Discuss in detail real time PCR (qPCR) including how PCR works, theory of qPCR, advantages, disadvantages, types of detection mechanisms used.

Let’s suppose that you were running RT-PCR and quatifying the level of a particular mRNA using qPCR. You run qPCR but you suspected that you are amplifying the wrong product.  What could you do to determine if the correct mRNA

Why is it medically important to distinguish between Streptococci and Staphylococci?

How would a competitive, irreversible inhibitor affect an enzyme? Please explain in detail.

What is transposition and what are the differences between replicative and non replicative transposition?

Bacteria can carry out gluconeogenesis using components of the citric acid cycle or amino acids, but unlike mammals, they can generate glucose from acetate via the glyoxylate pathway. Because bacteria have no organelles, the enzymes of the citric acid cycle and the glyoxylate pathway are not compartmentalized. (a) Why is regulation of the glyoxylate pathway necessary in bacteria? (b) Studies show that bacterial isocitrate lyase is allosterically inhibited by high concentrations of phosphoenolpyruvate. Would you expect to see the inhibition of isocitrate lyase when bacteria are utilizing glucose as a sole carbon source? Why? (c) Would you expect the glyoxylate pathway to be more active than the citric acid cycle when bacteria are growing on acetate? Why? (d) Would you expect to find glucose-6-phosphatase in bacteria?

Lipid bilayers can exist in a gel-like state or a more fluid-like state, which is a function of both temperature and lipid composition. Which of these states is more common in a biological membrane and why? Specifically address the advantages this may provide for associated membrane proteins

Oxidative Phosphorylation (McKee 374-378).  

1. Describe how the relatively high concentration of protons are prohibited from returning to the matrix of the mitochondria based on the permeability of the inner mitochondrial membrane
2. Explain the route taken by the proton gradient based on the proton channel of the ATP synthase complex.
3. Describe the location of the rotor portion of the ATP synthase (F₀) based on the membranes and compartments of the mitochondria.
4. Describe how the rotor portion of the ATP turns based on H⁺ flowing though the proton channel.
5. Describe the location of the catalytic sites for ATP synthesis based on the rotor and stator (F1) of the ATP synthase complex.
6. Describe the location of the F1 portion of the ATP synthase complex based on the aqueous compartments of the mitochondria.
7. Describe how the turning rotor transfers the energy required for ATP formation based on conformational changes in the catalytic sites that have substrates, ADP and inorganic phosphate (Pi), bound.
8. Describe how the electron transport chain and ATP synthase complex cooperate in the process of oxidative phosphorylation

At times a ribosome may get stuck with an mRNA that has been damaged so that there is no stop codon. What happens to this ribosome to fix this problem?

Explain why the frequency of color blindness is higher in males than in females in the human population?

1. Lab Review:

A) Explain why– control E. coli cells cannot grow on LBA+amp and LBA+amp+X-Gal.

B) Name a procedure which can replace the heat shock process and achieve the same goal:

C) If you used the pBLU plasmid as a vector to carry a desirable human gene into E. coli recipient cells. The insertion site is inside the β-galactosidase gene on the p-BLU plasmid. After the transformation, you plate the cells on LBA+amp+X-Gal to screen for E. coli cells with the desirable gene. You saw both blue and white colonies on the plate. Which type of colonies carry the desirable human gene?
A. White        B. Blue             C. both             D. neither one

Explain WHY?

Cellular communication and division

In one paragraph connect the following: Mitochondria and Anaphase.

Hints

1. what is going on in anaphase
2. what is required to have that happen
3. how does mitochondria provide anaphase with energy

Sample Random Mating Lab

P generation is 2 male and 2 females of sepia eyed, white eyed, irregular facets, vestigial, dumpy, and black body.

1a) The most common phenotype in the F1 generation is usually wild type. Explain why this occurs based on allele frequencies even though the P generation had no wild type.

1b) Explain why different methods can be used to calculate only irregular facets, the allele counting method, compared to other phenotypes

What is the purpose of a transformation control with pGAP?

1. What is one big difference between how frogs and fish gastrulate? (1-2 sentences) (Hint -explain how each of these organisms gastrulates and the difference will be obvious!)

2. Number the following steps of germ cell development in the appropriate order.

A. The primordial germ cells undergo meiosis.

B. The primordial germ cells are specified

C. The primordial germ cells migrate to where the gonads are developing

3.

What are the signals that are required for the induction of the organizer?

4. How did C. Easley make sperm-like cells from human foreskin fibroblasts? (2-3 sentences)

5. What is special about how the genes (whose mutations result in the flies above) are arranged in the fly genome and how they are expressed in the developing embryo? (1-2 sentences)