Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| Cell cycle step: protein & RNA synthesis |
|
Definition
|
|
Term
| Cell cycle step: DNA replication |
|
Definition
|
|
Term
|
Definition
|
|
Term
| Cell cycle step: cytokinesis |
|
Definition
|
|
Term
| Cell cycle step: terminally differentiated cells |
|
Definition
|
|
Term
|
Definition
| Protein that controls cell cycle |
|
|
Term
| Cyclin dependent protein kinase (CDK) |
|
Definition
| Kinases driven by cyclins that effect the cycle cell |
|
|
Term
| What things control the cell cycle (2) |
|
Definition
| 1) Cyclins, 2) cyclin dependent protein kinases |
|
|
Term
| What controls cyclin dependent protein kinases |
|
Definition
|
|
Term
|
Definition
| Ubiquitin-proteosome pathway |
|
|
Term
| Li-Fraumeni cancer syndrome |
|
Definition
| Inherited p53 mutation: multiple cancers early in life |
|
|
Term
| Inherited p53 mutation: multiple cancers early in life |
|
Definition
| Li-Fraumeni cancer syndrome |
|
|
Term
|
Definition
| 1) Bound by cyclin, 2) synthesis, 3) phosphorylation, 4) other proteins (e.g., p21) |
|
|
Term
|
Definition
| 1) G2-M boundary, 2) mitosis, 3) mid-G1, 4) S |
|
|
Term
| DNA damage: activates or inactivates p53 |
|
Definition
|
|
Term
| Activated p53 inactivates _____ through ______ and _____ |
|
Definition
| E2F through inactivated cyclin E and un-phosphorylated pRb |
|
|
Term
| Mutations of p53: increase or decrease cancer/tumor rate |
|
Definition
|
|
Term
| Skipping G1 and S checkpoints can lead to what |
|
Definition
| Cell recplication with DNA damage |
|
|
Term
|
Definition
|
|
Term
|
Definition
| 1) DNA damage 2) blocked replication forks |
|
|
Term
| p53 activated by what checkpoints (2) |
|
Definition
|
|
Term
| Majority of human tumors have mutation in what |
|
Definition
|
|
Term
| Steps of DNA damage checkpointing (4) |
|
Definition
| 1) Bind to DNA damage, 2) recruit transducer kinases, 3) activate effector kinases, 4) activate protein effectors |
|
|
Term
|
Definition
| Activated by DNA damage sensor proteins |
|
|
Term
| Transducer kinase examples (2) |
|
Definition
|
|
Term
|
Definition
| Activated by transducer kinases |
|
|
Term
| Effector kinase examples (2) |
|
Definition
|
|
Term
|
Definition
| Activated by effector kinases |
|
|
Term
| Protein effector examples (3) |
|
Definition
|
|
Term
| p53, Cdk, and BRCA1 are examples of what |
|
Definition
|
|
Term
| ChK1 and ChK2 are examples of what |
|
Definition
|
|
Term
| ATM and ATR are examples of what |
|
Definition
|
|
Term
|
Definition
|
|
Term
| Sensor proteins bind to what |
|
Definition
|
|
Term
| Caffeine reduces carcinogenesis through ____ of ____ |
|
Definition
|
|
Term
| Inhibition of replication checkpoint function can suppress |
|
Definition
|
|
Term
| Parts of a nucleic acid (3) |
|
Definition
| 1) Phosphate, 2) ribose/2'-deoxyribose, 3) purine/pyrimidine |
|
|
Term
| Base, nucleoside, and nucleotide: A |
|
Definition
| Base: Adenine, Nucleoside: adenosine, Nucleotide: adenylate |
|
|
Term
| Base, nucleoside, and nucleotide: C |
|
Definition
| Base: cytosine, Nucleoside: cytidine, Nucleotide: cytidylate |
|
|
Term
| Base, nucleoside, and nucleotide: G |
|
Definition
| Base: guanine, Nucleoside: guanosine, Nucleotide: guanylate |
|
|
Term
| Base, nucleoside, and nucleotide: T |
|
Definition
| Base: thymine, Nucleoside: thymidine, Nucleotide: thymidylate |
|
|
Term
| Base, nucleoside, and nucleotide: U |
|
Definition
| Base: uracil, Nucleoside: uridine, Nucleotide: uridylate |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| # of hyrogen bonds in A-T/A-U |
|
Definition
|
|
Term
| # of hydrogen bonds in C-G |
|
Definition
|
|
Term
|
Definition
|
|
Term
| Major and minor grooves result from angle of what |
|
Definition
| Angle between 1' of bases |
|
|
Term
| More energetically stable: A-T or C-G |
|
Definition
|
|
Term
| Denaturing of DNA: increase or decrease UV absorbance |
|
Definition
|
|
Term
| Many disease could be a result or related to non B-form DNA (6) |
|
Definition
| 1) Fragile X, 2) Prader-Willi, 3) myotonic dystrophy, 4) Friedriech's ataxia, 5) Huntington's, 6) Burkitt's lymphoma |
|
|
Term
|
Definition
| The linking number (L) of DNA is equivalent to the sum of the twist (T) and writhing number (W) |
|
|
Term
| L cannot change without doing what |
|
Definition
| Breaking strand(s) of the DNA |
|
|
Term
| DNA molecules that differ only in linking number are called |
|
Definition
|
|
Term
| Enzymes that affect linking number are called |
|
Definition
|
|
Term
| Topoisomerases adjuct what topology number |
|
Definition
|
|
Term
| Twist increases with ____ base pairs in B-form |
|
Definition
| 10.4 base pairs per +1 of twist |
|
|
Term
| DNA with no write is called |
|
Definition
|
|
Term
| Relaxed DNA has what property |
|
Definition
|
|
Term
| What two numbers are interconvertable depending upon conditions: L, T, W |
|
Definition
|
|
Term
| Lower linking number than relaxed B-form DNA yields what (2) |
|
Definition
| 1) Underwound DNA, 2) cruciform DNA |
|
|
Term
|
Definition
|
|
Term
| DNA wrapped around ("beads on a string") |
|
Definition
|
|
Term
|
Definition
|
|
Term
| Histones throughout species: highly or lowly conserved |
|
Definition
|
|
Term
| Histones forming nucleosome core (4x2) |
|
Definition
| 2 each of: H2A, H2B, H3, H4 |
|
|
Term
| Modification of histones (5) |
|
Definition
| 1) Methylation, 2) AP-ribosylation, 3) phosphorylation, 4) glycosylation, 5) acetylation |
|
|
Term
| One nucleosome per ____ bp |
|
Definition
|
|
Term
| ___ bp wound ___ times around a nucleosome |
|
Definition
|
|
Term
| Key site of histone modification: N- or C-terminal |
|
Definition
| N-terminal (C-terminal can be modified though) |
|
|
Term
| Wrapping DNA around histones increases ____ and requires ____ to "fix" |
|
Definition
| Linking number (L) and requires topoisomerases |
|
|
Term
|
Definition
| Condenses 11 nm fiber into 30 nm fiber with 20-100 kbp loops |
|
|
Term
| Names of DNA condensation (6) |
|
Definition
| 1) 11 nm fiber, 2) 30 nm fiber, 3) loop (75 kbp), 4) rosette (6 loops), 5) Coil (30 rosettes), 6) chromatid (10 coils |
|
|
Term
|
Definition
| M-FISH to individually identify each chromosome |
|
|
Term
| Types of recombination (3) |
|
Definition
| 1) Homolgous, 2) site-specific, 3) DNA transposition |
|
|
Term
| Formation of antibody genes is what type of recombination |
|
Definition
| Site-specific recombination |
|
|
Term
| Recombinases used for antibody genes |
|
Definition
|
|
Term
| Fidelity of antibody recombination: high fidelity or error-prone |
|
Definition
| Error-prone (produces larger variation) |
|
|
Term
| Cre works with the ____ sites and ____ the DNA between them |
|
Definition
|
|
Term
| Types of transponsons (2) |
|
Definition
| 1) DNA transposons, 2) retrotransposons |
|
|
Term
| DNA transposons found mostly in: bacteria or most eukaryotes |
|
Definition
|
|
Term
| Retrotransposons found mostly in: bacteria or most eukaryotes |
|
Definition
|
|
Term
| Recombine into random sites: DNA transposons or retrotransposons |
|
Definition
|
|
Term
| Related to RNA intermediate: DNA transposons or retrotransposons |
|
Definition
|
|
Term
| Enocdes a transposase: DNA transposons or retrotransposons |
|
Definition
|
|
Term
| Transposases are a type of what enzyme |
|
Definition
|
|
Term
| Non-site specific recombination aka |
|
Definition
|
|
Term
| Holliday junctions as intermediates for what |
|
Definition
| Recombination between two strands of DNA by cleaving and cross-bonding strands |
|
|
Term
| Homologous recombination catalyzed by |
|
Definition
|
|
Term
| Homologous recombination has (4) |
|
Definition
| 1) dsDNA break, 2) DNA synthesis, 3) branch migration, 4) Holliday junction resolution |
|
|
Term
| Site-specific recombination can have changes to DNA (3) |
|
Definition
| 1) Inversions, 2) deletions, 3) insertions |
|
|
Term
| Homologous recombination can have what outcomes after Holliday junction resolution (2) |
|
Definition
| 1) Crossover, 2) non-crossover |
|
|
Term
| Which recombination methods manipulate DNA |
|
Definition
|
|
Term
| Which recombination methods require breakage of at least one strand of DNA |
|
Definition
|
|
Term
| Which recombination methods require a double-strand break |
|
Definition
| Homologous for sure, not sure on the others (exact method not given) |
|
|
Term
| Which recombination methods requires DNA synthesis |
|
Definition
| DNA transposons and homologous recombination |
|
|
Term
| Ways in which site-specific recombination and homologous recombination are different (2) |
|
Definition
| 1) SSR functions at a specific site, HR functions at many sites; 2) SSR operates on a single DNA strand, HR operates on two strands |
|
|
Term
| DNA polymerase reads: 3'-to-5' or 5'-to-3' |
|
Definition
|
|
Term
| DNA polymerase synthesizes: 3'-to-5' or 5'-to-3' |
|
Definition
|
|
Term
| Lagging strand of DNA replication: continuous or discontinuous |
|
Definition
|
|
Term
| Leading strand of DNA replication: continuous or discontinuous |
|
Definition
|
|
Term
| Short fragments of DNA on lagging strand |
|
Definition
|
|
Term
| Stages of DNA replication (3) |
|
Definition
| 1) Initiation of replication, 2) elongation, 3) termination |
|
|
Term
| Classes of DNA polymerases (2) |
|
Definition
| 1) Classical, 2) translesion |
|
|
Term
| DNA polymerase class typically involved in undamaged DNA replication: classical or translesion |
|
Definition
|
|
Term
| DNA polymerase class typically involved in repair and synthesis of damaged DNA: classical or translesion |
|
Definition
|
|
Term
| Has 3 classical DNA polymerases: bacteria or mammals |
|
Definition
|
|
Term
| Has 5 classical DNA polymerases: bacteria or mammals |
|
Definition
|
|
Term
| Has 2 translesion DNA polymerases: bacteria or mammals |
|
Definition
|
|
Term
| Has 10+ translesion DNA polymerases: bacteria or mammals |
|
Definition
|
|
Term
| Bacteria has __ classical and __ translesion DNA polymerases |
|
Definition
| 3 classical and 2 translesion |
|
|
Term
| Mammals has __ classical and __ translesion DNA polymerases |
|
Definition
| 5 classical and 10+ translesion |
|
|
Term
| 3'-to-5' exonuclease activity is fancy talk for what one-word process? |
|
Definition
|
|
Term
|
Definition
| Inhibitor of herpes DNA polymerase |
|
|
Term
| Inhibitor of herpes DNA polymerase |
|
Definition
|
|
Term
|
Definition
| Inhibitor of hepatitis B DNA polymerase |
|
|
Term
| Inhibitor of hepatitis B DNA polymerase |
|
Definition
|
|
Term
| Eukaryotic DNA polymerase for DNA replication initiation |
|
Definition
|
|
Term
| Eukaryotic DNA polymerase for chromosomal DNA replication (2) |
|
Definition
|
|
Term
| Eukaryotic DNA polymerase: delta does which strand: leading or lagging |
|
Definition
|
|
Term
| Eukaryotic DNA polymerase: epsilon does which strand: leading or lagging |
|
Definition
|
|
Term
| Accessory factors to DNA polymerase (2) |
|
Definition
| 1) Sliding clamps, 2) clamp loader |
|
|
Term
| Accessory factors to DNA polymerase do what |
|
Definition
| Hold DNA polymerase to the DNA |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| Primases are usually found where |
|
Definition
| At the protein complex at the replication fork |
|
|
Term
| Does helicase require energy input: yes or no |
|
Definition
|
|
Term
| Helicases are: unidirectional or bidirectional |
|
Definition
| Unidirectional (different helicases do each direction) |
|
|
Term
| Prevents DNA from forming secondary structures |
|
Definition
| SSBs (ssDNA binding proteins) |
|
|
Term
| Kinds of DNA nucleases (2) |
|
Definition
| 1) Endonuclease, 2) exonuclease |
|
|
Term
| What DNA nuclease is required for DNA replication (direction & kind) and removes what |
|
Definition
| 5'-to-3' exonuclease to remove RNA primers |
|
|
Term
| Forms phosphodiester bonds across ssDNA breaks |
|
Definition
|
|
Term
| DNA ligases form ____ bonds |
|
Definition
|
|
Term
| DNA ligases require ATP: yes or no |
|
Definition
|
|
Term
| Quinolones and fluoroquinolones: what do they do and what purpose |
|
Definition
| Topoisomerase inhibitors as antibiotics (notes imply Topo I, but Wikipedia states Topo II) |
|
|
Term
| Camptothecin: what does it do and what purpose |
|
Definition
| Topisomerase I inhibitors as chemotherapeutics |
|
|
Term
| Change linking number by 1's: type I or II topoisomerase |
|
Definition
|
|
Term
| Change linking number by 2's: type I or II topoisomerase |
|
Definition
|
|
Term
| Performs a ssDNA break: type I or II topoisomerase |
|
Definition
|
|
Term
| Performs a dsDNA break: type I or II topoisomerase |
|
Definition
|
|
Term
| Etoposide phosphate: what does it do and what purpose |
|
Definition
| Topoisomerase II inhibitors as chemotherapeutic |
|
|
Term
| Forms a covalent intermediate: type I or II topoisomerase |
|
Definition
|
|
Term
| Separates DNA strands during DNA replication |
|
Definition
|
|
Term
| DNA repliation proteins are functionally highly conserved: yes or no |
|
Definition
|
|
Term
| PCNA antibody: binds to what and for what purpose |
|
Definition
| Human sliding clamp protein and marks proliferating cells |
|
|
Term
| Primosome contains what (2) |
|
Definition
|
|
Term
| Okazaki fragment processing requires (3) |
|
Definition
| 1) Nuclease, 2) DNA polymerase, 3) ligase |
|
|
Term
| Okazaki fragment processing requires what in E. Coli (2) |
|
Definition
| 1) DNA pol I (exonuclease + polymerase), 2) ligase |
|
|
Term
| 8 hour S phase: eukaryote or prokaryote |
|
Definition
|
|
Term
| 20-30 minute doubling time: eukaryote or prokaryote |
|
Definition
|
|
Term
| Larger genome: eukaryote or prokaryote |
|
Definition
|
|
Term
| Smaller genome: eukaryote or prokaryote |
|
Definition
|
|
Term
| Multiple origins of replication: eukaryote or prokaryote |
|
Definition
|
|
Term
| Single origin of replication: eukaryote or prokaryote |
|
Definition
|
|
Term
| Prevents multiple DNA replications in eukaryotes |
|
Definition
| Separation of initiation and elongation |
|
|
Term
| Origin recognition complex (ORC) required for what |
|
Definition
|
|
Term
| Initiation requires what complex |
|
Definition
| Origin recognition complex (ORC) |
|
|
Term
| Licensing of DNA replication performed when |
|
Definition
|
|
Term
| Initiation of DNA replication performed when |
|
Definition
|
|
Term
| What protein is loaded during "licensing" of DNA replication |
|
Definition
|
|
Term
|
Definition
| primordial dwarfism, ORC mutations, reduction in # of cells (?): short stature, small ears, absent/small patellae, skeletal abnormalities |
|
|
Term
| Unfixed damage leads to what after DNA replication (2) |
|
Definition
| 1) Mutations, 2) replication fork arrest |
|
|
Term
|
Definition
|
|
Term
| Factors that lead to 10^9 accuracy of DNA polymerase (4) |
|
Definition
| 1) Base pairing, 2) enzyme selectivity, 3) 3'-to-5' exonuclease, 4) mismatch repair |
|
|
Term
| Mismatch repair creates ___ in the DNA strand with the mismatch and must be fixed by ____ |
|
Definition
| A gap in DNA that must be filled in by a DNA polymerase |
|
|
Term
| Hereditary nonpolyposis colon cancer (HNPCC) |
|
Definition
| 5% of colon cancers, mutations in genes involved in mismatch repair; autosomal dominant |
|
|
Term
| Bulky adducts caused by (3) |
|
Definition
| 1) UV, 2) alkylation, 3) oxidative damage |
|
|
Term
| Nucleotide excision repair steps (4) |
|
Definition
| 1) Excinuclease to make nicks, 2) helicase to remove segment, 3) DNA polymerase (I in E coli; epsilon in human), 4) DNA ligase |
|
|
Term
| Excinuclease used in what major pathway |
|
Definition
| Nucleotide excision repair |
|
|
Term
| Nucleotide excision repair removes what (3) |
|
Definition
| 1) Pyrimidine dimers, 2) alkylation, 3) bulky adducts |
|
|
Term
|
Definition
| Defects in nucleotide excision repair pathway; thin, uneven pigmented skin; telangiectasia; very rare |
|
|
Term
| Base excision repair steps (4) |
|
Definition
| 1) DNA glycosylase, 2) AP endonuclease, 3) DNA polymerase, 4) DNA ligase |
|
|
Term
|
Definition
| Breaks nucleic base and ribose link |
|
|
Term
|
Definition
| Nicks ssDNA at abasic site |
|
|
Term
|
Definition
| A site in DNA that is missing a base |
|
|
Term
| Breaks nucleic base and ribose link |
|
Definition
|
|
Term
| Nicks ssDNA at abasic site |
|
Definition
|
|
Term
| Deamination of cytosine yields |
|
Definition
|
|
Term
| Deamination of methylated cytosine yields |
|
Definition
|
|
Term
| Cytosine deamination is recognized as damage in DNA: yes or no |
|
Definition
|
|
Term
| Methylated cytosine deamination is recognized as damage in DNA: yes or no |
|
Definition
|
|
Term
| Methylated cytosine to thymine accounts for ___% of mutations |
|
Definition
|
|
Term
|
Definition
| Use light to reverse light-induced pyrimidine dimers (not in mammals) |
|
|
Term
| Transcription coupled repair |
|
Definition
| Transcribed strand repair more efficient than non-transcribed strand |
|
|
Term
|
Definition
| Defect in transcription couple repair; similar to xeroderma pigmentosum |
|
|
Term
|
Definition
| Form of aplastic anemia; defect in inter-strand crosslink repair |
|
|
Term
| Cisplatin: what does it do and what purpose |
|
Definition
| Forms DNA crosslinks; chemotherapy |
|
|
Term
| Last-ditch effort to fix DNA errors that lead to replication fork arrest; what is needed |
|
Definition
| Error prone repair; translesion DNA polymerase |
|
|
Term
| Pathways of dsDNA repair (2) |
|
Definition
| 1) Homologous end-joining, 2) Non-homologous end-joining |
|
|
Term
| Which form of dsDNA repair uses BRCA: homologous or non-homologous end-joining |
|
Definition
|
|
Term
| Which dsDNA repair pathway uses a second copy as a template: homologous or non-homologous end-joining |
|
Definition
|
|
Term
| Which dsDNA repair pathway loses some nucleotides: homologous or non-homologous end-joining |
|
Definition
| Non-homologous end-joining |
|
|
Term
| Which dsDNA repair pathway involves a Holliday junction: homologous or non-homologous end-joining |
|
Definition
|
|
Term
| Overall phenotypes resulting from DNA repair problems (6) |
|
Definition
| 1) Genomic instability, 2) increased cancer, 3) premature aging, 4) developmental defects, 5) neurological defects, 6) immunological defects |
|
|
Term
|
Definition
| Unit of genetic information that encodes something useful |
|
|
Term
|
Definition
|
|
Term
| Dominant form of RNA in a cell: rRNA, mRNA, tRNA |
|
Definition
|
|
Term
| Most variable form of RNA in a cell: rRNA, mRNA, tRNA |
|
Definition
| mRNA (different with every gene) |
|
|
Term
| RNA polymerase synthesizes: 3'-to-5' or 5'-to-3' |
|
Definition
|
|
Term
| RNA polymerase reads: 3'-to-5' or 5'-to-3' |
|
Definition
|
|
Term
| Sigma subunit of E. coli. RNA polymerase |
|
Definition
| Initiation of transcription (-10 and -35 regions) |
|
|
Term
| Rho subunit of E. coli. RNA polymerase |
|
Definition
| Termination of transcription at some sites |
|
|
Term
| Faster: DNA or RNA polymerase |
|
Definition
|
|
Term
| Higher fidelity: DNA or RNA polymerase |
|
Definition
|
|
Term
| Does not require a primer: DNA or RNA polymerase |
|
Definition
|
|
Term
| E. coli. RNA polymerase subunit for initiation of transcription |
|
Definition
|
|
Term
| E. coli. RNA polymerase subunit for termination of transcription at some sites |
|
Definition
|
|
Term
| DNA strand read by RNA polymerase: template or coding strand |
|
Definition
|
|
Term
| DNA strand corresponding to RNA transcription: template or coding strand |
|
Definition
|
|
Term
| RNA synthesis starts at what sites |
|
Definition
|
|
Term
| Binds to -10 and -35 regions of DNA |
|
Definition
| Sigma subunit of RNA polymerase |
|
|
Term
| Binds to upstream promoter (UP) |
|
Definition
| Alpha subunit of RNA polymerase |
|
|
Term
| Alpha subunit of E. coli. RNA polymerase |
|
Definition
| Binds to upstream promoter (UP) |
|
|
Term
| E. coli. RNA polymerase promoter strength depends on what |
|
Definition
| Degree of matching to UP, -10, and -35 regions |
|
|
Term
|
Definition
| RNA polymerase bound to dsDNA |
|
|
Term
|
Definition
| RNA polymerase bound to ssDNA with a 10 nt window |
|
|
Term
|
Definition
| Inhibits E. coli. RNA polymerase |
|
|
Term
|
Definition
| Inhibits reverse transcriptase (of HIV) |
|
|
Term
|
Definition
| Inhibits hepatitis C growth |
|
|
Term
| Rho subunit of E. coli. RNA polymerase has what activity |
|
Definition
|
|
Term
| Termination of E. coli. RNA polymerase forms what RNA structure |
|
Definition
|
|
Term
| The RNA hairpin does what to E. coli. RNA polymerase |
|
Definition
| Pauses RNA synthesis (then see termination options) |
|
|
Term
| Rho-independent termination of E. coli. RNA polymerase (4) |
|
Definition
| 1) Forms hairpin, 2) synthesis paused, 3) A-rich sequence disrupts binding, 4) termination |
|
|
Term
| Rho-dependent termination of E. coli. RNA polymerase (4) |
|
Definition
| 1) Forms hairpin, 2) CA-rich sequence, 3) synthesis paused, 4) Rho (5'-to-3' helicase) catches up, 5) termination |
|
|
Term
| Which RNA transcripts are processed in E. coli.: rRNA, mRNA, tRNA |
|
Definition
|
|
Term
|
Definition
| Unit of genetic expression in prokaryotes |
|
|
Term
|
Definition
| 1) Promoter, 2) genes, 3) regulatory sites |
|
|
Term
| What things operate on operon regulatory sites (2) |
|
Definition
| 1) Activators, 2) repressors |
|
|
Term
|
Definition
| Co-regulation of genes/operons by the same regulatory proteins |
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Term
| Co-regulation of genes/operons by the same regulatory proteins |
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Definition
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Term
| Unit of genetic expression in prokaryotes |
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Definition
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Term
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Definition
| Cause binding or release of regulatory proteins |
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Term
| Examples of small molecule effectors (2 common examples) |
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Definition
| 1) Lactose (Lac operon), 2) tryptophan (Trp operon) |
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Term
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Definition
| Transcription regulation using a polypeptide leader |
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Term
| Transcription regulation using a polypeptide leader |
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Definition
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Term
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Definition
| Multiple proteins from one mRNA through multiple reading frames |
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Term
| Trp attenuation: full mRNA transcription when Trp is: high or low concentration |
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Definition
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Term
| Trp attenuation: partial mRNA transcription when Trp is: high or low concentration |
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Definition
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Term
| Trp attenuation: Rho-independent termination when Trp is: high or low concentration |
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Definition
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Term
| Trp attenuation: stalling of translation leads to what with transcription |
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Definition
| Rho-independent termination |
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Term
| Trp operon: attenuation and Trp repression: complementary or antagonistic |
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Definition
| Complementary: attenuation and repression occur when lots of Trp is available |
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Term
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Definition
| Alteration of surface proteins to evade host immune system |
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Term
| Alteration of surface proteins to evade host immune system |
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Definition
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Term
| S. typhimurium expresses ____ repressor to repress ____ flagellin and transcribes ____ flagellin instead |
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Definition
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Term
| S. typhimurium changes ____ to achieve ____ |
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Definition
| Flagellin protein; antigenic variation |
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Term
| Eukaryotes: which RNA polymerase to make rRNA: Pol I, Pol II, Pol III |
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Definition
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Term
| Eukaryotes: which RNA polymerase to make mRNA: Pol I, Pol II, Pol III |
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Definition
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Term
| Eukaryotes: which RNA polymerase to make tRNA: Pol I, Pol II, Pol III |
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Definition
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Term
| Eukaryotes: which RNA polymerase to make siRNA: Pol I, Pol II, Pol III |
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Definition
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Term
| Eukaryotes: which RNA polymerase to make miRNA: Pol I, Pol II, Pol III |
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Definition
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Term
| Eukaryotes: what RNA's does Pol I make |
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Definition
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Term
| Eukaryotes: what RNA's does Pol II make |
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Definition
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Term
| Eukaryotes: what RNA's does Pol III make |
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Definition
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Term
| Eukaryotes: which RNA polymerase to make 5S rRNA: Pol I, Pol II, Pol III |
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Definition
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Term
| Eukaryotes: which RNA polymerase works with the TATA box: Pol I, Pol II, Pol III |
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Definition
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Term
| Eukaryotes: which RNA polymerase works with the Inr sequence: Pol I, Pol II, Pol III |
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Definition
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Term
| Proteins required for eukaryotic RNA Pol II (2) |
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Definition
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Term
| Protein that binds to TATA box |
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Definition
| TBP (TATA-binding protein) |
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Term
| Protein that helps create the transcription bubble in eukaryotes |
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Definition
| TFIIH (transcription factor II H) |
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Term
| Protein that phosphorylates the CTD on Pol II |
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Definition
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Term
| Phosphorylation of what part of Pol II is required for initiation of transcription |
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Definition
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Term
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Definition
| C-terminal domain [of Pol II] |
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Term
| Mutation in TFIIH can lead to (2) |
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Definition
| 1) Xeroderma pigmentosum, 2) Cockayne's syndrome |
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Term
| TFIIH is required for (3) |
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Definition
| 1) Initiation of mRNA synthesis, 2) DNA repair, 3) nucleotide excision repair |
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Term
| Most eukaryotic genes have preassembled, paused polymerases ready to elongate when activates: yes or no |
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Definition
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Term
| Flavopridol: what is it and what could it be used for |
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Definition
| Inhibitor of cdks that regulate elongation; anti-cancer therapy |
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Term
| Actinomycin: what is it and what is it used for |
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Definition
| Intercalator; inhibits bacterial RNA polyermase & chemotherapy |
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Term
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Definition
| Inhibits beta subunit of bacterial RNA polymerases |
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Term
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Definition
| Inhibits Euk Pol II & III |
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Term
| Features of a mature eukaryotic mRNA (3) |
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Definition
| 1) 5' cap, 2) poly-A tail, 3) spliced (INTRONS BE GONE!) |
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Term
| More details of the "5' cap" |
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Definition
| 7-methylguanosine linked through a 5',5' triphosphate linkage |
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Term
| 5' cap is bound to what during transcription |
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Definition
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Term
| 5' cap and poly-A tail do what to the mRNA |
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Definition
| Enhances stability and translation |
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Term
| Spliceosomes interect with what and do what to mRNA |
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Definition
| Interact with CTD; remove introns |
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Term
| Duchenne muscular dystrophy: what goes awry |
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Definition
| Open reading frame disruption of the DMD gene |
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Term
| Retroviruses have: RNA or DNA |
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Definition
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Term
| Retrovirus reverse transcriptase error rate: high or low |
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Definition
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Term
| Aberrant expression of host genes due to a retrovirus is caused by what |
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Definition
| LTR (long terminal repeat) |
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Term
| Which is more condensed: euchromatin or heterochromatin |
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Definition
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Term
| Features of remodeling complexes of chromatin (2) |
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Definition
| 1) Requires ATP, 2) changes remain until changed again |
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Term
| Acetylation of histones: activating or silencing |
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Definition
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Term
| Methylation of histones: activating or silencing |
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Definition
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Term
| Acetylation of histones: what enzyme |
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Definition
| Histone acetyltransferase (HAT) |
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Term
| De-acetylation of histones: what enzyme |
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Definition
| Histone deacetylase (HDAC) |
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Term
| SAHA (suberoylanilide hydroxamic acid): what is it and what is it used for |
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Definition
| HDAC inhibitor and induces p21 to inhibit cell cycle; chemotherapy |
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Term
| Default transcription of human genome: transcribed or not |
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Definition
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Term
| Average # of promoters for a human gene |
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Definition
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Term
| Which is near the promoter: enhancer or UAS |
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Definition
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Term
| Which can be far from the promoter: enhancer or UAS |
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Definition
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Term
| Helix-turn-helix is an example of which: DNA binding or protein interaction domain |
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Definition
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Term
| Zinc finger is an example of which: DNA binding or protein interaction domain |
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Definition
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Term
| Homeodomain is an example of which: DNA binding or protein interaction domain |
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Definition
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Term
| Leucine zipper is an example of which: DNA binding or protein interaction domain |
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Definition
| Protein interaction domain |
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Term
| Acidic activation domain is an example of which: DNA binding or protein interaction domain |
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Definition
| Protein interaction domain |
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Term
| Proline-rich activation domain is an example of which: DNA binding or protein interaction domain |
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Definition
| Protein interaction domain |
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Term
| What binds to UAS and enhancer sites |
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Definition
| DNA binding transactivators |
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Term
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Definition
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Term
| RNA-induced silencing complex (RISC) |
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Definition
| Silences mRNA by binding miRNA to it |
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Term
| dsRNA processed by what protein family |
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Definition
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Term
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Definition
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Term
| siRNA can be added to artificially do what |
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Definition
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Term
| Pleuropulmonary blastoma (PPB) |
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Definition
| Disrupted DICER1; alters expression of growth factors? |
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Term
| Anticodon A matches what codon letters |
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Definition
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Term
| Anticodon C matches what codon letters |
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Definition
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Term
| Anticodon G matches what codon letters |
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Definition
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Term
| Anticodon I matches what codon letters |
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Definition
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Term
| Anticodon U matches what codon letters |
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Definition
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Term
| Anticodon I is what compound |
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Definition
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Term
| Mutation: cause no change in the amino acid sequence |
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Definition
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Term
| Mutation: change the amino acid sequence |
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Definition
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Term
| Mutation: change an amino acid to a STOP codon |
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Definition
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Term
| Mutation: change reading frame |
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Definition
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Term
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Definition
| No change in amno acid sequence |
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Term
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Definition
| Change the amino acid sequence |
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Term
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Definition
| Change the amino acid to a STOP codon |
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Term
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Definition
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Term
| Which mutation almost always changes a protein's function profoundly (2) |
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Definition
| 1) Nonsense, 2) frame shift |
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Term
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Definition
| Modified tRNA that alter translation |
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Term
| Suppressor tRNA examples (2) |
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Definition
| 1) Nonsense suppressor, 2) frameshift suppressor |
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Term
| Examples of nonsense mutation diseases (4) |
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Definition
| 1) Cystic fibrosis, 2) Duchenne muscular dystrophy, 3) beta thalassemias, 4) Hurler syndrome |
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Term
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Definition
| Skips nonsense mutations to continue normal translation (does not correct mutation) |
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Term
| Translational frame shifting by retroviruses |
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Definition
| Frame shift during translation to get a second protein by skipping a STOP codon |
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Term
| Steps of protein synthesis (5) |
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Definition
| 1) tRNA activation, 2) initiation, 3) elongation, 4) termination & release, 5) folding & processing |
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Term
| Steps of activation of tRNAs (3) |
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Definition
| 1) Activation through adenylation, 2) adding AA to tRNA, 3) |
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Term
| What enzyme adds charged AA to tRNA |
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Definition
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Term
| If aminoacyl-tRNA synthetase adds wrong AA to tRNA, what can it do? |
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Definition
| Hydrolase activity of aminoactyl-tRNA synthetase has proofreading ability to remove AA |
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Term
| Aminoacyl-tRNA is bound to which group of the AA: NH2 or COOH? |
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Definition
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Term
| Ribosomes have what enzymatic activity |
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Definition
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Term
| Peptidyl transferse describes what structure in protein synthesis |
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Definition
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Term
| Initiation of protein synthesis starts with mRNA binding to which subunit |
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Definition
| Small ribosome sunbunit (16S) |
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Term
| Initiation of protein synthesis requires what energy source |
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Definition
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Term
| The tRNA for the START codon binds to what ribosome site |
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Definition
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Term
| Internal ribosome entry sites (IRES) |
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Definition
| Internal (i.e., alternate) AUG sites in which translation can start |
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Term
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Definition
| 1) Incoming aminoacyl-tRNA into A site, 2) new AA added to C-terminal, 3) large subunit shifts, 4) small subunit advances along mRNA, 5) spent tRNA ejected from E site |
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Term
| Most abundant proteins in a cell |
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Definition
| Elongation factors (for protein synthesis) |
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Term
| Each residue added to a protein directly costs how much NTP |
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Definition
| 4 = 2 ATP to activate tRNA + 2 GTP to elongate with EF |
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Term
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Definition
| Depurinates residues in the 28S rRNA -> inactivates |
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Term
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Definition
| Binds to a STOP codon and hydrolyzes off polypeptide |
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Term
| How many release factors do eukaryotes have |
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Definition
|
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Term
| How many release factors do prokaryotes have |
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Definition
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Term
| Aconitase binds to ferritin mRNA when: low or high iron |
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Definition
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Term
| Aconitase not binds to ferritin mRNA when: low or high iron |
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Definition
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Term
| Aconitase binds to transferrin receptor mRNA when: low or high iron |
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Definition
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Term
| Aconitase not binds to transferrin receptor mRNA when: low or high iron |
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Definition
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Term
| Aconitase bound to ferritin mRNA, ferritin: translated or not translated |
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Definition
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Term
| Aconitase not bound to ferritin mRNA, ferritin: translated or not translated |
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Definition
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Term
| Aconitase bound to transferrin receptor mRNA, transferrin receptor: translated or not translated |
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Definition
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Term
| Aconitase not bound to transferrin receptor mRNA, transferrin receptor: translated or not translated |
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Definition
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Term
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Definition
| Multiple simultaneous translations of an mRNA |
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Term
| More severe phenotype if nonsense mutation at: 5' or 3' end |
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Definition
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Term
| More likely to be autosomal dominant if nonsense mutation at: 5' or 3' end |
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Definition
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Term
| More likely to be autosomal recessive if nonsense mutation at: 5' or 3' end |
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Definition
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Term
| Less severe phenotype if nonsense mutation at: 5' or 3' end |
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Definition
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Term
| Nonsense-mediate mRNA decay |
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Definition
| Detection of nonsense mutations near splice junctions -> degradation of mRNA |
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Term
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Definition
| Modification of mRNA after transcription |
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Term
| Cytosine deaminase in intestine: what does it do and what specifically does it do |
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Definition
| RNA editing; converts Gln to STOP codon in apoB protein |
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Term
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Definition
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Term
|
Definition
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Term
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Definition
| Provides favorable environment for protein to correctly fold |
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Term
| 26S proteosome components (2) |
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Definition
| 1) 20S core, 2) 19S regulatory |
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Term
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Definition
| Highly conserved 76 AA protein indicating attached protein to be degraded by proteosome |
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Term
| What signals 26S proteosome degradation |
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Definition
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Term
| Does a single ubiquitin indicate degradation: yes or no |
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Definition
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Term
| Signal sequence for protein secretion: at N- or C-terminal |
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Definition
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Term
| ______ indicates protein should be secreted |
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Definition
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Term
| Indicates protein to be synthesized into ER lumen |
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Definition
| SRP (signal recognition particle) |
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Term
| SRP (signal recognition particle) |
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Definition
| Indicates protein to be synthesized into ER lumen |
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Term
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Definition
| Cleaves a 4-8 bp dsDNA site |
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Term
| Restriction endonucleases can produce what ends (3) |
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Definition
| 1) Flush/blunt, 2) 5' overhang, 3) 3' overhang |
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Term
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Definition
| 1) Replication origin, 2) selectable marker(s), 3) restriction sites |
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Term
| PCR requires what kind of special polymerase |
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Definition
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Term
| PCR requires how many primers and what is the implication of this |
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Definition
| 2 primers; something about the sequence must be known |
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Term
| cDNA requires 3 things and produces what |
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Definition
| 1) dsDNA, 2) restriction enzymes, 3) plasmids; yields recombinant plasmids |
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Term
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Definition
| Apart of the molecule itself (e.g., radioactive isotope) |
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Term
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Definition
| Attaches to molecule of interest (e.g., antibody) |
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Term
| Oligonucleotide probe is what type of labelling: direct or indirect |
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Definition
| Indirect (it binds to the molecule of interest through denaturing & annealing) |
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Term
| Allele-specific oligonucleotide probe |
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Definition
| Identify mutant alleles (by them not binding) |
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Term
| Southern blot: DNA, RNA, protein |
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Definition
|
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Term
| Northern blot: DNA, RNA, protein |
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Definition
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Term
| Western blot: DNA, RNA, protein |
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Definition
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Term
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Definition
| 1) Grow bacteria on agar, 2) blot to membrane, 3) denature membrane, 4) test DNA, 5) map back to agar plate to find colony |
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Term
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Definition
| Southern blot post restriction digestion |
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Term
| Current DNA fingerpriting |
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Definition
| PCR of highly repetitive minisatellite DNA |
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Term
| Protein to DNA, useful uses (3) |
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Definition
| 1) Make complementary olonucleotide, 2) generate antibodies, 3) search genome database |
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Term
| Uses of determining DNA sequences (3) |
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Definition
| 1) Find open reading frames, 2) predict protein sequence, 3) find conserved sequences aka signature sequences (key one of the three) |
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Term
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Definition
| Placed under control of regulatory sequences of gene of interest: watch what happens |
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Term
| DNA microarrays: absolute or relative expression |
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Definition
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