biochemistry - How does a plant grow before photosynthesis is possible?

There are quite a few questions and thoughts in there, I'll try to cover them all:

First, to correct your initial word equation: During photosynthesis, a plant translates CO₂ and water into O₂ and carbon compounds using energy from light (photons).

You are correct to assume the C is further used for the growing process; it is used to make sugars which store energy in their bonds. That energy is then released when required to power other reactions, which is how a plant lives and grows. C is also incorporated into all the organic molecules in the plant.

Plants require several things to live: CO2, light, water and minerals. If any of those things is missing for a sustained period, growth will suffer. Most molecules in a plant require some carbon, which comes originally from CO₂, and also an assortment of other elements which come from the mineral nutrients in the soil. So the plant is completely reliant on minerals.

Most plants, before a leaf is established or roots develop, grow using energy and nutrients stored in the endosperm and cotyledons of the seed. I whipped up a rough diagram below. Cotyledons are primitive leaves inside the seed. The endosperm is a starchy tissue used only for storage of nutrients and energy. The radicle is the juvenile root. The embryo is the baby plant.

When the seed germinates the embryo elongates, the endosperm depletes, the testa ruptures, and the cotyledons emerge from the seed. The cotyledons are green, and like leaves can photosynthesise, so as soon as they are in the light the plant is able to make carbon compounds. The radicle elongates at the same time, and becomes the root, so the plant is very quickly able to obtain fresh nutrients from the soil (or whatever it's growing in).

At all stages of a plant's life it is using both energy stored in carbon compounds (from CO₂) and nutrients which it took up via its roots. At no point does the plant start to depend solely on the CO₂ in the air for its growth.

You are right that the way in which plants acquire energy and nutrients prior to leaves and roots being established varies between plants. Above I outlined the way most plants use. But there are lots of variations. For example, orchids have very tiny seeds, some barely visible to the naked eye, like specks of dust. They have no endosperm or storage tissue, so they have to rely on a symbiotic mycorrhizal fungus to get carbon and nutrients. The fungus grows through the coat of the orchid seed, then provides everything the growing plant needs until it has its own leaves. Then the orchid repays the fungus by providing sugars.

There are lots of other examples, but we could go on all day!

structural biology - Can protein structure be determined by X-Ray Diffraction in a single image?

Not by analysing a single protein. There is work with x-ray lasers.

You have to take a simultaneous image of millions of proteins and use that to get a structure. It's not quite prime time. People are also doing this with electron beams in electron microscopes.

These methods will reconstruct 3D models of the molecules, sometimes in states which cannot be obtained from crystallography. Examples being the structure of the many megadalton nuclear pore complex, and the f-actin fiber. The classic study is 3d model of bacteriorhodopsin, the first membrane protein structure which was at molecular resolution (this was a crystalline sample though).

While in principle, it sounds much simpler - get a pure sample of your protein, or complex and freeze it down and zap it with an Xray or Electron beam, its a lot more work to reconstruct the image and can take as long or longer than getting an x-ray structure. The resolution is also usually poor as the crystal will reinforce coherence, that is all the proteins are aligned in the same way and have close to the same 3d shape in a crystal.

gel electrophoresis - How do I deal with sticky and viscous samples from cell lysates?

To check a protein expression I pelleted a small amount of E. coli before and after induction and lysed them by redissolving them in SDS-PAGE loading buffer and heating them to 95 °C for 1 minute.

This lead to a solution with some very sticky and viscous parts in it, that make pipetting the sample into the gel wells extremely annoying. As far as I heard, this is probably genomic DNA, and my usual way to deal with this is to centrifuge the samples and only pipet a small part out from the top. This does seem to help sometimes, but not always.

How can I avoid the formation of that sticky and viscious stuff or how can I avoid pipetting that stuff into my wells?

pharmacology - In what ways, if any, does administration of rapamycin *not* mimic calorie restriction?

Rapamycin specifically inhibits the mTOR pathway (mTOR = mammalian target of rapamycin), which has numerous downstream functions including protein biogenesis, regulation of cell cycle, immune function and apoptosis. The upstream effectors of mTOR include growth factors and amino acid availability, so you can certainly see that the lifespan enhancing effects of caloric restriction will be (at least in part) mediated by the mTOR pathway.

But there are key differences. mTOR also receives signals relating to DNA damage and inflammatory changes (to name just 2) that are essential for healthy survival. So any direct inhibition of this pathway will affect all the functions - I can't find the reference now, but I have definitel read in one of the numerous rodent studies that rapamycin treated mice have reduced immune function (i.e. the lifespan increased effects can only be seen in a controlled lab environment - in the wild mTOR-inhibition to this degree would be a disadvantage).

I think therefore it is fair to say that the effects of caloric restriction on longevity are mediated by mTOR, but administration of rapamycin is not an equivalent treatment.

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Update

Really great review came out last month (http://www.ncbi.nlm.nih.gov/pubmed/22500797) - I recommend you give that a skim if you want detail!

human biology - How are proteins formed?

Essentially, yes, "proteins that we consume form new proteins that are different".

The processes are each of them topics for themselves. In short, consumed proteins are digested by peptidases (enzymes) in the stomach, breaking them down into their consituent amino acids. These are absorbed in the gut and transported in the blood to all cells. These take up amino acids and attach them to tRNA molecules which are used in translation to form new body proteins.

human biology - Why do people look different after a long sleep?

What happens during a long sleep that makes people look odd when they have just woken up? Why doesn't the same phenomenon occur in the case of a person who lies down for an extended period of time, but stays awake? I've noticed that some nights seem to make a bigger difference than others in the appearance of the sleeper, but haven't noticed a pattern.

biochemistry - ATP cost for gene expression

The cost of transcribing and translating a hypothetical average gene in yeast has been calculated as 551 activated phosphate bonds ~P per second (Wagner, 2005).

The median length of a yeast RNA molecule is 1,474 nucleotides, and
the median cost of precursor synthesis per nucleotide (derived from
the base composition of yeast-coding regions) is 49.3 ∼P. With a
median mRNA abundance of R = 1.2 mRNA molecules per cell and a median
mRNA decay constant of dR = 5.6 × 10−4 s−1, the mRNA synthesis costs
calculates as 49.3 × 1,474 × 1.2 × (5.6 × 10−4) = 48.8 ∼P per second
and cell. This is a fraction 48.8/1.34 × 107 = 3.6 × 10−6 of the total
RNA synthesis cost per second. The median length of a yeast protein is
385 amino acids, with a combined biosynthesis and polymerization cost
of 30.3 ∼P per amino acid. The median abundance is 2,460 protein
molecules per cell. No currently available data allows a meaningful
estimate of the median protein half-life, but a protein of an
intermediate half-life (see below) of 10 h (decay constant dP = 1.92 ×
10−5 s−1) yields an overall synthesis cost of 30.3 × 385 × 2,460 ×
(1.92 × 10−5) = 551 ∼P s−1.

For your question about a single gene, the cost would be 49.3 * 1474 ~P for the mRNA and 30.3 * 385 ~P for the translation, which would result in around 84 thousand ~P. This is probably a very misleading statistic as you can transcribe multiple proteins from a single mRNA.

How the cost of mRNA synthesis and translation are calculated is described in detail in the paper. A large part of the cost comes from the synthesis of the basic building blocks, the nucleotides and the amino acids.

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