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70 Cards in this Set
- Front
- Back
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Base Excision Repair
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-Parent Cell
1. DNA Glycolase removes incorrect base 2. APE1 Endonuclease chops sugar backbone 3. AP Lyase removes backbone 4 DNA poly and ligase repair. |
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Mismatch Repair in Humans
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-Daughter Cell
1. MSH2 and MSH6 recognize incorrect bases on 1 strand 2. MLH1 and PMS2 recruit helicase and exonuclease to unwind and remove incorrect section 3. DNA poly and ligase repair |
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Nucleotide Excision Repair
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-Occurs when bases cross link
1. Initial dmg recognized and 23B and XP-C form a complex around 2. DNA is opened using TFIIH, RPA binding proteins and XP-G exonuclease, recruits XP-F 3. XP-F and XP-G remove dmgd section 4. DNA Poly and Ligase fix |
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Error Prone Repari
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Repair units are saturated due to large amnt of dmg in short amount of time. Causes increased errors
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Double Strand Break by Homologous recombination
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1. Double strand breaks after replication
2. Nucleoprotein filament formed by RAD 51 and other proteins 3. RAD 52 and RAD 54 search for homolgy of nucleoprotein filament within sister chromatid, pairs up 4. DNA poly elongates strand using sister chromatid 5. Repaired strand base pairs with 2nd broken strand. 6. Poly elongates and ligase fuses |
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Double Strand Break Repair by End Joining
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-Error Prone
1. Double Strand Breaks 2. DNA-PK (kinase enzyme) and KU80/KU70 synapse to broken ends 3. Other proteins recognize and make strands equivalent 4. Ligase binds |
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Topisomerase I
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-Cleaves one strand of DNA
-No energy required -Camptochin-inhibits topo I anti yumor agent |
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Topoisomerase II
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-Binds two strands of DNA so that both become more relaxed, breaks and rejoins
-novobiocin0blocks binding of ATP to gyrase(topoisomerase) ciprofloxin-interferes with breakage and rejoining |
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PCNA
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Molecule that DNA moves through during replication, encircles DNA and stabilizes
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RPA
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Single stranded binding proteins
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Pol delta
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Polymerase in replication of human DNA
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Large T antigen
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helicase function in DNA replication
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Trombone Slide
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Moves lagging strand so that leading strand can continue duplication
prevents polymers from running into each other |
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Ori Sites
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-Repeats rich in AT facilitates unwinding
-9bp Serve as binding site for DNA A protein |
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Initiation of Translation
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-IF3 binds to 30s section and IF6 binds to 50s
-IF1 binds to 30s and IF2 brings in Met tRNA with GTP -IF4 brings in mRNA -GTP is hydrolyzed -IF6 and IF5 bring in 50s segment and hydrolyze together |
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Elongation of Translation
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-tRNA is brought in using an EF1 charged.
-hydrolyzes to change ribosome conformation -ribosome catalyzes peptide bond formation -EF2 hydrolyzes conformational change moving tRNA's along |
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Termination/Release of Translation
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RF1 and RF3 fill in at active site with GTP
-Hydrolyzes breaking apart ribosome and releasing mRNA and protein |
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Aminoacyl-tRNA synthase
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binds to tRNA to transfer amino acid, bind to two sides of face of tRNA
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Wobble
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Ability of third site on mRNA codon to be read by multiple base pairs, adds flexibility and need for almost half as many tRNA types
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DNA types
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A-shortened
B-normal Z-left handed |
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Conformations of DNA
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2ndary structures-hairpin and stem loop
tertiary-pseudoknot |
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AT and CG base pairs
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AT-2 H-bonds
CG-3 Hbonds |
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Vitamin K Antagonists
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-Needed for sythnesis of prothrombin and other clotting factors
-carboxylation of glutamate on tail of prothrombin -without this reaction prothrombin does not chelate calcium well which is needed to anchor to cell walls |
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TPA
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Changes plasminogen to plasmin which degrades the fibrin clot to peptides
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Hemophelia
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Lacks factor VIII which effects activation of X
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Zymogen-regulation type
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Inactive form of enzyme, requires cleaveage for activation
-digestive-chymotrypsin -irreversible |
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Regulation by Phosphorolation
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Phosphorylation activates enzyme by freeing it for activation
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Isoenzymes
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-Variations of enzymes with same functionality, varying degrees though-asian flush
-Can be used to determine site of injuries |
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Indinavir
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drug for HIV which binds to protease changing symmetry of catalytic triad
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Catalytic triad
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Asp, His, Ser
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Transition State Analog
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Resembles transition state acting as an inhibitor. Very Specifice
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Irreversible Inhibitoe
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Pennecilin, binds with very high affinity
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Vmax and Km and kcat
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Vmax-max velocity of rxn
Km-concentration needed to occupy half of the active sites of an enzyme kcat-turnover rate |
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competive inhibitor
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effects km, binds to the active site
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noncompetitive inhibitor
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effects Vmax, binds to a site other than the active site
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Types Enzyme fitting
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Induced Fit
Lock and Key |
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Thalassemias
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Defective synthesis of either alpha or beta chain of hemoglobin, gene is present but synthesis is impaired
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Sickle Cell
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Glu to Val, causes sickling as hydrophobic valine causes a stciky patch to form, Hb clump forming fibers leading to sickling
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Sequential Model for cooperative binding
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Each subunit of hemoglobin changes conformation when bound to O2 and effects only neighboring units
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Concerted Method for Cooperative binding
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Entire hemoglobin moleculec changes conformation.
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INtermediat Filaments
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-Acidic and BAsic Filaments-epithelial
-Desmin, GFAP, Vimentin-muscle, glial cells, mesenchymal -Neurofilaments-neuorons -Lamins-nucleus |
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collagen structure
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-structure triple helix using glycine and hydroxyproline and hydroxylysine
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Collagen sythesis
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-sythesized by ribosomes in rER
-Assemble into procollagen, with propepeptides on ends to prevent formation of fibrils -move to golgi for glycosylation and transport out of cell -propeptides removed when moved to cytoplasm to form fibrils |
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Huntington's Disease
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Extended Gln strands cause protein aggregation
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Ehler's Danlos Type IV
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replacement of glycine in residues disrupting triple helix anc from exon skipping wich shortens strands
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Osteogenesis Imperfecta
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Shortened alpha1 chains are produced preventing normal collagen formation
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Scurvy
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Vitamin C deficiency
Needed for hydroxyproline formation |
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Ehlers Danlos Type VI
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Deficiency in lysyl hadroxylase
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Ehlers Danlos Type VII
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Incomplete removal of propeptides
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Ehlers Danlos IX
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Occipital Horn Syndrom-deficiency in lysyl oxidase activity, defect in Cu transport
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Mad Cow Disease
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Bad Beta sheet prions from cow are introduced and cause human alpha helix prions to change to b-sheet, causes aggregations
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Alzheimer's
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Amyloid deposits form in the brain causing plaque formations
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GroEL
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bacterial complex that aids in folding
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GroES
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Caps GroEL to aid in protein folding
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HSP-70
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Bind to unfolded proteins keeping sticky parts seperate
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Peptidyl Prolyl Isomerase
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changes peptide bonds from cis to trans quickly
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Peptide Disulfide Isomerase
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reforms incorrect sulfide bonds into correct folding
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Amino Acid Size and Charge
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Effect what kind of structure amino acid can be found in: sheet, helix or turn
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Progressive Stabilization of Intermediates
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Proteins form intermediates which stay stable as the protein folds to the correct shape
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Aspartic and Glutamic Acid Pka
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4.1
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Histadine Pka
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6.0
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Cystein pKa
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8.0
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Tyrosine pKa
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10.9
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Lysine pKa
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10.8
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Arginine pKa
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12.5
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Histadine Pka
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6.0
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Cystein pKa
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8.0
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Tyrosine pKa
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10.9
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Lysine pKa
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10.8
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Arginine pKa
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12.5
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