Question 1 (Chapter 1 Exercise 2)

One important exercise a bioinformatician performs is to compare amino acid sequences. One reason to make comparisons is to determine the parts of the proteins that are critical for function. These regions are generally conserved within proteins that perform the same duties. Conserved regions are those that have nearly the same amino acid sequences. Proteins that perform the same duties are called homologs and can be found in different species. For example, p53 from humans and p53 from frogs perform the same functions. There are some regions within these proteins that will be similar in both humans and frogs. We call these regions conserved sequences. A multiple sequence alignment allows the bioinformatician to readily line up amino acid sequences of related proteins. The conserved regions are identified in the alignment. For this exercise, perform a multiple sequence alignment of three homologs of cytochrome C. The three homologs are from human, yeast, and dog, and the accession numbers for these sequences are AAA35732, NP_001183974, and 1YCC. The first two sequences can be found in the protein database at the NCBI. The last sequence can be found in the structure database at the Protein Data Bank. ***Print out your multiple sequence alignment result and attach a short paragraph. EXPLAIN how the alignment gives you a clue as to which parts of the cytochrome C protein are MOST important to its function.*** (The function is the same in all three organisms.)

For those of you unfamiliar with NCBI, here are specific instructions:

Go to the NCBI website.

Use the dropdown menu to search in the “Protein” database.

Enter the accession number and click “Search.”

Change the format to FASTA.

Copy the FASTA output into a sequence alignment window of a website that hosts a sequence alignment program. Make sure the header (the line with the > symbol) is placed on top of the sequence within the window.

Repeat for each FASTA output of the remaining two proteins.

Once all three sequences are pasted into the sequence alignment input window, run the program

***please help I starred the portion in the paragraph that I do not know how to answer.

11. In healthy individual, which two events are likely to occur at the same time?

a. Glycogenesis and gluconeogenesis

b. Lipolysis and increased plasma glucagon levels

c. Release of fatty acids from the adipose tissue and increased plasma insulin levels  

13. Why is the liver less likely to produce ATP from fatty acid oxidation?

a. The liver prefers to oxidize glycogen stored in the tissue

b. Oxaloacetate levels in the liver is too low to produce ATP from fatty acids

c. Access to fatty acids in the liver is limited due to the absence of a fatty acid transporter

Describe the fate of a single molecule of glucose as it goes through glycolysis and exits the Krebs cycle. Include the inputs to each reaction and all end products including all created energy storage molecules.

I have to write out a lab plan for an upcoming experiment! and complete the table below

Experiment 9: Introduction to Acids, Bases, and pH Learning

Objectives

» to gain experience with a wide variety of acids and bases

» to learn how to predict the principal species in a solution

»to learn how to measure acidity, basicity, and pH

» to predict what will happen when different acid and base solutions are mixed

Be sure to record all data in your own notebook. Materials Lots of acids and bases in various concentrations, litmus paper, well plates and pH meters.

Introduction to Acids and Bases Acids and bases are all around us. They are present in the fruits and vegetables we eat, in the sodas we drink, and in the various commercially available products that we use to unclog our kitchen sinks! Acids are characterized with respect to their ability to produce hydronium ions (H3O + ). Bases are characterized with respect to their ability to produce hydroxide ions (OH– ). Both acids and bases can be classified as “strong” or “weak,” which are allusions to whether the species is a strong electrolyte (placing many ions in solutions, see (1) below) or a weak electrolyte (placing a small number of ions in solution, see (2), below). (1) HCl(aq) + H2O()  H3O + (aq) + Cl (aq) Production of hydronium ion by a strong acid (2) NH3 (g) + H2O() NH4 + (aq) + OH (aq) Production of hydroxide ion by a weak base Strong acids produce large amounts of hydronium ions because their reaction with water goes essentially to completion, thus producing a stoichiometric number of ions. Weak acids react with water in the same type of proton-transfer process, but the equilibrium constant is not as large and only a minimal number of ions are created. The same can be said for strong and weak bases with respect to the amount of hydroxide formed. The chemical structure of the acid or base plays a large role in its ability to lose or attract a proton. 9-2 Introduction to Acids, Bases and pH In order for you to predict the principal species in solution, you must know if a particular acid or base is strong or weak. It is best to just memorize the strong ones: Strong Acids HCl hydrochloric acid HBr hydrobromic acid HI hydroiodic acid HNO3 nitric acid HClO4 perchloric acid H2SO4 sulfuric acid Strong Bases NaOH sodium hydroxide KOH potassium hydroxide Strong acids and strong bases are strong electrolytes; their principal species in solution are the fully dissociated ions – H3O + , Br– NO3 – , ClO4 – , HSO4 – , Na+ , K+ , OH– , etc. IT IS CRITICAL THAT YOU MEMORIZE THE NAMES AND FORMULAS OF THESE STRONG ACIDS AND BASES AND ALSO KNOW WHAT IONS THEY PRODUCE. DO IT NOW. Pretty much anything else that has a name that ends with “acid” – hydrofluoric acid, acetic acid, formic acid, nitrous (rather than nitric) acid, phosphoric acid, etc. – is a weak acid. Just about anything else containing nitrogen in it is a weak base. Weak acids and weak bases are weak electrolytes. Their principal species in solution is just themselves. The lower the pH of a solution, the more acidic it is. Conversely, the higher the pH of a solution, the more basic it is. A pH of 7 indicates that the concentrations of H3O + and OH– are equal; such solutions are called “neutral.” Acids and bases react with each other to form neutral solutions with salts and water as the products. (Can you write the reaction equation between HCl and NaOH?) Salts in solution will also form acidic, basic or neutral solutions depending on the properties of the ions. This will be apparent in some of the work carried out in today’s experiment.

Procedures Part 1: Acid, Base, or Neutral?

Types of substances in this table include neutral salts, strong acids, strong bases, weak acids (might be a salt), and weak bases (might be a salt). Water is present in large quantities in any aqueous system, so you need not list H2Omolecules as a principal species.

Solution Type of Substance Principal Specie(s) in Solution Prediction Measured pH

a 0.1 M HCl Strong acid H3O + , Cl– acidic

b 0.1 M H3PO4 Weak acid

c 0.1 M CH3CO2H Weak acid

d 0.1 M NH4Cl Salt (acidic) NH4 + , Cl–

f 0.1 M NaCl Salt (neutral) Na+, Cl– neutral

g 0.1 M NaO2CCH3 Salt (basic)

h 0.1 M NH3 Weak base NH3

i 0.1 M NaOH Strong base

When you get to lab, discuss your predictions with your partner and try to come to a consensus on your best guesses. Then measure the pH of each solution using a pH meter (Read the pH Meter Blue Pages! The use of these meters will also be demonstrated for you.) Record your predictions and observations in tabular form in your notebook. Note any surprises, as you will need to explain them later!

In an imaginary pathway the intermediate E is a substrate of both enzyme 1 and enzyme 2, creating products F and G respectively. Intermediate E is present at 1.2 mM and the Km values for this substrate for enzymes 1 and 2 are 0.2 mM and 3 mM respectively.

Question: What would the effect of an increase in the concentration of E have on the relative populations of the products F and G?

1. Only the population of G would increase as enzyme 1 is already working a maximum.
2. Both F and G would increase to equal amounts of each product.
3. Both F and G would increase but the amount of F would be greater than G
4. You cannot predict the relative populations of F and G from the information given.

Carboxylic Acids. Lipids are a macromolecule we need to survive and many of them happen to contain carboxylic acids. Choose one lipid - could be a particular steroid, fatty acid, or tri-glyceride and discuss its structure and potential reactivity. please cite on source using APA citation format.

Two persons differ in several SNPs (single nucleotide polymorphisms), however, after their proteins are compared, you realize that only some SNPs induce changes in amino acid sequence. What is going on here? How come some SNPs induce amino acid change while others don't? (GENETICS QUESTION)

Does AUG occur only at the start of a protein?  How can a ribosome “know” which AUGs represent start codons? What is the actual link between the amino acid and the mRNA molecule? (IOW=What are the “translating” tools that translate RNA language into amino acid(protein) language?hint#2=there are 64 of them)

(a) Derive a Maxwell relation from the exact differential da = edx + gdy.

(b) A gas container is separated by a partition and the volume of the left side is half of the volume as of the right side. The left column is filled with a 1 mole of helium gas and 2 moles of argon can be found in the right column. Consider that the system is thermally isolated, calculate the change in entropy using appropriate Maxwell relation under ideal gases.

3 reservoir problem

Reservoir A: 150m

Reservoir B : 125m

Reservoir C : 75m

The pipes from each reservoir meet at junction J. The characteristics are as follows (all in meters:

La Lb Lc. Da Db Dc

500 1000. 750.  0.75 1 1  

What are the friction factors for each pipe?

What is the correct elevation of J in meters ?

What are the flows in each pipe?