# Chemistry and Life sciences

Look deep into nature, and then you will understand everything better, Albert Einstein.

Animals are such agreeable friends — they ask no questions, they make no criticisms, George Elliot.

# Chemistry

Chemistry is the study of substances -that is, elements and compounds- while biology is the study of living things. It studies the composition, structure, and properties of matter, and the changes it undergoes. Let’s see some resources to learn and study Chemistry.

• Atomiks is a faithful remake of, and a tribute to, Atomix, a classic puzzle or, more specifically, a molecule building game; in other words, you need to build molecules out of single atoms. It is a fun and educational science-based game. If you are using GNU/Linux, you could install atomix. atomix is built for Gnome desktops (GNU/Linux).

“The player is tasked with assembling a molecule from the atoms; more specifically, the atoms must be arranged into a specific shape, identical with the shape of the molecule displayed on the left side of the screen. The player can choose an atom and move it in any of the four cardinal directions; however, a moved atom keeps sliding in one direction until it hits a wall or another atom. Solving the puzzles requires strategic planning in moving the atoms, and on later levels with little free space, even finding room for the completed molecule can be a problem,” (extracted from Wikipedia).

• Periodica (Windows) and Kalzium (GNU/Linux) are similar programs that show you the Periodic Table of Elements. Click on an element and you will get detailed information about its properties.

Kalzium has a molecular weight calculator: Tools, Perform Calculations… The molecular mass is the mass of one molecule of a substance expressed in atomic mass units (u). It is the sum of the atomic masses of all the atoms present in the molecule.

For example, to find the molecular mass of ammonia NH3 = (1 * the atomic mass of nitrogen N) + (3 * the atomic mass of hydrogen H) = (1 x 14.0067) + (3 x 1.00794) = 14.0067 + 3.02382 = 17.0305u. The molecular mass of sulfuric acid is H2SO4 = (2 * the atomic mass of hydrogen) + (1 * the atomic mass of sulfur) + (4 * the atomic mass of oxygen) = (2 * 1.00794) + (1 * 32.065) + (4 * 15.9994) = 98.0785 u (98.07848).

Kalzium has a Chemical Equation Balancer, too. In a chemical reaction, the quantity of each element does not change. Thus, each side of the equation must represent the same quantity of any particular element. 2H2O -> 2H2 + O2 and P4 + 5O2 -> 2P2O5 are balanced equations because there is an equal number of atoms of each element on the left- and right-hand sides of both equations.

• RasMol is a molecular graphics program intended for the visualization of proteins, nucleic acids, and small molecules.

In order to view a molecule, you need a separate file that specifies the structure of the molecule, that is, the position of every atom in the molecule as Cartesian coordinates X, Y, and Z. The program reads these molecular coordinate files and interactively displays the molecule on the screen in a variety of representations and color schemes. Launch your favorite browser and go to RCSB PDB. For example, I searched for 5T6Q and found the following entry, 5T6Q, Structure of cytochrome P450 4B1 (CYP4B1) complexed with octane: An n-Alkane and fatty acid omega-hydroxylase with a covalently bound heme, and click on Download Files, PDB Format.

This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease.

Once you have installed RasMol, launch it, and select File, Open… Then, navigate to the file that you have just downloaded, e.g., 5t6q.pdb. The default download folder is usually ‘My Documents,’ accessible through the file explorer.

• Avogadro is a free, open-source, and advanced molecular editor and visualization tool, designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high-quality rendering and a powerful plugin architecture.

First, we are going to open a file and navigate around the molecule. To do this, click on the File menu and select Open…

The screenshot shows the ethanol.cml (C2H6O) file already opened up and displayed using the Cartoons and Ball and Stick display type.

Molecules can be built and edited with the draw tool (pencil). You can begin creating a molecule by left-clicking on the black display. This will generate a carbon atom. If the “Adjust Hydrogens” box is checked, hydrogens in the molecule are automatically adjusted to satisfy valency. The result is Methane, a chemical compound with the chemical formula CH4.

Left-clicking and dragging the mouse will generate a bond to another carbon atom. In other words, two carbon atoms that are bonded to one another. The result is Ethane, C2H6. Repeat the process and it is going to adjust the number of hydrogens. Keep going and close the cycle to generate Cyclohexane, C6H12. Select under the Extensions menu, the Optimize Geometry option, and the geometry of the molecule would be optimized.

If you want a different atom, let’s say Oxygen, select Oxygen (8) from the drop-down Element menu and click on the black display. If the “Adjust Hydrogens” box is checked, hydrogens in the molecule are automatically adjusted to satisfy valency and the result is Water, H2O.

You can also use the navigation tool to pan, rotate, and scale the view of a molecule.

# Life sciences

Life sciences are the study of life and living organisms, such as microorganisms, plants, and animals including human beings, and how they interact with each other and their environment. They deal with every aspect of living organisms. Biology is the science of life.

There are many different branches of life sciences: botany (the study of plants), zoology (the study of animals), ecology (the study of how organisms interact with their environment), microbiology (the study of microorganisms. Microorganisms are those organisms that are too small to be seen with the naked eye, such as bacteria, fungi, and viruses), epidemiology (the study of diseases in populations -humans or other animals-, specifically how, when, and where they occur), paleontology (the study of ancient life preserved as fossils), biochemistry (the study of the chemistry of living things, a sub-discipline of both chemistry and biology), etc.

Read our free ebooks A wonderful journey and Life for a gentle introduction to this topic.

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