BIO101: Introduction to Molecular and Cellular Biology

3a. List the characteristics of water that make it important to life as we know it

• What is special about water?
• What is the electrical charge distribution on a water molecule?
• Why does the polarity of water make it well suited to its functions in biology?

Water is so indispensable for life that our primary method for searching for life outside of earth is to search for evidence of water.

A water molecule is composed of one oxygen atom that is simultaneously bonded to two hydrogen atoms. The covalent bonds between the oxygen and each hydrogen are polar because the sharing of electrons between oxygen and hydrogen is not equal. Because of this unequal sharing, the oxygen atom is partially negatively charged, and each hydrogen atom is partially positively charged. This makes the overall water molecule polar. This gives water several special characteristics:

• Water molecules can form hydrogen bonds with other polar molecules, including other water molecules.

• Water is less dense in the frozen state than in the liquid state. Because of this, bodies of water freeze from the top down, and thaw during seasonal warming.

• Water has a high specific heat capacity, requiring more energy than most substances to change its temperature. This stabilizes the temperature of bodies of water more than landmasses.

• Water has a high cohesion. This can create capillary attraction which can lift water through vessels to the tops of the tallest trees.

• Water is an excellent solvent. The chemistry of life is mostly aqueous solution chemistry.

• Water has high surface tension. This allows small organisms to walk on the surface of water.

• Water has a high latent heat of vaporization. This means water requires a lot of energy to change its state from liquid to gas. This allows for effective evaporative cooling by sweating.

• Water exists in all three states (solid, liquid, and gas) within a comparatively narrow range of temperatures that organisms can tolerate.

Because of these special characteristics, it is no surprise that life evolved in the water of the ocean. We can think of every living cell as a tiny bag of water and biological molecules. Keep these special properties in mind as you study biology, and be sure to review polarity and how it underlies these properties.

Review this material in Water and The Properties of Water.

3b. Describe the role of acids, bases, and buffers in biological systems

• What are the definitions of an acid and base?
• How do buffers work?

In aqueous solutions, the hydrogen atom shifts from one water molecule to another. This creates H+ and OH- ions that are very reactive. These ions are equal in pure water, but an imbalance in concentration occurs when certain solutes are added. Acids increase the H+ concentration; bases decrease H+ concentration. Different environments in living organisms have different amounts of acids and bases.

For example, the stomach requires high amounts of acid to break down food. The bloodstream is a different environment. Buffers are chemicals that resist the changes that acids and bases make in a solution of the body environment.

Review this material in Acids, Bases, and the pH Scale, pH, pOH, and pKw, and Electrolytes and pH.

3c. Define pH and the role of hydrogen ions in living systems

• What is the definition of pH?
• How do acids and bases alter the hydrogen ion concentration in a solution?

pH measures the H+ ion concentration in a solution. We define it as the negative log of H+ concentration. This creates an inverse comparison. When the H+ ion concentration increases, the pH value is low. When the H+ concentration is low, the pH value increases.

The pH scale is from zero to 14. Pure water has a pH of seven because the H+ concentration equals the OH- concentration. Acids increase the H+ ion concentration by 10 fold and lowers the pH, while bases decrease the H+ concentration. The pH of the stomach is two while the blood is around seven. Buffers are needed to maintain the pH in both of these environments.

Review Hydrogen Atoms in Acids and Bases, which describes the modification of H+ concentrations.

3d. Recognize the structure of the four major biological macromolecules

• What are the four classes of biological macromolecules?
• What are the structural differences between the different classes of biological macromolecules?

All organisms feature four major classes of large biological molecules, or macromolecules:

1. Lipids are made up of a diverse set of hydrocarbon molecules (containing hydrogen and carbon). This makes them largely partially non-polar because the covalent bonds in hydrocarbons (between two carbon atoms or between a carbon atom and a hydrogen atom) share electrons equally.

2. Polysaccharides are complex carbohydrates made up of carbon, hydrogen, and oxygen in a 1:2:1 ratio, giving them an empirical formula generalized as (CH₂O)_n.

3. Proteins are enormously diverse in structure and function, yet they all feature the substructure of amino acids. Each amino acid features a central carbon atom simultaneously connected to a hydrogen atom, an amino group, a carboxyl group, and a variable $R$ group.

4. Nucleic acids are informational molecules with a basic structure in which each subunit includes a five-carbon sugar (either ribose or deoxyribose) attached to a phosphate group and a nitrogenous base.

Knowing the chemical structure that underlies these essential biomolecules not only allows you to recognize them. It allows you to understand how they are constructed within cells and how they chemically interact with each other in metabolism and to give rise to structural components of organisms.

Review this material in Biological Polymers, Carbohydrates, Lipids, Proteins, and Nucleic Acids.

3e. Describe the functions of the four major biological macromolecules

• What are the major functions of the four classes of biological macromolecules?

Lipids are important for storing energy, thermal insulation, and providing protective padding. Phospholipids form the infrastructure of all cell membranes. Lipids also make up natural waxes and oils and many hormones.

Some polysaccharides (such as cellulose and chitin) are important for their structural strength, whereas other polysaccharides (such as starch and glycogen) are important for storing energy. Polysaccharides also serve as important identity markers on the surfaces of cells, so they play a role in immunity.

Proteins perform an impressively long list of biological functions. They function as enzymes, structural elements, chemical signals, transporters, and receptors. They also play important roles in cell-to-cell adhesion and immunity.

Nucleic acids include various DNA and RNA molecules. They serve informational purposes. DNA stores the genetic code, and various types of RNA help in the process of interpreting that code to build proteins. Certain RNA's can also function as catalysts.

Review these major functions in Lipids, Carbohydrates, Proteins, and Nucleic Acids. Try to make sense of why each macromolecule's basic structure is well suited to its particular function.

3f. Indicate the monomers and polymers of carbohydrates, proteins, and nucleic acids

• What are the monomers that make up polysaccharides?
• What are the monomers that make up proteins?
• What are the monomers that make up nucleic acids?

A polymer is a particular category of macromolecule that is built by connecting together many ("poly-" means "many") smaller subunits, called monomers. Only three of the four biological macromolecules we have been studying are polymers. Lipids are not polymers, but the others are.

Polysaccharides are macromolecular carbohydrates. Be careful with the words "polysaccharide" and "carbohydrate". Sometimes these words are used interchangeably, but they should not be since they are different.

Carbohydrates include small and large molecules (macromolecules). Put another way, all polysaccharides are carbohydrates, but not all carbohydrates are polysaccharides. As the name implies, polysaccharides are polymers made up of multiple monosaccharides. Monosaccharides are monomers, and they can be connected in either a linear or branched arrangement.

Proteins are polymers that are made up of monomers called amino acids. Unlike polysaccharides, which may be branched, a protein must be a linear (or end-to-end) arrangement of amino acids. Organisms use 20 different kinds of amino acids (in an unlimited number of combinations and orders) to construct their proteins.

We can also call a nucleic acid a polynucleotide. This alternative name indicates it is a polymer made up of many nucleotides. In the case of DNA, the monomers are nucleotides that contain the pentose (five-carbon sugar) called deoxyribose. For RNA, the nucleotides contain ribose instead of deoxyribose. Although there are only four commonly used DNA nucleotides (and four commonly used RNA nucleotides), a typical DNA molecule contains millions of nucleotides. So there is an unlimited number of sequences of such nucleotides.

Be sure you can match each type of monomer to the type of polymer that can be made from such monomers. In addition to reviewing the various monomers, refresh your memory about how polymers are constructed using dehydration reactions and deconstructed using hydrolysis reactions in Biological Polymers.

3g. Describe the four levels of protein structure

• What are the four levels of protein structure?
• How is each level distinct?

As a polymer, a protein is a large and complex molecule, and proteins have the most complex and most variable shapes among the three classes of biological polymers. Any given protein has its particular function because of its particular shape (also called its conformation). This is why proteins have such diverse functions. Some proteins function as enzymes, which are biological catalysts. We can describe protein structure up to four different levels:

• Primary structure refers to the particular sequence of amino acids (both the number and the order) making up a single polypeptide. A polypeptide is one continuous strand made up of some number of amino acids connected end-to-end in a particular order. If a protein consists of just one polypeptide, then that "polypeptide" is itself a "protein".
  

• Secondary structure refers to repeating patterns found within a polypeptide. The repeating patterns include alpha helices (a singular helix) and beta-pleated sheets.
  

• Tertiary structure refers to the particular three-dimensional structure of a single polypeptide. In other words, the particular shape that a single polypeptide assumes when it bends and folds is called its tertiary structure.

Every protein includes at least one polypeptide, so every protein features a primary, secondary, and tertiary structure. Only some proteins (called multimeric proteins) are made up of two or more polypeptides. For multimeric proteins, there is a fourth level of structure in addition to the other three levels.

• Quaternary structure refers to the particular way in which multiple individual polypeptides (each with their own primary, secondary, and tertiary structures) come together to form the overall shape of a multimeric protein. In this case, "polypeptide" and "protein" are not interchangeable terms. The polypeptides are just parts of the overall protein.

Review the section on protein structure in Proteins. Keep in mind that a protein cannot function properly unless it has the correct shape, regardless of its job in the cell.

Unit 3 Vocabulary

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

• amino acid
• amino group
• carbohydrate
• carboxyl group
• catalyst
• cohesion
• deoxyribose
• DNA
• enzyme
• hydrogen bond
• latent heat of vaporization
• lipid
• monomer
• monosaccharide
• multimeric
• nitrogenous base
• non-polar
• nucleic acid
• nucleotide
• phospholipid
• polar
• polymer
• polynucleotide
• polypeptide
• polysaccharide
• primary structure
• protein
• quaternary structure
• ribose
• RNA
• secondary structure
• solvent
• specific heat capacity
• surface tension
• tertiary structure