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