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Biochem Match
Biochem Matching
| Column A | Column B |
|---|---|
| Prokaryotic DNA melting site | Three 13-base-pair repeat sequences |
| OriC | Characterized by a tandem array of three 13-base-pair repeats and four 9-base-pair repeats |
| Nucleus | Aminoacylation of tRNA happens here |
| 50S ribosomal subunit | Binds 30S initiation complex to form 70S initiation complex |
| Prokaryotic DnaA protein binding site | Four 9-base-pair repeat sequences |
| Aminoacyl-tRNA synthetase | One for each amino acid |
| Inosine | Important for the wobble effect |
| N10-formyl-tetrahydrofolate | Helps formylate methionine |
| Transformylase | Adds formylated methionine to tRNA |
| Formamide | Destabilizes hydrogen-bonding |
| Transversion | Missense mutation; purine to pyrimidine or pyrimidine to purine |
| Werner syndrome | Premature aging disease |
| Transition | Missense mutation; purine to purine or pyrimidine to pyrimidine |
| Xeroderma pigmentosum | Cannot remove UV-induced thymine dimers with this disease |
| Cockayne syndrome | Associated with mutations in ERCC6 & ERCC8 genes |
| G1 | Longest phase |
| S phase | Characterized by DNA replication |
| G2 | Cell prepares for division |
| M phase | Shortest phase |
| Checkpoint | Ensures fidelity of cell division |
| Topoisomerase II | Nicks two strands of DNA molecule |
| Topoisomerase I | Nicks a single strand of DNA molecule |
| Helicase | Binds to DNA to begin replication |
| Single strand binding protein | Prevents re-annealing of DNA strands |
| Pre-priming complex | Polypeptides n, n', n'', and n''' |
| Replication bubble | Direct result of Helicase (DnaB/DnaC complex) |
| 5'-Cap | Attached via a 5'-5' triphosphate bridge |
| Noncoding RNA sequence | Directly regulates protein synthesis |
| DNA open reading frame | Gives rise to RNA coding sequence |
| Promoter | Non-transcribed upstream sequence |
| Rho protein | ATP-dependent helicase |
| Eukaryotic polymerase alpha | Elongates primer for about 20 nucleotides |
| Eukaryotic polymerase beta | Used for general DNA repair |
| Eukaryotic polymerase gamma | Used for DNA repair in mitochondria |
| Primase | Specialized RNA polymerase |
| 500 nucleotides per second | Speed of replication fork in E. coli |
| DNA polymerase I | DNA polymerase with the lowest processivity and a moderate polymerization rate |
| 50 nucleotides per second | Speed of replication fork in eukaryotes |
| DNA polymerase III | DNA polymerase with the highest processivity and highest polymerization rate |
| DNA polymerase II | DNA polymerase with a moderate processivity and lowest polymerization rate |
| IF3 | Prevents re-association of prokaryotic ribosome |
| 30S-IF3-IF1 complex | Attaches to mRNA, guiding the 5'-AUG to the P-site |
| IF2-GTP complex | Binds charged initiator tRNA |
| IF2-GTP-fMet-tRNA complex | Binds (30S subunit)-(IF3)-(IF1) complex, forming 30S initiation complex |
| IF3/IF1 | Binds to the 30S ribosomal subunit and dissociates the 70S prokaryotic ribosome |
| TTAGGG | Tandem repeats of this sequence is a characteristic of telomeres |
| AGGAGG | All or part of the Shine-Dalgarno sequence |
| UCCUCC | Anti-Shine-Dalgarno sequence on 3' end of ribosomal 16S rRNA |
| AAUAAA | Signal for polyadenylation |
| CCA | Sequence at 3' amino acid acceptor stem of tRNA |
| TTGACA | -35 |
| TATAAT | -10 |
| GC box | -100 |
| CAAT box | -75 |
| TATA box | -25 |
| tRNA | 15% of total RNA in cell |
| mRNA | 5% of total RNA in cell |
| dsRNA | Always A-type double helix |
| Histone mRNA | Lacks a poly(A) tail |
| rRNA | 80% of total RNA in cell |
| Hb Cranston | A-G dinucleotide insertion between codons 144 & 145 |
| Sickle cell anemia | G-A-G at position 6 replaced with G-U-G |
| Hypochromicity | Due to close stacking of bases along DNA helix |
| Electrostatic intrastrand repulsion | Responsible for rod-like conformation |
| Beta+ Thalassemia | Result of four different TATA box mutations |
| 6-4 photoproduct type thymine dimer | Repaired by nucleotide excision |
| Sigma 70 | Most common at 37 degrees C |
| Sigma 32 | Most common at 50 degrees C |
| Spliceosome | Contains U1, U2, U4, U5, and U6 snRNPs |
| Cyclobutane-type thymine dimer | Can be directly repaired |
| UVrD | Helicase; removes damaged portion of DNA |
| UVrC | Triggers another UVr to cut 5 nucleotides downstream and 8 nucleotides upstream of thymine dimer |
| UVrAB | Scans DNA for damage |
| UVrA | Recognizes thymine dimer |
| UVrB | Helps another UVr bind to DNA |
| T4N5 | Viral DNA repair enzyme; helpful for individuals with xeroderma pigmentosum |
| Guanylyl transferase | In nucleus, attaches 7-methyl-guanosine 5'-Cap via a 5'-5' triphosphate linkage |
| Guanine-7-methyl-transferase | In cytoplasm, acts on S-Adenosylmethionine and 5'-Cap |
| DNA photolyase | Recognizes cyclobutane-type thymine dimer |
| CGRP (calcitonin gene related peptide) | Vasodilator in brain |
| 5-bromouracil | Base analog; thymine substitute; converts A-T to G-C |
| Nitrous acid (HNO2) | Chemical modifier; converts A-T to C-G |
| Ethidium bromide | Chemical modifier; intercalating |
| 2-aminopurine | Base analog; pairs with thymine or cytosine; converts A-T to G-C |
| Benzopyrene | In cigarette smoke; damages p53 |
| Proleukin | Melanoma immunotherapy; mimics a T-cell cytokine |
| Irinotecan (Camptosar) | Topoisomerase I inhibitor (chemotherapy) |
| Dicarbazine | Melanoma chemotherapy agent; cross-links DNA strands; alkylating agent |
| Doxorubicin (Adriamycin) | Topoisomerase II inhibitor (chemotherapy) |
| Quinolones/Fluoroquinolones | Inhibit prokaryotic gyrase/topoisomerase (antibiotics) |
| p53 | Tumor suppressor gene; induces G1 arrest or apoptosis |
| Sigma factor | Enables RNA polymerase to recognize promoter regions on DNA template |
| cDNA | Synthesized by reverse transcription |
| Shine-Dalgarno sequence | About 7 bases upstream from AUG codon on mRNA strand |
| Calcitonin gene pre-mRNA | Contains 6 exons |
| Telomerase | Has a protein similar to reverse transcriptase |
| Transcription factors | Bind to promoter |
| Endonuclease | Cleaves 20 bases downstream of AAUAAA during transcription |
| Etoposide (Eposin) | Topoisomerase II inhibitor (chemotherapy) |
| Topotecan (Hycamtin) | Topoisomerase I inhibitor (chemotherapy) |
| Phosphodiester bond | Formed by condensation reaction |
| Hairpin loop | Most common secondary structure of RNA |
| 5' untranslated region | Derived from space in between promoter and open reading frame |
| Cloverleaf | Secondary structure of tRNA |
| UAC anticodon in fMet-tRNA (initiator tRNA) | Hydrogen-bonds AUG initiation codon in mRNA strand |
| Tissue-specific transcription factors | Globin genes |
| Constitutive transcription factors | "House-keeping" genes |
| RNA polymerase III | In nucleoplasm; mildly sensitive to alpha-amanitin |
| RNA polymerase I | In nucleolus; alpha-amanitin insensitive |
| RNA polymerase II | In nucleoplasm; highly sensitive to alpha-amanitin |
| TFIIA | Stabilizes binding of the transcription factor to bind before it |
| TFIIB | Attaches over the start site for the coding region |
| TFIID | Necessary for RNA polymerase II; binds TATA box |
| TFIIF | Establishes a complex with RNA polymerase II |
| TFIIH, TFIIE, and TFIIJ | Must be present for transcription to occur |
| 60S ribosomal subunit | Comprised of 28S rRNA, 5.8S rRNA, and 5S rRNA |
| 30S ribosomal subunit | Comprised of 16S rRNA |
| 40S ribosomal subunit | Comprised of 18S rRNA |
| 50S ribosomal subunit | Comprised of 23S rRNA and 5S rRNA |
| 20S ribosomal subunit | Does not actually exist |
| Streptolydigin | Blocks prokaryotic RNA elongation by inhibiting RNA polymerase II (antibiotic, effective against gram positive bacteria) |
| Actinomycin D | Binds duplex DNA at G-C rich regions in initiation complex; intercalates between bases; blocks transcription by preventing RNA polymerase elongation (chemotherapy & antibiotic) |
| Rifamycin/Rifampicin | Binds prokaryotic RNA polymerase β-subunit; blocks initial phosphodiester bond, halting transcription (used for tuberculosis & other gram positive bacteria) Note: Cannot stop mRNA elongation if binding to DNA template strand was already initiated |
| AZT (azidothymidine) | Nucleoside analog reverse transcriptase inhibitor; blocks phosphodiester bond so DNA cannot replicate (used for HIV/AIDS) |
| Camptothecin (CPT) | From Chinese yew tree (aka: Happy Tree), topoisomerase I inhibitor (chemotherapy) |
| ARA-C (cytosine arabinoside) | C-nucleotide “mimic”; cytosine base with arabinose sugar; gets incorporated; stops DNA synthesis (chemotherapy) |
| Methotrexate (MTX) | Prevent cells from making nucleotides by inhibiting folic acid (chemotherapy) |
| Acridine orange | Chemical modifier; intercalating |
| Hydroxylamine (NH2OH) | Chemical modifier; converts A-T to C-G |
| T4N5 Liposome Lotion (Dimericine) | Increases DNA repair of UV damage |
| Peptidyl transferase | 23S ribosomal component; helps bind amino acids during elongation |
| Peptidyl-tRNA | Found at P site |
| Aminoacyl-tRNA synthetase | Demonstrates proofreading activity |
| Aminoacyl-AMP | Amino acid complex; formation catalyzed by aminoacyl-tRNA synthetase |
| Aminoacyl-tRNA | Has amino acid bound via ester linkage |
| eIF4F | Eukaryotic complex of eIF4A, eIF4G, and cap binding protein |
| eIF4E | Eukaryotic cap binding protein during initiation of translation |
| PABP | Binds to poly(A) tail in eukaryotic initiation of translation |
| eIF4A | Exhibits helicase activity |
| eIF1, eIF2, eIF3, & eIF5 | Involved in final initiation step of eukaryotic translation |
| EF-Tu | Using GTP, mediates entry of charged tRNA into A-site |
| EF-Ts & EF-Tu | Facilitate release of GTP once charged tRNA is bound |
| EF-G | Translocase that helps shift ribosome during elongation; uses GTP |
| RF-1 | Recognizes UAG & UAA in prokaryotes |
| RF-2 | Recognizes AGA & UAA in prokaryotes |
| RF-3 | Helps hydrolyze peptide-tRNA ester bond in prokaryotes |
| eRF | Recognizes all three termination codons in eukaryotes |
| Streptomycin/Neomycin | Prevents binding of fMet-tRNA to P-site; blocks initiation (antibiotic) |
| Chloramphenicol | Binds 50S subunit near P-site; blocks elongation (antibiotic) |
| Tetracycline | Binds 30S subunit near A-site; blocks elongation (antibiotic) |
| Erythromycin | Binds 50S subunit; blocks translocation (antibiotic) |
| Cycloheximide | Inhibits peptidyl transferase at 60S subunit; blocks elongation (toxin) |
| Diphtheria | Inactivates eEF2 by ADP-ribosylation; blocks elongation (exotoxin) |
| Ricin | Catalyzes cleavage of 60S rRNA (toxin) |
| Puromycin | Resembles aminoacyl-tRNA; binds to A-site; blocks elongation (toxin & antibiotic) |
| Genomic library | Prepared from total DNA of a cell/tissue |
| Southern blotting | Locates particular DNA sequences by transferring DNA fragments from a gel to a nylon membrane |
| NaOH | Denatures DNA |
| Northern blotting | Detects and quantifies mRNA levels by transferring RNA molecules from a gel to a nylon membrane |
| Western blotting | Detects and quantifies protein levels by transferring protein molecules from a gel to a nylon membrane |
| CCTNAGG | Recognized by Mst II |
| CCTGAGG | Normal beta-globin gene |
| CCTGTGG | Sickle cell mutation; not recognized by Mst II |
| Algometric dT nucleotide coated resin | Purification of mRNA |
| Oligo-dT | Complementary primer; binds poly(A) tail |
| SNPs | Occur in at least 1% of population |
Created by:
kesselmb
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