Saturday, 22 March 2014

Ecology and Environment

Ecology and Environment - Today we hear people from all walks of life using the terms ecology and environment. Students, homeowners, politicians, planners, and union leaders speak of “environmental issues” and “ecological concerns.” Often these terms are interpreted in different ways, so we need to establish some basic definitions.

ecology

Ecology is the branch of biology that studies the relationships between organisms and their environments. This is a very simple definition for a very complex branch of science. Most ecologists define the word environment very broadly as anything that affects an organism during its lifetime.

These environmental influences can be divided into two categories. Other living things that affect an organism are called biotic factors, and nonliving influences are called abiotic factors (figure 14.1). If we consider a fish in a stream, we can identify many environmental factors that are important to its life. The temperature of the water is extremely important as an abiotic factor, but it may be influenced by the presence of trees (biotic factor) along the stream bank that shade the stream and prevent the Sun from heating it. Obviously, the kind and number of food organisms in the stream are important biotic factors as well. The type of material that makes up the stream bottom and the amount of oxygen dissolved in the water are other important abiotic factors, both of which are related to how rapidly the water is flowing.

As you can see, characterizing the environment of an organism is a complex and challenging process; everything seems to be influenced or modified by other factors. A plant is influenced by many different factors during its lifetime: the types and amounts of minerals in the soil; the amount of sunlight hitting the plant; the animals that eat the plant; and the wind, water, and temperature. Each item on this list can be further subdivided into other areas of study. For instance, water is important in the life of plants, so rainfall is studied in plant ecology. But even the study of rainfall is not simple. The rain could come during one part of the year, or it could be evenly distributed throughout the year. The rainfall could be hard and driving, or it could come as gentle, misty showers of long duration. The water could soak into the soil for later use, or it could run off into streams and be carried away.

Temperature is also very important to the life of a plant. For example, two areas of the world can have the same average daily temperature of 10°C* but not have the same plants because of different temperature extremes. In one area, the temperature may be 13°C during the day and 7°C at night, for a 10°C average. In another area, the temperature may be 20°C in the daytime and only 0°C at night, for a 10°C average. Plants react to extremes in temperature as well as to the daily average. Furthermore, different parts of a plant may respond differently to temperature. Tomato plants will grow at temperatures below 13°C but will not begin to develop fruit below 13°C.

The animals in an area are influenced as much by abiotic factors as are the plants. If nonliving factors do not favor the growth of plants, there will be little food and few hiding places for animal life. Two types of areas that support only small numbers of living animals are deserts and polar regions. Near the polar regions of the earth, the low temperature and short growing season inhibits growth; therefore, there are relatively few species of animals with relatively small numbers of individuals. Deserts receive little rainfall and therefore have poor plant growth and low concentrations of animals. On the other hand, tropical rainforests have high rates of plant growth and large numbers of animals of many kinds.

As you can see, living things are themselves part of the environment of other living things. If there are too many animals in an area, they can demand such large amounts of food that they destroy the plant life, and the animals themselves will die. So far we have discussed how organisms interact with their environments in rather general terms. cologists have developed several concepts that help us understand how biotic and abiotic factors interrelate in a complex system.

Friday, 21 March 2014

MOLECULAR REPLACEMENT: CALCULATING PHASES USING A HOMOLOGOUS STRUCTURE

The use of heavy atom derivatives is just one way to obtain a set of starting phases for the calculation of electron density maps. If coordinates of a homologous protein are known, it is possible to avoid the use of heavy atom derivatives. This involves some rather complex calculations but the principal steps are shown in Fig. 2.6. The success of the method appears to be related to the degree of conformational homology between the unknown protein and the known probe molecule.

The computational steps in crystal structure determination by molecular replacement require two sets of information: (1) the coordinates of the atoms in the probe molecule, and (2) an X-ray diffraction data set from crystals of the unknown protein.

The protocol for obtaining a set of phases for an unknown protein by molecular replacement is as follows:
1. Measure X-ray data from crystals of the native protein.
2. Compare the Patterson function of the unknown protein with that of a known
 protein to obtain a rotational transformation, placing the probe molecule in the correct orientation in the unknown unit cell; see Fig. 2.6. Remember, to calculate the Patterson function of a known crystalline structure, no phase information is needed. The relationship is similar to that described in Eq. (2.7) for a difference Patterson. Replace Puvw with Puvw, and Fhkl with Fhkl(calc) in Eq. (2.7). The Patterson function of the probe molecule in molecular replacement is obtained from the calculated structure factors, which in turn were obtained from the coordinates of the known structure. The Patterson function of the unknown is calculated from the observed structure amplitudes, which in turn were measured from a crystal of the unknown molecule. The three-dimensional Patterson function of the probe molecule is rotated until maximum overlap is observed between it and the Patterson from the unknown crystal. This formulation is called a rotation function. It is a time-consuming calculation even on fast computers. If it works, the orientation (but not the position) of the known protein in the unknown unit cell is determined.
3. Now find the correct translational position of the properly oriented probe molecule in the unknown unit cell. This can be done by trial and error. Structure factors are calculated at different increments on a three-dimensional grid, using the atomic coordinates of the correctly oriented probe molecule. The calculated |F(probe)| values are compared with the |F(obs)| values until a good correlation is found.
4. Calculate a set of test phases, (test, hkl), using the oriented and translated coordinates of the probe molecule in the unknown unit cell. The amplitudes for the unknown crystal, Fhkl(obs) are combined with the aforementioned phases to produce a trial electron density map.

Source: LEONARD J. BANASZAK. Foundations of Structural Biology. New York: Academic press