BIO 311c 1st Edition Exam #4 Study GuideDNA Structure and Replication1. What is Chargaff’s rule?2. X-ray crystallography of DNA by _________________ helped lead to discoveries on the shape and structure.3. Adenine is paired with ____________.4. Adenine is a (purine/pyramidine)5. Name two pyramidines6. Explain why two pyramidines cannot be paired with one another.7. What portion of a nucleotide is hydrophobic? Is this on the interior or exterior of the double helix?8. DNA is antiparallel 9. Nucleotides of a DNA strand are held together by covalent bonds10. Nitrogenous base pairs are attracted to one another by hydrogen bonds11. Meselson and Stahl believe in the ____________model of DNA replication12. Origin of Replication=short sequences of DNA where the replication bubble beginsa. How many origins of replication do prokaryotes have?b. How many origins of replication do eukaryotes have?c. Why are they different?13. Replicationa. What is the function of helicase?b. ___________ is the enzyme that relieves the highly twisted DNAc. single strand binding protein=prevent the two complimentary strands of DNA from repairingd. Draw a picture of the replication bubble and the proteins listed so far.e. The leading strandi. DNA can only be synthesized by adding new nucleotidesto which end of an existing nucleotide?ii. The synthesis of the leading strand is continuousiii. The new DNA strand is laid down (toward/away) from the replication forkiv. DNA polymerase III is responsible for laying down the new DNAf. The lagging strandi. The strand is synthesized away from the replication forkii. New DNA nucleotides can ONLY be laid down in the 5’-3’directioniii. Lagging strand is 5’ at the origin of replicationiv. RNA primase lays down RNA primer on the lagging strandv. Why is RNA primer required on the lagging strand and not the leading strand?vi. Define an okazaki fragment?vii. DNA polymerase III begins laying down new nucleotides starting from the RNA primerviii. DNA polymerase ___ replaces the RNA primerix. What is the role of DNA ligase?g. Telomerei. Telomeres are the result of DNA polymerase not being able to add a new nucleotide where there is not a 3’ end.For example where the first RNA primer was laid down.ii. Telomere is a single stranded portion that can now not be replicated and as a result the new DNA is shorteriii. How does DNA prepare before hand how to deal with this shortening after each replication?iv. What is the role of telomerase?v. Telomerase may be helpful for cancer treatment because if they are able to make telomerase inactive in cancer cells then it can inhibit them from efficiently dividing.h. Repairi. DNA proofreading1. DNA polymerase III proofreads as it lays down DNA and can replace incorrect matches on the spotii. Mismatch repair1. Enzymes remove segment with incorrect nucleotidea. nuclease2. DNA polymerase places new/correct nucleotidesiii. Excision repair1. DNA is constantly exposed to damage2. Example two thymines laid down instead of one3. Segment is cut out and replaced with DNA polymerase Iiv. DNA nuclease is the enzyme responsible for cleaving the DNA in some of the repair mechanisms14. Explain the benefits of mutation in the DNA15.DNA Transcription and Translation1. List three differences between RNA and DNA2. What is a codon?3. Which is correct; a codon codes for only one amino acid or for every amino acid there is only one codon?a. The genetic code has redundancy but not ambiguity4. Crick’s central dogmaa. DNA->RNA->protein5. Transcriptiona. RNA is synthesized in the 5’->3’ directionb. RNA polymerase does not need a primer like DNA polymerasec. Define “promotor”d. RNA polymerase II binds to promoter region of DNAe. Elongation occurs by adding new RNA nucleotides to the ___ end f. Termination occursg. Differences between eukaryotes and prokaryotesi. In bacteria transcription and translation can occur some what simultaneously ii. Bacteria has a termination sequence but eukaryotes had code for polyadenilationiii. Eukaryotes modify the mRNA that is producediv. Eukaryotes require transcription factors1. What is an enhancer?h. RNA modificationi. Why is modified guanine added to the 5’ end of the pre-mRNA?ii. What modification occurs at the 3’ end?iii. Modifications can1. Facilitate where the mRNA is transported to2. Protection from hydrolytic enzymes3. Help ribosomes attach in the cytosoliv. What is a UTR region?v. Differentiate between an intron and an exonvi. RNA splicing is removing large portions of nonexpressive RNAvii. Define alternative RNA splicing6. Translationa. mRNA moves to cytosolb. mRNA + tRNA with start amino acid +small subunit of ribosome +large unit of ribosomec. elongation occurs as tRNA enters the ribosomei. tRNA bonds with amino acids floating around in cytosolii. What is an anticodon?iii. What amino acid is the start codon?iv. A site=new tRNA enters sitev. P=site where growing amino acid chain beginsvi. E=exit sitevii. Causes energy expenditure7. A functional proteina. Coils during synthesisi. What is the primary structure of a protein?b. Proteins may have additions such as sugar, lipids, or phosphates. Also may combine or cleavec. If a protein is may in a free ribosome where is that proteins final destination?i. Bound ribosomes?ii. What is a signal recognition particle?8. Mutationsa. Substitutioni. Define1. Silent2. Missense3. nonsenseb. Insertion/deletioni. Define the effect of an insertion or deletion on a reading frameGene expression/bacteria1. Operon=grouped genes with related functionsa. Operator+promoter+genesb. Operator= switch within the promoter that controls access of RNA polymerase2. Repressor=protein that can switch off operon. Binds to operator and blocks RNA polymerase3. Regulatory gene=produces repressor-> repressor may require corepressor4. Repressible operona. =usually on…able to be turned offb. example=tryptophanc. bacteria continuously produces tryptophan however when tryptophanis present it acts as a corepressor and activates the repressor that was produced by the regulatory gene. With the repressor active the operon(can/cannot) be expressed. d. Explain how this kind of control would be beneficial and efficient for a cell.e. This is a form of negative controlf. Usually seen in _________ pathways5. Inducible operona. =usually off…must be turned onb. example= lac operonc. A cell prefers to use glucose for energy. When glucose is present there are low levels of cyclic AMP in the cell. cAMP