The Chemical Basis of Life: Atoms, Molecules, and Water

I. Summary


Atoms
Biology is the study of life, and to understand it, we have to know a little bit about chemistry and physics; as they help us understand how atoms and molecules interact. All living organisms are composed of matter, anything that takes up space and has mass. Matter is made up of atoms, which are the smallest functional units of all living things. Atoms are made up of tiny little particles. Atoms can also bond together to create molecules. Examples of some atoms are Hydrogen, Carbon, Nitrogen, and Oxygen. These specific types of atoms are called elements, pure substances of only one kind of atom. Protons, neutrons, and electrons can be found within an atom. The protons and neutrons can be found within the atomic nucleus and the electrons occupy orbitals around an atom's nucleus. Orbitals are the regions around the nucleus where the electrons are most likely to be found. They are almost like rings around the nucleus. Orbitals occupy energy shells, or energy levels.  The electrons in the outermost shell are called valence electrons. These are the most important electrons that we need to know for this chapter. They determine whether an atom can bond with other atoms.
The atomic number is the number of protons an atom contains. The atomic mass is an atom's mass relative to other atoms. This is usually confused with weight, which is the the gravitational pull on a given mass. The atomic mass is measured in daltons. A Dalton, also known as atomic mass unit, is equivalent to 1/12 the mass of a carbon atom. A mole of any substance contains the same number of particles as there are atoms in exactly 12g of carbon. <------ this is something that I'm still a little iffy about!
Traditionally, the number of neutrons are the same as the number of protons, in any given atom. However, variations of an element in their numbers of neutrons, can exist; these are called isotopes. An isotope found in nature that is inherently unstable and usually does not exist for long periods of time is called a radioisotope. They decay and emit energy in the form of radiation.
Oxygen, Nitrogen, Carbon, and Hydrogen make up the majority of atoms in all living organisms. Hydrogen and oxygen we know form water, carbon is the building block of all living matter, and nitrogen is vital in proteins. Trace elements are also necessary for normal function in all living organisms, but is only needed in small quantities. Iron and copper are examples of trace elements.
Chemical Bonds and Molecules

A molecular formula is a representation of a molecule that consists of the chemical symbols for all of the atoms present and and subscripts that indicate how many of those atoms are present. A molecule that is composed of two or more different elements is called a compound. Water is a compound as it contains two hydrogen molecules and one oxygen molecule. Chemical bonds are what hold atoms in molecules together.

Covalent bonds are where atoms share electrons. This is the strongest type of chemical bond.

For most atoms, 8 electrons are needed to fill their outer most shells. The octet rule states that atoms are stable when they have 8 electrons in their outermost shell. Keep in mind, this rule doesn't always apply (hydrogen only needs 2 electrons to fill its valence shell).
A double bond is when the atoms of a molecule share two pairs of electrons, rather than one. An atom's ability to attract electrons, electronegativity, is not the same for each atom. In a covalent bond, although the two atoms are sharing electrons, they don't always necessarily share electrons evenly. Sometimes one atom's electronegativity is greater than the other and the shared electrons spend more time around one atom than the other. This phenomenon is called a polar covalent bond. Water is a great example of a polar covalent bond. Although hydrogen is sharing its electrons with oxygen, oxygen has a greater electronegativity and therefore hydrogen's two electrons spend more time orbiting oxygen's nucleus than they do their own. Nonpolar covalent bonds are where the electrons shared in a covalent bond, are shared equally because the electronegativity of the two atoms are similar. A single molecule can have areas with nonpolar bonds and areas with polar bonds. When the bonds in a molecule are predominantly nonpolar, it is called a nonpolar molecule. Vice versa is referred to as a polar molecule.
Hydrogen bonds are the weakest bonds and form when a hydrogen atom from one polar molecule is electrically attracted to an electronegative atom in another polar molecule. The strength of hydrogen bonds increases relative directly as the number of bonds increase. AKA 3 hydrogen bonds are stronger than 2 hydrogen bonds. A good example is DNA; it takes considerable amount of energy to pry the two strands apart because of the amount of hydrogen bonds. Enzymes are proteins that either facilitate or catalyze chemical reaction in a cell. Van der Waals forces are attractive forces between molecules in close proximity of each other, caused by the variations in the distribution of electron density around individual atoms. <------ another unclear topic!
An ion is when an atom or molecule gains or loses electrons, giving it a net electric charge. Cations are ions that have a net positive charge and anions are ions that have a net negative charge. What helps me remember that cations are the positive ones and anions the negative is that cations has a t which kind of looks like a +, for positive. Yes, every time I read cation I read it like ca+tion! Ionic bonds occur when a cation bonds to an anion. Essentially one atom is giving electrons and the other is recieving. This exchange of electrons will change it's charge.
A free radical is an atom that only has one valence electron. Free radicals steal electrons from other atoms until their valence shell is full.
A chemical reaction is the formation and breaking of chemical bonds, resulting in a change in the composition of substances. This can be when two elements combine to form a compound, or when a compound is broken down into elements. Chemical reactions require energy, which is partly provided through heat. Heat energy allows atoms and molecules to move and vibrate; this is known as Brownian motion. Chemical reactions also need to be catalyzed. Chemical reactions proceed in a particular direction and will eventually reach a state of equilibrium unless something happens to prevent equilibrium. A reactant is something that participates in a chemical reaction and becomes changed by that reaction and a product is the end result of the reaction. Chemical equilibrium is a state in the chemical reaction where the rate of formation of products equals the rate of formation of reactants.
Properties of Water
A substance dissolved in a liquid is a solute and a solvent is the liquid in which a solute is dissolved. A solution is a liquid that contains one or more dissolved solutes. Aqueous solutions are solutions made with water. Ions and molecules that contain polar covalent bonds and WILL dissolve in water are known as hydrophilic. Molecules that don't have partial charges and are not attracted to water molecules are hydrophobic. They are composed of carbon and hydrogen and are relatively insoluble in water. Cohesion is when water molecules are attracted to each other and adhesion is when water adheres to a surface that is not electrically charged. Water also has a very high specific heat which is the amount of heat energy needed to raise the temperature of 1g by one degree Celsius. DON'T GET THIS CONFUSED WITH heat capacity which is the amount of heat energy needed to raise the temperature of an entire object or substance.
The colligative properties of water are dependent on the number of dissolved solutes and allow water to function as an anti-freeze in certain organisms. Water's high heat of vaporization and high heat of fusion help it be very stable while in liquid form. Hydrolysis is the breaking down of large molecules into smaller units and a dehydration reaction combines smaller molecules into a larger one.
The pH of a solution refers to it's concentration of hydrogen ions. The pH scale is from 0-14. 0 is acidic and contains the most H+ ions, whereas 14 is basic, or alkaline, and has more OH- ions. PH balance can be regulated by using a buffer. A buffer is a compound that minimizes pH fluctuations in fluids of living organisms; they can raise or lower pH, as needed.

II. Useful Materials


Above, I mentioned how the concept of a mole was still a little unclear to me. This song demonstrates how to find a mole, gives the definition, and helps remember everything. Its super catchy, LISTEN TO IT!!!

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I also mentioned how I didn't quite understand the van der Waals force. Here's a video that actually explains and clarifies it. He digresses a little but, in the end he actually helped! He pretty much said that the van der Waals force is a weak attractive force between atoms of nonpolar molecules caused by a temporary change in dipole moment from a brief shift of orbital electrons to one side of an atom or molecule, creating a similar shift in adjacent atoms/molecules.

III. Article


This article is about physicists that came about creating the heaviest isotope of magnesium. While experimenting, however, an isotope of aluminum also showed up. How exciting! This could help us come closer to understanding occasional X-ray emissions from neutron stars that are growing in mass.
On the 5th day of a 7-day-long experiment in Michigan State University, an isotope of aluminum appeared unexpectedly. Most theories predicted that aluminum-42 wouldn't exist; this is why it's appearance was so shocking. In sum, the discovery of aluminum-42 suggested that even heavier aluminum isotopes could exist and maybe even other elements, that are higher in the periodic table, would be able to accommodate more neutrons than expected.