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70 Cards in this Set
- Front
- Back
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In Griffith's transformation experiment, he heat killed the S strain, mixed it with a small number of R strain cells and injected a mouse. What happened to the mouse?
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it died
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What type of cell was isolated from the mouse's lung?
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S cells
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If Griffith had heat killed the R strain and mixed it with a small amount of S strain cells, what would you predict happen to the mouse?
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It would die
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What type of cells would you expect to find in the mouse's lung?
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S cells, the R cells would be destroyed by the immune system.
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If this second experiment were done in vitro, and the cells plated on media, what types of colonies might you expect to find?
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Mostly smooth colonies, but a few R colonies as well.
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Amino acids form building blocks for proteins. Using the one letter code, name the acidic amino acids and state what functional group makes them acidic.
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D, E, carboxyl group
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Using the one letter code, name the polar amino acids and state what functional group makes each amino acid polar.
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S, T, Y: hydroxyl group.......Q, N; amide group
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All amino acids except glycine are stereoisomers in the L configuration. What is different about glycine in this respect?
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It has two hydrogens attached to the C-alpha, so its not a chiral center.
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All amino acids except glycine are stereoisomers in the L configuration. What is different about glycine in this respect?
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It has two hydrogens attached to the C-alpha, so its not a chiral center.
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Cysteine is also unique in its own way. What makes cysteine different from the rest of the amino acids?
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It can be oxidized when two cysteines are close to form a disulfide bond.
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RNA plays a key role in gene expression. Name three advantages for an RNA as an intermediate during gene expression.
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Regulate amount of expression. Allows an amplification step. Allows formation of alternative forms of a protein through alternative splicing.
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Name three ways in which the structure of RNA differs from DNA.
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single stranded instead of double stranded. Ribose instead of deoxyribose. Uracil instead of thymine.
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All amino acids have a C-alpha carbon. What are the four groups that are attached to the C-alpha carbon?
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Hydrogen, amino group, carboxyl group, side chain.
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What is unique about proline in regards to the C-alpha carbon?
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Its side chain is covalently linked to the amino group preventing free rotation around the C-alpha.
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What is unique about glycine with regards to the C-alpha carbon?
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Since its side chain is a hydrogen, the C-alpha is not a chiral center.
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Why are the -10 and -35 regions of prokaryotic promoters conserved?
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This is the site at which sigma factor interacts directly with the DNA. Since most promoters are bound by the same holoenzyme, the sequence in this region is conserved.
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RNA synthesis involves a nucleophilic attack. What acts as the nucleohile and what is attacked?
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The 3'OH on the first nucleotide (or growing chain) acts as a nucleophile and attacks the first phosphate attached to the 5"C on the incoming nucleoside triphosphate.
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For each of the growth condition listed, what proteins would be bound near the lac promoter? Glucose?
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lac repressor
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lactose
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CAP-cAMP
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glucose + lactose
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no proteins bound
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For the lac operon, distinguish between a substrate and an inducer.
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A substrate is any molecule that is hydrolyzed (or converted to product) by beta-galactosidase, such as lactose, ONPG, and XG. An inducer is any molecule that can bind to lac repressor and induce conformational change, such as allolactose and IPTG. (alternatively an inducer is any molecule that can lead to an increase in transcription.)
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RNA functions in many key steps in both translation and splicing. How is binding of the small ribosomal subunit to the Shine-Delgarno sequence facilitated by RNA?
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The RNA sequence at the end of the 16S rRNA is complementary to the shine-dalgarno sequence. Therefore, the 30S recognition of the S-D sequence is through base pairing.
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What is another step in translation where RNA is centrally involved?
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Catalysist of the peptide bond.
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List the similarities of the DNA double helix and the alpha-helix.
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Both right handed, both held together by hydrogen bonds, both form independent of sequence.
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List the differences between the DNA double helix and the protein alpha-helix
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protein single strand, DNA double strand, H-bonds parallel to axis in protein, H-bond perpendicular to axis in DNA, R-groups stick into the helix in DNA, alpha helix rigid, DNA is flexible.
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Describe the composition of the eukaryotic nucleosome
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2 of each...H2A, H2B, H3, H4
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What types of post translational modifications can be found on nucleosomes or cucleosomal proteins?
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methylation, acetylation, phosphorylation, (optional ubiquitination, adenylation.
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Whats the purpose of these modifications?
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Provide binding site for proteins, modulate how tightly DNA binds to histones.
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What are the three fundamental differences between RNA and DNA?
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ribose instead of deoxyribose, uracil instead of thymine, single stranded instead of double stranded, complex secondary structure.
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How can RNA folding express gene expression?
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Attenuator, Riboswitch
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Describe Attenuation
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Two alternative stem loops can form in the leader region, one of these is a rho-independent terminator. Which structure forms is dependent on translation of a leader peptide which contains two or more codons for the amino acid that the genes in the operon are responsible for synthesizing. When the amino acid is plentiful, the ribosome does not pause and the terminator stem loop forms causing termination. When the amino acid is in low supply, the ribosome pauses at the aa codons allow the alternative structure to form and the full length mRNA to be synthesized.
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Describe Riboswitch
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Two alternative stem loops can form in the leader region, one of these is a rho-independent terminator. Which structure forms is dependent upon binding of a small molecule to the aptamer.
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RNA is inherently less stable than DNA. What is the basis of this instability and under what conditions does RNA degrade?
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2' OH, under basic conditions it can attack the P and break the phosphodiester bond.
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Name the radioactive precursor or molecule that could be used to label specifically DNA.
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3H-thymine, 14C-thymine
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Name the radioactive precursor or molecule that could be used to label specifically RNA.
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3H-uracil, 14C-uracil
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Name the radioactive precursor or molecule that could be used to label specifically proteins.
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35S-methionine, 3H-methionine, 14C-methionine
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If you wanted to label RNA in vitro with 32P-CTP, would you want the 32P in the alpha, beta, or gamma phosphate?
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alpha phosphate, since on the alpha phosphate remains after the phosphodiester bond is formed. (CTP is not used to start proteins.)
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When egg whites are cooked, they harden. This process can be reversed by heating the hardened egg white in a solution with a strong detergent such as SDS and B-mercaptoethanol. Neither agent alone has any effect.
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2 questions
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Why do you suppose heating egg whites cause them to harden?
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The proteins denature and their Cysteines become oxidized. This causes disulfide bonds to form and create a network much like acrylamide.
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Why does it require both a detergent and a reducing agent to dissolve the hardened egg whites?
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The reducing agent breaks the disulfide bonds and the detergent coats the denatured proteins allowing them to go into solution.
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It is a common observation that antiparallel strands in B-sheet are connected by short loops, but parallel strands are connected by alpha helices. Why do you think this is?
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A polypeptide can fold back on itself to form two B-stands that are antiparallel, requiring only a short loop at the end. For the same polypeptide to form parallel strands it has to fold back from one end of the strand to the other. This is sufficient distance to allow and alpha helix to form.
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RNA pol in bacteria are faily simple enzymes compared to their eukaryotic homologs. What are the names of the subunits found in the core enzyme?
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B, B', alpha-2, w
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The addition of what subunit creates the holoenzyme?
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sigma
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Why is the replacement of this last subunit under special conditions considered a form of regulation?
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Different sigma factors recognize different sequences, so when sigma-70 is replaced with a different sigma factor, it will transcribe a different set of genes.
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Consider an E.coli cell growing in each of the following media. For each operon, state which activators or repressors would be bound and what level of transcription would be (basal, repressed, activated)
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ready...
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Lac Operon (arabinose as sole carbon source, and tryptophan as an added supplement)
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CAP-cAMP, lac repressor, repressed
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Trp operon (arabinose as sole carbon source, and tryptophan as an added supplement)
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Trp repressor (plus trp), repressed
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AraBAD operon (arabinose as sole carbon source, and tryptophan as an added supplement)
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CAP-cAMP, AraC-arabinose, activated
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Lac operon (glucose, lactose)
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no proteins bound, basal
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Trp (glucose, lactose)
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no proteins bound, basal
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AraBAD operon (glucose, lactose)
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AraC bound as a repressor.
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Lac operon (lactose, arabinose)
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CAP-cAMP, activated
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Trp operon (arabinose, lactose)
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no proteins bound, basal
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AraBAD operon (lactose, arabinose)
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CAP-cAMP, AraC-arabinose as activator, activated.
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Supose you added the following RNA to in vitro translation system: 5'-AUGUUUUUUUUUUUU-3'. What polypeptide would be synthesized if UUU=phe?
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met-phe-phe-phe-phe
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If you added a drug to your translation system that locked formation of the 70S ribosomal complex, what product would you get?
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none
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If you added a drug to your translation system that block translocation, what product would you get?
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met-phe
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Describe an example discussed in class involving regulation of translation initiation.
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Some riboswitches alternate between two structures depending on binding of a small molecule to the aptamer. In one configuration, translation initiates normally, in the alternative form, ribosome binding site is involved in a stem loop structure and unavailable to interact with the 16S rRNA.
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How does the ribosome distinguish between an internal AUG and one that signals the start of an ORF?
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The ribosome only initiates protein synthesis at AUG which are preceded by a ribosome binding site. This sequence base pairs with the 1S rRNA and positions the AUG in the P site of the ribosome.
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Why is the Met on the initiator tRNA modified with a formyl group?
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The formyl group mimics a peptide bond and makes the interaction at the P site stronger.
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For each of the reactions, name he atom that acts as a nucleophile and the atom it attacks.
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ready....
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Phosphodiester bond formed during RNA synthesis
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nucleophile 3'O, attacks the alpha phosphate of the nucleotide triphosphate.
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Peptide bond formed during protein synthesis.
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nucleophile: N from the amino terminus, attacts the C of the carbonyl group attached to the tRNA.
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Charging of tRNAs is coupled to ATP hydrolysis. What portion of the ATP is transferred to the amino acid in the first step of the reaction?
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AMP
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Distinguish between the pairs
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ready...
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Gene and genome
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A gene is all the information required to synthesize a prtotein or RNA (includes promoter, 5'UTR, ORF, 3'UTR, termination signal. A genomes is all the genetic information for a given species.
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Translation and translocation
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Translation is the process of synthesizing proteins from an mRNA template. Translocation refers to the movement of the ribosome one codon at a time down the mRNA.
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Hybridization and renaturation
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Hybridization is when DNA from two different sources anneal together. Renaturation is when DNA that has been denatured anneals together.
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Motif and domain
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Motif is a small structure that has specific function and is found in many proteins. Domain is either an independently folding region of a protein or a region that has a defined function (or both).
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Antibody and enzyme
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An antibody is a protein that binds an antigen extremely tightly (high affinity). An enzyme is a protein that catalyzes a reaction.
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