Study Guide

Biomolecules and the Chemistry of Life Themes

  • Unity and Diversity

    As you think about biological molecules, it’s easy to see how the theme of unity and diversity applies. For starters, all biological molecules use a relatively small number of building blocks—our favorite word, monomers—to make a diverse array of larger polymers. You might even call them biopolymers. Within each class of biomolecules, carbohydrates, lipids, proteins, and nucleic acids, there is unity in the fact that the same monomers are used again and again, and diversity results from putting the monomers together in different ways.

    Carbohydrates exemplify this theme, so let’s take a closer look at the wide variety of polysaccharides that exist and what gives rise to this diversity. We mentioned earlier, in the In Depth section, that polysaccharides are used for energy storage. The polysaccharide of choice for plants is starch. Starch is basically a whole bunch of glucose monomers stuck together. When plants need energy, they use enzymes to break the bonds between glucose molecules one by one. Plants will only release as much glucose as they need at the moment, which is kind of nifty when you think about it. Plants are practical like that. Most animals also have enzymes that allow them to break plant starch into sugars, which is the reason that starchy foods like grains and potatoes are such a good source of energy.

    It turns out that there are different kinds of starches, and these different types arise partly as the result of chemical bonds. Remember that monosaccharides form rings before they bond together; depending on which carbon in the first monomer binds with the second monomer, you can get pretty different structures.

    Now, let us be the Friz to your Arnold. Seatbelts everyone! Glucose is a 6-carbon ring. Therefore, if the fourth carbon of one glucose monomer binds with the first carbon of a second glucose monomer, and this happens lots and lots of times so that lots and lots of bonds form, we will have a chain with no branches. (In fact, this starch is called amylose.) However, if some glucose molecules deviate from this bonding pattern, we can get a branched form of starch. Different starches are united by the fact that they have the exact same building blocks, and diversity arises when those building blocks are assembled in different ways.

    In animals, the storage polysaccharide is called glycogen. Glycogen has lots of branches and is stored in liver and muscle cells. We animals are like plants in that we can release glucose from the polysaccharide as needed, but glycogen stores do not last very long: less than a day in humans, and far less in some other animals. Shucks.

    So far, we’ve seen how carbohydrates can be used immediately or stored for later use. On top of the majorly important task of providing energy, some carbohydrates play an important role in providing structural support. In plants, the main structural polysaccharide is cellulose. Cellulose constitutes most of the cell walls of plants (animal cells don't have cell walls). Ecologists, or those guys who study how organisms relate to their physical surroundings, that want to impress their friends like to say that over a trillion tons of cellulose are produced on Earth each year – that is more than the weight of 200 billion elephants. That’s a lot of elephants.

    Cellulose, like starch and glycogen, is made from glucose monomers, but they bond together in a different way. In the storage molecules starch and glycogen, all the glucose molecules are right-side-up, and animals have enzymes that can deal with these kinds of bonds. In cellulose, however, every other glucose monomer is upside down, creating a different sort of bond. Animal enzymes are perplexed by this and cannot figure out how to break these bonds. Some animals, like cows, have microbes in their digestive tracts that are able to break these bonds, and they are some of a very few that can get a little energy from cellulose. For everyone who isn’t lucky enough to have a little clan of helpful, cellulose-digesting microbes, including us humans, cellulose passes through our systems undigested. This cellulose is famously known as fiber. Metamucil, anyone?

    Picture time! Here are the chemical structures for these sugars. Remember, no central atom means it is carbon, and any needed hydrogen atoms are "assumed."

    Chitin is another structural polysaccharide, but this one is found in fungi (mushrooms and whatnot) and some animals. It’s made of glucose like the other polysaccharides but has some nitrogen thrown in the mix for good measure. Chitin comprises the hard exoskeleton of arthropods, like insects and crustaceans, and strengthens the cell walls of fungi. Since fungi and animals share a more recent common ancestor than either one shares with plants, it makes some evolutionary sense that animals and fungi share this important structural polysaccharide. Yes, you read that correctly. A mushroom is more closely related to you than it is to any plant. Hey, everyone’s extended family has a few nuts. Er, mushrooms.

    The take-home point here is that there is an array of storage and structural polysaccharides, but they are unified by a common monosaccharide building block: glucose.

    Unity and diversity apply to other biomolecules, too. Think about DNA: the same four nucleotides combined in different ways are the basis for all the diverse life forms on Earth! Similarly, just 22 amino acids serve as the common building blocks for a plethora of protein structures. There is also unity in the way that monomers tend to be bound together. In all the biological molecules we looked at, monomers were assembled by dehydration synthesis. The fact that so much of life’s diversity is attributable to so few building blocks and processes is truly amazing. It would be like building New Orleans, with all its richness, color, and vigor, out of 3D puzzle pieces. Let’s be glad that Mother Nature is a more skilled architect than we are!

  • Structure and Function

    We have talked a lot about the structures and functions of biological molecules, but 'til now, we haven’t spent much time thinking about how structure and function relate to each other. Don't fret; biological molecules provide some great examples of this theme.

    Take the phospholipid bilayer. Recall that phospholipids are one kind of lipid; they have a glycerol backbone with two fatty acid "tails" and a phosphate "head." How does the structure of a phospholipid allow it to carry out its function?

    1. The fact that the tails are hydrophobic means that they do not interact with water. When a bunch of phospholipids are floating around in water, they try to arrange themselves in a bilayer that shields the hydrophobic parts from water-based, or aqueous, surroundings.

    2. The heads are hydrophilic and can then interact with water and other polar or charged substances on either side of the bilayer. The bilayer acts as a barrier that allows cells to maintain internal conditions that are different from external conditions, which is monumentally important for cells to operate properly. Everything from nerve impulse conduction to muscle firing to cellular metabolism depends on the cell's ability to maintain different conditions on opposite sides of the bilayer.

    3. Phospholipids demonstrate the intersection of structure and function in another way, too. We already know that fatty acids can be saturated or unsaturated and that unsaturated fatty acids have bends in their chains. Those bends prevent fatty acids from packing closely together, which causes cell membranes (membrane = phospholipid bilayer + other stuff) that contain lots of unsaturated fatty acids to be more "fluid." Fluid describes fatty acids that cannot pack in as tightly, and as a result, they move more freely over the surface of the cell.

    It might be weird to think about cell membranes as fluids, but actually, this property is really important for proper membrane functioning. Enzymes need to move around in order to work, and if a membrane is not fluid enough, it might become impermeable (walled off) to certain substances that normally pass through the bilayer easily. In sum, the fact that phospholipids structurally have polar and nonpolar parts, and the fact that fatty acids can structurally be saturated or unsaturated, allow phospholipid bilayers to properly function in regulating a cell’s contents.

    Proteins provide another great example of the intersection between structure and function. As we already know, proteins have four levels of structure: primary, or the sequence of amino acids; secondary, or the coils and folds from bonds between backbone elements; tertiary, or the coils and folds from bonds between R groups; and quaternary, or the conglomeration of more than one folded subunit. A protein is not a protein without its 3D structure, and regardless of what function it has, a protein is useless if its structure is somehow incorrect. Scientists in the field actually refer to proteins as having structure-function relationships. You don't get more thematic than that.

    Enzymes, for example, function by binding to a particular substrate, or substance. If the enzyme is misshapen, the substrate will not be able to find its binding site on the enzyme, and that reaction will never be catalyzed, or kick-started. Cellular receptors are also good examples. Receptors function much in the same way as enzymes: they have a specific site where a signal molecule can bind, and once that signal is bound, it sets off a chain reaction that conveys information to other parts of a cell, or to other cells in the organism. If a receptor protein has the wrong shape, the signal molecule cannot bind, and the flow of information will cease. That spells trouble for the cell.

    What causes a protein to have the wrong shape? There are a couple conditions that can cause this misshaping to happen. If a mutation (read: unexpected alteration) in the genetic code causes the wrong amino acids to be incorporated into the protein’s primary structure, later folding may be affected by that change. Sickle cell anemia is a blood disease caused by an incorrect amino acid in one of the subunits of hemoglobin.

    Hemoglobin has two subunits, and together, the protein's combined function is to bind to oxygen and deliver it to cells all over your body. Hemoglobin is present in your red blood cells, or RBCs for short, that circulate through your blood vessels, delivering oxygen to all your organs and tissues. People with sickle cell anemia have a valine amino acid instead of a glutamic amino acid at a certain position along the polypeptide chain. This alteration causes improper folding of the hemoglobin subunit that leads to two problems:

    1. Reduced oxygen-carrying capacity
       
    2. Red blood cells that have the wrong shape

    Yes, you read correctly. In this case, proteins of the wrong shape lead to whole cells that are the wrong shape! Those misshapen cells clog blood vessels and prevent proper circulation.

    Even if the sequence of the amino acids in the polypeptide chain is correct, proteins can still fold incorrectly if they are surrounded by bad influences. When proteins are forming and taking on their 3D shapes, they can be strongly influenced by environmental factors. Yes, proteins experience peer pressure, too. If environmental conditions are poor, blossoming proteins may go down the wrong path and fold incorrectly, rendering themselves useless. Luckily, there are special proteins, called chaperonins, that help other proteins fold correctly. Chaperonins are shaped like little capsules, and they provide a safe environment for proteins to fold correctly, away from all the bad outside influences. Once the synthesized proteins are properly formed in terms of structure, they are released into the wider world of the body they live in and carry out their functions normally.

    Here is how a chaperonin usually operates.

    And here is what a chaperonin usually looks like.

    As we have seen, structure and function relate to each other in different ways in lipids and proteins. Might there be other ways in which structure and function unite in carbohydrates? How about in nucleic acids? Keep thinking about structure and function as you learn more about DNA replication and protein synthesis.