Biochemistry 2

kcunnu's version from 2015-05-19 07:11

Section 1

Question Answer
CDKscyclin-dependent kinases, constitutive and inactive
Cyclinsregulatory proteins that control cell cycle events, phase specific, activate CDKs
Tumor suppressorsp53 and RB normally inhibit G1 to S progression
Stable or quiescent cellsenter G1 from G0 when stimulated, ex hepatocytes and lymphos
Labile cellsNever go to G0, divide rapidly with short G1, ex BM, gut, epithelium, hair, skin
Permanent cellsremain in G0, regenerate from stem cells, ex neurons, skeletal/cardiac mm., RBCs
Nissl BodiesRER in neurons, makes enzymes and peptide NTs
SERsmooth ER for making steroids and detox

Section 2

Question Answer
COP1vesular trafficking protein that is retrograde from golgi-->ER
COP2anterograde vesicular transport from RER-->cis Golgi
Clathrinvesicular trafficking protein from trans Golgi-->lysosomes, also for receptor mediated endocytosis (plasma membrane-->endosome)
I-Cell diseaseinclusion cell disease, inherited lysosomal storage disease, failure to add mannose6P to lysosome proteins, will see coarse facial features, clouded cornea, restricted jt movement, high levels of plasma lyso enzyme, often fatal in childhood
golgi functiondistrubtion of proteins from ER to membrane/lysosome/vesicles, modifies N-oligosacchs on asparagine, adds O-oligos to ser/thr, adds mannose6P to lysosomal proteins, proteoglycan assembly from core proteins, sulfation of sugars in proteoglycans
MT structurepolymerized dimers of alpha/beta tubulin, each dimer has 2 GTP bound, incorporated into flagella, cilia, mitotic spindles, grows slowly/collapses quickly
Dynein vs kinesinretrograde to MT (+ to -) vs anterograde (- to +)
Mebendazole/thiabendazoleantihelminthic that acts on MTs
Griseofulvinantifungal that acts on MTs

Section 3

Question Answer
Vincristin/vinblastineanticancer that acts on MTs
Paclitaxelanti-breast cancer that acts on MTs
Colchicineanti-gout that acts on MTs
Chediak higashi syndromeMT polymerization defect resulting in decreased phagocytosis, results in recurrent pyogenic infxns, partial albinism, and peripheral neuropathy
Cilia structure9+2 arrangment, axonemal dynein is an ATPase that links peripheral 9 doublets causing bending of cilium by differential sliding of doublets
Kartagener's syndromeimmotile cilia due to dynein arm defect, male/female infertility, bronchiectasis, recurrent sinusitis, sotus inversus
Actin/myosin functionsmicrovilli, m. contraction, cytokinesis, adherens junctions
Intermediate filaments functionvinmentin, desmin, cytokeratin, glial fibrillary acid proteins (GFAP), neurofilaments
Plasma membrane characteristicsasymmetric fluid bilayer, cholesterol (50%), phsospholipids (50%), sphingo/glycolipids, proteins, high cholesterol or long saturated FA content--> high melting point, less fluidity
Stains for what cell type? vinmentin, desmin, cytokeratin, GFAP, neurofilamentsconnective tissue, muscle, epithelial cells, neuroglia, neurons

Section 4

Question Answer
Sodium pumpfor each ATP, 3 Na out and 2 K in, during cycle pump is phosphorylated
Ouabaininhibits Na/K pump by binding to K site
Cardiac glycosidesex digoxin/digitoxin inhibit Na/K ATPase directly, leads to indirect inhibition of Na/Ca exchange, increased intracellular Ca-->increased cardiac contractility
Collagen typesBe So Totally Cool Read Books, Type 1 (90%) is in Bone/Skin/Tendon, Type 2 is in Cartilage, Type 3 is in Reticulin (skin/vessels/uterus/fetal tissue), Type 4 is in Basement membrane (type 4 under the Floor)
Collagen synthesisinside fibroblasts is synthesis (RER), hydroxylation (ER), glycosylation (ER), and exocytosis- outside fibroblasts is proteolytic processing (procollagen-->tropocollagen) and cross-linking (make collagen fibrils from tropocollagen, covalent bonds are lysine-hydroxylysine)
Cross-linking to make collagenreinforce tropocollagen by covalent lysine-hydroxylysine cross-links (by lysyl oxidase) to make colalgen fibrils, occurs outside fibroblast
Synthesis of collagen (1st step)inside fibroblast, translation of collagen alpha chains (preprocollagen)- usually Gly-X-Y polypeptide where X/Y are pro/hydroxypro/hydroxylysine
Hydroxylation step in collagen synthesisinside fibroblast at ER, 2nd step, hydroxylation of specific proline/lysine residues, *requires Vit C*
Glycosylation3rd step in collagen synthesis in fibroblast at ER, glycosylation of pro-alpha chain lysine residues and forming procolalgen (triple helix of 3 collagen alpha chains)
Exocytosis of collagen4th step in synthesis inside fibroblast, exocytose procollagen into extracellular space

Section 5

Question Answer
Scurvyhydroxylation of pro/lys residues is inhibited because of Vit C deficiency
Osteogenesis imperfectagenetic bone disorder, auto dominant with abnormal type 1 collagen causes multiple fractures w/minimal trauma, blue sclera, hearing loss, dental imperfections (less dentin), Type 2 is fatal in utero, generally glycosylation step is affected
Ehler Danlosfaulty collagen synth causing hyperextensible skin, easy bleeding/bruising, hypermobile joints, 6 types that vary in inheritance/severity, Type 3 collagen is most frequently affected
Alport's syndromedifferent gene defects causing abnormal type 4 collagen (in basement membrane of kidney/ears/eyes), one would have progressive hereditary nephritis and deafness, also ocular disturbance
Elastinstretchy protein in lungs/large aa./elastic ligaments/vocal cords/ligamenta flava, rich in pro/glycine, broken down by elastase which is inhibited by alpha-antitrypsin
Marfan's syndromedefect in fibrillin
Emphysemaalpha1-antitrypsin deficiency so excess elastase activity (too much elastin breakdown)

Section 6

Question Answer
PCRamplify fragment of DNA, denature-anneal (excess premade DNA primers anneal to specific sequence on each strand to be amplified)- elongate (heat-stable DNA poly replicates DNA sequence following each primer)
Southern blotfor DNA, sample is electrophoresed on gel and transferred to filter, filter soaked in denaturant and exposed to a labeled DNA probe that recognizes/anneals to complementary strand, resulting dblstranded labeled DNA is visualised when filter is exposed to film
Western blotfor protein, sample protein separated by electrophoresis and transferred to filter, labeled Ab is used to bind to relevant protein
Northern blotfor RNA, radioactive DNA probe binds to sample RNA
Microarray1000s of nucleic acid sequences arranged in grids on glass/silicon, DNA/RNA probes hybridize to chip and scanner detects amts of complementary binding, used to profile gene expression levels to detect SNPs
ELISAtests for Ag-Ab reactivity, blood sample probed with either test Ag (to see if immune system recognizes it) or test Ab (to see if certain Ag is present), if target substance is present then test solution will have intense color rxn-->+ result
FISHfluorescent DNA or RNA probe binds to specific gene site of interest, to localize genes and directly visualize anomalies at molecular level (when deletion is too small to be seen on karyotype), fluorescence=gene present, no fluorescence= gene deletion
Cloning methodsproduce recombinant DNA molecule that is self-perpetuating, 1. insert DNA fragment into plasmid that has Ab-resistance genes, select for plasmids using media containing Ab and amplify them, 2. restriction enzymes cleave DNA and allow for insertion of fragment into plasmid, 3. tissue mRNA isolated/exposed to reverse trans forming a cDNA library (w/o introns)
Sanger DNA sequencingdideoxynucleotides halt DNA polymerization at each base making sequences of differnt lengths that encompass whole original sequence, terminated fragments are electrophoresed and original sequence can then be determined
Karyotypingmetaphase xsomes are stained/ordered/#ed by morphology/size/arm-length ratio/banding pattern, can be performed on blood/BM/amniotic fluid/placental tissue, dx xsomal imbalances
RNAidsRNA is synthesized complementary to mRNA sequence of interest, when transfected into human cells dsRNA separates and promotes degradation of target mRNA-->knock down gene expression