hi, trying to understand the proccess of crebs cycle..

a. If Isocitrate dehydrogenase is inhibited by axcess of citrate, and alpha ketogluterate by axcess of Suc-CoA, what exactly happeneds with the already made citrate and Suc-CoA? do they go back to being Acetyl coA and Alphaketogluterate respectively (and also become into fatty acids, amino acids and purins)?

b. I also don't get how calcium signals for more production of Acethyl coA? who gets this signal? is that the Icam somthing...?

c. in HIF1 degradation in the proteosome, what exactly pVHL and PHD2 do? like what is done individually and what tougether?

d. does HIF1 stop crebs cycle? I only know it encourages anaerobic respiration.. so what proccess does it stop if so? is directly or indirectly?

e. is there any other important substances in the crebs cycle? i remember something said about Fumarate and Succinate is there something worth remembering?

thanks in advance, I am very very lost and my summery is just confusing me.

schematize the following passage:

Ketogenic diet is well known for rapid weight loss. The diet protocol restricts carbohydrate consumption to 30 gm per day for an 80 kg adult. In order to protect the lean body mass, the protein intake should fall between 1.2-1.7 gm per kg BW per day, less than that may cause a loss of lean muscles. The protein intake should be moderate as an excessive amount of protein is metabolized to convert into amino acids, which are required for gluconeogenesis high-fat diet results in the shift of metabolism, depleted levels of glucose and enhanced oxidation of fatty acids that form ketone bodies to provide energy. The use of electrolytes such as sodium and potassium is highly recommended for maintaining nitrogen balance with the preservation of the fuctional tissue in the body.

Samreen Aziz, and Hina Rehman. “Mechanism and Benefits of Ketogenic Diet for Weight Loss and Health.” Rewal Medical Journal, vol. 44, no. 4, 2019, pp. 880–882., http://www.rmj.org.pk/fulltext/27-1545295565.pdf?1583710925.

“Lactose repressor protein (LacI) utilizes an allosteric mechanism to regulate transcription in E. coli, and the transition between inducer- and operator-bound states has been simulated by targeted molecular dynamics (TMD). The side chains of amino acids 149 and 193 interact and were predicted by TMD simulation to play a critical role in the early stages of the LacI conformational change. D149 contacts IPTG directly, and variations at this site provide the opportunity to dissect its role in inducer binding and signal transduction. Single mutants at D149 or S193 exhibit minimal change in operator binding, and alterations in inducer binding parallel changes in operator release, indicating normal allosteric response. The observation that the double mutant D149A/S193A exhibits wild-type properties excludes the requirement for inter-residue hydrogen bond formation in the allosteric response. The double mutant D149C/S193C purified from cell extracts shows decreased sensitivity to inducer binding, while retaining wild-type binding affinities and kinetic constants for both operator and inducer. By manipulating cysteine oxidation, we show that the more reduced state of D149C/ S193C responds to inducer more similarly to wild-type protein, whereas the more oxidized state displays diminished inducer sensitivity. These features of D149C/S193C indicate that the novel disulfide bond formed in this mutant impedes the allosteric transition, consistent with the role of this

region predicted by TMD simulation. Together, these results establish the requirement for flexibility of spatial relationship between D149 and S193 rather than a specific D149-S193 interaction in the LacI allosteric response to inducer.” Biochemistry 48:4988.

(4 points) What is allosteric regulation?

(4 points) How does the lactose repressor protein (LacI) use an allosteric mechanism to regulate transcription?

(6 points) How do the side chains of amino acids 149 and 193, of the lactose repressor protein, play a role in the LacI conformational change.

(6 points) What would you predict would happen if either amino acid 149 or 193 were mutated?

CHAPTER 6 Multiphase Systems(Elementary princilples of Chemical Engineering 4th Ed)

6.88) Serine (Ser, molecular weight=105.1g/mol) is a non-essential amino acid (seeFootnote16) produced by fermentation. As with many other fermentation products, substantial downstream processing is required to meet specifications on product purity. Crystallization from an aqueous solution is useful in meeting those specifications. The following table shows how serine solubility in water varies with temperature:

(a) Prepare a plot of solubility as a function of temperature that can be used for interpolation.

(b) An aqueous solution of serine containing 60 g Ser/100 g H2O is pumped into a batch cooling crystallizer, and the temperature is reduced slowly to 10°C, causing the formation of crystals of the monohydrated salt Ser H2O.Using the given solubility data, estimate the mass of crystals produced per unit mass of feed solution and the fraction of serine fed that is recovered as crystalline product.

(c) The molecular structure of serine makes it much more hydrophilic than other amino acids, and therefore its solubility is about an order of magnitude greater than that of most other amino acids. The addition of methanol to reduce the solubility in the solution has been suggested. Experimental data show that the solubility of Ser as a function of methanol content is given by the correlation S/S₀ =exp(-4.8x_m)where x_m is the mass fraction of methanol in a methanol–water solvent mixture,S₀ (g/g solvent) is serine solubility in water at a given temperature, and S is the solubility in the methanol–water solvent. In an alternative to the processing scheme described in Part(b), sufficient methanol is added to the crystallizer after it has reached 10°C to produce a final solution that has a methanol-to-water mass ratio of 55:45, and the resulting system is allowed to come to equilibrium. Estimate the mass of crystals produced per unit mass of feed solution and the fraction of serine fed that is recovered as crystalline product.

Chymotrypsin serves as a catalyst in the "Hydrolysis" of pepdite bonds - found in carboxylic groups of amino acids, which consist of aromatic pedand groups and large hydrophobic groups. Chymotrypsin is also known to serve as a catalyst in the Hydrolysis of "ester - and amide bonds" , found in hydrophobic groups.

1. Would you expect the K_Mof the reactions of Chymotrypsin with the different substrates to have the same value ? explain your reasoning.

2. Would you expect the V_maxof the reactions of Chymotrypsin with the different substrates to have the same value ? explain your reasoning.

3. Would you expect the " pH-dependence " of the "hydrolysis - reactions" of the different substrates to be the same for all substrates ? explain your reasoning.

Given the non-template strand of DNA, draw the template strand with the 5' and 3' ends labeled. Draw the RNA molecule with the proper 5' and 3' ends labeled

Non-Template Strand: 3'- AAT GCT CGT AGC TTC GAT CGG ATC GA-5'

My answers: Template= 5'- TAT CGA GCA TCG AAG CTA GCC TAG CT-3'

RNA Molecule= 3'- AUA GCU CGU UGC UUC GAU CGG AUC GA-5'

Next it asks, how many amino acids would the RNA molecule code for? - how would I figure this out?

Superoxide dismutase is a very unique protein. It is the only protein that can catalyze faster than the rate of diffusion, which is usually a limiting rate for proteins since you cannot catalyze something faster than the amount of time it takes for your substrate to arrive at the active site. However, superoxide dismutase is able to do this. If you look at a diagram of superoxide dismutase, you will find a large cluster of basic amino acids surrounding the active site where the substrate binds. First, state the purpose of superoxide dismutase and what its substrate is. Then discuss how you think superoxide dismutase is able to have a kcat/Km that is faster than the diffusion limit.

The role of Voltage Sensitive Na⁺ Channels (VSSC in neuron signaling) is:             

a) Initiation of depolarization   

b) propagation of depolarization       

c) space from an axonal membrane of a neuron to dendrite membrane of next neuron                

d) release of neurotransmitter

ATP production during aerobic respiration is by which mechanism:       

a) substrate level phosphorylation   

b) oxidative-phosphorylation  

c) both substrate-level and oxidative-phosphorylation  

d) This depends upon the temperature

e) this depends upon the pH

ATP production during glycolysis is by which mechanism:

a) substrate-level phosphorylation   

b) oxidative-phosphorylation  

c) both substrate-level  and oxidative-phosphorylation  

d) this depends upon the temperature

e) this depends upon the pH

Which is not a postulate of cell theory:

a) all life is made of cells

b) heredity is controlled by genes

c) all cells come from pre-existing cells   

d) all cells are microscopic  

If a molecule has a molecular weight (mw) of 3,685 daltons (Da), then how many grams are required to make 1.0 mole:

a)  3,685 g   

b) 368.5 g   

c) 36.85 g    

d) 3.7 g

Questions 9 to 13 are in reference to the DNA sequence shown in Question 8.

Here is Question 8.

Question 8:

The top strand of the following segment of DNA serves as the template strand:

3’ TACACCTTGGCGACGACT 5’

5’ ATGTGGAACCGCTGCTGA 3’

We will refer to this segment of DNA as the original (or unmutated) sequence.

Please answer the following questions:

(a) What is the mRNA sequence?

The mRNA sequence is  5'  3'.

**Please enter your sequence in the 5' to 3' direction. Deductions will be made if a sequence is inputted in the wrong direction.**

(b) Using the mRNA sequence you determined in part (a) of this question, give the sequence of the protein that would be translated.

The amino acid sequence for this protein is N-terminus  C-terminus.

**Please note**

The N-terminus refers to the beginning of the primary sequence for a protein, and the C-terminus refers to the end of the primary sequence for a protein.

i.e. input the amino acids in the order that they would be translated.

If a codon encodes for a stop codon, type STOP.

When inputting your sequence, separate each amino acid with a hyphen (e.g. Ser-Tyr-STOP).

You will need to consult the genetic code to answer this question.

Question 10:

The original (unmutated) DNA sequence (shown above in Question 8) has been mutated to the following (this represents the template strand):

3’ TACGACCTTGGCGACGACT 5’

We will refer to this sequence as mutation #2.

Please note that for simplicity only the template strand for this mutated segment of DNA is shown.

Answer the following questions:

(a) What is the complete mRNA sequence for the mutated segment mutation #2?

The mutated mRNA sequence is  5'  3'.

**Please enter your sequence in the 5' to 3' direction. Deductions will be made if a sequence is inputted in the wrong direction.**

(b) Using the mRNA sequence you determined in part (a) of this question, give the sequence of the protein that would be translated.

The amino acid sequence for this protein is N-terminus  C-terminus.

**Please note**

The N-terminus refers to the beginning of the primary sequence for a protein, and the C-terminus refers to the end of the primary sequence for a protein.

i.e. input the amino acids in the order that they would be translated.

If a codon encodes for a stop codon, type STOP.

When inputting your sequence, separate each amino acid with a hyphen (e.g. Ser-Tyr-STOP).

You will need to consult the genetic code to answer this question.

4 points   

QUESTION 11

Questions 9 to 13 are in reference to the DNA sequence shown in Question 8.

Question 11:

The original (unmutated) DNA sequence (shown above in Question 8) has been mutated to the following (this represents the template strand):

3’ TACACCTTAGCGACGACT 5’.

We will refer to this sequence as mutation #3.

Please note that for simplicity only the template strand for this mutated segment of DNA is shown.

Answer the following questions:

(a) What is the complete mRNA sequence for the mutated segment mutation #3?

The mutated mRNA sequence is  5'  3'.

**Please enter your sequence in the 5' to 3' direction. Deductions will be made if a sequence is inputted in the wrong direction.**

(b) Using the mRNA sequence you determined in part (a) of this question, give the sequence of the protein that would be translated.

The amino acid sequence for this protein is N-terminus  C-terminus.

**Please note**

The N-terminus refers to the beginning of the primary sequence for a protein, and the C-terminus refers to the end of the primary sequence for a protein.

i.e. input the amino acids in the order that they would be translated.

If a codon encodes for a stop codon, type STOP.

When inputting your sequence, separate each amino acid with a hyphen (e.g. Ser-Tyr-STOP).

You will need to consult the genetic code to answer this question.

4 points   

QUESTION 12

Questions 9 to 13 are in reference to the DNA sequence shown in Question 8.

Question 12:

(1 mark each)

In reference to the original sequence (shown in Question 8), classify each type of mutation present from Questions 9 to 11. Choose the best option for each.

QUESTION 13

Questions 9 to 13 are in reference to the DNA sequence shown in Question 8.

Question 13:

Most mutations have a neutral effect on the phenotype, function or survival of an organism because they do not elicit any noticeable change. Whereas other mutations can have a positive effect on an organism leading to new versions of proteins that help an organism adapt to changes in its environment; while other mutations can have a negative effect on the organism and result in a protein that does not function normally or at all.

Answer the following questions based on the responses you gave above in Questions 8 to 12.

(a) Based on the protein sequences that were produced as a result of mutation #1, mutation #2, or mutation #3, describe the effect, if any, these mutations would likely have on the function of the protein within the cell. Support your answer.

(b) If these mutations occurred within a germline cell and not a somatic cell, how would the effects of these mutations differ?