BIO101: Introduction to Molecular and Cellular Biology

2a. List the major components of an atom and their locations

• What are the three primary subatomic particles?
• What are the major differences between the various subatomic particles?
• Where are the various subatomic particles located within an atom?
• What is an electron shell?
• What is a subshell?
• What is an orbital?

The universe is made up of matter and energy. Matter (all of the material in the universe) is composed of almost unimaginably small particles called atoms. As tiny as atoms are, even smaller particles make up each atom. We call them subatomic particles because they are smaller than atoms.

The primary subatomic particles are protons, neutrons, and electrons. Protons and neutrons make up the nucleus of an atom. Electrons are 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.

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.

Review the atomic structure and orbitals in Elements and Atoms, More on the Atom, and Protons, Neutrons, and Electrons.

2b. List the different types of bonds and how they lead to the formation of molecules and compounds

• What is a compound?
• How is a compound different from an element?
• How are compounds formed?

Atoms are the building blocks of elements, which are pure substances made up of only one kind of atom. Although there are just more than one hundred different elements, there are countless different substances in the universe. Most of these substances are compounds, not elements.

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 different properties compared to the properties of the constituent elements.

For example, sodium chloride (table salt) is comprised of the elements sodium and chlorine, but sodium chloride (the compound) is different from each 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 electrons 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. Ions are charged elements.

• Covalent bonds form when two different atoms share one or more pairs of electrons which hold 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 the same or different elements) held together by covalent bonds. For example, a molecule of water consists of an oxygen atom which is covalently and separately bonded to two hydrogen atoms.

You should appreciate the distinction between atoms, ions, molecules, elements, and compounds.

Review this material in Orbitals, More on Orbitals and Electron Configuration, Valence Electrons, Isotopes, Ions, and Molecules, Ionic, Covalent, and Metallic Bonds, Chemical Notation, and Balancing Chemical Equations.

2c. Describe the primary concepts of thermodynamics as they relate to heat, temperature, energy, and work

• What is energy?
• What is heat?
• What is temperature?
• What is work?
• What are the laws of thermodynamics?

Thermodynamics is the branch of science concerned with energy and energy transfer between objects. Although thermodynamics applies throughout the universe, we study it within biology because organisms are involved in many energy transactions. In other words, organisms are thermodynamic systems.

These are fundamental questions of thermodynamics. We can define energy as the capacity to do work. Work 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 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.

Two of the four laws of thermodynamics are important in biology:

• The First Law of Thermodynamics states that energy cannot be created or destroyed, though 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. An implication of this second law is that every energy transaction involves some loss of usable energy as heat, so no energetic process (including those occurring in organisms) can ever be perfectly efficient.

These thermodynamic concepts are important for understanding living things.

Review this material in Energy and Metabolism, More on Energy, The First Law of Thermodynamics, and Gibbs Free Energy.

Unit 2 Vocabulary

You should be familiar with these terms as you prepare for the final exam.

• atom
• chemical bond
• compound
• covalent bond
• electron
• element
• energy
• heat
• ion
• ionic bond
• metallic bond
• molecule
• neutron
• orbital
• proton
• shell
• subshell
• temperature
• thermodynamics
• work