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Biochemistry 1
Enzymes of DNA and RNA synthesis, etc
69
Biochemistry
Graduate
10/06/2011

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Term
Endonuclease
Definition
Enzymes that digest DNA by putting nicks or breaks in the phosphodiester bonds. Can attack single strands of DNA or double stranded DNA.
Term
Exonucleases
Definition
Enzymes that digest DNA from the ends. Can be specific for double or single stranded DNA. Can operate 5' to 3' or 3' to 5'
Term
RNaseH
Definition
A special type of nuclease that removes the primer for Okazaki fragments. Digests the RNA strand of a RNA/DNA hybrid in the 5' --> 3' direction. In bacteria it is part of a DNA polymerase. In mammals it is its own separate enzyme.
Term
Ligase
Definition
An enzyme that forms a phosphodiester bond withough adding new nucleotides.
Term
Single Stranded DNA Binding Protein (SSB)
Definition
A protein that binds to single stranded DNA. Protects DNA from nucleases that degrade the phosphodiester bonds. Protects DNA from folding back onto itself. Facilitates action of DNA replication enzymes.
Term
Helicase
Definition
Enzymes that form single stranded regions of DNA. Require ATP. Wrap around DNA and translocate along DNA to strip it apart. Requires a free end of DNA to load onto or an accessory protein . Cannot unwind circular double stranded DNA without another enzyme. Cannot change topology.
Term
Topoisomerase
Definition
Enzymes that change the linking number of DNA. Act by splicing a strand of DNA in half and then passing the other strand through, then rejoining the first piece.
Term
DNA Polymerase
Definition
Enzymes that carry out the synthesis of DNA. Only work in the 5'->3' direction. They must have a primer, thus cannot perform de novo synthesis. They must also have a template.
Term
Primase
Definition
Enzymes that synthesize short RNA primers to be used by DNA polymerase for DNA synthesis.
Term
Sliding Clamp (DNA Clamp)
Definition
Proteins that wrap around the DNA and bind to the DNA polymerase. Increases processivity of the DNA polymerase. This stays tightly wrapped on the leading strand (high processivity). On the lagging strand, it collides with 5'RNA end of the next Okazaki fragment and then breaks apart and detaches from the DNA and releases the DNA polymerase.
Term
Clamp Loader
Definition
Attaches and removes sliding clamp from the DNA polymerase. Signals to the clamp to remove after bumping into the next Okazaki fragment.
Term
Reverse Transcriptase
Definition
An enzyme that makes a DNA copy of an RNA template. Uses a tRNA molecule from the last host as an initial primer.
Term
DnaA
Definition
An enzyme that binds to specific origin sites on the DNA to wedge the two DNA strands apart. Allows a helicase to unzip the DNA.
Term
Telomerase
Definition
Enzymes that have a built in RNA template to create long strands of repeating noncoding sequences on the 3' end of the linear chromosomes.
Term
Recombinase
Definition
Enzyme that attaches one end of the strand broken during recombination, searches for a homologous part on the recipient strand, and catalyzes the formation of a D-loop.
Term
Resolvase
Definition
Enzymes that facilitate the resolution of a Holliday Junction
Term
Peptidyl Transferase
Definition
RNA enzyme in protein synthesis that catalyzes the formation of peptide bonds.
Term
RNA polymerase I
Definition
Enzyme that transcribes large rRNAs (18S, 28S, 5.85S)
Term
RNA Polymerase II
Definition
Enzyme that transcribes mRNA in eukaryotes
Term
RNA Polymerase III
Definition
Enzyme that transcribes small RNAs (tRNAs and 5S rRNAs in eukaryotes.)
Term
S-Adenosyl Methionine (SAM)
Definition
Methylates the 45S rRNA precursor transcribed by RNA Polymerase I to form a 41S precursor which is then cleaved.
Term
Nucleotidyltransferase
Definition
Enzyme that adds a CCA segment to the 3'OH of tRNA precursor to form mature tRNA
Term
RNaseP
Definition
Enzyme that cleaves a large transcript to produce tRNA in prokaryotes.
Term
Actinomycin D
Definition
Intercalates (slips between DNA base pairs) and prevents DNA from functioning as a template for replication or transcription. Very toxic in both eukaryotic and prokaryotic organisms.
Term
Rifampicin
Definition
Binds to bacterial RNA polymerase and prevents initiation of RNA synthesis. Used as an antibiotic. Eukaryotic cells are not affected. It can also inhibit synthesis of mitochondrial RNA, but the concentration required is higher than that required to kill bacteria.
Term
Streptolydigin
Definition
Binds to bacterial RNA polymerase and prevents elongation of RNA chains that are in the process of being transcribed.
Term
alpha-Amanitin
Definition
Derived from poisonous mushrooms, inhibits eukaryotic RNA polymerases, especially RNA II.
Term
tRNA synthetase
Definition
Enzyme that catalyzes the covalent attachment of amino acids to tRNA. Each amino acid has a different enzyme. This enzyme catalyzes both of the steps required in activating a tRNA. It can attach an amino acid to the 2'OH or 3'OH
Term
eIF2
Definition
To initiate protein synthesis in eukaryotes, binds Met-tRNA and GTP. Carries these two to the 5' end of mRNA
Term
EF1a (EF1alpha)
Definition
Factor that binds to a charged tRNA and GTP molecule in eukaryotes. Carries the amino acid to the A site of tRNA
Term
EF2
Definition
Factor that is involved in translocation during protein synthesis
Term
Streptomycin
Definition
Binds to 16S rRNA in 30S ribosomal subunits, blocks formation of functional initiation complexes, and causes misreading of mRNA (bactericidal)
Term
Tetracycline
Definition
Binds to 30S ribosomal subunits and prevents binding of aminoacyl tRNA at the A site. (bacteriostatic)
Term
Chloramphenicol and Lincomycin
Definition
Bind to 23S rRNA in 50S ribosomal subunits in the peptidyl transferase site. They prevent the aminoacyl group in the A site from approaching the peptidyl ester group in the P site, thereby blocking formation of the peptide bond. (bacteriostatic)
Term
Erythromycin
Definition
Binds to 23S rRNA in the 50S ribosomal subunit, near the binding site for chloramphenicol. This does not inhibit peptide bond formation but rather inhibits translocation. (bacteriostatic)
Term
Puromycin
Definition
Antibiotic used in research. Resembles 3' end of an aminoacylated tRNA. This can add to a growing polypeptide on a ribosome, but subsequent amino acids cannot be added to it; hence it terminates the synthesis of a polypeptide into which it is incorporated, both in prokaryotes and eukaryotes
Term
Cycloheximide
Definition
Used in research. Inhibitor of eukaryotic protein synthesis. Blocks translocation
Term
Signal Peptidase
Definition
Cleaves the signal off of a polypeptide chain.
Term
Glycosyl Transferase
Definition
Attaches sugars to the end of a protein one at a time.
Term
Proteasome
Definition
Protein that recognizes a polyubiquitinated protein and cleaves it into small peptides.
Term
Sigma Factor
Definition
Accessory proteins that help RNA polymerase bind with high specificity to promoter
Term
Promoter
Definition
DNA sites that RNA polymerase binds to at which transcription begins
Term
Operator
Definition
DNA sites at or near the promoter that bind repressors
Term
Activator Site
Definition
DNA sites at or near the promoter that bind activators
Term
Operon
Definition
Cluster of genes that is transcribed to give a polycistronic mRNA
Term
Polycistronic mRNA
Definition
mRNA that encodes several proteins (contains many start and stop codons)
Term
Repressor
Definition
Bind to operator sequences and decrease the rate of transcription
Term
Activator
Definition
Bind to activator site and increase rate of transcription
Term
Inducer
Definition
Bind to repressor and inhibits it from binding to operator
Term
Corepressor
Definition
Binds to repressor and allows it to bind to operator
Term
Effector
Definition
Bind to activators and allow them to bind to activator site.
Term
Attenuation
Definition
Process in which transcription begins but it is terminated before the first coding sequences of the operon
Term
Catabolite Repression
Definition
Inhibition of protein synthesis of enzymes involved in the catabolism of carbon source other than the preferred one (ex: glucose > lactose)
Term
CpG islands
Definition
Areas of the DNA that are associated with methylated Cytosines and decreased transcription
Term
Cryptic Splice Site
Definition
A splice site that is not normally used but is unmasked when a mutation removes the normal splice site from an mRNA
Term
siRNA (short interfering RNA)
Definition
Short (21-26 nucleotide) RNA molecules derived from double stranded RNA (dsRNA) that has been processed by a dicer. This molecule perfectly basepairs with a target mRNA and results in cleavage of that mRNA by a RISC complex
Term
miRNA (microRNA)
Definition
RNA that is derived from transcripts that form stem loop structures. Form incomplete Watson-Crick base pairing with a target mRNA and causes the translation of this mRNA to be inhibited. Can rarely form perfect base pairing with mRNA and then will degrade that mRNA
Term
Restriction enzyme
Definition
Enzyme that cuts double stranded DNA at specific locations (if the sequence is not methylated) every time that sequence is encountered. Produces "sticky" or "blunt" ends.
Term
Transactivation Domain
Definition
A structural domain in ALL activators and repressors. Binds to DNA polymerase or corepressor/coactivator
Term
DNA Binding Domain
Definition
Structural domain in ALL transcriptional activators and repressors. Binds to the DNA sequence
Term
Dimerization Domain
Definition
Structural domain in some transcriptional activators or repressors. Protein-protein interaction with other transcription factors.
Term
Ligand Binding Domain
Definition
Structural domain of some transcriptional activators and repressors. Recognizes regulatory molecules such as steroids or hormones.
Term
Dicer
Definition
Enzyme that cleaves double stranded RNA (dsRNA) into siRNA along with an ATP molecule.
Term
RISC
Definition
A complex that binds a single strand of siRNA or miRNA, and is also activated by an ATP. The complex then searches for complementary DNA basepairs to the RNA template, and cleaves at that point.
Term
Genomic Imprinting
Definition
When certain genes from only one chromosome (maternal or paternal) are expressed due to methylation on the opposite chromosome.
Term
Glycosylase
Definition
In excision repair (base excision repair), cleaves the bond between a damaged base and the deoxyribose sugar. There are 8 different kinds of these enzymes, one for each type of DNA damage.
Term
TFIIH
Definition
Enzyme that can recruit excision repair during RNA transcription in eukaryotes when a lesion is discovered.
Term
Photolyases
Definition
An enzyme responsible for direct repair of DNA in prokaryotes. Uses light to cleave pyrimidine dimers.
Term
Werner Syndrome
Definition
Premature aging disease. Autosomal recessive trait. The responsible gene is RECQL2 which is a predicated helicase involved in NHEJ. High frequency of balanced translocations.
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