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Biochem Match

Biochem Matching

Column AColumn 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 on 2011-08-22



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