-
purines (which, how do they pair, synthesis components, synth disruption)
- AG (PURe As Gold)
- A with T (2 H bonds)
- G with C (3 H bonds) (G and C look similar=stronger "bond")
- Aspartate, Glycine, GlutAmine (AG and GA are purines)
- tetrahydrofolate required
- 6 mercaptopurine (6 MP) disrupts IMP
- mycophenolate and ribavirin disrupt IMP to GMP (not AMP) (inosine monophosphate dehydrogenase)
- hydroxyurea disrupts pyrimidines and purines (ribonucleotide reductase)
-
pyrimidines (which, how do they pair, synthesis components, synth disruption)
- CUT
- T with A (2 H bonds)
- C with G (3 H bonds) (G and C look similar=stronger "bond")
- aspartate, carbamoyl phosphate
- CUT carbs and phosphate out of your diet and CUT the asparagus py (pie)
- leflunomide inhibits dyhydroorotate dehydrogenase
- methotrexate, trimethoprim, and pyrimethamine inhibit dihydrofolate reducatase (DHF to THF) inhibiting formation of dTMP (deoxythymidine monophosphate)
- 5-FU forms 5-F-dUMP to also inhibit formation of dTMP by direct inhibition of thymidylate synthase
-
adenosine deaminase deficiency
- adenosine deaminase (ADA) converts adenosine and deoxyadenosine to inosine for purine salvage
- instead goes to dATP, which is toxic to lymphocytes->SCID (AR)
-
Lesch-Nyhan syndrome
- deficiency of hypoxanthine guanine phosphoribosyltransferase part of AMP (adenosine to hypoxanthine) and GMP (guanine) salvage
- converts these to IMP and GMP respectively, instead hypoxanthine and guanine are converted to xanthine by xanthine oxidase
- xanthine oxidase then converts them to uric acid
- gout, hyperuricemia, orange sand (sodium urate) in diaper, retardation, self-mutilation, aggression, dystonia
-
transition DNA mutation
- purine to purine or pyrimidine to pyrimidine
- (opposed to trasnversion)
-
transversion DNA mutation
- purine to pyrimidine or pyrimidine to purine
- (opposed to trasition)
-
nucleotide excision repair (and what is disease?)
- fixes bulky helix distorting lesions during G1
- endonucleases relase oligonucleotides
- DNA pol and ligase fill and reseal
- xeroderma pigmentosum
-
base excision repair
- occurs throughout cell cycle
- base-specific glycosylase creates apurinic/apyrimidinic (AP) site
- AP endonuclease cleaves 5’
- lyase cleaves 3’
- DNA polymerase-β fills and lyase seals
-
mismatch repair (and what disease?)
- predominantly G2 phase
- newly synthed strand (that’s why G2 phase) recognized and mismatched removed
- gap filled and resealed
- Lynch syndrome (hereditary nonpolyposis colorectal cancer)
-
non-homologous end joining (and what disease?)
- lack a sister chromatid (so probably G1
- lose some DNA but shove two ends together after chewing a bit off so they stick
- ataxia telangiectaseia, Fanconi anemia
-
mRNA reading and protein synth directions
- mRNA read 5 to 3! (that way the first codon that you made from DNA is the first one read)
- protein N to C
- unlike DNA 3 to 5 read and 5 to 3 synth
-
mRNA start and stop codons
- start AUG or GUG (rare) make methionine (N-formylmethionine in prokaryotes fMet [fMet induces neutroph chemotaxis]…we’re way off topic by now!)
- stop UGA, UAG, UAA
- you go away, you are going, you are away
-
gene promoter seq, start codon, begining and end of introns, polyadenylation
- promoter CAAT box and TATAAT box (“TATA”)
- start codon ATG
- intron start GT
- intron end AG
- polyA signal AATAAA
-
enhancer
- binds transcription factors
- can be in introns even
-
gene silencer
- same as an enhancer, but binds negative regulators aka repressors
- can be in introns even
-
RNA pol I (what does it make, what inhibits it?)
- rRNA (most common type of RNA)
- used for ribosomes
- Actinomycin D
-
RNA pol II (what does it make, what inhibits it?)
- mRNA (longest RNA)
- opens DNA at promoter site
- alpha amantinin
- Actinomycin D
-
RNA pol III (what does it make, what inhibits it?)
- tRNA and 5SrRNA
- Actinomycin D
-
prokaryote RNA pol (what does it make, what inhibits it?)
- they only have one RNA pol to make all types of RNA
- inhibited by rifampin
-
hnRNA to mRNA
- heterogenous nuclear RNA aka pre-mRNA is capped at 5’ (7 methylguanosine)
- tailed at 3’ (poly adenosine) (no template just slap it on the AAUAAA)
- spliced (lose introns)
- then it’s mRNA and transported out
-
mRNA quality control
- cytoplasmic processing bodies (P-bodies) with exonucleases, decapping enzymes, microRNAs
- P-bodies can also store mRNA
-
antibodies against spliceosome components
- SLE antiSmith is anti snRNP
- mixed CTD has anti-U1 RNP
-
microRNA (where are they found)
can be found in introns
-
tRNA structure
- CCA at 3’ binds amino acid (A binds) [3’ has OH 5’ has PO4 btw]
- Can Carry Amino acids
- T-arm ribothymidine, pseudouridine, cytidine for tRNA-ribosome binding
- Touch arm
- D-arm dihydrouridine for tRNA recognition by correct aminoacyl-tRNA synthetase (charging [requires ATP])
- Determinant arm
-
protein synth (initiation, elongation, termination)
- initiation uses GTP to assemble 40S and 60S (80S)
- aminoacyl-tRNA methionine binds to P site
- subsequent aminoacyl-tRNAs bind to A site
- ribozyme (rRNA) catalyzes peptide bond, puts growing protein on aa in A site
- everything slides down 3 nucleotides (P to E for exit, A with protein to P)
- release factor recognizes stop codon
-
cyclin dependent kinase
- constituitively expressed
- CDK is inactive until cyclin complexes with it
-
cyclin
- only expressed when need to move through cell cycle
- activates CDK by complexing, then the cyclin-CDK complex phosphorylates
-
p53
- induces p21 to inhibit CDKs leading to hypophosphorylation of Rb
- when hypophosphorylated Rb binds E2F halting G1 to S
-
G0
- quiescent (stable) or permanent cells hang out in this phase
- labile cells never go into G0 (gut, marrow, skin, hair, germ cells)
-
G1
- growth phase getting ready for S phase
- quiescent (stable) cells can move from G0 to this
- labile cells have a short G1 (gut, marrow, skin, hair, germ cells)
-
G2
two chromatids, getting ready for mitosis
-
RER (job, other names)
- synthesis for secretory proteins (goblet cells are rich in RER)
- aka Nissl bodies
-
smooth ER (job, assoc. cells)
- steroid synthesis
- detox
- hepatocytes, adrenal cortex, gonads
-
I-cell disease
- aka mucolipidosis type II; inclusion cell disease
- lysosomal storage disorder
- golgi lacks N-acetylglucosaminy-1-phosphotransferase, can’t phosphorylate mannose residues
- glycoproteins lack mannose-6-phosphate (normally signal that protein goes to lysosome)
- proteins secreted instead of put in lysosomes, so lysosomes lack normal enzymes and get filled with junk
- high levels of lysosome enzymes in serum
- coarce facies, short trunk, clouded cornea, restricted joint movement, hepatosplenomegally, enlarged heart valves, respiratory tract infection/CHF fatal in childhood (age 7)
-
microfilament
- actin, microvilli
- muscle contraction, cytokinesis
-
vimentin (tissue type)
- mesenchymal
- also endometrial carcinoma, RCC, meningioma
- intermediate filament
-
desmin (tissue type)
- muscle
- intermediate filament
-
cytokeratin (tissue type)
- epithelial
- intermediate filament
-
glial fibrillary acid proteins
- GFAP
- astrocytes, ependymal
- also found in Schwann cells, oligodendroglia
- intermediate filament
-
neurofilaments (tissue type)
- neurons but not glia
- intermediate filament
-
intermediate filaments
- lamins (nuclear envelope)
- cytoskeleton for structure (staining)
-
microtubules
- axonal trafficking, cilia, flagella, mitotic spindle, centrioles
- dynein (-) and kinesin (+)
- alpha and beta tubulin with 2 GTP
- movement, cell division
-
cilia (structure, function)
- 9+2 microtubule doublets
- doublets linked by ATPase axonemal dynein to bend
- basal body is 9 triplets without central microtubules
-
Na-K-ATPase inhibitors
- Ouabain binding to K site
- digoxin/digitoxin (indirectly inhibit Na-C exchange to increase contractility)
-
Type I collagen (where used, disorder)
- bone (osteoblasts make it), skin, tendon, dentin, fascia, cornea/sclera, late wound repair
- osteogenesis imperfecta 1 (defect in preprocollagen triple helix formation)
-
Type II collagen (where used)
cartilage (including hyaline), vitreous body, nucleus pulposus
-
Type III collagen (where used, disorder)
- reticulin, blood vessels, uterus, fetal tissue, granulation tissue
- uncommon vascular type of Ehlers-Danlos (vascular, organ rupture)
-
Type IV collagen (where used, disorder)
- BM, basal lamina (“BM” of skin), lens
- Alport syndrome defective, targeted in Good pasture
-
Type V collagen (disorder, affected tissue)
- Ehlers Danlos classic type AD or AR (tropocollagen cross-linking problem)
- joint disolaction, berry aneurysm, aortic aneurysm, organ rupture, easy bleeding, hyperextensible skin
-
collagen synthesis
- alpha chains aka preprocollagen Gly-X-Y (proline and lysine often, but if you wanna know how much collagen someone has, check the glycine) I digress, moved into RER
- hydroxylation (OH) of proline and lysine (VIT C) in RER
- glycosylation (sugar) of hyroxylysine in RER
- hydrogen bonds and disulfide bonds to form triple helix in RER = procollagen
- exocytosis via golgi
- disulfide rich terminals cleaved extracellularly forming tropocollagen (the part you keep)
- tropocollagen covalent lysine-hyroxylysine by copper with lysyl oxidase forming collagen fibrils
- wrinkles are from decreased collagen and elastin production
-
Menkes disease
- XR lack ATP7A, impaired copper absorption and transport
- low lysyl oxidase activity, less tropocollagen covalent crosslinking
- kinky brittle hair, growth retardation, hypotonia, sagging facies, metaphyseal widening, intellectual disability, seizures
-
elastin (use, structure, synth, diseases)
- stretchy protein in skin lungs, large arteries, elastic ligaments, vocal cords, ligamenta flava (connect vertebrae)
- nonhydroxylated proline, lysine, glycine
- cross linking of tropoelastin is extracellular
- elastase breaks down (alpha 1 antitrypsin inhibition)
- Marfan defect of fibrillin, a sheath around elastin
- emphysema by alpha 1 antitrypsin deficiency
- wrinkles are from decreased collagen and elastin production
-
PCR temperatures
- 95 denature
- 55 anneal
- 72 elongation
-
southern blot
- first electrophoresis then
- radiolabeled DNA probe
- filter exposed to film to see dsDNA bound probe
-
northern blot
- electrophorese RNA sample
- radiolabled probe binds RNA
- filter exposed to film to see RNA bound probe
-
western blot
- electrophorese protein sample
- labeled antibody to bind protein target
- confirmatory for ELISA
-
southwestern blot
- electrophoresis
- radiolabeled oligonucleotides to bind DNA-binding proteins (xscription factors)
-
flow cy
- tag cell with antibody, tag antibody with fluorescent label
- laser records each cell and how many tags
- plot as histogram (1 measure)
- scatter (2 measures)
-
enzyme-linked immunosorbent assay
- aka ELISA. woah
- antibody (linked to enzyme) against antigen (HBsAg) or antibody (anti-HBs) in blood sample
- color change or some signal that enzyme is going
- can be indirect (detect antigen)(add antibody, then enzyme-linked anti-antibody antibody, wash, then substate)
- direct (add enzyme-linked anti-antibody antibody, wash, then substate)
- sandwich (detect antibody) (add antigen to bind to target antibody, then enzyme-linked antibody against antigen, wash, then substrate)
- competitive (detect antibody) (incubate test antigen with antibody to form complex, add complex to well with antigen [if antibodies didn’t bind antigen, then they will bind well antigen], wash, then enzyme-linked anti-antibody antibody, then substate looking for less color change)
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