Question

3. Nitrogen Fixation is a process by which some bacteria can convert N2 into ammonia. This process is very important in making the element nitrogen, a component of amino acids and nucleotides, available to ecosystems. Even though N2 makes up 80% of the atmosphere, nitrogen is the limiting nutrient in many ecosystems. Because nitrogen fixation is so energetically expensive, bacteria will only synthesize the proteins needed for this process if there is no available source of already fixed nitrogen, such as ammonia, nitrate, or proteins. Some bacteria use the concentration of glutamine, an amino acid with N in its R group, to help judge whether they are nitrogen starved or not. The concentration of glutamine goes down rapidly in a cell that is not taking in enough nitrogen. Your first task is to create models (i.e. hypothetical systems that might exist) for how a N2 fixation operon might be regulated. Imagine that you have an operon that consists of a promoter, operator, and the structural genes nifH, nifD and nifK. Part 1: Draw and explain three different models. Model 1 should involve a DNA- binding protein that acts as a negative regulator, and Model 2 should involve a DNA-binding protein that acts as a positive regulator. Model 3 should involve an RNA molecule that has a 5' UTR that can directly bind to an effector and regulate translation. In each case, state what the effector molecule is, what it does, and whether the operon will be transcribed and translated. State this separately for when the cells are exposed to nitrogen -rich and nitrogen-poor environments. (9 pt)

Answer 1

Answer:                 This question i have to write pointswise because it's easy to understand you...

Model 1:

• In this model, a regulatory protein nihA, is always bound to the operator region of the nih operon.
• Glutamine is the effector molecule.
• nihR uses Glutamine as a co-repressor. When cells are in nitrogen-rich environments, Glutamine levels are high.
• In this scenario, Glutamine remains bound to nihA and nihA-Glutamine bind to the operator, preventing transcription and translation.
• In Nitrogen-poor conditions, Glutamine levels are low and enough Glutamine is not present to bind to nihA.

• Thus, nihA is unable to bind to the operator region of the nih operon and transcription and translation are allowed to proceed.

Model 2:

• In this model, nihB is a constitutively expressed positive regulator of the nih operon. nih senses Glutamine levels (Glutamine is the effector molecule).
• When Nitrogen is sufficient, Glutimine binds to nihB and prevents nihB from binding to the promoter of the nih operon and recruiting RNA polymerase.
• However, under low-Nitrogen conditions, nihB is not bound by Glutamine, and binds the Promoter sequence of the nih operon.
• nihB then recruits RNA polymerase to initiate transcription and translation.

Model 3:

• In this model, Glutamine acts as an effector molecule by binding to the 5' Leader Sequence present in the operator site of the nih operon.
• When the cell is in a Nitrogen rich environment, Glutamine levels are high. In this environment, Glutamine binds to the Leader sequence downstream of the promoter and promotes the formation of an hairpin structure that inhibits translation by ribosomes.
• Here, transcription is constant, but protein is not produced.
• When Nitrogen is low, no hairpin structure is formed at the leader sequence and transcription and translation continue.

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