The Cell 9-8

The Cell (Alberts) 9-8 question Antibodies that bind to specific proteins are important tools for defining the locations of molecules in cells. The sensitivity of primary antibody, the antibody that reacts with the target molecule, is often enhanced by using labeled secondary antibodies that bind to it. What are the advantages and disadvantages of using secondary antibodies that carry fluorescent tags versus those that carry bound enzymes? Show answer

A lot of useful information can be found on Wikipedia article Immunohistochemistry . Fluorescent tags on secondary antibody allow for higher signal and labeling multiple targets using orthogonal pairs of antibodies. For example, we can label at the same time tubulin and actin. Secondary antibodies, though, are bulkier and can decrease resolution, especially in super-resolution microscopy. Using multiple antibodies also can increase chance of off-target labeling (when antibody binds elsewhere rather than it's antigen).

Questionnaire #1

That is first series of short (with short description as well as answer) questions from GRE Subject Test.
#5

Most of the dry mass in the trunk of a tree was originally derived from
(A) the soil
(B) light energy
(C) amino acids
(D) CO2
(E) glucose

Show answer

As soon as dry mass of the trunk of a tree consists mainly of oligosaccharides its source should contain carbon and hydrogen. Soil is too much common answer for me. Light energy can't be right answer because energy is not converted into matter easily. Amino acids is strange idea also. So let's check two options: CO2 and glucose. As this question – obviously – touches photosynthesize process, which yields glucose and other carbohydrates, I pick up CO2 as an answer.

#13

Which of the following types of molecules is always found in virions?
(A) Lipid
(B) Protein
(C) Carbohydrate
(D) DNA
(E) RNA

Show answer

First, we should define what virion is. Surprisingly, it is just one instance of object virus. So you talk about virus (e.g. fag T4) properties, but when you meet one in the shop, it is virion.
What do we know about virions? They are simple systems which are not really cells because of lack of membrane and other important compartments as well as functions and facilitates. They have got capsid – hard-breaking protein-lipid armor around internal stuff. Inside they have some proteins and nucleic acid: either DNA or RNA, either single- or double-strained molecules. So the answer is proteins as molecules, that are found in all viruses and thus virions.

#31

The difference between the molecular weight of sucrose and that of the sum of the molecular weights of its components (glucose and fructose) is
(A) 0
(B) 1
(C) 16
(D) 18
(E) 180

Show answer

If you remember scheme structure of sucrose as O_O (:-) you get the idea of question. The reaction of such polymerization looks like that:
Glu-OH + OH-Fru = Glu-O-Fru + HOH
Thus, difference is in one water molecule which is 2 hydrogen atoms and 1 oxygen. The answer is D: 18 = 2*1 + 16.

#34

An alpha-helical conformation of a globular protein in solution is best determined by which of the following?
(A) Ultraviolet-visible absorbance spectroscopy
(B) Fluorescence spectroscopy
(C) Electron microscopy
(D) Analytical ultracentrifugation
(E) Circular dichroism

Show answer

I really looooove fluorescence. So I hope it is the right answer, but lets be patient.
Electron microscopy is not good idea, because it can't show us structure of the protein as x-ray crystallography make it possible.
Ultracentrifugation, I suppose, will not help us because it will just sediment peptides and nothing more.
Circular dichroism is damn strange stuff I don't know much about. But google fetched me nice page about circular dichroism. I got the idea of that method: difference in absorbances of left- and right-polarized light is higher if peptide is structured. It is rather similar to fluorescence anisotropy. High anisotropy shows that fluorophore is fixed in space (and time :-) It can also predict stable structures as alpha-helices or beta-layers.