Biology - Molecules and Cells


 Terms and Concepts 




Cell Functions




The world of atoms and molecules is one mostly of empty space - particles fly about in space, when they can, at relatively high rates of speed and bump into each other and into the matrix formed when particles crowd together into what we up in the macro world call a barrier.  In some barriers, the particles are so crowded (aided by their shared or almost-shared electron zones) that very little can squeeze through - these barriers would seem fairly solid to us, and would be largely impermeable, a term meaning that nothing (at least nothing significant or practical) could get through it.  Some barriers are hardly barriers at all, being for all intents and purposes permeable.  These two extremes are not absolutes - could anything be truly either of them? - but are useful as concepts.  Between these extremes, in barriers that stop some particles - that are impermeable to that type of particle - but allow others through - be permeable to those - we have the term semipermeable, and many barriers in living systems can change permeability according to needs, making them selectively permeable.

Selective permeability (video).

How permeability can lead to potentials and voltages (video).

But what moves the particles in the first place?  As discussed before, particles just move, each with its own tiny kinetic energy - speeding them up or slowing them down is associated with changes in temperature, which is a measure of the average particle speeds in the measured medium;  warmer equals faster.  And particles, when placed as a clump into a medium through which they can move, will tend to spread out, randomly distributing themselves from a crowded area to available less crowded areas.  This tendency to spread out, to appear to move from areas of high concentration to areas of low concentration, has a name:  diffusion.  We've all seen it at work:  a drop of ink or food coloring, or tea from a tea bag, spreading through the water around it, spreading throughout a cup whether we help it by stirring or not.  When there is a permeable barrier with an imbalance of particles on each side, there will be a net diffusion movement through the barrier - a movement called flux - until the concentrations are equal on both sides.  At this point, the material is in equilibrium, which means particles keep moving through the barrier but for each one going one way, there's one coming back.   As a diffusion exchange moves toward equilibrium, flux slows down.

Temperature effects on molecules (animation video).

Diffusion (animation video).

Introduction to flux.

Introduction to flux equilibrium.

The barrier that will be the main focus of this chapter is the cell membrane, a lipid-based barrier with water-based (aqueous) solutions on either side.  Flux through a barrier can be increased in several ways, some of which apply easily to cells and some of which don't.  For instance, the size of the particles affect the flux - smaller particles move faster - but living things can't usually change particle size in order to move something more quickly.  It should be obvious that speeding the particles up - raising the temperature -  will speed the flux, but that would have other effects on biological systems, so few cells or systems speed diffusion by warming themselves on demand.  

Diffusion through a membrane (video).

How flux factors are calculated.

But there are approaches that cells can use to increase flux.  One way to speed flux is to increase the concentration gradient, which keeps the net movement of material speeding from a crowded area into a much emptier one.  Cells do this by either processing particles just as they've crossed, or carrying them off, as blood systems do with cellular wastes, or sequestering them in other less-accessible parts of the cell that they can't come back from.  Sometimes, by being permeable in just one direction, the rate of entry slows as the amounts available to enter drop, but particles are not lost in a return flux.  Another feature of flux through a barrier is the limitations presented by the surface to be penetrated - the more surface area, the more particles can move through.  Cells commonly increase surface area (for example, with microvilli) to increase particle movement in or out.

Diffusion Theory background.


Many cells with microvilli.

A particular type of diffusion concerns a type of particle that follows all of the diffusion rules we just discussed, but sometimes gets ignored because it is the solvent rather than the solute.  Osmosis is the diffusion of water, moving from highly dilute areas to areas less so.  Typical cell membranes are permeable to water, and if the dilution of cell contents and that of cell surroundings are not in balance, there will be osmosis.  It should be no surprise that many organisms in the oceans have water concentrations inside that match the water concentrations outside (although the solutes will be different), so no net flux of water in or out has to be dealt with.

Osmosis in action (animation).


Osmosis (animation video).

Solutions can be labeled according to their particle concentrations - balanced solutions are isotonic.  If surroundings get too many solutes, as happens in some inland salt-water lakes, they are hypertonic to cytoplasm, and cells can lose so much water by osmosis that cell chemistry is affected.  If surroundings are too dilute, or hypotonic, water can flood into a cell, interfering with chemical interactions or even swelling it to the breaking point.  Organisms exposed to fresh water must somehow deal with osmosis, or they will die.  The flow of water inward can be so strong that it exerts an osmotic pressure.  In small plants, the flow from groundwater into the roots - root pressure - can be strong enough to push water up the plant against the pull of gravity (usually not very far, maybe half a meter).  Plants will also use water pressure (turgor pressure) in a central vacuole to provide a stiffness to their structure.  This is done by pumping particles, mostly potassium ions, into the vacuole, so that water diffuses in.

Basics of solutions.

Solution categories.

Red blood cells under the three conditions (video).

Time-lapse turgor pressure (video).

ADAPTATIONS TO DEAL WITH INCOMING OSMOSIS - In small fresh-water organisms, a few mechanisms will stem the flux.  One is a structure like a cell wall - a rigid retainer that will not let the cell expand beyond a certain size.  Many plants and bacteria need no other way to keep themselves from overfilling with water.  But animal cells, which lack cell walls, have a problem.  Some animals do produce casings to prevent swelling.  For other animals, two basic approaches work:  first, water can be pumped out as it enters, such as with a contractile vacuole;  second, in multicellular systems, the outer surfaces can be largely waterproofed.  In animals such as fish or crustaceans, only a few outer surfaces, such as respiratory or digestive linings, are not waterproofed.  They can't be, as a waterproof surface is also impermeable to oxygen and nutrients.  Any extra water that enters by osmosis across those surfaces is pumped out by structures like kidneys.

Contractile vacuoles in action (video).

Cell casings that can resist osmotic pressure.

Adaptations to fresh water or the changing dilutions of tidal pools would have "set up" a capability to deal with no surrounding water at all - a fish or crustacean waterproofed against osmosis in fresh water would also be resistant to drying out in the air.  For this reason, animal life on land almost certainly moved there from tidal and / or freshwater environments.




The Cell Membrane, also referred to as a plasma membrane or plasmalemma, is the primary interface between all cells and their environments.  This is the barrier through which materials have to pass, and it is a barrier to water and solutes mostly due to its lipid nature.

Intro to the membrane (animation).

The lipid part of a membrane is actually two layers, and each layer is made up of phospholipid molecules.  In these phospholipids, two carbons on the glycerol hold hydrophobic fatty acids, which tend to extend in the same direction, while the hydrophilic phosphate groups on the middle carbon face outward toward the surrounding water.  In the membrane, the inside and outside surfaces are phosphate groups, and the middle of the membrane is two layers of fatty acids.  Just the phobic reaction to water tends to form the membrane overall into a bubble shape - the molecules do not need to be bonded to each other, and in fact they flow around each other like floating balls in a very crowded barrel.  In the molecular model of membrane structure, the fluid mosaic model, these free-floating lipids are the "fluid" part.  The fatty acid components, which may be "kinked," can determine how tightly the molecules cluster and how permeable the basic membrane is.  The flow and looseness of the phospholipids can also be changed by cholesterol molecules floating in the hydrophobic layers.

Membrane structure.

Phospholipid structure.

Fluid mosaic model (animation video).

More on membranes (animation video).

And more, with cholesterol discussed.

But a membrane cannot be simply phospholipids, because it would be too impermeable - very few solutes could penetrate such a barrier.  Some very small, uncharged particles, like oxygen, carbon dioxide, even the occasional water molecule can slip through a pure phospholipid membrane, and particles that are themselves lipids, such as steroid hormones, can dissolve through, but there are many other things that need to get in or out of a cell, and many ways that a cell needs to interact with the environment other than serving as gatekeeper.  Those additional needs are served by a wide variety of proteins embedded in the membrane.  These proteins almost always have hydrophobic domains which fit them into the middle layer.  Some of the proteins float on a surface, while many penetrate through from one side to the other - they are the "mosaic" part of the fluid mosaic model, presenting a meaningful pattern out of small bits on the surface.  Embedded proteins may be involved in transport, as pores, or gates, or carriers, or pumps, etc;  they may be receptors, picking up and relaying messages to the other side;  they may be markers, allowing cells to tell one another apart;  they may be connectors in multicellular systems;  and the list goes on an on.

Permeability of "just" the lipid bilayer.

A hydrophobic domain.

More on transmembrane proteins.

Pores, also called channels, are essentially small holes through the membrane, but the edges often have charged domains that exclude many ions - for life that evolved in an environment full of sodium and chloride ions, that would have been a must - so only small uncharged or slightly charged particles pass through easily.  These particles would follow a diffusion flux - oxygen and other nutrients flow in (and are used, which lowers their concentrations and preserves the gradients), wastes flow out and spread or get carried away.

Pores built when a cell must die.

Gates are pores that can be opened or closed as necessary.  A nerve impulse travels down a nerve as a wave of gates opening and closing, letting an imbalance of ions suddenly but temporarily diffuse through and change the overall charge of the membrane.  Muscle cells activate in a similar way.

More on gates.

Carriers are used to pass materials that can't get through the pores.  Carriers tend to be specific for particular materials, and in fact are in many ways like enzymes.  What would be an active site on an enzyme is called a binding site on a carrier or receptor, and the substrates are often referred to with the more general term ligands.  Such molecules also follow Michaelis - Menten Kinetic patterns.  Some carriers are single-step passers, while others may involve a sequence of surface and intramembrane molecules.  If a material flows with such help in the direction diffusion should move it, the process is called facilitated diffusion and, although it may require some energy to accomplish, is generally considered passive transport, like all diffusion-oriented movement through the membrane.  Some carriers do double duty as enzymes, helping to change the materials as they get passed through - this process is called group translocation.

More on carriers.

Introduction to Michaelis - Menten Kinetics.

Group translocation in action (video).

Pumps move materials through a membrane opposite to the direction the materials would diffuse;  driving them against the normal flux takes energy, and this process is called active transport.  Sometimes pumps are linked to other carriers, in either the same or opposite direction, which may supply some pumping power from their own flux, or pumps are linked and help each other work - these cooperative systems are called coupled channels.

A coupled pump (animation video).

Endocytosis (and the reverse, exocytosis) is a form of active transport that forms vacuoles from cell membrane around something that has no dedicated carriers.  It does require cellular energy to accomplish.

More on exo- and endocytosis.









Cells only arise from similar pre-existing cells - that's part of the Cell Theory, and its as reliable as any rule in biology can be.  But how do cells make new cells that can do all the same things they can do?

Well, sometimes they don't.  In multicelled organisms, not all cells make new cells.  In humans, for instance, few or no new nerve or muscle cells are made after infancy.  And many cells, like blood cells, are made from cells that are not functionally blood cells.

But in cells that will reproduce, the requirement is that the root of all functions, the information center from which everything can be built, the DNA, must be copied, and complete copies must be distributed properly to the new cells.  The process of DNA copying is called replication.

Replication animation.

Replicating DNA follows a process called semiconservative, which means that each "copy" is half new and half original, but the two sides are not duplicates of each other.  Enzymes start the process - topoisomerase allows most of the heavy unravelling of DNA from its coiled form, and helicase straightens the helical structure and causes the strands to separate.  This can all be done on a short length of a chromosome at a time.  Primase attaches small RNA priming sequences on each strand.  DNA polymerase, starting at the primers, puts a new strand across from the old strand.  Replication can move in only one direction along the strands, which means that one side can be replicated from the primer along the entire length of the chromosome (areas open ahead of it and close behind it), but the other side must be made in bits and pieces the other way while stretches are open, going "backwards" with multiple primers.  Those bits are called Okazaki fragments.   Eventually, a second DNA polymerase replaces the RNA primers with DNA bits, telomerase (if active) makes sure the chromosome ends (telomeres) are finished where the polymerase was attached, and two chromosomes exist where one was.  These two chromosomes remain attached to one another at the centromere.

Replication (CGI video).

Topoisomerase (video).



DNA polymerase.

Okazaki fragments.

More on telomeres and telomerase.

In many multicelled systems, a multi-level "check" occurs to tell whether the cell should make copies - cell damage, especially DNA damage, may block the process.  The cell might be "flagged" for apoptosis or removal instead.  In many organisms, telomerase stops being made in some cell populations, which degrades the chromosome tips and prevents new cell production, so the system can no longer repair damage - this is implicated in many aging processes.  In some cells, the damage-detection-and-response system stops working - this can cause damaged cells to make more damaged cells, leading to cancer.



A cell that's doing what the cell is supposed to do is almost always in interphase, the stage between cell divisions when the DNA is accessible, proteins can be made, and activities of various sorts can happen.  An ameba crawling across a pebble, a photosynthesizing leaf cell, a skin cell being pushed to the surface, are all in interphase.  If a particular cell is going to divide, its interphase can be subdivided into stages, with the first called the G1 Stage.  If the cell is going to divide, certain critical RNAs and enzymes are made in this stage.  If the cell is not going to divide, it stays in this stage until it dies.  But in dividing cells, there is an S Stage, when DNA is replicated, followed by a G2 Stage, another active stage that also includes preparation for the division.

Animation of cell cycle.

Interphase (Video).

Interphase stages (interactive animation).

The division of a eukaryote cell requires the division of the nucleus first, a process called mitosis.  Once the cell heads toward division, the progress follows a set pattern of new phases -

Videos of dividing cells.

PROPHASEThis will set up the cell so that a complete complement of chromosomes can be placed on each side of the division plane, an area called the cell equator.  As prophase progresses, the DNA-protein complex of the cell winds up tighter and tighter, condensing first down to visible-in-a-light-microscope strands which were the first objects to be called chromatin (now the term applies to the DNA-protein complex that's always there, visible or not), and eventually becoming visible as separate, double-stranded chromosomes,  each one with two chromatids connected at a centromere.  At the "ends" of the cell away from the equator, the cell poles, microtubule-organizing centers called centrioles, inside a complex known as a centrosome, have moved into position (the cell had started with one from the last division, and a copy has been made during interphase) and begin to grow microtubules, called spindle fibers, in all directions.  Some of the spindle will attach to the cell membrane and hold the centrioles in place - others will attach to structures on the chromosomes centromeres called kinetochores.  But at the start, there is something in the way - the nuclear envelope is between the microtubules and the chromosomes, and nuclear structures such as the nucleolus and the nuclear matrix surround them.  All of these structures will "disappear" during prophase, although what exactly happens to them isn't clear - are they broken into bits and dispersed within the cell or broken down entirely?  Probably both, to varying degrees in different cells.  But once these obstructions are removed, the microtubules attach to the chromosomes and start to pull on them - the longer the microtubule, the stronger the pull, and the ensuing "tug of war" will go on until each chromosome has equal-length microtubules on each side, putting the chromosomes on the equator of the cell.



Chromosome-spindle interactions.


Prophase (video).


Prophase (light micrograph).

METAPHASEOnce the chromosomes are close to centered in a cell (arranged in a disc, although it looks like a line from the side), the cell is considered to be in metaphase.  This phase lasts until the cell signals the chromatids to separate.  The centromeres "pop" apart;  now each single-stranded chromosome is attached to microtubules hauling it toward a particular pole, and once they are separate and moving away from each other, it's the next phase...


ANAPHASEDuring this stage the separate groups of chromosomes are drawn toward the poles, away from the equatorial division line.  In plant cells, the beginnings of the cell wall that will separate the two new cells, the cell plate, begins to form.


TELOPHASEThis phase puts things back the way they were before prophase, so much of what happens is like the steps of prophase, but in reverse.  The spindle detaches from the chromosomes and disassembles.  The nuclear envelope reforms around the chromosomes, which loosen up into chromatin and seem under a light microscope to disappear, while the nucleolus reappears.  Eventually, conditions are back in interphase.


CYTOKINESISActual division of the cell may not take place during mitosis, or it may occur in anaphase, telophase, or the next interphase.  Some cells use mitosis, which is technically just production of new nuclei, to produce a multi-nucleated cell that may or may not divide at some point.  When cells divide, microfilaments usually pinch the membrane until separate cells are made.  If the division is in two and equal daughter cells are made, its called binary fission;  if unequal (as in yeast), budding;  if multiple cells are produced all at once, fragmentation or multiple fission.  Budding and fragmentation are also forms of asexual reproduction in multicelled organisms, producing multicelled offspring but following the same patterns.

Mitosis and cytokinesis (video).

In PROKARYOTES, where there is only one chromosome, cell division follows a different course.  DNA is replicated, producing two separate looped chromosomes, but each then attaches to the cell membrane well away from where the cell will divide by binary fission.  After division, the chromosome releases into the new daughter cell.

Prokaryote division.





When reproduction is going to be sexual, then a mixing of genetic materials will occur, usually an all-out one-for-one mix that involves an entire set of chromosomes from one source mixing with a full set from another.  This is one of the reasons that eukaryotes are diploid, carrying two sets of matched chromosomes.  One set can be separated out to mix with one set from the other source (note that the word is "source" rather than "parent," as this can be done with just one individual).  Whether this is done with the mixing of nuclei directly, as happens with some protozoans or fungi, or done with cells to carry nuclei, as in animals and plants, the process requires nuclei that are haploid (also called monoploid), with just one set of chromosomes rather than two.  The process to make these is called meiosis, sometimes called a reduction division.

Diploid, defined by the over-qualified.


Meiosis animation.

Meiosis begins like mitosis, with an interphase that, among other things, replicates DNA.  This means that the cell undergoing meiosis starts with its two sets of chromosomes doubled - it's going to have to make four nuclei if each will have only one set each.  Meiosis gets to four nuclei by going through two division stages - one to two nuclei / cells, then another to four - that are called Meiosis I and Meiosis II.  Both divisions go through the prophase, metaphase, anaphase, telophase order, but there are some differences compared to mitosis.

Premeiotic interphase.

Ciliate protists do a very complicated meiosis dance.

MEIOSIS I -   During prophase, chromosomes are not just hauled to the equator, but pairs of homologous chromosomes are set up next to one another (synapsis), where they may swap pieces by crossing over.  Crossing over separates linked alleles.  The odds that two linked alleles will separate depends on how far apart they are - separation rates can be used to map locations of genes on chromosomes.  During metaphase, the chromosomes do not separate into single strands - homologous chromosomes are pulled away from each other and eventually wind up in different nuclei.  These nuclei are haploid (one set), but the chromosomes are double-stranded.  A short interphase follows, just a bridge to the next division.

Meiosis tutorial.

Crossing over.

More crossing over.


MEIOSIS II -  This looks like a typical mitosis, except that there's only one set of chromosomes present - at metaphase, single strands pop apart and are pulled away from each other.  Four nuclei (usually in 4 cells), each with a single set of single-stranded chromosomes, are produced.

Differences between mitosis and meiosis.

FUSION happens when two nuclei from meiosis merge together, mixing their chromosomes.  This can happen when nuclei are exchanged between protozoans, when non-gendered cells cross fungal bridging fibers, or when a sperm cell nucleus has entered an egg cell.

The meiosis-mitosis cycle.

SEX WITH GENDER -  Most organisms that reproduce sexually also do it through the use of genders, roles played by participants during sexual reproduction.  Male / female is the most common but not only gender system.  But what makes males male and females female is not what you probably think it is.  Remember, maleness and femaleness are terms that have to apply not just to people and dogs but to trees, and flower parts, and organ systems in animals that are male and female simultaneously (monoecious, what used to be called hermaphroditic, as opposed to separate-gendered dioecious species).  And don't assume it always involves "X" and "Y" chromosomes, which is just one way of several to set up gender.  Simply put, male and female are defined by the gametes, the sex cells, that are made - everything else is peripheral to that.  Many of the "regular" differences between males and females can easily be traced to the differences in their gametes.

Research into gender.


Gender determinants in humans.

Females BY DEFINITION make...

Males BY DEFINITION make...



Are much bigger, since this is where the food for the next generation is stored.

Are much smaller, since they have to be more mobile.

Just need to be somewhere that sperm can reach them.

Need to be able to get to where the egg cells are.  This is done in various ways.

Are produced in much lower numbers, since each is a bigger investment of resources.

Are produced in much larger numbers, since their individual chances of reaching an egg cell is low.

During meiotic production, one cell retains all of the food and becomes an actual egg cell, while three polar bodies are used to discard "extra" sets of chromosomes.

Each meiosis produces four functional sperm cells.

When organisms moved from a water-based environment up onto "dry" land, it seems that the hardest change to adapt to was the lack of a support medium that sperm could swim through to reach the egg cell.  It was the last problem definitively solved in the evolution of vertebrate land animals (female internal fluids substitute for outside water, eggs don't dry out or poison themselves) and land plants (sperm are sealed into pollen).

Family tree of land-living vertebrates.


Terms and Concepts

In the order they were covered.

Selectively Permeable  
Effects on Flux  
Flux Effects in Cells  
Solutions & Osmosis  
Osmotic Pressure  
Root Pressure  
Adaptations Against Osmosis  
Osmosis Resistance & Life on Land  
Cell Membranes  
Phospholipid Molecules  
Fluid Mosaic Model  
Membranes - Embedded Proteins  
Binding Sites  
Facilitated Diffusion  
Passive Transport  
Group Translocation  
Active Transport  
Coupled Channels  
DNA Replication  
DNA Polymerase  
Okazaki Fragments  
Cell Cycle  
G1 Stage 
S Stage 
G2 Stage  
Cell Equator  
Cell Poles  
Spindle Fibers  
Cell Plate  
Daughter Cells  
Binary Fission  
Cell Division in Prokaryotes  
Haploid / Monoploid  
Meiosis I  
Crossing Over  
Meiosis II  
Male (Sperm) vs Female (Egg Cell)  
Polar Bodies



General Biology 2 - Molecules and Cells

Copyright 2013 - 2019, Michael McDarby.

Reproduction and/or dissemination without permission is prohibited.  Linking to this page is fine.



Hit Counter