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UNC MS1 Exam 1

Various important information for exam 1

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
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
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
Translesion Synthesis Replication fork progresses through damaged sites error prone may need special DNA polymerase
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
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
Gaucher's Disease defective pathway is Cer-Glc
Krabbe's Disease defective pathway is cerebroside (psychosine builds up via alternative toxic catabolic pathway)
Metachromatic leukpdystrophy (MLD) defective pathway is sulfatide
Tay Sachs Disease defective pathway is ganglioside
Niemann-Pick A & B diseases defective pathway is sphingomyelin
Histidine (His) Basic, polar amino acid
Leucine (Leu) non-polar amino acid
Serine (Ser) uncharged, polar amino acid
Phenylalanine (Phe) non-polar amino acid
Tryptophan (Trp) non-polar amino acid
Glutamate (Glu) Acidic, polar amino acid
Glutamine (Gln) uncharged, polar amino acid
Tyrosine (Tyr) uncharged, polar amino acid
Arginine (Arg) Basic, polar amino acid
Valine (Val) non-polar amino acid
Alanine (Ala) non-polar amino acid
Asparagine (Asn) uncharged, polar amino acid
Aspartate (Asp) Acidic, polar amino acid
Glycine (Gly) non-polar amino acid, small size lead to flexibility of chain, found in tight turns of proteins
Methionine (Met) non-polar amino acid
Isoleucine (Ile) non-polar amino acid
Threonine (Thr) uncharged, polar amino acid
Proline (Pro) non-polar amino acid, proline is a rigid residue causes inflexibility in the chain
Lysine (Lys) basic, polar amino acid
Cysteine (Cys) uncharged, polar amino acid, forms disulfide bonds with other cysteines, tends to happed in oxidizing environments (extracellular), can stabilize or strain chains
topoisomerase I relaxes supercoiled DNA in replication, cuts one strand, passes other through and reseals
topoisomerase II relaxes supercoiled DNA, cuts duplex DNA, passes other duplex DNA through and reseals --> target of etoposide (cancer drug)
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
Primase enzyme that lays down 3' OH RNA primer for replication
DNA Polymerase Delta Performs bulk of eukaryotic DNA synthesis, associates with PCNA clamp, has 3'->5' exonuclease proofreading
DNA Polymerase Epsilon Can substitute for Pol Delta, processive without PCNA clamp association, has 3'->5' exonuclease proofreading
PCNA clamp proliferating cell nuclear antigen, stabilizes association of DNA polymerase and DNA
Okazaki fragments fragments of daughter strand DNA created on lagging strand during replication
Ligase I enzyme that seals nicks in DNA
The Replisome @ minimum includes: helicase, 2 polymerases (with associated PCNA clamps), and primase
Cell Cycle M phase, G1 phase, S phase, and G2 phase
Replication Licensing Method by which initiation of replication is controled, ensure that each segment of the genome is only replicated once a cell cycle
ORC Origin Recognition Complex - attracts licensing factor (cdc6) for initiation of replication
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
Deamination spontaneous DNA damage, amine group is lost from a base causing a transition mutation -->changes base pairing properties
Base Loss Spontaneous DNA damage, base falls off, leaving DNA backbone intact (depurination most common form)
ROS Reactive Oxygen Species, generated by normal cell metabolism or ionizing radiation, cause strand breaks or base damage
Ionizing radiation Gamma Rays or X-rays, lead to formation of ROS used for cancer therapy
UV causes photoactivation of DNA, forming pyrimidine dimers (cyclobutane products btwn adj Ts, and 6,4 products btwn T and C)
Carcinogens chemicals that form adducts in DNA, can be taken in directly or form from cellular metabolism of a chemical)
Alkylating agents carcinogens that add alkyl groups by covalent bond to DNA cancer drug cytoxan is alkylating agent
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
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
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
p53 gene that is critical mediator of cellular response to DNA damage, activation leads to cell cycle arrest or apoptosis, mutation of p53 --> cancer
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
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)
V(D)J recombination process by which multiple versions of coding segments are put together to achieve variable domains on lymphocytes
V(D)J mechanism RAG1 and RAG2 make ds breaks between signals and coding segments, the pieces are joined via EJ
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
Alpha Helix residues separated by 4 positions form h-bonds
Beta Sheet h-bonds between adjacent beta strands (hydrophillic and phobic residues alternate)
Globular Proteins hydrophobic residues in center of protein, aa side chains closely packed in center, buried O and N h-bonds are satisfied
Fibrous Proteins elongated molecules that function as structural materials, have repetitive amino acid sequences
Integral Membrane Proteins have hydrophobic domains where protein is in membrane
post translational modifications proteolysis, phosphorylation, methylation, hydroxylation
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
MSA multiple sequence alignment - compares sequences of homologous proteins
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
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
heat shock protein 70 (Hsp70) binds to proteins as they emerge from the ribosome preventing aggregation and misfolding before the end of translation
GroEL Chaperonins cylindrical protein complexes that contain the protein while it folds
ligand anything that binds specifically with a protein
cofactor non-protein molecule bound by an enzyme that participates in rxns or influences their rate
allosteric effectors of Hb BPG, Bohr effect (pH), temperature, CO2
HbS Delay time time it takes the deoxygenated HbS to start polymerizing, shortened by heat increase
Hydroxyurea drug that increases percentage of HbF
RNA Polymerase I transcribes single gene that codes for rRNA
RNA Polymerase II synthesizes mRNA
RNA Polymerase III synthesizes tRNAs and other small nuclear RNAs
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
RNA poly I promoter binding binding involves association of two UBFs and subsequent attraction of protein complex including TBP that attracts RNA polyI
RNA poly III promoter binding TFIIC binds and attracts complex with TBF which attracts RNA polyIII
mRNA 5' cap 7-CH3-guanosine linked 5'->5' triphosphate protects 5' end from degradation by making it look like a 3' end
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
positive control binding of trans factor upregulates gene expression
negative control binding of trans factor down regulates gene expression
pinocytosis cellular uptake of fluid without changing cellular concentrations
potocytosis uptake of small molecules in caveolae, often for transcytosis
phagocytosis cellular uptake of large particles, generally by association with receptors
RME Receptor Mediated Endocytosis - binding of protein to specific receptor resulting in cellular uptake
coated pit region wher RME occurs, coated in clathrin which is involved in pinching off of vesicles
endosomes vesicle that has lost its clathrin coat
primary lysosome spherical or oval with uniform staining
secondary lysosomes uneven staining with EM, contain material that is being digested
mucopolysaccharidoses Hunter's Syndrome, Hurler's Syndrome
glycosaminoglycans repeating disaccharide units, highly negatively charged
O-linked glycoproteins carbohydrate chains on the OH of Ser or Thr (eg. blood antigens)
N-linked glycoproteins carbo chains on NH2 of Asn, includes most glycoproteins
sphingolipid polar sugar head, hydrophobic tail consisting of an FA and a sphingosine(long chain amino alcohol)
ceramide sphingosine + FA (base of sphingolipids)
cerebroside gal+ceremide (major myelin lipid)
sulfatide sulfated cerebroside
ganglioside glycolipid with large sugar head (contain sialic acid)
sphingomyelin ceramide-p-choline (lots found in myelin)
Competitive Inhibition of Enzymes Km changes, Vmax constant, can be overcome by increasing substrate
Non-Competitive Inhibition of Enzymes Vmax changes, Km constant
Created by: MouserKat