Biomolecules

What should students in introductory biology courses know about the universal constituents of cells?

This is an initial attempt to explore whether we can reach consensus on the core learning goals on biological molecules and macromolecules, roughly corresponding to Chapter 5 of Biology by Campbell, Reece et al. (8th ed).  At Georgia Tech, our Intro to Biological Principles, Biol 1510, begins with modules on evolution and ecology, and this starts the third module, on cells and bioenergetics. I welcome feedback about what should be added/omitted/modified, and any questions from students about the content.

1. All living organisms are made of organic molecules.

Students should be able to distinguish organic from inorganic molecules.

  • Organic molecules must have C and H, and may have O, N, P, S
  • Organic molecules have at least one bond between C and H or C and C (the carbon atom is in a reduced state, rather than fully oxidized as in O=C=O)

2. Organic molecules can arise from abiotic synthesis (see Miller-Urey expt), but in the biosphere, most organic molecules are synthesized by living organisms.

Synthesis of organic molecules from inorganic molecules requires energy, and chemical reducing power (redox reactions), as the carbon atoms in organic molecules are in reduced form compared to inorganic carbon (carbon dioxide). For a review of redox reactions from a biology point of view, see this Khan Academy video.

3. Small organic molecules are assembled (polymerized) into large biological macromolecules.

One recent study concluded that cells are composed of 68 distinct organic molecules (http://ucsdnews.ucsd.edu/newsrel/health/09-0868Molecules.asp) that are assembled into macromolecules and lipid structures (membranes).

Polymerization of monomers into polymers occurs by dehydration reactions – a molecule of water results from the addition of each monomer to a growing polymer.

Cleavage of polymers back to monomers occurs by hydrolysis reactions – a molecule of water is consumed.

4. Living organisms assemble these small organic molecule building blocks into 3 types of biological macromolecules (polymers):

a. glycans, also called polysaccharides (starch, cellulose, chitin, etc.) – carbohydrates may refer either to monomers (monosaccharides) of the composition Cn(H2O)n or polymers (polysaccharides) made by linking monosacchardiges via glycosidic bonds.

b. polypeptides (proteins) are polymers of amino acids, joined together by peptide bonds.

c. nucleic acids (RNA and DNA) are polymers made by joining nucleotides in a phosphodiester linkage

Students should be able to distinguish among these macromolecules, and identify the monomers that build each type of macromolecule.

Students should also identify what non-covalent bonds/interactions stabilize each types of macromolecular structure.

My lecture video on this topic:

5. Living organisms also contain lipid bilayer membranes made of phospholipids.

The lipids create boundaries and a hydrophobic  environment that separates the aqueous environment of the cytosol from the outside of the cell, and also separates distinct intracellular organelle compartments in eukaryotic cells. Such compartmentalization is essential to maintain thermodynamic disequilibrium for cellular energy metabolism.

Students should be able to identify hydrophilic versus hydrophobic (lipid) molecules.

6. Cells use the different classes of biological macromolecules in different ways.

a. Polysaccharides are used primarily for energy storage (glycogen, starch) and static structures (such as cellulose, chitin), but can also play important roles in cell-cell recognition/adhesion and signaling.

b. Proteins are used primarily for enzymatic activities, signaling, and dynamic structural components. A separate post on protein structure and function will follow.

c. Nucleic acids are used for genetic information storage (DNA) and retrieval (RNA). Catalytic RNAs play some key roles in information processing (RNA splicing, translation).

d. Lipids are used to define the cell’s boundary, compartmentalize the cell (in eukaryotes), for energy storage, and signaling.

Questions for review, further research and thought:

1. Do all living organisms synthesize organic molecules from inorganic molecules?

2. What processes created organic molecules before life arose? In what environments?

3. Why do proteins have enzymatic activities, but generally not polysaccharides or nucleic acids?

4. Carbon atoms are in their most reduced form in which type of organic molecules?

5. Which macromolecules often have branching structures?

6. If you heat a dilute cell extract to boiling for a few minutes, what will be the effect on the 3 types of macromolecules?

7. How will changes in pH or salt concentrations affect solutions of each type of macromolecule?

8. Speculate as to how the different macromolecules evolved – did one class evolve before the others? This is an open question in biology and the origin of life.

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About jchoigt

I'm an Associate Professor in the School of Biology at Georgia Tech, and Faculty Coordinator of the Professional MS Bioinformatics degree program.
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3 Responses to Biomolecules

  1. I like the ideas so far, Jung. One concept that I’d like freshmen to build from this material + their learning on photosynthesis and ecology is about how the three major classes of biomolecules differ not just in terms of their bonding patterns and “shapes” (which I think freshmen typically memorize in a general way, since they haven’t yet had enough organic chemistry to understand how differently these bonds react) – but also in terms of their atomic composition. The 3 major types of biomolecules all contain C, H, O., but carbohydrates don’t contain any N or P, proteins typically contain N but not P, nucleic acids both N & P. Yet synthesizing carbs requires proteins (enzymes) so can be N-limited, and cell division requires new nucleic acids which can be N and P limited… The relevance of the different atomic composition of these 3 types of biomolecules is something that freshmen CAN recognize despite little organic chem knowledge and which can help them understand how plant growth may be limited by N or P (can’t make proteins or nucleic acids), yet mature plant tissue is fairly rich in carbs… And why plants that are rich in carbs and have limited protein content makes poor food for animals, who need to synthesize animal tissue (high in proteins) from plant tissue (high in carbs). Which then explains why cows graze all day eating tons of grass and poop constantly (dumping excess useless carbs all the while), while a lion can sleep 20 hours per day and then hunt a little at night to get what it needs. Not that it’s easy being a lion, stealing from all those hyenas all the time.

    • jchoigt says:

      Good idea, although polysaccharides like chitin do contain N (N-acetylglucosamine). I do ask students to apply this concept of the different elemental composition of the major macromolecules, when I discuss the Hershey-Chase expt. and how P-32 and S-35 label nucleic acids and proteins, respectively. Some metabolic labeling questions would address this, as well as a discussion of nutritional requirements, and how increased atmospheric carbon dioxide concentrations will not necessarily lead to increased plant growth or crop yields.

  2. Mirjana Brockett says:

    This is a good conceptual map for Ch. 5. I would make it clear where do organic molecules come from first and in this place recognize that they are part of the four molecules of life.
    As a second concept, bulding upon, you could say about early Earth’s conditions and the possibility of “de-novo” synthesis in such conditions (supported by the S-U experiment).
    It would be possible to make a good relation with nutrition, as well as types of nutrition and evolution of it…?

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