B&B Cell Bio Flashcards
Which cell cycle checkpoint is blocked by p53?<div><br></br></div><div>{{c1::G1 to S}}</div>
“<div><i>Hence a mutation can cause uncontrolled cell division</i><br></br></div><div><i>Also blocked by hypophosphorylated Rb <br></br></i><div><img></img></div></div>”
Which cell cycle checkpoint is blocked by hypophosphorylated Rb?<div><br></br></div><div>{{c1::G1 to S}}</div>
“<div><i>Hence a mutation can cause uncontrolled cell division</i><br></br></div><div><img></img></div>”
<div><b>Rhabdomyoblasts</b> are characterized by positive IHC staining for <b>{{c1::desmin}}</b> and <b>{{c1::myogenin}}</b> </div>
“<i>desmin is an intermediate filament of muscles cells; </i><i>malignant rhabdomyoblasts cause embryonal </i><b><i>rhabdomyosarcoma</i></b><div><b><i><br></br></i></b></div><div><i>myogenin<b> </b>is a transcription factor present in immature muscle cells</i></div>”
<div>What process is used by <b>mismatch repair enzymes</b> to distinguish between <u>old</u> and <u>new</u> <b>DNA strands</b> in prokaryotes?</div>
<div><br></br></div>
<div>{{c1::DNA methylation}}</div>
template strand <b>cytosine</b> and <b>adenine</b> are methylated for this very purpose
<div>What process takes <b>DNA</b> and makes more <b>DNA</b>? </div>
<div><br></br></div>
<div>{{c1::Replication}}</div>
“<img></img>”
<div><div>What process takes <b>DNA</b> and makes <b>RNA</b>? </div><div><br></br></div><div>{{c1::transcription}}</div></div>
“<img></img>”
<div><div>What process takes <b>RNA</b> and makes <b>protein</b>? </div><div><br></br></div><div>{{c1::translation}}</div></div>
“<img></img>”
<div><div><div>DNA & RNA are made of <b>{{c1::nucleotide monophosphates}}</b> connected via a(n) {{c2::<b>phosphodiester</b>}} bond</div></div></div>
“<img></img>”
<div>One feature of the <b>genetic code</b> is that it is {{c1::degenerate/redundant}}: most amino acids are coded by <i>multiple</i> codons </div>
<i><u>exceptions</u>: methionine and tryptophan are encoded by only 1 codon (AUG and UGG, respectively)</i>
<div>One feature of the <b>genetic code</b> is that it is {{c1::commaless, nonoverlapping}}: it is read from a fixed starting point as a continuous sequence of bases</div>
<i><u>exceptions</u>: some viruses</i>
<div>One feature of the <b>genetic code</b> is that it is {{c1::universal}}: genetic code is conserved throughout evolution</div>
<i>exceptions: mitochondria (in humans)</i>
<div>What does <b>AUG</b> encode for in <i>eukaryotes</i>?</div>
<div><br></br></div>
<div>{{c1::Methionine (start codon)}}</div>
<i>rarely GUG is a start codon as well</i>
<div><div>What does <b>AUG</b> encode for in <i>prokaryotes</i>?</div><div><br></br></div><div>{{c1::N-formylmethionine, or fMet (start codon)}}</div></div>
<i>fMet also stimulates neutrophil chemotaxis</i>
<div>Which <u>three</u> sequences of bases are mRNA <b>stop codons</b>? </div>
<div><br></br></div>
<div>{{c1::<b>UGA</b>, <b>UAA</b>, <b>UAG</b>}}</div>
“<i>”“<b>U G</b>o <b>A</b>way, <b>U</b> <b>A</b>re <b>A</b>way, <b>U</b> <b>A</b>re <b>G</b>one””</i> “
<div>The {{c1::origin of replication}} is a particular consensus sequence of base pairs in a genome where <b>DNA replication begins</b> </div>
“<div><i>may be <u>single</u> (prokaryotes) or <u>multiple</u> (eukaryotes)</i> </div><div><img></img></div>”
<div>{{c1::AT}}-rich sequences are found in <b>promoters</b> and <b>origins</b> <b>of replication</b></div>
AT has 2 bonds vs 3 in GC-easier to break apart
<div>The {{c1::replication fork}} is a Y-shaped region along the DNA template where <b>leading</b> and <b>lagging strands are synthesized</b> </div>
“<img></img>”
<div>Which enzyme is responsible for <b>unwinding the DNA template</b> at the replication fork? </div>
<div><br></br></div>
<div>{{c1::Helicase}} </div>
“<img></img>”
<div>{{c1::Single-stranded binding}} proteins <u>prevent</u><b> DNA strands from reannealing</b> during replication </div>
“<img></img>”
<div>Which enzyme is responsible for <b>relaxing the DNA strand</b> by creating single- or double-stranded breaks in the DNA helix to add/remove supercoils? </div>
<div><br></br></div>
<div>{{c1::Topoisomerase}} </div>
“<div><img></img></div>”
<div>Which enzyme is responsible for <b>making an RNA primer</b> on which DNA polymerase III can initiate replication (<u>prokaryotes</u>)? </div>
<div><br></br></div>
<div>{{c1::Primase}}</div>
“<img></img>”
<div>Which enzyme is responsible for <b>elongating the DNA strand</b>? </div>
<div><br></br></div>
<div>{{c1::DNA polymerase (specifically, DNA polymerase III in <u>prokaryotes</u>)}}</div>
“<div><i>DNA polymerase uses <b>dNTP</b> substrates to add <b>monophosphates</b>; In the process, inorganic pyrophosphate (PPi) is given off</i></div><div><i><img></img></i></div>”
<div><div><div><b>{{c2::DNA}} polymerase</b> <i>must</i> see a(n) {{c1::<b>RNA primer</b>}} to bind, which is <b>complementary</b> and <b>antiparallel</b> to the polymerase</div></div></div>
“Technically it doesn’t need to be an <u>RNA</u> primer, just any primer with a 3’-OH group (i.e. PCR)<div><img></img></div>”
“<div><div><div><b>DNA polymerase </b>pauses and checks (““<b>proof-reads</b>””) via {{c1::3’ -> 5’ exonuclease}} activity</div><div></div></div></div>”
“<img></img>”
<div>Which enzymes are responsible for <b>removing the RNA primer</b> in <i><u>eukaryotes</u></i>? </div>
<div><br></br></div>
<div>{{c1::RNase H and FEN-1::2}}</div>
“<div>*<i>note: this is probably pretty low yield for step 1</i></div><div><br></br></div><div>Removal of primers</div><div>Prokaryotes: RNase H and DNA polymerase I (5’→3’ exonuclease activity)</div><div>Eukaryotes: RNase H and FEN-1 (flap endonuclease-1)</div><div><br></br></div><div>Gaps between fragments are filled after primer removal</div><div>Prokaryotes : DNA polymerase I</div><div>Eukaryotes : Polymerase δ</div><div><img></img></div>”
<div>Which enzyme catalyzes the formation of a phosphodiester bond between <b>Okazaki</b> <b>fragments</b>?</div>
<div><br></br></div>
<div>{{c1::DNA ligase}}</div>
“<div><i>this is the <b>lagging strand</b> and is synthesized in the direction <u>away</u> from the replication fork</i> </div><div><img></img></div>”
“<div>The enzyme which adds {{c2::<u>TTAGGG</u>::sequence}} to 3’ ends of chromosomes to <b>avoid loss of genetic material</b> with every duplication is known as {{c1::<b>Telomerase</b>}}</div>”
<i>- eukaryotes only; prokaryotes have circular DNA</i> <div><br></br></div><div>- critically shortening in telomere length –> signal for programmed cell death (TP53 becomes activated –> apoptosis)</div>
<div><div>Which replication enzyme is a <b>RNA-dependent</b> <b>DNA</b> <b>polymerase</b>, and thus a major example of reverse transcriptase activity, in humans? </div><div><br></br></div><div>{{c1::Telomerase}} </div></div>
- endogenously expressed in cells that need to divide regularly(ex. <b>germ cells, </b>certain adult <b>stem cells</b>), allowing them to proliferate indefinitely in a controlled manner
<div><div><div>Telomerase is a rare example where <b>{{c1::reverse transcriptase::enzyme}}</b> activity occurs <i>endogenously</i> in humans </div></div></div>
This is found in <b>eukaryotes only</b>
<div><div><div>What pathology is associated with <u>increased</u> telomerase activity?</div><div><br></br></div><div>{{c1::Cancer}}</div></div></div>
> 90% of cancer cells contain increased telomerase activity, allowing for continued proliferation without apoptosis
“<div><div><div><div><b>{{c1::RNA}} polymerase</b> <u>doesn't have to</u> see a <b>RNA primer</b> to bind</div><div></div></div></div></div>”
“binds to promoter regions and requires transcription factors<div><img></img></div>”
<div>Which type of <b>DNA</b> <b>mutation</b> causes the <u>least</u> severe damage? </div>
<div><br></br></div>
<div>{{c1::Silent mutations}}</div>
<i>silent «_space;missense < nonsense < frameshift</i>
<div><div>Which type of <b>DNA</b> <b>mutation</b> causes the <u>most</u> severe damage? </div><div><br></br></div><div>{{c1::frameshift mutations}}</div></div>
<i>silent «_space;missense < nonsense < frameshift</i>
<div>A(n)<b>{{c1::silent}} mutation</b> occurs when a nucleotide substitution codes for the <u>same</u> amino acid</div>
“<div><i>often a base change in 3rd position of codon (tRNA wobble)</i></div><div><i><img></img></i></div>”
<div>A(n)<b>{{c1::missense}} mutation</b> occurs when a nucleotide substitution codes for a <u>different</u> amino acid</div>
“<div><i>e.g. sickle cell disease (substitution of glutamic acid with valine)</i></div><div><i><img></img></i></div>”
<div>A(n)<b>{{c1::nonsense}} mutation</b> occurs when a nucleotide substitution codes for a <b>stop</b> codon</div>
“<div><i>usually results in a nonfunctional protein</i></div><div><img></img> </div>”
<div>A(n)<b>{{c1::frameshift}} mutation</b> occurs when there is a <u>deletion</u> or <u>insertion</u> of a number of nucleotides <b>not divisible by {{c2::3}}</b>, resulting in misreading of all nucleotides downstream</div>
“<div><i>protein may be shorter or longer, and its function may be disrupted or altered; examples include </i><b>duchenne muscular dystrophy</b><i> and </i><b>Tay-sachs disease</b> </div><div><br></br></div><div><img></img></div><div><br></br></div><div><img></img></div>”
<div><div>A mutation at a(n) {{c1::splice site}} results in a <b>retained intron</b> in the mRNA, leading to a protein with impaired or altered function</div></div>
“<i>rare cause of cancers, dementia, epilepsy, and some types of </i><b>β-thalassemia</b> “
<div><div>The enzyme that <u>recognizes</u> and <u>excises</u> <b>pyrimidine dimer</b> mutations is {{c1::excision endonuclease}}</div></div>
<i>nucleotide excision repair</i>
<div><div>What phase of the cell cycle do <b><u>nucleotide</u> excision repairs</b> occur?</div><div><br></br></div><div>{{c1::G1}}</div></div>
“In contrast, BER occurs in all phases of the cell cycle and Mismatch Repair occurs predominantly in S<br></br><div><br></br></div><div><img></img></div>”
<b>Xeroderma Pigmentosum</b> is an inherited pathology due to a defective {{c1::Nucleotide Excision Repair}} pathway
“<div><div><i>- This is inherited in an <b>autosomal recessive </b>manner </i></div><div><i><br></br></i></div><div><i>- can diagnose by measurement of repair mechanisms in WBCs</i></div></div><div><i><br></br></i></div><div><i><img></img></i></div>”
<div><div><div>What form of <b>DNA repair</b> fixes mutations due to DNA replication errors?</div><div><br></br></div><div>{{c1::Mismatch repair}}</div></div></div>
very important for maintaining <b>microsatellite stability</b> (DNA slippage can occur easily at these sites). Problems with this can lead to <u>colon cancer</u>
<div><div><u>Recognition</u> and <u>facilitation of excision</u> of <b>{{c2::mismatched nucleotides}}</b> occur via enzymes found on <b>two</b> genes: {{c1::<b>MSH2 (MutS)</b>}} or {{c1::<b>MLH1 (MutL)</b>}} </div></div>
<i>- <b>MutS</b> recognizes the mismatch on the newly created daughter strand (distinguished from parent strand by occasional nicks in the daughter strand phosphodiester bonds), <b>MutL</b> is then recruited and the complex slides along the DNA until 1 of daughter strand nicks is encountered</i><div><i><br></br></i></div><div><i>- <b>exonuclease 1 </b>is then loaded onto the repair complex and activated, which then excises the mismatch<br></br></i><div><i><br></br></i></div><div><i>Mutations in these genes account for 90% of cases of Lynch syndrome</i></div></div>
<div><div>What pathology is characterized by a deficiency of the <u>enzymes</u> used in <b>mismatch base repair</b>? </div><div><br></br></div><div>{{c1::Lynch syndrome (hereditary nonpolyposis colorectal cancer [HNPCC])}}</div></div>
leads to colon cancer with <b>microsatellite instability</b> (DNA slippage can occur easily at these sites). Problems with this can lead to <u>colon cancer</u>
<div><div>What phase of the cell cycle do <b>mismatch base repairs</b> <u>predominantly</u> occur?</div><div><br></br></div><div>{{c1::S}}</div></div>
”- <b>some also occur in G2</b>; whereas NER occurs in G1 and BER occurs throughout cell cycle<div><br></br></div><div><img></img></div>”
<div><div><div>What form of <b>DNA repair</b> fixes mutations due to spontaneous/toxic deamination?</div><div><br></br></div><div>{{c1::Base excision repair}}</div></div></div>
i.e. deamination, oxidation, etc
<div><div>In <b>base excision repair</b>, base-specific {{c1::glycosylases}} <u>remove</u> the altered base and create a(n) {{c2::AP (apurinic/apyrimidinic)}} site </div></div>
“<i>ex. cytosine deamination is repaired with uracil glycosylase</i><div><div><i><img></img></i></div><div><i><br></br></i></div><div><i><img></img></i></div></div>”
“<div><div>Which <b>base excision repair </b>enzyme is responsible for <u>removing nucleotides</u> at the <b>5’ end</b>?</div><div><br></br></div><div>{{c1::AP-endonuclease}} </div></div>”
“<img></img><div><img></img></div>”
“<div><div><div>Which <b>base excision repair </b>enzyme is responsible for <u>removing nucleotides</u> at the <b>3’ end</b>?</div><div><br></br></div><div>{{c1::Lyase}} </div></div></div>”
“<img></img><div><img></img></div>”
<div><div>What phase of the cell cycle do <b><u>base</u> excision repairs</b> occur?</div><div><br></br></div><div>{{c1::Throughout the cell cycle}}</div></div>
“Whereas NER occurs in G1, and mismatch occurs predominantly in S<br></br><div><br></br></div><div><img></img></div>”
<div><div>Which forms of <b>DNA repair</b> repairs double-stranded breaks (due to <u>ionizing radiation)</u>?</div><div><br></br></div><div>{{c1::Nonhomologous end joining}} and {{c2::homologous recombination}}</div></div>
“<div><i>Nonhomologous End Joining depicted below</i></div><div><i><br></br></i></div><div><i><img></img></i></div><div><i>Homologous Recombination depicted below</i></div><div><i><img></img></i></div>”
<div>Mechanisms to repair {{c1::dsDNA}} breaks are defective in Ataxia telangiectasia, Fanconi anemia, and SCID</div>
<i>- Due to defects in the ATM protein, FANC enzymes, and Artemis enzyme respectively</i>
<div>The {{c1::template}} strand is the dsDNA strand used for transcription; it is <b>complementary</b> and <b>antiparallel</b> to mRNA</div>
“<img></img>”
<div>The {{c1::coding}} strand is the strand of dsDNA that is <u>NOT</u> used during transcription, but is <b>identical to mRNA</b> (substitute T/U)</div>
“<img></img>”
<div><div><u>Practice</u>: If a DNA template sequence is TAGC, what is the mRNA sequence?</div><div><br></br></div><div>{{c1::GCUA}}</div></div>
“<i>AUCG is wrong because the strand is <u>built</u> in the 5’ to 3’ direction</i> “
<div>The {{c1::untranslated region (UTR)}} of m<b>RNA </b>is the portion of mRNA which contains no protein information</div>
“<div><div><i>every RNA contains a <b>5’ </b>and <b>3’ UTR</b></i></div></div><div><i><img></img></i></div>”
“<div><div>In <i>eukaryotes</i>, each gene has it’s <i>own</i> {{c1::promoter}}, to which RNA polymerase II may bind </div></div>”
<i>in prokaryotes, there may be one promoter for many genes (<u>operons</u>)</i>
<div>The <b>promoter</b> is an AT-rich upstream sequence with {{c1::TATA}} and {{c1::CAAT}} boxes </div>
“<div>- TATA (Hogness) is located approximately 25 bases upstream, CAAT is located 70-80 bases upstream</div><div><br></br></div><div>- these regions of weak A:T bonds are where RNA polymerase binds (easy to open up vs stronger G:C bonds)</div><div><br></br></div><div><img></img></div>”
<div><div><b>Promoters</b> serve as binding sites for {{c1::general::general/specific}} transcription factors</div></div>
“<div><i>they are present in <u>all cells with a nucleus</u> and are involved in basal transcription</i></div><div><br></br></div><div><img></img></div>”
<div><div>{{c1::Enhancers}}<b> </b>are stretches of DNA that <b>increase</b> <b>gene</b> <b>expression</b> by binding <i>specific </i>transcription factors</div></div>
“These bind regulatory activator proteins which stabilize RNA polymerase<div><br></br></div><div><img></img></div>”
<div><div>{{c1::Silencers}} are sites where <b>negative</b> <b>regulators</b> (repressors) bind to DNA</div></div>
<div>These <b>decrease</b> expression of a gene on the same chromosome by preventing RNA polymerase from binding</div>
<div><div><b>Enhancers</b> increase transcription via enhanced activity of the enzyme {{c1::RNA polymerase II}}</div></div>
”- enhancers bind regulatory Activator proteins that stabilize transcription factors / RNA pol<div><br></br></div><div><img></img></div>”
<div><div><b>Enhancers</b> serve as binding sites for {{c1::specific::specific/general}} transcription factors</div><div></div></div>
“<img></img>”
<div><div>Are <b>enhancers</b>/<b>silencers</b> <i>close</i> or <i>far</i> from the gene it regulates?</div><div><br></br></div><div>{{c1::May be close to, far from, or within the gene (in an intron)}}</div></div>
“<div>- Because of DNA coiling, many are geometrically close but many nucleotides away from gene</div><div><br></br></div><div>- enhancer sequences can also bind activator proteins that facilitate bending of DNA</div><div><br></br></div><div><img></img></div>”
<div><div><div>How can <b>enhancers</b> be far away from the gene it regulates?</div><div><u><br></br></u></div><div>{{c1::DNA will bend to bring enhancer to promoter}} </div></div></div>
“<img></img>”
<div>RNA polymerase {{c1::I}} makes {{c2::r}}RNA </div>
“<i>rRNA is the <u>most numerous</u> RNA; this is restricted to the <b>Nucleolus </b>and thus in Cancer, malignant cells with high mitotic activity have a large # of active rRNA and <b>prominent nucleoli</b></i><div><br></br><div><img></img></div></div>”
<div>RNA polymerase {{c1::II}} makes {{c2::m}}RNA </div>
“<i>mRNA is the <u>largest</u> RNA; this enzyme is inhibited by the <b>amanita phalloides (death cap mushroom) amatoxin</b></i><div><b><i><br></br></i></b><div> <img></img></div></div>”
<div>RNA polymerase {{c1::III}} makes {{c2::t}}RNA and 5S rRNA </div>
<div></div>
“<i>tRNA is the <u>smallest</u> RNA</i><div><img></img></div>”
<div>In <i>eukaryotes</i>, <b>{{c2::RNA polymerase II}}</b> may be <u>inhibited</u> by {{c1::<b>α-amanitin</b>}}</div>
<i><div></div></i><i>- absorbed into GI tract, amatoxins are transported to liver by portal circulation whereby active transport by organic anion transporting polypeptide (OATP) and sodium taurocholate cotransporter (NTCP) concentrate toxin within liver cells</i><div><i><br></br></i></div>- found in Amanita phalloides (<b>death cap mushrooms</b>); causes severe <u>hepatotoxicity</u> if ingested (6-24 hours post ingestion, abdominal pain, vomiting, and cholera like diarrhea)
<div>What drug is an <u>inhibitor</u> of <i>prokaryotic</i> <b>RNA polymerase</b>? </div>
<div><br></br></div>
<div>{{c1::Rifampin}}</div>
<i>therefore, rifampin blocks prokaryotic transcription</i>
“<div><div><div>One <i>co-transcriptional modification</i> is the addition of a(n)<b>{{c1::7-methylguanosine cap}}</b> at the <b>{{c2::5}}’ end</b> </div></div></div>”
“<img></img><div>- occurs in 2 stages, adding GTP, then methylation</div><div><br></br></div><div>- capping occurs in the nucleus as RNA is being transcribed; functions as protection against cellular degradation / allow escape from nucleus</div>”
“<div><div><div>One <i>post-transcriptional modification</i> is the addition of a(n)<b>{{c1::poly-A tail}}</b> at the <b>3’ end</b> </div></div></div>”
“<div><i>- synthesized by poly-A polymerase in the nucleus</i></div><div><i><br></br></i></div><div><i>- <b>protects mRNA from degradation within the cytoplasm</b> after it exits the nucleus</i> </div><img></img>”
<div><div><div>What sequence of bases represents a <b>polyadenylation signal</b>?</div><div><br></br></div><div>{{c1::AAUAAA::6}}</div></div></div>
telomeres are TTAGGG
<div><div><div>mRNA <b>quality control</b> occurs at {{c1::cytoplasmic processing bodies (P-bodies)}}, which contain exonucleases, decapping enzymes, and microRNAs</div></div></div>
- these are involved in regulation and turnover of mRNA; particularly in translation repression and mRNA decay<div><br></br></div><div>- additionally, certain constituents are involved in microRNA induced mRNA silence</div>
<div><div><div>mRNAs may be <b>stored</b> in {{c1::P-bodies}} for future translation</div></div></div>
- typically mRNA once entering cytosol associates with ribosomes, certain mRNA associated with proteins found in P bodies<div><br></br></div><div>- P bodies can partake in mRNA quality control, but also act to store mRNA to later release for further translation</div>
<div><div><div><div><div>In the <i>first</i> step of <b>alternative</b> <b>splicing</b>, the primary transcript (hnRNA) combines with {{c1::<b>small nuclear ribonucleoproteins</b> (snRNPS)}} and other proteins to form the <b>{{c2::spliceosome}}</b> </div></div></div></div></div>
“<div><i><b>Anti-snRNP antibodies are known as anti-Smith antibodies (SLE)</b></i></div><br></br><div><img></img></div>”
<div><div><div><div><div>After the <b>spliceosome</b> has been formed in <u>alternative splicing</u>, a(n) {{c1::lariat-shaped (looped)}} intermediate is generated</div></div></div></div></div>
“<img></img>”
<div><div><div><div><div>In the <i>final</i> step of <b>alternative splicing</b>, the {{c2::lariat}} is released to precisely remove the {{c1::intron}} and join <u>two</u> {{c1::exons}}</div></div></div></div></div>
“<img></img><div>Spliceosomes remove introns containing <b>GU </b>at the 5’ splice site and <b>AG</b> at the 3’ splice site</div><div><br></br></div>”
<div><div><div><div><div>Antibodies to <b>spliceosomal snRNPs</b>, also known as <b>{{c2::anti-Smith}} antibodies</b>, are highly specific for {{c1::<b>SLE</b>}}</div></div></div></div></div>
Lupus
<div><div><div><div>Different <i>exons</i> are frequently combined by {{c1::alternative splicing}} to produce a larger number of <u>unique</u> proteins </div></div></div></div>
“<div><i>allows for </i><b>multiple</b><i>, </i><b>different</b><i> </i><b>proteins</b><i> to be generated from a </i><b>single</b><i> </i><b>gene</b> </div><div><img></img></div>”
<div><div><div><div><div>One <u>hematological pathology</u> that is due to <b>abnormal splicing variants</b> is {{c1::β-thalassemia}}</div></div></div></div></div>
“<i>mutation in 5’ splice donor site of intron 1, therefore intron 1 is not removed</i><div><i><br></br></i></div><div><i>others include; Gaucher disease, Tay-Sachs Disease, Marfan syndrome</i></div>”
<div><div>{{c1::microRNAs}} are small, <i>noncoding</i> <b>RNA</b> <b>molecules</b> that <i>post-transcriptionally</i> regulate <b>protein</b> expression</div></div>
“<i><b>introns</b> can contain microRNA (miRNA) genes</i><div><div><img></img></div></div>”
<div><b>microRNA</b> often leads to the {{c1::silencing/inactivation}} of <i>target</i> <i>mRNA</i>, thus causing {{c1::<u>decreased</u>}} translation into protein</div>
<div><i>can have multiple mRNA targets, typically</i></div>
<div><i>related to complementary base pairing</i> </div>
<div><div>{{c1::tRNAs}} are the <i>smallest</i> RNAs and have a <u>clover-leaf structure</u> </div></div>
“<img></img>”
<div><div>At the <u>base</u> of a <b>tRNA molecule</b> is a(n)<b>{{c1::anti-codon loop}}</b>, which base pairs with a codon of mRNA in a <i>complementary</i>, <i>antiparallel</i> fashion</div></div>
“<img></img>”
“<div>At the <b>{{c2::3}}’ end</b> of a <b>tRNA molecule</b> is a(n)<b>{{c1::5’-CCA-3’}} sequence</b>, which<i> </i>is the amino acid <i>acceptor stem</i></div>”
“<div><i>CCA = <b>C</b>an <b>C</b>arry <b>A</b>mino acids</i> </div><div><br></br></div><div>The -OH of A links to the amino acid</div><div><br></br></div><div><img></img></div>”
<div><div>The <b>{{c1::T-arm}}</b> of <b>tRNA</b> contains the <u><b>TΨC</b> </u><u><b>sequence</b></u> (<b>ribothymidine</b>, <b>pseudouridine</b>, <b>cytidine</b>) necessary for tRNA-ribosome binding</div></div>
“<img></img>”
<div><div>What is the function of the <b>T-arm</b> of <b>tRNA</b>? </div><div><br></br></div><div>{{c1::tRNA-ribosome binding}}</div></div>
“<img></img>”
<div><div>The <b>{{c1::D-arm}}</b> of <b>tRNA</b> contains <u>dihydrouridine</u> residues necessary for tRNA recognition by the correct aminoacyl-tRNA synthetase</div></div>
“<img></img>”
<div><div><div><b>Aminoacyl-tRNA synthetase</b> requires {{c1::ATP}} and releases inorganic PPi</div></div></div>
“<div><i>scrutinizes an amino acid before and after it binds to tRNA; if incorrect, bond is hydrolyzed</i></div><div><img></img></div>”
“<div><div>Accurate base pairing is usually required only in the first <b>two</b> nucleotide positions of a <u>mRNA codon</u> because codons differing in the <b>3rd</b> “”{{c1::wobble}}”” position may code for the same amino acid</div></div>”
“<img></img>”
<div><b>Peptide bond formation</b> is facilitated by the <b>ribozyme</b> <i>{{c1::peptidyl transferase}}</i></div>
“<div><i>a <b>ribozyme </b>is RNA carrying out a catalytic reaction (enzyme is a protein)</i></div><div><img></img></div>”
<div><div><div>What is the <u>smaller</u> <b>ribosomal subunit</b> used in <i>prokaryotic</i> translation? </div><div><br></br></div><div>{{c1::30s}}</div></div></div>
<i>this subunit recognizes the shine dalgarno sequence</i>
<div><div><div>What is the <u>total</u> size of the <b>ribosome</b> used in <i>prokaryotic </i>translation?</div><div><br></br></div><div>{{c1::70s}}</div></div></div>
“<img></img>”
<div><div><div>What is the <u>smaller</u> <b>ribosomal subunit</b> used in <i>eukaryotic</i> translation? </div><div><br></br></div><div>{{c1::40s}}</div></div></div>
“<i>this subunit recognizes the 5’-7-Methyl-G-cap</i> “
<div><div><div><div>What is the <u>larger</u> <b>ribosomal subunit</b> used in <i>eukaryotic</i> translation? </div><div><br></br></div><div>{{c1::60s}}</div></div></div></div>
“<i>this is the target of </i><b>shiga</b><i> </i><b>toxins</b><i> and </i><i>verotoxin</i> “
<div><div><div><div>What is the <u>total</u> size of the <b>ribosome</b> used in <i>eukaryotic </i>translation?</div><div><br></br></div><div>{{c1::80s}}</div></div></div></div>
“<img></img>”
<div><div><i>Eukaryotic</i> {{c1::Initiation Factors}} help <u>assemble</u> the <b>40s</b> <b>ribosomal subunit</b> with the initiator tRNA</div></div>
“<i><div></div></i><i>- IF’s identify either the 5’ cap or an internal ribosome entry site (IRES - often located in 5’-UTR); Uses GTP to assemble the structure</i><div><br></br></div>- initiation factors are released when the mRNA and the ribosomal 60S subunit assemble with the complex <div><br></br></div><div><br></br></div><div><img></img></div><div><img></img></div>”
<div><div><b>Translation</b> is initiated by {{c1::GTP}} hydrolysis </div></div>
“<img></img>”
<div><div>At what <u>site</u> of the <i>ribosome</i> does tRNA bind to for translation <b>initiation</b>? </div><div><br></br></div><div>{{c1::P site}}</div></div>
”"”prepare”” site- the ““peptidyl”” site<div><img></img></div>”
<div><div>In the <u>first</u> step of strand <b>elongation</b>, a(n) {{c1::aminoacyl-tRNA}} binds to the <b>A</b> site </div></div>
“<img></img>”
<div><div>After aminoacyl-tRNA binds to the A site of the ribosome, {{c1::peptidyl transferase}}, a <b>ribozyme</b>, catalyzes peptide bond formation (translation)</div></div>
“<img></img>”
“<div><div>In the final step of translation <b>elongation</b>, {{c1::translocation}} of the ribosome occurs, advancing the ribosome 3 nucleotides towards the 3’ end of mRNA</div></div>”
“<div><i>requires GTP and elongation factors</i></div><div><i><br></br></i></div><img></img>”
<div><div>In addition to GTP, <b>translocation</b> of the ribosome during <i>translation</i> also requires eukaryotic {{c1::elongation factor 2 (eEF-2)}}</div></div>
“<div><i>- pseudomonas exotoxin A and diphtheria toxin act via inhibition of eukaryotic enlongation factor 2 </i><i>via <b>ADP ribosylation</b></i></div><div><br></br></div><div>- translocation occurs when Ribosome advances 3 nucleotides towards 3’ end, moving the peptidyl tRNA to the P site (A site is now empty)</div><div><img></img></div><div><br></br></div><div><img></img></div>”
<div><div>In the <i>final</i> step of <b>translation</b>, a stop codon is recognized by {{c1::release factor}} and the completed polypeptide is released from the ribosome</div><div><div><div></div></div></div></div>
“<img></img>”
<div>A(n)<b>{{c1::chaperone}} protein</b>, is an intracellular protein involved in facilitating and/or maintaining <b>protein</b> <b>{{c2::folding}}</b> </div>
<i>in yeast, <b>heat shock proteins (e.g. Hsp60)</b> are expressed at high temperatures to prevent protein denaturing/misfolding</i>
<div><div><div><div><div>What is the <u>shortest</u> phase of the <b>cell cycle</b>?</div><div><br></br></div><div>{{c1::M phase (mitosis + cytokinesis)}}</div></div></div></div></div>
“<img></img>”
<div><div><div><div><div>Which <b>cell cycle phase</b> is characterized by resting, non-dividing cells?</div><div><br></br></div><div>{{c1::G0}} </div></div></div></div></div>
“<img></img>”
<div><div><div><div><div>What <u>cell type</u> remains in G0 and can only regenerate from stem cells?</div><div><br></br></div><div>{{c1::Permanent}}</div></div></div></div></div>
<i>examples include neurons, skeletal/cardiac muscle, and RBCs</i>
<div><div><div><div><div><div>What <u>cell type</u> enters G1 from G0 when stimulated?</div><div><br></br></div><div>{{c1::Stable (quiescent)}}</div></div></div></div></div></div>
<i>examples include hepatocytes, lymphocytes, renal tubular cells, periosteal cells</i>
<div><div><div><div><div><div>What <u>cell type</u> <i>never</i> enters G0 and divides rapidly with a short G1?</div><div><br></br></div><div>{{c1::Labile}}</div><div></div></div></div></div></div></div>
<i>examples include bone marrow, gut epithelium, skin, hair follicles, and germ cells</i>
<div><div><div><div><div><div>Which <b>cell cycle phase</b> is characterized by DNA synthesis and replication?</div><div><br></br></div><div>{{c1::S}} </div></div></div></div></div></div>
<i><u>46</u> chromosomes/chromosomes per cell before S phase; <u>92</u> <b>chromatids </b>per cell after S phase (still 46 chromosomes)</i>
<div><div><div><div><div>Which <b>cell cycle phase(s)</b> are part of <b>interphase</b>? </div><div><br></br></div><div>{{c1::G1, S, G2}}</div></div></div></div></div>
“<div>- G1 - cells in this phase prepare building blocks for DNA synthesis (synthesis of RNA, protein, lipid, and carbs)</div><div><br></br></div><div>- S - DNA replication occurs during this phase</div><div><br></br></div><div>- G2 - DNA is checked for errors and corrections are made if possible, if corrections cannot be made, then apoptosis will result; ATP synthesis occurs here</div><div><br></br></div><div><img></img></div>”
<div><div><div><div><div><div>Which <b>cell cycle phase(s)</b> are <u>NOT</u> part of <b>interphase</b>? </div><div><br></br></div><div>{{c1::M}}</div></div></div></div></div></div>
“<img></img>”
<div>{{c1::<b>Free</b>}} <b>ribosomes</b> are unattached to any membrane and are the site of <u>synthesis</u> for <b>cytosolic</b> and <b>organellar </b><b>proteins</b></div>
“<img></img>”
<div>What part of the cell is the site of <b>steroid synthesis</b> and <b>detoxification </b>of drugs and poisons?</div>
<div><br></br></div>
<div>{{c1::Smooth endoplasmic reticulum}}</div>
<i>liver hepatocytes and steroid hormone-producing cells of the adrenal cortex and gonads are rich in SER</i>
<div>When proteins are <b>misfolded</b>, multiple {{c1::ubiquitins}} are added, which aids in trafficking to the <i>proteasome</i></div>
“<img></img>”
<div>The {{c1::proteasome}} is a barrel-shaped protein complex that degrades damaged or <b>ubiquitin-tagged</b> proteins</div>
“<img></img>”
<u>Defects</u> in the <b>ubiquitin-proteasome system </b>have been implicated in some cases of {{c1::Parkinson}} disease
<i>defects in the <b>Parkin</b>, <b>PINK1</b>, and <b>DJ-1</b> genes specifically</i>
<div><div>On the <b>N terminal side</b> of <i>newly synthesized protein</i>, a stretch of 10-15 <b>hydrophobic</b> <b>amino acids</b> forms the {{c1::<b>N-terminal signa</b>l}} <b>sequence</b></div></div>
“<img></img>”
<div><div>The <b>N-terminal signal</b> <b>sequence</b> of a newly synthesized protein is bound by a(n) {{c1::<b>signal recognition particle (SRP</b>)}}, which attaches the complex to the {{c2::ER}} membrane </div></div>
“<div><i>once the <u>SRP-protein complex</u> is bound to the ER, the signal sequence is removed and the protein enters the ER (co-translational)</i> </div><div><img></img></div>”
<div><div>Which enzyme <b>phosphorylates</b> <b>mannose</b> in the <u>Golgi apparatus</u>, facilitating protein trafficking? </div><div><br></br></div><div>{{c1::Phosphotransferase}}</div></div>
<i>specifically, N-acetylglucosaminyl-1-phosphotransferase</i>
“<div><div><div>What pathology is associated with a defect in the enzyme <i>N-acetylglucosaminyl-1-phosphotransferase</i>?</div><div><br></br></div><div>{{c1::I-cell disease (inclusion cell disease/mucolipidosis type II)}}</div></div></div>”
<i>failure of the Golgi to phosphorylate mannose residues (i.e. mannose-6-phosphate) on glycoproteins</i>
<div><div><div><b>{{c1::Endosomes}}</b> are <b>sorting</b> <b>centers</b> for material from outside the cell or from the Golgi, sending it to lysosomes for destruction or back to the membrane/Golgi for further use</div></div></div>
“<img></img>”
<div><div><div>Which inherited <u>lysosomal storage disorder</u> is characterized by <b>coarse facial features</b>, <b>clouded</b> <b>corneas</b>, and restricted joint movement with <u>high</u> serum levels of <i>multiple</i> lysosomal enzymes? </div><div><br></br></div><div>{{c1::I-cell disease}}</div></div></div>
“<i><div><i>- often fatal in childhood (typically due to <u>severe dilated cardiomyopathy)</u></i><br></br></div></i><div><i><u><br></br></u></i></div><div><i><u><img></img></u></i></div>”
<div><div><div><b>I-cell disease</b> is characterized by high plasma levels of {{c1::lysosomal}} enzymes</div></div></div>
<i>proteins are secreted extracellularly rather than delivered to lysosomes</i>
<div>Which <b>vesicular trafficking protein</b> is responsible for <i><u>retrograde</u> Golgi transport</i> (<i>cis-</i><i>Golgi and ER) and intra-Golgi transport</i>? </div>
<div><br></br></div>
<div>{{c1::COPI}}</div>
“<div>Normally, Proteins are made at the ER, packaged / modified in the Golgi, and then routed to different locations (lysosomes, secretory vesicles, plasma membrane)</div><div><br></br></div><div>COPI aids in taking proteins that are packaged / modified in the golgi and sending them back to the ER for use there, or to another spot on the golgi apparatus</div><div><div><br></br></div></div><div><img></img></div>”
<div><div>Which <b>vesicular trafficking protein</b> is responsible for <i><u>anterograde</u> Golgi transport</i> (ER to cis Golgi)?</div><div><br></br></div><div>{{c1::COPII}}</div></div>
“<img></img>”
<div><div>Which <b>vesicular trafficking protein</b> is responsible for transport between the <i>trans-Golgi</i> and <i>lysosomes</i>? </div><div><br></br></div><div>{{c1::Clathrin}}</div></div>
“<img></img>”
<div><div>Which <b>vesicular trafficking protein</b> is responsible for transport between the <i>plasma membrane</i> and <i>endosomes</i> (receptor-mediated endocytosis)?</div><div><br></br></div><div>{{c1::Clathrin}}</div></div>
“<img></img>”
<div><div>Which type of <u>filament</u> is predominantly involved in <b>maintainence of cell structure</b>? </div><div><br></br></div><div>{{c1::Intermediate filaments (e.g. desmin, cytokeratin)}}</div></div>
<i>other examples include vimentin, lamins, glial fibrillary acid proteins (GFAP), and neurofilaments</i>
<div><div>Which type of <u>filament</u> is predominantly involved in <b>movement</b> and <b>cell division</b>? </div><div><br></br></div><div>{{c1::Microtubules (e.g. cilia, flagella)}}</div></div>
<i>other examples include <b>mitotic</b> <b>spindles</b>, <b>axonal</b> <b>trafficking</b>, and centrioles</i>
<div><div>What type of <u>filament</u> are <b>cilia</b> and <b>flagella</b>?</div><div><br></br></div><div>{{c1::Microtubule}}</div></div>
“In contrast, villi are actin filaments<div><br></br></div><div><img></img></div>”
<div><b>{{c1::Microtubules}}</b> are a cylindrical outer structure composed of a helical array of polymerized heterodimers of <b>{{c2::α-}}</b> and <b>{{c2::β-tubulin}}</b></div>
“<img></img>”
<div>Each <b>α-</b> and <b>β-tubulin</b> heterodimer of a <u>microtubule</u> has 2 {{c1::GTP}} bound</div>
GDP bound tubulin will dissociate
<div>Which <b>molecular motor</b> <b>protein</b> is responsible for <i>retrograde</i> transport to the microtubule (+ to -)?</div>
<div><br></br></div>
<div>{{c1::Dynein}} </div>
“<img></img>”
<div><div>Which <b>molecular motor</b> <b>protein</b> is responsible for <i>anterograde</i> transport to the microtubule (- to +)?</div><div><br></br></div><div>{{c1::Kinesin}} </div></div>
“<img></img>”
<div><b>{{c1::Cilia}}</b> are organized in a(n)<b>{{c2::9+2}} arrangement</b> of microtubule doublets</div>
<div></div>
“<div>Flagella as well; </div><div><br></br></div><div><img></img></div><div><br></br></div><div><img></img></div>”
<div>The base of a <b>cilium</b> below the cell membrane, called the {{c1::basal body}}, consists of 9 microtubule triplets with no central microtubules</div>
“<img></img>”
<div><b>Axonemal</b> <b>{{c2::dynein}}</b> is a(n)<b>{{c1::ATPase}}</b> that links peripheral 9 doublets and causes <u>bending of cilium</u> (movement)</div>
“Coordinated ciliary beating is facilitated by <b><span>gap junctions</span></b> <br></br> <div> <br></br> </div> <div><img></img></div> <div> <br></br> </div> <div><img></img></div> “
<div><b>{{c1::Kartagener}} syndrome</b> is a(n) {{c3::autosomal recessive::inheritance}} disease characterized by <u>immotile cilia</u> due to a(n)<b>{{c2::dynein arm}} defect</b></div>
<i>also known as primary ciliary dyskinesia; dynein is important for cilia function, thus anything that requires cilia will be dysfunctional (organogenesis, mucociliary tract, fallopian tubes)</i>
<div><b>Kartagener syndrome</b> results in <u>decreased</u> male and female {{c1::fertility}}</div>
<i>due to <b>immotile sperm</b> and dysfunctional fallopian tube cilia, respectively</i>
<div>Which developmental pathology is characterized by <b>bronchiectasis</b>, <b>recurrent sinusitis</b>, and <b>situs inversus</b>? </div>
<div><br></br></div>
<div>{{c1::Kartagener syndrome}}</div>
“<div><i>an example of situs inversus is <b>dextrocardia</b> on CXR</i> </div><div><img></img></div>”
<div>What is the <b>most abundant protein</b> in the human body?</div>
<div><br></br></div>
<div>{{c1::Collagen}}</div>
<i>extensively modified by post-translational modification</i>
<div>What <u>type</u> of <b>collagen</b> is the most common (90%)? </div>
<div><br></br></div>
<div>{{c1::Type I}}</div>
- Found in <b>Bone</b>, <b>Skin</b>, <b>Tendon</b>, <b>Ligaments</b>, Dentin, Fascia
<div>What <u>type</u> of <b>collagen</b> makes up <b>bone</b>, <b>skin</b>, and <b>tendon</b>? </div>
<div><br></br></div>
<div>{{c1::Type I}}</div>
<i>also makes up <b>dentin</b>, fascia, cornea, and is part of <u>late</u> wound repair</i> <div><br></br></div><div>this is defective in <b>Osteogenia Imperfecta</b></div>
<div>What <u>type</u> of <b>collagen</b> makes up <b>cartilage</b>? </div>
<div><br></br></div>
<div>{{c1::Type II}}</div>
<i>also makes up the vitreous body, pubic symphysis, nucleus pulposus</i> <div><br></br></div><div>Autoantibodies to type II collagen can be seen in patients with <b>relapsing polychondritis</b></div>
<div>What <u>type</u> of <b>collagen</b> makes up <b>skin</b> and <b>blood vessels</b>? </div>
<div><br></br></div>
<div>{{c1::Type III}}</div>
<i><div></div></i><i>- Also makes up <u>uterus</u>, <u>fetal tissue</u> (growing fetus need to be able to stretch), <u>granulation tissue</u></i><div><i><u><br></br></u></i></div><div><i>- defective in Vascular Ehlers Danlos</i></div>
<div>What <u>type</u> of <b>collagen</b> makes up <b>reticulin fibers</b>?</div>
<div><br></br></div>
<div>{{c1::Type III}}</div>
This is a very pliable structure
<div>What <u>type</u> of <b>collagen</b> makes up the <b>basement membrane</b>?</div>
<div><br></br></div>
<div>{{c1::Type IV}}</div>
<i>also makes up the basal lamina and lens</i>
<div>The <u>{{c3::vascular}}</u> type of Ehlers-Danlos Syndrome that is caused by a <u>deficiency</u> of <b>type {{c4::III}} collagen</b> can lead to:</div>
<div><br></br></div>
<div>- the formation and rupture of {{c1::<u>aneurysms</u>}} </div>
<div>- rupture of <u>organs</u> (ex. in women the {{c2::uterus::specific organ}} during birth)</div>
<i>- Both <u>Berry</u> and <u>Aortic</u> Aneurysms</i><div><i><br></br></i><div><i>- Pregnant patients with vascular Ehlers-Danlos can rupture their <u>Uterus</u></i></div></div>
<div>What <u>type</u> of collagen is <i>decreased</i> in <b>osteogenesis imperfecta type I</b>?</div>
<div><br></br></div>
<div>{{c1::Type I}}</div>
<i>- collagen is <u>normal</u> but production is decreased</i><div><i><br></br></i></div><div><i>- type I collagen is the predominant collagen in <b>osteoid </b>(organic portion of bone matrix)</i></div>
<div><div>What pathology is characterized by a <u>defective</u> <b>type IV collagen</b>? </div><div><br></br></div><div>{{c1::Alport syndrome}}</div></div>
- Cant See (Lens)<div>- Cant Pee (Basement membrane of the Glomerulus)<br></br><div>- Cant Hear a Bee (Cochlea)</div></div>
<div><b>Type {{c1::IV}} collagen</b> is targeted by <u>autoantibodies</u> in <b>{{c2::Goodpasture}} syndrome</b> </div>
<i>specifically, the <b>alpha 3 chain</b> of <b>type IV collagen</b> is targeted</i> <div>- found in lungs (hemoptysis) and glomeruli (GBM)</div>
<div><div><div><div><div><b>Collagen</b> is a repeat of a <i>tripeptide</i> following the pattern {{c1::Gly-X-Y}}, made by <b>fibroblasts</b></div></div></div></div></div>
<i>- X and Y are usually proline or lysine</i><div>- also have signal molecules </div>
<div><div><div><div><div>One third of the <b>collagen</b> <b>strand</b> is made of the amino acid {{c1::glycine}}</div></div></div></div></div>
<i>glycine has the smallest side chain, therefore easy to form a triple helix (very little <b>steric hindrance</b>)</i>
<div><div><div><div><div>In the first step of <u>collagen synthesis</u>, translation of <b>collagen</b> <b>alpha chains</b> forms {{c1::preprocollagen}}</div></div></div></div></div>
“<div>- Collagen mRNA is first translated in the RER to preprocollagen</div><div>- Signal molecules direct it into the ER lumen, and the structure is now the ““Pro-Alpha chain””</div><div><br></br></div><div><img></img></div>”
<div><div><div><div><u>Collagen Synthesis</u>: After the collagen alpha chains are synthesized, specific residues of the amino acids <b>{{c1::proline}}</b> and <b>{{c1::lysine}}</b> are <b>{{c2::hydroxylated}}</b> </div></div></div></div>
“This step requires <b>Vitamin C </b>(deficient in <u>Scurvy</u>)<br></br><div><br></br></div><div><img></img></div>”
<div><div><div><div><u>Collagen Synthesis</u>: <b>Hydroxylation</b> of selected <u>prolines</u> and <u>lysines</u> during collagen synthesis requires vitamin {{c1::C}}</div></div></div></div>
“<i>deficiency of vitamin C causes </i><b>scurvy</b> as these patients will have <u>defective pro-alpha chains</u> that can’t form a triple helix, resulting in collagen being degraded instead of secreted”
<div><div><div><div><u>Collagen Synthesis</u>: Following hydroxylation of proline and lysine, there is {{c1::<b>glycosylation</b>}} of pro-α-chain {{c2::<b>hydroxylysine</b>}} residues </div></div></div></div>
“<img></img>”
<div><div><div><div><u>Collagen Synthesis</u>: After <i>hydroxylation</i> and <i>glycosylation</i>, <b><u>hydrogen</u></b> and <b><u>disulfide</u></b> <b>bonds</b> help form a(n) {{c1::<b>triple</b> <b>helix</b>}} of <b>collagen α chains</b> (<b>procollagen</b>) </div></div></div></div>
“<div><i>problems forming the triple helix may be indicative of <b>osteogenesis imperfecta</b></i><b> </b>- glycine is swapped out with a bulkier amino acid causing steric hindrance that makes a faulty triple helix structure for type I collagen</div><div><b><br></br></b></div><div><img></img></div>”
<div><div><div><div><u>Collagen Synthesis</u>: <i>After</i> the <b>triple helix</b> is formed, the procollagen is {{c1::exocytosed}} into the extracellular space</div></div></div></div>
“<div><img></img><br></br></div>”
<div><div><div><div>Where in the cell does <b>synthesis</b>, <b>hydroxylation</b>, and <b>glycosylation</b> of <u>preprocollagen</u> occur?</div><div><br></br></div><div>{{c1::Rough endoplasmic reticulum}}</div></div></div></div>
“<img></img>”
<div><div><div><div><u>Collagen Synthesis</u>: Once in the extracellular space, <u>cleavage</u> of disulfide-rich terminal regions of <b>procollagen</b> by {{c2::<u>procollagen peptidase</u>}} forms the <i>insoluble</i> <b>{{c1::tropocollagen}}</b> </div></div></div></div>
“<div>These are individual triple helix alpha chain molecules that haven’t been crosslinked at this point </div><div><br></br></div><div>problems with cleavage of procollagen to tropocollagen due to defects in procollagen peptidase result in <b>Ehlers-Danlos</b></div><div><br></br></div><div><img></img></div>”
<div><div><div><div><u>Collagen Synthesis</u>: Staggered <b>tropocollagen</b> molecules are reinforced by covalent {{c1::lysine-hydroxylysine}} {{c2::cross-linkages}} to make <b>collagen fibrils</b> </div></div></div></div>
“<div><b>- </b>this step is catalyzed by Lysyl oxidase and is deficient in Menkes disease</div><b><div><b><br></br></b></div>- Collagen fibrils</b> self assemble to form <b>Collagen Fibers</b><br></br><div><br></br></div><div><img></img></div>”
<div><div><div><div>Formation of <b>lysine-hydroxylysine cross-linkages</b> (collagen synthesis) requires both {{c1::copper}} and the enzyme <i>{{c1::lysyl oxidase}}</i></div></div></div></div>
“<i>copper deficiency leads to <b>Menkes</b> <b>disease</b></i><div><i><b><br></br></b></i></div><div><i><b><img></img></b></i></div><div><i><b><br></br></b></i></div><div><i><b><img></img></b></i></div>”
<div>Where in the cell does the <b>synthesis</b> and <b>formation</b> of<u>tropocollagen</u> and <u>collagen fibrils</u> occur?</div>
<div><br></br></div>
<div>{{c1::Extracellular space}}</div>
“<img></img>”
<div>Which <u>collagen synthesis</u> pathologies are associated with <b>problems with cross-linking</b>?</div>
<div><br></br></div>
<div>{{c1::Ehlers-Danlos syndrome, Menkes disease::2}}</div>
- Ehlers-Danlos is problems with proteolytic cleavage (deficiency in procollagen propeptidase) to generate the insoluble tropocollagen substrate from procollagen<div><br></br></div><div>- Menkes Disease results in copper deficiency (resulting in a dysfunctional Lysyl Oxidase), making it impossible to cross link tropocollagens into collagen fibrils</div>
<div>Which <u>collagen synthesis</u> pathologies are associated with <b>problems forming the triple helix</b>?</div>
<div><br></br></div>
<div>{{c1::Osteogenesis imperfecta and Scurvy}}</div>
“<div>-in osteogenesis imperfecta; Deficient Type 1 Collagen replaces Glycine with a bulky amino acid, creating steric hindrance that prevents 3 pro-alpha chains from properly linking into the triple helix procollagen; This improper collagen structure is either destroyed in the fibroblast, or is faultily incorporated into bone with hydroxyapatite causing brittleness</div><div><br></br></div><div>In scurvy, These patients can’t hydroxylate pro-alpha chains (hydroxylation of proline or lysine requires vit C), thus they can’t form the triple helix and the nascent collagen is degraded in the cell without being secreted</div>”
<div><b>Osteogenesis imperfecta</b> is most commonly caused by gene defects in <i>{{c1::COL1A1}}</i> and <i>{{c1::COL1A2}}</i></div>
- <u>COL1</u> = type 1 collagen, type 1 collagen is the predominant collagen in <b>osteoid</b>, which allows the bone to be somewhat flexible while maintaining strength
<div>What is the<i> inheritance</i> of <b>osteogenesis imperfecta</b> (most common)? </div>
<div><br></br></div>
<div>{{c1::Autosomal dominant}}</div>
<i>with decreased production of otherwise normal type 1 collagen</i>
<div><b>Osteogenesis imperfecta</b> is characterized by multiple recurrent {{c1::fractures}} with <u>minimal</u> trauma </div>
“<div><i>treat with <b>bisphosphonates</b> to <u>reduce fracture risk</u></i></div><div><i><br></br></i></div><div><i>may occur during the birth process; can mimic child abuse, but bruising is <u>absent</u></i> </div><div><img></img></div>”
<div><b>{{c2::Osteogenesis imperfecta}}</b> may present with {{c1::<b>blue</b> <b>sclerae</b>}} due to <i>translucent</i> connective tissue over <u>choroidal</u> veins</div>
“<img></img>”
<div><b>Osteogenesis imperfecta</b> may present with {{c1::hearing loss}} due to abnormal ossicles</div>
<i>bones of the middle ear fracture easily</i>
<div>Some forms of <i>osteogenesis</i> <i>imperfecta</i> have <b>tooth</b><b>abnormalities</b>, including <u>opalescent teeth</u> that wear easily due to lack of {{c1::dentin}}</div>
“<div><i>this is known as </i><b><i>dentinogenesis imperfecta</i> </b></div><div><b><img></img></b></div>”
<div>The <b>{{c1::classical}} type</b> of <b>Ehlers-Danlos syndrome</b> (joint and skin symptoms) is caused by a mutation in <b>type {{c2::V}} collagen</b></div>
<i>the classical type includes Ehlers-Danlos types 1 & 2</i>
<div>What type of <b>Ehlers-Danlos syndrome</b> is the most common type?</div>
<div><br></br></div>
<div>{{c1::Hypermobility type (joint instability)}}</div>
<i>this is also known as Ehlers-Danlos type 3</i>
<div><b>Ehlers-Danlos syndrome</b> is characterized by <u>faulty collagen synthesis</u> causing {{c1::hyperextensible}} skin</div>
“<img></img>”
<div><b>Ehlers-Danlos syndrome</b> is characterized by <u>faulty collagen synthesis</u> causing {{c1::hypermobile}} joints</div>
“<img></img>”
<div>The classical and vascular forms of <b>Ehlers-Danlos syndrome</b> are inherited in a(n) {{c1::autosomal dominant}} manner</div>
However, other types of Ehlers-Danlos can be inherited in Autosomal Recessive manner; remember the classical and vascular forms involve structural proteins
<div>What is the <i>inheritance</i> of <b>Menkes disease</b>? </div>
<div><br></br></div>
<div>{{c1::X-linked recessive}}</div>
<u>Men</u>kes. Men are more likely to get it
<div>What gene is defective in <b>Menkes disease</b>? </div>
<div><br></br></div>
<div>{{c1::ATP7A}} </div>
<i>not to be confused with ATP7B (Wilson disease)</i>
“<div><b>{{c2::Menkes}} disease</b> results in {{c1::brittle, ““kinky””}} hair, growth retardation, and hypotonia</div><div></div>”
“<img></img>”
<div>{{c1::Elastin}} is a <b>stretchy protein</b> within skin, lungs, large arteries, elastic ligaments, vocal cords, and ligamentum flava</div>
”- dominant elastic protein in the arteries, makes up 50% of aortic tissue <br></br><div><br></br></div><div>- Ligamentum flava has lots of elastin, allowing it to connect vertebrae to allow relaxed and stretched conformations</div><div><br></br></div><div><img></img></div><div><img></img></div>”
<div><b>Elastin</b> is rich in <i>non-hydroxylated</i> {{c1::proline}}, {{c1::glycine}}, and {{c1::lysine}} residues (amino acids)</div>
“In comparison to collagen<div><br></br><div>- mostly non-hydroxylated amino acids (some hydroxyproline, no hydroxylysine)</div><div><br></br></div><div>- no glycosylation (surrounding network of fibrillin microfibrils)</div><div><br></br></div><div>- elastin is secreted as <b>tropoelastin</b>, whose unique polypeptide backbone when cross linked causes random coiling (giving it its elastic property)</div></div><div><br></br></div><div><img></img></div>”
<div><b>Elastin</b> is <i>tropoelastin</i> with {{c1::fibrillin}} scaffolding</div>
”- Elastin has an unusual polypeptide backbone that causes random coiling when crosslinked - giving it it’s elastic properties<div><br></br><div>- central core of tropoelastin has two unique amino acids that crosslink and provide stability<br></br><div><br></br></div><div><img></img></div></div></div>”
“<div>What gives <b>elastin</b> its elastic ““rubber-like”” properties?</div><div><br></br></div><div>{{c1::Cross-linking}}</div>”
“<div><i>- mediated by <b>lysyl oxidase </b>which <u>deaminates</u> <b>lysine residues</b> of tropoelastin, facilitating formation of <b>desmosine cross-links </b></i></div><div><i><b><br></br></b></i></div><div><i>- allows for elastin fibers to be stretched to several times original length and then recoil once stretching forces are withdrawn</i></div><img></img><div><img></img></div>”
<div>Where in the cell does <u>cross-linking</u> of <b>elastin</b> take place? </div>
<div><br></br></div>
<div>{{c1::Extracellular space}}</div>
“<div><img></img></div>”
{{c1::<b>Wrinkles</b>}}<b> of</b> <b>aging</b> are due to <u>decreased</u> <b>{{c2::collagen}}</b> and <b>elastin</b> production
“<i>decreased collagen production and increased collagenases secondary to UV-A radiation induced inflammatory damage</i> <div><img></img></div>”
<div><div><b>Gel electrophoresis </b>separates fragments on the basis of {{c1::size}} </div></div>
<i>all DNA/RNA/protein fragments used are negatively charged</i>
<div><div>When using <b>blotting procedures</b>, the {{c1::probe}} determines what sequences are detected </div></div>
“<div><div><i>the probe is complementary to the gene sequence of interest</i></div></div><div><i><b><img></img></b></i></div>”
<div>A(n)<b>{{c2::Southern}} blot</b> is used to analyze {{c1::DNA}}</div>
“<i>Used in genetic testing of diseases, forensics (DNA identification - microsatellite analysis can also be used here)</i><div><i><br></br></i></div><div><i>Can use to observe inheritance of <b>RFLP </b>markers</i></div><div><i><br></br></i></div><div><i><img></img></i></div>”
<div>A(n)<b>{{c2::Northern}} blot</b> is used to analyze {{c1::RNA}}</div>
<i>measure mRNA levels (<b>gene</b> <b>expression</b>)</i>
<div><div>Does a <b>Southern blot</b> require <u>gel electrophoresis</u> before analysis? </div><div><br></br></div><div>{{c1::Yes}}</div></div>
“<img></img>”
<div><div>What type of <i>probe</i> is used to bind <u>protein</u> when using a <b>Western blot</b>? </div><div><br></br></div><div>{{c1::Labeled antibody}}</div></div>
“<div><i>binds protein that has been separated by gel electrophoresis and transferred to a membrane</i></div><div><img></img></div>”
<div><div><div>What type of <i>probe</i> is used to bind <u>DNA/RNA</u> when using a<b>Southern/Northern blot</b>? </div><div><br></br></div><div>{{c1::Labeled single stranded DNA / RNA oligonucleotide}}</div></div></div>
“This can be radioactive or fluorescently labeled<div><br></br></div><div><img></img></div>”
<div><div>The <b>{{c1::Western}} blot</b>*used to be* the confirmatory test for HIV after a positive ELISA</div></div>
“FA 2019: Western blot tests are no longer recommended by the CDC for confirmatory testing. Presumptive diagnosis is made with HIV-1/2 Ag/Ab immunoassays. These assays detect viral p24 Ag capsid protein and IgG Abs to HIV-1/2.”
<div><div>Does a <b>Dot (slot) blot</b> require <u>gel electrophoresis</u> before analysis?</div><div><br></br></div><div>{{c1::No!}}</div></div>
“<div><i>useful for analyzing DNA, RNA, or protein but must know the <u>specific</u> mutation being looked for; e.g. <b>Hemochromatosis</b> (person #3 is homozygous mutant for the C282Y mutation) </i> </div><div><img></img></div><div><br></br></div>”
<div>A(n)<b>{{c1::Southwestern}} blot</b> is used to identify <b>{{c2::DNA-binding}} proteins</b> using labeled oligonucleotide probes</div>
“<i>useful for identifying </i><u>transcription factors</u> “
<div><div><div>In the <u>first</u> step of <b>PCR</b>, DNA is {{c1::denatured}} by using {{c2::heat}} to separate the strands</div></div></div>
“<div><i>temperature is approximately 95° C</i> </div><div><img></img></div>”
<div><div><div>In the <u>second</u> step of <b>PCR</b>, {{c2::<u>DNA</u> primers}} <b>{{c1::anneal}}</b> to <i>specific sequences</i> on each DNA strand to be amplified</div></div></div>
“<div><i>temperature is approximately 55° C</i> </div><div><img></img></div>”
<div><div><div>In the <u>final</u> step of <b>PCR</b>, heat-stable {{c2::Taq DNA polymerase}} <b>{{c1::elongates}}</b> the DNA sequence following each primer </div></div></div>
“<div><i>temperature is approximately 72° C</i> </div><div><img></img></div>”
<div><div><div>What <u>type</u> of <b>primer</b> is used in a polymerase chain reaction (PCR)?</div><div><br></br></div><div>{{c1::DNA primer}}</div></div></div>
“<div><i>in the body, RNA primers are used; in the test tube, DNA primers are used</i> </div><div><img></img></div>”
“<div><div><div>Which end of the DNA strand does the <b>DNA primer</b> bind to during PCR?</div><div><br></br></div><div>{{c1::3’ end}}</div></div></div>”
“<img></img>”
<div><div><div><b>PCR</b> requires the addition of all <u>four</u> {{c1::deoxynucleotide triphosphates (dNTPs)}} for DNA synthesis</div></div></div>
“<div><div><i>also requires DNA polymerase and primers</i> ; PCR is repeated until DNA sample size is sufficient</div></div><div><img></img></div>”
<div><div><b>{{c1::Flow cytometry}}</b> is a laboratory technique used to assess size, granularity, and protein expression of <u>individual</u> cells in a sample</div></div>
“<div><i>commonly used in the workup of <b>hematologic</b> <b>abnormalities</b> and <b>immunodeficiencies</b></i> </div><div><img></img></div>”
<div><div>In <b>flow cytometry</b>, cells are tagged with {{c1::antibodies}} specific to surface or intracellular proteins </div></div>
“<img></img>”
<div><div>In <b>flow cytometry</b>, <u>antibodies</u> are tagged with a unique {{c1::fluorescent dye}}, which is detected and counted during analysis </div></div>
“<img></img>”
“<div><div><div><u>Flow Cytometry Example</u>: Cells in the <b>right lower quadrant</b> are CD3{{c1::-}} and CD8{{c1::+}} </div><div><br></br></div><div><img></img></div></div></div>”
<i>all CD8 expressing cells also express CD3, hence why this quadrant is empty</i>
<div><div><div><b>{{c1::Microarrays}}</b> analyze <u>thousands</u> of nucleic acid sequences arranged in <i>grids</i> on glass or silicon</div></div></div>
“<div><i>useful for genotyping, clinical genetic testing, forensic analysis, cancer mutations, and genetic linkage analysis</i></div><div><img></img> </div>”
<div><div><div><div><b>{{c1::Microarrays}}</b> are a laboratory technique used to profile <b>gene expression</b> levels of <u>thousands</u> of genes <i>simultaneously</i> to study certain diseases and treatments</div></div></div></div>
“<img></img>”
<div><div><div><b>Microarrays</b> use a(n) {{c1::labeled DNA/RNA}} probe, which is hybridized to the chip, and a scanner detects the relative amounts of complementary binding</div><div></div></div></div>
“<img></img>”
<div><div><div>What <u>two</u> types of variations in DNA are detected when using <b>microarrays</b>? (DNA markers)</div><div><br></br></div><div>{{c1::<div> - Single nucleotide polymorphisms (SNPs)</div><div> - Copy number variations (CNVs)</div>}}</div></div></div>
disadvantage: cannot detect translocation or inversions, only can detect <u>gain or loss</u> of material
“<div>{{c1::Enzyme-linked immunosorbent assay (ELISA)::not Coombs}} is an <u>immunologic test</u> used to detect the presence of either a <i>specific</i> <b>antigen</b> or <b>antibody</b> in a patient’s blood sample</div>”
<i>major ELISA variations include direct, sandwich, and competitive; can have high sensitivity and specificity</i>
<div>When using <b>ELISA</b>, detection involves the use of a(n) {{c1::antibody}} linked to a(n) {{c2::enzyme}} </div>
“<div><i>added <b>substrate</b> then reacts with enzyme, producing a detectable signal (e.g. color change)</i></div><div><br></br></div><div><img></img></div>”
<div>{{c1::Fluorescence in situ hybridization (FISH)}} uses a <b>fluorescent DNA/RNA probe</b> to bind to a specific gene of interest on chromosomes</div>
“<img></img>”
<div>{{c1::Fluoresence in situ hybridization (FISH)}} is a laboratory technique used for specific <u>localization</u> of genes and direct <u>visualization</u> of chromosomal anomalies</div>
**vs Karyotyping it is <u>higher resolution</u> and can be done in <u>interphase</u>
<div>A(n) {{c1::microdeletion}} is detected with <b>FISH</b> as <u>no fluorescence</u> on a chromosome compared to fluorescence at the same locus on the second copy of that chromosome</div>
“<img></img>”
<div>A(n) {{c1::translocation}} is detected with <b>FISH</b> as fluorescence <u>outside</u> the original chromosome</div>
“white arrows in image [A] show fragments of chromosome 17 that have been translocated to chromosome 19<div><br></br><div><img></img></div><div><img></img></div></div>”
<div>A(n) {{c1::duplication}} is detected with <b>FISH</b> as an <u>extra site</u> of fluorescence on one chromosome relative to its homologous chromosome</div>
“Can result in a <b>trisomy</b> or <b>tetrasomy</b> (blue arrows in image [A])<br></br><div><br></br></div><div><img></img></div><div><br></br></div><div><img></img></div>”
<div>What protein is defective in <b>Marfan syndrome</b>?</div>
<div><br></br></div>
<div>{{c1::Fibrillin (scaffold for elastin)}}</div>
“<i>connective tissue disorder affecting skeleton, heart, and eyes</i> <div><img></img><div><i><img></img></i></div></div>”
<div>What pathology is associated with <b>long, tapering fingers and toes </b>(arachnodactyly) and <b>subluxation</b> <b>of lenses</b>?</div>
<div><br></br></div>
<div>{{c1::Marfan syndrome}}</div>
“<i>other findings include tall with long extremities, pectus carinatum or excavatum, hypermobile joints, and cystic medial necrosis of the aorta</i> <div><img></img></div>”
<div><b>Marfan syndrome</b> typically presents with subluxation of the lenses {{c1::upward::direction}} and {{c1::temporally::direction}}</div>
<i>versus homocystinuria which is usually downward and inward</i>
<div><b>Marfan syndrome</b> is associated with a floppy {{c1::mitral}} valve</div>
<i>also associated with aortic incompetence and dissecting aortic aneurysms </i>
<div>What is the <u>mode of inheritance</u> of <b>Marfan syndrome</b>?</div>
<div><br></br></div>
<div>{{c1::Autosomal dominant}}</div>
chromosome 15<div>missense=dominant</div>
<div><div>What <i>class</i> of diseases is <b>Huntington disease</b> a part of?</div><div><br></br></div><div>{{c1::Trinucleotide repeat expansion diseases}}</div></div>
<i><b>Try</b> (trinucleotide) <b>hunting</b> for <b>my</b> <b>fried</b> <b>eggs</b> (X)</i>
<div><div>What <i>class</i> of diseases is <b>Friedreich ataxia</b> a part of?</div><div><br></br></div><div>{{c1::Trinucleotide repeat expansion diseases}}</div></div>
<i><b>Try</b> (trinucleotide) <b>hunting</b> for <b>my</b> <b>fried</b> <b>eggs</b> (X)</i>
<div>The influx of calcium during the<b> plateau phase</b> of a <u>myocardial action potential</u> triggers release of Ca2+ from the {{c1::sarcoplasmic reticulum}}, causing<b> myocyte {{c2::contraction}}</b></div>
<i>Ca2+-induced Ca2+ release</i>
<div>A defect in <b>left-right dynein</b> during <u>heart morphogenesis</u> can result in {{c1::dextrocardia}}</div>
<i>e.g. Kartagener syndrome (primary ciliary dyskinesia)</i>
<div>In the <b>{{c1::peroxisome}}</b>, <u>ethanol</u> may be converted to <u>acetaldehyde</u> via the enzyme <b>{{c2::catalase}}</b></div>
“<img></img>”
<div><b>Cystic fibrosis </b>most commonly occurs due to a(n) {{c2::<u>in-frame</u>}} <u>deletion</u> of {{c1::Phe508}}</div>
”- This results in a <b>impaired post translational processing: </b>improper folding and glycolyslation of CFTR results in misfolded protein that gets retained in the RER and marked for proteasomal degradation<div><br></br><div>- thus there is decreased CFTR transported to the cell membrane; decreased Cl secreted at mucosal epithelium, decrease Cl reabsorbed at sweat glands</div></div><div><br></br></div><div><img></img></div><div><img></img></div>”
<div><div><div>Following binding of <b>LDL </b>to its <b>LDL receptor</b>, the ligand-receptor complex is <u>endocytosed</u> in <b>{{c1::clathrin}}-coated pits</b></div></div></div>
“<img></img>”
<div><div><div>The <b>LDL-containing</b> <u>clathrin-coated pits</u> fuse with <b>{{c1::lysosomes}}</b>, which break down <b>cholesterol ester</b> into <b>cholesterol</b> </div></div></div>
“<div><i>via the enzyme lysosomal esterase</i></div><div><img></img> </div>”
<div><b>Sickle cell anemia</b> occurs due to a<i> </i><u>point mutation</u> that substitutes <b>{{c1::glutamic acid}} </b>(hydrophilic) with <b>{{c1::valine}}</b> (hydrophobic) </div>
“<b>glutamic acid</b><i> (HbA) is </i><u>negatively</u><i> charged; </i><b>valine</b><i> (HbS) is </i><u>neutral</u><i> </i>”
<div><b>{{c1::Paroxysmal nocturnal hemoglobinuria}}</b> may be confirmed via {{c3::<u>flow cytometry</u>}}, which detects a <u>lack</u> of <b>CD-{{c2::55}}</b> and <b>CD-{{c2::59}}</b></div>
“DAF and MIRL<div><img></img></div>”
<div><b>Aplastic anemia</b> may be caused by <b>{{c2::Fanconi}} anemia</b>, which occurs due to a(n) {{c1::<u>dsDNA repair</u>}}<u> defect</u>, resulting in bone marrow failure</div>
“<i>- defect in <b>homologous recombination </b>(double stranded break repair)</i><div><i><br></br></i></div><div><div><i>- dsDNA breaks can be detected by the FA Core Complex, acting as a nidus to recruit BRCA repair enzymes</i></div><div><i><br></br></i></div><div><i><img></img></i></div></div>”
<div>The <b>{{c3::cell body}}</b> and <b>{{c3::dendrites}}</b> of a <u>neuron</u> can be seen histologically with <b>{{c1::Nissl}} staining</b>, which stains {{c2::RER}} </div>
“<div><i>RER is not present in the axon</i> </div><div><img></img></div>”
<div><b>Lynch syndrome</b> and <i>some</i> <u>sporadic</u><b> colorectal carcinomas</b> arise via the {{c1::microsatellite}} instability pathway </div>
<i>i.e. the serrated polyp pathway</i>
<div><div>The <b>{{c2::microsatellite}} instability pathway</b> of <u>colorectal cancer</u> is characterized by <i>mutations</i> or <i>methylation</i> of {{c1::<b>mismatch</b> <b>repair</b>}} <b>genes</b> </div></div>
<i>e.g. MLH1, MSH2</i>
<div><b>Free radicals</b> cause cellular injury via {{c1::<u>peroxidation</u>}} of <b>lipids</b> and {{c2::<u>oxidation</u>}} of <b>DNA</b> and <b>proteins</b></div>
<i><b>DNA</b> <b>damage</b> is implicated in <b>aging</b> and <b>oncogenesis</b></i>
<div>During phagocytosis, <b>pseudopods</b> extend from <u>leukocytes</u> to form <b>{{c1::phagosomes}}</b>, which are <i>internalized</i> and merged with <b>{{c2::lysosomes}}</b> </div>
“<div><i>thus producing a </i><b>phagolysosome</b> </div><div><img></img></div>”
<div><b>{{c2::Ataxia-Telangiectasia}}</b> is due to <u>defects</u> in the <b><i>{{c1::ATM}} </i>gene</b></div>
failure in <b>nonhomologous end joining</b>
<div>Which <u>immunodeficiency</u> is caused by <b>failure to repair DNA double strand breaks</b>? </div>
<div><br></br></div>
<div>{{c1::Ataxia-telangiectasia}}</div>
<i>results in <b>unrestricted cell cycle progression</b> (resulting in mutations accumulating) </i> and <b>DNA hypersensitivity </b>to <u>ionizing radiation</u><div><u><br></br></u></div><div>VDJ recombination requires double strand breaks to occur, without ATM these are hard to repair (resulting in a weakened immune system)</div>
“<div><b>Ataxia-TelangiectasiA</b> presents with a <u>triad</u> of:</div><div>- {{c1::cerebellar defects (<b>A</b>taxia)}}</div><div>- {{c2::spider angiomas (<b>T</b>elangiectasia)}}</div><div>- {{c3::Ig<b>A</b> deficiency}} </div>”
<i>lymphopenia and cerebellar atrophy</i> <div><br></br></div><div><div>- Toddlers wobble and sway when walking (almost appear drunk)</div><div><br></br></div><div>- patients present also with slurred distorted speech, swallowing, dysarthria, and oculomotor apraxia</div><div><br></br></div><div>- Telangiectasias erupt on skin and eye, early aging (premature greying of hair)</div></div>
<div>What <i>type</i> of tissue is comprised of <b>stem cells</b> that can <u>continuously cycle</u> to <b>regenerate tissue</b>? </div>
<div><br></br></div>
<div>{{c1::Labile}}</div>
<i>e.g. small and large bowel, skin, bone marrow</i>
<div><b>{{c1::Duchenne}} muscular dystrophy</b> is typically due to <u>frameshift</u> or <u>non-sense</u> mutations, resulting in a <b>truncated</b> or <b>absent dystrophin protein</b> </div>
“<i>”“<b>D</b>uchenne = <b>D</b>eleted <b>D</b>ystrophin”” (vs. Becker, where dystrophin is mutated)</i> “
<div><b>{{c1::Liposarcoma}}</b> is a <u>malignant</u> tumor of <b>adipose tissue</b> </div>
<i>characterized histologically by nuclear indentations and <b>scalloping</b> of the nuclear membrane</i>
<div>{{c1::<b>Ubiquitin</b>}}-ation of proteins recruits the {{c2::<b>proteasome</b>}} to degrade them</div>
“<img></img>”
<div><b>Irinotecan, </b>a(n) {{c2::<b>Topoisomerase I</b>}} <b>inhibitor</b>, is used to treat {{c1::<b>Colon</b>}} <b>Cancer</b></div>
“<img></img>”
<div><div><b>Vinca Alkaloids</b> are antineoplastics that prevent cell cycle progression at the {{c2::<b>M</b>}} <b>phase</b></div></div>
“<i>ex. include <b>Vinblastine </b>and <b>Vincristine</b></i><div><i><img></img></i></div>”
<div><div><div>A general rule of chemotherapeutic side effects is that they will affect all {{c1::rapidly}} dividing cells</div></div></div>
These are known as <b>Labile </b>cells; thus side affects at the skin, GI tract, bone marrow
<b>Growth Factors </b>induce cellular {{c1::growth}}<div><br></br></div><div><i>vs mitogen</i></div>
<div>- Examples include EGF, IGF-1, NGF</div>
<div><br></br></div>
- Note, <b>mitogens</b> induce cellular division, compounds can be growth factors and mitogens
<div>The <b>Cell Cycle</b> is regulated by <u>Cyclins</u> and<u>Cyclin-Dependent Kinases (CDKs)</u> which when {{c2::<b>complexed</b>}} allow cells to bypass {{c1::<u>restriction points</u> (checkpoints)}}</div>
”- Thus, these proteins are an important point of regulation by the cell in order to avoid tumorigenesis<br></br><div><br></br></div><div>- restriction points occur near the end of <b>G1</b>, near the end of G2, and within M metaphase</div><div><br></br></div><div><img></img></div>”
The <b>G1 restriction point</b> of the cell cycle is regulated by the <u>tumor suppressors</u> {{c1::<b>p53</b>}} and {{c1::<b>Rb</b>}}
“<div>This allows the cell to verify:</div><div>- should I be going into S phase?</div><div>- would I be carrying any mutations into S phase?</div><div><br></br></div><div><img></img></div>”
p53 restricts the cell cycle to <b>G1</b> by engendering the inhibition of {{c2::<b>CDK4</b>}}, maintaining the <u>{{c1::hypo}}phosphorylated</u> state of Rb
“However when stimulated, CDK4 binds Cyclin D1 to initiate the hyperphosphorylation of Rb (**this leads to Rb leaving and E2F acting as a transcription factor for things needed in S phase)<br></br><div><br></br></div><div><img></img></div>”
In response to <b>DNA damage</b>, p53 initially attempts to {{c1::<u>halt</u>}}<u> the cell cycle</u> and <u>facilitates the activity of {{c2::DNA repair}} enzymes</u><div><u><br></br></u></div><div>*<i>bonus-what does it <u>induce</u> that inhibits the cell cycle?</i></div>
”- <u>induces P21</u> which inhibits CDK complexes important for release of E2F from RB<div><br></br></div><div>- facilitates NER, BER, Mismatch Repair, dsDNA repair pathways<br></br><div><br></br></div><div><img></img></div></div>”
If <b>DNA repair</b> is not possible, p53 induces {{c1::apoptosis}}
“<img></img>”
<b>Growth Factors </b>stimulate G1 phase by increasing the levels of the {{c1::Cyclins}}
”- Once cyclins (ex <b>Cyclin D1</b>) reach a sufficient level, these activate <b>CDKs</b> to stimulate progression past the G1 restriction point<div><br></br></div><div>- growth factors include EGF, PDGF, EPO</div><div><br></br></div><div><img></img></div>”
Once levels of <b>Cyclins</b> reach an appropriate level, these complex with {{c1::Cyclin-Dependent Kinases}} to hyperphosphorylate <u>Rb</u>
”- <u>Cyclin D / CDK4</u> monophosphorylate Rb, which is followed by hyperphosphorylation by <u>Cyclin E / CDK2</u><div><br></br></div><div>- this causes a conformational change that releases sequestered E2F from Rb<br></br><div><div><br></br></div><div><img></img></div></div></div>”
<b>Tumor suppressor </b>genes {{c1::regulate}} cell growth
”- These <u>decrease</u> (““suppress””) risk of tumor formation (ex. p53 / Rb)<div><br></br></div><div>- as opposed to proto-oncogenes which promote cell growth</div>”
<div>When performing <b>Immunohistochemistry</b>; a(n) {{c1::Cytokeratin}} stain can be used to identify <u>Epithelial tumors (ex Squamous Cell Carcinoma)</u></div>
“<div><div>- ex. SCC of the head and neck, cervical cancer, lung, skin, esophagus</div><div><br></br></div><div><u><img></img></u></div></div>”
<div>When performing <b>Immunohistochemistry</b>; a(n) {{c1::Vimentin}} stain can be used to identify <u>Sarcomas, Endometrial Carcinoma, RCC, Meningioma</u></div>
“These are tumors of <u>mesenchymal tissue</u><div><u><br></br></u><div><img></img></div></div>”
<div>When performing <b>Immunohistochemistry</b>; a(n) {{c1::Desmin}} stain can be used to identify <u>Rhabdomyosarcomas, Leiomyomas, Leiomyosarcomas</u></div>
“These are tumors of <u>muscle tissue</u> <div><u><br></br></u><div><img></img></div></div>”
<div>When performing <b>Immunohistochemistry</b>; a(n) {{c1::Glial Fibrillary Acidic Protein (GFAP)}} stain can be used to identify <u>Astrocytomas, Glioblastomas, Oligodendrogliomas, Ependymomas</u></div>
“<div>These are tumors of <u>neuroglia</u> <div><u><br></br></u><div><img></img></div></div></div>”
<div>When performing <b>Immunohistochemistry</b>; a(n) {{c1::Neurofilament}} stain can be used to identify <u>neuroblastomas, medulloblastomas, retinoblastomas</u></div>
“These are tumors of <u>neurons</u> <div><u><br></br></u><div><img></img></div></div>”
<div><b>Colchicine</b> works by inhibiting intracellular {{c1::<b>microtubule</b>}} polymerization through binding and stabilizing {{c1::<b>tubulin</b>}}</div>
<div><br></br></div>
“<div>- this prevents <u>polymerization</u> of microtubules, thus cells that rely on microtubule polymerization (ex <b>Neutrophils</b>) will be strongly affected</div><div><br></br><div><img></img></div></div>”
The exotoxin <b>Diphtheria</b> toxin causes {{c2::<u>ADP-ribosylation</u> (and therefore inhibition)}} of <u>{{c2::elongation factor-2 (EF2)}}</u>
“EF2 is needed for protein synthesis, therefore protein synthesis is inhibited by the exotoxin<div><img></img></div>”
<u>Diagnosis of HIV</u>previouslywas made initially with {{c1::<b>ELISA</b>}}; <i>positive results</i> are <u>confirmed</u> with a(n)<b>{{c2::Western}} blot</b>
“FA 2019: <span>Western blot</span> tests are no longer recommended by the <span>CDC</span> for <span>confirmatory testing</span>. <b>Presumptive diagnosis is made with <span>HIV</span>-1/2 Ag/Ab immunoassays</b>. These assays detect viral <span>p24</span> Ag <span>capsid</span> protein and <span>IgG</span> Abs to <span>HIV</span>-1/2. <br></br> <div><img></img><img></img></div> “
{{c1::PCR}} is the gold standard used in the diagnosis of <b>Herpes Simplex Virus</b>
“<img></img>”
<b>Colchicine</b> binds {{c1::<b>tubulin</b>}}, preventing <i>polymerization</i> of <u>{{c2::microtubules}}</u>
“<img></img>”
Which <b>gout drug</b> binds <u>tubulin</u> and inhibits intracellular <u>microtubule polymerization</u>?<div><br></br></div><div>{{c1::Colchicine}}</div>
“<div><i>thus inhibiting neutrophil entry and inflammation due to MSU crystal deposition</i></div><div><br></br></div><img></img>”
What used to be the <b>rule out</b> test for <u>HIV</u>?<div><br></br></div><div>{{c1::ELISA}}</div>
“<div>FA 2019: Western blot tests are no longer recommended by the CDC for confirmatory testing. Presumptive diagnosis is made with HIV-1/2 Ag/Ab immunoassays. These assays detect viral p24 Ag capsid protein and IgG Abs to HIV-1/2.</div><div><br></br></div><div>sensitive (SNout)</div><img></img>”
<b>{{c2::Ionizing}} radiation</b> results in the formation of <u>double-stranded</u> <b>breaks</b> in DNA and <u>{{c1::hydroxyl free radicals}}</u> which <b>damage DNA</b>
“H2O in tissues hit with ionizing radiation -> *OH free radicals generated<div><br></br></div><div>associated with AML, CML, and papillary thyroid carcinoma</div><div><img></img><br></br></div>”
{{c1::Xeroderma pigmentosum}} results from lack of <b>excision endonuclease</b> activity to remove <u>pyrimidine dimers</u>
“<div>defective nucleotide excision repair</div><img></img>”
{{c1::<b>Sarcoma</b>}} implies the cancer is of <u>mesenchymal</u> origin
soft tissues (e.g. fat, musle, bone, etc)
<b>Li-Fraumeni syndrome</b> is characterized by <u>multiple malignancies</u> at a(n) {{c1::early}} age
“<img></img>”
Which enzyme is inhibited by <b>topotecan</b>?<div><br></br></div><div>{{c1::topoisomerase I}}</div>
“<img></img>”
Which enzyme is inhibited by <b>irinotecan</b>?<div><br></br></div><div>{{c1::topoisomerase I}}</div>
“<img></img>”
Which of the cytotoxic microtubule inhibitors <u>bind</u> <b>β-tubulin</b> and <u>inhibit</u><b> polymerization</b>?<div><br></br></div><div>{{c1::Vincristine; Vinblastine::2}}</div>
“<div>thus preventing mitotic spindle formation</div><img></img>”
Which of the cytotoxic microtubule inhibitors <u>prevent</u> <b>mitotic spindle formation</b>?<div><br></br></div><div>{{c1::Vincristine; Vinblastine}}</div>
“<div>via binding to <b>β</b>-tubulin and inhibit its<b> </b>polymerization</div><img></img>”
Which phase of the <u>cell cycle</u> do <b>vincristine</b> and <b>vinblastine</b> act at?<div><br></br></div><div>{{c1::M phase}}</div>
“<div>prevent mitotic spindle formation (specifically the <u>prophase</u> of mitosis)</div><img></img>”
Which of the cytotoxic microtubule inhibitors <u>bind</u> <b>microtubules</b> and <u>inhibit</u> their<b> depolymerization</b>?<div><br></br></div><div>{{c1::Paclitaxel (taxanes)}}</div>
“<img></img>”
Which of the cytotoxic microtubule inhibitors <u>enhance</u> <b>mitotic spindle formation</b>?<br></br><div><br></br></div><div>{{c1::Paclitaxel (taxanes)}}</div>
“<img></img>”
Which phase of the <u>cell cycle</u> does <b>paclitaxel</b> (taxanes) act at?<div><br></br></div><div>{{c1::M phase}}</div>
“<img></img>”
Which <u>antifungal</u> works by <i>disrupting</i> <b>mitotic spindles</b>?<div><br></br></div><div>{{c1::Griseofulvin}}</div>
“<div><br></br></div><div><br></br></div><img></img>”
<b>{{c1::Mesenchyme}} </b>is the embryonic connective tissue
- not found in adults except for mesenchymal stem cells<div><br></br><div>- <b>mostly</b> derives from <u>mesoderm</u></div></div>
The <b>Mesenchyme </b>gives rise to <i>most</i> <b>{{c1::connective tissue}}</b>
- bones, cartilage, lymphatic, and circulatory systems<div><br></br><div>- cells of the mesenchyme are surrounded by protein and fluid</div></div>
Patients with <b>Xeroderma Pigmentosum</b> often present with <u>freckled and dry</u> skin, <u>extreme</u> <b>{{c1::sunlight}} sensitivity, </b>and {{c2::<b>corneal</b>}} <b>ulcers</b>
”- patients will typically be light skinned<div><br></br></div><div><i><img></img></i></div>”
Patients with <b>xerodermapigmentosum</b>are at risk for which type/s of skin cancer?<div><br></br></div><div>{{c1::All :)}}</div>
- Melanoma, Basal Cell Carcinoma, Squamous Carcinoma
Patients with <b>Xeroderma Pigmentosum</b> cannot repair {{c1::Thymidine Dimers}} formed as a result of <u>UV-B</u> exposure
“<div>These patients either have a defective enzyme that recognizes <u>helix distortions</u> (XPC / XPA) or have a defective <u>excision endonuclease</u> (XPB, XPD-XPG)</div><div><br></br></div><div><img></img></div><div><img></img></div>”
<b>Nonhomologous End Joining (NHEJ)</b> occurs {{c1::before::before/after?}} S phase of the cell cycle
”- There is NO requirement for homology<div><br></br></div><div><img></img></div>”
Is <b>Nonhomologous End Joining </b><u>error prone</u>?<div><br></br></div><div>{{c1::Yes}}</div>
HIGHLY error prone; this has no template strand to compare to
<u>Nonhomologous End Joining</u> is defective in {{c1::<b>SCID</b>}} and {{c2::<b>Ataxia Telangiectasia</b>}}
”- Ex. defect in the <u>Artemis</u> protein or <u>ATM</u><br></br><div><br></br></div><div><img></img></div>”
The <u>intermediate filament</u> <b>Cytokeratin</b> is found in {{c1::Epithelial}} cells
”- Thus IHC stains can be developed for tumors of epithelial cells<div><br></br></div><div>- Keratin proteins are highly abundant in exposed stratified squamous epithelium (such as epidermis, oral mucosa) and are less abundant but still present in simple epithelium (such as liver, gut, pancreas)</div><div><br></br></div><div><img></img></div>”
The <u>intermediate filament</u> <b>Vimentin</b> is found in {{c1::mesenchymal}} tissue
“<div>(ex fibroblasts, endothelial cells, macrophages)</div><div>- Thus IHC stains can be developed for tumors of mesenchymal origin</div><div><br></br></div><div>- endogenously, Vimentin’s role is to maintain cell structure in mesenchymal cells</div><div><br></br></div><div><img></img></div>”
The <u>intermediate filament</u> <b>Desmin</b> is found in {{c1::muscle}} cells
”- Thus IHC stains can be developed for tumors of muscle cells<div><br></br></div><div>- endogenously, Desmins role is to maintain cell structure in muscle cells (Smooth, cardiac, skeletal)</div><div><br></br></div><div><img></img></div>”
The <u>intermediate filament</u> <b>Glial Fibrillary Acidic Protein (GFAP)</b> is found in {{c1::neuroglial}} cells (ex. astrocytes, Schwann cells, oligodendrocytes)
”- Thus IHC stains can be developed for tumors of neuroglial cells; do not rely on this for schwannoma as it also has S-100<div><br></br></div><div>- endogenously, GFAPs role is to maintain cell structure in Neuroglia</div><div><br></br></div><div><img></img></div>”
The <u>intermediate filament</u> <b>Neurofilament</b> is found in {{c1::neurons}}
- Thus IHC stains can be developed for tumors of neurons (ex. Neuroblastoma)<div><br></br></div><div>- endogenously, Neurofilaments role is to maintain cell structure in neurons</div>
The <b>Peroxisome</b> is a cytosolic membrane involved in the β-oxidation of {{c1::Very-long-chain fatty acids (VLCFA)}}
<div>- this is defective in <b>Adrenoleukodystrophy</b> - VLCFA build up and cause pathology</div>
Which cellular organelle is responsible for catabolism of <u>branched-chain fatty acids</u>, <u>amino acids</u>, and <u>ethanol</u>?<div><br></br></div><div>{{c1::Peroxisome}}</div>
An example of a branched-chain fatty acid = Phytanic Acid
A <u>germline P53 mutation</u> predisposes you to what tumor <i>syndrome</i>?<div><br></br></div><div><b>{{c1::Li-Fraumeni (SBLA) Syndrome}}</b></div>
When patients develop a somatic hit of the normal P53, the absence of both alleles of this tumor suppressor results in pathology
“<b>Li-Fraumeni Syndrome</b> is also known as ““<b>SBLA</b>”” Syndrome, which stands for:<div style=""><div class=""><div><br></br></div><div><b>S</b> - {{c1::Sarcoma}}</div><div><b>B </b>- {{c2::Breast Cancer}}</div><div><b>L </b>- {{c3::Leukemia}}</div><div><b>A </b>- {{c4::Adrenal Gland tumor}}</div></div></div>”
Loss of the P53 tumor suppressor results in a constellation of tumors due to absence of G1-S checkpoint regulation
In regards to <b>wrinkles of aging</b>, there is <u>{{c1::decreased}}</u> synthesis of collagen fibrils and <u>{{c2::increased}}</u> crosslinking of collagen
“<div>In contrast to FA2018, UWORLD says there is increased cross linking of collagen</div><div>- in aging, the atrophic dermis and increased collagen cross linking + dessication of stratum corneum produce the characteristic wrinkling of photoaged skin</div><div><br></br></div><div><img></img></div>”
A <b>direct ELISA</b> tests for a(n) {{c1::antigen}}, whereas the <b>indirect ELISA</b> tests for a(n) {{c2::antibody against an antigen}}
The antibodies for an indirect ELISA are easier to acquire
Patients with <b>ataxia-telangiectasia</b> have vitiligo, granulomas, and a high recurrence of {{c1::sinopulmonary}} infections
recurrent sinopulmonary infections can lead to bronchiectasis; due to being IgA, IgG, and IgE deficient
<b>Anthracyclines</b> (-rubicin) bind {{c1::topoisomerase II}} to cause <b>cleavage</b> of DNA
“<div>in addition to binding Fe -> free radical formation</div><img></img>”
<b>Depurination</b> results in the loss of {{c1::purine}} bases
occurs thousands of times per day- sugar phosphate stays in the backbone
