1. You have the following prokaryotic DNA sequence: 5-GGACTAGACAATAGGGACCTAGAGAT
ID: 94897 • Letter: 1
Question
1. You have the following prokaryotic DNA sequence: 5-GGACTAGACAATAGGGACCTAGAGATTCCGAAA-3 3-CCTGATCTGTTATCCCTGGATCTCTAAGGCTTT-5 If the top strand is the template strand which sequence below is the correct mRNA transcript? A. 5-GGACUAGACAAUAGGGACCUAGAGAUUCCGAAA–3 B. 5'-UUUCGGAAUCUCUAGGUCCCUAUUGUCUAGUCC-3' C. 5'-CCUGAUCUGUUAUCCCUGGAUCUCUAAGGCUUU-3' D. None of the above are correct
2.Starting in the cytoplasm with a fully mature mRNA explain the process of translation initiation and then elongation and termination to me.
3.Prior to export from the nucleus, pre-mRNA must be processed. What specifically does this entail?
4.The biosynthetic pathway for the two amino acids E and H is shown schematically in the figure. You are able to show experimentally that E inhibits enzyme V, and H inhibits enzyme X. The most logical hypothesis regarding the regulation of Enzyme T would be that it is most likely subject to feedback inhibition by E alone. True or False?
5. A. kinase B. ligase C. polymerase D. oxido-reductase E. Phosphatase F. protease G. nuclease H. ATPase 1. Removes a phosphate group from a molecule 2. Hydrolyzes ATP 3. Hydrolyzes bonds between nucleotides 4. Adds phosphate groups to molecules 5. Catalyzes reactions in which one molecule is oxidized and another is reduced 6. Hydrolyzes peptide bonds 7. Joins two ends of DNA together 8. Catalyzes the synthesis of polymers such as RNA and DNA
6. Looking at the figure showing the change in reaction rate for two different enzymes that both utilize the same substrate, answer the following questions. a. What is the approximate Vmax for enzyme B ? b. What is the approximate Vmax for enzyme A ? c. What is the approximate Km for the enzyme which has a higher affinity for the substrate uM.
7. Answer the following question either yes or no (spell out the word, do not abbreviate as y or n). Looking at the following coupled reaction: Luciferase luciferin + O 2 ==========> oxyluciferin + light G = + + Mg2+ ATP <=> AMP + PPi G = - - - a. Based on your knowledge of free energy change and reactions would this coupled reaction occur ? b. Would changing the second step from ATP<=> AMP + PPi G = - - - to ATP <=> ADP + Pi G = - change your answer
7.Spontaneous reactions by definition will happen instantaneously. Why false?
8. Each of the following questions apply to the image of the channel protein. The purple sphere is a charged ion. Type your response to each question in the blank provided. a. Based you on what you know about cells and ions, what does the tri-lobed red and white molecule represent (although there aren't anywhere near enough of them shown) ? b. Since the question stated the purple sphere was a charged particle, using what you know about the tri-lobed red and white molecule what is the charge of the purples sphere c. On the extracellular space, on the right side of the purple sphere, there are two tri-lobed red and white molecules in close proximity to one another. The red of one appears to be attracted to the white of the other. What type of bond is this ? d. Based on your knowledge of proteins that interact with the membrane and the properties of the membrane, to what family of amino acids would the amino acid marked by A. most likely belong? ?
Explanation / Answer
1. Option C is correct. The mRNA synthesized from DNA is the complimentry of the tempelate strand with the occurance of uracil instead of thymine. Hence option c is correct.
2. Translation can be categorized into three stages: I. Initiation II. Elongation and III. Termination
I. Initiation: This is the first phase of translation. Start or initiation codon [AUG] is responsible for initiation of translation process. Initiation of translation involves the assembly of the components of the translation system which are: the two ribosomal subunits (small and large), the mRNA to be translated, the first (formyl) aminoacyl tRNA (the tRNA charged with the first amino acid), GTP (as a source of energy), and three initiation factors (IF 1, IF 2 and IF 3) which help the assembly of the initiation complex.
II. Elongation: This is the second phase or middle phase of translation. Elongation begins after the formation of the initiation complex. Elongation of the polypeptide chain involves addition of amino acids to the carboxyl end of the growing chain. The growing protein exits the ribosome through the polypeptide exit tunnel in the large subunit.Elongation starts when the fmet-tRNA enters the P site, causing a conformational change which opens the A site for the new aminoacyl-tRNA to bind. This binding is facilitated by elongation factor-T4 (EF-T4), a small GTPase. Now the P site contains the beginning of the peptide chain of the protein to be encoded and the A site has the next amino acid to be added to the peptide chain.
III. Termination: This is the last phase of translation. Termination occurs when one of the three termination codons moves into the A site. These codons are not recognized by any tRNAs. Instead, they are recognized by proteins called release factors, namely RF1 (recognizing the UAA and UAG stop codons) or RF2 (recognizing the UAA and UGA stop codons).These factors trigger the hydrolysis of the ester bond in peptidyl-tRNA and the release of the newly synthesized protein from the ribosome. A third release factor RF-3 catalyzes the release of RF-1 and RF-2 at the end of the termination process.
3. Since the DNA is transcribed into mRNA in the nucleus, and protein synthesis takes place in the cytoplasm, the mRNA has to exit the nucleus to the cytoplasm. The environment in the nucleus differs in many ways from that of the cytoplasm. To separate these two environments from each other the nucleus is enclosed by a double membrane, and the only connection to the surrounding cytoplasm is through channels called the nuclear pore complex (NPC).When it is time for the mRNA to leave the nucleus, the mRNA is believed to be "tagged" by proteins (Ran protein) which serve as export signals, directing the mRNA to the nuclear pore complex that the mRNA is to leave. The mRNA and it's bound export proteins then attaches to export receptors and the whole complex (RNA, export signal proteins and export receptors) is translocated through the nuclear pore complex. The mRNA is released into the cytoplasm and is immediately ready for the next step.
5. A. Kinase: Adds phosphate groups to molecules
B. Ligase: Joins two ends of DNA together
C. Polymerase: Catalyzes the synthesis of polymers such as RNA and DNA
D. Oxidoreductase: Catalyzes reactions in which one molecule is oxidized and another is reduced
E. Phosphatase: Removes a phosphate group from a molecule
F. Protease: Hydrolyzes peptide bonds
G. Nuclease: Hydrolyzes bonds between nucleotides
H. ATP ase: Hydrolyzes ATP
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