Unit 3: Biological Molecules

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

  • What is special about water?
  • What is the electrical charge distribution on a water molecule?
  • What does it mean that water is a universal solvent?
  • Why does water's polarity make it well suited to its functions in biology?

Water is so indispensable for life that our primary method for searching for life outside Earth is to look 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 oxygen and hydrogen are polar because the sharing of electrons between oxygen and hydrogen is not equal. This unequal sharing means the oxygen atom is partially negatively charged, and each hydrogen atom is partially positively charged. This makes the water molecule polar and 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. Consequently, 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 a capillary attraction that 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 it requires a lot of energy to change its state from liquid to gas, allowing 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.

Due to 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. Be sure to review polarity and how it underlies these properties.

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

  • What are acids and bases?
  • What does the addition of Hydrogen ions (H+) or Hydroxyl ions (OH-) do to the pH of a solution?
  • 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 the H+ concentration. Different parts of 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's environment.

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

  • What is pH?
  • How do acids and bases alter the hydrogen ion concentration in a solution?
  • What values are considered acid?
  • What values are considered basic?
  • What value is neutral?

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

The pH scale is from 0 to 14. Pure water has a pH of 7 because the H+ concentration equals the OH- concentration. Acids increase the H+ ion concentration by tenfold and lower the pH, while bases decrease the H+ concentration. The stomach's pH is 2, while the blood is around 7. Buffers are needed to maintain the pH in these environments.

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3d. Describe 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?
  • Where can each of the four biological macromolecules be found in the human body?

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

  1. Lipids are composed of a diverse set of hydrocarbon molecules (containing hydrogen and carbon). This makes them partially non-polar because the covalent bonds in hydrocarbons (between two carbon atoms and 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 will help you recognize them. It also explains how they are constructed within cells, interact chemically with each other in metabolism, and form structural components of organisms.

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3e. Describe the functions of the four major biological macromolecules as they relate to our physical requirements for health

  • What are the primary functions of the four classes of biological macromolecules?
  • Where is each macromolecule class located in the body?
  • Which foods contain each of the four classes of biological macromolecules?
  • What amount of each macromolecule is essential for sustaining human life?

Lipids (fats) store energy and provide thermal insulation and protective padding. Phospholipids form the infrastructure of all cell membranes. Lipids also make up natural waxes, oils, and many hormones.

Some polysaccharides, or complex sugars (such as the cellulose in plants and chitin in fungi), are important for their structural strength, whereas other polysaccharides (such as starch, which plants create to store carbohydrates, and glycogen, used for the same function in animals) are important for storing energy. Polysaccharides also serve as identity markers on the surfaces of cells, so they play a role in immunity.

Proteins, composed of chains of amino acids, perform an impressive 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 interpret that code to build proteins through transcription and translation. Specific RNAs can also function as catalysts.

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

  • Which monomers make up polysaccharides?
  • Which monomers make up proteins?
  • Which monomers make up nucleic acids?

A polymer is a category of macromolecule that is built by connecting 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 since they do not contain repeating chains of monomers.

Polysaccharides are macromolecular carbohydrates – polymers made up of multiple monosaccharides. Monosaccharides are monomers, and they can be connected in a linear or branched arrangement.

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 of multiple monosaccharides. Monosaccharides are monomers, and they can be connected in 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 (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 they can form. In addition to reviewing various monomers, study how polymers are constructed using dehydration reactions and deconstructed using hydrolysis reactions.

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3g. Describe the four levels of protein structure and how this relates to enzyme function

  • What are the four levels of protein structure?
  • How is each level distinct?
  • Why is an enzyme particular to a certain substrate or class of substrates?
  • What happens when a protein is denatured?

As a polymer, a protein is a large and complex molecule. Proteins have the most intricate and variable shapes among the three classes of biological polymers. Each protein has its particular function due to its specific shape (its conformation). This is why proteins have such diverse functions. Some proteins function as enzymes, which are biological catalysts.

We describe protein structure up to four levels:

  • Primary structure is the sequence of amino acids (the number and order) for a single polypeptide. A polypeptide is one continuous strand made of a number of amino acids connected end-to-end in a certain order. If a protein is just one polypeptide, the "polypeptide" is a "protein."

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

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

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

  • Quaternary structure is the way multiple individual polypeptides (each with their own primary, secondary, and tertiary structures) 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.

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

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Unit 3 Vocabulary

This vocabulary list includes terms you will need to know to successfully complete the final exam.

  • acid
  • amino acid
  • base
  • buffer
  • carbohydrate
  • DNA
  • enzyme
  • lipid
  • monomer
  • monosaccharide
  • nucleic acid
  • pH
  • pH scale
  • polymer
  • polynucleotide
  • polypeptide
  • polysaccharide
  • primary structure
  • protein
  • quaternary structure
  • RNA
  • secondary structure
  • tertiary structure
  • water