The inside of a cell is extremely crowded. We will try to gain some insight for exactly how crowded by considering some numbers that are estimates of the situation in the common bacterium E. coli. One can estimate the total number of proteins present in a cell in several ways. For example, one can measure the dry mass of a cell (the amount of material left once the cell is dried out), analyze the composition to determine what fraction is amino acids, estimate the average molecular weight of a protein, and use all these numbers to calculate the total number of protein molecules present. Alternatively, one can use experimental analysis to determine the approximate amount of proteins present in a sample consisting of a known number of cells. All of these methods agree that a typical E. coli bacterial cell contains about 3 x 10⁶ proteins.

a) We can estimate the volume of an E. coli cell to be about 1 µm³, that is, equivalent to a cube of 1 µm on each side. Convert that volume to liters, and assuming there are 3 x 10⁶ total proteins present, calculate the total molar concentration of proteins contained in a bacterial cell.

b) Take the reciprocal of the molar concentration obtained in part a, and convert units to find the number of cubic nanometers per protein molecule.

c) One way to think about the volume per protein molecule found in part b is that if you divided up the total volume of the cell into tiny cubes, with each cube having the volume found in part b, then on averge, each cube would contain one protein. The length of each side of one of these cubes would just be the cube root of the volume per protein molecule. Further, the length of each side of the cube is an estimate of the center-to-center separation distance of each protein molecule. From the volume per protein obtained in part b, use this approach to estimate the center-to-center distance between protein molecules (on average) in an E. coli cell.

d) Averaged across a cell's inventory of proteins, the average protein molecular weight is about 30000 grams per mole (i.e., 30 kiloDaltons). For proteins, an average mass density is found of about 1.4 g/cm³. Use these numbers, after appropriate unit conversions, to calculate the average volume of a protein molecule in cubic nanometers. Compare this number to the value obtained in part b, and estimate what fraction of the total volume of a cell is filled with proteins.

Calculate the Theoretical Yield and Percent Yield for the reaction of p-Amino Benzoic Acid (PABA) + Ethanol + Sulfuric Acid to create Benzocaine. Is Sulfuric Acid simply a catalyst in this reaction? 

Molar Mass Benzocaine: 165.19g/mol

Molar Mass PABA: 139.14g/mol

Molar Mass Ethanol: 46.07g/mol

Molar Mass of Sulfuric Acid: 98.079g/mol

Mass of PABA Used: 0.5093g (0.00366 moles)

Volume of Ethanol Used: 7.0 mL (5.523g) (0.11986 moles) Ethanol is in excess here.

Volume of Sulfuric Acid Used: 0.50 mL (0.92g) (0.00938 moles)

Mass of Benzocaine collected: 0.3722g

12. (4) For each of the situations described below: 1) Which process would be primarily affected: RNA Processing, Translation Initiation, Translation Elongation, Translation Termination and 2) Describe the effect/consequence of the change

a) Deletion of a 5’splice site in a pre-mRNA

b) The underlined mutation in the protein-coding region whose reading frame is shown 5’- AUG-CCA-UAU-ACA-3’ 5’- AUG-CCU-UAA-ACA-3’

c) A mutation that removes the Shine-Delgarno sequence

d) A mutation in the tRNA for the amino acid lysine that changes the anticodon sequence from 3′-UUU-5′ to 3′-UAU-5′

Which of the following statements about mutations and genetic disease are correct?

CHECK ALL THAT APPLY!

Check all that apply

Transcription is the process of RNA synthesis.  Translation is the cytoplasmic process of protein synthesis. Both processes can be divided into three stages, Initiation, Elongation, and Termination.  For each of the events listed below write which process it occurs in (either transcription or translation) and in which stage the event occurs (initiation, elongation, termination).

1. Release factor binds to the stop codon in the amino acyl site and cuts away the protein from the transfer RNA.

2. Transfer RNA anticodons bind to the messenger RNA codons.

3. A hairpin loop forms in the messenger RNA.

4. The small subunit of the ribosome scans the messenger RNA to find the AUG start codon.

1. Interpret the infrared and NMR spectra of benzocaine.

2.What is the structure of the precipitate that forms after the sulfuric acid has been added?

3. When 10% sodium carbonate solution is added, a gas evolves. What is the gas? Give a balanced equation for this reaction.

4. Explain why benzocaine precipitates during the neutralization.

5. Refer to the structure of procaine in the table in the essay “Local Anesthetics.” Using p-aminobenzoic acid, give equations showing how procaine and procaine monohydrochloride could be prepared. Which of the two possible amino functional groups in procaine will be protonated first? Defend your choice. (Hint: Consider resonance.)

R-plasmids are plasmid vectors which encode what type of genes? (user thinks genes for replicases)

Homologous recombination results in a protein with which attributes? (user thinks it a protein with amino acid sequence)

Transduction is the process best described as? (the uptake of DNA by infection)

Ribosomal RNA sequencing is utilized to create phylogenetic relationships between organisnms due to the fact these genes are some conserved throughout evolution. T or F ( user thinks true)

5.) What domian contain Chromosomes consist of Exons and Introns (user thinks archea and bacteria)

Can someone just please help me better understand these questions?

Which has a wider array of structures: proteins, DNA, or RNA? Explain why.

In your own words, explain common functional relatedness, structural relatedness, and ancestral gene relatedness of conserved regions of proteins.

Explain why protein domains that contain structurally or functionally important amino acid sequences would be conserved between organisms that are very distantly related.

Why are cysteines important to the structure of a protein?

Explain the role of p53 and how its mutation leads to increased growth rate in the cell.

Which mutations most commonly lead to cancer – somatic cell or germ-line?

How do mutations lead to natural selection?

7. Suppose that you have just graduated from college and have started working at a biotechnology firm. Your first job assignment is to clone the pig gene for the hormone prolactin. Assume that the pig gene for prolactin has not yet been isolated, sequenced, or mapped; however, the mouse gene for prolactin has been cloned, and the amino acid sequence of mouse prolactin is known. Briefly explain two different strategies that you might use to find and clone the pig gene for prolactin.

8. Describe how the genome of an organism of your choice has been successfully engineered to improve a trait of economic importance in the organism.