Unit 2: Basic Chemistry
Nature is not based on one field of study. It incorporates biology, physics, chemistry, and other academic disciplines. Life is multidisciplinary and is driven by chemical processes. Since so many biology topics overlap with basic principles of chemistry, you need a basic understanding and appreciation of chemistry to fully understand biology. For example, in Unit 1 we discussed that the atom is the first part of the biological hierarchy. In this unit, we provide an understanding of this foundational level of organization.
Completing this unit should take you approximately 5 hours.
Upon successful completion of this unit, you will be able to:
- list the major components of an atom and their locations;
- list the different types of bonds and how they lead to the formation of molecules and compounds; and
- describe the primary concepts of thermodynamics as they relate to heat, temperature, energy, and work.
2.1: Atoms and Molecules
Atoms and elements are the smallest structures in the universe. These substances cannot be broken down any further. Elements come together to form molecules which are the building blocks of the lowest level of life, the cell. To understand biology, you need to understand these foundation elements that form the structures of life.
The primary subatomic particles are protons, neutrons, and electrons. Protons and neutrons make up the nucleus of an atom. Electrons are found outside the nucleus. A proton has an electrical charge of +1. A neutron is nearly identical in size to a proton, but it has no charge. An electron is much smaller than a proton or neutron. An electron is also a charged particle. Despite being much smaller than a proton, the charge of an electron is equal in magnitude to the charge of a proton. However, the charge is opposite, so each electron has a charge of -1.
Watch this lecture, which introduces the atom and discusses the relationship between atoms and elements. What do you think the periodic table represents?
Watch this video, which discusses the subatomic particles of the atom.
Watch these short videos for an overview of the elements within an atom: protons, neutrons, and electrons. Make sure you understand the definitions for the proton, neutron, and electron. You should also be able to define atomic measurements, such as atomic number and mass, and calculate the number of subatomic particles based on this number.
Atoms have a specific structure that determines their behavior in an element or compound. Electrons occupy spaces around the nucleus. These spaces have a hierarchical arrangement. An orbital is a space that can be occupied by electrons. Each orbital can contain up to two electrons.
There are different types and shapes of orbitals: s, p, d, and f. There is only one kind of s orbital, but there are three kinds of p orbital, five d orbitals, and seven f orbitals. A collection of orbitals of the same type makes up a subshell, and a collection of subshells makes up a shell (also called an energy level). The first shell includes only one subshell (the s subshell), which is made up of only one s orbital. The second shell is made up of two subshells (an s and a p subshell), with the s subshell being made up of one s orbital and the p subshell being made up of three p orbitals. Since different shells contain different numbers of orbitals, each shell has a different maximum number of electrons it can hold.
Watch this lecture to learn about orbitals and review the structure of an atom.
Living structures are three-dimensional (3D), and electrons fly in three-dimensional orbitals. This feature is critical because it explains how elements join to form 3D molecules that build the 3D tissues and organs of life. Watch this lecture, which describes how the electrons fly in different orbitals.
Watch this lecture to learn about electron configuration and valence electrons.
Read this section, which describes how atoms and elements form different types of bonds between atoms.
After you read, see if you can answer these questions: What makes ionic bonds different from covalent bonds? Why are hydrogen bonds and van der Waals interactions necessary for cells? How do buffers help prevent drastic swings in pH? Why can some insects walk on water? What property of carbon makes it essential for organic life? Compare and contrast saturated and unsaturated triglycerides.
Watch this lecture to learn about the details of ionic, covalent, and metallic bonds, and how to balance chemical equations.
A compound is a substance made up of two or more different kinds of atoms. This is the fundamental distinction between an element and a compound. Rather than simply being a mixture of two or more kinds of atoms, compounds are formed when different kinds of atoms interact. This interaction gives the compound properties that differ from the properties of the constituent elements. For example, sodium chloride (table salt) is made up of the elements sodium and chlorine, but sodium chloride (the compound) is different from both of these elements. The interactions between atoms in a compound are called chemical bonds.
There are three major categories of chemical bonds:
- Ionic bonds form when one or more electron from one atom is transferred to another atom, creating a positive ion and a negative ion that are attracted to each other because of their opposite charges.
- Covalent bonds form when one or more pairs of electrons are shared by two different atoms, holding the two atoms together more strongly than an ionic bond.
- Metallic bonds consist of a "sea" of electrons that move about from one metallic atom to another, holding together many metallic atoms.
Molecules are particles that are bigger than atoms. They are made up of multiple atoms (of either the same or different elements) held together by covalent bonds. A molecule of water, for example, consists of an oxygen atom covalently (and separately) bonded to two hydrogen atoms.Be sure you understand the distinction between atoms, ions, molecules, elements, and compounds.
- Ionic bonds form when one or more electron from one atom is transferred to another atom, creating a positive ion and a negative ion that are attracted to each other because of their opposite charges.
Now that you have learned about atoms and their structures, watch this overview of how to write and draw atoms, molecules, and chemicals correctly.
Now, let's learn how to balance chemical reactions. Elements come together to form molecules called products. It is important to make sure the same amount of elements are found on both sides of the chemical reaction.
2.2: Thermodynamics
Thermodynamics is the branch of science that studies how energy is transformed from one form to another. We study thermodynamics in biology because organisms are involved in many energy transactions. In other words, organisms are thermodynamic systems. Biochemical reactions must follow the laws of thermodynamics to predict whether reactions will occur spontaneously, or without any energy required.
For example, living things need the ability to move. Energy gives this power, but it must be harnessed and transformed from one form of energy to another. Living things need usable forms of energy.
Two of the four laws of thermodynamics are especially important in biology:
- The first law of thermodynamics states that energy cannot be created or destroyed, although it can be transferred and transformed. This is also known as the law of conservation of energy.
- The second law of thermodynamics states that every energy transaction increases the entropy (disorder) of the universe. This second law implies that every energy transaction involved some loss of usable energy as heat, so no energetic process (including those occurring in organisms) can ever be perfectly efficient.
We will review thermodynamics again in Unit 5 when we study metabolism and metabolic pathways.Energy is a basic process common among all living organisms. We define energy as the capacity to do work, which refers to some sort of change. For example, moving an object from one place to another requires work, and energy is required for that work. Heat is energy in the form of the movement of particles (atoms, ions, or molecules) within a substance.
Heat is energy that is unavailable for performing work. Temperature is a measure of the average speed of the particles in an object. Temperature and heat are not the same thing. Temperature does not depend on how much matter is present, whereas heat does.
For example, a swimming pool has the same temperature as a cup of water from that swimming pool, but the swimming pool contains much more heat than the cup of water because it contains much more matter.
Read this section to learn how energy flows through a living system and how enzymes catalyze chemical reactions.
Energy can be readily converted between forms. For example, a book that falls from a shelf converts potential energy into kinetic energy. When a person moves the book back to the shelf, they convert kinetic energy into potential energy. The metabolism of life involves countless interactions between matter and energy and countless conversions between energy forms, so it is important to understand the distinction between matter and energy.
Watch this video, which offers an overview of the concept of energy and discusses how it relates to atoms and molecules. All atoms and molecules have kinetic energy or movement. We measure kinetic energy as temperature.
Watch this lecture, which explains the importance of the first law of thermodynamics to living organisms. Many scientists call the first law of thermodynamics the law of conservation of energy since It states that energy can be neither created nor destroyed, but it may change form. For example, imagine a campfire: the energy is stored in chemical bonds in the wood and is released as light and heat.
After watching the video, make sure you can identify the different forms of energy and how they are transferred and transformed.
Watch this video for a discussion of the Gibbs Law of Free Energy. After you have read this section, you should be able to write and define each component (G, H, S, T) of the equation for free-energy change, distinguish between exergonic and endergonic reactions in terms of free energy change, predict which reactions are spontaneous, and explain why organisms do not violate the second law of thermodynamics.