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**Molecular Set 3
Exam 1
| Question | Answer |
|---|---|
| C-value Paradox | C-value=DNA content per haploid cell. The C-value paradox is generally explained not by extra genes, but by extra NONCODING DNA in some organisms. |
| what is reliable way to estimate the number of genes in an organism | is to estimate the number of different types of mRNAs. The only way to a RNA molecule if there is a gene that codes for the RNA (1:1 ratio). |
| how much DNA do humans have that are "extra" and do not code for anything | 25,000-40,000 genes and 50 times that of extra material |
| what are the two parent purine nucleotides of nucleic acids? | Adenosine 5’-monophosphate (AMP) and guanosine 5’ (GMP) |
| how does De novo purine nucleotide biosynthesis start? | with the molecule phosphoribosyl pyrophosphate (abbreviated PRPP) |
| PRPP pathway? | -an amino group is donated by glutamine and this group is then attached to C-1 of PRPP. -making the 5-phosphoribosylamine is EXTREMELY unstable, with a half-life of 30s at pH 7.5 - the remainder of the purine rig is built up on this structure. |
| what are the molecule that aid in the ring structure | • Amide supplies 2 N (1 each ring) • Formate donates 2 C (1 each ting) • Asparatate donates N on the left ring • Top C comes from CO2 • Trip of C=C-N comes from Glycine |
| what is the first intermediate in the de novo purine pathway to have a complete purine ring | Inosinate (IMP) |
| what are made from Inosinate? | AMP and GMP |
| what is the second intermidates in the PRPP pathway | Pyrimidines nucleotides. they are synthesized from aspartate, PRPP, and carbamoyl phosphate |
| what is made in Pyrimidines pathway? | - Cytidine 5’- monophosphate (CMP) and uridine 5’-monophosphate (UMP) are made in this pathway. - The pyrimidine ring is made first then it is attached to ribose 5-phosphate. |
| what is the precursor of deoxyribonucleotides | Ribonucleotides - The reduction of NDP to dNDP is catalyzed by ribonucleotide reductase. |
| what is yielded during the purines degradation pathway | Uric Acid |
| what is yielded during the pyrimidines degradation pathway | Urea |
| what are formed from the degradation of nucleotides | free purines and pyrimidines |
| what is salvaged and reused to for "new" nucleotides | free bases y a simpler reaction than required during de novo synthesis. |
| what is an example of a salvaged pathway? | Adenine(used base) + PRPP → AMP + PPi catalyzed by adenosine phosphoribosyltransferase |
| what conditions are needed for DNA replication? | High fidelity, Highly processive, relatively fast |
| explain why high fidelity is needed for DNA replication | • Change that happen is harmless • One nucleotide change could be very detrimental or lethal • Whatever mistake happens could be a beneficial mistake and improve the particular part of the DNA. |
| explain why highly processivness is needed for DNA replication | • makes reference to a property to DNA polymerase that allows it to stay stuck on the template DNA for long periods of time. • If this didn’t happen it would fall off after replication of a small amount of DNA then it needs to rebind and then repeats. |
| explain why relatively fast condition be needed for DNA replication | • Must be fast in order for it to be successful |
| what is implied knowing the DNA is a double stranded helix? | each stand can serve as a template for making its own “partner strand” because they are complimentary to each other |
| Semiconservative (partner strand) | the manner in which DNA replicates itself |
| what ways are hypothesized on how DNA replicates? | SEMICONSEVATIVELY CONSERVATIVELY DISPERSIVELY |
| Meselson and Stahl | demonstrated that replication is semiconservative |
| how did Meselson and Stahl demonstrate replication is semiconservative | by employing CsCl gradient ultracentrifugation of DNA labeled with HEAVY nitrogen (15N) and then grown in normal Light (14N) |
| what other possibilities were discovered on how DNA replicated by Meselson and Stahl | replication could possibly proceed: continuously, semidiscontinuously, discontinuous |
| what did Okazaki propose with DNA Replication | DNA polymerase could make one strand of DNA CONTINUOULDY in the 5’-3’ direction but that the other strand must be made discontinuously in the 5’->3’ direction |
| what is the continuously synthesized strand called | leading strand |
| what is the discontinuously synthesized strand called | lagging strand |
| what was the first prediction that Okazaki's model suggest about replication | If short pieces of DAN are synthesized on the lagging strand, then it should be possible to “catch” these short pieces f DNA before they are linked together by employing short pulses of radiolabeling. |
| what was the second prediction that Okazaki's model suggest about replication | If the enzyme DNA ligase is eliminated from the replication process, then the short pieces of DNA made ought to be detectable even longer labeling periods. |
| What must be done in order for DNA replication to commence | RNA primers must be laid down on the template strands to provide a double-stranded region for DNA polymerase to bind. |
| DNA Replication is _______ and occurring at __ ___________________ | Bidirectional 2 replication forks |
| oriC | initiated location within the DNA that replication starts |
| Cairns | labeled replicating E. coli DNA with a radioactive DNA precursor and at selected times observed the DNA using autoradiography. |
| What did Cairns discover during DNA replication process? | • At a certain point during replication, a structure resembling the greek letter theta is seen Θ (Theta) -Theta Mode of replication. - you have two indentical circular pieces of DNA |
| Gyurasits and Wake | radiolabeled replicating DNA for a short time with low levels of radioactive precursor, followed by high levels of radioactive precursor. |
| ColE1 | one example of unidirectional replication that occurs in a plasmid |
| Rolling Circle Replication | alternative way or DNA replication present in circular DNA. |
| example of Rolling circle replication | ΦX174 one stand of double stranded DNA is nicked and the 3’ end is extended. • The intact stand of DNA is used as the template. • A full length, single stranded circle of DNA is released. |
| How does the single strand circular DNA go to a double stranded circular DNA | • In λ phage the displace strand serves as the template for discontinuous lagging strand synthesis, as opposed to using the intact DNA strand as template shown in the precious example for ΦX174. |
| ds replicative form (RFI) | this is a double stranded circular DNA form that was produced by a ssDNA from the phage ΦX174 |
| What are the enzymes and other protein that are required for DNA replication | helicase, ssDNA-binding protein, Topoisomerases, DNA polymerase, |
| Helicase enzymes | • An ATP-dependant enzyme that separates the DNA strands in advance of the replication fork. |
| example of a helicase | • The DNA-B gene (protein) product in E. coli is the helicase required for DNA replication |
| ssDNA -binding proteins (SSBs) | bind to single stranded regions of DNA, hold open the replication point and prevent it from reforming double-stranded DNA. -stimulates replication |
| where does the ssDNA binding protein come from | ssDNA bidning protien of E coli. |
| how does the binding of ssDNA binding proteins work | COOPERATIVE "bees swarming on the beekeeper" the infinity increases of the binding protein molecules makes it more attractive for additional protein binding 1000 fold once the first protein binds. |
| Are SSBs found in Eukaryotes? | no only found in prokaryotes. |
| Topoisomerases | the enzyme that relieves the strain introduced into DNA molecules as they unwind. |
| how do topoisomerase work | introduce TEMPORY single- or double- stranded breaks in DNA, allowing it to change topology (shape. No longer has the bump) |
| what are the types of Topoismerases | • Type 1 Topoisomerases - introduce single-stranded breaks • Type 2 Topoisomerases – introduce double-stranded breaks |
| what is an example of type 2 Topoisomerase | DNA Gyrase from E coli |
| What are the three types of DNA Polymerases found in E. coli? | • DNA polymerase 1 (DNA repair, primer excision) • DNA polymerase 2 (SOS repair ?) • DNA polymerase 3 holoenzyme pol 3 is the polymerase required for DNA replication in E. coli. |
| Holoenzymes? | means that the polymerase is composed of multiple subunits. (Holo- entire. ) 3 polypeptides (α, ε, and θ subunits) |
| α-subunit | has the DNA polymerase activity |
| ε-subunit | has the 3’→5’ exonuclease proofreading activity |
| what are the 5 DNA polymerase in Eukaryotes | 1. DNA polymerase α (priming) 2. DNA polymerase δ(elongation) 3. DNA polymerase β (repair) 4. DNA polymerase ε(repair) 5. DNA polymerase γ(mitochondria) |
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kort
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