Atomic Structure
The history of the atom goes back centuries. You can read about it here, but basically what you need to know is its basic structure. The Bohr model of the atom is a nice model to use (though not the accepted model today) because it can be represented two-dimensionally. Atoms consist of protons and neutrons in the nucleus and electrons orbiting around the nucleus in what is essentially a probability cloud. Protons are positively charged particles, electrons are negatively charged, and neutrons have no charge. Atoms are electrically neutral, meaning that they have no charge. To the right is a Bohr model of a nitrogen atom. Nitrogen has seven protons, which gives it an atomic number of 7. Adding neutrons to the nucleus adds mass to the atom but not any additional charge. This means that nitrogen has an atomic mass of 14 amu, but the atomic number remains seven because there are still seven protons balancing out seven electrons. The Periodic Table of Elements is a list of all the known elements. Elements are the simplest of all substances. Ionic Bonding & Covalent BondingIonic bonding occurs between metals and nonmetals. Metals, which form cations, will transfer their valence (outermost) electrons to nonmetals, which form anions. Ionic bonds are very, very strong, resulting in compounds with high boiling and melting points, and strong crystalline structures.
Covalent bonding occurs between nonmetals. In this case, valence electrons are shared between elements. Covalent bonds can be strong, but are oftentimes weaker than ionic bonds. Molecules are atoms that are held together by covalent bonds. See the image to the right. |
Ion FormationBear in mind that adding or subtracting protons changes the fundamental nature of the element. Oxygen is oxygen because it has eight protons. Adding a proton changes it to fluorine and subtracting a proton changes it to nitrogen. Electrons, however, can be added or subtracted without the element losing its character. What it does, however, is affect the element's ability to react with other elements.
When elements are added to or taken away from electrons, ions are formed. Positive ions, called cations, are formed when electrons are lost. Negative ions, called anions, are formed when electrons are gained. Check out the below image from chemcool.com. To the left are specific examples using sodium (Na, #11) and chlorine (Cl, #17). Sodium loses an electron and chlorine gains an electron. Whether an element loses or gains an electron is dependent on its location to the nearest noble gas. Elements in groups 1-13 tend to lose electrons and elements in groups 15-17 gain electrons. |
van der Waals Forces
The bonding that occurs between molecules are called van der Waals forces. The strength of the attraction depends on the size, shape and orientation of the molecules. They are not as strong as covalent bonds or ionic bonds, but they are essential in biological processes.
Water is a polar molecule (see the image to the left). This means that there is a net charge on one end of the molecule due to the uneven pull of unshared electrons. This charged end is attracted to the uncharged end on another water molecule. Water molecules are held together by van der Waals forces. But the atoms that make up a water molecule are covalently bonded. |
Chemical Reactions
Chemical reactions are the process by which elements and/or compounds change into new substances. Chemical equations are written representations of chemical reactions and you can see that the atoms are rearranged. The substances on the left are called reactants and the substances on the right are called products.
In biology, there are two key chemical reactions that you need to be aware of: photosynthesis & respiration. They are complementary processes. Photosynthesis takes place in chloroplasts and respiration takes place in mitochondria. Photosynthesis requires carbon dioxide, water and energy (in the form of sunlight) to produce glucose (a simple sugar) and oxygen. Respiration requires glucose and oxygen and transforms it into carbon dioxide, water and energy (in the form of ATP).
As you can see, both equations are balanced. Any chemical equation must be balanced because mass is always conserved.
In biology, there are two key chemical reactions that you need to be aware of: photosynthesis & respiration. They are complementary processes. Photosynthesis takes place in chloroplasts and respiration takes place in mitochondria. Photosynthesis requires carbon dioxide, water and energy (in the form of sunlight) to produce glucose (a simple sugar) and oxygen. Respiration requires glucose and oxygen and transforms it into carbon dioxide, water and energy (in the form of ATP).
As you can see, both equations are balanced. Any chemical equation must be balanced because mass is always conserved.
Chemical reactions require energy. The minimum amount of energy needed for reactants to form products is called activation energy. (Ea) Once this threshold is reached, no further input of energy is required. If you are looking at an energy curve, the peak represents activation energy. Exothermic reactions are reactions where energy is released because the energy of the reactants is higher than the energy of the products. Endothermic reactions are reactions where energy is absorbed because the energy of the products is higher than the energy of the reactants.
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Some chemical reactions proceed very, very slowly because the activation energy is so high, or proceed super fast, because the Ea is so low. Either way, we cannot observe what is taking place. In order to get any work done with these reactions, additional substances are required to reduce the activation energy. Catalysts reduce the Ea and speed up reactions. Inhibitors raise the Ea and slow down reactions. These substances do not affect the outcome of the reaction and does not get used up.
Special proteins called enzymes are biological catalysts. They are essential to life and their names typically describe what they do. Most enzymes are specific to one reaction. For example, amylase, which is in saliva, speeds up the breakdown of amylose, which is in starch. Reactants that bind to the enzyme are called substrates, and where they bind is called the active site. Because the enzyme and the substrate have complementary shapes, they bind in a precise manner. Once this happens, the enzyme-substrate complex is formed and the chemical reaction takes place. Then the enzyme releases the products.
Image courtesy of kenpitts.net.
Special proteins called enzymes are biological catalysts. They are essential to life and their names typically describe what they do. Most enzymes are specific to one reaction. For example, amylase, which is in saliva, speeds up the breakdown of amylose, which is in starch. Reactants that bind to the enzyme are called substrates, and where they bind is called the active site. Because the enzyme and the substrate have complementary shapes, they bind in a precise manner. Once this happens, the enzyme-substrate complex is formed and the chemical reaction takes place. Then the enzyme releases the products.
Image courtesy of kenpitts.net.