Biology - Molecules and Cells


 Terms and Concepts 



CHAPTER 5 - Major Organic Molecule Classes




There are four basic types of molecules that are the major players in biological systems:  carbohydrates, lipids, proteins, and nucleic acids.  These molecule types each have at least two major functions and all interact in complex ways, sometimes producing combined molecules as well.




A stable molecule, big or small, will have electrons in all appropriate places (all of the orbitals will be occupied by electrons, native or borrowed), and not spontaneously link with other molecules.  When the bigger organic molecules are being made from small pieces, bonds in the original component molecules must be broken and parts taken off to provide places for new bonds to form.  This is how large molecules are built from smaller components.

Such construction of molecules, a process called synthesis, is done almost universally with a process called dehydration synthesis,  with the removal of a hydrogen from one component and a hydroxyl from the other (H + OH combine to form H2O, so the components lose water or dehydrate).

When large molecules are broken down, the process happens in reverse - the bond between parts is broken, with a hydrogen placed on one and hydroxide on the other.  Since water is "split" to do this, the process is called hydrolysis ("water breaking") and occurs in such processes as digestion, and when molecules are not useful and get broken down in cells for use as energy or to build new molecules. 

Dehydration synthesis. (Video)

Dehydration synthesis. (Odd Video)

More on hydrolysis.

Hydrolysis of non-organic material. (Video)




Carbohydrates tend to be the least complicated type of major biological molecule.  As smaller molecules, they take the form of individual rings with carbon "corners," with one oxygen acting as a sort of "clasp";  when these rings open up, which they do occasionally (molecules, remember, are always moving and shaking, so the rings occasionally pop open), it tends to be at the oxygen spot.  In simple ring form, the basic formula takes the pattern of CXH2XOX ;  this is where the name comes from, carbon + water (hydrate).  Typically the "X" ranges from 4 to 6.  These molecules are also called saccharides.  They can be strung together in disaccharides, trisaccharides, etc., but as small molecules they are usually called sugars.  As individual molecules are strung together, the loss of water for every connecting bond (that's why it's called dehydration synthesis) alters the X-2X-X ratio, but the numbers stay close to the base relationship.  Carbohydrate types are commonly named with words ending in -ose.  Not every carbohydrate does this - sugars follow the rule a bit more reliably than starches - but if you see a molecule name with -ose on the end you should know that it's a carbohydrate.

Introduction to carbohydrates. (Animation)

Glucose image.



Sugar basics.

Sugars are extremely important as sources of semi-immediate energy for cell processes by way of the process of respiration.  Respiration on a cellular level breaks down sugar molecules and transfers much of the bond energy to ATP, which can be used to supply energy more directly to cell chemistry.  Short strings of sugars are also sometimes attached to proteins to make identification marker molecules on cells.  Sugars are mostly built by a process that, as a reaction, is a mirror image to respiration:  photosynthesis.  Photosynthesis uses energy that starts as light but gets transformed into energy to "glue" parts of carbon dioxide (CO2) and hydrogen from water molecules together into sugars, with oxygen as a "leftover" product.  The most advanced type of respiration uses oxygen and breaks sugar down, sending the bond energy that way-back-when was in light form into bonds of ATP, and producing CO2 and H2O as products.

Respiration does not always involve oxygen.

Respiration with oxygen.

Basics of photosynthesis.

Starches are long strings of sugar molecules, which can be organized as simple strings, branched strings or interconnected strings.  Any molecules that exist as strings of the same or similar subunits are called polymers; starch, proteins, and nucleic acids are all polymers, as are many artificial materials, such as plastics.  It's a relatively easy way to build big molecules.  Starches have two major uses in organisms:  they serve as a storage place for sugars and therefore energy (extra sugar in your blood is stored as starch in your liver, and seeds, nuts, and roots are starchy to store energy for plant metabolism), and they can be used for structural support.

More on starches.




More complex forms.

Sugars can be connected with two different three-dimensional arrangements to make starches, and it is not easy to explain or show in two dimensions the differences.  First, the loss of hydrogen from one side in each is from a hydroxyl group, leaving oxygen to form the "bridge" between the sugars - the position of that oxygen between each sugar is different between alpha linkages, which are found in starches, and beta linkages, which are found in major structural carbohydrates, such as the wood and grass fiber cellulose.  You could say that plants use photosynthesis mostly for making plant structural tissue, and that using their starch for energy is only important during sprouting and when the suns gone down.  Humans and most animals have digestive processes to break alpha linkages and release the sugars, but almost no animals have their own processes to deal with cellulose.  The ability to process fiber has evolved mostly in a few fungi, protozoans, and bacteria, and fiber-eating animals like cows use bacteria "buddies" (called symbiotes, members of a relationship where both participants benefit - cows get sugars and bacteria get a great place to live) to do the digesting for them.

Polysaccharide basics.

How the bonds work.

Alpha linkage image.

Beta linkage.

More on cellulose.

Cellulose digestion in insects. (Abstract)

Carbohydrates often show up as parts of other materials, as you will see in nucleic acids, and there are several types of molecules that are mostly carbohydrate in nature but which may have other characteristics as well.  These include mucopolysaccharides, more correctly known as glycosaminoglycans, which carry sulfate and amino groups and give distinct characteristics to such materials as mucus and other types of slippery, viscous mucins, or to another structural material, chitin, used both to reinforce cells in fungi and as skeletal elements in arthropods, including insects.

Mucopolysaccharides and human health.

More on glycosaminoglycans.





Of the four major organic molecule types, carbohydrates and lipids are both fairly simple.  Lipids have two major constituent molecules:  glycerol, a 3-carbon molecule with alcohol groups on each carbon;  and, attached to the carbons of the glycerol through the oxygens of the alcohol groups, three fatty acids,  unbranched chains of a few or many carbons with various attached groups and a carboxyl group (the acid) at the far end.  Generally the middle fatty acid points away from the top and bottom ones - although, again, in three dimensions it may not be exactly opposite.  3-fatty-acid lipid molecules (variants may have other components attached to one or more of the glycerol carbons) are virtually nonpolar, which makes them not mix with water.  The fatty acid molecules may be saturated (no carbon-carbon double bonds) or unsaturated.  If one of the glycerol carbons is carrying a group that is not a fatty acid, this is still a lipid-type molecule, such as the phospholipids that make up cell membranes.

More on lipids.


The pieces of the molecule.


Fatty acids and human health.

Lipids have several uses in living things.  A major use is as water barriers, as happens in cell membranes, but these are usually made of lipids whose central fatty acid is a phosphate-containing chain that is hydrophilic while the other two chains are hydrophobic.  Lipids are also used for extra waterproofing, as waxes and oils, when water entry or water loss is a special problem, or as insulation around nerves, trapping a complex soup of water and ions and keeping it close to the nerve membrane where it is needed.  Lipids are often used in animals for long-term storage of energy in the form of fat:  fat in cell inclusions is close to chemically inert, which makes it ideal for long storage, and it has physical properties that can be taken advantage of as well.  When necessary, fats can be broken down into molecules similar to breakdown intermediates of respiration and fed into respiratory processes for energy.  While stored, fats can be used as cushions, as is the fat between your eyeballs and the bony sockets they are in, or as heat insulation, important in animals like us who generate and maintain a constant body temperature.  Several types of messenger molecules, including steroid hormones (most hormones are proteins, but some are lipids or combinations), are lipid-based molecules as well.




The next two molecule types are typically much larger and much more complicated than the first two, and the most complicated of these two are the proteins, whose functions are tied to their three-dimensional shapes and whose shapes are virtually infinite in variety.

Like many very complicated things in living systems, proteins are built in discrete and often simple steps.  For instance, although a protein presents a complex "surface" to the world, inside it is actually a single, sometimes a few, strings of small simple molecules bound in sequence. 

Slideshow about proteins.


Basics of protein structure.

Amino acids are the "building blocks" of that long string, making proteins another type of polymer.  All amino acids share a basic structure:  a central carbon, called the alpha carbon, holds three critical components (and a hydrogen):  on one side, an amino group; on the other, a carboxyl group; above, a variable R group that determines just which amino acid it is.  Theoretically, there could be many R groups there, producing huge numbers of different amino acids, but in earthly life only about 20 different types are found.  The charge characteristics of various amino acids varies, producing different polarities and solubilities, which can give different regions (domains) of proteins different properties.

As introduced last chapter, any molecule with a bond around which opposite sides can rotate exhibits what is called chirality:  with all of the same atoms bound together in different ways, called isomers (because of how the bonds form, there are limited ways that the twistings can set up), you can still have "mirror image" forms of the molecules, stereoisomers or enantiomers.   Chiral molecules can be L-isomers ("left-hand" twist) or D-isomers ("right-hand" twist);  if you were to synthesize amino acids in a test tube, you would get about a 50-50 split of L- and D-isomers, and there would be almost no chemical difference between them.  However, proteins in living things are almost exclusively made up of L-isomers, and no one is sure why.

Amino acids. (Animation)

Chemistry of amino acids.

The 20 types of biologically common amino acids.

Enantiomers. (Video)


One explanation for why Life's isomers are left-handed.

Another explanation. (Abstract)


On the first level of protein complexity, called primary structure, proteins are a string of amino acids in a particular order, starting from the free amino end (called the N-terminus or the amino terminus) and running to the free carboxyl end (the C-terminus or the carboxyl terminus).  Biologists had to originally pick an end to work from in describing the sequences, before anyone knew how they get made, and were lucky to pick a directionality that turned out to match the way that the amino acids are actually connected together as proteins in cells.  Since amino acids can also be called peptides, the bond of one carboxyl to the next amino, from the carbon directly to the nitrogen (no oxygen bridge, with the OH being lost from the carboxyl side and the H from the amino side in dehydration synthesis) in the primary structure is called a peptide bond.

As has been covered and will be dealt with in more detail later, the information from which proteins are built is carried in genes:  a gene codes for a type of protein, but those codes can vary, with the code variations called alleles.  Although many alleles exist that have no effect on primary structure, for reasons the will be explained later, what is important is that alleles may change primary structure in a variety of ways, from "swapping" a single amino acid for another, up to changing the entire sequence.  How much that affects what the protein does depends on how much the higher orders of structure are changed.

Structural levels.


Primary structure. (Research image)


Importance of the N-terminus.


Protein with ends labeled. (Image)


Peptide bond. (Video)

Amino acids connect in a string but how the bonds form puts each amino acid at a particular angle to the next.  Each peptide bond is stable in space, a condition called "rigid," so the connections in space along the sequence between known amino acids are predictable.  Sometimes a sequence of connections causes the string to spiral, forming a helix; sometimes the connections angle back and forth in a nearly flat plane and cross-connect to a similar part of the string, forming a pleated sheet.  These very localized patterns are called secondary structure of the protein.  The angled bonds will also generally cause some parts of the protein to bend around back toward itself.

The main contributing patterns to secondary structure. (Image)

As the string of amino acids bends, kinks, and twists, often different sections of the string come close enough to each other to interact.  Different attractive forces may bind parts of the protein into bundles, called domains, that themselves can interact.  Domains commonly have specific activities, and a single protein may have several domains that do different things and even influence each other.  The attractions involved can include weak forces of atoms in close quarters, the clumping of hydrophobic areas in solution, hydrogen bonds of various strengths, up to full charge-charge interactions of ionic bonds, bridging of trapped water molecules, or, as mentioned before, covalent bridges.  These interactions lead to an overall "external shape" for the molecules, an outer face that interacts with the molecular world, called their tertiary structure.  The stability of tertiary structure varies, and may be disrupted by several factors:  temperature (both high and low), pH, and attaching other molecules, among others, can disrupt connections and cause tertiary structure to alter.  An unwinding of protein structure (and loss of the function associated with that structure) is called denaturation.  Denaturation doesn't change primary structure, but the change in tertiary structure may be irreversible, as when egg-white albumin is boiled, but it may be reversible - a common way to "turn off" a proteins function is by temporarily changing its shape, followed by renaturation.  

Sometimes other non-peptide atoms or molecules wind up integrated into the protein's tertiary structure - many dietary minerals do this - and are called prosthetic groups.  Many proteins have a function that requires binding to other molecules and forming complexes that may be fleeting or permanent.

Peptide bond connections and secondary structure. (Video, Indian lecture)


More on secondary structure (Video).


Tertiary structure. (Images)


Protein denaturation. (Video)


Prosthetic group (heme).  (Image)

If a functional protein is made up of more than one discrete amino acid string, the protein has a quaternary structure more complex than a single string would have.  Not all proteins have quaternary structure, since many are single strings.

The particular shapes that tertiary and quaternary structure provides underlie many of the almost infinite numbers of functions that proteins can do.  Many proteins act by attaching to other molecules, often represented by a "lock and key" model, but there is much more going on here than simple complementary shapes - when substrates connect to proteins, the electron interactions and changes in shapes that happen after the connection are an extremely important part of what's going on.

Usefulness of quaternary structure.

Quaternary structure. (Video)

Protein structure in motion. (Video)

Many visualizations of protein structure. (Video)


Protein synthesis, since it involves converting genetic sequences to primary structure, will be covered in more detail after nucleic acids have been discussed;  however, some details are pertinent here.  Proteins are constructed one amino acid at a time, but the final tertiary structure of the protein, the shape it needs to take to do its job, rarely just "happens."  A class of proteins called chaperonins are involved in making certain that proteins coming out of the production phase form their proper shapes.  The molecules also may as heat-shock proteins work in overheated cells, such as cells in hot-spring environments, to restore proper shape to denatured proteins.

Chaperonins in action. (Images)


Lots of information (too much, really) about protein folding. (Slideshow)




In molecules with a limitless range of potential shapes, the things that can be accomplished are just as limitless.  Here we will deal with just a few very important but general applications to which proteins are put in living systems, and please note that these designations are artificial labels and some proteins can reasonably be included in more than one group:

Some protein types have relatively stable forms and functions:

STRUCTURAL ELEMENTS, especially on small scales such as on and inside cells.  On a cellular level, proteins take the forms you might associate with construction materials:  cables, struts, and sheets.  Cells that have particular forms are held in those shapes by proteins.  Above the cell level, proteins are common in structural elements, such as cartilage, but there are non-proteins found at that level as well, like the cellulose in plants or calcium carbonate, a salt, in bones.

Picture of fluorescing structural proteins.


Collagen is a structural protein.


MOVEMENT ELEMENTS.  With very few exceptions, any kind of visible movement in living things, whether the movement of microscopic cell parts or the movement of your own arm, is produced by protein systems.  Force for movement is generally exerted as a pull, which can come from compression of a spring-like protein or the movement of two proteins across one another, shortening the length of the complex.

How the proteins in skeletal muscles work. (Video)

COMMUNICATION MOLECULES.  These may work several different ways, and this is a function often performed by non-proteins as well.  Communication may be over distances, as is done by protein-based hormones, smell-message pheromones, or neurotransmitters carrying nerve impulse messages across tiny gaps (synapses) between nerves in a sequence, or communication may be across barriers, as is accomplished by many proteins embedded in cell membranes that carry signals into and out of the cell.  Another type of protein that could be considered in this group are antibodies, which are created by the immune system.  Antibodies have two active domains.  One end of the molecule has domains specifically built to attach to antigens, molecules (usually protein-based) that have gotten into the body but which are different from any of the body's molecules - they are foreign, and automatically treated as being dangerous.  An important source of antigens is external molecules on disease-causing invaders like viruses and bacteria, but any foreign molecule of sufficient size can stimulate an antibody response.  The other antibody domain is the communications domain, activated when antibody-antigen binding changes the shape of the antibody molecule;  this marks antigens and the invaders carrying them for various responses designed to remove them.  If your immune system is working properly, you currently have antibodies in circulation to every disease organism (among other things) that you have even been exposed to, which will prevent new individuals that might cause an "old" disease from being able to "set up shop" in your system.  Simply put, the antibodies will "flag" returning invaders for immediate removal.  In allergies, environmental molecules (called allergens) that should not set off a response do.

A growth hormone molecule.


More on pheromones (article).


A LOT of stuff about neurotransmitters.


Antibody molecule.


How immune response works.



Some proteins function through changes and transitional forms.   Most of these are capable of temporarily binding other molecules, called substrates or ligands, and doing something with them, as antibodies above were mentioned doing:

CARRIERS / TRANSPORTERS.  Proteins may form temporary complexes with atoms and molecules that increase solubility, to move materials around in circulation fluids, or may pass materials through barriers such as cell membranes.  In humans, lipoproteins, help lipid and lipid components dissolve in the blood and tissue fluids.  These lipid carriers do not make the lipids fully soluble, though, and are implicated in circulation problems that arise when lipids settle out and build up on arterial linings.

How lipoproteins work.

RECEPTORS.  These proteins change in response to some input, often when other molecules connect to them temporarily.  Living things have many different types of receptors, for things like communication molecules, nutrients, smells and tastes, and even wavelengths ("colors"), levels of light, and magnetic fields.

A receptor in action.

CONTROL AND REGULATION MOLECULES.  These are directly involved in adjusting the function of metabolic systems, often by attaching to molecules that are vital to the flow of a particular process or pathway.

A pathway, with enzymes.

ENZYMES.   Important enough that several later sections will be spent discussing their operations, these are the catalysts used in almost every known biological systems.  A catalyst speeds up the rate at which a chemical reaction takes place by reducing the amount of energy it takes to get it started (activation energy).  Enzymes bind to substrates, bringing potential pieces together in synthesis reactions (anabolism) so that they bind together, or grabbing larger molecules and stressing them in ways that encourage them to split into separate pieces in breakdown reactions (catabolism) It can be said that any kind of chemistry that occurs in organisms only occurs because specific enzymes exist for any given step of the processes.  Enzymes are usually very specific for substrates;  very few will react with multiple substrates.  This three-dimensional pickiness, which is also found in things like receptors and other binding proteins, is called specificity or stereospecificity.  For example, sucrase is a digestive enzyme used to break down table sugar, sucrose, but it cannot react with the similar molecule in sucralose, known commercially as SplendaTM Enzyme types are usually named with an -ase ending;  like carbohydrates, however, all enzymes don't have this ending, but chemicals with this ending are all enzymes.  Like any catalyst, when an enzyme has contributed to a chemical change and released the product(s), it returns to its original form, ready to help again.  However, just because an enzyme emerges from a reaction in the same form it started as does not mean that it doesn't change while the reaction is going on.  The old image of a solid lock-and-key system does not give a truly accurate idea of how these molecules work.

An introduction to catalysts.

More on activation energy.

An enzyme-substrate complex.

A series of enzyme-aided steps, with alternative pathways along the way.

Sucrase at work.

How the sucrose - sucrase connection works.

Splenda (sucralose, similar but different enough.

PRIONSThese were at one time important functional proteins, but accidentally became twisted into a dangerous new form that could cause other copies of the proteins to themselves change to prions - these are the closest thing nature gets to actual zombies!  These can cause diseases by shutting down the function of important proteins, and some cause infectious diseases.

The Big Battle - Prions against Lichens!!

As mentioned earlier, this is just a list of major functions performed by proteins, without getting into the long list of more minor activity, and proteins often resist categorization and could be put into multiple classes from this list.




A bit has already been said about how nucleic acids - or DNA, one type of nucleic acid - hold the information from which proteins are made.  But there's more to it than that.

Nucleic acids are another type of polymer, another long string of repeating subunits.  The subunits in this case are nucleotides, which are themselves made up of three pieces:  a five-carbon ribose sugar - ribose or deoxyribose, which is where the names of the 2 major types come from;  a phosphate group that actually links the string of sugars together;  and one of five possible nitrogenous bases, attached to the sugar and capable of cross-linking to bases on other strings.  Three of the five bases, adenine, cytosine, and guanine, are found in both DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Acid);  the remaining two are similar, but thymine (not to be confused with thiamine, the vitamin) is found only on DNA while uracil takes the same "spot" on RNA.

An introduction to nucleic acids.

Nucleotide definition.

Nucleotide structure and DNA.

How the bases cross-connect.

In RNA, the polymer is a single string, commonly called a strand;  DNA is double-stranded, held by hydrogen bonds in a spiral (helix) and cross-connected between bases on strands "running" in opposite directions, so there is a double helix.  The cross connections are very particular:  adenine on one side only bonds to thymine on the other (and vice versa), while cytosine only bonds to guanine.  This means that if you know which base is on one side, you can accurately predict which one is on the other.  Adenine will only link to thymine in DNA and uracil in RNA;  cytosine only links to guanine (and vice versa).  This set-up of complementary strands produces excellent copying potential:  copies of DNA are made by separating strands and then building new ones across from each old one, and the new strands will be duplicates of the "peeled off" strands.

RNA molecules.


Double-strands of DNA.


DNA and evolution.

Briefly, with details in a later chapter, DNA carries the genes, codes from which proteins can be built.  Genes exist as stretches of DNA (or multiple stretches that can be combined) on very long structures called chromosomes.  There may be a number of variant sequences for the same gene - those variants are called alleles, and the variations may or may not significantly affect the protein coded for.  Chromosomes carry more than just genes (and any given chromosome will house hundreds to thousands of separate genes):  one of the cutting-edge aspects of genetics is figuring out what all of the "extra" DNA is there for.  In a story that is sadly all too common, until recently the extra DNA was called "Junk DNA," which shows how a common hypothesis following, "we can't figure out why this is here," is "well, then it must have no purpose."  Much of that unknown has been explained:  there are templates for many functional RNA molecules, remnants of viral DNA long shut off, old genes no longer used, sections involved in chromosome structure or gene processing, and many bits that are essentially molecular parasites, existing just to reproduce and spread among the genome.

The coding process depends upon codons, three-base sequences along one strand of the DNA (sort of) that convey three basic codes:  a) one codon for where the gene code starts;  b) various codons that can each be translated into an amino acid in the protein sequence;  c)  one codon for where the gene sequence ends.  This means that any coding gene has three times more bases in the sequence than the protein will have amino acids.  Except, of course, that this is biology, and the truth is much more complicated and confusing than that.

Information about fluorescently-labeled chromosomes.


More on what's known about the "junk."


The process of DNA code - to - protein sequence.

While DNA for the most part has a single basic form and function, RNA has a range of roles, mostly involving DNA processing.  When a protein must be made in a cell, the two strands of the gene responsible are separated.  Using the actual code strand, a strand of messenger RNA (mRNA) is made in a step called transcription.  The mRNA then moves to where the actual protein will be made (ribosomes, cell structures which themselves have RNA in their construction), and a small type of RNA performs most of the next step, translation.  It is transfer RNA (tRNA), with a codon-based connector on one end and an amino acid carrier on the other, that allows base sequence code to become amino acid sequence reality.

RNA molecules can be active beyond their coding and decoding roles, but not much is known yet about that aspect of the molecules.  Recent research hints that some short-strand RNA molecules, called microRNAs, may be used by many types of cells to block the replication of RNA viruses.

More about transcription. 

Making messenger RNA. 

Transfer RNA at work. 

RNA has its own scientific journal!

RNA Variety.

Even circular RNA.




The reason that this section appears early is not to "weed out" students who may not have the preparation to grasp such concepts (that can be a side effect, though), but because the ideas and terms here will be important immediately and often in even the most basic discussion of living systems.  This can all be quite overwhelming, but you will need a basic understanding of the roles of sugars, starches, lipids, proteins, and nucleic acids for the next sections to really make sense.


Terms and Concepts

In the order they were covered.

Dehydration Synthesis  
Sugar Uses  
Sugars and Respiration  
Sugars and ATP  
Sugars and Photosynthesis   
Starch Uses  
Alpha vs Beta Linkages  
Symbiotes / Symbionts  
Lipid Components  
Fatty Acids  
Lipid Uses  
Amino Acid Structure  
Alpha Carbon  
R Group  
Isomer Types  
Primary Structure  
N-Terminus / Amino Terminus  
C-Terminus / Carboxyl Terminus  
Peptide Bond  
Proteins & Genes  
Proteins & Alleles  
Secondary Structure  
Tertiary Structure  
Prosthetic Groups  
Quaternary Structure  
Protein Synthesis  
Protein Uses  
Protein Substrates  
Activation Energy  
Specificity / Stereospecificity  
Nitrogenous Bases  
DNA / Deoxyribonucleic Acid  
RNA / Ribonucleic Acid  
DNA Structure  
Complementary Strands  
Junk DNA  
RNA Uses  
Messenger RNA (mRNA)  
Transfer RNA (tRNA)  



General Biology 2 - Molecules and Cells

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