biology question and need an explanation and answer to help me learn. Instructions: Download this problem set, keep the questions in the document and please type your answers in a

biology question and need an explanation and answer to help me learn.
Instructions:
Download this problem set, keep the questions in the document and please type your answers in a color other than black so that your answers are easily discernable.
Complete this entire problem set ? give robust, detailed responses ? this is practice so use it as such.
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Complete the entire problem set. For grading, a problem or two will be randomly chosen for grading of 10 points and will be graded for completeness and originality worth 5 points; 15 points total.
Due date: Sunday, January by 11:59pm
Question 1: General Questions About Transcriptional Regulation
A. Explain whether RNA polymerase is a sequence-specific DNA-binding protein or not, and why the answer to this question is important for the process of transcription.
B. Explain the basic process by which transcription is controlled by transcription factors: what are transcription factors, what do they do, and how do they control transcription (you can keep this explanation general).
Question 2: Positive and Negative Control of Transcription
Explain the difference between positive and negative control of transcription as described in the lectures and notes for this topic.
Question 3: The lac Operon Regulatory System
In this topic, well use the lac operon in E. coli as an example of transcriptional regulation.
For this regulatory system, explain whether or not the (i) sigma factor (sigma 70), the (ii) lac repressor and the (iii) CAP protein are negative regulators of transcription, positive regulators of transcription or neither.
*Note that sigma factor is not considered a regulatory transcription factor (its a general transcription factor), but think about what it does and whether it fits into either one of these two categories as defined in Question 2.
Question 4: lacI Mutants
Researchers have studied mutants in the lacI gene to understand the function of the Lac repressor protein and how it regulates transcription at the lac operon in E. coli.
A. One of these types of mutants is a loss of function mutation in the Lac repressor protein (the protein is no longer functional). This is called a lacI- mutant. How would the lacI- mutant affect the function of the lac operon?
B. How well would lacI- mutants do in an environment that has lactose as its sole sugar source? Would it be able to survive if lactose were the sole energy source in the cell? Explain your reasoning.
C. One of those types of mutants is called LacIS mutants (S? stands for super-repressor). These repressor proteins continue to bind to the operator in the lac operon promoter, even in the presence of the inducer (i.e. lactose). How would the lacIS mutant affect the function of the lac operon?
D. How well would lacIS mutants do in an environment that has lactose as its sole sugar source? Would it be able to survive if lactose were the sole energy source in the cell? Explain your reasoning.
E. What would happen if there were a loss of function in the sigma70 binding site in the lacI promoter? What effect would this have on regulation of the lac operon?
Question 5: cAMP Regulation of the lac Operon
Describe how cAMP regulates the lac operon and why it makes sense that both lactose (directly) and glucose (indirectly) affect the transcription levels of this operon.
Question 6: lac operon Mutants
Researchers create mutations to understand how processes like transcriptional regulation work in the cell. This is certainly true for the lac operon, which was one of the first transcriptional regulation systems studied in cells.
You are given 6 mutants in E. coli, which carry one or more mutations in the lac operon or the lacI gene.
For each strain, indicate whether the lacZ gene product (B-gal) will be expressed in the presence of lactose and whether it will be expressed in the absence of lactose. Explain your reasoning in each case.
A plus? superscript indicates normal functioning part of operon or repressor gene
A minus? superscript indicates loss of function
P? region is where the RNA polymerase binds (sigma70 binding site)
O? is the operator
I? is the lacI gene
Z? is the lacZ gene
Oc? means operator-constitutive? mutant which means that the operator is mutated such that the repressor cant bind
Is? means super-repressor? which binds the operator, but doesnt bind lactose (so never dissociates from the operator)
Part I: A-F

A. I+P+O+Z+
B. IsP+O+Z+
C. I+P+OcZ+
D. I-P+O+Z+
E. IsP+OcZ+
F. I+P-O+Z+
Part II: In which of these mutant strains would you see low constitutive levels of expression (not completely off, but not fully on ? like a 3? on our scale from 0 to 10) in the absence of lactose and presence of glucose?
Question 7: Hypothetical Operon Transcriptional Regulation System
Now we are going to work on an example of transcriptional regulation at a different operon. This chromosomal region is in bacteria and contains two genes, fadA and fadB, which are necessary for the breakdown of oleic acid, a fatty acid energy source.
** Note that an operator? is a term used in prokaryotes to describe a binding site for a regulatory transcription factor, and that these transcription factors can be either negative or positive regulators.
The FadX protein, encoded for within the FadX gene, which sits just upstream of the FadAB operon, is continuously produced. It binds to the operator of the FadAB operon in the presence of oleic acid.
A. FadX is a regulator of transcription at this operon. Do you think that FadX serves as a repressor or an activator of this operon based on the information you are given in this question? Briefly explain your reasoning.
B. As described above, it is common to work with mutants to understand how regulation of transcription at this operon works.
For each of the following mutants (mutants 1-4), predict the level of FadA and FadB (low or high) in the presence of oleic acid. Explain your reasoning.
mutant1: O is deleted (meaning that the operator region of the promoter of the FadAB operon is no longer present)
mutant2: Loss-of-function mutation in the FadX gene
mutant3: P is deleted (meaning that the promoter region of the FadAB operon is no longer present)
mutant4: FadX is always bound to O (no matter what else is happening)
Question 8: Introduction to Eukaryotic Transcriptional Regulation
Eukaryotic transcription regulation with transcription factors works in very similar ways as compared to prokaryotes except for a few interesting differences. There is also some different terminology used?
A. What are the general transcription factors in eukaryotes? What are they called and how do they work?
B. Describe the terms enhancer?, silencer?, and promoter-proximal element? as it relates to eukaryotes transcription regulation. Where do these DNA sequences reside in relation to the promoter(s) that they regulate? How is this different than the situation in prokaryotes?
C. An enhancer may increase the frequency of transcription initiation for its associated gene when? (indicate true or false for each finishing of the statement and explain your answer?)
A. ?it is located 10,000 nucleotides upstream of the genes core promoter.
B. …it is located 10,000 nucleotides downstream of the genes core promoter.
C. ?it is in a genes intronic region (the region of the gene that codes for an intron).
D. ?no promoter is present.
E. ?it causes looping out of the intervening DNA.
Question 9: A Hypothetical Eukaryotic Transcriptional Control System
Use the eukaryotic transcription regulation model for the following questions:??
?
A. What is the function of transcription factors B and C and why are they needed in this hypothetical model of eukaryotic transcription regulation?? Do they disrupt each others function if both are bound at the same time?
?
?
B. What is the function of transcription factors D and E and why are they needed in this hypothetical model of eukaryotic transcription regulation?? Do they disrupt each others function if both are bound at the same time?
?
??
C. Which gene(s) are expressed in skin cells?? Explain your reasoning for each gene (yes or no, explain).
?
D. A mutation occurs in Gene 1 that changes the ACGC binding site for Transcription Factor C (TF-C can no longer bind there). Which cell types would change their expression of Gene 1? Explain your answer for each cell type (yes or not, explain your reasoning).

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