Various important information for exam 1
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| Base Excision Repair (BER) | repairs single base alterations with specific glycosylases
usually targets deaminations
removes abberrant base creating AP site, cuts backbone, polymerase fills in
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| Nucleotide Excision Repair (NER) | targets UV photoproducts
protein comples removes DNA before and after damage
USUALLY coupled to transcription
repairs template strand more efficiently than complementary strand
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| Mismatch Repair (MMR) | targets misincorporation errors that occur during replication
recognizes heteroduplex bubbles in DNA, looks for gaps in strand to determine which is newly synthesized
exonuclease removes large patch up and downstream
of damage, polymerase fills in
HN
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| Translesion Synthesis | Replication fork progresses through damaged sites
error prone
may need special DNA polymerase
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| Homologous Recombination (HR) | occurs at dsDNA breaks (intentional or unintentiomal), at the break the homologous region of the homologous chromosome or sister chromatid is used as a repair template
restricted to S phase cells
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| End Joining (EJ) | At a dsDNA break a nuclease removes damaged ends, a polymerase makes them compatible for ligation
very error prone, but it is fast and easy, and can occur at anytime
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| Gaucher's Disease | defective pathway is Cer-Glc
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| Krabbe's Disease | defective pathway is cerebroside (psychosine builds up via alternative toxic catabolic pathway)
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| Metachromatic leukpdystrophy (MLD) | defective pathway is sulfatide
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| Tay Sachs Disease | defective pathway is ganglioside
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| Niemann-Pick A & B diseases | defective pathway is sphingomyelin
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| Histidine | (His) Basic, polar amino acid
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| Leucine | (Leu) non-polar amino acid
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| Serine | (Ser) uncharged, polar amino acid
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| Phenylalanine | (Phe) non-polar amino acid
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| Tryptophan | (Trp) non-polar amino acid
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| Glutamate | (Glu) Acidic, polar amino acid
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| Glutamine | (Gln) uncharged, polar amino acid
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| Tyrosine | (Tyr) uncharged, polar amino acid
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| Arginine | (Arg) Basic, polar amino acid
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| Valine | (Val) non-polar amino acid
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| Alanine | (Ala) non-polar amino acid
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| Asparagine | (Asn) uncharged, polar amino acid
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| Aspartate | (Asp) Acidic, polar amino acid
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| Glycine | (Gly) non-polar amino acid, small size lead to flexibility of chain, found in tight turns of proteins
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| Methionine | (Met) non-polar amino acid
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| Isoleucine | (Ile) non-polar amino acid
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| Threonine | (Thr) uncharged, polar amino acid
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| Proline | (Pro) non-polar amino acid, proline is a rigid residue causes inflexibility in the chain
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| Lysine | (Lys) basic, polar amino acid
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| Cysteine | (Cys) uncharged, polar amino acid, forms disulfide bonds with other cysteines, tends to happed in oxidizing environments (extracellular), can stabilize or strain chains
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| topoisomerase I | relaxes supercoiled DNA in replication, cuts one strand, passes other through and reseals
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| topoisomerase II | relaxes supercoiled DNA, cuts duplex DNA, passes other duplex DNA through and reseals --> target of etoposide (cancer drug)
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| DNA Polymerase Alpha | associates with Primase to synthesize short stretch of DNA, error prone but tolerated because the DNA gets removed with the RNA primer
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| Primase | enzyme that lays down 3' OH RNA primer for replication
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| DNA Polymerase Delta | Performs bulk of eukaryotic DNA synthesis, associates with PCNA clamp, has 3'->5' exonuclease proofreading
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| DNA Polymerase Epsilon | Can substitute for Pol Delta, processive without PCNA clamp association, has 3'->5' exonuclease proofreading
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| PCNA clamp | proliferating cell nuclear antigen, stabilizes association of DNA polymerase and DNA
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| Okazaki fragments | fragments of daughter strand DNA created on lagging strand during replication
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| Ligase I | enzyme that seals nicks in DNA
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| The Replisome | @ minimum includes: helicase, 2 polymerases (with associated PCNA clamps), and primase
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| Cell Cycle | M phase, G1 phase, S phase, and G2 phase
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| Replication Licensing | Method by which initiation of replication is controled, ensure that each segment of the genome is only replicated once a cell cycle
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| ORC | Origin Recognition Complex - attracts licensing factor (cdc6) for initiation of replication
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| cdc6 | licensing factor, must be activated by CDK, binds to ORC to assemble prereplication complex (helicase and associated proteins), after replication begins cdc6 is destroyed, ensuring that the particular ORC will only start replication once that cell cycle
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| Deamination | spontaneous DNA damage, amine group is lost from a base causing a transition mutation -->changes base pairing properties
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| Base Loss | Spontaneous DNA damage, base falls off, leaving DNA backbone intact (depurination most common form)
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| ROS | Reactive Oxygen Species, generated by normal cell metabolism or ionizing radiation, cause strand breaks or base damage
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| Ionizing radiation | Gamma Rays or X-rays, lead to formation of ROS
used for cancer therapy
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| UV | causes photoactivation of DNA, forming pyrimidine dimers (cyclobutane products btwn adj Ts, and 6,4 products btwn T and C)
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| Carcinogens | chemicals that form adducts in DNA, can be taken in directly or form from cellular metabolism of a chemical)
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| Alkylating agents | carcinogens that add alkyl groups by covalent bond to DNA
cancer drug cytoxan is alkylating agent
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| Cross-linking agents | carcinogens that are bifunctional, bond to two positions in the DNA forming inter (worst kind) or intrastrand cross-links
cancer drug - cis platin
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| Replication Errors | polymerase error - enzyme adds wrong base (often a tautomer of the appropriate base) Microsatellite instability - primer strand slips during highly repetitive sequences -->deletion or expansion of repeats can occur
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| Celluar response to DNA damage | damage sensors recognize abnormal DNA, they activate Transducers which phosphorylate Mediators that instruct activation or repression of gene products that lead to checkpoints and DNA repair pathways
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| p53 | gene that is critical mediator of cellular response to DNA damage, activation leads to cell cycle arrest or apoptosis, mutation of p53 --> cancer
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| transposon | mobile DNA element that excises from one site and inserts in another, encodes transposase - an enzyme responsible for excising the transposon and inserting it elsewhere
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| retro element | mobile DNA element that is not excised, it is copied by cell during transcription, reverse transcriptase then makes a DNA copy and inserts the new copy else where (two kinds retroviral elements and retroposons)
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| V(D)J recombination | process by which multiple versions of coding segments are put together to achieve variable domains on lymphocytes
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| V(D)J mechanism | RAG1 and RAG2 make ds breaks between signals and coding segments, the pieces are joined via EJ
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| Basic Protein Structure | primary=amino acid sequence
secondary=local spatial arrangement (alpha helices and beta strands)
tertiary=3D structure of entire peptide chain
quaternary=spatial arrangement and association of two or more peptide chains
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| Alpha Helix | residues separated by 4 positions form h-bonds
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| Beta Sheet | h-bonds between adjacent beta strands (hydrophillic and phobic residues alternate)
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| Globular Proteins | hydrophobic residues in center of protein, aa side chains closely packed in center, buried O and N h-bonds are satisfied
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| Fibrous Proteins | elongated molecules that function as structural materials, have repetitive amino acid sequences
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| Integral Membrane Proteins | have hydrophobic domains where protein is in membrane
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| post translational modifications | proteolysis, phosphorylation, methylation, hydroxylation
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| Protein Folding Stability Factors | hydrophobic effect - favors folded
conformational entropy - favors unfolded
h-bonding - which ever state satifies most h-bonds
electrostatics - generally folded state
steric repulsion - determines viability of folded
torsional strain - favors unfold
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| MSA | multiple sequence alignment - compares sequences of homologous proteins
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| How to improve solubility of protein therapeutics | mutate cys->ser, prevents dimer formation
replace surface hydrophobic with hydrophillic
Change pI -> make charged at cellular pH
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| How to improve stability of protein therapeutics | remove cysteines ->prevent misfolding
use computer model to find ideal states
remove protease recognition sites and shorten loops
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| heat shock protein 70 (Hsp70) | binds to proteins as they emerge from the ribosome preventing aggregation and misfolding before the end of translation
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| GroEL Chaperonins | cylindrical protein complexes that contain the protein while it folds
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| ligand | anything that binds specifically with a protein
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| cofactor | non-protein molecule bound by an enzyme that participates in rxns or influences their rate
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| allosteric effectors of Hb | BPG, Bohr effect (pH), temperature, CO2
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| HbS Delay time | time it takes the deoxygenated HbS to start polymerizing, shortened by heat increase
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| Hydroxyurea | drug that increases percentage of HbF
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| RNA Polymerase I | transcribes single gene that codes for rRNA
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| RNA Polymerase II | synthesizes mRNA
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| RNA Polymerase III | synthesizes tRNAs and other small nuclear RNAs
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| RNA poly II promoter binding | TFIID(TBP and associated TAFS) bind at TATA or are attracted by other protein complex (for non TATA promoters)
TFIID attracts RNA polyII
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| RNA poly I promoter binding | binding involves association of two UBFs and subsequent attraction of protein complex including TBP that attracts RNA polyI
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| RNA poly III promoter binding | TFIIC binds and attracts complex with TBF which attracts RNA polyIII
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| mRNA 5' cap | 7-CH3-guanosine linked 5'->5' triphosphate protects 5' end from degradation by making it look like a 3' end
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| mRNA poly A tail | cleavage-polyadenylation encoded by pre-mRNA, signals on mRNA induce cleavage followed by addition of poly A tail, tail is important for translation and mRNA 1/2 life determination
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| positive control | binding of trans factor upregulates gene expression
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| negative control | binding of trans factor down regulates gene expression
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| pinocytosis | cellular uptake of fluid without changing cellular concentrations
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| potocytosis | uptake of small molecules in caveolae, often for transcytosis
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| phagocytosis | cellular uptake of large particles, generally by association with receptors
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| RME | Receptor Mediated Endocytosis - binding of protein to specific receptor resulting in cellular uptake
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| coated pit | region wher RME occurs, coated in clathrin which is involved in pinching off of vesicles
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| endosomes | vesicle that has lost its clathrin coat
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| primary lysosome | spherical or oval with uniform staining
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| secondary lysosomes | uneven staining with EM, contain material that is being digested
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| mucopolysaccharidoses | Hunter's Syndrome, Hurler's Syndrome
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| glycosaminoglycans | repeating disaccharide units, highly negatively charged
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| O-linked glycoproteins | carbohydrate chains on the OH of Ser or Thr (eg. blood antigens)
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| N-linked glycoproteins | carbo chains on NH2 of Asn, includes most glycoproteins
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| sphingolipid | polar sugar head, hydrophobic tail consisting of an FA and a sphingosine(long chain amino alcohol)
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| ceramide | sphingosine + FA (base of sphingolipids)
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| cerebroside | gal+ceremide (major myelin lipid)
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| sulfatide | sulfated cerebroside
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| ganglioside | glycolipid with large sugar head (contain sialic acid)
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| sphingomyelin | ceramide-p-choline (lots found in myelin)
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| Competitive Inhibition of Enzymes | Km changes, Vmax constant, can be overcome by increasing substrate
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| Non-Competitive Inhibition of Enzymes | Vmax changes, Km constant
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