BIO 330 Exam 1Questions And Detailed Correct Answers.

What are the characteristics of a gene? - correct answers 1. Replication 2. Storage of materials 3. Expression of information 4.Variation by mutation What experiments demonstrated that nucleic acid is the genetic material? - correct answers -Griffith -Avery, McLeod, McCarty -Hershey and Chase -Tobacco Mosaic Virus What did the Griffith experiment study and conclude? - correct answers Studied strains of pneumoniae and injected mice with virulent S, and non virulent R strain. Found that mice injected with Type R and heat treated S still died, but mice injected with Type R alone where still alive. Confirmed: Transformation Principle: bacteria are capable of transferring genetic information What did the Avery, MacLeod, and McCarty experiment show and conclude? - correct answers Experiment was similiar to Griffith experiment but with alterations. ● Agglutination Assay o Agglutination assay makes use of the fact that antibodies recognize certain macromolecules on cells o First, isolated and heat killed SIII cells, and recovered the filtrate o Then, they performed multiple similar experiments by treating the filtrate with different enzymes to isolate which macromolecule of a cell might be the genetic material (used proteases to remove proteins, nucleases to break down nucleic acids, etc.) o Spinning RII and anti RII gives a pellet with anti RII bound to multiple RII ▪ When pellet isn't there, RII isn't there ▪ Antibodies are specific for RII ▪ Can check the pellet to see if any SIII present Concluded: Nucleic Acid is the Genetic Material What did Hershey and Chase experiment entail and conclude? - correct answers Radioactively labeled protein and DNA in a bacteriophage (32P for DNA, 35S for protein). Allowed bacteriophage to inject bacteria, then centrifuged. Showed most of 32P was transferred into cells. Conclusion: DNA is genetic material Tobacco Mosaic Virus - correct answers studied two types of virus 1) wild type- lacks methionine 2)mutant-contains methionine showed mixed protein coat + RNA gives an active virus Conclusion: RNA is the genetic material in viruses Watson and Crick - correct answers Used x-ray diffraction from Rosalind Franklin, Chargaff's Principle and discovered DNA is a double helix, with base pairing between strands, and is antiparallel What bases are purines? - correct answers Adenine and Guanine What bases are pyrimidines? - correct answers Cytosine Thymine and Uracil What are some differences between DNA and RNA? - correct answers 1. DNA is double stranded, RNA single stranded 2. RNA sugar is ribose, DNA sugar is deoxyribose 2. DNA bases A-T, C-G, RNA bases A-U, C-G What are the components of a nucleotide? - correct answers nitrogenous base, pentose sugar, and phosphate group What type of bond links nucleotides? - correct answers phosphodiester bonds What type of bond links bases? - correct answers hydrogen bonds The sugar-phosphate backbone is.. - correct answers hydrophilic The nitrogenous bases are.... - correct answers hydrophobic How is the phosphodiester bond created in DNA? - correct answers Bond is broken between alpha and beta phosphate (which is used to catalyze next steps) two remaining phosphates are kicked off. 1) The 5' group of nucleotide triphosphate is held close to the free 3' hydroxyl group of a nucleotide chain 2) 3' OH group forms a bond to the phosphorus atom of the free nucleotide closest to the 5' oxygen atom Why did some people think protein was the genetic material? - correct answers There are many proteins, and there is so much variation between species Chargaff's Rule - correct answers A=T and C=G 5' Nearest Neighbor Experiment - correct answers Tries to determine is DNA is parallel or antiparallel Phosphate at the 5' end of a certain base is radioactively labeled. Details: When a nucleotide is incorporated, the alpha phosphate stays with the DNA and becomes attached to the 3' nucleotide position that precedes it, the alpha phosphate of T's 5' nn is marked with p32 (radioactive), then when incorporated into newly synthesized DNA the new phosphate with be added to 5' end of the 5' nearest neighbor Next, the enzyme spleenphospdextrouse, that will cleave the bond between a base and the 3' phosphate and raise the pH or temperature so that the base pair with separate. It will cleave the DNA and will have individual nucleotides in the test tube and ALL 5' nn of T would be radioactive. Showed that the strand is antiparallel because the frequency of C as 5'nn of T= frequency of A as 5'nn of G ● If they're parallel then every time 5' is the nearest neighbor of C is the 5'nn of T, G will be the 5'nn of A, if and only if the strands are parallel ● If parallel, the frequency of C is 5'nn of T= to the frequency of G is the 5'nn of A on any DNA strand Conclusion: DNA is antiparallel What are some predictions made by Watson and Crick? - correct answers DNA is genetic material DNA looks like a double helix (sometimes true) Base pairs are perpindicular to phosphodiester bonds (sometimes true) Messelson and Stahl Experiment - correct answers Examined 15N and 14N isotopes of DNA density over generations Showed a band of intermediate in density Conclusion; Semiconservative model for replication What are some requirements of DNA Replication? - correct answers 1. Origin of replication (more than one in eukaryotes), 2. Way to unwind strand 3. Way to hold strands apart 4. "Something to do stuff" What are the various types of DNA? - correct answers A,B, D, C and Z-DNA. All have varying angles between base pairs and not all are perpendicular, but ALL are right handed helices True/False DNA replication is bidirectional? - correct answers True What enzymes are required for DNA replication? - correct answers Helicase Single Stranded Binding Proteins DNA Polymerases Primase DNA Ligase What is the function of helicase? - correct answers Unwind DNA creating a replication fork What is the function of single stranded binding proteins? - correct answers Hold DNA strands apart What is the function of DNA polymerase III? - correct answers Major enzyme doing replication Which reaction is catalyzed by DNA polymerase? - correct answers Phosphodiester bond between a phosphate on 5' sugar and 3' OH end of new base What is the function of DNA polymerase 1? - correct answers To remove the RNA primers and replace them with DNA, also acts as a proofreader What is the function of DNA ligase? - correct answers DNA ligase joins the Okazaki fragments on the lagging strand together. What is a plasmid? - correct answers a genetic structure in a cell that can replicate independently of the chromosomes, typically a small circular DNA strand in the cytoplasm of a bacterium or protozoan. Plasmids are much used in the laboratory manipulation of genes. What is the function of a telomere? - correct answers Telomeres prevent the ends of chromosomes from being damaged. rolling circle replicationW - correct answers Replication of plasmid, circular DNA that is initiated by a break in one of the nucleotide strands, producing a double-stranded circular DNA molecule and a single-stranded linear DNA molecule, the latter of which may circularize and serve as a template for the synthesis of a complementary strand. Homologous Recombination - correct answers Exchange of genetic information between homologous DNA molecules. Allows for increased variability RecA homologous recombination - correct answers RecA- protein used for DNA repair and maintenance...... Transcription - correct answers the organic process where DNA is used as a template to create RNA What enzymes are required for transcription? - correct answers RNA polymerase What subunits make up the core enzyme of RNA polymerase? - correct answers two alpha subunits, a beta subunit What subunits make up the holoenzyme of RNA polymerase? - correct answers two alpha, beta, and sigma** this is the active form of RNA polymerase What does the sigma subunit of RNA polymerase do? - correct answers Provides specificity for start sites Where is the pribnow box located? - correct answers -10 Upstream from initiation site What is located at -35? - correct answers Binding region Describe the initiation steps of prokaryotic transcription - correct answers o Initiation ▪ (1) First step, the holoenzyme (using sigma to guide it, sigma will recognize the pribnow box) will look for promoters (pribnow box) ▪ (2) Then, the holoenzyme will bind to the binding region ▪ RNA polymerase, when is stretches itself out it will cover about 50bp ▪ Need to separate the two strands of DNA to be able to add RNA base pairs ▪ (3) Unwind the two strandsàRNA polymerase does this too ▪ (4) Keep the strands unboundàRNA polymerase does this too ▪ Suggests as RNA polymerase moves down DNA, it is unwinding, but after the RNA polymerase moves down the DNA it doesn't keep the DNA unwound ▪ Get unwinding from the pribnow box to about +6 ▪ Only Ts and As in the initiation site, H bonds, easier to open up ▪ Purine (A or G) will be the first RNA base, the first DNA base will be a C or t ▪ If +2 on DNA is A, then the second ribonucleic triphosphate will be U on RNA ▪ Need to form a covalent bond between the first two ribonucleic triphosphates ▪ RNA polymerase will facilitate the covalent phosphodiester bond ▪ (4) RNA polymerase does NOT need a primer to bring in the first ribonucleoside triphosphate and second NTP ▪ The core enzyme loves to do transcription, does it very quickly, lacks in specificity b/c its fast ▪ Therefore, sigma shows it the correct place to start, but it slows RNA polymerase down ▪ (5) Holoenzyme adds NTPs, but then stops, make 8-10 nucleotide RNA short pieces, then aborts and retries ▪ (6) sigma will leave the holoenzyme, initiation is complete ▪ After sigma leaves, core enzyme can carry out elongation Describe the elongation steps of prokaryotic transcription - correct answers o ▪ Core enzyme ▪ As RNA moves, the DNA strands will whip back together, therefore kicking the RNA in between the strands is kicked out of the way (which is fine b/c its bonded to the other RNA nucleotides) ▪ The RNA (which is no longer bound to DNA) can have ribosomes bound to it to start making proteins (b/c no membrane separating it like in eukaryotes) ▪ It can also take on other structures and bind to itself Describe the termination steps of prokaryotic transcription - correct answers ▪ Depends upon the structure that RNA has taken on after its been kicked out of the DNA ▪ Lollipop/stemmed loop structure formed by RNA ▪ Stem and loop structure are a necessary component of termination (help signal) What is the Rho-dependent termination signal? - correct answers ▪ Rho-dependent termination signal: G and C only in stem, not just Us on RNA after the stem - Rho wants to terminate transcription, but it needs to find RNA polymerase in the middle of transcription What is the Rho-independent termination signal? - correct answers : G and C only in the stem, following the stem and loop there are 6 Us - NusA is looking out and will pause the RNA polymerase o If there is an abrupt stop b/c of NusA, RNA polymerase isn't as stable (kind of like whip lash) What is the function of NusA? - correct answers - NusA will recognize the sequence and make the RNA polymerase pause What determines how prokaryotic transcription is stopped? - correct answers Rho dependent or Rho independent signal Rho-dependent termination - correct answers - Rho wants to terminate transcription, but it needs to find RNA polymerase in the middle of transcription o Rho binds to 5' end of RNA o Like a blood hound (tracker), uses the 5' end of the RNA to use as a trail until it finds the RNA polymerase o Problem: it is slow, no way it will catch the polymerase unless it is forced to pause (by NusA), then Rho can catch up o When Rho catches up, it will kick the RNA polymerase off o Rho binds when RNA is available (like if no ribosomes) Rho-independent termination - correct answers o NusA is looking out and will pause the RNA polymerase o If there is an abrupt stop b/c of NusA, RNA polymerase isn't as stable (kind of like whip lash) o Strong bonds in stem (C and G), but the 6 Us after are bound to 6 As on the DNA o H bond between RNA and DNA, RNA polymerase provides stability b/c H bond (between A and U) are weak o When the RNA polymerase is shaken up, this is enough to terminate transcription (in Rho dependent b/c of the A-U H bonding region) What are some differences between prokaryotic and eukaryotic transcription? - correct answers In prokaryotic transcription, ● RNA holoenzyme directly binds to DNA b/c has sigma ● Transcription not in nucleus (b/c they have no nucleus) No poly(A) tail or 5' cap In Eukaryotic transcription, ● Promoter- don't necessarily need all these pieces in every promoter ● RNA polymerase doesn't directly bind to the promoter (instead, transcription factors bind to the promoter) ● Transcription factors bind to recruit RNA polymerase ● -25 TATA box: recognition ● -70 to -80 (CAAT box) ● -110 (GC box) ● Problems: ● Transcription takes place in nucleus ● (1) Need mechanism to transfer RNA to cytoplasm (polyA tail) ● (2) Once in cytoplasm, RNA might be degraded, needs protection (polyA tail) ● (3) Need to specify where the ribosome attaches (7 methylguanisine cap, added at 5' end for ribosome binding) If 1 codon represented 1 nucleotides, - correct answers There would only be 4 combinations If one codon represented 2 nucleotides, - correct answers There would be 16 possible combinations If one codon represented 3 nucleotides - correct answers There would be 64 possible combinations Is the code degenerate? - correct answers Yes What did Nirenburg and Matthei study? - correct answers Synthesized RNA in the lab and used it to translate proteins and see what they got. 1st experiment: Use CCC--Pro Use AAA--Lys Use GGG--Gly Showed a correlation between a codon and an amino acid 2nd experiment 5A:1C randomly and predict who will be the most and least common codons AAA(most common) AAC, ACA, CAA CCA, CAC, ACC CCC(least common)