Biology - Molecules and Cells


 Terms and Concepts 





History of Genetics


In keeping with the concept that people of earlier ages were not stupid, it was long understood that most reproduction produced offspring that somehow displayed combinations of the traits of the parents.  If you bred individuals with some particular trait in common, you increased the chance that such a trait would be prominent in the offspring, but it didn't always work that way.  You could make plant cuttings and pretty much get a duplicate plant, traitwise, but pollination produced the same sort of mixtures that animal reproduction gave.  How did it all work?  Were there hidden rules that could be discovered and applied?

Gregor Mendel was fascinated with science and Nature, but in order to get enough training he had to enter a monastery in what was then Austria (now Brno of Czechia).  In a classic example of using the materials at hand, Mendel took advantage of the monastery's production of peas:  for years he bred peas in special separate plots, focusing on a few one-or-the-other features (such as Tall / Short, or Wrinkly Pea / Smooth Pea) that he could isolate in a "pure" form.  After hundreds of tests, with new plots of hybrid plants and plots of hybrid-hybrid crosses, Mendel developed the first basic rules of what would come to be called genetics.

Mendel mini-biography.

More on Mendel's tests.

Mendel's rules.

Mendel decided that traits were determined by some sort of internal code pieces which he called genes.  For any particular trait, there might be code variations of a trait, like leaf color, or degree of the trait, such as a variation in the Height Gene for Tall and one for Short.  These variations he called alleles, which, he realized, are carried in each individual in pairs (although there may be way more than two allele variations in a whole population, each individual generally just gets two, one from each parent), of which only one is passed on to each offspring.  For each trait that is determined by a single gene, an individual's particular version of that trait is a product of their two alleles.  Mendel thought that every single allele pair was sorted separately for reproduction, which turned out later to not be true, but many of them do sort independently.

More on Mendel.

Mendel's Laws and terms.

Mendel "tells you" his work (animation).

As a side effect of Mendel's choice of pea traits, he also discovered a genetic feature called dominance, where the presence of a dominant allele can completely hide the presence of a recessive allele.  This either-or condition was necessary to his working out genetic rules, but it has since been found (and he almost certainly realized) that many traits don't follow such a simple pattern.  Many allele effects are not that strong or weak, but rather blend to produce the trait.  (In human eye color, very dark alleles can be dominant over very light alleles - brown can dominate blue - but middle-strength alleles blend, such as when green and light brown produce hazel)  It also turns out that many traits, in fact most traits, are a product of at least two genes working together, two alleles per gene;  these multiple-gene traits (also called polygenic) do follow rules based upon Mendel's discoveries, but the complex mixing of many alleles makes predictions of offspring traits a matter of complex probability.  With all that we know of genetics, breeding racehorses is still a matter of mating parents with desired traits and hoping everything mixes properly in the offspring (racing ability is a multiple-gene trait), which is what they have been doing since before Mendel was born.

Dominant / recessive human traits (most probably not that strongly).

How gene patterns (genotypes) affect visible features (phenotypes).

A few types of inheritance.

Human height - a multiple-gene trait

Mendel wrote and published several papers on his discoveries, but no one in the scientific community noticed, possibly because no one had taken such a mathematical approach to biology before.  When he died, as far as he knew his research and findings would make no difference to the world.  However, in the very early 1900's, three scientists investigating the same sorts of processes discovered Mendel's papers, and those papers became the foundations of what is now called genetics.

Following Mendel.

We know a bit more about genes today.  The researchers who followed up on Mendel's work through the 20th century discovered some additional details:

A genetics timeline.

Groups of genes are linked together.  Researchers in Britain and the Netherlands, building upon Mendel's rules, found that seemingly unrelated alleles sometimes follow inheritance patterns that suggests  they were connected to each other in some way.  It turns out that our cells do not carry thousands of separate codes floating about;   genes are bound together along the lengths of chromosomes.  This is called linkage:  for example, genes that are found on sex chromosomes (many of which have no direct effect on gender) exhibit what's called sex linkage.

One feature of any species is its characteristic chromosome number, usually an even number in sexually-reproducing species because of the pairs  (humans have a chromosome number of 46, for 23 pairs).  There are advantages and disadvantages to both low and high chromosome numbers:  with low numbers, the distribution of copies that must happen whenever new cells are made is easier - there are fewer chromosomes to copy and fewer copies to distribute properly;  but with higher numbers, the sorting becomes more complicated, increasing variability in offspring, which increases evolutionary flexibility.  The numbers vary widely, including some plants with amazingly high numbers.


How linkage is used.

Sex linkage.

Some chromosome numbers.

Extreme chromosome numbers.

For each chromosome gotten from one parent, there''s one from the other that "matches" it, with spots for all of the same genes even if the alleles differ.  These pairs are called homologous chromosomes.

About twenty years later, as it became obvious that linkages could occasionally be broken, it was discovered that pieces of  homologous chromosomes could be swapped during certain cell events.  This process, called crossing over, supplied yet another way that alleles could be recombined.

Homologous chromosomes.

Crossing over.

One weakness of Darwin's original theory is that it could not explain where "new" features (which turn out to be old features, dramatically changed) came from - natural variations couldn't really explain how feathers evolved from scales, for instance.  But many years later, in work mostly with fruit flies, mutations were discovered:  spontaneous changes in genetic material, producing new alleles that produced new variations on traits, sometimes distinctly new traits.  Soon it was found that x-rays could induce mutations, with greater doses making more changes.  We now consider any change in DNA, whether it is in genes or not, to be a mutation, and it is known that mutations to a gene will usually have no effect on the coded trait, will tend to have a bad effect if an effect exists, but occasionally will produce a valuable change.  And a particular type of mutation from crossing over can produce duplicate genes in offspring, allowing for the mutational change of an existing trait (say, snake saliva to venom through changes of the "extra" saliva gene) while preserving the original action (not losing the original saliva protein).  This might also explain why more "advanced" organisms seem to have more genes than more "primitive" ones.    Genetic redundancy works these two ways - coding is redundant (for reasons covered when the details of code-to-protein are covered) and is hard to effectively alter, and "extra" or redundant genes may be produced by duplication.  The extra genes, according to recent research, have at least 4 functions if they are not shut off or deleted:  they can help produce more of the coded protein;  they can be available to perform if the "original" fails;   they can become involved in differential expression, allowing fine-tuned regulation of production (especially in multi-step chemical pathways);  and they can develop a new function, possibly dramatically different from the original, which was mentioned above as important to evolutionary "jumps." 

Discovery of mutations.


One way that redundancy can work (abstract).


Redundancy in plants.


Code redundancy.


Recent redundancy research.

Work with a bread mold, Neurospora, in the 1940's, led to the discovery that allele mutations were producing changed traits by affecting single enzymes (which are proteins) in the mold's metabolic pathways, leading to a clear idea of what exactly a gene is:  a code that is used to make particular proteins.  Cells then use those proteins to create the "traits" that Mendel connected to genes.  Mendel's height gene, for instance, codes for a type of plant growth hormone protein.  What makes alleles different is that they produce proteins that have slight (or major) molecular differences, changing how they work.  The definition of "gene" itself has continued to evolve;  this simple one works at the introduction level.

As mentioned, the Neurospora mutations affected single enzymes in a pathway that used several.  The fact is that many if not most traits are the result of pathway processes;  even what seems like single-gene traits are actually multiple-gene traits.

Images of Neurospora.

All about Neurospora.

How discoveries of functional RNAs is changing the term "gene."

A glossary of genetics terms.


DNA had long been suspected of being the coding material in cells, but when broken down to its handful of components, it seemed too simple to be able to carry such complex information.  However, during the late 1940's, work done with phages, viruses that use bacterial cells as sources to produce more viruses, showed that in many circumstances the only viral material getting into the host cell was DNA, and that supplied all that was necessary for the cell to make and assemble the next generation of viruses.  DNA, it was confirmed, could act as a code, and it could carry all necessary information all by itself.

Intro to phages (on a site suggesting they should replace antibiotics, a real thing but maybe not from this place).

During the 1950's, work done by James Watson, Francis Crick, Maurice Wilkin, and Rosalind Franklin led to an understanding of how DNA can hold complex information on a molecular level.  They found that the molecule was a two-stranded, cross-connected spiral, called  a double helix, and that a type of component called a nitrogenous base, in only 4 varieties, produced the code from their sequential order along one strand.  Since each base type will only connect to one other type across the way, the two strands could be separated and a new strand added on that would exactly duplicate the old complement.  Most mutations arise when some aspect of the sequence is changed.

A page from the Nobel Prize people on this discovery.

Image of the double helix.

The four nitrogenous bases (there is a fifth, used in RNA) are Adenine, which cross-connects only to Thymine (and vice versa), and Cytosine, which only connects to Guanine.   In RNA, Uracil replaces Thymine and cross-connects to Adenine.   Inside an actual gene sequence, each 3-base sequence on the DNA strand is a codon (actually, its a codon once its transcribed to RNA) that will be translated into one amino acid of the protein coded for.  Often a single base-change in a codon will translate to exactly the same amino acid (or one very similar), which is the molecular basis of that one type of genetic redundancy.  More detail on how this all works appears in the next chapter.







Since Mendel, it has been discovered that in some circumstances for an individual, having two different alleles for a trait can be better than a matched pair of the same alleles, a condition called hybrid vigor (also heterozygote advantage or heterosis).  This often is the reason that human genetic diseases have spread through a population.  For example, the gene for the oxygen carrier hemoglobin has a allele that makes a nonround version of the protein when oxygen is not attached;  if you get a pair of these alleles, it gives you sickle-cell anemia, a dangerous disease that affects the shape of entire red blood cells and impairs circulation.  In areas where malaria, a disease caused by a blood parasite, is common, people carrying one regular hemoglobin allele and one sickle-cell allele have more resistance to malaria than those with two regular alleles, giving them an advantage that passes sickle-cell alleles to their offspring.  Other genetic diseases may have similar effects:  cystic fibrosis alleles might make single-carriers resistant to diarrheal diseases (which kill huge numbers across the world), Tay-Sachs seems to produce a tuberculosis resistance, and schizophrenia (which is a multiple-gene trait and harder to sort out) may in some combinations increase creativity and the willingness to take risks, important features for some individuals in human societies.

More on hybrid vigor.

How this applies to cystic fibrosis.


And sickle-cell anemia.

And Tay-Sachs disease.

And schizophrenia-?

Over recent decades, the role of genetics in traits of all kinds has become a major focus of research.  As a bridge to answering those questions, lots of high-profile work has been done in the analysis of genomes, or the total DNA carried by particular species of organisms (or, really, by an individual selected as a representative).  Genomes have been determined for many disease organisms and popular research organisms, as well as through the Human Genome Project.  Of course, knowing the sequence of all of human DNA doesn't tell you which gene does what, or even what all of the non-gene DNA does, but it's a useful step.

The Human Genome Project.

The mouse genome.

Even E. coli!

Very recent work has led to the hypothesis that changes in parts of the DNA involved in regulating gene expression, especially a type called a cis-regulatory element, may be even more important to evolutionary changes than gene mutations.   It may not be so much what we have as how we use it.  The idea that development, with its environmental-response gene expression, is a major player in evolution is called evo-devo.

Research on cis-regulatory elements (abstract).




Warning:  prepare to abandon your preconceived notions about reproduction!!!

There are two basic forms of reproduction in living things, asexual reproduction and sexual reproduction.

ASEXUAL REPRODUCTION.   If you're thinking "reproduction without intercourse," now's a good time to abandon that idea - most sexually-reproducing organisms do it without intercourse.  No, "doing it" is not any part of the definitions here.  In asexual reproduction, offspring are genetic copies of the original. They may or may not be physical copies - all of your cells, produced asexually, have the same genetic make-up, but they are not physically identical (you'd be a formless blob if they were).  This ability to exactly pass on a parent's genes to offspring is a huge evolutionary advantage - it's the only form of reproduction that really is reproduction.  But there is a problem:  evolution, adapting to changing environments, depends upon variation, and there just isn't much in this approach.  A change that can hurt one individual offspring should be equally damaging to all of them.  To survive over the long haul, asexual reproducers have tended to  compensate by producing huge numbers of offspring.  This allows some variation, from mutation (which rarely is good, but if you make a trillion offspring your odds for a beneficial change get better) and often spreads offspring out so harmful local changes will miss some.  This evolutionary need to generate offspring on a large scale usually keeps such reproducers small, also.  Some have also survived in those rare places where variation is barely important:  extremely stable ecosystems or microenvironments.


When two modes seems to appear in subgroups, it gets very complicated.


Some think that sexual reproduction first appeared in parasites (unlikely).

SEXUAL REPRODUCTION.  No, it does not require two parents;  many, many sexual reproducers can accomplish it with just one that is simultaneously male and female.  Additionally, even genders are not required - many sexually- reproducing protistans and fungi do not have male and female forms.  In sexual reproduction, single sets of alleles from two sources are combined in offspring.  The huge advantage here is the mixing aspect of the allele sets:  potentially, every individual produced can be different from every other one, even from a single parent reproducing alone, increasing the variation that evolutionary processes need.  This allows evolution to work while only small numbers of offspring are made, a necessity in the making of larger organisms.  The disadvantage, of course, is that exact genetic copies cannot be made, even of extremely successful individuals.  You can't pass on everything that makes you what you are, or even preferentially the best aspects - it's all luck, even if natural selection drives the odds in favor of beneficial alleles over time.

An explanation of the costs and benefits of sexual reproduction (pdf).


Generating variation.

In general, asexual reproducers are small, often tiny, and capable of producing the huge amounts of offspring needed for meaningful variation.  Sexual reproducers exist across the range of organism sizes (although sexual reproduction in usually-asexual prokaryotes is only a sort-of sexual reproduction - they swap bits of DNA, just a gene, maybe a couple, with each other in the small chromosome-like packets called plasmids), and produce offspring numbers roughly according to their chances of surviving long enough to make offspring on their own.  Some organisms are capable of reproducing either way according to circumstances - one wonders why this option isn't more common - and a few groups of organisms reproduce first asexually, then sexually, then asexually again, and so on, following a pattern called Alternation of Generations.

Plasmid sharing and antibiotic resistance.


Plasmids in genetic engineering.

Of the three major circumstances under which alternation of generations has evolved, only one seems connected to the evolutionary advantages of being able to make offspring both ways:  several types of parasites, organisms that live by stealing resources from other, larger organisms, will go through an asexual stage in one host then a sexual phase in another, then back to a host of the first type, etc.  Making copies of a successful form alternates with mixing genes from successful forms, worthwhile for complex life cycles with the odds stacked against them.  The other two circumstances where alternation of generations is common involve life cycles with at least one stage unable to move.  In animals, an example would be found in corals, which asexually produce huge colonies, then generate swimming jellyfish-like forms that swim off and mate sexually and help to distribute offspring away from the original site.  In the first land plants, which were still tied to using open water for sperm to swim through during mating, larger asexual reproducers could spread by way of airborne spores, but the sexual reproducing forms stayed small and in places where open water could accumulate to support sperm. 

Alternation of generations in a parasite.


Coral life cycle.


Alternation of Generations in plants (video).




 Today, relationships among organisms are often determine by comparative biochemistry, which can be done by looking at three different types of molecules:

- Metabolic molecules.  Snakes might be grouped according to similarities in their venoms, for instance.

- Proteins.  These long sequential molecules provide lots of comparison points.

- DNA.  Also a long sequential molecule, its assumed that close relatives will share similar sequences, but once two groups lose contact, they will accumulate differing mutations at a predictable regular rate over time, especially in non-coding areas (which may or may not be true).  Differences in DNA sequences are used like molecular clocks to decide when the family tree forked, how far back in time two organisms shared an ancestor.  There's a huge amount of uniformitarianism in the assumptions involved, but for the moment folks seem to accept the calculations as trustworthy.

Comparisons of sea snake venoms (note it does not turn out to be taxonomically useful). 

Intro to molecular clocks.

A critique of believing too much in the regularity of molecular clocks.

A molecular clock leads to an estimate of when humans began to wear clothes.




It was soon recognized that what really changed in an evolving population was the frequencies at which certain alleles appeared, since they were what produced Darwin's selected traits.  But what might influence how allele frequencies might change over time?

Godfrey H. Hardy, an English mathematician, and Wilhelm Weinberg, a German doctor, developed a set of rules under which the allele frequencies in a population would stay the same indefinitely:  this is called Hardy-Weinberg Equilibrium, sometimes the Hardy-Weinberg Law.  It kind of has had a backwards effect on evolutionary theory.  We know that allele frequencies do change as species evolve - this law about the conditions under which they would not change tells us what factors must be involved in keeping certain "new" alleles present until such time as changing conditions select them as advanatgeous.

Hardy biography.

Weinberg was otherwise, maybe, not so nice.

More on Hardy-Weinberg.

NO NATURAL SELECTION.  Well, obviously natural selection has an impact on evolution.  But if a new allele has no real survival impact, it won't disappear over time.

NO MATING SELECTION.  (Also, all population  members breed and produce the same number of offspring)  This amount to No Sexual Selection.  Mathematically, all members must reproduce as well.  Again, it's the persistance of unique mutations that's really important here.

NO MIGRATION of members in or out.  This would remove alleles from a population or bring in others.  This led to the realization that the more isolated a population is, the more chance that the other evolutionary effects could work without blending with alleles from populations adapted to perhaps different conditions.  It also became obvious that connections between populations in somewhat different environments might preserve a "type" suited to both but not particularly suited to either.  Something else can happen in isolated groups evolving in similar environments:  genetic drift comes from the unique combinations and mutations (which, after all, occur randomly) that change the flow of evolution in each group, producing separate species when it would seem that natural selection would have kept them the same.

NO MUTATION.  This process actually alters alleles.  Even though the odds for a beneficial mutation are not good, it still can have a profound effect on how a group evolves.  And once a mutated allele appears, the odds of it mutating again to disappear is vanishingly small.

POPULATION MUST BE HUGE.  In a population of only 100, any lost individual will have a strong effect on the allele ratios, the gene pool, of the group;  the more individuals in the group, the harder it is for chance occurrences to strongly affect the gene pool.  This also means that all of the other factors will affect a small group more powerfully than a large one.  Some processes are based upon this principle:

- The founder effect is used to describe what happens when a small group breaks off from a large population and becomes isolated.  The group's gene pool probably is not an exact duplicate of the larger group's allele mix, changing the possible combinations and altering the potential direction of the founder group's evolution.

- The bottleneck effect is made when some catastrophe reduces a population to a much smaller group, which then evolves based on that restricted gene pool.

Founder and bottleneck effects. 

Founder effect and genetic drift.




Basically, any situation that reproductively isolates one group from another allows them to set up their own separately-evolving gene pool.  It turns out that this can be done in more than the obvious way...

- Geographic isolation.  When groups become physically isolated from one another - one winds up on an island, or separated by a river, mountain range, desert, whatever - this will give you separate breeding populations.

Geographic isolation in salamanders.

- Niche isolation.  A niche is a functional "spot" or "job," a role in an ecosystem that can be performed by some type of living thing.  Niches are determined by place, time, and relationships.  Most ecosystems have a top predator, for instance, although just what species occupies that niche varies in different places, and in a single place that may change from day to night or season to season.   Darwin's finches represent a founding population whose descendants split into different specialist species, a process called adaptive radiation.

Niche isolation leads to adaptive radiation.

- Temporal isolation (time-based).  This term is sometimes applied as type of niche isolation, if a single species begins to break into a day-active group and a night-active group.  Usually, however, it refers to when parts of a group vary by breeding periods, which is not a type of niche isolation.  If subgroups are reproducing at different times, they easily become separate gene pools.

More on temporal isolation (abstract).

- Behavioral isolation can arise from many different types of behavior:  groups with different courtship rituals, or which cease to recognize each other as potential mates, are examples.

More on behavioral isolation.

- Mechanical isolation.  These are issues of physical form that prevent successful mating.  In groups that copulate (and many do not), occasionally changes in the physical features of genitals can isolate a group.  There are species of beetle that show this isolation.  It can also apply to flowers whose shape shifts the use of particular types of pollinators.

More on mechanical isolation.

- Chemical / Immunological isolation.  Sometimes a mutational change in chemistry will cause a rejection of sperm or zygote (the first cell of the next generation) so that one group can no longer reproduce with the other.  This may be more common with plants, where acceptance or rejection of pollen can be an important trait.

How the concept applies to human reproduction.

These ideas have led to a biology discipline called biogeography, which is concerned with the broader distribution of living things.  Biogeography has been a huge source of evidence for the theory of evolution by natural selection, by showing how often features of organisms in an ecosystem reflect the nature of the environment.

The International Biogeography Society.




You have inherited features that are not in your genes - a particular language and culture, a particular community and physical location, things that came to you both from parents and from others.  These can be passed down through generations, but are not passed as packets of DNA;  factors such as these are called epigenetic factors.  This term is new and going through quite a bit of fluctuations of meaning - more and more, this refers to the details of DNA processing, packaging, and regulation mentioned above.  To others, this is a broad area including anything heritable but not necessarily carried by  DNA primary gene sequences.

Introduction to epigenetics.


Using epigenetics to fight tumors.

Other organisms can pass along epigenetic factors through learning, placement, and other things (this area seems to be gradually being separated from the "mainstream" definition of epigenetic).  Sometimes cells pass altered parts on to offspring, which duplicate the altered parts and pass them on also.  The maternal environment around developing seeds, eggs, or embryos can affect developmental processes.  This is, in a way, the inheritance that Lamarck's theories were based upon, so he wasn't completely wrong.

Cytoplasmic epigenetics (video lecture).

Epigenetics against viruses.

An entire subdiscipline, memetics, has grown up around this idea, with memes being essentially inherited non-genetic information.  Whether such inheritance can really be described in classic evolutionary terms is a bit controversial still, but the term has caught on big time in cyberspace.  This term seems to be more and more separating out as what was one of the broader bits of epigenetics.

More on memetics.

Memes used to mean something.




A TIMELINE of genetics discoveries.

Did Mendel alter his own data?

Manic-Depressive Disorder as a Multiple-Gene Trait.



Terms and Concepts
In the order they were covered.

   Gregor Mendel (mid to late 1800s)
Dominant / Recessive Alleles
Multiple-Gene Traits
Crossing Over   
Chromosome Number
Homologous Chromosomes
Genetic Redundancy   
Gene - Modern Definition  
DNA as Hereditary Carrier   
DNA:  Double Helix   
DNA:  Nitrogenous Bases   
Genetic Redundancy - Molecular Basis   
Hybrid Vigor  
Human Genome Project   
Asexual vs Sexual Reproduction
Alternation of Generations
Reproduction Types and Evolution
Comparative Biochemistry
Molecular Clocks
Hardy-Weinberg Law
Evolution & Isolation
Genetic Drift
Gene Pool
Evolution and Chance
Founder Effect
Bottleneck Effect
Isolation Types
Adaptive Radiation 
Epigenetic Factors



General Biology 2 - Molecules and Cells

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