Transcription and translation in numbers

In this section we will describe the basic production apparatus of the cell the mechanisms of transcription and translation. These processes are the action of huge molecular motors, which work their way along a one-dimensional string, using this as a template, for generating another one-dimensional string. This, of course, demands energy. Energy is, however, abundant in the cell in form of huge amounts of ATP and GTP. Also, production demands the presence of some building blocks the bases to...

Calorimetry denaturation by heating

Schematic melting curve for a typical protein. On the left we show energy (enthalpy) per protein on the right we show the heat capacity. Latent heat Q is indicated by the shaded area. Notice the gap in heat capacity A Cp between the folded and unfolded states, reflecting the exposure of hydrophobic residues upon unfolding. The peak heat capacity is counted from the midpoint of the transition, as indicated. Throughout the text we focus on the part of the heat capacity that is...

Kramers formula

Escape from a potential well is an old and important problem in physics, as well as in chemistry. It has also recently proven important in a number of biological Figure A4. Escape over a one-dimensional potential, where a particle is confined at A, but is allowed to escape over barrier C to the outside of the well. In the figure we show a number of particles, to illustrate the approach by Kramers. Figure A4. Escape over a one-dimensional potential, where a particle is confined at A, but is...

Nonspecific binding to DNA

Gene control involves transcription factors, i.e. proteins that bind to specific DNA sites and thereby activate or repress the transcription machinery at that point. Thus binding of a particular protein to a specific site is needed. In practice it is possible to obtain quite high specific binding energies, but not arbitrarily high if specific binding is very high, then often the protein will also bind substantially to nonspecific DNA sites. The non-specific binding can be taken into account by...

The Fokker Planck equation and the Einstein relation

The alternative approach to the relation between mobility and noise is through the Fokker-Planck equation. If x fulfils a Langevin equation with < n(t)rj(t')> S(t t') then one can construct a probability distribution for x at a given time t P(x, t)dx probability for x e x, x + dx at time t (A64) By using the physical insights we have for the two terms in the Langevin equation in terms of loss and gain terms to a given x coordinate, P will evolve according to the Fokker-Planck equation At...

Or3 Or2

-9.7 -11.0 -12.8 AG -3.3 -2.6 AG AGdim -11.1 -9.7 -11.0 -12.8 AG -3.3 -2.6 AG AGdim -11.1 Figure 7.13. Illustration of data on AG (in kcal mol) involved in OR regulation from Darling et al. (2000). The top part shows Cro bindings, with Gi being individual bindings, and AGij being additional cooperative bindings. The lower part shows corresponding numbers for CI and RNAp respectively. Total AG for a state is obtained by summing individual contributions. Notice that the cooperative bindings are...

Rb69 Infection E Coli

Many phages could coexist in some E. coli. However, many also try to take control of the E. coli. P4 is particularly specialized, as it acts as a parasite on P2, and relies on many of the larger phages' genes. Phages are often related phage taxonomy of 144 known phages can be found at http salmonella.utmem.edu phage tree. Some phages are very similar, for example the lambdoid phages that include A, 80, 434, HK97, 21, 82, 933W, HK022 and H19-B. Another phage group consist of the T4 relatives...

The genetic switch of the Aphage

With about 5 x 1030 prokaryotes on Earth, these relatively simple single-celled organisms are a dominating life form. However, not even for bacteria is the world a safe place The bacteria are exposed to their own parasites, the bacteriophages. The number of phages exceed the number of bacteria by several orders of magnitude, and their diversity and ability to manipulate genetic information probably makes these simple information carriers an important force in shaping the global ecosystem....

Molecular motors energy from ATP

Proteins can be grouped into a few broad categories with respect to their function. Some are regulatory, some are enzymes, some are structural, and some proteins do mechanical work. It is this latter group that we now discuss. Molecular motors include kinesin, myosin, dynein, the motors connected to DNA replication, to gene transcription and to translation. The motors are mostly driven by ATP hydrolysis ATP ADP P, a process with AG 13 kcal mol for typical conditions in the cell. Exactly how the...