HB1-exam 1 note cards.txt

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  1. proteolytic cleavage
    done by proteases, example: removal of methionine after translation
  2. Zymogens
    inactive precursors that are activated by proteolytic cleavage, ex. clotting cascade (serine proteases cleave inactive zymogens)
  3. Clotting cascade (main point)
    To stimulate a thrombin burst-->convert fibrinogen to fibrin-->fibrin cross linkages create clot
  4. Acylation
    When a methionine is removed it is replaced by an acetyl group at the N-terminus (donated by acetyl CoA)
  5. Mryristylation
    Lipid anchors. Myristyl anchors embed themselves in the lipid bilayer; allows a protein that would normally not associate with the lipid bilayer to be attracted to that area
  6. Prenylation
    Prenylation attaches the cysteine residue and prenyl (15 residue farnesyl) group via a thioester. Fti inhibitors for Progeria try to block prenylation.
  7. Example of prenylation
    Prenylation is known to occur on proteins of the RAB family of RAS-related G-proteins, oncogenic GTP-binding and hydrolyzing protein RAS which is farnesylated
  8. DNA methylation
    Adding methyl group at CPG islands to DNA causes steric hinderance -->allows for transcription factors to bind-->STOP TRANSCRIPTION
  9. Histone acetylation
    When you acetylate histones (using HATS)->shields their charge->decreases their affinity for DNA->activate them-> ENHANCE TRANSCRIPTION, to deactylate use HDACs
  10. Histone methylation
    When histones are methylated, histones are deacetylated, DNA is methylated--> allows binding of transcription factors on outer DNA helix gene silencing (NO TRANSCRIPTION)!
  11. Phosphorylation
    Most common post translational modification, proteins are phosphorylated by kinases, AAs that are phosphorylatable are serine, threonine, tyrosine
  12. Physiological Example of Phosphorylation
    Phosphorylations that occur in glycogen synthase and glycogen phosphorylase in hepatocytes in response to glucagon release from the pancreas
  13. Ubiquitination
    ATP-dependent process that is major mechanisms for the destruction of cellular proteins, involves a complex structure referred to as the proteosome, ubiquitin carrier protein attaches ubiquitin to the protein with ubiquitin ligase
  14. Lactose
    glucose-galactose cleaved by lactase (non-inducible, brush border disaccharidase), rate limiting step in its digestioon is its hydrolysis not the transport of glucose and galactose
  15. Glycogen
    glucose molecules linked by alpha-1,4 glycosidic bonds (amylose), digestion promoted by amylase
  16. Primary monosaccharides
    glucose, fructose, galactose
  17. Glucose
    monosaccharide Na+ dependent glucose transported across brush border from mucosa-->enterocyte
  18. Galactose
    monosaccharide Na+ dependent transported across brush border from mucosa-->enterocyte
  19. Fructose
    monosaccharide Na+ independent facilitated diffusion (uses GLUT5) transported across brush border membrane from mucosa-->enterocyte
  20. Glycoprotein
    proteins with sugars covalently linked to their AAs, MOST CELL SURFACE MEMBRANES, usually contain amino sugars (N-Acetylglucosamine, N-acetylgalactoseamine), neutral sugars (D-galactose, D-mannose, L-fucose) or acidic sugars (sialic acid)
  21. Functions of Glycoprotein
    Hormone receptors at the cell surface, cell-cell interaction
  22. Proteoglycan
    long unbranched sugar chains, hallmark of disaccharide repeats, MOST ER and Golgi membrane proteins
  23. Functions of Proteoglycans
    Many of ER and Golgi membrane proteins, also proteins secreted from the cell like serum and mucus proteins, Glycosylation is the major enzymatic modification in the body
  24. N-linked proteins
    N-glycosidically linked oligosaccharides widespread in nature, characteristic of membrane and secretory proteins, linked by N-acetylglucosamine (GlcNAc)--connected to asparagine
  25. O-linked proteins
    O-linked found in mucous fluids, but can also be present in membrane and secretory proteins, 3 or more sugars linked by N-acetylglalactosamine (GalNAc)--connected to serine, theronine. O-linked found a lot in collagen
  26. Collagen Synthesis
    First procollagen (N-linked glycoprotein)-->N linke oligosaccharide is removed ("N")-->only O linked remain in mature collagen
  27. Collagen glycosylation
    Degree of glycosylation impacts structure--> less glycosylated collagen=ordered fibrous structure (tendons) while heavily glycosylated are more like meshwork structure in basement membrane
  28. N-linked protein in hormones
    GlcNAc is linked to serine residue that become phosphorylated by protein kinases in hormonal stimulation
  29. High mannose N-linked protein
    all N-linked glycoproteins have oligosaccharide chains coming off a common core 3 mannose residues+2 GlcNAc, high mannose is how they all start some glycoproteins are modified further after this
  30. Tetra-antennary type N-linked protein
    Complex chains which have terminal trisaccharide sequence of sialic acid0galactose-GlcNAc attached to branched core mannoses
  31. LDL receptor glycoprotein structure
    has 2 N-linked oligosaccharides near LDL-binding domain (not involved in binding) and cluster of O-linked oligosaccharides near membrane spanning region (sialic acid residues to hold it up)
  32. Biosynthesis of N-linked glycoproteins
    Synthesized in the ER. Dolihcol is the anchor in the lipid bilayer of the ER membrane-->first sugar is GlcNAc-1-P-->another GlcNAc-1-P --> 4 or 5 mannose residues--> 3 glucose residues (which are later removed) NEXT STEP modificaton in the ER-->sent to Golgi-->elongation
  33. Biosynthesis of O-linked glycoproteins
    Occurs in the Golgi occurs in stepwise fashion of addition of sugars
  34. High mannose oligosaccharides in Lysosomes
    Lysosomal enzymes are N-linked oligosaccharides are synthesized in the ER and Golgi
  35. Lapatinib (HERCEPTIN)
    Small molecule drug to treat HER2 resistant breast cancer by bind to ATP recptors-->Blocks the tyrosine kinase from binding
  36. Imatinib
    Small molecule drug to treat CML by bind to ATP recptors-->Blocks the tyrosine kinase from binding
  37. Proteoglycans
    Gel forming compounds made of protein backbone with covalently bound sugars, oligosaccharide chains have disaccharides repeats usually composed of amino sugar and uronic acid
  38. Glycosaminoglycans (GAGs)
    the carbohydrate part of proteoglycans, each has unique disaccharide repeat, usually includes hexosamine and uronic acid (EXCEPT FOR KERATAN SULFATE), amino sugars are usually glucosamine (GlcNH2) or galctosamine (GalNH2) present in their N-acetylated form
  39. Hyaluronic acid
    proteoglycan, no sulfation--located in joint and ocular fluids
  40. Chondroitin sulfates
    proteoglycan, located in cartilage, tendons, bone
  41. Dermatan sulfate
    proteoglycan, located in skin, valves, blood vessels
  42. Heparan sulfate
    proteoglycan, amino group sulfated (not acetylated) located in cell surfaces
  43. Heparin
    proteoglycan, amino group sulfated (not acetylated) located in mast cells and liver
  44. Keratan sulfate
    proteoglycan, uronic acid replaced by galactose, located in cartilage, cornea
  45. Synthesis of proteoglycans
    synthesized by a series of glycosyl transferases, epimerases, sulfo transferases. Synthesis of core oligosaccharide while still in the RER, then synthesis of the repeating oligosccahride and other modifications take place in the Golgi
  46. Germline mosaicism
    X-inactivation causes one X chromosome to be inactivated in some tissues and the other X chromosome to active in others
  47. X-linked mental retardation
    X chromosome has a high frequency of mutations, microdeletions, duplication that cause X linked mental retardation
  48. LDL receptor
    defects in this receptor are responsible for familial hypercholesterolemia (autosomeal dominant) it's a transmembrane glycoprotein!
  49. factor VIII
    Allel coding for this causes hemophilia A--X-linked recessive, usually seen in males not females
  50. X-linked recessive (can females ever have phenotype)?
    If the father is a carrier on his X and the mother is a carrier then female offspring would be homozygous affected (rare because of the low incidence of X-linked recessive disorders)
  51. Skewed X-inactivation
    X inactivation (usually random) the fraction of mutant alleles that remain active is much greater than normal, the deleterious allele finds itself located on active X, if this is present in pertinent tissues then you will have disease
  52. Unstable repeat expansions
    Genetic diseases caused by the expansion within an affected gene of DNA with repeating units of three or more nucleotides in tandem (CAG or CCG)-->primarily neurological conditions result
  53. Unstable repeat expansion diseases
    Myotonic dystrophy, fragile X syndrome, Huntington's Disease (polyglutamine disoder), spinocerebellar ataxias (polyglutamine disoder)
  54. Anticipation
    Genetic term referrring to the progressive severity and decrease in the age of onset for diseases that are passed through the pedigree
  55. Disease associated with Anticipation
    Fragile X, Myotonic Dystrophy, Huntington's
  56. Huntington's disease
    CAG repeats
  57. Spinocerebellar ataxia
    CAG repeats
  58. Fragile X
    CGG repeats
  59. Myotonic Dystrophy
    CTG repeats
  60. Fatty acid synthesis
    Step 1: turn acetyl CoA--> malonyl CoA (using Biotin and acetyl CoA carboxylase), Step 2: elongation of fatty acid chain in two
  61. Phospholipid synthesis
    occurs on the cytoplasmic face of the ER, uses CDP-->CMP and flippases who flip the phospholipid one leaflet of the bilayer to the other
  62. Cholestrol
    Phospholipid, has a polar head group and a largely non-polar hydrocarbon tail. When it enters the bilayer, it causes stiffening. It will sit in hydrophobic tail region. It exists at quite a high level at the bilayer. By stiffening the bilayer, you alter the properties, even changing membrane permeability.
  63. Fluid mosaic model
    Singer, Nicholson said that the phospholipid bilayer has assymetry that is caused by differential packing of p-serine vs. p-choline
  64. Phospholipids in the bilyaer
    phosphotidyl serin phosphotidyl choline
  65. lipid rafs
    another example of asymmetry--mobile--float around bilayer, environment inside rafts is different from outside- Caveoli
  66. Dominant negative effect
    Mutation in gene regulatory region, If you get a mutation in the regulatory region it has an enhanced effec as a result of kinase activity
  67. Dominant negative effect (disease example)
    Amylotrphic lateral sclerosis, causes proteins to aggregate and interfere with cellular function
  68. PDZ Domain
    scaffold protein to bind ion channels to membrane, 80-90 AAs 6 strand Beta sandwich flanked by alpha helices, recognizes the C-terminus of receptors, involved in anchoring the CFTR in lung epithelial cells
  69. SALT BRIDGE in Hb
    ionic bond between lysine and glutamate
  70. Hemoglobin
    Oxygen carrier, iron in heaxcoordinate (binds 4 porphyrin, 1 proximal histidine, 1 oxygen) porphyrin ring is tetra coordinate
  71. Cooperativity
    When the binding of one oxygen molecule increases the binding affinity of the other sites, tense (low affinity), relaxed (high affinity)
  72. Allosterism:
    when the binding of one molecule at a site other than the active site increases or decreases the finction there
  73. Bonding between base pairs in DNA
    Hydrogen bonding
  74. Alpha helix (macrodipole)
    N terminus is positive, C terminus is negative
  75. Hydrophobic interactions
    Ex. oil in water-->increase entropy of system by liberating water molecules, all aromatice molecules are nonpolar (hydrophobic)
  76. Sterochemistry of enantiomers
    Animals are almost exclusively L-amino acids, sugars are all D-sugars
  77. # exons in B-globin gene
  78. # exons in BRCA1
  79. # exons in B-myosin heavy chain (MYH7)
  80. Prokaryotic vs. Eukaryotic DNA
    Prokaryotic Genes On, Eukaryotic OFF, Prokaryotic no DNA-protein complexes, Eukaryotic has DNA-protein complexes
  81. Stop codons
    UGA, UAA, UAG (you go away, you are away, you are gone)
  82. Kozak sequence
    Sequnce that the AUG start codon in included within (in the 5'UTR region)
  83. Exon-Intron splice
    GT (3' end of exon, 5'end of intron)----->AG(5' end of exon, 3'end of intron)
  84. Transcription factors
    TATA box (complimented by iniator), CAAT box, GC rich
  85. Large genes (>100bp)
    Factor VIII, CFTR, Dystrophin, BRCA1
  86. Small genes (<10 kb)
    B-globin, insulin
  87. Medium gene (10-100bp)
    collagen, LDL receptor
  88. Avergae number of exons per gene
    10 exons
  89. Pseudogene
    transcribed but not translated or not transcribed at all--can lead to unequal crossing over
  90. Unequal crossing over
    misalignment of two alpha globin genes on a chromsome causes alpha-thalassemia
  91. tandem repeats
    Repetitive DNA sequences-satellite DNA near centromeres
  92. SINEs
    short interspersed nucleotide repeats (10% human DNA), can interfere with crossing over, ex. Alu repeats SINEs cause familial hypercholesterolemia
  93. Which exon is lost in the unequal crossing over Familial Hypsercholesterolemia
    exon 5
  94. LINEs
    long interspersed nucleotide repeats (20% human DNA), can be transposable elements
  95. Mitochondrial DNA
    37 genes, amternal inheritance, no introns, highly conserved, makes more mutations, 2 strands heavy-guanine rich and light-cytosine rich
  96. Heteroplasmy
    the mixed population or normal and mutant mtDNA
  97. Types of DNA
  98. Z DNA
    left handed turn
  99. Histones (#)
    two copites of each of the four core histone (H2A, H2B, H3, H4)
  100. Histones that can substituted
    H3 and H2A
  101. Histones that can be chemically modified
    H3 and H4
  102. Histone code
    the pattern of major and specialized histone types and their modifications
  103. Cell division
    4-6 hours to reproduce 6.4 Gb
  104. High fidelity
    DNAs ability to reliably replicate
  105. DNA error rate
    1 in 10^9 is the limit, actual rate is 1 in 10^6 it fixes it by proofreading!
  106. DNA licensing
    ensure that DNA replication is limited to once/cycle
  107. Replication origin
    replication origins are rich in A-T (easier to break)
  108. Number of replication sites (Prokaryotic vs. Eukaryotic)
    E. coli have 1, humans have 100,000
  109. Steps of DNA Replication
    1. unwinding & replication forks, 2. stabilization with SSBPs, 3. Iniation (priming with DNA polymerase alpha), 4. Elongation (5'-->3'), 5. Lagging strand synthesis (3'-->5'' semgents) discontinuous, 6. Licensing: ensuring each replicates only once/cell cycle
  110. Helicase
    DNA strands are separated in ATP-dependent fashion
  111. Topoisomerase
    prevent DNA from becoming supercoiled
  112. Single stranded binding protein
    stabilize leading strand
  113. DNA Polymerase
    Can only add to the 3' end nucleotides, needs Magnesium to function
  114. DNA Pol alpha
    AKA RNA primase, synthesizes an RNA primer and then acts as a DNA pol to elongate for about 20 bp
  115. DNA Pol delta
    Lagging strand synthesis, Highly processive, proofreading 3'-->5'
  116. DNA Pol E
    Leading strand synthesis, Highly processive, proofreading 3'-->5'
  117. Processivity
    stays on strand longer
  118. PCNA (clamps)
    ATP-dependent way to increase the processivity of the Polymerase (stay on the strand)
  119. Prokaryotic Polymerazes
    DNA Pol 1, II, III
  120. Main polymerase in bacteria
    DNA Pol III
  121. RNAase H
    takes off the small RNA primer and DNA pol delta and epsilon fill it in
  122. Semi-discontinuous synthesis
    Lagging strand is built in segments (Okazaki fragments)
  123. Okazaki fragments
    segments of DNA on the lagging strand
  124. DNA Ligase
    glues together Okazaki fragments
  125. Replisome
    the whole complex of helicase, SSBPs, Polymerase, PCNAs
  126. Replication
    4-6 hours for 6.4 Gb, 100,000 replicons, during S phase
  127. CDC 6
    CDC6 recruited to form pre-replication complex, licensing to ensure 1 DNA replication/cell cycle, by the end of G2 there is no CDC6 left
  128. Type of DNA Damage
    Spontaneous, Exogenous (UV, Radiation, Chemical)
  129. Spontaneous DNA damage
    Deamination (standard bases are exchanged for nonstandard bases), base loss (Depurination>depyrimidation), ROS
  130. Ionizing radiation
    Causes double strand breaks by hydrolysis of water which breaks down into ROS
  131. UV Radiation
    Photo activate nucleotides, causes thymine (pyrimidine) dimer formations
  132. Adduct formation
    covalent attachment to DNA nucleotides, ex. benzo[a]pyrene
  133. Alkylating agents
    Carbn comound group to one of the bases-->disrupts structures, Ex. CYTOXAN
  134. Crosslinking
    Bi functional-->2 adduct forming entities can bond two 2 positions on DNA (can be inter or intra strand), Ex. CISPLATIN
  135. Type II topoisomerase inhibitor
  136. Microsatelitte Instability
    Occurs during replication of repetitive sequences, Forward slippage (parent) causes deletion, backwards slippage (daughter) causes insertion
  137. Translesion synthesis
    DNA backbone is still intact but you will get replication error
  138. DNA Double strand break
    caused by ionizing radiation, most deleterious form of DNA damage-->leads to aneuploidy
  139. Cell cycle checkpoint
    Eukaryotes have cell cycle checkpoints at G1 and G2, focus on checkpoint for G2--if you have mutations in the genes that code for checkpoints
  140. Why use alkylating agents, crosslinking agents in cancer therapy?
    Tumor cells grow faster than normal counterparts, should be more susceptible to checkpoint
  141. DNA Repai pathways
    Base Excision repait, Nucleotide Excision Repair, Translesion Synthesis, Mismatch Repair, Homologous Recombination, End joining
  142. Base Excision Repair
    Deaminations, depurinations-->uses glycosylases to cut out damaged base (least flexible)
  143. Nucleotide Excision Repair
    UV photoproducts, cross links-->RNA pol encounters DNA lesion, stops, uses a multiprotein complex (>10 proteins) for primary repair mechansim of UV photoproducts, cuts 5 bases 3' of the damage and 23 bases 5' of the damage, gaps filled by DNA pol
  144. Mismatch Repair
    Replication error (ex. Lynch Syndrome)
  145. Homologous recombination
    Double strand break, adducts, cross links
  146. End joining
    Double strand breaks
  147. Translesion synthesis
    Not high fideltity, can pass by damage, very error prone, non-templated manner
  148. XPA and XPC addount for (%) of all XP cases
  149. How to test for XP?
    Unscheduled DNA synthesis with skin biopsy (use radiolabeled thymine)
  150. Where is rRNA synthesized?
  151. Where does capping and polyA tail are added after transcription, where?
  152. Transcriptional unit
    TATA, GC, CAAT box, Enhacers and Silencers (on the DNA), TFIID
  153. Transcription Termination sequence
  154. RNA Polymerases
  155. What causes mushroom poisoning?
    alpha-Amanitin, is a mushroom poisoning RNA pol II inhibitor-->block mRNA transcription
  156. RNA polymerases
    Enzymes that synthesize the RNA strand from a DNA template during transcription
  157. RNA pol II transcribes which RNA?
  158. mRNA is transcribed using what RNA Polymerase?
    RNA Pol II
  159. RNA pol II transcribes which RNA?
    mRNA and microRNA
  160. RNA pol III transcribes which RNA?
    tRNA and ribozymes
  161. Stages of transcription
    1. initiation (construction of RNApol complex on the promoter, recruitment of transcription factors), 2. Elongation, 3. Termination (cessation of RNA transcription with CG repeats)
  162. Does RNA Polymerase has its own helicase activity?
  163. TATA Box
    10-20% of human promoters, 25-30 bases upstream of trranscription start site, allows correct positionaing of RNA pol
  164. TBP
    TATA binding protein, first to bind the DNA, causes the DNA to bend-->recruits TFIID and other transcriiption factors
  165. General transcription factors (GTFs)
    required for PolII in a test tue are TFIIA, B,D, E, F, and H (but basal level is achieved with purified B and F)
  166. Elongation
    RNA pol requires energy to add ribonucleotise to the 3' end of the growing strand, 17 bp transcription complex with 8 bp DNA-RNA hybrid
  167. Abortive transcription
    RNApol shows strong binding to promoter and generates short 9bp RNA fragments-->eventually it clears the promoter
  168. Rho factor (prokaryotic)
    Termination factor dependent for termination, used in bacteria
  169. How is transcription different in prokaryotes
    RNA pol directly recognizes sequences in DNS for binding and transcription, no nuclear envelope, no introns, transcription/translation occur simultaneously, use of polycystronic messages (like the LAC operon)
  170. Antibiotic that target prokaryotic transcription
    Rifampin binds to beta subunit of prokaryotic RNApoly, Dactinomycin (actinomysin D) binds to DNA template and interferes with RNApol progression
  171. Reverse Transcription
    Viral RNA used reverse transcriptase. Take mRNA strand and reverses transcription to turn it into DNA. Then it inserts itself into our genome
  172. Gene Regulatory Proteins
    Helix turn helix, zinc finger, leucine zipper, winged helix, winged helix turn helix, helix loop helix
  173. Helixa turn helix
    Repressor protein
  174. Zinc Finger
    Zn ion to stabilize structure/finger/specific triplet of base pairs, Zn ion causes secondary structure, bind major groove
  175. Leucine zipper
    Leucine every 7th residue, "zips" up to dimerize the protein, needs a dimer to inhibit DNA
  176. Winged Helix
    4 helices and two strand beta sheet
  177. Winged helix turn helix:
    3 helical bundle and 4-strand beta sheet
  178. Methylate histone
    Block charge-->activate transcription
  179. Acetylates histone
    Block charge-->activate transcription
  180. Methylate DNA
    Methylate DNA at the CpG island-->inhibit transcription
  181. Nucleosome
    Histone complex (8 total) with the DNA wrapped around it
  182. Histone acetyltransferases (HATS)
    Acetylate histones
  183. DNA Binding Proteins (enhancer/silencers)
    Regions that can contain multiple elements for assemply of large protein complexes--can be 1000s of bps away
  184. Multi-domain proteins
    activators and repressors can have multiple functions besides serving as transcriptional regulators
  185. Polycystronic message
    message with a length of RNA with whole process associated through several consecutive genes--all related to same process
  186. Lac Operon
    B-galactosidase cleaves lactose into allolactose-->bind repressor subunits to prevent assembly-->cAMP starvation signal forms CAP cAMP and promotes RNA pol attachment--> RNA pol transcribes genes to produce B-Galactosidase, permease and acetylase
  187. Halflife of RNA
    10 hours
  188. Chronic Myeloid Leukemia
    15-20% of all adult leukemias, BCR-ABL-->ABL (tyrosine kinase) --> speeds up cell division and inhibits DNA repair
  189. Regulation of RNA turnover- AUUUA sequences
    Experiment deomstrating the destabilizing effect of AUUUA sequences-->shortened the halflife of B-globin mRNA from 10h-->1.5h
  190. Nonsense Mutation
    is when you get a stop codon before you should
  191. Nonsense mediated decay
    Inserting stop codon where they shouldn't be
  192. Regulation of RNA turnover-- IRE-bps
    In high iron, the mRNA that codes for transferrin is off. When you have low iron, you want to pump the iron in so the IREbps stabilize the stem loops and turn the transferrin on-->you get lots of transferrin and protect your little iron
  193. What exon is removed through alternative splicing in CF?
    exon 9
  194. RNA splicing-Lariat
    Just 5' of acceptor site is pyrimidine rich acceptorregion that forms lariat site, branch site a single A binding is sitting just upstream of the pyrimidine rich region and is where the lariat lands
  195. What is the reason for alternate splicing?
    The human genome is limited
  196. Alternate RNA Splicing include or exclude certain exons?
    Ex. alpha-tropomyosin, alpha-TM Exon Gene organization uses alternate splicing to produced different types of muscles fibers
  197. Exonic splicing enhancers (ESEs)
    Enhance recognition of splice site- can bind directly or indirectly
  198. Intronic splicing enhancers (ISEs)
    Enhance recognition of splice site- can bind directly or indirectly
  199. Exonic splicing silencers (ESSs)
    Silence recognition of splice site- can bind directly or indirectly
  200. Intronic splicing silencers (ISSs)
    Silence recognition of splice site- can bind directly or indirectly
  201. Cryptic splice site
    splice site that is not supposed to be there, causes competition between splice sites
  202. Gain of function mutation
    Creation of cryptic splice site
  203. Loss of function mutation
    A splice site is weakened or destroyed
  204. In CF, regulation of splice site
    A splice site in intron 8 regulates inclusion of exon 9, in CF you don't get exon 9 included
  205. CF compound heterozygote, R117H and 7T
    mild presentation of disease, congentical bilateral absence of vas deferans
  206. CF compound heterozygote, R117H and 5T
    mild CF, disease symptoms present
  207. deltaF508
    most severe mutation that is associated with CF
  208. MAPT
    codes for tau protein, chromosome 17, involved splicing for exon 2, 3, 10 mutations can disrupt the balance of isoforms and cause disease--> ALZHEIMERS
  209. miRNA synthesis
    Synthesized in the nucleus as double stranded RNA, forms hair pin loops in nucleus, Drosha suts the hair pin loops in the nucleus, Exportin 5 sends it out to the cytoplasm where Dicer cuts it into 20-30 bp fragments, transciptional cleavage, now the miRNA can recognize its homologous RNA on the RISC complex
  210. Drosha
    cuts the hairpin loops of Pri miRNA in the nucleus to turn it Pre-miRNA
  211. Exportin 5
    Exports Pre-miRNA into the cytoplasm
  212. Dicer
    chops up the Pre miRNA into 20-30 bp fragments
  213. RISC
    complex that the anti sense strand binds to-->blocks translation
  214. Epigenetic
    study of heritables changes in gene function that occur without a change in the sequence of DNA
  215. CpG island
    C and G rich area in the 5' regulatory region close to the promoter region of DNA that gets methylated-- YOU METHYLATE THE C (cytosine)
  216. Location of LncRNAs
    Located in the nucleus and then trafficked to the cytoplasm
  217. Heterochromatin
    Highly compacted DNase resistant DNA
  218. When you acetylate histones which residue do you tag?
  219. When you methylate the histone, which residue do you tag?
    Cytosine (the C's of the CpG islands)
  220. Can drugs demethylate DNA?
    yes-through drug reversal you can restore transcription
  221. Rett Syndrome
    MECP2--Methyl CpG binding protein--no males can have Rett Syndrome unless they have Klinefelters (XXY) because if you have only on mutant X you won't have any normal protein
  222. What gets ADP ribosylated in Cholera?
    G protein
  223. Sumoylation, Small Ubiquitin like Modifier (SUMO)
    ADP ribosylation
  224. What genetic condition are likely to have epigenetic component?
    Imprinted genes--prader willie and angelman (7 genes missing on chromosome 15, in normal the maternal allele is expressed, paternal allele is silenced-when the maternal allel is lost you get Angelman)
  225. Example of secondar structure of RNA
    Stem-loop and small subunit of rRNA
  226. rRNA
    structural RNA (80% of all processed DNA)
  227. tRNA is the only RNA with non standard bases, what are they?
    Inosine and pseudouridine
  228. Are tRNA's aminoacylated?
    Yes, it uses ATP to give a high energy bond to the AA which is transferred to the RNA
  229. aminoacyl tRNA synthetase
    What glues the AAs onto the tRNA. There is one for each amino acid
  230. How many tRNAs do we need?
  231. How many tRNAs do we have?
  232. Wobble
    Since we need 61 tRNAs and only have 31, we have to alternate position 3 with the inosine and pseudouridine
  233. Prokaryotic Ribosome
    30S and 50S subunits, total 70S
  234. Eukaryotic Ribosome
    40S and 60S subunits, total 80S
  235. Svedburg coefficient
    centrifugation coefficient used in antibiotics
  236. Shine-Dalgardo Sequence
    What prokaryotic DNA use to determine start sequence (like the eukaryotic Kozak sequence)
  237. Ribosome scanning
    Small ribosomal subunit scans (with tRNA attached) by ribosome scanning the mRNA 5' UTR to look for start AUG codon
  238. What happens once tRNA find start sequence?
    Important Initiation factors are recruited (EIF Ii) and then the 60S is recruited
  239. What does every protein start with?
  240. A-site
    donor tRNA-amino acid (amino acid)
  241. P-site
    tRNA growing peptide chain (peptide)
  242. E-site
    tRNA (exit)
  243. Peptidyl transferase
    anzyme that is responsible for elongating the polypeptide chain
  244. Release factor
    Once the stop codon comes into A site, RF Binds to the A site with the help of GTP
  245. Ubiquitination
    sends proteins to be destructed in the proteosome
  246. Secondary structure of proteins
    relies on hydrogen bonding interactions, defined by rotation restriction around phi and psi, alpha helix (interchain H bonding) and Beta sheets (interchain H bonding)
  247. Ramachandran plot
    used to calculate the islands stability of stability by minimizing steric hindrance
  248. Tertiary structure
    3-D structure, relies on the interactions between side chains (not the backbone)
  249. Only covalent bonds in tertiary structure
    Disulfide bonds, cysteine-cystine
  250. Quaternary structure
    Several multiple protein subunits, ex. human hemoglobin, heterotetramer (2 alpha and 2 beta)
  251. Two sites of protein translation
    ribosomes in the cytoplasm and ribosomes on the RER
  252. Direction of protein translation, ribosomes move
    from 5'-->3' (synthesis of protein from N terminus-->C terminus)
  253. Signal recognition protein (SRP)
    Signal sequence at the beginning of the protein signals SRP used
  254. Chemical environment of the mitochondria
  255. Chemical environment of the cytoplasm
  256. ER tanslation
    Signal recogniition sequence on the protein recognized by the SRP-->direct protein into the ER membrane--> enzyme signal peptidase suts off the signal sequence at the beginning of protein
  257. Translation termination
    Once translation is complete, the ribosomal subunits dissociate-->completed protein is sent to the Golgi-->trafficked out of the cell
  258. Protein folding
    goal is to get to the local minimum energy conformation-->decrease Gibb's free energy and increase entropy (of water molecules)
  259. Disulfide bonds
    Don't want to be in the cytoplasm, weaker thand C-C bonds-->mostly found in secretory proteins, lysosomal proteins and exoplasmic domains on the membrane proteins
  260. Where do disulfide bond form in the protein?
    In the hydrophobic interior region of the protein-->they have lower energy
  261. Connotoxin
    importnat for pain management-->uses disulfide bonds to hold peptide architectures together
  262. Anfinsen experiment
    Taugh us how primary protein structure dictates tertiary structure. Used urea to denature protein and break disulfide bonds, then removed urea, and oxidized (protein went back to original conformation)--then used urea to denature, then oxidized before removing urea, message was scrambled
  263. Secondary vs. tertiary protein structure
    secondary structure has to do with backbone, tertiary has to do with side chains
  264. Ramachandran plot
    certain bond angles are preferred for kinky plates to align, most common are alpha helix, beta sheet and beta turns
  265. Misfolded proteins
    Have hydrophobic surface exposed
  266. What happens to misfolded protein? (two choices)
    sent to proteosome for degradation or refolded using chaperones (GroEl is bacteria or HSPs in humans)
  267. Heat Shock Proteins
    help to correctly fold the protein. Done by altering the polarity (switches from hydrophobic to hydrophilic) of interior surface (massage the outside of the barrel changes the protein on the inside)
  268. What percentage of proteins get refolded by HSPs?
  269. Group I chaperonins (Chaperones)
    prokaryotic- GroEl (Hsp 60) has a detachable lid (GroEs)
  270. GroEl action
    unfolded protein binds to the GroEl pocket not blocked yb GroEs-->ATP binds to each subunit of the Groel heptamer-->ATP hydrolysis (14)leads to the release of GroEs-->7 ATP and GroES bind to pocket-->lid is reannelaed and shaken up by ATP hydrolysis--> protein refolds inside enclosure
  271. Group II chaperonins (chaperones)
    found in eurkaryotes--TriC, are lidless and rely on apical protrusions to cap chaperonin
  272. Most misfolded proteins are sent to chaperones or degraded?
  273. Why would a protein be misfolded?
    Inappropriately modified with glyoclytic compounds, modified via prroducts of lipid peroxidation during oxidative stress, part of brief repsonse to hormones, contain the PEST sequence
  274. PEST sequence
    ProGlUSerThr--marks proteins for rapid turnover
  275. Proteasome
    the place where cytosolic proteins go to get degraded, have proteases within the barrel motif (like garbage disposal)
  276. Ubiquitination
    uses ubiquitin carrier protein, ubiquitin ligase to add ubiquitin to a misfolded protein (uses ATP)
  277. Protein interactions
    binding can be tight or weak, long or short, but is always highly specific
  278. Protein binding
    singles site on one protein or multiple complex interactions
  279. PDZ domain
    FUNCTIONAL PROTEIN DOMAIN,80-90 AA domains found in over 150 different human proteins (including CFTR) 6 strand B sandwiches flanked by 2 alpha helices-->recognize specific sequence (4-5 AA) on the C-terminal of protein
  280. Anitbody-Antigen interaction
    protein-protein interaction
  281. Antibody structure
    Heavy chain on the inside, light chain on the outside, divalent (two binding sites) held together by DISULFIDE BONDS! variable domain in the arm, constant domain on the stem, antigen recognizes the NH2 amino site at the antigen binding site, alpha helices make up C term
  282. Enzymes
    proteins that catalyze covalent bond breakage or makeage
  283. Gene Regulatory Proteins
    is. Zinc finger, TFIID, molecules that bind DNA or other proteins to regulate gene expression
  284. Structural protein
    provides mechanical support inside and outside of cells
  285. Signal proteins
    ligans, receptor for signal trasnduction
  286. Motor proteins
    ex. dynein and kinesin, generate movement in cells and tissues
  287. Cellular adhesion molecule
    example of combining active domains to specify function/structureL Ig combined with FNIII (fibronectin type III), Igs originally evolved in cell adhesion
  288. Function of PDZ domains in CFTR
    Microvilli in alveoli in the lung, Plasma membrane has midrodaomins to localize CFTR to microvilli-->PDZ domain anchors the CFTR here
  289. Ankyrin repeats
    functional protein domain
  290. Immunoglobulin domain
  291. DNA binding domains
    Variable, ex Zinc finger, leucine zipper
  292. Spectrin repeats
    STRUCTURAL DOMAIN, 106-110 AA, triple helix, spectrin dystophin, anchors ion channel proteins in the membrane
  293. Coiled-coiled domain
    STRUCTURAL DOMAIN, protein protein association, ex. Leucine zipper
  294. Transmembrane domain
    Membrane spanning regions
  295. Dominant negative effect
    mutations in gene regulatory regions-->aberrant or absence of product, ex. one domain is regulatory region, one domain is a kinase region, enhaced effect of kinase EX. ALS, causes protein aggregates
  296. Nonsense mutation
    Unstable mRNA reduced or absent product, truncated proteins, degraded as proteolytically unstable (can only be in a coding region)
  297. Missense mutations
    Unstable mRNA, reduced or absent product
  298. Function begats strucute
    Human erythrocyte: biconcave disk (gas exchange, deformability (to get through the sinusoidal slits)
  299. Hereditary spherocytosis
    Autosomal dominant (1/2000)--results in splenomegaly, hemolytic anemia
  300. Hereditary ellipsocytosis
    Autosomal dominant (1/2000-1/10000)--results in hemolysis, splenomegaly, hemolytic anemia
  301. Hereditary Pyropolykilocytosis
    looks like sever burns, rare member of the HE family
  302. Erythrocyte shape-structure
    RBCs have scaffold of filamentous proteins that crosslink short actin filaments and underlies plasma membrane, give shape, strength and organization of lipid bilayer
  303. Band 3
    membrane protein in bilayer of RBCs linked to plasma membrane
  304. Spectrin (alpha and Beta)
    long, filamentous molecule, two subunits (a and B) both which have 106 repeats) heterotetramer of two dimers key to maintain RBC structure, a and B organized counter parallel to each other to form spectrin dimer
  305. Spectrin self association site
    allows you to bring together the alpha and beta subunit in head to head association. One molecule contributes 2 alpha helix which form a spectrin repeat and one molecule contributes 2 Beta sheets
  306. Ankyrin
    connected to the B helix of spectrin
  307. Defects in spectrin self association site
    lead to HE
  308. Missense mutation at spectrin self association site
    PROLINE HELIX BREAKERS at the N terminus of a-spectrin subunit--> this mutation affects the ability of spectrin to form the heterotetramer
  309. Mutations in Band 3 and Ankyrin
    Associated with HS--can occur at the cytoplasmic or transmembrane domains in Band 3 or at the membrane bidning, spectrin binding, or regulatory regions of Ankyrin
  310. Myristoylation
    post-translation modification that promotes the association of proteins with plasma membrane
  311. Most common bond used in protein folding/post translational modification
    • Disulfide bonds-->cysteines
    • Phosphorylation
    • post translational modification that adds phosphate group to a specific molecular site-->activates gene (reversible)
  312. Ubiquitination
    non-reversible post translational protein modification-->leads to proteosome mediated proteolysis
  313. Clotting cascade (ex of post-translation modification)
    example of proteolytic cleavage post translational modification, platelets recruits-->platelet factors form-->recruit clotting factor-->continuously break peptide bonds in platelets to turn pro-thrombin to thrombin (thrombin burst)-->convert fibrinogen to fibrin
  314. Coagulation factors
    serine proteases that convert the Zymogens to active forms
  315. Proinsulin
    Secreted by B-cells in pancreashas signal peptide+active sequence+connecting polypeptide+another active sequence
  316. Insulin modification (ex. post translational modifcation)
    Insulin is a secreted protein, Insulin protein folds into loop, connects active sites by disulfide bonds-->cleaves the signal sequence after insertion in the ER-->endopeptidases cleave the connecting polypeptide
  317. What do we use for insulin in diabetes?
    recombinant protein--used to use pig insulin because this type of processing does not occur in the bacterial system
  318. Phosphorylation
    addition of a negatively charged phosphate group to a serin, threonine or tyrosine residue
  319. Kinases
    molecules that phosphorylate proteins--usually activate proteins
  320. Phosphatases
    molecules that remove phosphoates--usually deactive proteins
  321. Phosphorylation and HER2
    HER2 neu recepotrs have an intracellular kinase domain--acts as a dimer with a neighboring receptor to cross phosphorylate eachother-->this is the beginning of the Tyr-Kin signaling cascade
  322. Myristylation
    Adding a lipid anchor to the amino terminus of the protein to promote the association of proteins with the plasma membrane--happens (ex. RAS important GTPases need the help of proteins in the plasma membrane)
  323. Prenylation
    Adding a lipid anchor to the cysteine residue (ex. FTI inhibitor block the process of Prenylation and block the activity of RAS, actually successful in Progeria)
  324. Acetylation
    Adding acetyl group (usually to the N-terminal alpah amine, NGlcAc) allows many drugs to cross the blood brain barrier (ex. acetylate histone on the lysine at the nucleosome-->increase transcription) (ex. Aspirin is an acetlyated sialic acid)
  325. Glycosylation
    BINDS TO ASPARAGINE--Modification of cell membrane for cell recognition, aid in protein folding, keep proteases away (ex. viruses and bacteria routinely use carbohydrate moities for entry into cell)
  326. Glycosylation
    Attaches to Asparagine, N-linked or O-linked
  327. Signal recognition protein (SRP)
    Recruited after recognizing signal sequence on protein--> SRP carried ribosome to the SRP receptor sending ribosome to the rER membrane--> attaches to translocon-->protein translation occurs directly into ER
  328. Glycosylation of membrane protein
    Once the polpeptide chain enters ER lumen-->it is glycosylated with oligosaccharides at the asparagine residues to the asparagines [Asn-X-Ser/Threonin]
  329. Dolichol
    glycolipid in the ER membrane that glycosylates the protein as it is translated through the translocon
  330. Glycosylated proteins trafficking
    After translation in ER, glycosylated proteins (secreted and membrane bound) are trafficked to the Golgi using kinesins (molecular motors)-->final modifcation-->sent to PM
  331. Specific modications in ER
    additoins of 2 GlcNAc's-->multiple mannoses (8)-->3 glucose cleaved off by glucosidase and 1 mannose by ER mannosidase before it enters Golgi
  332. Specific modifications in Golgi
    3 more mannose cleaved off-->one GlcNAc added-->two mannose sugars are removed to indicate ENDO H RESISTANCE!
  333. Glycation
    Non-enxymatic glycosylation when fructose and glucose (reducing agents) can be added to proteins and lipids-->form AGE complex (ex. cooking sugars)
  334. EExogenous glycation
    Cooking sugars with proteins/lipids-->absorbed by the body
  335. Endogenous glycation
    In the blood stream-->slow reactions form AGEs (advanced glycation endproducts) the long lived cells (Schwann cells, brain cells) and proteins (eye, collagen) are susceptible to damage
  336. Endogenous glycation and Diabetes
    bindinng of endogenous glycation products (AGEs) in bloodstream of patients with diabetes, AGEs in Schwann cells can cause diabetic neuropathy
  337. Problems with protein based drugs
    source (human, animal, contamination), purification (co-factors, stability), administration (direct injection)
  338. Expression systems
    Bacteria (not for glycosylated proteins, yeast, mammalian cells, transgenic animals and plants
  339. Types of protein based drugs
    Mabs, enzymes (for enzyme replacement therapy), hormones, clotting factors vaccines
  340. Recombinants that replces animal/human sources
    HGH, Human insulin, follicle stimulating hormone, Factor VIII
  341. Original recombinant
    EPO (for kidney diseases stimulates hematopoeisis in bone marrow, Glucocerebrosidase (used to treat Gaucher's Disease)
  342. Monoclonal aanitbodies as drugs--Tsyabri (natalizumab)
    Used to treat MS (autoimmune disease affecting myelin sheath), drug blocked the affinity btwn leukocytes and vessel wall-->problem PML-patients started dying because you need the recruitment of WBCs
  343. Monoclonal antiboides to block function--Trastuzimab
    Targets HER2 (in the family of EGFRs involved in controlling cell growth and differentiation)--anti HER2 antibody inhibits the overamplification of HER2
  344. Glucocerebrosidase deficiency
    Lack of this ezyme results in fatty accumulation in the spleen, liver, kidenys, lungs, brain-->GAUCHER'S DISEASE
  345. Enzyme replacement therapy- Ceredase
    Genzyme made Ceredase (out of human placenta)-->replaced with recombinant therapy Cerenzyme
  346. Hormone replacement therapy-EPO
    Epo is a hormone produced by the kidney in response to low O2 in the blood-->drives differentiation of RBCs from progenitor cells
  347. Recombinant Epo
    used to treat sever anemia, suspected in illegal doping
  348. Detecting recombinant EPO
    use highly glycosylation of recombinant Epo as compareed to endogenous to detect illegal doping
  349. Fusion Proteins
    use the active domains of some proteins to improve or modify function
  350. Etanercept
    fusion protein (combined Fc domain of TNF alpha and IgG)-->used as a fake receptor for TNF alpha and soaks up all the extra TNF alpha produced, used to treat Rheumatoid arthritis
  351. Hemoglobin vs. Myoglobin (function)
    Hemoglobin is a carrier/transporter we get 10X the amount of O2 carrying capacity, Myoglobin is an O2 storage molecule
  352. Hemoglobin vs. Myoglobin (location)
    Hb in blood, Mb in skeletal and cardiac muscle
  353. Hemoglobin vs. Myoglobin (location)
    Hb is quaternary tetramer, Mb is monomer
  354. Hematocrit
    the % volume of RBCs in the blood (25mM)
  355. Human oxygen requirements
    260mL of O2/min at rest, 4000 mL/min by athletes
  356. Cytoglobin and Neuroglobin
    In the brain and peripheral tissues
  357. Hb structure
    quaternary strucutre of 2 dimers of 2 monomers a and B--the Hb monomers are touching and this allows communication to be possible
  358. Cooperativity
    as one monomer binds an O2, it increases the affinity in the other monomers
  359. Hb SALT BRIDE
    lysine and glutamate (think Salt Bridge is like glue)--IONIC BOND
  360. Salt Bridge=Tense
    No O2 binding--low affinity
  361. Salt Bridge=Relaxed
    O2 binding --> high affinity, O2 binding breaks the salt bridge
  362. Fe needs to be------to bind oxygens
    reduced (Fe2+)
  363. Heme
    Porphyrin ring that is planar and has 4 coordination bonds
  364. Fe
    hexacoordinate, makes 4 bonds with Heme, 1 with proximal histidine, one with O2
  365. Cooperativity
    binding of ligand (O2) to one monomer of a multimeric protein affects the affinity at the other binding sites (can be positive or negative)--positive for Hb
  366. Why do different types of Hb exist/
    to address the specific tissue demands at different times during development
  367. Adult Hb
  368. Fetal Hb
    HbF (exists as ~1% of adult blood)
  369. Allosteric Protein
    protein that exhibits changes in ligan affinity under the influence of small molecules
  370. Allosteric effectors (regulators)
    Bind to proteins at a site OTHER than the active site--alter ligan binding via Long-range conformational effects
  371. Allosterica regulator has a shape______than the substrate molecule
    different than
  372. Hb S-Shaped
    because of multimeric cooperativity
  373. Mb hyperbolic
    because of monomeric, reversible binding
  374. Shifting the curve-->Lower the affinity
    Negative allosteric effect-->shifts curve to right
  375. Shifting the curve-->Increasing the affinity
    Positive allosteric effect-->shifts the curve left
  376. Increasing these, shifts the curve right
    Temp, H+, CO2, BPG
  377. At high altitudes (low pO2, need to get more O2 to tissue)
    high levels of BPG-->shift the curve to the right-->lower affinity for O2-->increase tissue O2
  378. 2,3 BPG
    metabolite in high concentrations in RBCs, principal allosteric effector for Hb-->stabilizes the T-form-->shifts T/R equilibrium to the T form-->binds btwn B subunits-->weakens affinity for O2 binding-->has little effect at high O2 levels-->has stronger effect at low O2 levels
  379. Carbamate formation
    Hb carries 15% of CO2 in blood as carbamate-->carbamate formation favor salt bridge formation (tense state)-->lowers O2 affinity of Hb
  380. Hb acts like a blood buffer
    binding protons-->Hb promotes the formation of bicarbonate
  381. Fetal Hb vs. Adult Hb
    2,3 BPG has a weaker binding to fetal Hb because of different aminoacids at the allosteric site, allosteric effect of 2,3BPG on HbFHbF has a slightly higher affinity for O2 than HbA
  382. Alteration in HbF
    The Histidine is replaced by Serine--->basically you took away positive charge-->less able to stick the O2
  383. Sickle cell Hb
    HbS-->replace Glutamine with Valine-->hydrophobic-->cells with sickle shape
  384. HbC
  385. B Thalassemias
    chromosome 11, two mutated B-globin genes (minor: heterozygote)
  386. A Thalassemias
    chromosome 16, progressive loss of alpha globin genes-->results in more severe anemias
  387. Why does HbS polymerize in the deoxy state
    When the Hb is deoxygenated that is when the Hb clumps together-->causes long polymers, in higher O2 concentrations is can disperse
  388. Which vessels are affected by HbS?
    Mostly venous occlusion because deoxyHb, especially venules
  389. Splenic involvement in HbS (SC)
    Red pulp is the clearinghouse (sinusoidal slits)--white pulp (splenic cord) has immune function, when RBCs migrate from snusoids-->chords they get stuck-->sent for destruction (hemolysis)
  390. Joint/Inflammatory involvement (SC)
    Increased RBC transit times in inflamed tissues
  391. Bone involvement (SC)
    Occlusion in bone marrow-->very painful
  392. Circulatory involvement (SC)
    Increased bilirubin because increased rate of hemolysis
  393. Sickle cell trait
    confers resistance to Malaria, presence of HbA and HbS, patients should over overly strenous physical activity
  394. Management of Sickle Cell
    Hydrate the patient! Dehydration is a huge issue-->hydrate with HYPOTONIC solution so it will enter cells, splenomegaly, ischemic tissue pain, leg ulcers
  395. Top ten symptoms to manage
    Vasoocclusive crisis and acute pain, chronic pain, chronic hemolytic anemia (transfusion, folate supplementation), treatment and prevention of infections (spleen is important for immune response), organ damage (most SC patients have gallbladder removed), diagnosis and prevention of stroke (dilute HbS and antiplatelet therapy), pulmonary hypertension (acute chest syndrome), iron overload (chelation therapy, from transfusions), awareness of sickle cell trait, health maintenance (psychosocial)
  396. Creuzfeld Jacob Disease-Scrapie-Prions
    transmissable spongiform encephalopathy
  397. Types of CJD
    spontaneous CJD, famlial fCJD, variant vCJD
  398. Monosaccharides
    glucose, fructose, galactose, mannose--exist as cyclic ring systems
  399. Sucrose
  400. Maltose
  401. Lactose
  402. Amylose
    glucose+glucose (alpha 1,4)
  403. How do gucose and galactose move from lumen-->enterocyte
    use Na+ depdent transporter enter the apical membrane of the enterocyte--->exit the basal membrane
  404. Lactase
    non-inducible, brush border enzyme-->can't make more of it if you ingested a lot of lactose-->lactose absorption is dependent upon lactose cleavage not onthe absorption of glucose and galactose
  405. Lactose intolerance
    deficiency in lactase enzyme
  406. Brain and RBC requirement for glucose-HYPOGLYCEMIA
  407. How long after ingestion is glucose absorption take place?
    2-3 hours
  408. Glycogen
    glucose storage polymer--stored as granules in the liver and muscle cells
  409. Where are Glycogenolytic and glycogenic enzymes stored?
    Bounds directly on granules of glycogen-->assures rapid change in glycogen metabolism in response to allosteric and hormone stimuli
  410. Glycosylation
    Can occur during protein synthesis in the ER or after protein synthesis in the Golgi, is the major post translational protein modification
  411. What is the function of glycosylation?
    guard against denaturation, signal tansport, cell-cell communication, maintain water solubility of hydrophobic proteins
  412. N-linked sugar on protein
    GlcNAc or GalNAc bound to asparagine-X-Ser/Thr
  413. O-linked sugar on protein
    bound to serine, usually membrane proteins and mucous secretions are O-linked
  414. LDL Receptor
    Found in the membrane of smooth muscle and fibroblasts-has 2 N-linked and 1 O-linked glycosylations, O linked encircle the protein chain to hold it up like a circulary floaty--deficiency in LDL receptor can lead to Smith Lenli Opits
  415. I-Cell disease
    lacking the GlcNAc 1-P transferase-->lysosomal enzymes do not get phosphorylated--> do not get the Man-6-P to target them to the lysosomes-->build up substrate in the lysosome-->dense inclusion bodies in the fibroblasts
  416. Collagen
    triple helix motif with N-linked and O-linked glycosylations--> N linked cleaved off
  417. Degree of glycosylation
    Highly glycosylated collagens-->meshwork (basement membranes), low glycosylated-->highly ordered (tendons
  418. Structure of collagen
    each monomer: left handed alpha helical (tertiary), mature collagen: triple stranded, right handed super helical, quaternary
  419. Procollagen
    Made first in RER-->sent to the Golgi-->N-linkages are removed
  420. Tropocollagen
    Present form in the Golgi, Second version of collagen after the nonhelical domains have been cleaved off-->self assemble into insoluble collagen fibrils
  421. Brittle Bone disease
    Can't synthesize Type I collagen
  422. Glycosylation & blood type
    Glycosylation determines blood types-the "decoration": on the H-substance lycosphingolipid
  423. Type A blood
    GalNAc (N-acetylgalactose)---develop antibodies in their plasma which agglutinate type B and AB
  424. Type B blood
    Galactose--develop antibodies in plasma against type A and type AB
  425. Type A-B blood
    GalNAc and Galactose--develop no antibodies (universal recipient)
  426. Type O blood
    neither--have only H substance (universal dOnor)
  427. Sialic acid
    impart negative charge via the carboxylate (in the GM receptor for the cholera pathway
  428. GABA
    inhibitory NT-increase Cl- influx into the channel
  429. GABA drugs
    propofol, neurosteroid
  430. GABA sites
    on alpha subunit
  431. Excitatory
    Ach, glutamate, serotonin
  432. Ionotropic (directly coupled ion channels)
  433. Metabotropic (linked to G-protein)
    Ach-muscarinic (ex. ACh in the parasympathetic innervation of the heart)
  434. subunits of ACh receptor
    alpha (2), beta, delta, gamma
  435. D-tubocurarine
    competitive inhibitor of ACh
  436. Ion channel primaarily responsible for resting membrane
    K+ leak channels (another is Na-K channels)
  437. Enzymes that synthesizes ACh, where is it synthesized
    cholinacetyltransferase in the presynaptic
  438. Where is it stored and how is it released?
    Stored in vesicles--released by increase Ca2+ (via voltage gated Ca2+ channels)
  439. Enzyme that degrades Ach, where is it synthesized
    achetylcholinesterase, in the synaptic cleft
  440. Synthesis of GABA
    GAD, formation of glutamate to GABA via decarboxylation
  441. Helix that lines the ion channel of ACh receptors
    M2 helix--it's an amphipathic helix and it has hydrophilic and hydrophobic domains (opens and closes)
  442. What is meant by allosteric regulation of the ACh gating mechanism
    ACh binding causes conformational change in M2 helix that allows hydrophilic ions in
  443. Differences between ACh and GABA(a)
    ACh lets in anion, GABA lets in cations,
  444. Similarities between ACh and GABA(a)
    both bind NTs, both have 5 subunits, they both have M2, they are both ionotropic,
  445. How does GABA decrease the probability of action potential?
    GABA opens up Chloride channels (Cl- goes into cell, membrane potential goes down)
  446. Two positive modulators of the GABA(a) receptor
    propafol and ethanol and benzodiazapenes, activate GABA(a) by binding to transmembrane receptor between alpha and gamma
  447. Disease involving a chloride channel
    CFTR--cystic fibrosis
  448. Disease involving ACh receptor
    Myastinia gravis-->autoimmune disease affecting the nicotinic receptor
  449. 3 systems in structural
    actin microfilaments, microtubules (the biggest), intermediate filaments
  450. Roadway analogy
    Microtubules are highways, actin are the side roads
  451. Actin
    does the membrane remodeling and movement (short distance movement)
  452. Myosin
    molecular motors for actin, almost always to the + end of the filament
  453. Microtubules
    alpha and beta tubulin heterodimers, alpha GTP does not hydrolyze to GDP, Beta GTP does hydrolyze, the highways
  454. Synthesis of microtubules
    Both subunits of heterodimer need to be in the GTP state for polymerization-->always adds to the GTP-bound Beta subunit-->lateral assembly of 13 protofilaments results in hollow tube-->creates polarity-->heterodimers added to + end
  455. Microtubule Catastrophe
    Rapid dissociation of the microtubules--rate of deletion is faster than the rate of addition
  456. Treadmilling
    adding to the positive and losing from the negative simultaneously to change microtubule length
  457. Cilia and flagella
    formed from doublet microtubules
  458. Kinesin
    move towards the +
  459. Microtubule associated disease
    Tau protien on chromosome 17-->causes Alzheimer's
  460. Microtubule organizing center
    in the centriole, responsible for pulling the DNA apart
  461. Centrioles
    organelles that pull the centromeres apart in mitosis, made up of gamma tubulin
  462. Kinetochore
    the protein that the microtubules bind to on the centromere
  463. Mitotic spindle motion
    uses dynein to pull apart
  464. Spindle poisons
    Taxol(Palitaxel), vinca alkaloids (vinblastine and vincristine), colchicine
  465. Taxol (Paclitaxel)
    hyper stabilizes microtubules by binding to b-tubulin
  466. Vincca alkaloids (Vinblastine and vincristine)
    used in the treatment of leukemia and lymphoma--binds to tubulin dimers to inhibit their assembly
  467. Colchicine
    membrane soluble, high affinity for tubulin, prevents polymerization extremely toxic, used for Gaut
  468. Genomic instability in Cancer
    uneven mutiplication of MT organizing centers-->leads to multipolar cell division-->causes cancer-->one of the earliest events detectable
  469. Basal body
    what cilia originate from, made of triplet microtubules
  470. Microvilli
    Actin based
  471. Cilia
    Microtubule based
  472. Motile cilia
    in the lungs
  473. Non-motile cilia
    Ex. in the kidney lumen, these cilia can couple to cell proliferation-->mutation in this results in polycystic kidney disease
  474. Dynein
    carry out long distance intracellular particle movement, retrograde motors-->move to the negative end, highly processive motors
  475. Kinesin
    carry out long distance intracellular particle movement, anterograde-->move to the positive end
  476. Cytoplasmic dynein
    found in the cytoplasm
  477. Axonemal dynein
    found in cilia
  478. Fast axonal transport
    the molecular motors (dynein and kinesin) move fast up and down axons
  479. Intermediate filaments
    2 dimers form a tetramer, 8 tetramers form a rope like filament, coil-coil structure, less dynamic and non polarized--components are extremely diverse and complex--provides mechanical strength to cell
  480. Type I and II intermediate filaments
  481. Type III -Intermediate filaments
    Desmin, Vimentin
  482. Type IV-Intermediate filaments
    nestin neurofilaments
  483. Type V-Intermediate filaments
    nuclear lamins
  484. Node of ranvier
    Achieved by dephosphorylating the intermediate filaments
  485. Epidermis Bullosa
    genetic disease that affects the keratin (type I and II intermediate filaments)-->skin becomes detacheched from dermis
  486. Cilia
    they have MTOC centrioles--basal bodies--composed of microtubules--9 doublets of microtubules arranged in a circle on the outside and 2 on the inside--highly energy dependent
  487. How do Cilia move?
    axonemal dynein acuases adjacent filaments to slide over each other--highly ATP driven
  488. Cilia and Situs Inversus
    Early embryo is symmetric L-R assymetry is established by a ciliated structure known as the node-->cilia mix up the contents-->mutations that affect dynein can cause cilia to beat the wrong direction
  489. Kartenger Syndrome
    Situs inversus--ciliopathy--when combined with chronic sinusitis and bronchiectasis (inability of the cilia to move mucous through the lungs)
  490. Primary Ciliary Dyskinesia
    Rare autosomal dominant ciliopathy encompassing 250 proteins-- chronic sinutsitis and bronchiestasis
  491. Crawling
    some cells that don't have cilia, rely on intrinsic propeties of the actin/microtubule cytoskeleton for their movement
  492. Example of crawling cells
    neutrophils migrating from the bloodstream to tissues when the "smell" diffusable molecules released from bacteria
  493. Where does fatty acid synthesis occur?
  494. Where does fatty acid oxidation occur?
  495. In fatty acid synthesis, where and how is Acetyl CoA transferred from mitochondria?
    Transferred to the cytoplasm as citrate through a citrate shuttle
  496. In fatty acid synthesis, what happens to citrate in cytoplasm?
    • It is converted to oxalacetate (ATP-driven).
    • Oxalacetate is converted to malate by malate dehydrogenase.
    • Reduced form of NADH disguised as malate can be shuttle through to the mitochondria through the Malate transporter
  497. What is the source of carbons in fatty acid synthesis?
    Acetyl CoA--acetyl is tethered by a thioester (SOCH3) to CoA
  498. The two building block for fatty acid synthesis
    Acetyl CoA and malonyl CoA
  499. How do you convert Acetyl CoA to malonyl CoA?
    Biotin as the carrier protein uses Biotin carboxylase
  500. What triggers fatty acid synthesis?
    insulin--the cells know you have energy
  501. What inhibits fatty acid synthesis?
    glucagon, epinephrine-->trigger phosphorylation of Acetyl CoA
  502. Acetyl CoA carboxylase
    Key ergulatory enzyme in fatty acid synthesis
  503. Fatty acid synthesis: elongation
    • Fatty acid synthase is like a wheel that uses CO2 has carbon source to elongate fatty acid chain, starts with 3 carbon malonyl CoA...
    • 1. condensation
    • 2. reduction
    • 3. dehydration
    • 4. reduction
    • REPEAT!
    • to
  504. How many cycles does fatty acid synthase have to comlete to build palmatate?
    7 cycles (start with 2C-->16C)
  505. Net reaction for fatty acid synthesis
    8AcCoA + 14 NADPH + 14H+ + 7 ATP-->palmitate+ 8CoA+ 14NADP+ + 7ADP +7 Pi+ 7 H2O
  506. How do humans convert fatty acids into triglycerides?
    • activate as thioester by converting palmitate to "fatty acid coA" using Fatty acid CoA synthetase (thiokinase)
    • acylate alcohol side chain-->reduce it with NADH-->acytlate-->reduce the ketone
    • makes a phosphatidic acid intermediate (2/3 of the way to triglyceride
  507. phosphatidic acid
    intermediate created during synthesis of triglycerides
  508. saturated vs. unsaturated
    saturated packs together tightly (butter) unsaturared is kinky (liquid, oil)
  509. lipoprotein lipase
    allows us to degrade triglycerise back to fatty acid
  510. Where are triglycerides stored? degraded?
    adipose tissue, degraded in blood, liver

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HB1-exam 1 note cards.txt
2010-09-08 03:23:23
hb1 exam notecards

hb1 exam notecards
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