Introduction to Biology

Molecules and Cells


Chapter 5 - Organic Molecules 


What makes a Molecule "Organic"?


As the science of chemistry was developing, there was an understandable fascination with chemistry that was unique to living things.  As more and more was learned about the elements that could be found in living things, it was realized that carbon was a major component, found in any type of organism that was analyzed, and even in every compound that was extracted.  Molecules with carbon in them were assumed to be associated with organisms, and so were called organic molecules.  We know that carbon, with its ability to bond to four other atoms, can form very complex molecular structures, making it the perfect candidate for building such molecules around.

But this is science, and no terms or ideas seem to last without some modification.  There did seem to be carbon compounds in minerals that were not derived from living things, so carbon alone wasn't enough;  organic molecules came to need both carbon and hydrogen.  We have since found methane, CH4, and other such materials, in the dust of space and on other planets and moons, but the old definition hasn't been changed.  It is now thought that when the Earth first formed, the oceans were full of the small organic molecules of space dust, forming primordial soup, from which truly living systems formed.  

More on organic molecules.

An article about organic molecules that shows how tricky it is to show 3-dimensional molecules in a 2-dimensional image. 

Organic molecules found on planet circling another star (video). 

More on the origins of Life on the planet.


Major Types of Organic Molecules

The organic molecules found in living things fall into four major classes.  Each class of molecule has features that determine its use in living systems.

The first class of molecules are called carbohydrates.  The simplest type of these, monosaccharide simple sugars, have a basic formula:  for every carbon atom, there are two hydrogens and one oxygen, or one water for each carbon.  Carbo - hydrate.  Glucose is a common carbohydrate that will show up again and again as we discuss cell chemistry:  its formula is C6H12O6.  Table sugar, sucrose, is two single sugars bound together:  a disaccharide simple sugar.  Sugars can be anything from a single sugar molecule up to several bound together.

When organic molecules are bound together, a bonding site must be freed up on each participant.  This happens by clipping a single hydrogen from one participant, and an oxygen-hydrogen piece (hydroxide) off of the other.  Where each bit used to be become the new bond, and the two freed pieces stick together as H2O.  This building process where water comes out is called dehydration synthesis, and is used whenever we build molecule from components.  When molecule chains need to be broken apart, such as happens in digestion, the opposite reaction happens:  the bond breaks, and one spot gets a hydrogen while the other gets hydroxide.  A water molecule breaks apart - in Latin, that's hydrolysis, and that's what this process is called.

Sugars can be bound together in long chains, which may form branches and even networks:  these huge carbohydrates are called starches.  Both sugars and starches are commonly used as sources of energy in cells:  sugars are broken apart for the bond energy, and starches are a way to store lots of sugars in a fairly inactive form.  Large, stiff starches can also be used as structural molecules:  cellulose is what hold most plants up.  That "-ose" ending is a giveaway that something is a carbohydrate, although they don't all end that way.

When the same type of molecule component is used over and over in a much bigger molecule, the bigger molecules are called polymers.  Starches, proteins, and nucleic acids are all different types of polymers.

There are other uses for carbohydrates in living systems, but energy and structure are by far the most common ones.

Monosaccharides, showing how they bond typically into a ring with an oxygen "bridge."

Formation of sucrose, showing dehydration synthesis (video).


More on carbs.


A bit of artwork based on polymer molecules.

The second class of organic molecules are called lipids.  Fats and oils are included in this class of molecules.  These have a fairly simple structure, starting with the 3-carbon glycerol molecule.  Each carbon picks up a bit called a fatty acid, which can be short or fairly long, and then it's a lipid molecule.  A pair of terms that can applied to other types of molecules often shows up in descriptions of lipids:  a saturated molecule has all of the atoms its carbons could possibly hold, and has only single bonds in the fatty acid chains;  an unsaturated molecule has at least one double bond between carbons, and so could hold at least one more hydrogen.  Not surprisingly, this alters the chemistry of the molecules.

Lipid molecules are usually hydrophobic:  they won't dissolve in water and tend to separate out from it (materials that will dissolve in water are hydrophilic).  Vegetable oil is a lipid - what happens when you mix them?  This makes them useful as water barriers, and they are found in cell membranes as well as such things as waxes and waterproofing oils.  Not mixing with water also reduces their chemistry, and lipid molecules can be a nice, nonreactive place to store extra energy:  the lipids in fat are constructed for longterm energy storage.  When energy is really needed, the fat molecules are broken apart and "fed" into the middle of the same process that gets energy from sugar molecules.

Some lipid molecules can dissolve well enough in water to move around, but also can dissolve through other lipids like those in cell membranes;  this makes lipids good signaling molecules.  Included in this group are steroid hormones.

Lipids also has other, varied uses, including insulation in organisms that need to hold onto heat in unusual conditions, like deep underwater.  Lipids are also commonly a holding point for lipid-soluble toxins, which can accumulate there to dangerous levels.  Many manufactured toxins, like pesticides, are lipid soluble:  it helps get them into the target organisms, but gets them into others as well.

Lipid basics.

Basic lipid molecule - note the main glycerol connecting the 3 fatty acids.

Saturated and unsaturated.

Fat molecules - each carbon bond holds a bit of usable energy.

Steroids get pretty complicated.

Technical abstract about the action of some lipid-soluble toxins.

Article on how pesticides may disrupt female reproductive function.

The last two classes of molecules are huge polymers.  Proteins are long chains of components called amino acids and have three to four levels of structure.  The first level of structure, called primary structure, is just the order of amino acids in each chain.  At the secondary structure level, amino acids in a particular region connect to each other and produce local formations, like pleated sheets of coils.   At the tertiary structure level, the entire molecule is pulled together into a particular three-dimensional shape, often through hydrogen bonds but sometimes through cross-connecting covalent bonds.  Only some proteins have a quaternary structure, where the molecule has more than a single chain of amino acids, but again the overall three-dimensional structure is critical, because the function of proteins is connected to their shapes.  When these shapes are changed, the functions may change or disappear;  this can happen when other molecules attach to them, when the proportion of ions around them changes (such as in pH shifts), or when a change in temperature shakes or compresses the shape.

The possible shapes that proteins can take is virtually infinite, so they have a broad array of possible functions.  What follows is just a partial list, some of the major things that proteins do in living systems.

Primary structure.

Secondary structure.

Tertiary structure.

Quaternary structure.

All the levels covered.

StructureMost cells have particular shapes, and those shapes are commonly held together by proteins that connect to the outer membrane and often to each other.  Cells are often held together with protein-based structures. Protein is an important component to structure in fungi, in animals in exoskeletons, and in things like tendons, ligaments, and cartilage.

Movement.  A single cell moves, or swims, using a protein-based movement system.  Animal muscle depends upon two proteins, actin and myosin, contracting cells.  Membranes have proteins that help move things through the barrier.

Communication.  Cells often send signals to each other using various types of proteins.  Many hormones are proteins, as well as pheromones (signals-by-scent) and alarmones (signals that alert other individuals).  Protein neurotransmitters carry signals between nerve cells.  Receptors may be at the target cell that will attach to the signal molecule, and there are receptors that pick up other things, such as the light receptors in visual systems.  Antibodies are proteins made specifically to attach to "foreign" molecules (the foreign molecules are called antigens);  once attached, the molecule changes to a shape that attaches to receptors on immune cells and activates them to attack whatever the antibody is attached to (in an autoimmune disease, a system makes antibodies to molecules on its own cells and calls attacks on them).

Chemistry.  The reactions that happen in cells often need a boost to get going, and that boost is supplied by enzymes, most of which are proteins.  Enzymes are catalysts, chemicals that activate and speed along reactions.  They typically are named to give some indication of the reaction they aid, and commonly have the ending -ase on their names. Almost every bit of chemistry done in cells is aided by enzymes.

Cell junctions with several proteins labeled.

Proteins in cilia, which help some cells swim.

Coronavirus spike protein attaching to human cell protein.

Activity of actin and myosin (Video).

An article about pheromones.

How neurotransmitters work.

Antibody structure.

How enzymes work.

The last class of organic molecules are the nucleic acids.  There are two varieties:  ribonucleic acid,  or RNA, and deoxyribonucleic acid, or DNA.  These polymers are long chains of components called bases, of which there are only five types.  RNA is a single-strand molecule;  DNA is a spiral of two cross-connected strands.

DNA carries information.  Part of the DNA in a cell is genes, which code for protein molecules.  Each type of receptor, or enzyme, or neurotransmitter, has a stretch of DNA in which its sequence of amino acids is coded.  The code-to-primary-structure ratio is three-to-one:  three bases (called a codon) per amino acid.  The codes proteins can vary, and code variations for a single type of protein are called alleles.  Different alleles can produce proteins that have the exact same amino acid sequence, have different sequences but no difference in activity, have different sequences that produce different levels of activity (including no activity at all), or produce a new type of activity.  These will be returned to in the chapter on genetics.

DNA is the code from which living things are made, since the DNA codes for proteins and the proteins are the foundation of cellular chemistry.  Carbohydrates, lipids, and nucleic acids are made by enzyme-driven systems. 

A huge proportion of the DNA on many chromosomes is not used for protein production.  This non-coding DNA is made up of many different types of DNA stretches:  some are critical to interacting with the proteins that hold chromosomes together;  some are codes that aren't used, either old sequences or dangerously mutated sequences or foreign sequences (invaders from disease organisms);  some are non-gene codes that work to get genes processed;  some produce functional stretches of RNA (see below);  some are short stretches that exists to propagate themselves, a kind of molecular parasite;  and a lot of what's there, no one knows what the origin or possible purpose is.  All of this used to be called junk DNA, but that term is going away as functions are discovered for these bits.

The other nucleic acid form, RNA, is used in getting DNA code to protein sequence.  RNA moves the code from where it is stored to where it is executed.  RNA is a critical component of the cell parts that takes the codes and makes the protein.  Small RNA molecules do all sorts of things in and around the genes;  some are ribozymes, having similar activity to enzymes.

More on nucleic acids. 

Nucleic acid roles in images. 

RNA and DNA structures. 


More on RNA functions. 

More on non-coding DNA.


Go On to Next Chapter - Cells


Introduction to Biology - Molecules & Cells.
For SCI-135.

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