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186 Cards in this Set
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BIOCHEMISTRY
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0
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Chromatin: In mitosis, the negatively charged DNA condenses by wrapping around…
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nucleosomes
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Chromatin: name the proteins nucleosomes are made of:
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Histones: H2A, H2B, H3, H4
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Chromatin: the structure that ties nucleosomes together to form chromatin:
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H1 (another histone)
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Chromatin: how long is a chromatin fiber?
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30 nm
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Chromatin: which one is transcriptionally active, heterochromatin or euchromatin?
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Euchromatin = true, active, less condensed, open Heterochromatin = condensed, darker/more color, inactive (less open)
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Nucleotides: the purines are
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A and G -- Pure As Gold = Purines
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Nucleotides: the pyrimidines are:
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C, U, T -- CUT the PY -rimidines
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Nucleotides: Which pair is stronger, G-C or A-T?
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GC has 3 H bonds. AT has 2 bonds. (AT = 2 points in Scrabble, GC = 6 points -- GC wins!)
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Nucleotides: significance of # of H bonds?
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higher GC content, more H bonds, higher melting temperature
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Nucleotides: guanine has this side group:
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ketone
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Nucleotides: thymine has this side group:
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methyl -- thymine has methyl
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Nucleotides: deamination of cytosine gives -->
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Uracil -- remember U before C in CUT (see above)
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Nucleotides: Nucleotides are held together by these bonds:
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3'-5' phosphodiesterase bond
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Transition vs. Transversion: substituting purine for purine, pyrimidine for pyrimidine is call:
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transition - staying inside the same class
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Transition vs. Transversion: substituting purine for pyrimidine, vice versa
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transversion - change from 1 type to another, 1 version to another version of nucleotide
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Genetic Code features: each codon specifies only 1 amino acid:
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Unambiguous
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Genetic Code features: more than 1 codon can code for the same amino acid:
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Degenerate
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Genetic Code features: all organisms have nonoverlapping, commaless nucleotides except for:
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viruses (are they really organisms? …)
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Genetic Code features: name 4 organisms/structures where a different genetic code is used:
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mitochondria, archaeobacteria, Mycoplasma, some yeasts
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Mutations in DNA: A silent mutation is…
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when the base change (usually @ 3rd codon) does not change the aa, thanks to the degenerate feature of the genetic code!
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Mutations in DNA: what's worse, nonsense, missense, or silent?
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nonsense > missense > silent
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Mutations in DNA: what is a conservative mutation?
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new amino acid is similar in structure (e.g. small vs. bulky, linear side chain vs. rings)
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Mutations in DNA: what is a missense mutation?
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changed amino acid - e.g. Glu-->Val in sickle cell anemia
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Mutations in DNA: what is a nonsense mutation?
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early stop codon. Nonsense = No meaning, no aa.
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Mutations in DNA: what happens if a frameshift mutation occurs?
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the open reading frame is shifted so that all the nucleotides are misread --> result is usually a truncated protein
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Prokaryotic DNA replication and DNA polymerases: how many origins of replications does a prokaryote (bacteria, viruses, plasmids) have?
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1
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Prokaryotic DNA replication and DNA polymerases: a primase makes…
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RNA primer on which DNA polymerase initiate replication
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Prokaryotic DNA replication and DNA polymerases: what is needed to replicate DNA on the lagging strand?
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Okazaki fragments
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Prokaryotic DNA replication and DNA polymerases: DNA polymerase III - action?
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has 5'-->3' synthesis ability -- reaches the primer of preceding "O" fragment. Also has 3'-->5' exonuclease proofreading ability!
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Prokaryotic DNA replication and DNA polymerases: RNA primers are degraded by:
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DNA polymerase I
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Prokaryotic DNA replication and DNA polymerases: the DNA fragments are sealed by:
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DNA ligase
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Prokaryotic DNA replication and DNA polymerases: proofreading of the DNA is done by:
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DNA polymerase III
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Prokaryotic DNA replication and DNA polymerases: What happens if there is a supercoil of the DNA, ready to snap?
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DNA topoisomerases -- create nick in the helix to relieve supercoils
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Eukaryoyic DNA polymerases:: DNA polymerase alpha
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replicates lagging strand and synthesizes RNA primers
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Eukaryoyic DNA polymerases:: DNA repair is done by:
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DNA polymerase beta and epsilon
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Eukaryoyic DNA polymerases:: When mitochondria divide we need this to replicate the mitochondrial DNA
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DNA polymerase gamma
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Eukaryoyic DNA polymerases:: This DNA polymerase replicates the leading strand:
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DNA polymerase delta
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DNA repair : single strand: to remove a damaged base:
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single-strand, excision repair-specific glycosylase
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DNA repair : single strand: Endonuclease - action?
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cleaves the DNA several bases to the 5' side
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DNA repair : single strand: Exonuclease - action?
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remove short stretches of nucleotide
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DNA repair : single strand: What can happen if both strands are damaged?
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repair --> recombination!
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DNA repair defects: defective uvr ABC endonuclease --> thymidine dimers seen in:
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Xeroderma pigmentosum -- autosomal recessive, inability to repair thymidine dimers which form when exposure to UV light
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Directions: Direction of transcription and translation?
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5' --> 3' ! (please BYOPhosphate from 5 to 3)
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Directions: Direction of protein synthesis?
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N to C - also 5 to 3
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types of RNA: what is the largest RNA?
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mRNA ( m = massive)
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types of RNA: what is the most abundant RNA?
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rRNA -- in ribosomes! R = Rampant
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types of RNA: what is the smallest RNA?
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tRNA -- T = Tiny
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RNA polymerases: Whose RNA is all made with one enzyme, prokaryote or eukaryote?
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Prokaryote! RNA polymerase makes all 3 RNAs
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RNA polymerases: RNA polymerases I, II, III (1, 2, 3) make (respectively):
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RMT -- rRNA, mRNA, tRNA
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RNA polymerases: RNA polymerase II has another talent with DNA:
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can initiate chain by opening DNA at promoter site (AT rich upstream sequences: TATA, CAAT)
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RNA polymerases: alpha-amanitin - action?
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inhibit RNA polymerase II
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Start and Stop Codons: start codon:
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AUG -- AUG inaugurates protein synthesis!
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Start and Stop Codons: What does the start codon code for?
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Methionine -- removed in eukaryotes; formyl-methionine in prokaryotes
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Start and Stop Codons: Stop codons - how to remember?
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UGA: U Go Away; UAA = U Are Away; UAG = U Are Gone
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Regulation of gene expression: What happens if a promoter is mutated?
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reduction in amount of gene transcribed -- this is where RNA polymerase and other transcription factors bind to DNA upstream from gene locus
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Regulation of gene expression: a stretch of DNA, far or near, that can alters gene expression by binding transcription factors is called:
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Enhancer
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Regulation of gene expression: AUTHOR
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Sarah Goldman
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Introns vs. Exons: Which part of DNA is transcribed to mRNA?
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Exons
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Introns vs. Exons: _______ are intervening noncoding segments of DNA
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Introns (INtrons stay IN the nucleus; EXons Exit and are EXpressed
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Splicing of mRNA: ________ facilitate splicing by binding to primary mRNA transcripts and forming spliceosomes
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Small nuclear ribonucleoprotein particles (snRNP)
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RNA processing (eukaryotes): Where does RNA processing occur?
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In the nucleus
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RNA processing (eukaryotes): What are the 3 steps of RNA processing, following transcription?
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1) caping on 5' end (7-methyl-G); 2) Polyadenylation on 3' end (200 A's); 3) Splicing out of introns
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RNA processing (eukaryotes): The initial transcript is called_________. The capped and tailed transcript is called_______.
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Heterogeneous nuclear RNA (hnRNA); mRNA
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tRNA structure: True or false: The anticodon end of tRNA is opposite the 5' end
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False. The anticodon end is oposite the 3' aminoacyl end
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tRNA structure: What codon is at the 3' end of all tRNAs?
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CCA and chemically modified bases
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tRNA structure: The amino acid is covalently bound to which end of the tRNA?
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3' end
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tRNA charging: What enzyme scrutinizes the amino acid before and after it binds to tRNA?
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Aminoacyl-tRNA-sythetase (1 per amino acid, uses ATP)
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tRNA charging: What happens if a tRNA is mischarged?
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It reads the usual codon, but inserts the wrong amino acid.
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tRNA Wobble: True or false: codons that differ in the 3rd position may code for the same tRNA/amino acid
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True. Accurate base pairing is required only in the first 2 nucleotide positions of an mRNA codon; the 3rd position is the "wobble" position.
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Protein synthesis: ATP vs. GTP: (a) ATP or (b) GTP is used in tRNA charging?
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(a) ATP (tRNA Activation)
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Protein synthesis: ATP vs. GTP: What energy form is required for binding of tRNA to the ribosome and for translocation?
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GTP (tRNA Griping and Going places)
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Polymerase chain reaction (PCR): What is the laboratory procedure used to synthesize many copies of a desired fragment of DNA?
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PCR
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Polymerase chain reaction (PCR): What are the 3 steps of PCR?
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1) DNA denatured by heating into 2 separate strands; 2) Annealing of premade DNA primers to a specific seqence of each strand, during cooling; 3)Heat-stable DNA polymerase replicates the DNA sequence following each primer
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Molecular biology techniques: Match the following techniques with the appropriate interaction: Techniques: a) Southern blot; b)Northern blot; c)Western blot; d)Southwestern blot Interactions: 1) DNA-RNA hybridization; 2)Antibody-protein hybridizaton; 3) DNA-protein interaction; 4)DNA-DNA hybridization
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a) Southern blot---4)DNA-DNA (Southern-Same) b)Northern blot---1)DNA-RNA c)Western blot---2)Antibody-protein d)Southwestern blot---3)DNA-protein interaction
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Enzyme-linked immunosorbent assay (ELISA): What interaction is tested by ELISA?
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antigen-antibody reactivity
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Enzyme-linked immunosorbent assay (ELISA): What indicates a positive test result?
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An intense color reaction in the test solution
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Modes of inheritance: What percentage of offspring from two carrier parents are affected by an autosomal recessive trait?
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0.25
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Modes of inheritance: Which mode of inheritance is often due to defects in structural genes, and affects many generations?
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Autosomal dominant
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Modes of inheritance: If a woman is heterozygous for an X-linked recessive disorder, what is the chance that her son will be affected?
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0.5
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Modes of inheritance: True or False: Females heterozygous for an X-linked trait may be affected by the disorder.
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TRUE
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Modes of inheritance: What mode of inheritance is transmitted only through the mother? What are some examples of such disorders?
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Mitochondrial inheritance; examples include Leber's hereditary optic neuropathy and mitochondrial myopathies
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Modes of inheritance: AUTHOR
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Lee Kiang
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Genetic Terms: Distinguish between variable expression and incomplete penetrance
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In variable expression, NATURE and SEVERITY of PHENOTYPE VARIES amongst individuals. In incomplete penetrance not all individuals with mutant GENOTYPE show mutant PHENOTYPE
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Genetic Terms: Define pleiotropy
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1 gene has > 1 effect on individual's phenotype
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Genetic Terms: Angelman's syndrome is an example of _______.
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Maternal imprinting. In imprinting, phenotype differs based on whether mutation is maternal or paternal.
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Genetic Terms: Give an example of Paternal imprinting
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Prader-Willi syndrome
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Genetic Terms: In Huntington's disease, severity worsens or age of onset becomes earlier with successive generations. This phenomenon is called________.
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Anticipation
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Genetic Terms: What is Loss of Heterozygosity, and in what situation does it not apply?
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With congenital or acquired mutation of tumor supressor gene, the completement allele must be deleted/mutated before the development of Ca. NOT TRUE with ONCOGENES.
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Genetic Terms: When the body cannot produce enough normal gene product with only one functional allele, there is a ______mutation. An example is the mutation COL1A1 in the disease _________.
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Dominant negative mutation; Osteogenesis Imperfecta.
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Genetic Terms: Define Linkage Disequilibrium
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Tendency for certain alleles at 2 linked loci to occur together more often than expected by chance. Measured in a population, not within a family; varies among pops.
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Genetic Terms: When cells in the body have a different genetic makeup, this is ________.
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Mosaicism
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Hardy-Weinberg population genetics: For a population in Hardy-Weinberg equilibrium, where p and q are separate alleles, what is the heterozygote prevalence?
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Hardy-Weinberg equation for alleles p and q: p^2 + 2pq + q ^ = 1; p+q=1. The heterozygote prevalence is 2pq
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Hardy-Weinberg population genetics: The Hardy-Weinberg law assumes 4 criteria. List them.
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1. No mutation at the locus; 2. No selection for any genotypes at the locus; 3. Mating completely random; 4. No migration into/out of population being considered
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Genetic Errors: What is a main risk factor for Trisomy 21?
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Down syndrome=Trisomy 21. Prevalence 1:800, increased risk with advanced maternal age.
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Genetic Errors: Name 3 genetic diseases that involve mental retardation
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Down Syndrome, Fragile-X, Phenylketonuria
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Genetic Errors: The mechanism of this disease involves failure to express gene-encoding RNA binding protein, due to progressive expansion of unstable DNA
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Fragile X-associated mental retardation
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Genetic Errors: A single missense mutation in beta globin, conferring susceptibility to infections, painful crises
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Sickle Cell anemia, 1:400 African-Americans
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Genetic Errors: Name 3 characteristics of the CF phenotype
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Recurrent pulmonary infection, exocrine pancreatic insufficiency, infertility.
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Genetic Errors: Characterized by café-au-lait spots, neurofibromas, increased tumor susceptibility- what is this, and what is the inheritance?
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Neurofibromatosis, prevalence 1:3000. AD, with 50% new mutations
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Genetic Errors: Name two X-linked genetic errors
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Fragile X, Duchenne's muscular dystrophy
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Genetic Errors: Characterized by increased susceptibility to fractures, connective tissue fragility:
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Osteogenesis Imperfecta
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Genetic Errors: Phenotype of Phenylketonuria
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Mental and growth retardation.
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Trinucleotide repeat expansion diseases: Name 4 trinucleotide repeat expansion diseases
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Freidreich's ataxia, Huntington's chorea, mytotonic dystrophy, fragile X syndrome
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Lysosomal Storage Diseases: What are the two categories of lysosomal storage diseases?
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1. Sphingolipidoses; 2. Mucopolysaccharidoses
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Lysosomal Storage Diseases: In _______disease, a deficiency of alpha-galactosidase A results in the clinical finding of _____.
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Fabry's disease; Renal Failure.
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Lysosomal Storage Diseases: What are the manifestations of the AR disease leading to accumulation of galactocerebroside in the brain?
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Krabbe's disease. Optic Atrophy, spasticity, early death.
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Lysosomal Storage Diseases: This disease leads to glucocerebroside accumulation in 4 sites, and has characteristic "crinkled paper" cells.
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Gaucher's disease. Glucocerebroside accumulation in brain, liver, spleen, bone marrow. Gaucher's cells have "crinkled paper" apearance with enlarged cytoplasm.
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Lysosomal Storage Diseases: Match: Galactocerebroside accumulation, Glucocerebroside accumulation to Gaucher's, Krabbe's
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galaKto = Krabbe. GlUco=GaUcher's.
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Lysosomal Storage Diseases: AR disease with buildup of sphingomyelin and cholesterol in reticuloendothelial and parenchymal cells and tissues
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Niemann-Pick disease. "NoMAN PICKs his nose with his sphinger"
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Lysosomal Storage Diseases: In _______disease, a deficiency of the enzyme _______results in a cherry-red spot on the macula and death by age 3.
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Tay-Sachs disease. "Tay-saX lacks heXoaminidase"
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Lysosomal Storage Diseases: Carrier rate for Tay-Sachs in Jews of European Descent
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1 in 30
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Lysosomal Storage Diseases: What is Metachromatic Leukodystrophy?
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Deficiency of arylsulfatase A results in accumulation of sulfatide in brain, kidney, liver and peripheral nerves.
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Lysosomal Storage Diseases: What are the two mucopolysaccharidoses?
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Hurler's and Hunter's syndromes
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Lysosomal Storage Diseases: Inheritance of Hurler's syndrome, clinical manifestation:
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AR, alpha-L-iduronidase results in corneal clouding, mental retardation.
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Lysosomal Storage Diseases: Inheritance of Hunter's, clinical manifestation:
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X-linked Recessive. "Hunters aim for the X" Deficiency of iduronate sulfatase- a milder form of Hurler's with no corneal clouding and with MILD mental retardation.
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Lysosomal Storage Diseases: AUTHOR
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Ronnie Gurevich
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Enzyme kinetics: Km = ___ at 1/2 Vmax
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[S]
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Enzyme kinetics: what is the relationship between affinity and Km?
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inverse correlation (lower Km = higher affinity)
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Enzyme kinetics: when adding a competitive inhibitor: what happens to Vmax and Km
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Vmax is unchanged; Km is increased
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Enzyme kinetics: when adding a non-competitive inhibitor: what happens to Vmax and Km
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Vmax is decreased; Km is unchanged
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Enzyme regulation methods: name 5 methods by which enzyme activity is regulated
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1. concentration alteration; 2. covalent modification; 3. proteolytic modification; 4. allosteric regulation; 5. transcriptional regulation
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Cell cycle phases: name the 5 phases of the cell cycle
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G1= growth, S = DNA synthesis, G2 = growth, Go = quiescent G1 stage, M= mitosis "G stands for Gap/Growth, S stands for synthesis"
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Cell cycle phases: which parts of the cell cycle are considered INTERPHASE
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G1, S, G2
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Cell cycle phases: what phase is usually the shortest? what phase is shortened in rapidly dividing cells?
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M; G1 (duration varies)
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Cell cycle phases: what phase are most cells in
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G0
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Plasma membrane composition: what is the percentage of cholesterol in the cell membrane? Phospholipids?
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~ 50% each
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Plasma membrane composition: which side of the membrane are glycosylated lipids on?
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the noncytoplasmic
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Phosphatidylcholine function: phosphatidylcholine (lecithin) is a major component of___ (list 4)
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RBC membranes, myelin, bile, surfactant (DpC).
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Phosphatidylcholine function: what does phosphatidylcholine esterify
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cholesterol
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Na-K-ATP pump: on what side of the cell membrane is the ATP pump phosphorylated (by ATP)
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the cytoplasmic
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Na-K-ATP pump: what is the ion exchange that goes on?
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3 Na out; 2 K in
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Na-K-ATP pump: what is a pump inhibitor that binds to the K site?
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Ouabain
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Na-K-ATP pump: how do cardiac glycosides work?
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(digoxin, digitoxin). They bind to the Na-K-ATP pump and increase cardiac contractility
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G protein linked 2nd messengers : what is the G protein class and main function of the alpha1 receptor
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class q; increase smooth muscle contraction
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G protein linked 2nd messengers : what is the G protein class and main function of the alpha 2 receptor
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class i; decrease sympathetic outflow, decrease insulin release
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G protein linked 2nd messengers : what is the G protein class and main function of the beta1 receptor
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class s; increase: heart rate, contractility, renin release, lipolysis, aqueous humor production
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G protein linked 2nd messengers : what is the G protein class and main function of the beta 2 receptor
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class s; vasodilation, bronchodilation, increase glucagon release
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G protein linked 2nd messengers : what is the G protein class and main function of the M1 receptor
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class q; CNS
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G protein linked 2nd messengers : what is the G protein class and main function of the M2 receptor
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class i; decrease heart rate
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G protein linked 2nd messengers : what is the G protein class and main function of the M3 receptor
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class q; increase exocrine gland production
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G protein linked 2nd messengers : what is the G protein class and main function of the D1 receptor
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class s; relax renal vascular smooth muscle
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G protein linked 2nd messengers : what is the G protein class and main function of the D2 receptor
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class i; modulates transmitter release, especially in the brain
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G protein linked 2nd messengers : what is the G protein class and main function of the H1 receptor
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class q; increase nasal and bronchial mucous production, contraction of bronchioles, pruritis, pain
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G protein linked 2nd messengers : what is the G protein class and main function of the H2 receptor
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class s; increase gastric acid secretion
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G protein linked 2nd messengers : what is the G protein class and main function of the V1 receptor
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class q; increase vascular smooth muscle contraction
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G protein linked 2nd messengers : what is the G protein class and main function of the V2 receptor
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class s; increase water permeability and reabsorption in the collecting tubules
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G protein linked 2nd messengers : how does Gq work?
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stimulates phospholipase C which causes cleavage of PIp 2.
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G protein linked 2nd messengers : how does Gs work?
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binds to adenylcyclase which converts ATP--> cAMP
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G protein linked 2nd messengers : how does Gi work?
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by inhibiting adenylcyclase
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G protein linked 2nd messengers : what do the 2 products of PIp 2 do?
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Ip 3 increases intracellular [Ca] DAG activates protein kinase C
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arachadonic acid products: name the enzyme that liberates AA from the cell membrane
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phospholipase A2
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arachadonic acid products: what does the lipoxygenase pathway yield
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leukotrienes (L for Lipoxygenase and Leukotrienes)
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arachadonic acid products: LTB4 is a____
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neutrophil chemotactic agent
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arachadonic acid products: which leukotrienes are involved in bronchoconstriction, vasoconstriction, smooth muscle contraction, and increased vascular permeability
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LT C4, D4, E4 (SRS-A)
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arachadonic acid products: what are the 3 products of the cyclooxygenase pathway?
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thromboxane, prostacyclin, prostaglandin
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arachadonic acid products: what are the 2 functions of TxA2
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platelet aggregation, vasoconstricion
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arachadonic acid products: what are the 2 functions of PGI2
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inhibition of platelet aggregation; vasodilation (Platelet Gathering Inhibitor)
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microtubule: what are the shape and dimensions of a microtubule?
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cylindrical, 24 nm in diameter, variable length.
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microtubule: what are the components of a microtubule
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polymerized dimers of alpha and beta tubulin (+2 GTPs per dimer)
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microtubule: where are microtubules found
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cilia, flagella, mitotic spindles, neuronal axons (slow axoplasmic transport)
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microtubule: antihelminthic drug that acts on microtubules
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mebendazole/thiabendazole
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microtubule: anti breast cancer drug that acts on microtubules (prevent disassembly)
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taxol
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microtubule: antifungal drug that acts on microtubules
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griseofluvin
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microtubule: anti cancer drug that acts on microtubules (prevent assembly)
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vincristine/vinblastine
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microtubule: anti gout drug that acts on microtubules
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cholchicine
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collagen synthesis and structure: hydroxylation of specific prolyl and lysyl residues in the ER requires ____
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vitamin C
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collagen synthesis and structure: how is collagen synthesized form procollagen
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procollagen is exocytosed into the EC space, and cleaved by procollagen peptidase to make tropocollagen which aggregates to form collagen fibrils.
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collagen synthesis and structure: what is the function of lysine-hydroxylysine in collagen
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it cross links tropocollagen and reinforces the fibrillar structure of collagen
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collagen synthesis and structure: a collagen fibril is made of many stagggered collagen molecules. What is a collagen molecule made of?
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3 collagen alpha chains, usually Gly-X-Y. X and Y- proline, hydroxyproline, hydroxylysine)
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Ehlers-Danlos syndrome: in this disease, faulty collagen synthesis causes what 3 things
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1. Hyperextensible skin; 2, tendency to bleed; 3. Hypermobile joints
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Ehlers-Danlos syndrome: what is the genetic inheritance of type IV EDS
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autosomal dominant
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Ehlers-Danlos syndrome: what is the genetic inheritance of type VI EDS
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autosomal recessive
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Ehlers-Danlos syndrome: what is the genetic inheritance of type IX EDS
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x linked
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Ehlers-Danlos syndrome: what type of cerebral vascular disorder is EDS associated with
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berry aneurysms
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Osteogenesis imperfecta: brittle bone disease causes____
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multiple fractures w/ minimal trauma
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Osteogenesis imperfecta: blue sclera is due to ______
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translucency of the connective tissue over the choroid
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Osteogenesis imperfecta: what is the main pathology in OI
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genetic defect in collagen synthesis
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Osteogenesis imperfecta: what is the most common form of OI
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autosomal dominant with abnormal type I collagen
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Osteogenesis imperfecta: the presentation of a child with OI may be confused with_____
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child abuse
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ATP: what are the units comprising ATP
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adenine base; ribose sugar; 3 phosphoryls
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ATP: what type of high energy bonds does ATP have
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2 phosphoanhydride bonds, 7 kcal/mol each
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ATP: how many ATPs are produced in aerobic glucose metabolism?
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38 via malate shuttle; 36 via G3P shuttle
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ATP: how many ATPs are produced in anaerobic glycolysis?
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2
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activated carriers: what is the active carrier of phosphoryls
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ATP
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activated carriers: what is the active carrier of electrons
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NADH, NADPH, FADH2
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