Biochemistry Flashcards – First Aid for the USMLE STEP 1

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  • "In the chromatin structure, which histones form the octamer, and which ties the nucleosome beads together in a string?"
    "octamer = 2 sets of H2A, H2B, H3, H4 - tie =H1"
  • What amino acid makes up most of the octamer
    lysine and arginine
  • "Which type of chromatin is condensed, transcriptionally inactive, sterically inaccessible?"
    heterochromatin = HighlyCondensed
  • "Which type of chromatin is less condensed, transcriptionally active, sterically accesible"
    euchromatin
  • What does PURe As Gold and CUT The Py stand for
    "purines= A, G pyrimidine = C, T (U)"
  • How many rings do purines have
    2 rings
  • How many rings do pyrimidines have
    1 ring
  • How does cytosine become uracil
    deamination
  • "What polar group does guanine have, and what non polar group does thymine have"
    "ketone, methyl"
  • Which bond is stronger AT or CG and why? What is the laboratory consequence of this?
    "CG- 3 > AT-2 - More CG content, melting point goes up"
  • What 3 amino acids are necessary for purine synthesis
    "glycine, aspartate, glutamine"
  • What makes up a nucleoside
    base + ribose
  • What makes up a nucleotide
    base + ribose + phosphate (3' -5') phosphodiester bond
  • What are purines made from
    IMP precursor
  • What are pyrimidines made from
    "orotate precursor, with PRPP added later"
  • What is made fir rNucleotides or deoxyrNucleotides and what enzyme is necessary to convert one to the next
    ribos first then deoxyribos with ribonucleotide reductase
  • "What two pathways is carbomoyl phosphate involved in, and what enzyme deficiency leads to a build of carbamoyl phosphate leading to what element in pyrimidine synthesis"
    "de novo pyrimidine synthesis and urea, ornithine transcarbamoyl def in the urea cycle leads to a build of CP, then converted to orotic acid in pyrimidine synthesis pathway"
  • Name 5 drugs that interfere with nucleotide synthesis
    "hydroxyurea - inhibits ribonucleotide reductase, 6 MP - blocks de novo purine synthesis, 5 FU inhibits thymidilate synthase, MTX - inhibits DHFR, Trimethroprin inhibits bacterial DHFR"
  • Inhibition of thymidilate synthase and and DHFR lead to decrease in what substance
    dTMP
  • Which step in the de novo purine and pyrimidine synthesis pathway requires just aspartate
    orotic acid to UMP
  • "Which step in the de novo purine and pyrimidine synthesis pathway requires aspartate, glycine, glutamine and THF"
    Ribose 5-P to PRPP
  • An inability to convert orotic acid to UMP would be caused by a deficiency either of which two enzymes
    orotic acid phosphoribosyltransferase or orotidine 5'-phosphate decarboxylase
  • How is orotic aciduria inherited
    AR
  • What are the findings in orotic aciduria
    "inc orotic acid in urine, megaloblastic anemia (does not correct with B12 or folate), failure to thrive"
  • What lab value can distinguish orotic aciduria from ornithine transcarbamoylase def?
    "OTC has hyperammonemia, orotic aciduira does not"
  • What is the treatment for orotic aciduria
    oral uridine administration
  • "What does Adenosine deaminase deficiency cause a build up of, and what does that lead to?"
    "excess ATP, dATP, feeback inhibits ribonucleotide reductase, no DNA synthesis"
  • Adenosine deaminase deficiency is an important cause of what immunodeficiency?
    "dec DNA, dec lymphos leads to SCID"
  • Leysh-Nyhan syndrome is a defect in which enzyme and what are the biochemical results
    "HGPRT, defective purine salvage, excess uric acid production"
  • What are the findings in Lesch-Nyhan
    "retardation, self mutilation, aggression, hyperuricemia, gout, choreoathetosis"
  • How is Lesch Neyhan inherited
    X-linked recessive
  • What enzyme converts adenine to AMP
    APRT + PRPP
  • What step of uric acid synthesis does xanthine oxidase catalyze
    hypoxanthine to xanthing and xanthine to uric acid
  • What reaction does adenosine deaminase normally catalyze
    adenosine to inosine
  • What does an umabiguous genetic code refer to
    each codon specifies only 1 amino acid
  • What does degenerate/rundant genetic code refer to
    more than 1 codon may code for the same amino acid
  • What is the exception to genetic redundancy
    methionine encode by only 1 codon (AUG)
  • "What does commaless, nonoverlapping genetic code refer to"
    read from a fixed starting point as a continuous sequence of bases
  • What does universal genetic code refer to and what are some exception
    "genetic code is conserved throughout evolution, except for mito, archaebacteria, mycoplasma, and some yeast"
  • What is a silent mutation
    "same AA, often base change in 3rd position of codon (tRNA wobble)"
  • What is a missense mutation
    changed AA (convservative - new AA is similar in chemical structure)
  • What is a nonsense mutation
    change resulting in early stop codon
  • What is a frame shift
    "change resulting in misreading of all nucleotides downstream, usually resulting in a truncated nonfxnal protein"
  • What is the order of severity for the different types of mutations
    nonsense > missense > silent
  • Eukaryotic and prokaryotic DNA synthesis is blank and involves both blank and blank strands
    "semiconservative, continuous and discontinuous strands (okazaki fragments)"
  • "For eukaryotes, where does replication begin?"
    consesus sequenec of base pairs
  • What is the origin of replication
    particular sequence of DNA where replicatino begins - may be single of multiple
  • Describe the replication fork
    Y shaped region along the DNA template where leading nad lagging strands are synthesized
  • What does helicase do
    unwinds DNA template at replcation fork
  • What do the single stranded binding proteins do
    prevent strands from reannealing
  • What do DNA topoisomerases do
    creat a nick in the helix to relieave supercoils created during replication
  • What does primase do
    makes RNA primer on which DNA poly III can initiate replication
  • What does DNA poly III do?
    "prokaryotic only - elongates leading strand by adding deoxnucTIDE to the 3' end. Elongates lagging strand until it reaches primer of preceeding fragment. 3' to 5' exonuclease activity ""proofreads"" each added nucTIDE"
  • What does DNA poly I do?
    prokaryotic only - degrades RNA primer and fills in the gap with DNA
  • What does DNA ligase do
    seals.
  • How do fluoroquinolones work
    inhibit DNA gyrase specific for prokaryotic topoisomerase
  • "In which single strand DNA repair mechanism do specific endonucleases release the oligonucTIDE containing bases and DNA poly and ligase fill and reseal, and what disease occures when this is mutated"
    nucleotide excision repair - xeroderma pigmentosum; unable to repair thymidine dimers caused by UV light
  • "In base excision repaire, what recognizes and removes damaged bases and what cuts the DNA to remove the empty sugar"
    "specific glycosylases, AP endonuclease"
  • "In mismatch repair, which strand is recognized and in what hereditary syndrome is this defective"
    "unmethylated, newly synthesized, HNPCC"
  • Is there any requirement for homology in NHEJ
    no - its non homologous
  • In what direction are DNA and RNA synthesized
    5' to 3'
  • Which carbon bears the triphosphate and the energy source for bond formation
    5' of the incoming nucleotide
  • What is the target of the 3' hydroxyl attack
    The triphosphate bond
  • In which direction is protein synthesized
    N to C
  • What is the most abundant type of RNA
    rRNA
  • What is the longest time of RNA and shortest
    "mRNA, tRNA"
  • What does the start codon code for in eukaryotes and prokaryotes
    "eu - methionine, pro - formyl-methionine"
  • What are the mRNA stop codons
    "UGA, UAA and UAG"
  • Which part of the DNA binds RNA polymerase and multiple other TFs upstream from gene locus
    "promotor - TATA box, and CAAT box, AT rich"
  • What stretch of DNA that alters gene expression by binding of transcription factors
    enhancers
  • This is the site where negative regulators bind
    silencers
  • "In eukaryotes, what does RNA poly I make"
    rRNA
  • "In eukaryotes, what does RNA poly II make"
    mRNA
  • "In eukaryotes, what does RNA poly III make"
    tRNA
  • Which RNA poly opens DNA at promotor site
    RNA poly II
  • "RNA poly can't proofread, but what can it do"
    initiate chains
  • "In prokaryotes, what does makes the different types of RNA"
    1 kind with multiple subunits
  • Why does alpha amanitin cause liver failure and where is it found
    "inhibits RNA polymerase II, found in death cap mushrooms"
  • What 3 steps in RNA processing occur after transcription
    1- capping on 5' (7-methyguanosine) 2 - polyadenylation on 3' end 3 - splicing out of introns
  • What is the initial transcript called and what is the capped and tailed transcript called
    "initial is heterogenous nuclear RNA, the capped and tailed is called mRNA"
  • Which enzyme involved in RNA synthesis does not require a template
    poly A polymerase - signal is AAUAA
  • What kind of RNA is transported out of the nucleus
    only processed RNA
  • What does the primary transcript combine with to form the spliceosome
    snRNPs and other proteins
  • What shape does the RNA generate during splicing and why?
    lariat shape in order and remove intron precisely and join 2 exons
  • Which aspect of the spliceosome do patients with lupus make antibodies against
    snRNPs
  • What part of the pre mRNA contains the actual genetic information coding for protein
    exons
  • How many nucTIDEs is a tRNA and what does the secondary sturcture form
    "75 to 90, cloverleaf"
  • Which end of the tRNA is the amino acid bound to
    3' end (with CCA)
  • "What does aminoacyl tRNA synthetase do the AA before and after it binds to tRNA, and what happens if it's the wrong the match"
    "scrutinizes, hydrolyzes the bond"
  • What does a mischarge tRNA do
    reads usual codon but inserts wrong AA
  • How do tetracyclines work
    bind 30s subunit preventing attachment of aminoacyl-tRNA
  • "Accurate base pairing is required only in the first two nucleotide positions of an mRNA codon, so conds differeing in the 3rd position may code for the same tRNA/AA due to degenerate genetic code"
    wobble
  • What initiates protein synthesis
    "GTP hydrolysis, initiation factors assemble 40S ribosomal subunit with initiator tRNA and are released with mRNA and ribosomal subunit assemble with the complex"
  • What happens in elongation of protein synthesis
    "Aminoacyl-tRNA binds A site, ribosomal rRNA catalyzes peptide bond formation, transfers growing peptide to AA in A site, ribosome advances 3 nucTIDE toward 3' end of RNA, moving peptidyl RNA to P side"
  • What happens in termination of proteins synthesis
    "stop codon is recognized by release factor, and completed protein is released from ribosome"
  • What ribosomes do eukaryotes have
    "40, 60, 80"
  • What ribosomes do prokaryotes have
    "30, 50, 70"
  • What is the energy source for tRNA actication (charging)
    ATP
  • What is the energy source for translocation
    GTP
  • How do aminoglycosides work
    by inhibiting formation of the initiation complex and cause misreading of mRNA
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