--you need lactose and cAMP to turn this thing on
--high glucose inhibits cAMP hence turns off the operon
--Beta-Galactosidase if the activity of this enzyme is high, then the operon is on, if its activity is low, then the operon is off.

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Regulation of Human Transcription

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ehancers and silencers
--must be in euchromatin form to act in transcription (loosely packed) form
--methylation turns genes off and demtheylation makes them active

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homeobox genes, homeotic genes

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--ehancer binding genes
--these genes make transcription factors that appear at certain times during fetal development that set down the body plan.

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leucine zipper or zing finger

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fat-soluble vitamins A and D, and thyroid hormones, and all steroids act as transcription factors.

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eukaryotic ribosomes

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even numbers: 80's, 60's, 40;s
number 8 sticks out

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prokaryotic ribosomes

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smaller and odd numbered:
70, 50, 30

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tRNA structure

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secondary: cloverleaf
tertiary: looks like an L with the CCA at the end.

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amino acid activation

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amino acids are attached to amino acyl tRNA synthases in the cytoplasm, which attach to the CCA end of the TrNA

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Anticodons

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each amino acid has it's own tRNA with oriented anitparallel to one another. Wobble position is at 1