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61 Cards in this Set
- Front
- Back
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Describe the termination phase.
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1) Stop codon has no tRNA 2) Stop codon causes elongation to stall 3) Peptide is held in the P-site attached to the tRNA 4) Release Factor (RF) diffuses in to the A-site RF allows peptidyl transferase to cleave ester bond between tRNA and the peptide GTP dependent activity 5) After release of the peptide, the ribosome dissociates into its subunits which may then begin a new round of translation
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What is the function of DNA gyrase in prokaryote cells?
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DNA gyrase aids in the suppercoiling of DNA.
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What is the function of DNA topoisomerase I in prokaryote cells?
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DNA topoisomerase aids in the suppercoiling of DNA.
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What is the function of HU proteins in prokaryote cells?
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HU proteins aid in the packaging of DNA when supercoiled.
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What is the function of aminoacyl-tRNA synthetase?
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Attaches the AA to the tRNA. Needs ATP
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What is the difference between negative and positive supercoiling?
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Negative supercoiling promotes strand separation Positive supercoiling makes DNA strand separation more difficult.
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What is the function of DNA gyrase in Eukaryote cells?
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Topoisomerase II (DNA gyrase): Introduces -ve supercoils. Activated when two double helices cross over each other. Makes a covalent linkage to both strands of one DNA helix and making a double stranded break. The second DNA helix is passed through the break. The break is resealed and the enzyme dissociates. Requires ATP hydrolysis.
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What is the function of DNA topoisomerase I in Eukaryote cells?
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Topoisomerase I forms a single covalent bond with tDNA Allowing free rotation of the DNA around the covalent backbone bonds. Does not require ATP because energy is stored in the phosphotyrosine linkage making the reaction reversible. Relaxes -ve supercoils
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Describe intrinsic termination.
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Hits a palindrome and everything falls off. Rho-independent
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What is chromatin?
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Chromatin is the complex of DNA and chromosomal proteins.
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Describe the process of compaction.
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1. Nucleosome forms from the core octamer, linker DNA and histone H1. Nucleosomes connected together by linker DNA and H1 histone to produce the beads-on-a-string extended form of chromatin. 2. Nucleosomes can associate with each other to form a more compact structure that has been termed, due to its size, the 30 nm fiber. This structure results from interactions between adjacent histone H1 proteins. 3. 300nm is extended section of chromosome 4. 700nm Condensed section of chromosome 5. 1400nm Metaphase chromosome
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Describe the translocation of the mRNA relative to the ribosome.
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EF-G is a GTPase protein. Hydrolysis of GTP is important for efficient translocation of the mRNA relative to the ribosome. EF-G is the prokaryotic protein In eukaryotes, EF-G is called EF-2
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What is Euchromatin?
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Decondensed and transcriptionally active
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What is Heterochromatin?
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Condensed and transcriptionally inactive
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What are heat shock proteins? What is the function of Hsp 70? Describe shape and function of Hsp60.
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Heat shock proteins are chaperones for specific folding of proteins. Hsp 70 prevents aggregation of unfolded protein. Hsp60 has a barrel shape and assists in the folding and refolding of proteins.
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What function does DNA methyltransferase enzyme perform?
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DNA methylation involves the modification of the DNA base cytosine to 5-methyl-cytosine. DNA methylation tags a region of the genome for histone modification that causes the formation of heterochromatin and turns off transcription.
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What is the function of DNA Polymerase-a?
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•Synthesizes RNA primer on leading and lagging strand •Subunit possesses primase activity and initiates DNA synthesis •Low processivity – falls off after sythesizing a short DNA segment •No exonuclease activity
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What does Decitabine do?
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Decitabine causes DNA hypomethylation and increased transcription
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What is the function of MeCP2
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MeCP2 acts as a transcriptional repressor and activator. The MeCP2 protein binds to forms of DNA that have been methylated.
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What is the purpose of histone acetylation?
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Reduces affinity between histone and DNA Increases transcription. Removes + charge on the lysine AA of the histone.
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What is required for DNA replication?
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The following components are required for the synthesis of DNA: 1) All four dNTPs (deoxynucleoside triphosphate) -building blocks of the DNA molecule 2) A fragment of DNA to act as template. 3) DNA polymerase 4) Magnesium ions (Mg2+).-required for DNA polymerase activity. 5) A primer providing a free 3' -OH group.
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What is the function of phosphatase during capping of mRNA?
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Removes one phosphate from the 5’ end of the RNA.
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What is the function of initiator proteins (DNaA protein) in prokaryotes?
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Binds to the origin of replication and breaks hydrogen bonds between bases.
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What is the function of DNA helicase (DNaB)in prokaryotes?
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Opens helix and binds primase to form primosome.
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What is the function of Guanine-7-methyl transferase during 5' capping.
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Adds a methyl group to the 7 position of the terminal guanine.
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What is the function of Helicase inhibitor (DNaC)in prokaryotes?
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Delivers helicase to DNA template
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What is the function of DNA primase in prokaryotes?
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A RNA polymerase that synthesizes a RNA primer on the lagging strand to enable DNA polymerase to synthesize DNA strand.
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What is the function of DNA polymerase I: in prokaryotes?
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Remove RNA primer and replace with DNA
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What is the function of DNA polymerase III in prokaryotes?
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Synthesis of leading and lagging strands of DNA
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What is the function of Single stranded binding protein (ssb) in prokaryotes?
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Binds to single stranded DNA in the replication bubble and prevents it from re-annealing or forming secondary structure.
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What is the function of DNA polymerase I in eukaryotes?
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DNA polymerase I removes the RNA primer (RNAseH and FEN1 protein in eukaryotes) and fills in the remaining gap.
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What is the function of DNA ligase?
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Joins Okazaki fragments Requires ATP
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What is the purpose of clamp protein?
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The Clamp protein tightly holds the DNA polymerase onto the template for synthesis and releases DNA pol when it stalls at a region of double stranded DNA.
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What is the function of sigma factor?
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Sigma factor enables RNA pol to recognise promoters
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What is the function of RNA polymerase I?
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Transcribes the 5.8S, 18S, and 28S rRNA genes
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What is the function of RNA polymerase II?
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Transcribes all protein-coding genes (mRNA), some snRNAs and microRNA (miRNA)
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What is the function of RNA polymerase III?
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Transcribes tRNA genes and some snRNAs
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What is the TATA box binding protein used for?
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A subunit of TFIID -binds to TATA box of gene promoter
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Describe the transcription initiation proteins in eukaryotes.
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1) TFIID Causes a distortion in the DNA helix allowing the recruitment of other transcription factors.
2) TFIIB Involved in RNA polymerase interactions Start site recognition 3) TFIIH Contains a DNA helicase to unwind DNA Activates RNA polymerase by phosphorylation 5) TFIIE Involved in positioning RNA polymerase |
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Describe the initiation of DNA transcription including the order that the initiation proteins bind to DNA.
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1. TFIID and TBP bind to TATA -25 2. TFIIA and TFIIB bind to promoter (recruitment and stabilizaiton 3. RNA polymerase, TFIIE, and TFIIH bind 4. TFIIH unwinds DNA 5. TFIIH phoshorylates RNA polymerase activating transcription. 6. Most transcription factors are released
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What is a palindromic region?
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1) Palindromic regions that form hairpins varying in length from 7 to 20 bps. 2) The stem loop structure includes a G-C rich region and is followed by a run of U residues. This is Intrinsic Termination of transription. Rho-independent
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What is extrinsic termination?
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1) Rho protein attaches to the recognition site on the RNA. 2) Rho moves along the RNA following RNA polymerase. 3) RNA polymerase pauses at terminator and Rho catches up. 4) Rho unwinds (helicase activity) the DNA-RNA hybrid and separates the RNA from the RNA polymerase. 5) Termination: RNA polymerase, Rho, and RNA are released.
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Describe the process of capping performed on mRNA.
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1) Phosphatase: removes one phosphate from the 5' end of the RNA. 2) Guanylyl transferase: adds a GMP in a reverse linkage (5' to 5' instead of 5' to 3'). 3) Guanine-7-methyl transferase: adds a methyl group to the 7 position of the terminal guanine.
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What is the purpose of the 5' cap?
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1) Regulates export of mRNA out of the nucleus. 2) Required for the efficient translation of the mRNA into protein. 3) Prevents 5' degradation.
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Describe the process of Polyadenylation.
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Cleavage Phase 1) Cleavage and polyadenylation specificity factor (CPSF) binds to the hexamer AAUAAA (the polyadenylation signal). 2) Cleavage stimulating factor F(CstF) binds the GU-rich element beyond the cleavage site. 3) Cleavage factors bind to the CA sequence at the cleavage site. Poly-adenylation 1) Poly-A-polymerase (PAP) adds approximately 200 A nucleotides to the 3' end produced by the cleavage. 2) Poly-A Binding Proteins (PABP) binds to the poly-A tail and assist in directing translation by the ribosome. 3) The cleaved fragment of the RNA is degraded in the nucleus.
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What are the functions of Polyadenylation?
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1) Increases the half life 2) Increases translation 3) Aids in transcription termination 4) Aids in export of the mRNA from the nucleus.
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Describe the Model for intron removal by the spliceosome.
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1) U1 snRNP binds to the 5' splice junctions and U2 binds to the branch point, respectively. 2) Interactions with U4/U6 snRNP and U5 snRNP binds U1 and U2 together to form a loop. 3) U4 dissociates forming the active spliceosome. 4) The spliceosome complex cleave the intron from exon 1 at the 5' splice junction. The free end binds to the A in the branch-point sequence (lariat). 5) The intron is excised by cleavage at the 3' splice junction and exons 1 and 2 are ligated. SnRNPs are released. The 5’ sequence always possesses a GU sequence & the 3’ always an AG sequence.
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What are the steps of RNA editing in Trypanosome mitochondria:
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1) Guide RNA complimentary base pairs with target RNA. 2) Endonuclease cleaves RNA at region of mispairing. 3) TUT (Terminal uridyltransferase) inserted uridine. 4) RNA ligase ligates substrate RNA.
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Describe the initiation phase in Prokaryotes.
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The 3 Initiation Factors, tRNAfMet and the mRNA binds to the 30S subunit first GTP is hydrolyzed as the 50S subunit joins to form the complete 70S ribosome tRNAf Met is the only free aminoacyl-tRNA to bind in the P site first
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Describe the elongation cycle.
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1. Binding of the aminoacyl tRNA 2. Formation of the peptide bond 3. Translocation of the ribosome
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What are the stop codons?
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UAA UAG UGA
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What does cytidine deaminase perform?
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Changes the C - U. This is a form of mRNA modification to increase protein variety.
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What does adenosine deaminase do?
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Changes A to I. This is a form of mRNA modification to increase protein variety.
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What is the function of EF-2?
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EF-2. aka EF-G, is a GTPase protein. Hydrolysis of GTP is important for efficient translocation of the mRNA relative to the ribosome
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What is the function of peptidyl transferase?
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Cleave ester bond between tRNA and the peptide GTP dependent activity
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Describe the formation of a peptide bond
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1. The aminoacyl-tRNA in the P-site has a free carboxyl group 2. The amino group of the A-site aminoacyl-tRNA is oriented to facilitate peptide bond formation 3. The P-site charged aminoacyl-tRNA is hydrolyzed 4. The peptide bond forms and the P-site now has a free tRNA
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What is the function of the Shine-Delgarno sequence and where it is found?
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The Shine-Delgarno sequence is found a few basses 5' to the start codon in prokaryotes. Used to align the ribosome with the start codon.
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What is the function of DNA Polymerase-delta?
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•Synthesizes DNA from leading and lagging strands •Main replicative enzyme •High processivity – can synthesize long stretches of DNA •3’-5’ exonuclease proofreading activity
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What is the function of DNA Polymerase-beta?
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DNA repair.
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What is the function of DNA polymerase-y.
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Mitochondria genome replication
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What is the function of Guanylyl transferase during 5' capping?
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Adds a GMP in a reverse linkage (5’ to 5’ instead of 5’ to 3’).
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