A cell stores the basic
information it needs to do everything it can do in DNA codes -
genes - that can be used to make all of its proteins, including
enzymes used to make almost everything else. But it doesn't
carry a bunch of separate pieces of DNA - the genes are stuck
together on chromosomes.
cell makes offspring cells, all of the genes need to be copied, and
a copy of each needs to get into each new cell. The fewer
pieces that must be copied and distributed, the better the chance
that it will be done properly. This is why genes are linked
together on chromosomes. Chromosomes also carry other
important pieces - stretches that control how genes are read and
spliced, stretches that allow interactions when other genes are
activated, stretches that code for many different types of
functional RNA. There is also a lot of DNA in a chromosome
whose function, if it exists, is unknown - those are often used for
genetic comparisons, since mutations in a non-functional part of a
chromosome should be passed along to offspring with no selection
acting on them.
Species have their own characteristic
chromosome number. For prokaryotes, it's typically one;
for eukaryotes, it's usually an even number, since they carry
matched pairs of homologous chromosomes. Low
chromosome numbers are better for cell division: fewer
pieces, fewer mistakes. High chromosome numbers tend
toward more mistakes, but can be sorted out in many more
combinations. This produces higher variation in offspring,
very important in evolution.
More on the relationship of genes to chromosomes, specifically in
Linkage of some disease-related alleles on human chromosomes.
Some different species' chromosome numbers.
Image of human chromosomes
(colors added), showing 22 types in homologous pairs plus the sex
Chromosomes are not just
DNA, but a complex of DNA and special packaging proteins called
histones that allow a long strand of DNA to be spooled and
coiled into a small place. These proteins produce chromosomes
with thick or thin spots, or even with light and dark stripes.
Chromosomes also have special structures, centromeres, that
hold copies together and are used to move them around during cell
division. Each species has a particular karyotype - an
analysis of their chromosomes by total number, then by the shape of
Since the packaging varies along
the chromosomes, some genes can be easier or more difficult to
access when the protein is produced. Changes in the packaging
patterns can happen, change how the gene is expressed, and affect
features without an actual change of the gene sequence.
Eukaryote chromosomes are
two-ended, and the ends have a special "cap" called a telomere.
Because of the way DNA gets copied, the very end would be uneven if
a special enzyme called telomerase didn't fix it. In
many species, including us, telomerase stops being produced in many
cells as we age, and our chromosomes "fray at the ends," until the
cells won't make new copies and so can't make cells to replace
damaged ones; this is one of the causes of aging.
Levels of chromosome structure.
More on structure.
Karyotype - actual spread and assembly of types.
Telomeres, aging, and cancer.
Telomerase used to extend mousey lifespans.
Telomeres and telomerase.
Homologous chromosomes are
sorted into single sets for sexual reproduction for a special type
of cell division called meiosis, whose steps will be covered
later in this chapter. One set will be mixed with another
single set, producing two sets in a new combination. Even in
organisms that sexually reproduce with themselves, offspring will
get new combinations of chromosomes.
Gender is a common factor in sexual reproduction (not always -
many fungi reproduce with no gender roles at all, and some use way
more than two), and usually there is a male role and a
female role. How can you tell which from which? It's
not what you're thinking (could you apply that to a tree?) - what
determines those genders is only what sort of
gametes (sex cells) they produce. Males produce
sperm, females produce egg cells, also called ova.
There are very particular features for each:
When two genders are not enough.
Produced in much higher
Fewer produced (although in some species many may be made,
it's always way fewer than sperm).
Are much smaller.
much bigger, because nutrients for offspring are stored
Have some way of getting to where the egg
be reached by sperm, don't go to them.
During production, each starting cell makes
four functional sperm.
During production, each starting cell makes one functional
egg cell and three polar bodies.
Egg cell production.
In many species with
gender, what makes an individual male or female involves interaction
with its environment while it's developing. In other species,
sex chromosomes determine gender. This may involve an
unmatched pair, where one gender has a matched pair and the
other has a unmatched set (such as in mammals, where males have the
unmatched pair, or birds, where females have it). In some
species, one gender gets a singlet, only one sex chromosome,
and the other gender gets a doublet, a matched pair.
Genes carried on sex chromosomes are said to be sex-linked,
and in show different genetic patterns than genes on the
other chromosomes (the other chromosomes are called autosomes;
humans have sex-linked disorders and autosomal chromosome
disorders that indicate where the genes are).
In the unmatched-pair form of gender expression, the
gender with two matched chromosomes may deactivate one of them, so
both genders only use one. In humans, the deactivated
chromosome can be stained, showing a Barr body that only
genetic females should have.
Human sex chromosomes.
Evolution of 3 different unmatched pairs.
Sex linkage for human Y chromosome (not seriously).
Some sex-linked disorders of humans.
More on the Barr Body.
DNA molecules are two strands
of nitrogenous bases cross-connected, set up like a twisted
ladder or helix (DNA is famously known as a double
helix molecule). In DNA there are four nitrogenous bases,
and they pair up in a set way: Adenine cross-connects
to thymine (A-T), and cytosine cross-connects to
guanine. This makes the molecules easy to copy reliably:
during replication, the strands are separated and new strands
are built across from the originals: wherever an A was across
from a T, only an A should fit there when the new strand is being
constructed. That means that every "copy" made is half new and
half old. Since this molecule contains almost every bit of
information needed for a new cell to be functional, it is critical
to make good copies of each chromosome for the new cells.
Eukaryote cells have an array of proteins that work
to make new DNA copies in preparation for making new cells.
There are the enzymes that do the actual work, as well as a number
of proofreading proteins that check that the copying goes
correctly. Even so, mistakes get made that are passed along to
the new cells: this is one type of mutation. Viruses use
the cell's copying enzymes to make DNA for new viruses, but they
often don't use the proofreaders. This is both good and bad
for the viruses, as a lot of mistakes will produce many
poorly-functioning offspring, but the rare improvement. What
often causes an HIV infection to progress to HIV-AIDS is the
production of what's called an escape mutant: a virus
that the body's defenses or treatments can't hold in check.
Lots on DNA structure.
Video showing DNA replication.
HIV escape mutants.
When a cell needs to make a particular protein, a chemical
message travels to the nucleus, and bits of a chromosome near the
gene for that protein activate. That part of the DNA molecule
separates, and on one side, a molecule of messenger RNA (mRNA)
is made from the gene sequence in a process called transcription.
Where there is a cytosine, there will be a guanine on the mRNA, and
vice versa; a thymine on the DNA will have an adenine
connected there; an adenine on the DNA will not have a
thymine across from it, but a similar base called uracil.
Every three bases on the mRNA are a codon. Most codons
code for particular amino acids in the final protein, but the first
and last codon have other functions. The first one in the
sequence is a start codon and marks where the mRNA will be
built (that codon inside the sequence, codes for the amino acid
methionine), and the last codon is a stop codon, which causes
transcription to stop.
The mRNA may get
manipulated before it leaves the nucleus. It isn't unusual for
some pieces to be clipped out and not used, and some to be spliced
together in a new sequence different from the original.
mRNA (actually, there should be at least two of them, from the
codes on homologous chromosomes) travel from the nucleus to the
ribosomes, where translation happens. The mRNA fits
into a furrow on the ribosome and crawls along and out; as it
is on the ribosome, molecules of transfer RNA (tRNA) attach
to it briefly with a 3-base sequence called an anticodon (again,
the bases pair up in a set way, and there are as many tRNAs as there
are codon sequences). Also attached to the tRNA is an amino
acid; as the tRNAs bind, one after the other, to the mRNA,
they bring in and leave a sequence of amino acids, building a
As the end of the mRNA feeds
through the ribosome, the protein sequence emerges with it. It
turns out that some amino acid sequences can, if just left alone,
curl up into many different shapes, only one of which is the one the
cell needs. There are special proteins called chaperonins
that make certain that the protein takes the proper functional
Prions are a type of infective protein that
apparently get into cells and change the shape of a functional into
a prion - you lose the protein function, and it can now do the same
thing to more proteins. Mad cow disease is thought to be a
mRNA codon-to-amino-acid table.
Test your understanding.
Possible prion diseases.
Mutations are a change in DNA - anything from a single
change in a single base on the sequence (a point mutation) up
to entire extra sets of chromosomes (which are associated with new
species in plants, but usually fatal to animals).
Point mutations may involve the wrong base
getting into a sequence, a substitution mutation. Most
point mutations happen in the non-coding parts of the DNA (since
there's more of it than the coding parts) and have little effect.
If a substitution changes the codon in a gene, the code has some
redundancy: often a changed codon codes for the same amino
acid, or a very similar one. This is probably how most new
alleles arise. When a substitution really changes one
amino acid into another, it still may not alter the function of the
final protein; human, cow, and pig insulin differ in some
amino acids, but have the same functionality. But changes can
really alter the effects of a protein. Recessive alleles
often produce non-functioning proteins; dominant
alleles produce proteins with comparatively powerful effects,
strong enough to cover the effects of a recessive. When
alleles produce proteins with different effects usually
there's more of a combination effect: these can be
called blended, intermediate, or codominant allele
effects. One particularly dangerous mutation changes a
regular codon into a stop codon, stopping the transcription at that
If a base is mistakenly cut out of a sequence (a
deletion) or a base is squeezed between two where it
shouldn't be (an addition), a frame shift occurs:
every codon "downstream" from the mutation is shifted over a spot.
This should produce a very different, probably non-functional
protein, although it might rarely produce a protein with a brand-new
yet useful function.
Types of mutations.
Animation of mutation effect.
Recessive & dominant inheritance.
Larger-scale mutations happen
as well. DNA molecules often break and need to be stuck back
together with DNA repair proteins. There is a limit to
what the repair mechanism can handle: multiple simultaneous
breaks may result in pieces being put back in the wrong place, being
put in backwards, or a piece being lost from its original
chromosome. Some chemicals or radiation types can cause many
DNA breaks, with such mutations. Since most DNA is non-coding
and in any given cell, only some codes get used, these mutation
often show effects only in cells that divide. During division,
loose pieces get copied but not properly distributed, and new cells
that have too many or too few copies of genes they need can make the
wrong amounts of proteins, hurting the cells. This can cause
cells to become cancerous, but it is also used to try to kill
Translocations happen when a
piece of a chromosome is moved to another place, usually on another
chromosome. These may produce position effects by
putting the piece in a place that is easier or harder to get to for
processing, increasing or decreasing its expression rate. It
may add genetic information as well, if an offspring gets an
"enhanced" chromosome from one homologous set but the unaffected
member of the pair the piece came from.
More on DNA repair.
Repair enzymes go where they are needed.
More on translocations.
Mutations on a whole-chromosome
level happen fairly often: a cell divides, but a chromosome
copy goes the wrong way, giving one cell extra genes and one cell
fewer. In an early stage of development, those genes are
likely to be used and the individual is likely to be damaged:
in humans, for instance, when an egg cell or sperm sends on an extra
or missing chromosome to offspring, those offspring often die early.
Of the 24 types of human chromosomes, we can usually only survive an
extra Number 21 (which even though small, still causes Down
Syndrome), an extra X (any more than one gets converted into a
non-functional Barr Body), and an extra Y (which only carries
male-related genes). Later in development, if cell division
mistakes send on extra or missing chromosomes, effects depend on
whether those chromosomes hold critical genes for that cell type.
One type of mosaicism, where an individual has patches of
genetically-different cells, is caused this way.
Karyotype of Down Syndrome.
the type of reproduction involved, there are two types of cell
reproduction: mitosis produces
cells that are genetically identical to the original, the definition
of asexual reproduction; when sexual reproduction produces a
mixture of genes, meiosis makes cells with just one set of
chromosomes, to be recombined with another set and get a new mix.
Technically, both are actually terms applied to making new
nuclei: mitosis produces two diploid (2X, two sets
of chromosomes) nuclei, and meiosis produces four haploid (1X,
one set of chromosomes) nuclei. However, it's common to use
the terms to describe cell divisions.
Cells that are going to make more cells go
through something called a cell cycle. The cycle is
divided into phases.
is the stage that most cells are in most of the time, because it is
the between-divisions stage during which a cell does its job.
A cell that is not going to divide just does its job in interphase
until it dies (many human cell types do this). If the cell is
going to divide, it chemically prepares during interphase, building
up the components it will need to make the structures active during
a division, including copies of its chromosomes.
Prophase is the first active stage of a
division. The copied chromosomes get gathered into extremely
condensed forms, so they can be easily moved around without
tangling. Chromosomes aren't visible under a light microscope
during interphase, but they become visible during prophase, first as
strands of chromatin, then as double-stranded chromosomes.
Each strand is called a chromatid.
Outside the nucleus, at opposite ends of the cell
(called the poles), centrioles begin to build
microtubules, which radiate out in all directions. These are
called spindle fibers or just spindle. Some of
them attach to the membrane and hold the centrioles in place;
others move across the cell and will connect to the centromeres
that hold the two strands of the double-stranded chromosomes
together. However, the chromosomes are in the nucleus and the
spindles are outside; the nuclear envelope must get out of the
way for them to get together. The nucleus and nucleoli
disassemble and disappear from view.
Spindles from both poles grab chromosomes by the
centromeres and pull on them, with longer spindles pulling harder.
Eventually the chromosomes stall in the middle zone (the equator)
of the cell, with equal-length spindles on each side.
Prophase is to set up this condition: put the copies where
they can be reliably separated and pulled apart.
Spindle chromosome connection.
Not a lot
happens during metaphase, and you
might think it should go by very quickly, but a cell might stall
here for a while. The length of time for each phase can vary
greatly from cell to cell. The cell is in metaphase from the
time that most of the chromosomes settle into the equator to the
time that a chemical release causes the centromeres to break apart,
separating the strands. Each copy is attached to an opposing
spindle, and they get pulled away from each other.
anaphase, the now single-stranded
chromosomes are moved well away from each other. Once they are
far enough apart, a cell could begin cytokinesis, the actual
division, but that could be done in the next two phases as well.
Plant cells generally begin constructed the cell wall that will be
between the new cells, the cell plate, in anaphase.
Cell plate forming.
Telophase is the stage that puts
everything back as it needs to be for the cell or cells to go back
to work, so most of what happened in prophase "unhappens" in
telophase: the nuclear envelopes reform around each group of
chromosomes; the chromosomes go from being tightly packaged
and visible with a light microscope to being loosely packaged,
accessible for transcription, and not visible; the spindles
get disassembled; the nucleoli get reassembled. The cell
returns to interphase.
Telophase with beginning cytokinesis.
Much of what
happens in mitosis also happens in meiosis. During
interphase, DNA gets copied, producing copies of two sets of
chromosomes, or four potential sets. Since the end-product
cells will only have one set each, the process will make four cells,
and there will two division stages.
Meiosis 1, prophase is very similar to
mitosis with one huge added detail: as chromosomes are pulled
into the equator zone, homologous chromosomes are pulled in next
to each other. As they sit waiting for the other ones to
get in place, the molecules may make contact and pieces may swap
between homologous pair members. This is called
crossing over. The chromosomes may exchange equal pieces
or unequal pieces. If a chromosome picks up a much bigger bit
than it lost, it will now have extra copies of genes on the
chromosome. If one copy mutates and acquires a new
function, the function of the "old" gene doesn't have to be lost,
since there's still one of those. This is one way that
organisms can get genetically are functionally more complex as they
evolve. This is also another type of genetic redundancy.
Going into anaphase, the strands don't get separated,
the sets do - one set of double-stranded chromosomes goes to
one pole, and the second goes to the other pole. Nuclei
reappear and the cells divide. In egg cell production, the
poles are close together and just under the cell membrane, and
division leaves one big, nutrient-carrying cell and one cell just
big enough to hold a set of double-stranded chromosomes, a polar
body. Polar bodies generally have no other use and die
soon after they are made.
Steps of meiosis.
"New" gene from old one's duplicate.
on the polar body.
Meiosis 2 starts with two cells, each
containing one set of double-stranded chromosomes. This
division proceeds just like a mitosis would, with the strands
separating into new cells. Two cells become four cells, each
with one set of "regular" chromosomes. In egg cells, another
polar body would divide off the larger cell from Meiosis 1.
Fertilization, usually involving a sperm
nucleus getting into the egg cell, leads to fusion of nuclei,
producing a zygote: the 2N first cell of the
Another meiosis video.
In multicelled organisms, the zygote
would go through mitosis, become an embryo, and for a while
would make a lot of similar cells. Eventually, different cells
would start to access different genes so that they could do
different jobs, a process called differentiation. The
cells would carry the same genes, but use different combinations of
them. This is why a genetic disease from an allele for a
non-functional protein would be carried by every cell, but only
affect some of them.
Blog entry on differentiation.
The basic rules of evolution by natural
selection were worked out long before genetics was understood, but
eventually the two areas were merged into what is often called
Biologist Richard Dawkins on Neo-Darwinism.
is a term applied to all the the DNA present in something. An
individual has a genome, a population has a genome, a species has a
genome. My genome will be different from your genome because I
would carry some alleles that are different from yours, and I might
have some mutations you don't (the farther back in time we have a
common ancestor, the more different mutations would be there).
A gene pool is all of the alleles in a particular
When Darwin talked about adaptations that helped or
hurt an individual in its environment, and which could be passed to
offspring, he was really talking about traits arising from different
alleles. A more fit individual would have a different mix of
alleles to send on to offspring, and each new generation would carry
a greater proportion of alleles "good" for their circumstances.
A mutation that produced an allele for a "better" trait would help
its owner survive, and they would pass it to offspring, who had a
better chance of surviving and passing it to their offspring, so in
a few generations it would go from being rare, in just one member of
the population, to being more common, being a bigger part of the
Evolution is now understood as a change in a
population's gene pool over time.
Project to map out the human genome.
How genomes are used to measure evolutionary relationships.
In trying to figure out how
gene pools change over time, two statisticians came up with some
rules called Hardy-Weinberg Equilibrium. These
stated the conditions under which the pool's alleles would not
change, but were obviously connected to what would make
them change over time. These are the needed restrictions:
to stay the same, a population had to have no Natural Selection,
Sexual Selection, or Mutations happening, which was no surprise.
The population also had to be very large, because
events of pure chance can affect small groups but not really big
ones. The impact of populations size hadn't really been
considered, and it was still a long time before it was realized
that, since the gene pool had a lot fewer alleles in it, a small
population can evolve much faster than a large population.
The remaining factor was known to be important
even from Darwin, but this focused attention on it: the
population could not have small groups migrating away or new
relative groups migrating in. An isolated
population would change in comparison with other related populations
(like an island group differing from the mainland groups).
More on Hardy-Weinberg.
A Hardy-Weinberg Lab Exercise
A few processes turned out to
be related to these "new" evolutionary rules:
When a small population starts out, it "sets" the
gene pool on which evolution will play. With a small migrating
group, if they move away and become isolated, the gene pool is
already different then the original group, and the descendants are
working with that limited genetic repertoire. This is called a
If something dramatically shrinks a population, a
near-extinction, whatever alleles are left in the survivors is the
new gene pool that passes to descendants. This is called a
More on these two effects.
It turns out
that the only critical isolation is reproductive isolation
- once populations can not pass alleles between them, they can
change along separate paths. There are a few different ways to
is the best know type - here, some sort of physical barrier
separates populations. This could be a desert, a widening
river, mountains, or sea expanses.
Niche isolation (also called
ecological isolation) happens when groups in what starts as a
single population in the same area begin to specialize in different
ways, to occupy different niches or ecological roles.
This might involve slightly different food types, or different
locations (such as treetops versus ground-browsing), or different
active times (such as day versus night). This may get the
groups reproductively isolated as the groups don't encounter each
other as much, but also as groups get specialized, behavior that
avoids cross-breeding become advantageous anyway.
Temporal isolation happens when a
subgroup becomes reproductively active at a different time than the
main population. If the timing works, the subgroup can become
a founder group without ever changing locations.
Behavioral isolation can happen
where behaviors factor strongly into reproduction (examples occur in
many animal phyla, from birds to spiders); a subgroup where a
different preference arises can separate from the main group.
Chemical isolation is based upon
reproductive "choosing" that is strongly based upon chemical
compatibility. Many plants, for example, accept or reject
sperm-carrying pollen grains using chemical interactions. In
some species, this isolation could be an immune reaction that
similarly rejects sperm in some females.
Mechanical isolation is known from a
few species, such as beetles, where the only separating feature
between two groups seems to be the way their reproductive anatomy is
built: males from one group cannot couple with females from
the other group.
More on isolation.
Geographic isolation example.
Niche isolation example.
Temporal isolation example.
Behavioral and chemical isolation at work.