Biology Terms

Auxin Definition
An auxin is a plant hormone derived from the amino acid tryptophan. An auxin

may be one of many molecules, but all auxin molecules are involved in some sort
of cellular regulation. Auxin molecules are one of five major types of plant
hormone. The other major groups are the gibberellins, cytokinins, ethylene, and
abscisic acid. Auxin was the first of these groups to be identified, and was
chemically isolated in the 1930’s.
The most widespread auxin is indoleacetic acid, or simply IAA. IAA is an auxin
which is very important in the growth and development of plant tissues. In
studying auxin molecules, scientist have been able to recreate similar structures,
called synthetic growth regulators. These “fake” auxins also stimulate growth in
plants and have been used in many agricultural and commercial applications.
Auxin Function
The auxin group of hormones has a wide range of uses in a plant. Auxin
molecules are found in all tissues in a plant. However, they tend to be
concentrated in the meristems, growth centers which are at the forefront of
growth. These centers release auxin molecules, which are then distributed
towards the roots. In this way, the plant can coordinate its size, and the growth
and development of different tissues based on the gradient of the auxin
concentration.
Auxin affects many different cellular processes. At the molecular level, auxin
molecules can affect cytoplasmic streaming , the movement of fluids within a cell,
and even the activity of various enzymes. This gives auxin direct control over the
growth, development, and proliferation of individual cells within the plant. The
auxin gradient directly affects processes such as flower initiation, fruit
development, and even tuber and bulb formation. Even on a daily basis, auxin
levels affect processes such as phototropism, which allows the plant to follow the
sun and gain the most energy. The auxin controls this process by concentrating
in the side of the plant away from the sun. This causes changes in the cells,
which bend the plant toward the light. This can be seen in the image below.
Another important feature which auxin gradients provide many plants is apical
dominance. Apical dominance is formed when a single meristem is growing
faster and more efficiently. Eventually, the auxin released from this meristem
inhibits any new shoots from budding off below it. If the stem is cut off, many
new shoot will erupt below the stem, as the auxin gradient has been disrupted
and the system must create a new leading shoot. The auxin gradient, when
established, determines how fast internodes grow, which determines the height
of the plant. When discussing the function of the auxin molecules in a plant, it is
almost easier to discuss the things they do not control.
Some scientist have even discussed the polar-auxin transport system as a plant-

like take on a nervous system. The way the auxin molecules move from cell to
cell is very similar to how a nerve signal is sent across an animal’s body. The
auxin molecule affects various tissues, and is usually converted into another
auxin. A “return signal” can then be generated. In this way, using the many
different versions of auxin and the other plant hormones, a plant could have a
feasibly robust nervous system for responding to external stimuli.
Auxin Structure
Native auxin molecules are normally derived from the amino acid tryptophan.
This amino acid has a six-sided carbon ring, attached to a 5-sided ring containing
carbon. This 5-sided ring has a group attached. The only difference between
most auxin molecules and tryptophan is what is attached to this ring. The
common auxin IAA can be seen below.
To create this molecule, two enzymes are needed to act on tryptophan. First,
an amino-transferase removes a nitrogen and a hydrogen from the side-chain
attached to the 5-sided ring. Then, a decarboxylase enzyme removes
the carboxyl group, leaving only COOH. A chloride ion attaches to the six-sided
ring, and IAA is born. Most auxins are some derivation of this molecule.
Synthetic Auxin Analogs

After studying the structure of natural auxin molecules, scientist were easily able
to produce molecules which were similar to natural auxins. These synthetic auxin
analogs have many applications. They can be used to encourage growth in
certain plants. Synthetic auxin treatment is used on many plant cuttings, to
induce rooting processes. In this way, scientist can make plant clones by taking
cuttings, and growing the cuttings into entire plants.
1-Naphthaleneacetic acid (NAA) is a coming rooting chemical, and a synthetic

auxin. This fake auxin is marketing to regular gardeners. While there are some
safety and handling concerns, fake auxin molecules have been used since the
1940’s to stimulate the growth of cuttings. Scientist also found that auxin
molecules could have anti-growth properties as well.
The synthetic auxin 2,4-D (2,4-Dichlorophenoxyacetic acid), is a common weed

killer. The auxin-like molecule affects only broadleaf weed species. This means it
can be applied around lawn, grassland, and other landscape plants without
affecting them. However, in the broadleaf plants it causes rapid growth in all the
wrong places. The plants quickly die off. There are many other synthetic auxin
compounds, which have a variety of marketed uses.
Quiz
1. What is one risk of using synthetic auxin molecules?
A. They can make a plant grow too big
B. They are absolutely toxic to the end consumer
C. They can leach off, into the water supply
Answer to Question #1
2. A scientist takes three cuttings of an unknown plant. On one cutting,
he puts no synthetic auxin. The second plant receives a light dose of
auxin, while the last is soaked in a high dose. Which plant will develop
the best roots?
A. Plant 2
B. Plant 3
C. Not enough info
C is correct. In this case, without knowing how the auxin affects the plant, there
is no way to say how it will respond. Some plants need high doses of auxin,
while others are stimulated at low doses. It depends on the exact auxin or
synthetic auxin that is used. If the plant species rejects it altogether, it may be
the untreated cutting which does the best.
3. How is the animal nervous system different from the theoretical

auxin-based nervous system described in this article?
A. Animal nervous system functions more efficiently
B. The animal system uses electrical impulses
C. Both nervous systems are the same
B is correct. In the case of the plant nervous system, the actions and reactions
of the system are based off the interaction of molecules with external stimuli. In
animals, these interactions are turned into electrical stimuli. This is why animal
nerve impulses move more quickly. However, just as much information can be
contained in the passage and movement of auxin molecules within the plant.
Definition of Speciation
Speciation is a process within evolution that leads to the formation of new,
distinct species that are reproductively isolated from one another.
Anagenesis, or ‘phyletic evolution’, occurs when evolution acts to create new
species, which are distinct from their ancestors, along a single lineage, through
gradual changes in physical or genetic traits. In this instance, there is no split in
the phylogenetic tree. Conversely, ‘speciation’ or cladogenesis arises from a
splitting event, where a parent species is split into two distinct species, often as
the result of geographic isolation or another driving force involving the
separation of populations.
The reproductive isolation that is integral to the process of speciation occurs due
to reproductive barriers, which are formed as a consequence of genetic,
behavioral or physical differences arising between the new species. These are
either pre-zygotic (pre-mating) mechanisms, for example, differences in
courtship rituals, non-compatible genitalia, or gametes, which are unable to
fertilize between species. Alternatively, they are post-zygotic (post-mating), for
example zygote mortality or the production of sterile offspring. Reproductive
isolation leads to reinforcement of the distinction between species
through natural selection and sexual selection.
Types of Speciation
Allopatric Speciation
Allopatric speciation occurs when members of a population become

geographically isolated from one another, to the extent that genetic exchange,
through mating, is prevented or interfered with. This may be a result of
geographical changes, such as the formation of a mountain by a volcano, island
formation, habitat separation by glaciers and rivers, or habitat fragmentation
caused by human activity. Alternatively, species members may emigrate,
resulting in population separation by dispersal; this is commonly known
as vicariance.
The separated populations then undergo divergence

in genotypic or phenotypic traits as a result of different selective pressures acting
upon populations. This leads natural selection to cause genetic drift as mutations
arise within populations. Over time, the separate populations may
develop morphologically distinct features due to adaption to their new
environment. The features may become so distinctively different that
reproductive isolation occurs, preventing the inbreeding of populations and thus
forming new species. If the populations become sufficiently different that they
are classified as new species, but not distinct enough for reproductive isolation to
occur, the species may come back into contact and mate, producing hybrids.
The extent of the effect that geographic barriers may have on a population often
depends on the dispersal ability of the organism; for example, the new formation
of a river in a landscape would create an impassable barrier for small terrestrial
mammals, insects and reptiles. However, birds and larger mammals would likely
disperse across the river with ease.
An elegant example of allopatric speciation, which first inspired Charles Darwin to

develop the theory of evolution and natural selection, is the divergent
populations of finches inhabiting the Galapagos Islands, and known as ‘Darwin’s
finches’. Darwin noticed that each of the Galapagos Islands hosted a population
of finches, which although relatively similar in morphology (compared with other
bird species), exhibited slight differences in features such as body size, color and
beak length or shape. He noted that there were different food sources available
for the birds on each of the different islands, and came to the conclusion that the
differences in beak shape were an adaption toward acquiring the particular food
source.
Sympatric Speciation
Sympatric speciation is the evolutionary process whereby species are formed

from a single ancestral species while inhabiting the same geographic area. In
contrast to allopatric speciation, the distribution ranges of species which evolve
through sympatry may be identical or they may only overlap. Rather than
geographic distance prompting a reduction of gene flow between populations,
sympatry occurs when members of one population make use of a new niche.
This could occur, for example, if a herbivorous insect begins to feed on a new or
novel plant source with which it was not ancestrally associated, or if a new
species of plant is introduced to the species’ geographic range. As insects
generally reproduce or lay eggs within the type of fruit that they were born in,
over time, the individuals would specialize in feeding and mating on particular
fruits. Consequently, gene flow between populations that specialize in different
fruits will be reduced, leading to reproductive isolation of the populations. It is
possible that the populations will also develop morphological differences as they
adapt to most effectively exploit the new niche. Although sympatric speciation
does sometimes occur, it is uncommon, especially within
large, multicellular organisms.
Parapatric Speciation
Parapatric speciation is an extremely rare case of speciation that occurs when a

population is continuously distributed within a geographic area without any
specific barriers to gene flow. Nonetheless, the population does not mate
randomly within the population, but rather individuals mate more commonly with
their closest geographic neighbors, resulting in uneven gene flow. Non-random
mating may increase the rate of dimorphism within populations, in which varied
morphological forms of the same species are displayed. The result of parapatric
speciation is one or more distinct sub-populations (known as ‘sister species’),
which have small, continuous overlaps in their biogeographic range and are
genotypically dimorphic.
Peripatric Speciation
Peripatric speciation is a form of allopatric speciation that occurs when

populations that have become isolated have very few individuals. Through this
process, the population goes through a genetic bottleneck. Within the small sub-
population, organisms which are able to survive within the new environment may
carry genes that were rare within the main population but that cause a slight
variation to behavior or morphology. Through repeated matings, the frequency
of these, once rare, genes increases within the small population. This is known
as the ‘founder effect’. Over time, the characteristic that was determined by the
gene becomes fixed within the population, leading to an isolated species that is
evolutionarily distinct from the main population.
Speciation modes
Artificial Speciation
Artificial speciation is the form of speciation that can be achieved by the input of
human influence. By separating populations, and thereby preventing breeding, or
by intentionally breeding individuals with desired morphological or genotypic
traits, humans can create new, distinct species. This is also known as ‘artificial
selection’; most modern domesticated animals and plants have undergone
artificial selection.
Although evolution of our modern crops and livestock has taken thousands of
years, it is possible to visualize the process of artificial selection in species that
have short life cycles. Artificial selection has been demonstrated most effectively
in species of Fruit Fly (Drosophila melanogaster). Experiments in which flies are
placed into environments which contain different resources or habitats show the
changes that occur when the flies adapt to each environment. After several
generations, the flies are removed from the experimental zone and are allowed
to cohabitate, although the populations are unable to mate due to the
reproductive isolation process that occurred while in isolation.
Drosophila speciation experiment
Related Biology Terms

 Morphology – A branch of biology that relates to the structure, form
and physical characteristics of an organism.
 Genotype – The set of genes within DNA that is responsible for
particular traits.
 Population – The community of animals or plants in which
interbreeding occurs.
 Species – The largest group of organisms in which individuals can
breed and produce fertile offspring.
Test your knowledge

1. If a population of rats is separated by the formation of a deep
canyon, this could result in:
A. Peripatric speciation
B. Artificial speciation
C. Allopatric speciation
D. Sympatric Speciation
C is correct. Allopatric speciation occurs when populations are separated by a
geographical barrier and cannot easily disperse across the barrier.
2. Parapatric speciation would be least likely to occur in:

A. Large mammals
B. Insects
C. Bacteria
D. None of the above
A is correct. Parapatric speciation is rare, and requires extreme gene flow
disruption to take place. Large mammals are likely not to specialize in one
particular niche; therefore, the novel niche would rarely be adopted as a sole
resource, and genetic or morphological adaptions to exploit the niche would be
unnecessary.
3. Which of the following is not a product of reproductive isolation?

A. Non-compatible genetalia
B. Fertile offspring
C. Zygote mortality
D. Changes to courtship rituals
B is correct. Reproductive isolation prevents newly formed species from mating
or reproducing successfully. If fertile offspring are produced, then reproductive
isolation has not occurred.
4. Speciation can result in changes to:

A. Body size
B. Leg length
C. Birdsong vocalizations
D. All of the above
D is correct. Speciation can lead to any difference in a species’ morphology or
genotype. It is partly responsible for the vast diversity of species we have today.
Apoptosis Definition
Apoptosis is a process that occurs in multicellular when a cell intentionally
“decides” to die. This often occurs for the greater good of the whole organism,
such as when the cell’s DNA has become damaged and it may become
cancerous.
Apoptosis is referred to as “programmed” cell death because it happens due to

biochemical instructions in the cell’s DNA; this is opposed to the process of
“necrosis,” when a cell dies due to outside trauma or deprivation.
Like many other complex cellular processes, apoptosis is triggered by signal

molecules that tell the cell it’s time to commit cellular “suicide.”
The two major types of apoptosis pathways are “intrinsic pathways,” where a cell
receives a signal to destroy itself from one of its own genes or proteins due to
detection of DNA damage; and “extrinsic pathways,” where a cell receives a
signal to start apoptosis from other cells in the organism. The extrinsic pathway
may be triggered when the organism recognizes that a cell has outlived its
usefulness or is no longer a good investment for the organism to support.
Apoptosis plays a role in causing and preventing some important medical

processes. In humans, apoptosis plays a major role in preventing cancer by
causing cells with damaged DNA to commit “suicide” before they can become
cancerous. It also plays a role in the atrophy of muscles, where the body decides
that it’s no longer a good idea to spend calories on maintaining muscle cells if
the cells are not being regularly used.
Because apoptosis can prevent cancer, and because problems with apoptosis can
lead to some diseases, apoptosis has been studied intensely by scientists since
the 1990s.
Function of Apoptosis
Apoptosis is an important evolutionary adaptation because it allows organisms to
destroy their own cells. At first glance, that may sound like a terrible idea. Why
would you destroy part of yourself?
Well, perhaps if that part of yourself had become dangerous to the rest, as in the
case of cells with damaged DNA that could become cancerous. Apoptosis is a
major killer of pre-cancerous cells, and people with mutations that prevent
apoptosis from functioning correctly are much more likely to get cancer.
Multicellular organisms may also wish to lose cells that are no longer useful to
the organism. We’ll share some really spectacular examples of when cell death is
a good thing below.
Examples of Apoptosis
From Tadpole to Frog
A spectacular example of this is found in frog tadpoles, which destroy and re-
absorb entire body structures as they undergo their transformation into frogs.
Cells from tadpole’s gills, fins, and tail are “told” to die by apoptosis signals as
the tadpole matures. The raw materials of these dissembled cells become
building materials and food for their new growing limbs.
Human Nervous System Development
During the early development of the human nervous system, huge numbers of

cells die through apoptosis. Why should that be so?
The truth is, scientists are not entirely sure why so much programmed cell death
occurs in the developing nervous system. Some think it is because forming the
correct connections is a complex and potentially difficult process for young
neurons; and because maximum efficiency of the nervous system is definitely in
the organism’s best interest.
Nerves require huge amounts of energy in order to function – in fact, the

nervous system consumes about 20-25% of all calories consumed in the human
body!
Neurons also have to find their way to very precise targets. Early in
development, neurons grow from furiously dividing stem cell “parents” and follow
chemical signals to try to find the correct target cells to connect with.
Connections must be formed between the brain and skin, between the brain and
muscles, between neurons in the brain and rod and cone cells in the retina, etc..
To create this incredibly complex targeting, the developing nervous system
simply grows way too many cells. Those that connect efficiently with the correct
targets are used frequently, and they are preserved. But those that don’t make
contact efficiently and are not used frequently die off away by apoptosis.
It may be that this theory about why neurons die during development is correct;
it may also be that scientists will make important discoveries we haven’t
dreamed of yet that will explain why there is so much apoptosis in the
developing nervous system. More research is certainly needed!
Mouse Feet
During embryonic development, the feet of mice start out as flat, spade-shaped
things. As development proceeds, the feet separate into five distinct toes by the
process of – you guessed it – apoptosis! Cells that connect the toes die off in
order to create the distinct gaps between them.
This is an example of how programmed cell death can be used to shape useful
structures and create useful features, in addition to getting rid of un-needed
ones.
Apoptosis and Cancer

One primary function of apoptosis is to destroy cells that are dangerous to the
rest of the organism. A common reason for apoptosis is when a cell recognizes
that its DNA has been badly damaged. In these cases, the DNA damage triggers
apoptosis pathways, ensuring that the cell cannot become a malignant cancer.
However, clearly this process sometimes fails. All instances of cancer are
presumably instances where a damaged cell did not commit apoptosis, but
instead went on to make more of itself.
Apoptosis may be unable to occur if essential genes required for it are among
those that are damaged. However, some doctors and scientists have been
studying apoptosis intensely in hopes that they may be able to learn to trigger it
specifically in cancer cells using new medications or other therapies.
As with all drugs designed to kill cancer cells, the challenge with drugs designed
to induce apoptosis is to ensure that these drugs only effect cancer cells. A
medication that causes healthy cells as well as cancerous ones to commit
programmed cell death could be very dangerous.
The picture may also not be quite as simple as “cancer occurs when apoptosis
fails.” Research has suggested that some cancers may arise in cell populations
where apoptosis occurs more easily than it should; possibly these cells have
been forced to “learn” to ignore over-enthusiastic apoptosis signals, and
subsequently don’t commit apoptosis even when they have sustained severe
damage.
Other research has revealed that cancer cells which die due to the effects of
medication often die by apoptosis – suggesting that cancers that are especially
apoptosis-resistant may also be especially treatment-resistant.
Much more research is needed on the subject of cancer treatment, and

understanding apoptosis pathways is one extremely promising avenue for
making new breakthroughs!
Apoptosis Pathway
There are two major types of apoptosis pathways, each of which illustrates an
important point about how apoptosis is triggered and why it is useful.
Both major pathways are illustrated in the graphic below. The steps are
discussed in more detail in the following lists:
Extrinsic Pathway
In the “extrinsic” pathway to apoptosis, a signal is received from outside the cell
instructing it to commit programmed cell death. This may occur if the cell is no
longer needed, or if it is diseased.
Like many pathways for bringing about complex changes in a cell, the extrinsic
pathway to apoptosis involves many steps, each of which can be “upregulated”
or “downregulated” by gene expression or by other molecules:
Step 1:
Like most signaling between cells, the extrinsic pathway of apoptosis starts with
a signal molecule binding to a receptor on the outside of the cell membrane.
Two common types of chemical messengers that trigger the extrinsic pathway to
apoptosis are FAS and TRAIL. These molecules may be excreted by neighboring
cells if a cell is damaged or no longer needed.
The receptors that bind to FAS and TRAIL are called “FASR” for “FAS Receptor”
or “TRAILR” for “TRAIL Receptor.”
As with most receptor proteins, when FASR and TRAILR encounter to their signal
molecule – sometimes called a “ligand” – they bind to it.
The binding process causes changes to the receptor’s intracellular domain.
Step 2:
In response to the changes in the intracellular domain of TRAILR or FASR, a

protein inside the cell called FADD also changes.
FADD’s name is either amusing or terrifying: it stands for “FAS-Associated Death

Domain” protein.
Once FADD has been activated by changes to the receptor, it interacts with two
additional proteins, which go on to start the process of cell death.
Step 3:
Pro-caspase-8 and pro-caspase-10 are inactive proteins until they interact with
an activated FADD. But if two of these molecules encounter an activated FADD,
the parts of the proteins that keep them inactive are “cleaved” or “cut” away.
The pro-caspases then become caspase-8 and caspase-10 – which have been
romantically referred to by scientists as “the beginning of the end” due to their
role in starting apoptosis.
Caspases-8 and -10 disperse through the cytoplasm and trigger changes to

several other molecules throughout the cell, including messengers that start the
breakdown of DNA after being activated by the caspases.
Step 4:
Another inactive molecule called BID is transformed into tBID when the activated
caspases cleave off the part of BID that keeps the molecule inactive.
After BID is transformed into tBID, tBID moves to the mitochondria. tBID

activates the molecules BAX and BAK.
The activation of BAX and BAK are the first steps shared by both the extrinsic
and intrinsic pathways to apoptosis.
Steps 1-4 listed here are unique to the extrinsic pathway. But after BAX and BAK
are activated, the subsequent steps are the same between both pathways.
As such, steps 3-7 of the intrinsic pathway, listed below, are also steps 5-9 of the
extrinsic pathway!
Intrinsic Pathway
Step 1:
The intrinsic pathway to apoptosis is triggered by stress or damage to the cell.

Types of stress and damage that can lead the cell to apoptosis include damage
to its DNA, oxygen deprivation, and other stresses that impair a cell’s ability to
function.
In response to these damages or stresses, the cell “decides” that its continued
existence might be dangerous or costly to the organism as a whole. It then
activates a set of proteins called “BH3-only proteins.”
Step 2:
BH3-only proteins are a class of proteins including several pro- and anti-
apoptosis proteins. Apoptosis can be encouraged or discouraged, depending on
which BH3-only proteins are activated or expressed.
Pro-apoptotic BH3-only proteins activate BAX and BAK – the same proteins that
are activated by tBID after it is created through the extrinsic pathway to
apoptosis.
Step 3:
Activated BAX and BAK cause a condition known as “MOMP.” MOMP stands for
“mitochondrial outer membrane permeability.”
MOMP is considered the “point of no return” for apoptosis. The steps leading up
to MOMP can be stopped in their tracks by inhibitor molecules, but once MOMP
has been achieved, the cell will complete the death process.
MOMP plays its key role in apoptosis by allowing the release of cytochrome C
into the cytoplasm.
Step 4:
Under normal circumstances, cytochrome C plays a key role in the

mitochondrial electron transport chain. During MOMP, however, cytochrome C
can escape the mitochondria and act as a signaling molecule in the cell
cytoplasm.
Cytochrome-C in the cell cytoplasm prompts the formation of the ominous-

sounding “apoptosome” – a complex of proteins that performs the final step to
beginning cellular breakdown.
Step 5:
The apoptosome, once it is formed, turns pro-caspase-9 into caspase-9.
Just as with the activation of caspases-8 and -10 in the extrinsic pathway to
apoptosis, caspase-9 is able to trigger further changes throughout the cell.
Step 6:
Caspase-9 performs several functions to promote apoptosis. Among the most

important is the activation of caspases-3 and -7.
Step 7:
Once activated, caspases-3 and -7 begin the breakdown of cellular materials.

Caspase-3 condenses and breaks down the cell’s DNA.
When Does Apoptosis Occur?

Apoptosis occurs when a cell’s existence is no longer useful to the organism. This
can occur for a few reasons.
If a cell has become badly stressed or damaged, it may commit apoptosis to

prevent itself from becoming dangerous to the organism as a whole. Cells with
DNA damage, for example, may become cancerous, so it is better for them to
commit apoptosis before that can happen.
Other cellular stresses, such as oxygen deprivation, can also cause a cell to
“decide” that it is dangerous or costly to the host. Cells that can’t function
properly may initiate apoptosis, just like cells that have experienced DNA
damage.
In a third scenario, cells may commit apoptosis because the organism doesn’t
need them anymore due to its natural development.
One famous example is that of the tadpole, whose gill, fin, and tail cells commit
apoptosis as the tadpole metamorphoses into a frog. These structures are
needed when the tadpole lives in water – but become costly and harmful when it
moves onto dry land.
Quiz
1. Which of the following would you NOT expect to trigger apoptosis?
A. Damage to a cell’s DNA
B. Long-term oxygen deprivation
C. An organism moving to a new stage of its life cycle, rendering some cells
obsolete
D is correct. All of the above are potential triggers for apoptosis.
2. Which of the following might occur if a mutation made apoptosis

impossible?
A. The nervous system might not develop properly
B. Cancer might become much more likely
C. An insect might not be able to undergo metamorphoses
D. All of the above
D is correct. All are possible consequences for an organism whose cells cannot
trigger apoptosis.
3. What is the difference between the extrinsic and intrinsic pathways

of apoptosis?
A. The extrinsic pathway is triggered by a signal from outside the cell, while the
intrinsic pathway is triggered by events inside the cell.
B. The extrinsic pathway has more steps because the signal must be relayed
from the cell membrane.
C. The extrinsic pathway activates BAK and BAX, while the intrinsic pathway
does not.
D. A and B
D is correct. Both A and B are true. However, C is not true – both the intrinsic
and extrinsic pathways to apoptosis must activate BAK and BAX for apoptosis to
be completed successfully.
Anticodon Definition
Anticodons are sequences of nucleotides that are complementary to codons.
They are found in tRNAs, and allow the tRNAs to bring the correct amino acid in
line with an mRNA during protein production.
During protein production, amino acids are bound together into a string, much

like beads on a necklace. It’s important that the correct amino acids be used in
the correct places, because amino acids have different properties. Putting the
wrong one in a spot can render a protein useless, or even dangerous to the cell.
This graphic shows a growing protein chain. Towards the bottom left, you can
see tRNAs carrying amino acids entering the ribosome complex. If all goes well,
only the tRNAs with the correct anticodons will bind successfully to the exposed
mRNA, so only the correct amino acids will be added:
tRNAs are responsible for bringing the correct amino acids to be added to the
protein, according to the mRNA’s instructions. Their anticodons, which pair-bond
with codons on mRNA, allow them to perform this function.
Function of Anticodons
The function of anticodons is to bring together the correct amino acids to create
a protein, based on the instructions carried in mRNA.
Each tRNA carries one amino acid, and has one anticodon. When the anticodon
successfully pairs up with an mRNA codon, the cellular machinery knows that the
correct amino acid is in place to be added to the growing protein.
Anticodons are necessary to complete the process of turning the information

stored in DNA into functional proteins that a cell can use to carry out its life
functions.
How Anticodons Work
When genetic information is to be turned into a protein, the sequence of events
goes like this:
1. Genetic information in the cell’s genome is transcribed into mobile

pieces of RNA using base-pairing rules. Each nucleotide has only one
other nucleotide which pairs up with it.
By pairing the correct RNA nucleotide with each DNA nucleotide, RNA
polymerase creates a strand of RNA that contains all the correct
information to make the protein.
This “messenger RNA,” or “mRNA,” then travels to a ribosome, the site
of protein production.
2. At the ribosome, the rules of base-pairing are again used to ensure a
correct transfer of information. Each three-nucleotide “codon” in the
mRNA is matched with an “anticodon” containing the complementary
bases.
The “transfer RNAs” or “tRNAs” that string proteins together each have
one anticodon that corresponds to one mRNA codon, and one amino
acid attached.
When the correct tRNA finds the mRNA, its amino acid is added to the
growing protein chain.
Enzymes catalyze the bonding of amino acids together as tRNA
anticodons bind to the correct mRNA codon.
When the tRNA’s amino acid has been added to the protein chain, the
tRNA leaves to pick up a new amino acid to bring to a new mRNA.
Interestingly, this means that the tRNA anticodon has the RNA version
of the same nucleotide sequence of the original gene.
Remember – the gene was transcribed using complementary
nucleotides to make RNA, which then had to bond with complementary
tRNA codons.
RNA Base Pairing Rules

Each RNA nucleotide can only hydrogen bond to one other nucleotide. It is by
bonding the correct nucleotides together that DNA and RNA successfully transfer
and use information.
The four bases of RNA are Adenine, Cytosine, Guanine, and Uracil. These bases
are often referred to by just their first letter, to make it easier to show sequences
of many bases. Base pairing rules for RNA are:
A–U
C–G
G–C
U–A
Put more simply, in RNA, A nucleotides always bond with U nucleotides, and C
nucleotides always bond with G nucleotides.
Differences Between RNA and DNA

Of note, in DNA, the “Uracil” base is a slightly different base called “Thymine.” In
DNA, A and T pair. RNA Adenine will also pair with DNA’s Thymine, and DNA
Adenine will pair with RNA’s Uracil.
The difference between Uracil and Thymine is that Thymine has an extra methyl
group, which makes it more stable than Uracil.
It is thought that DNA uses Thymine instead of Uracil because, as the cell’s
“master blueprints,” information stored in DNA must remain stable over a long
period of time. RNAs are only copies of DNA made for specific purposes, and are
used by the cell for only a short period of time before being discarded.
Examples of Anticodons
Let’s look at some examples of DNA base triplets, mRNA codons, and tRNA
codons to see if you can fill in the missing information using base pairing rules.
You might find it useful to use a pencil and paper to allow you to transcribe each
nucleotide’s complement instead of doing it in your head.
1. mRNA codon: GCU

What is the tRNA anticodon that will bind to this mRNA codon?
CGA. The codon GCU codes for the amino acid alanine, so the tRNA with the
corresponding anticodon will be carrying that amino acid.
2. mRNA codon: ACA

What is the corresponding tRNA anticodon?
UCU. The codon CGA codes for the amino acid cysteine, so a tRNA with
anticodon UCU will be carrying cysteine.
3. DNA base triplet: CTT

What is the mRNA codon that will be transcribed from this DNA triplet?
GAA. This mRNA codon codes for the amino acid glutamate.
4. Based on the information in the answers to the question above, what

is one anticodon for a tRNA that carries glutamate?
CUU. This anticodon that is complementary to an mRNA codon for glutamate.

 Amino Acid – The building blocks of protein. Different amino acids
have different properties, which allow cells to build proteins to serve
many different functions by stringing the right combinations of amino
acids together
 Codon – A three-nucleotide sequence in an mRNA molecule that codes
for a particular amino acid. Most amino acids have more than one
codon that codes for them, although methionine only has one.
 DNA – The substance used to store the permanent operating
instructions of a cell. Information stored in DNA is stable, and can be
copied to make new blueprints for daughter cells using nucleotide base
pairing rules.
Quiz
1. Which of the following is NOT true of anticodons?
A. They are found on tRNAs.
B. They are complementary to codons.
C. They have the RNA equivalent of the same nucleotide sequence as the
original DNA instructions for the amino acid.
D. They have the same nucleotide sequence as codons.
D is correct. Anticodons are complementary to codons, NOT the same as them.
2. Which of the following sequences is complementary to: GCUCGU

A. GGAGCA
B. CCACGA
C. CGAGCA
D. CGUGCU
C is correct. It’s helpful to transcribe the sequence letter by letter before
answering multiple choice questions like these.
3. Which of the following is something that would NOT be coded for by
a codon?
A. Glutamine
B. Glucose
C. Alanine
D. Stop protein production
B is correct. tRNAs do not carry sugars. Sugars may be added to proteins later to
form important substances like glycoproteins, but that is done during a later step
of protein processing.
ACTIVE TRANSPORT
Definition
Active transport is the process of transferring substances into, out of, and
between cells, using energy. In some cases, the movement of substances can be
accomplished by passive transport, which uses no energy. However, the cell
often needs to transport materials against their concentration gradient. In these
cases, active transport is required.
Active Transport 3D model
Process of Active Transport

Active transport requires energy to move substances from a low concentration of
that substance to a high concentration of that substance, in contrast with the
process of osmosis. Active transport is most commonly accomplished by a
transport protein that undergoes a change in shape when it binds with the cell’s
“fuel,” a molecule called adenosine triphosphate (ATP).
For example, one type of active transport channel in the cell membrane will bind
to the molecule it is supposed to transport – such as a sodium ion – and hold
onto it until a molecule of ATP comes along and binds to the protein. The energy
stored in ATP then allows the channel to change shape, spitting the sodium ion
out on the opposite side of the cell membrane. This type of active transport
directly uses ATP and is called “primary” active transport.
Another type of active transport is “secondary” active transport. In this type of

active transport, the protein pump does not use ATP itself, but the cell must
utilize ATP in order to keep it functioning. This will be explained in more depth in
the section on Symport Pumps below.
Lastly, active transport can be accomplished through processes called

endocytosis and exocytosis. In exocytosis, a cell moves something outside of
itself in large quantities by wrapping it in a membrane called a vesicle and
“spitting out” the vesicle. In endocytosis, a cell “eats” something by wrapping
and re-forming its membrane around the substance or item.
Each type of active transport is explained in more detail below.
Types of Active Transport

Antiport Pumps
Active transport by
antiport pumps
Antiport pumps are a type of transmembrane co-transporter protein. They pump
one substance in one direction, while transporting another substance in the
opposite direction. These pumps are extremely efficient because many of them
can use one ATP molecule to fuel these two different tasks.
One important type of antiport pump is the sodium-potassium pump, which is

discussed in more detail under “Examples of Active Transport.”
Symport Pumps
Symport pumps take advantage of diffusion gradients to move substances.

Diffusion gradients are differences in concentration that cause substances to
naturally move from areas of high to low concentration.
In the case of a symport pump, a substance that “wants” to move from an area
of high concentration to low concentration down its concentration gradient is
used to “carry” another substance against its concentration gradient.
One example of a symport pump – that of the sodium-glucose transport protein
– is discussed below under “Examples of Active Transport.”
Active transport by
symporter pumps
Endocytosis
In the third type of active transport, large items, or large amounts of

extracellular fluid, may be taken into a cell through the process of endocytosis.
In endocytosis, the cell uses proteins in its membrane to fold the membrane into
the shape of a pocket. This pocket forms around the contents to be taken into
the cell. The pocket grows until it is pinched off, re-forming the cell membrane
around it and trapping the pocket and its contents inside the cell. These
membrane pockets, which carry materials inside of or between cells, are called
“vesicles.”
The folding of the cell membrane is accomplished in a mechanism similar to the

antiport transport of potassium and sodium ions. Molecules of ATP bind to
proteins in the cell membrane, causing them to change their shape. The
conformational changes of many proteins together change the shape of the cell
membrane until a vesicle is created.
In receptor-mediated endocytosis, a cell’s receptor may recognize a specific

molecule that the cell “wants” to take in, and form a vesicle around the area
where it recognizes the molecule. In other types of endocytosis, the cell relies on
other cues to recognize and engulf a particular molecule.
Exocytosis
Exocytosis is the opposite of endocytosis. In exocytosis, the cell creates a vesicle

to enclose something inside the cell, for the purpose of moving it outside of the
cell, across the membrane. This most commonly occurs when a cell wants to
“export” an important product, such as cells that synthesize and export enzymes
and hormones that are needed throughout the body.
In eukaryotic cells, protein products are made in the endoplasmic reticulum.

They are often packaged by the endoplasmic reticulum into vesicles and sent to
the Golgi apparatus.
The Golgi apparatus can be thought of like a cellular “post office.” It receives
packages from the endoplasmic reticulum, processes them, and “addresses”
them by adding molecules that will be recognized by receptors on the membrane
of the cell intended to receive the product.
The Golgi apparatus then packages the finished “addressed” products into
vesicles of its own. These vesicles move towards the cell membrane, dock, and
fuse with it, allowing the vesicle membrane to become part of the cell
membrane. The vesicle’s contents are then spilled into the extracellular space.
Endocytosis and
exocytosis are examples of active transport mechanisms
Examples of Active Transport

Sodium Potassium Pump
One of the most important active transport proteins in animals is the sodium-
potassium pump. As animals, our nervous system functions by maintaining a
difference in ion concentrations between the inside and outside of nerve cells.
It is this gradient that allows our nerve cells to fire, creating muscle contractions,
sensations, and even thoughts. Even our heart muscle relies upon these ion
gradients to contract!
The ability of the sodium-potassium pump to transport potassium into cells while
transporting sodium out of cells is so important that some estimates suggest we
spend a total of 20-25% of all the energy we get from food just performing this
one task! In neurons, a great majority of the cell’s energy is used to power
sodium-potassium pumps.
This might sound like a lot of energy, but it is an important and monumental
task; it is this pump that allows us to move, think, pump blood throughout our
bodies, and perceive the world around us.
Sodium-Glucose Transport Protein
A famous example of a symport pump is that of the sodium-glucose transport

protein. This protein binds to two sodium ions, which “want” to move into the
cell, and one glucose molecule, which “wants” to stay outside of the cell. It
represents an important method of sugar transport in the body, required to
provide energy for cellular respiration.
The natural diffusion of sodium ions inside the cell facilitates the movement of
glucose into the cell. Glucose can be carried into the cell with the sodium without
the transport protein expending ATP. However, ATP must be utilized by the
sodium-potassium pump elsewhere in the cell to keep up the sodium gradient in
place. Without the sodium gradient, sodium-glucose transport could not function.
White Blood Cells Destroying Pathogens

An important example of endocytosis is the process by which white blood cells
“eat” pathogens. When white blood cells recognize a foreign object inside the
body, such as a bacterium, they fold their cell membrane around it to take it into
their cytoplasm.
They then merge the vesicle containing the invader with a lysosome – a vesicle
containing strong chemicals and enzymes that can break down and digest
organic matter. They have essentially just created a cellular “stomach” to
“digest” the invader!
What is the Difference Between Active Transport

and Passive Transport?
Active transport moves substances from a region of lower concentration to a
higher concentration, i.e., against the concentration gradient. There is an energy
requirement for this process, as it does not occur naturally in the absence of
active forces.
In contrast, passive transport occurs naturally, as substances move down a

concentration gradient in the absence of energy. Therefore, the primary
difference in active transport vs passive transport is the energy requirement.
Quiz

Share
Thank you for taking Active Transport Quiz! You got 2 questions correct out
of 3. The result is shown below:
1. Active transport requires energy
 A. Truecorrect
 B. False
Active transport is called “active” because it requires the cell to spend energy to
make it happen. Active transport is transport that would not happen on its own,
without cellular energy.
2. All forms of active transport must directly use ATP to accomplish
their goal.
 A. Truewrong
 B. Falsecorrect
Secondary active transport may use ATP indirectly, as in the case of the sodium-
glucose pump.
This pump does not use ATP itself, but it does use the concentration gradient of
sodium – which is created by the sodium-potassium pump that does use ATP –
to accomplish its goal.
This form of transport would not work without ATP. It's just that the ATP is spent
by a different transport protein. The sodium-glucose pump then takes advantage
of this work.
3. A molecule of ATP can be used many times and still retain its ability
to power action within the cell.
 A. True
 B. Falsecorrect
Like firewood that has been burned, the energy of ATP is “spent” after it is used
to power a chemical reaction.
Unlike firewood, the adenosine phosphate “backbone” of ATP can be re-charged
by having more energy added to it in the form of more phosphate groups.
To re-charge ATP, however, cells must collect more energy from the
environment, such as from sunlight or food. Without energy from the
environment, cellular actions powered by ATP cannot occur.
ATP Synthase Definition

ATP synthase is an enzyme that directly generates adenosine triphosphate (ATP)
during the process of cellular respiration. ATP is the main energy molecule used
in cells. ATP synthase forms ATP from adenosine diphosphate (ADP) and an
inorganic phosphate (Pi) through oxidative phosphorylation, which is a process in
which enzymes oxidize nutrients to form ATP. ATP synthase is found in all
lifeforms and powers all cellular activities.
Function of ATP Synthase

The function of ATP synthase is to produce ATP. ATP is necessary to power all
cellular processes, so it is constantly being used by cells and constantly needs to
be produced. Each ATP synthase can produce about 100 molecules of ATP every
second. Eukaryotes, such as plants, animals, and fungi, have organelles
called mitochondria that mainly function as ATP producers. Plants also have
chloroplasts that contain ATP synthase and can produce ATP from sunlight and
carbon dioxide. Bacteria and archaea, which make up the prokaryotes, do not
have mitochondria but produce ATP through similar cellular respiration processes
in their plasma membrane. Across all forms of life, ATP synthase has basically
the same structure and function. Therefore, it is thought to have evolved early
on in the evolution of life, and would have been found in the last common
ancestor of all life on Earth.
Structure of ATP Synthase
ATP Synthase has two parts. The part embedded within the membrane of the
mitochondria (in eukaryotes), thylakoid membrane of the chloroplast (only in
plants), or plasma membrane (in prokaryotes) is called F O. This is a motor that is
powered by H+ ions flowing across the membrane. The part within the
mitochondria, stroma of the chloroplast, or inside the bacterial or archaeal cell is
called F1-ATPase. This is another motor that is used to generate ATP. These two
parts are thought to have been two separate structures with two different
functions that eventually evolved into ATP synthase. The FO region is similar to
DNA helicases (enzymes that unzip DNA so that it can be used as a template for
reproduction), while the F1-ATPase region is similar to the H+ motors that allow
flagella, arm-like appendages on some bacteria, to move. F 1-ATPase has a
central stalk and rotor that, when turned, converts ADP and P i into ATP.
This is a rendering of the structure of ATP synthase. FO is shown in blue and
purple, while F1-ATPase is shown in red.
ATP Synthesis
ATP is produced through different methods: through cellular respiration in the
mitochondria, during photosynthesis in the chloroplasts of plants, and across the
inner membrane of bacteria and archaea, which do not have mitochondria.
Although the methods of ATP production vary across different types of
organisms, they all follow a similar basic procedure.
In the mitochondria of eukaryotes, the molecules NADH and FADH 2, which are
products of the citric acid cycle, pass electrons down an electron transport chain,
where they travel through three different protein complexes. This process
releases energy, and this energy allows protons (H+ ions) to travel down a proton
gradient through the protein complexes, which act as proton pumps. The flow of
these protons down the gradient turns the rotor and stalk of the ATP synthase,
which makes it possible for a phosphate group to join with adenosine
diphosphate (ADP), forming ATP. In chloroplasts, the process is similar, except
light energy is the type of energy that excites electrons, causing them to flow
down the electron transport chain and enable H+ ions to travel through a
membrane in the chloroplast. These methods are similar in very different
organisms since the ability to generate ATP existed in the common ancestor of
all living organisms.

 Adenosine triphosphate (ATP) – The main energy molecule used by
the cell.
 Eukaryotes – Organisms that have eukaryotic cells, which are complex
cells with a true nucleus and organelles.
 Mitochondria – The organelle in the cells of eukaryotes that produces
ATP.
 Chloroplast – The organelle in plant cells that, in addition to
mitochondria, produces ATP through photosynthesis.
Quiz
1. Which organisms do not have mitochondria?
A. Bacteria
B. Animals
C. Plants
D. Fungi
A is correct. Bacteria do not have mitochondria, and instead produce ATP
through ATP synthase molecules that are lodged in their inner membranes.
Archaea, not a listed choice above, do not have mitochondria either; archaea and
bacteria are both prokaryotes and do not have a true nucleus or other cell
organelles.
2. Which component is not part of the ATP synthesis process?

A. Electron transport chain
B. Proton gradient
C. Flagella
D. Rotor and stalk of ATP synthase
C is correct. Choices A, B, and D are all steps in the synthesis of ATP. Flagella
are arm-like appendages that some bacteria have; they allow bacteria to move.
Flagella have H+ motors that are similar to F1-ATPase, one of the components of
ATP synthase.
3. Which part of ATP synthase is a motor?

A. FO
B. F1-ATPase
C. Both
D. Neither
C is correct. Both parts of ATP synthase, FO and F1-ATPase, are motors. FO is a
motor that is powered by the proton gradient across the membrane, which
occurs because the electron transport chain releases energy. F 1-ATPase is also a
motor; it is similar to the motors in the flagella of some bacteria. The action of
FO turns F1-ATPase into a generator of ATP.
Cell Cycle Definition

The cell cycle is a cycle of stages that cells pass through to allow them to divide
and produce new cells. It is sometimes referred to as the “cell division cycle” for
that reason.
New cells are born through the division of their “parent” cell, producing two
“daughter” cells from one single “parent” cell.
Daughter cells start life small, containing only half of the parent

cell’s cytoplasm and only one copy of the DNA that is the cell’s “blueprint” or
“source code” for survival. In order to divide and produce “daughter cells” of
their own, the newborn cells must grow and produce more copies of vital cellular
machinery – including their DNA.
The two main parts of the cell cycle are mitosis and interphase.
Mitosis is the phase of cell division, during which a “parent cell” divides to create
two “daughter cells.”
The longest part of the cell cycle is called “interphase” – the phase of growth
and DNA replication between mitotic cell divisions.
Both mitosis and interphase are divided into smaller sub-phases which need to
be executed in order for cell division, growth, and development to proceed
smoothly. Here we will focus on interphase, as the phases of mitosis have been
covered in our “Mitosis” article.
Interphase consists of at least three distinct stages during which the cell grows,
produces new organelles, replicates its DNA, and finally divides.
Only after the cell has grown by absorbing nutrients, and copied its DNA and
other essential cellular machinery, can this “daughter cell” divide, becoming
“parent” to two “daughter cells” of its own.
The graphic below shows a visual representation of the cell cycle. The small
section labeled “M” represents mitosis, while interphase is shown subdivided into
its major components: the G1, S, and G2 phases.
This cell cycle is used by all eukaryotic cells to produce new cells. Prokaryotic
cells such as bacteria use a process called “binary fission.”
For some unicellular eukaryotes, the cell cycle is the same as the reproductive

cycle. Their “daughter cells” are independent organisms that will go on to
reproduce themselves through mitosis.
In other organisms, the cell cycle is used for growth and development of a
single organism, while other methods are used to reproduce the organism.
Animals and some plants, for example, create new offspring through a process
of sexual reproduction which involves the creation and combination of special sex
cells.
But animals and plants still use the cell cycle to produce new cells within their
tissues. This allows these multicellular organisms grow and heal throughout their
lifespans.
Function of Cell Cycle

Because cells reproduce by dividing, new “daughter” cells are smaller than their
parent cells, and may inherit the bare minimum of cellular machinery they need
to survive.
Before these daughter cells can divide to produce still more cells, they need to
grow and reproduce their cellular machinery.
The importance of the cell cycle can be understood by doing simple math about
cell division. If cells did not grow in between divisions, each generation of
“daughter” cells would be only half the size of the parent generation. This would
become unsustainable pretty quickly!
In order to accomplish this growth and prepare for cell division, cells divide their
metabolic activities into distinct phases of Gap 1, Synthesis, Gap 2 between cell
divisions.
The complete cell division cycle will be discussed below.
Phases of Cell Cycle

Mitosis
Let’s start this cell cycle with “birth.”
During mitosis, the “parent” cell goes through a complex series of steps to
ensure that each “daughter” cell will get the materials it needs to survive,
including a copy of each chromosome. Once the materials are properly sorted,
the “parent” cell divides down the middle, pinching its membrane in two.
You can read more about the detailed steps of mitosis and how a parent cell
makes sure its daughter cells will inherit what they need to survive in our article
on Mitosis (https://biologydictionary.net/mitosis/).
Each of the new “daughters” are now independently living cells. But they’re
small, and have only one copy of their genetic material.
This means they can’t divide to produce their own “daughters” right away. First,
they must pass through “interphase” – the phase between divisions, which
consists of three distinct phases.
G1 Phase
In G1 phase, the newly formed daughter cell grows. The “G” is most often said to
stand for “gap,” since these phases appear to an outside observer with a light
microscope to be relatively inactive “gaps” in the cell’s activity.
However given what we know today, it might be more accurate to say the “G”
stands for “growth” – for the “G” phases are flurries of protein
and organelle production as well as literal increase in the size of the cell.
During the first “growth” or “gap” phase, the cell produces many essential
materials such as proteins and ribosomes. Cells that rely on specialized
organelles such as chloroplasts and mitochondria make a lot more of those
organelles during G1 as well. The cell’s size may increase as it assimilates more
material from its environment into its machinery for life.
This allows the cell to increase its energy production and overall metabolism,
preparing it for…
S Phase
During S phase, the cell replicates its DNA. The “S” stands for “synthesis” –
referring to the synthesis of new chromosomes from raw materials.
This is a very energy-intensive operation, since many nucleotides need to by
synthesized. Many eukaryotic cells have dozens of chromosomes – huge masses
of DNA – that must be copied.
Production of other substances and organelles is slowed greatly during this time
as the cell focuses on replicating its entire genome.
When the S phase is completed, the cell will have two complete sets of its
genetic material. This is crucial for cell division, as it ensures that both daughter
cells can receive a copy of the “blueprint” they need to survive and reproduce.
However, replicating its DNA can leave the cell a little bit depleted. That’s why it
has to go through…
G2 Phase
Just like the first “gap” phase of the cell cycle, the G2 phase is characterized by
lots of protein production.
During G2, many cells also check to make sure that both copies of their DNA are
correct and intact. If a cell’s DNA is found to be damaged, it may fail its “G 2/M
checkpoint” – so named because the this “checkpoint” happens at the end of the
G2 phase, right between G2 and “M phase” or “Mitosis.”
This “G2/M checkpoint” is a very important safety measure for multicellular

organisms like animals. Cancers, which can result in the death of the entire
organism, can occur when cells with damaged DNA reproduce. By checking to
see if a cells’ DNA has been damaged immediately before replication, animals
and some other organisms reduce the risk of cancer.
Interestingly, some organisms can skip G2 altogether and go straight into mitosis
after DNA is synthesized during S phase. Most organisms, however, find it safer
to use G2 and its associated checkpoint!
If the G2/M checkpoint is passed, the cell cycle begins again. The cell divides
through mitosis, and new daughter cells begin the cycle that will take them
through G1, S, and G2 phases to produce new daughter cells of their own.
Unless of course they’re meant for…
An Alternative Path: G0 Phase
After being born through mitosis, some cells are not meant to divide themselves
to produce daughter cells.
Neurons, for example – animal nerve cells – do not divide. Their “parent cells”
are stem cells, and the “daughter” neuron cells are programmed not to go
through the cell cycle themselves because uncontrolled neuron growth and cell
division could be very dangerous for the organism.
So instead of entering G1 phase after being “born,” neurons enter a phase

scientists call “G0 phase.” This is a metabolic state meant only to maintain the
daughter cell, not prepare for cell division.
Neurons and other non-dividing cell types may spend their whole lives in
G0 phase, performing their function for the overall organism without ever dividing
or reproducing themselves.
Cell Cycle Regulation

It’s very important for the survival of cells and organisms that the cell cycle be
regulated.
Organisms need to be able to stop cell division when the cell in question is
damaged, or when there isn’t enough food to support new growth; they must
also be able to start up cell division when growth or wound healing are needed.
To accomplish this, cells use a variety of chemical “signal cascades” where

multiple links in a chain create complex effects based on simple signals.
In these regulatory cascades, a single protein may change the function of many
other proteins, bringing about widespread changes to the functioning or even
structure of the cell.
This allows these proteins – such as cyclins and cyclin-dependent kinases – to

act as “stop points.” If the cyclins or cyclin-dependent kinases don’t give the go-
ahead, the cell cannot progress to subsequent stages of the cell cycle.
Some examples of cell cycle regulation are given below.
Cell Cycle Examples

Here we’ll discuss common examples of how cells regulate their cell cycles, using
a complex cascade of signal molecules, protein-activating enzymes, and signal-
destroying molecules.
p53
p53 is a protein that is well-known to scientists for its role in stopping cells with
severe DNA damage from reproducing.
When DNA is damaged, p53 works with cyclin-dependent protein kinases and
other proteins to initiate repair and protection functions – and can also stop the
cell from entering mitosis, ensuring that cells with DNA damage do not
reproduce.
Cyclins
Cyclins are a group of proteins that are produced at different points in the cell
cycle. There are cyclins unique to most phases of the cell cycle – G 1 cyclins, G1 /S
cyclins that regulate the transition from G1 into S, S cyclins, and M cyclins that
regulate the progress through the stages of mitosis.
Most cyclins are found in the cell at very low concentrations during other phases
of the cell cycle, but then spike suddenly when they’re needed to give the go-
ahead to the next stage of the cell cycle. Certain types of DNA damage may
prevent these cyclins from appearing to move the cell cycle forward, or may
prevent them from activating their cyclin-dependent protein kinases.
A few others, such as G1 cyclins, remain high as a constant “go ahead” signal
from G1 until mitosis.
Cyclin-Dependent Protein Kinases
The cell’s cyclins ultimately do their jobs by interacting with Cyclin-Dependent

Protein Kinases – that is, kinases that activate certain enzymes and proteins
when they bind to a cyclin. This allows cyclins to function as the “go” signal for
many changes in cellular activity that happens throughout the cell cycle.
Protein kinases are a special set of enzymes that “activate” other enzymes and
proteins by affixing phosphate groups to them. When an enzyme or other protein
is “activated” by a kinase, its behavior changes until it returns to its inactivated
form.
The system by which one protein kinase can change the activities of many other
proteins allows simple signals, such as cyclins, to produce complex changes to
cellular activity. Signal-dependent protein kinases are used to coordinate many
complex cellular activities.
Maturation-Promoting Factor
One example of a protein kinase at work is the Maturation-Promoting Factor, or

MPF. MPF is a protein kinase that is activated by an M cyclin, meaning that it is
activated during mitosis.
When MPF is activated, it in turn activates several different proteins in the

nuclear envelop of its host cell. The changes to these proteins result in the
disintegration of the nuclear envelope.
This is something that would be very dangerous at other points in the cell cycle,
but which is necessary during mitosis so that the chromosomes can be sorted to
ensure that each daughter cell receives a copy of each chromosome.
If M cyclins do not appear, MPF does not activate, and mitosis cannot go
forward. This is a good example of how cyclins and cyclin-dependent kinases
work together to coordinate – or stop – the cell cycle.
Anaphase-Promoting Complex/Cyclosome
Ingeniously, the protein kinase MPF doesn’t just ensure that the nuclear
envelope breaks down during mitosis – it also ensures that MPF levels will fall
after the nuclear envelope is broken down. It does this by activating
the Anaphase-Promoting Complex/Cyclosome, or “APC/C” for short.
As its name suggests, the APC/C promotes passage into Anaphase – and one of
the ways it does that is by breaking down MPF, a messenger from a previous
phase. So MPF actually activates the very proteins that destroy it.
The destruction of MPF by the APC/C ensures that the actions MPF promotes –
such as the disintegration of the nuclear envelope – do not happen again until
the daughter cell makes more MPF after passing through G1 phase, S phase, and
G2 phase.
By activating the APC/C, MPF regulates itself!
Quiz
1. Which of the following is NOT a reason why interphase is necessary?
A. Daughter cells begin life with only one copy of their DNA.
B. Daughter cells begin life small, without sufficient cellular machinery to pass on
to daughter cells.
C. If cells performed mitosis repeatedly without going through interphase, each
generation of daughter cells would be progressively smaller.
D. All of the above.
D is correct. Cells must go through interphase in order to grow, copy their DNA,
and ensure that they are prepared to create a healthy new generation of
daughter cells.
2. Which of the following organism would you NOT expect to use the
cell cycle described here?
A. A daisy
B. A kitten
C. An archaebacteria
C is correct. Archaebacteria and “true bacteria” are prokaryotes. They reproduce
using a similar, but simpler cycle of growth and division.
3. Which of the following is true of the G2 phase?

A. It is when the cell’s DNA is copied.
B. It is the first phase of the cell cycle after mitosis.
C. It contains the important G2/M checkpoint which checks the cell for DNA
damage before allowing it to reproduce.
D. None of the above.
C is correct. The G2 phase is the last phase before mitosis – and the site of the
vital G2/M, which makes cancer less likely by preventing cells with severe DNA
damage from reproducing.
ell Division Definition

Cell division is the process cells go through to divide. There are several types of
cell division, depending upon what type of organism is dividing. Organisms have
evolved over time to have different and more complex forms of cell division.
Most prokaryotes, or bacteria, use binary fission to divide the cell. Eukaryotes of
all sizes use mitosis to divide. Sexually-reproducing eukaryotes use a special
form of cell division called meiosis to reduce the genetic content in the cell. This
is necessary in sexual reproduction because each parent must give only half of
the required genetic material, otherwise the offspring would have too much DNA,
which can be a problem. These different types of cell division are discussed
below.
Types of Cell Division

Prokaryotic Cell Division
Prokaryotes replicate through a type of cell division known as binary fission.

Prokaryotes are simple organism, with only one membrane and no division
internally. Thus, when a prokaryote divides, it simply replicates the DNA and
splits in half. The process is a little more complicated than this, as DNA must first
be unwound by special proteins. Although the DNA in prokaryotes usually exists
in a ring, it can get quite tangled when it is being used by the cell. To copy the
DNA efficiently, it must be stretched out. This also allows the two new rings of
DNA created to be separated after they are produced. The two strands of DNA
separate into two different sides of the prokaryote cell. The cell then gets longer,
and divides in the middle. The process can be seen in the image below.
The DNA is the tangled line. The other components are labeled. Plasmids are
small rings of DNA that also get copied during binary fission and can be picked
up in the environment, from dead cells that break apart. These plasmids can
then be further replicated. If a plasmid is beneficial, it will increase in
a population. This is in part how antibiotic resistance in bacteria happens. The
ribosomes are small protein structures that help produce proteins. They are also
replicated so each cell can have enough to function.
Eukaryotic Cell Division: Mitosis
Eukaryotic organisms have membrane bound organelles and DNA that exists on
chromosomes, which makes cell division harder. Eukaryotes must replicate their
DNA, organelles, and cell mechanisms before dividing. Many of the organelles
divide using a process that is essentially binary fission, leading scientist to
believe that eukaryotes were formed by prokaryotes living inside of other
prokaryotes.
After the DNA and organelles are replicated during interphase of the cell cycle,
the eukaryote can begin the process of mitosis. The process begins
during prophase, when the chromosomes condense. If mitosis proceeded
without the chromosomes condensing, the DNA would become tangled and
break. Eukaryotic DNA is associated with many proteins which can fold it into
complex structures. As mitosis proceeds to metaphase the chromosomes are
lined up in the middle of the cell. Each half of a chromosome, known as sister
chromatids because they are replicated copies of each other, gets separated into
each half of the cell as mitosis proceeds. At the end of mitosis, another process
called cytokinesis divides the cell into two new daughter cells.
All eukaryotic organisms use mitosis to divide their cells. However, only single-
celled organisms use mitosis as a form of reproduction.
Most multicellular organisms are sexually reproducing and combine their DNA
with that of another organism to reproduce. In these cases, organisms need a
different method of cell division. Mitosis yields identical cells, but meiosis
produces cells with half the genetic information of a regular cell, allowing two
cells from different organisms of the same species to combine.
Eukaryotic Cell Division: Meiosis
In sexually reproducing animals, it is usually necessary to reduce the genetic

information before fertilization. Some plants can exist with too many copies of
the genetic code, but in most organisms it is highly detrimental to have too many
copies. Humans with even one extra copy of one chromosome can experience
detrimental changes to their body. To counteract this, sexually reproducing
organisms undergo a type of cell division known as meiosis. As before mitosis,
the DNA and organelles are replicated. The process of meiosis contains two
different cell divisions, which happen back-to-back. The first meiosis, meiosis I,
separates homologous chromosomes. The homologous chromosomes present in
a cell represent the two alleles of each gene an organism has. These alleles are
recombined and separated, so the resulting daughter cells have only
one allele for each gene, and no homologous pairs of chromosomes. The second
division, meiosis II, separated the two copies of DNA, much like in mitosis. The
end result of meiosis in one cell is 4 cells, each with only one copy of the
genome, which is half the normal number.
Organisms typically package these cells into gametes, which can travel into the
environment to find other gametes. When two gametes of the right type meet,
one will fertilize the other and produce a zygote. The zygote is a single cell that
will undergo mitosis to produce the millions of cells necessary for a large
organism. Thus, most eukaryotes use both mitosis and meiosis, but at different
stages of their lifecycle.
Cell Division Stages

Depending upon which type of cell division an organism uses, the stages can be
slightly different.
Mitosis Stages
Mitosis starts with prophase in which the chromosome is condensed. The cell

proceeds to metaphase where the chromosomes are aligned on the metaphase
plate. Then the chromosomes are separated in anaphase and the
cell’s cytoplasm is pinched apart during telophase. Cytokinesis is the final process
that breaks the cell membrane and divides the cell into two.
Meiosis Stages
The stages of meiosis are similar to mitosis, but the chromosomes act differently.
Meiosis has two phases, which include two separate cell divisions without the
DNA replicating between them. Meiosis I and meiosis II have the same 4 stages
as mitosis: prophase, metaphase, anaphase, and telophase. Cytokinesis
concludes both rounds of meiosis.
In prophase I, the chromosomes are condensed. In metaphase I, the

chromosomes line up across from their homologous pairs. When they are
separated in anaphase I and telophase I, there is only one form of each gene in
each cell, known as a reduction division. Meiosis II proceeds in the same manner
as mitosis, which sister chromatids dividing on the metaphase plate. By
telophase II, there are 4 cells, each with half of the alleles as the parent cell and
only a single copy of the genome. The cells can now become gametes and fuse
together to create new organisms.
Quiz
1. Somatic cells are cells that fill the body, and must reproduce to
repair damage. Gametic cells are cells that produce gametes. Which
type of cell division do each type of cell undergo?
A. Somatic= mitosis; Gametic= meiosis
B. Somatic= mitosis; Gametic= meiosis and mitosis
C. Somatic= mitosis and meiosis; Gametic= meiosis and mitosis
B is correct. Somatic cells only ever undergo mitosis. They only reproduce when
healing an injury or developing more tissue while an organism is growing.
Gametic cells must do these basic tasks as well. Therefore, they undergo mitosis.
They also can undergo meiosis to produce gametes. Organisms typically produce
thousands to millions of gametes, requiring many gametic diploid cells to start.
Once a cell becomes a haploid gamete, another diploid cell is needed to create
more gametes.
2. Mitochondria are organelles in cells that create ATP, a molecule used

for energy. Mitochondria must replicate inside the cell, separate from
mitosis or meiosis, to regulate the amount of energy being delivered.
In mitochondria, there is a ring of DNA that controls the mitochondrial
metabolism. This mtDNA is replicated, the mitochondria elongates, and
divides in half. What type of cell division is this?
A. Binary Fission
B. Mitosis
C. Meiosis
A is correct. Mitochondria must reproduce many times inside of a cell to provide
it with enough energy. The simple form of division displayed is binary fission. No
chromosomes are sorted, or reduced. The organelle is simply enlarged and split
in half, with the DNA that controls it being duplicated as well.
3. Evolution depends on the successful replication of DNA. In fact, all

DNA on Earth comes from only one or two original cells, and most
organisms are related to each other. What is responsible for the
different forms of life?
A. Mutation
B. Genetic Recombination
C. Both
C is correct. The majority of the variety on Earth is caused by both mutations
and genetic recombination. Organisms that undergo meiosis can undergo events
known as recombination in which parts of chromosomes are swapped. Even in
asexual organisms, mutations and spontaneous recombination of DNA sometimes
produce very successful organisms.
Chemiosmosis Definition
Chemiosmosis is when ions move by diffusion across a semi-permeable
membrane, such as the membrane inside mitochondria. Ions are molecules with
a net electric charge, such as Na+, Cl–, or specifically in chemiosmosis that
generates energy, H+. During chemiosmosis, ions move down an electrochemical
gradient, which is a gradient of electrochemical potential (a form of potential
energy). Since chemiosmosis is a type of diffusion, ions will move across a
membrane from areas of high concentration to areas of low concentration. Ions
also move to balance out the electric charge across a membrane.
Function of Chemiosmosis
Chemiosmosis is involved in the production of adenosine triphosphate (ATP),
which is the main molecule used for energy by the cell. In eukaryotes, ATP is
produced through the process of cellular respiration in the mitochondria. First,
the molecules NADH and FADH2, obtained from the citric acid cycle, pass
electrons down an electron transport chain, which releases energy. This energy
allows protons (H+) to travel down a proton gradient via chemiosmosis. This in
turn provides the energy for the enzyme ATP synthase to make ATP. The flow of
these protons down the gradient turns the rotor and stalk of the ATP synthase,
which makes it possible for a phosphate group to join with adenosine
diphosphate (ADP), forming ATP. The production of ATP during respiration is
called oxidative phosphorylation. Through oxygen and glucose, ATP is ultimately
created through the phosphorylation of ADP. In aerobic respiration, 38 ATP
molecules are formed per glucose molecule. Since chemiosmosis plays a role in
the creation of ATP during this process, without chemiosmosis, organisms would
not be able to produce the energy that they need to live.
The idea that ATP is synthesized through chemiosmosis was first proposed in
1961 by Dr. Peter D. Mitchell. At the time, this was controversial, because it was
more widely accepted that there was some intermediate molecule that stored
energy from the electron transport chain. However, an intermediate molecule
was never found, and eventually research showed that the chemiosmosis theory
was correct. Mitchell would later go on to win the Nobel Prize in Chemistry in
1976 for his contributions to science.
This images shows, very generally, ions moving from high to low concentration
during chemiosmosis.
Examples of Chemiosmosis
Although chemiosmosis is often generally defined as the movement of ions
across a membrane, it is really only used in the context of talking about the
movement of H+ ions during the production of ATP. The most common method
involving chemiosmosis in the production of ATP is cellular respiration in the
mitochondria, the process of which is discussed above. All eukaryotic organisms
have mitochondria, so chemiosmosis is involved in ATP production through
cellular respiration in the vast majority of different types of organisms, from
animals to plants to fungi to protists. However, even though archaea
and bacteria do not have mitochondria, they also use chemiosmosis to produce
ATP through photophosphorylation. This process also involves an electron
transport chain, proton gradient, and chemiosmosis of H+, but it takes place
across the inner membrane of the bacterium or archaeon, since they have no
mitochondria.
Plants produce ATP during photosynthesis in the chloroplast in addition to the

ATP they generate through cellular respiration in mitochondria. The process is
again similar: during photosynthesis, light energy excites electrons, which flow
down an electron transport chain, which in turn allows H+ ions to travel through a
membrane in the chloroplast. Some bacteria, such as cyanobacteria, also use
photosynthesis.
The similarities between these ATP production methods are more than just
coincidence; both mitochondria and chloroplasts are thought to have evolved
from free-living bacteria. This theory is called the endosymbiotic theory. This
theory hypothesizes that that had symbiotic relationships with other cells, aiding
them by producing energy in return for a place to live inside the cell. Over time,
these bacteria became inextricable from the cells they resided in. The fact that
mitochondria and chloroplasts have their own, separate, DNA supports this idea.
This is why the chemiosmosis is used in generally the same way whether ATP is
being produced in a mitochondrion, chloroplast, or bacterium.

 Glucose – A simple sugar that has an important role in metabolism and
energy production.
 Adenosine triphosphate (ATP) – The main molecule used for energy
in cells.
 Ion – A molecule with a net electric charge due to gaining or losing an
electron.
 Diffusion – Movement of molecules from an area of high concentration
to an area of low concentration.
Quiz
1. Which organism does not have mitochondria?
A. Human
B. Mushroom
C. Bacteria
D. Fern
C is correct. Bacteria do not have mitochondria. However, they still produce
energy though a similar process involving chemiosmosis. It is thought that
mitochondria actually evolved from bacteria that were once free-living; this
theory is called the endosymbiotic theory.
2. Chemiosmosis involving what ion is part of the process of generating

ATP?
A. Na+
B. H+
C. Cl–
D. H–
B is correct. During cellular respiration, protons (H+) travel down a proton
gradient by chemiosmosis. This causes the enzyme ATP synthase to turn and join
a phosphate group to adenosine diphosphate (ADP), forming ATP. Choice D, H –,
refers to electrons, which are also involved in the production of ATP but travel
down the electron transport chain, not through chemiosmosis.
3. Chemiosmosis can occur in what cell organelle?

A. Mitochondrion
B. Chloroplast
C. Nucleus
D. Choices A and B
D is correct. Chemiosmosis occurs in mitochondria during cellular respiration and
in chloroplasts during photosynthesis. Both of these processes generate ATP.
Channel Protein Definition

A channel protein is a special arrangement of amino acids which embeds in
the cell membrane, providing a hydrophilic passageway for water and small,
polar ions. Like all transport proteins, each channel protein has a size and shape
which excludes all but the most specific molecules. A generic channel protein is
seen below, embedded within the membrane. Ions, the small green hexagons,
travel through the channel protein. They move from an area of high
concentration to an area with a lower concentration.
Types of Channel Protein

Non-gated
Like the image above, a channel protein may exist in a state which stays open all
the time. This is called a non-gated channel protein. These proteins allow ions
and water to flow through the cell membrane, which is normally hydrophobic and
would resist the passage of these molecules. A non-gated channel protein is
needed whenever the balance of water and ions must be assisted by the
constant passage of water and ions into or out of the cell. However, it is often a
disadvantage to leave a channel open all the time. The second type of channel
protein addresses this problem.
Gated
A gated channel protein remains closed, until it receives a special chemical or

electrical signal. These channel proteins are extremely important in many cellular
functions. The ability to gate an ion channel allows electrical energy to be built
up inside the cell. Nerve function is entirely based on this fact. Channel proteins
on the surface of nerve cells react to electrical signals created by the flooding of
ions through the membrane next to them. As they open, ions spill through and
continue the electrical disturbance. This passes a signal very quickly through the
body. A gated channel protein reacting to a signal molecule can be seen in the
image below.
Channel Protein Function

Depending on whether it is gated or non-gated, a channel protein has a slightly
different function. A non-gated channel protein simple allows ions and water to
flow freely from one side of a membrane to another. While these type of
channels are not often found on the external cell membrane, they are more
often found within organelles and places where ion gradients are not maintained.
When an ion gradient needs to be maintained, gated channel proteins serve the
role of holding back the tide of ions until they are signaled to open. A closed
channel acts as corked bottle. Water and ions move slowly through the plasma
membrane, or not at all. If the channel protein is closed, they have little chance
of obtaining an equilibrium. Cells use these proteins in many ways, everything
from balancing their water content to actively building up charges.
Channel Protein Structure

Most channel proteins are made of several identical protein subunits which form
a hydrophilic region in their center. Gated channels function by changing
conformation upon receiving a signal, allowing access to the hydrophilic
passageway. Non-gated channels are usually formed from identical subunits,
which attach to each other in a circle. While the inside of the circle is hydrophilic,
the amino acids exposed within the hydrophobic cell membrane are also non-
polar. This helps to anchor the protein within the membrane. If the protein tried
to slip out of the membrane, it would be pushed by polar forces back into place.
Channel Protein Example

When your muscles contract, this is the result of the action of gated channel
proteins within your muscle cells. These cells respond to the
neurotransmitter acetylcholine, which is present in high amount as the end of
nerve cells. At the synapse or space where they release the neurotransmitter,
the opposing nerve cell contains many channel proteins set to receive the signal.
An electrical signal coming down the nerve (also driven by a type of channel
protein) causes the acetylcholine to be released.
The neurotransmitter diffuses quickly across the synapse, and reaches channel
proteins on the other side. Each channel protein opens, releasing sodium and
potassium ions. The electrical disturbance travels down special channels within
muscles, carrying the signal to each muscle cell. Here, another set of channel
proteins is activated. These release sodium, causing the
proteins actin and myosin to start their crawling motion against each other,
contracting each cell. The full result is a full muscle contraction, moving a limb or
operating a part of the body.
Channel Proteins and Carrier Proteins

There are four types of transport that occur within cells. Simple diffusion occurs
with small gas molecules, such as oxygen and carbon dioxide, as well as many
non-polar chemicals such as steroid hormones and medicinal drugs. These
molecules have the right chemistry and size to pass right through the cell
membrane.
More charged molecules, which are hydrophilic, have a hard time passing
through the membrane. These include ions, water, and sugars such as glucose.
Channel proteins carry out the majority of facilitated diffusion. While the
chemicals are still moving in the direction of their concentration (from high to
low), they are given a passageway through the cell membrane. This allows them
to move at near diffusion speeds.
However, not all facilitated diffusion is carried out by channel proteins. Carrier

proteins, proteins which bind and transport molecules across the membrane, are
also involved in facilitated diffusion. Large molecules like glucose cannot pass
through the narrow passageway created by channel proteins. Carrier proteins
known as uniporters bind to glucose molecules one at a time. The binding action
causes a conformational change in the protein, which causes it to deposit the
molecule on the opposite side of the cell. These carrier proteins operate without
energy, and move molecules down their concentration gradient.
When substances need to be moved against their concentration gradient, more

complicated carrier proteins are needed. Active transport is the process of using
a carrier protein and powering it with an interaction with ATP to move a
molecule against the gradient. The energy is needed because molecules naturally
want to diffuse, and spread out. It takes a lot of energy to move some ions and
molecules, but is necessary for the way life has evolved. Other carrier proteins
have evolved for cotransport. By transporting a molecule down its concentration
gradient, another molecule can be moved against its gradient. This carrier
protein type allows cells to transport materials using the ion gradient they build
with other ATP carrier proteins.
The major difference between a channel protein and a carrier protein

is stereospecificity. While channel proteins only allow certain sized molecules to
pass, they do not bind the molecules. Carrier proteins have an active site, which
the chemical to be transported must bind to. This site will bind specifically to
only one molecule, and seeks to transport this molecule alone. The binding
action is what allows the passage of the large molecule through the cell
membrane.
Quiz
1. What is the difference between a channel protein and a carrier
protein?
A. They move different types of molecules
B. A channel protein does not need energy
C. A channel protein does not bind the molecules it transports
C is correct. Channel proteins are simply that: channels. Like a straw, or the
drain on a tub, they simply allow water and ions to pass through them. While
they can be gated or non-gated, they do not need energy to operate, but neither
do uniporters nor other carrier proteins. Channel proteins and carrier proteins
can move the same types of molecules.
2. A mutation in a person causes their ion channels to malfunction. Will

this be a problem?
A. Yes
B. No
C. They can treat it
A is correct. This is the cause of a terrible disease known as Cystic Fibrosis.
Sufferers of this disease cannot regulate ions in their mucous membranes,
causing suffocating phlegm buildups and organ failures at a young age. Channel
proteins are very important for many other functions, and most of them are
required to work for normal bodily functions.
3. In an experiment, a scientist separates two bodies of water with a

thin phospholipid membrane, such as that found in a cell. He pours salt
in one of the bodies of water. The membrane has channel proteins
embedded. His control experiment is two bodies of water separated by
the same membrane, but without the channel proteins. He adds salt to
this control as well. Which of the following would you expect to
happen?
A. In both experiments, the salt will quickly come to equilibrium between the
bodies
B. In the control, equilibrium will come more slowly than the experimental
membrane
C. The control will come to equilibrium faster
B is correct. The control will come to equilibrium more slowly because it lacks a
channel protein. These proteins will allow the ions in salt to distribute right
through the membrane along with water. These two substances will work their
way back and forth across the membrane until they are equal. Without the
proteins, the membrane holds back water and ions, and the process will happen
much more slowly, if it happens at all.
CRISPR Definition
Clustered regularly interspaced short palindromic repeats (CRISPR) are short,
repeating stretches of DNA found in most archaea and many bacteria. CRISPR
and CRISPR-associated proteins (Cas) form an adaptive immune system that
protects against foreign genetic elements such as viruses, plasmids, and
transposons. The CRISPR/Cas9 system also provides the basis for a genome
editing tool that can be used to permanently modify genes in a specific, targeted
manner.
Features of CRISPR Loci

CRISPR loci are composed of an AT-rich leader sequence followed by multiple,
short nucleotide repeats separated by spacer regions. Many of the repeats are
palindromic, with predicted RNA hairpin secondary structure, while others lack
symmetry and are predicted to form unstructured RNA. Repeats are conserved
within a CRISPR locus, while the spacers are highly variable and correspond to
DNA acquired from exposure to foreign DNA, such as viruses and plasmids. The
length of CRISPR repeats and spacers varies; repeats are 23-55 basepairs long,
and spacers are 21-72 basepairs long. CRISPR arrays are usually located
adjacent to clusters of Cas genes. The Cas genes encode a wide variety of
proteins that have functional domains found in helicases, nucleases, polymerases
and other nucleotide-binding proteins. Cas proteins have functions in acquiring
spacer DNA, RNA processing, and target binding and cleavage. CRISPR loci have
been identified in approximately 90% of Archaea and 40% of Bacteria, and
an organism’s genome may contain one or many CRISPR loci (up to 18 have
been observed in a single organism).
CRISPR Classes and Types

There are two classes of CRISPR/Cas systems, termed Class 1 and Class 2. Class
1 systems utilize multiple Cas proteins to cleave foreign DNA, while Class 2
systems use a single Cas protein. The classes are divided into types; Class 1
contains types I, III, and IV, and Class 2 contains types II, V, and VI. Types are
defined by a gene generally found only within that type, as well as the additional
Cas genes present. The types are further divided in 19 subtypes.
Function and Mechanism of CRISPR in Prokaryotes

CRISPR provides prokaryotes with acquired immunity against invasive genetic
elements. These loci incorporate genetic material from viruses and plasmids, and
use it to target foreign genetic elements in a sequence-specific manner. The
steps involved in protecting against foreign genetic elements using the
CRISPR/Cas system are acquisition of spacer DNA from the invading virus,
biogenesis of CRISPR RNA (crRNA), which will allow for recognition of foreign
DNA, and interference, in which the invasive DNA is recognized and cleaved.
Acquisition of Spacer DNA
When a prokaryotic cell is invaded by a virus, portions of the viral DNA are
sampled and incorporated into the spacer regions of the CRISPR locus. The
nuclease enzymes Cas1 and Cas2 are involved in spacer acquisition in E. coli and
likely all CRISPR/Cas systems, as they are the only Cas proteins found to be
conserved across all systems. The DNA that is sampled and incorporated into
CRISPR loci as spacers may be located next to protospacer adjacent motifs
(PAMs) within the viral genome; PAMs are important in selection of foreign
nucleic acids in type I and type II systems. Spacers are usually added next to the
leader sequence, though the new spacer may also be inserted randomly into the
repeat-spacer array.
crRNA Biogenesis
Following incorporation of foreign DNA into a CRISPR locus, the CRISPR

sequence is transcribed and processed into small interfering crRNAs. The repeat-
spacer array is initially transcribed into a single transcript, which is then
processed by Cas proteins into crRNAs, which later serve as a guide in targeting
foreign nucleic acids. Biogenesis of crRNA differs in different CRISPR systems. In
certain type I systems, Cas proteins cleave at the edge of stem-loops in the long
transcript to produce smaller crRNAs. In type II systems, a trans-activating
crRNA (tracrRNA) is transcribed that is complementary to the CRISPR repeats,
resulting in the formation of double stranded RNA (dsRNA). The dsRNA is
cleaved by RNaseIII to produce crRNAs.
Interference
During the interference stage, crRNAs associate with Cas proteins to form a
complex that recognizes, targets, and destroys viral genetic material. The crRNA
basepairs with the complementary sequence in the viral DNA, marking it for
destruction. Recognition of the PAM sequence may also be required for
recognition of the foreign DNA. In type II systems, Cas9 carries out the
interference step using both a crRNA and tracrRNA which allows it to recognize
foreign DNA. In addition to recognizing target sequences, Cas9 has endonuclease
activity and cleaves the foreign DNA.
The figure depicts how the CRISPR/Cas system defends against foreign genetic
elements in prokaryotes.
CRISPR/Cas9 System as a Genome Editing Tool

The CRISPR/Cas system has been exploited as a molecular biology technique for
targeted genome editing. Genome editing is carried out using CRISPR/Cas9
system. The Cas9 protein is a DNA endonuclease that uses a guide RNA to target
and cleave DNA. Native Cas9 utilizes a guide RNA composed of crRNA and trans-
activating CRISPR RNA (tracrRNA); for the purposes of genome editing, this
system was simplified by fusing crRNA and tracrRNA to form a single guide RNA.
The CRISPR/Cas9 system may also include a repair template, which is utilized in
DNA repair via non-homologous end joining or homology directed repair. By
altering the sequence of the guide RNA, the CRISPR/Cas9 system can be used to
target any DNA sequence, and knockdown, activate, or mutate the desired
sequence. The components of the CRISPR/Cas9 system are often incorporated
into a plasmid that is used to transfect cells for genome editing. Multiple changes
can be made simultaneously; in one case 62 genes were modified at once.
Gene Activation and Repression

CRISPR that lacks nuclease activity (termed dCas9) can be used to target a
specific sequence for activation or suppression. By eliminating the ability to cut
DNA, the CRISPR/Cas9 system can be used to target genes without cleaving
them. Cas9 lacking nuclease activity alone blocks transcription in bacterial cells;
in mammalian cells additional proteins are incorporated. Transcription factors
may also be coupled to Cas9, allowing for activation of target genes.
Altering the Genetic Sequence
A DNA repair template can be included in the CRISPR/Cas9 system which allows
for this DNA sequence to be incorporated at the desired location. The repair
template extends beyond the location of the cleaved section of DNA. Once the
DNA break is introduced, the cell’s DNA repair machinery uses the template to
repair the DNA, thereby permanently altering the sequence of the DNA.
CRISPR Applications
CRISPR technology can be used to make precise genetic alterations in diverse
cell types and organisms, including mice, plants, fish, and human cells. CRISPR
can be used to generate animal models of disease by knocking down or targeting
a gene of interest. CRISPR can also be used to generate cell lines that contain
disease-causing mutations and can be use to study the molecular mechanisms of
the disease. CRISPRs also have promising therapeutics applications; they may be
effective in targeting viruses such as herpesvirus and preventing their replication
in humans, have been used to treat genetic disorders in animals, and have been
approved for clinical trials in the treatment of cancer. Apart from biomedical
applications, CRISPR can also be used to engineer biofuel-producing yeast
strains as well as food crops.
Quiz
1. The CRISPR/Cas system provides adaptive immunity against foreign
genetic elements in what types of organisms?
A. Bacteria
B. Archaea
C. Eukaryotes
D. A and B
D is correct. CRISPR loci are found in ~40% of bacteria and ~90% of archaea,
where they provide the organism with acquired immunity against viruses and
plasmids.
2. What does Cas9 do after binding DNA that is complementary to its

guide RNA?
A. Replicates it
B. Cuts it
C. Transcribes it
D. All of the above
B is correct. Cas9 is a DNA endonucleases that cleaves DNA it detects to be
complementary to its guide RNA.
3. Which of the following is not a feature of CRISPR?

A. Contain palindromic DNA repeats
B. Have highly conserved spacer regions
C. Provide adaptive immunity to Bacteria and Archaea
D. Used as a molecular biology tool for genome editing
B is correct. CRISPR loci contain spacer regions that are not conserved.
Conversely, they are highly variable, and correspond to invasive genetic
elements acquired from viruses and plasmids.
Coenzyme Definition
A coenzyme is an organic non-protein compound that binds with an enzyme to
catalyze a reaction. Coenzymes are often broadly called cofactors, but they are
chemically different. A coenzyme cannot function alone, but can be reused
several times when paired with an enzyme.
Functions of Coenzymes
An enzyme without a coenzyme is called an apoenzyme. Without coenzymes or
cofactors, enzymes cannot catalyze reactions effectively. In fact, the enzyme
may not function at all. If reactions cannot occur at the normal catalyzed rate,
then an organism will have difficulty sustaining life.
When an enzyme gains a coenzyme, it then becomes a holoenzyme, or active

enzyme. Active enzymes change substrates into the products an organism needs
to carry out essential functions, whether chemical or physiological. Coenzymes,
like enzymes, can be reused and recycled without changing reaction rate or
effectiveness. They attach to a portion of the active site on an enzyme, which
enables the catalyzed reaction to occur. When an enzyme is denatured by
extreme temperature or pH, the coenzyme can no longer attach to the active
site.
Types of Enzymes
Cofactors are molecules that attach to an enzyme during chemical reactions. In
general, all compounds that help enzymes are called cofactors. However,
cofactors can be broken down into three subgroups based on chemical makeup
and function:
Coenzymes
These are reusable non-protein molecules that contain carbon (organic). They
bind loosely to an enzyme at the active site to help catalyze reactions. Most are
vitamins, vitamin derivatives, or form from nucleotides.
Cofactors
Unlike coenzymes, true cofactors are reusable non-protein molecules that do not
contain carbon (inorganic). Usually, cofactors are metal ions such as iron, zinc,
cobalt, and copper that loosely bind to an enzyme’s active site. They must also
be supplemented in the diet as most organisms do not naturally synthesize metal
ions.
Prosthetic groups
These can be organic vitamins, sugars, lipids, or inorganic metal ions. However,
unlike coenzymes or cofactors, these groups bind very tightly or covalently to an
enzyme to aid in catalyzing reactions. These groups are often used in cellular
respiration and photosynthesis.
Examples of Coenzymes
Most organisms cannot produce coenzymes naturally in large enough quantities
to be effective. Instead, they are introduced to an organism in two ways:
Vitamins
Many coenzymes, though not all, are vitamins or derived from vitamins. If
vitamin intake is too low, then an organism will not have the coenzymes needed
to catalyze reactions. Water-soluble vitamins, which include all B complex
vitamins and vitamin C, lead to the production of coenzymes. Two of the most
important and widespread vitamin-derived coenzymes are nicotinamide adenine
dinucleotide (NAD) and coenzyme A.
NAD is derived from vitamin B3 and functions as one of the most important
coenzymes in a cell when turned into its two alternate forms. When NAD loses
an electron, the low energy coenzyme called NAD+ is formed. When NAD gains
an electron, a high-energy coenzyme called NADH is formed.
NAD+ primarily transfers electrons needed for redox reactions, especially those

involved in parts of the citric acid cycle (TAC). TAC results in other coenzymes,
such as ATP. If an organism has a NAD+ deficiency, then mitochondria become
less functional and provide less energy for cell functions.
When NAD+ gains electrons through a redox reaction, NADH is formed. NADH,

often called coenzyme 1, has numerous functions. In fact, it is considered the
number one coenzyme in the human body because it is necessary for so many
different things. This coenzyme primarily carries electrons for reactions and
produces energy from food. For example, the electron transport chain can only
begin with the delivery of electrons from NADH. A lack of NADH causes energy
deficits in cells, resulting in widespread fatigue. Additionally, this coenzyme is
recognized as the most powerful biological antioxidant for protecting cells against
harmful or damaging substances.
Coenzyme A, also known as acetyl-CoA, naturally derives from vitamin B5. This
coenzyme has several different functions. First, it is responsible for initiating fatty
acid production within cells. Fatty acids form the phospholipid bilayer that
comprises the cell membrane, a feature necessary for life. Coenzyme A also
initiates the citric acid cycle, resulting in the production of ATP.
Non-Vitamins
Non-vitamin coenzymes typically aid in chemical transfer for enzymes. They

ensure physiological functions, like blood clotting and metabolism, occur in an
organism. These coenzymes can be produced from nucleotides such as
adenosine, uracil, guanine, or inosine.
Adenosine triphosphate (ATP) is an example of an essential non-vitamin

coenzyme. In fact, it is the most widely distributed coenzyme in the human body.
It transports substances and supplies energy needed for necessary chemical
reactions and muscle contraction. To do this, ATP carries both a phosphate and
energy to various locations within a cell. When the phosphate is removed, the
energy is also released. This process is result of the electron transport chain.
Without the coenzyme ATP, there would be little energy available at the cellular
level and normal life functions could not occur.
Here is an example of the electron transport chain. The vitamin-derived

coenzyme NADH begins the process by delivering electrons. ATP is the final
resulting product:
 Catalyze – To cause or accelerate a reaction.
 Enzyme – A protein that catalyzes chemical reactions within an
organism.
 Active Site – The region on an enzyme where substrates bind during a
reaction.
 Substrate – The substance on which an enzyme acts to make a new
product.
Quiz
1. Why are coenzymes necessary?
A. They catalyze reactions in an organism
B. They attach to an enzyme which catalyzes a reaction
C. They make vitamins and nucleotides
D. They stop unnecessary reactions
B is correct. Coenzymes cannot function unless they are attached to an enzyme.
2. A coenzyme is a protein.
A. True
B. False
False. Coenzymes are nonprotein molecules that bind to an enzyme.
3. Coenzymes can be which of the following?

A. Reused and recycled in an organism
B. Only used once in a reaction
C. Metal ions
D. Molecules tightly bound to an enzyme
A is correct. Coenzymes attach loosely to enzymes so they can break free after a reaction and be
used again.
Cofactor Definition
A cofactor is a non-protein chemical that assists with a biological chemical
reaction. Co-factors may be metal ions, organic compounds, or other chemicals
that have helpful properties not usually found in amino acids. Some cofactors
can be made inside the body, such as ATP, while others must be consumed in
food.
Minerals, for example, come from the environment, and cannot be made from
scratch by any living cell. The organic compounds we refer to as “vitamins” are
cofactors that our own bodies cannot make, so we must consume them from
food in order for our cells to be able to perform essential life functions.
At the biochemical level, cofactors are important in understanding how biological

reactions proceed. The presence or absence of cofactors may determine how
quickly reactions proceed from their reactant to their product.
At the biological level, understanding cofactors is important to understanding
health. Without the proper cofactors, humans and other animals can develop
serious diseases and even death.
Function of Cofactors
Cofactors generally serve the purpose of supplying chemical groups or properties
that are not found in other chemical groups.
ATP, for example, is a cofactor with a unique ability to transfer energy to drive
chemical processes such as the activity of enzymes and transport proteins.
Heme, on the other hand, is a chemical complex that contains iron, which allows
heme to bond to oxygen molecules in a unique way. Heme is necessary for
our blood cells to carry oxygen through our bodies.
There are dozens of known cofactors, each of which may be necessary for
multiple biochemical reactions, as illustrated below.
As a result, the functions of cofactors may be as diverse as their chemical
structures and properties.
The wide-ranging effects of cofactors can be seen by studying vitamin

deficiencies: deficiencies of different vitamins, many of which are cofactors, have
many different negative effects on human health.
Types of Cofactor
Vitamins
Vitamins are organic compounds that are co-factors for necessary biochemical
reactions. Vitamins typically need to be consumed in the diet, because they
cannot be made inside the body.
Many vitamins are cofactors which help enzymes to catalyze reactions, such as
the production of important proteins. Vitamin C, for example, is a cofactor for the
production of the connective tissue collagen.
This is why people who get scurvy – a severe form of vitamin C deficiency – may
experience connective tissue problems, including muscle weakness, muscle
soreness, and even unexplained bleeding as the connective tissues of blood
vessels cannot be replaced.
Vitamin deficiencies are a good illustration of the effects of co-factor deficiency.

Just as there are many possible vitamin deficiencies with many different
symptoms, there are many different co-factors that our body needs to carry out
its diverse necessary biochemical reactions.
The body’s requirement for diverse vitamin cofactors is also the reason why
nutritionists counsel people to “eat the rainbow” – many plants’ colors are
produced by cofactors, so by eating fruits and vegetables in a wide variety of
colors helps to ensure that we consume a healthy variety of cofactors.
Minerals
Like vitamins, minerals are chemicals from outside of the body that must be
ingested to allow our cells to function properly. The difference is that while
vitamins are organic molecules – molecules containing carbon, which are often
made by other living things – minerals are inorganic substances that occur
naturally, and are often found in rocks and soil.
Minerals often enter our diets from plants, which draw them up out of the
ground through their roots along with water. In some rare cases, people with
vitamin deficiencies may feel the urge to eat certain types of soil to obtain the
minerals from the soil directly.
Minerals that are important for human health include copper, which is necessary
for the function of some important liver enzymes that break down toxins; iron,
which is necessary for the function of some important metabolic enzymes;
magnesium, which is necessary for the function of DNA polymerase and other
enzymes; and zinc, which is also necessary for DNA polymerase as well as some
liver enzymes.
As with vitamins, there can be too much of a good thing – while minerals are
necessary in small amounts for our metabolisms to function, taking large doses
of them can result in toxicity and death. Indeed, overdoses of iron-containing
multivitamins are a leading cause of death in children under 4, who may mistake
these multivitamins for candy.
Organic Non-Vitamin Cofactors
Some cofactors are organic substances not classified as enzymes. Some of these
may be made inside our own bodies, and so not qualified as vitamins.
Organic non-vitamin cofactors include ATP – an essential assistant to many

biochemical processes, which transfers energy to numerous enzymes, transport
proteins, and more; coenzyme Q, which plays a vital role in the mitochondrial
transport chain; and heme, which is a complex iron-containing compound that is
necessary for our blood cells to carry oxygen throughout our bodies.
Examples of Cofactors
Thiamine (Vitamin B3)
Thiamine is a vitamin found primarily in edible seeds such as beans, corn, and
rice. To improve public health, thiamine is often artificially added to wheat-
containing products such as breakfast cereals.
In the body, thiamine is used to make many co-enzymes that assist with
important processes. It is made into thiamine pyrophosphate, which is necessary
to break down sugars and amino acids.
Severe thiamine deficiency is one cause of Korsakoff Syndrome – a rare

neurological disorder seen in people with severe alcohol addiction. In Korsakoff
Syndrome, severe malnutrition, lack of thiamine, and brain damage from overuse
of alcohol combine to produce severe symptoms, including memory impairment.
Some sufferers of Koraskoff Syndrome are not able to form new memories
because the metabolism of their brain is so impaired.
Folic Acid (Vitamin B9)
Folic acid is another vitamin which is now often added to food to improve public
health. It is necessary for the body to produce DNA, RNA, and amino acids,
which are necessary for growth and cell division.
This makes folic acid particularly essential for pregnant women, whose fetuses
are producing new cells and tissues very quickly. Deficiencies in folic acid can
lead to birth defects in babies, or to anemia in pregnant women who may not be
able to make enough new blood cells to supply both them and the baby.
For this reason, it is recommended that all women of childbearing age talk to
their doctors about taking folic acid supplements. Pregnancy outcomes are best
when sufficient folic acid is present in the mother’s body even before pregnancy
begins.
Iron-Sulfur Clusters
Iron-sulfur clusters are – you guessed it – clusters of iron and sulfur ions which
can form stable arrangements. These clusters have many unique properties that
are not found in amino acids or other organic compounds.
The unique properties of iron-sulfur clusters make them very useful for biological
reactions involving electron transfers. Both iron and sulfur are able to store and
release electrons with greater eases than more common atoms such as carbon.
This makes iron-sulfur clusters a vital part of cofactors and enzymes involved in
electron transfer and energy transfer, including NADH dehydrogenase, coenzyme
Q, cytochrome C, and Complex I and Complex II in the mitochondria.

 Enzyme – A protein which increases the rate of a chemical reaction.
Enzymes make life possible by catalyzing reactions that would otherwise
proceed very slowly.
 Mineral – A naturally occurring inorganic substance, often found in
rocks. Some minerals have chemical properties that are used by cells to
facilitate their life processes.
 Vitamin – An organic compound that is essential for biological activity.
Vitamins must be consumed in an organism’s diet if the organism
cannot manufacture them themselves.
Quiz
1. Which if the following is NOT likely to be a cofactor?
A. Vitamin A
B. Iron
C. ATP
D. None of the above.
D is correct. Vitamins, minerals, and ATP are all examples of cofactors. ATP
functions as a cofactor by transferring energy to chemical reactions.
2. Why might a mineral be useful as a cofactor?

A. Minerals can have very different chemical properties from organic compounds
such as carbon.
B. Some minerals are better at accepting and donating electrons than organic
compounds.
C. Minerals include atoms that cannot be produced by living things, but most be
obtained from the environment.
D is correct. Minerals can only be created through nuclear fusion in the cores of
stars. As such, they have unique properties, and must be obtained from the
environment. Atoms with these unique properties cannot be made by living
creatures.
3. Why is it important to eat a variety of fruits and vegetables?

A. Because fruits and vegetables contain minerals which they take up from the
soil through their roots.
B. Because fruits and vegetables contain organic compounds which animals do
not make themselves.
C. Because different fruits and vegetables include different cofactors that are
necessary to human health.
D is correct. All of the above are reasons why eating a variety of fruits and
vegetables is important for the healthy functioning of human metabolism.
Cytoplasm Definition
Cytoplasm refers to the fluid that fills the cell, which includes the cytosol along
with filaments, proteins, ions and macromolecular structures as well as the
organelles suspended in the cytosol.
In eukaryotic cells, cytoplasm refers to the contents of the cell with the exception
of the nucleus. Eukaryotes have elaborate mechanisms for maintaining a distinct
nuclear compartment separate from the cytoplasm. Active transport is involved in
the creation of these subcellular structures and for maintaining homeostasis with
the cytoplasm. For prokaryotic cells, since they do not have a defined nuclear
membrane, the cytoplasm also contains the cell’s primary genetic material. These
cells are usually smaller in comparison to eukaryotes, and have a simpler internal
organization of the cytoplasm.
Structure of Cytoplasm
The cytoplasm is unusual because it is unlike any other fluid found in the
physical world. Liquids that are studied to understand diffusion usually contain a
few solutes in an aqueous environment. However, the cytoplasm is a complex
and crowded system containing a wide range of particles – from ions and small
molecules, to proteins as well as giant multi protein complexes and organelles.
These constituents are moved across the cell depending on the requirements of
the cell along an elaborate cytoskeleton with the help of specialized motor
proteins. The movement of such large particles also changes the physical
properties of the cytosol.
The physical nature of the cytoplasm is variable. Sometimes, there is quick

diffusion across the cell, making the cytoplasm resemble a colloidal solution. At
other times, it appears to take on the properties of a gel-like or glass-like
substance. It is said to have the properties of viscous as well as elastic materials
– capable of deforming slowly under external force in addition to regaining its
original shape with minimal loss of energy. Parts of the cytoplasm close to
the plasma membrane are also ‘stiffer’ while the regions near the interior
resemble free flowing liquids. These changes in the cytoplasm appear to be
dependent on the metabolic processes within the cell and play an important role
in carrying out specific functions and protecting the cell from stressors.
The cytoplasm can be divided into three components:
1. The cytoskeleton with its associated motor proteins

2. Organelles and other large multi-protein complexes
3. Cytoplasmic inclusions and dissolved solutes
Cytoskeleton and Motor Proteins
The basic shape of the cell is provided by its cytoskeleton formed primarily by
three types of polymers – actin filaments, microtubules and intermediate
filaments.
Actin filaments or microfilaments are 7 nm in width and are made of double

stranded polymers of F-actin. These filaments are associated with a number of
other proteins that help in filament assembly and are also involved in anchoring
them close to the plasma membrane. This cytoplasmic location helps the
microfilaments become involved in rapid responses to signal molecules from the
extracellular environment and produce cellular responses through signal
transduction or chemotaxis. In addition, myosin, an ATP-based motor protein
transmits cargo and vesicles along the microfilament and is also involved
in muscle contraction.
Microtubules are polymers of α and β tubulin, which form a hollow tube by the
lateral association of 13 protofilaments. Each protofilament is a polymer of
alternating α and β tubulin molecules. The inner diameter of a microtubule is 12
nm and its outer diameter is 24 nm.
Microtubule structure
Microtubules radiate towards the periphery of the cell from microtubule
organizing centers (MTOCs) located close to the nucleus, and provide structure
and shape to the cell.
Fluorescent Cells
This image shows the nucleus in blue, the actin filaments on the cell periphery
are labeled red and the extensive microtubule network is marked green. The
cytoplasm undergoes rapid reorganization during cell division with microtubules
forming the spindle, which binds to chromosomes and segregates them into
two daughter cells.
Kinetochore
Similar to the previous image, chromosomes are stained blue and microtubules
are green. Tiny red dots are kinetochores.
Microtubules are involved in cytoplasmic transport, chromosome segregation and

in forming structures such as cilia and flagella for cellular movement.
Intermediate filaments are larger than microfilaments but smaller than

microtubules and are formed by a group of proteins that share structural
features. Though they are not involved in cell motility, they are important for
cells to come together as tissues and to remain anchored to the extracellular
matrix.
Organelles and Multi-protein Complexes
Most eukaryotic cells have a number of organelles that provide compartments

within the cytoplasm for specialized microenvironments. For instance, lysosomes
contain a number of hydrolases in an acidic environment that is ideal for their
enzymatic activity. These hydrolases are actively transported into
the lysosome after being synthesized in the cytoplasm. Mitochondria, while
containing their own genome, also need many enzymes synthesized in the
cytosol, which are then selectively moved into the organelle. These organelles
are placed in specific locations due to the physical gel-like nature of the
cytoplasm and by anchoring to the cytoskeleton.
In addition, the cytoplasm also plays host to multi-protein complexes like the
proteasome and ribosomes. Ribosomes are large complexes of RNA and protein
that are important for the translation of mRNA code into amino acid sequences
of proteins. Proteasomes are giant molecular structures about 20,000 kilodaltons
in mass and 15 nm in diameter. Proteasomes are important for targeted
destruction of proteins that are no longer needed by the cell.
Cytoplasmic Inclusions
Cytoplasmic inclusions can include a wide range of biochemicals – from small

crystals of proteins, to pigments, carbohydrates and fats. All cells, especially
in tissue like the adipose, contain droplets of lipids in their triglyceride form.
These are used to create cellular membranes and are an excellent energy store.
Lipids can generate twice as many ATP molecules per gram when compared to
carbohydrates. However, the process of releasing this energy from triglycerides
in intensive in oxygen consumption and therefore the cell also contains stores
of glycogen as cytoplasmic inclusions. Glycogen inclusions are particularly
important in cells like the skeletal and cardiac muscle cells where there can be a
sudden increase in demand for glucose. Glycogen can be quickly broken down
into individual molecules of glucose and used in cellular respiration before the
cell can obtain more glucose reserves from the body.
Crystals are another type of cytoplasmic inclusion found in many cells, and have
special function in cells of the inner ear (maintaining balance). Presence of
crystals in cells of the testis appears to be linked with morbidity and infertility.
Finally, the cytoplasm also contains pigments such as melanin, which lead to the
pigmented cells of the skin. These pigments protect the cell and internal body
structures from the deleterious effects of ultraviolet radiation. Pigments are also
prominent in the cells of the iris that surround the pupil of the eye.
Each of these components affects the functioning of the cytoplasm in different

ways, making it a dynamic region that plays a role in, and is influenced by the
cell’s overall metabolic activity.
Functions of Cytoplasm
The cytoplasm is the site for most of the enzymatic reactions and metabolic
activity of the cell. Cellular respiration begins in the cytoplasm with anaerobic
respiration or glycolysis. This reaction provides the intermediates that are used
by the mitochondria to generate ATP. In addition, the translation of mRNA into
proteins on ribosomes also occurs mostly in the cytoplasm. Some of it happens
on free ribosomes suspended in the cytosol while the rest happens on ribosomes
anchored on the endoplasmic reticulum.
The cytoplasm also contains the monomers that go on to generate the

cytoskeleton. The cytoskeleton, in addition to being important for the normal
activities of the cell is crucial for cells that have a specialized shape. For instance,
neurons with their long axons need the presence of intermediate filaments,
microtubules, and actin filaments in order to provide a rigid framework for
the action potential to be transmitted to the next cell. Additionally,
some epithelial cells contain small cilia or flagella to move the cell or remove
foreign particles through coordinated activity of cytoplasmic extrusions formed
through the cytoskeleton.
The cytoplasm also plays a role in creating order within the cell with specific
locations for different organelles. For instance, the nucleus is usually seen
towards the center of the cell, with a centrosome nearby. The extensive
endoplasmic reticulum and Golgi network are also placed in relation to the
nucleus, with the vesicles radiating out towards the plasma membrane.
Cytoplasmic Streaming
Movement within the cytoplasm also occurs in bulk, through the directed
movement of cytosol around the nucleus or vacuole. This is particularly
important in large single celled organisms such as some species of green algae,
which can be nearly 10 cm in length. Cytoplasmic streaming is also important for
positioning chloroplasts close to the plasma membrane to
optimize photosynthesis and for distributing nutrients through the entire cell. In
some cells, such as mouse oocytes, cytoplasmic streaming is expected to have a
role in the formation of cellular sub-compartments and in organelle positioning as
well.
Cytoplasmic Inheritance
The cytoplasm plays hosts to two organelles that contain their own genomes –
the chloroplast and mitochondria. These organelles are inherited directly from
the mother through the oocyte and therefore constitute genes that are inherited
outside the nucleus. These organelles replicate independent of the nucleus and
respond to the needs of the cell. Cytoplasmic or extranuclear inheritance,
therefore, forms an unbroken genetic line that has not undergone mixing or
recombination with the male parent.
 Chemotaxis – Movement of a cell in response to a chemical signal.
 Intermediate Filaments – Cytoskeletal components formed by a
family of proteins sharing structural and functional features larger than
actin fibers and smaller than microtubules.
 Kinesin – A group of motor proteins that can travel along a
microtubule and are important for the movement of cellular
components, especially during cell division.
 Syncytium – A multinucleated cell formed by the fusion of the plasma
membrane of multiple cells. Syncytia can also be formed through the
interconnections between cells containing specialized gap junctions,
allowing the cells to behave synchronously as a single unit.
Quiz
1. Which of these biomolecules are NOT present as cytoplasmic
inclusions?
A. Lipids
B. Carbohydrates
C. Nucleic acids
D. Crystals
C is correct. Cytoplasmic inclusions can have crystals of inorganic compounds or
proteins. They can contain carbohydrates such as glycogen and triglycerides and
other lipids. However, nucleic acids have not yet been reported in cytoplasmic
inclusions.
2. What are microtubules made of?

A. Polymers of G- and F-actin
B. Polymers of dynein
C. Polymers of α and β tubulin
D. Polymers of kinesin
C is correct. G- and F-actin contribute towards the formation of the actin
cytoskeleton, while dynein and kinesin are motor proteins that traverse the
length of microtubules. However, microtubules are large tubular structures are
formed by 13 protofilaments made of alternating α and β tubulin monomers.
3. Which of these statements is true about nucleic acids in the

cytoplasm?
A. All cells contain cytoplasmic nucleic acids
B. Only some organelles within the cytoplasm such as mitochondria or
chloroplasts contain nucleic acids
C. Nucleic acids are never found in the cytoplasm
D. None of these statements is always true
A is correct. Nucleic acids include RNA in addition to DNA and therefore every
cell contains nucleic acids in its cytoplasm. Many proteins required for the cell to
function normally are synthesized by translating RNA molecules in the cytoplasm.
Mitochondria and chloroplasts are special because they contain their own
genomic DNA, however, even red blood cells that have lost all their organelles
contain RNA and continue to produce proteins in their cytoplasm.
Endosymbiotic Theory Definition

Endosymbiotic theory is the unified and widely accepted theory of how
organelles arose in organisms, differing prokaryotic organisms
from eukaryotic organisms. In endosymbiotic theory, consistent with general
evolutionary theory, all organisms arose from a single common ancestor. This
ancestor probably resembled a bacteria, or prokaryote with a single strand of
DNA surrounded by a plasma membrane. Throughout time, these bacteria
diverged in form and function. Some bacteria acquired the ability to process
energy from the environment in novel ways. Photosynthetic bacteria developed
the pathways that enabled the production of sugar from sunlight. Other
organisms developed novel ways to use this sugar is oxidative phosphorylation,
which produced ATP from the breakdown of sugar with oxygen. ATP can then be
used to supply energy to other reactions in the cell.
Both of these novel pathways led to organisms that could reproduce at a higher
rate than standard bacteria. Other species, not being able
to photosynthesis sugars or break them down through oxidative phosphorylation,
decreased in abundance until they developed a novel adaptation of their own.
The ability of endocytosis, or to capture other cells through the enfolding of the
plasma membrane, is thought to have evolved around this time. These cells now
had the ability to phagocytize, or eat, other cells. In some cells, the bacteria that
were ingested were not eaten, but utilized. By providing the bacteria with the
right conditions, the cells could benefit from their excessive production of sugar
and ATP. One cell living inside of another is called endosymbiosis if both
organisms benefit, hence the name of the theory. Endosymbiotic theory
continues further, stating that genes can be transferred between the host and
the symbiont throughout time.
This gives rise to the final part of endosymbiotic theory, which explains the
variable DNA and double membranes found in various organelles in eukaryotes.
While the majority of cell products start in the nucleus,
the mitochondria and chloroplast make many of their own genetic products. The
nucleus, chloroplasts, and mitochondria of cells all contain DNA of different types
and are also surrounded by double membranes, while other organelles are
surrounded by only one membrane. Endosymbiotic theory postulates that these
membranes are the residual membranes from the ancestral bacterial
endosymbiont. If a bacteria was engulfed via endocytosis, it would be
surrounded by two membranes. The theory states that these membranes
survived evolutionary time because each organism retained the maintenance of
its membrane, even while losing other genes entirely or transferring them to the
nucleus. Endosymbiotic theory is supported by a large body of evidence. The
general process can be seen in the following graphic.
Endosymbiotic Theory Evidence

The most convincing evidence supporting endosymbiotic theory has been
obtained relatively recently, with the invention of DNA sequencing. DNA
sequencing allows us to directly compare two molecules of DNA, and look at
their exact sequences of amino acids. Logically, if two organism share a
sequence of DNA exactly, it is more likely that the sequence was inherited
through common descent than the sequence arose independently. If two
unrelated organisms need to complete the same function, the enzyme they
evolve does not have to look the same or be from the same DNA to fill the same
role. Thus, it is much more likely that organisms who share sequences of DNA
inherited them from an ancestor who found them useful.
This can be seen when analyzing the mitochondrial DNA (mtDNA) and
chloroplast DNA of different organisms. When compared to known bacteria, the
mtDNA from a wide variety of organisms contains a number of sequences also
found in Rickettsiaceae bacteria. Fitting with endosymbiotic theory, these
bacteria are obligate intracellular parasites. This means they must live within
a vesicle of an organism that engulfs them through endocytosis. Like bacterial
DNA, mtDNA and the DNA in chloroplasts is circular. Eukaryotic DNA is typically
linear. The only genes missing from the mtDNA and those of the bacteria are
for nucleotide, lipid, and amino acid biosynthesis. An endosymbiotic organism
would lose these functions over time, because they are provided for by the host
cell.
Further analysis of the proteins, RNA and DNA left in organelles reveals that
some of it is too hydrophobic to cross the external membrane of the organelle,
meaning the gene could never get transferred to the nucleus, as the cell would
have no way of importing certain hydrophobic proteins into the organelle. In
fact, chloroplasts and mitochondria have their own genetic code, and their own
ribosomes to produce proteins. These proteins are not exported from the
mitochondria or chloroplasts, but are needed for their functions. The ribosomes
of mitochondria and chloroplasts also resemble the smaller ribosomes of
bacteria, and not the large eukaryotic ribosomes. This is more evidence that the
DNA originated inside of the organelles, and is separate completely from the
eukaryotic DNA. This is consistent with endosymbiotic theory.
Lastly, the position and structure of these organelles lends to the endosymbiotic
theory. The mitochondria, chloroplasts, and nuclei of cells are all surrounded in
double membranes. All three contain their DNA in the center of the cytoplasm,
much like bacterial cells. Although less evidence exists linking the nucleus to any
kind of extant species, both chloroplasts and mitochondria greatly resemble
several species of intracellular bacteria, existing in much the same manner. The
nucleus is thought to have arisen through enfolding of the cell membrane, as
seen in the graphic above. Throughout the world, there are various
endosymbiont bacteria, all of which live inside other organisms. Bacteria exist
almost everywhere, from the soil to inside our gut. Many have found unique
niches within the cells of other organisms, and this is the basis of endosymbiotic
theory.

 Endosymbiont – An organism that lives with another organism, cause
both organisms to receive benefits.
 Cyanobacteria – Still extant, cyanobacteria are photosynthetic
bacteria whose ancestors probably became the chloroplasts
of plant cells.
 Proteobacteria – The bacterial ancestor to the mitochondria
organelle.
 Eukaryote – An organism with membrane bound organelles, thought
to have evolved from endosymbiotic interactions.
Quiz
1. Some people refute the theory that similar DNA is due to common
descent, a cornerstone of endosymbiotic theory. They say that similar
sequences of DNA can arise through convergent evolution, or pressure
from similar sources. Why is this improbable?
A. Genetic recombination and mutations are the only things that are known to
give rise to new DNA.
B. There are so many DNA bases, the combinations are endless.
C. Similar evolutionary circumstances are unlikely to need similar proteins.
A is correct. The only documented cases of new genes arising come from
mutations of DNA that is already present. As mutations take a long time to add
functional material to a genome, it is much more likely that existing proteins will
be modified to fit the task. While there are only 4 DNA base molecules, a
single mutation in DNA can cause a large functional change in a protein, which
can lead to novel chemical pathways. To build an entirely new gene from scratch
that is identical to that found in a similar species would mean the process of
mutation and selection would have to take place almost identically in both
populations, for thousands of DNA base molecules in a specific order. Since
mutations are entirely random, this is nearly impossible. However, proteins with
similar functions are often created from seemingly unrelated proteins in different
groups of animals.
2. A bacterial cell is ingested by a human. The bacteria travels to the

intestine, where it is endocytosed by an intestinal cell. The bacteria is
not destroyed, and lives in an endosymbiotic relationship with the
human cell. Did endosymbiotic theory just happen before our eyes?
A. Yes
B. No
C. This may be the first step
C is correct. Many organisms in nature exist in endosymbiotic relationships with
another species. Endosymbiotic theory specifies that over time these
endosymbionts lose the ability to live independently of the host, and the host
becomes reliant on the endosymbiont. Further, the genome of the endosymbiont
will be greatly reduced, as the host will provide the majority of the proteins it
needs to function.
3. Mitochondria and chloroplasts divide separately from the normal cell
cycle. During mitosis, they are distributed more or less evenly to each
new cell. Does this support endosymbiotic theory?
A. Yes, the separate cycle suggests a different lineage.
B. No, the mitochondria and chloroplasts are simply needed for energy at all
times.
C. Maybe? Both seem like good answers.
C is correct. While this may seem unimportant, this remains a disputed area in
endosymbiotic theory. Some critics suggest that the differing reproductive rates
of mitochondria and chloroplasts is simply to preserve the flow of energy that the
cell needs during division. If the flow of energy was lost because all of the
mitochondria were dividing, the entire cell would have to stop in the middle of
division. Proponents of endosymbiotic theory point to the fact that the DNA is
different in these organelles as well, which suggests that they never reproduced
in a eukaryotic fashion.
Exon Definition
An exon is a coding region of a gene that contains the information required to
encode a protein. In eukaryotes, genes are made up of coding exons
interspersed with non-coding introns. These introns are then removed to make a
functioning messenger RNA (mRNA) that can be translated into a protein.
Exon Structure
Exons are made up of stretches of DNA that will ultimately be translated
into amino acids and proteins. In the DNA of eukaryotic organisms, exons can be
together in a continuous gene or separated by introns in a discontinuous gene.
When the gene is transcribed into pre-mRNA the transcript contains both introns
and exons. The pre-mRNA is then processed and the introns are spliced out of
the molecule. Mature mRNAs can be a few hundred to several thousand
nucleotides long.
The mature mRNA consists of exons and short untranslated regions (UTRs) on
either end. The exons make up the final reading frame which consists of
nucleotides arranged in triplets. The reading frame begins with a start
codon (usually AUG) and ends in a termination codon. The nucleotides are
arranged in triplets as each amino acid is coded for by a three-
nucleotide sequence.
The figure depicts a gene made up of three exons. The resulting gene is 1317 bp
in length despite an initial gene length of over 13,000 bp.
Exon Function
Exons are pieces of coding DNA that encode proteins. Different exons code for
different domains of a protein. The domains may be encoded by a single exon or
multiple exons spliced together. The presence of exons and introns allows for
greater molecular evolution through the process of exon shuffling. Exon shuffling
occurs when exons on sister chromosomes are exchanged during recombination.
This allows for the formation of new genes.
Exons also allow for multiple proteins to be translated from the same gene
through alternative splicing. This process allows the exons to be arranged in
different combinations when the introns are removed. The different
configurations can include the complete removal of an exon, the inclusion of part
of an exon, or the inclusion of part of an intron. Alternative splicing can occur in
the same location to produce different variants of a gene with a similar role, such
as the human slo gene, or it can occur in different cell or tissue types, such as
the mouse alpha-amylase gene. Alternative splicing, and defects in alternative
splicing, can result in a number of diseases including alcoholism and cancer.
The figure depicts possible alternative splicing mechanisms which can result in
alternative proteins being translated.
Human slo gene
An example of extreme alternative splicing is the human slo gene which encodes

a transmembrane protein involved in regulation of potassium entry in the hair
cells of the inner ear, resulting in frequency perception. The gene consists of 35
exons which can combine to form over 500 mRNAs through the excision of one
to eight exons. The different mRNAs control which sound frequencies can be
heard.
Mouse alpha-amylase gene
The mouse alpha-amylase gene encodes two different mRNAs – one in

the salivary glands and one in the liver. Which of the mRNA transcripts is formed
is controlled by different promoters specific to the tissue type. In this case the
processed mRNA contains the same two exons, resulting in the same protein, but
it is regulated by a tissue-specific promoter.
Quiz
1. A protein is coded for by how many exons?
A. 1
B. 2
C. 10
D. All of the above
D is correct. Proteins are coded for by exons. A simple protein may be coded for
by a single exon, while complex proteins may be coded for by tens of exons.
2. How can new genes be formed?

A. Alternative splicing
B. Exon shuffling
C. Splicing
B is correct. Alternative gene variants can be formed by exon shuffling. This
occurs when two sister chromatids exchange one or more exons resulting in a
new gene form. Alternative splicing is the formation of multiple proteins from the
same gene.
3. What sequence is commonly found at the beginning of an exon?
A. AUG
B. UAG
C. UAA
D. UGA
A is correct. Exons begin with start codons. The vertebrate start codon is AUG,
while UAG, UAA, and UGA are all termination codes. The genetic codes vary
slightly among groups.
Facilitated Diffusion Definition

Facilitated diffusion is a form of facilitated transport involving the passive
movement of molecules along their concentration gradient, guided by the
presence of another molecule – usually an integral membrane protein forming a
pore or channel.
Facilitated diffusion does not directly involve high-energy molecules like

adenosine triphosphate (ATP) or guanosine triphosphate (GTP) since the
molecules are moving along their concentration gradient.
Factors Affecting Diffusion

The driving force behind diffusion of fluids is simply the probability behind
Brownian motion. All molecules have some degree of erratic, random movement,
largely dependent on temperature. As temperature increases, the energy of
these molecules increases.
When a substance is highly concentrated in a certain region, molecular
movement, especially at the periphery, will lead to the gradual spread of the
substance. When all the molecules within the region are moving randomly, some
are bound to move outwards, into a region where its concentration is low. On
the other hand, it is less likely that random molecular movement will result in the
directional movement from a region of low concentration specifically towards
regions of high concentration.
For instance, when someone walks into a room wearing a strong perfume, the
odorous molecules diffuse outwards, from the skin or clothes. The people in the
room perceive some of these randomly moving molecules when they trigger the
sensory receptors in the nose. When there is a high density of scented molecules
in a region, there is a chance that a few will move away due to the innate kinetic
energy of these molecules. However, the likelihood that these few stray
molecules will move in a directed manner, back towards the sleeve or cuff of the
person wearing the perfume is relatively small. The end result is a cloud of
progressively decreasing concentration away from the person wearing the
perfume.
As seen in the example, the diffusion of a molecule needs a concentration

gradient. If everyone in the room wears the same perfume, there would be a
minimal effect from a new person entering the room. In addition, temperature
increases the rate of diffusion. So, on hot days the perfume would diffuse quickly
across the room. Diffusion is also dependent on the size of the molecule itself
and the nature of the medium.
However, it does not depend on the concentration of any other substance in the
medium. In the previous example, the aftershave of the person next to you will
not influence the rate of diffusion of the perfume towards you. Though this could
be an unpleasant experience, independent diffusion is an important property of
molecules that allows cells to take in nutrients (diffusing in one direction), while
at the same time, expelling metabolic waste products (diffusing outwards in the
opposite direction).
Facilitated Diffusion Across Membranes

Diffusion is ubiquitous across the biosphere. It is seen in the movement of air
and water, and is a necessary force driving global weather patterns. Within living
systems, the presence of lipid-based membranes creates compartments that
allow the selective concentration of water-soluble substances. For instance,
mitochondrial membranes can create 2 distinct regions within the organelle – the
inner matrix and the inter-membrane space. Each of these sub-compartments
has a specific composition and function, distinct from the adjoining spaces. The
generation of order in this manner is one of the hallmarks of nearly every unit of
the living world – from organelles within a cell to entire organ systems and
organisms.
However, this automatically means that ions, small molecules, proteins and other
solutes have differential concentrations across lipid bilayers. Moreover, polar,
charged or hydrophilic molecules cannot traverse biological membranes. While
this is useful for maintaining the integrity of each compartment, it is equally
necessary for molecules to move across membranes, along their concentration
gradient, when needed.
Diffusion of Gases
An excellent example of this is the movement of oxygen and carbon dioxide in
actively respiring tissues and cells. These cells need the input of oxygen and
glucose while carbon dioxide needs to be removed and expelled from the body.
Since each of these molecules are moving from regions of high concentration
towards areas with low concentration, there is no direct involvement of ATP or
other energy currency molecules. However, they do need to cross multiple lipid
bilayers – from mitochondrial membranes, to the plasma membrane of the cell,
and then the lipid bilayers of endothelial cells lining blood capillaries, the plasma
membranes of red blood cells and finally the membranes of cells forming the
alveolar sacs in lungs.
Need for Facilitated Diffusion
Cell membranes are only freely permeable to a very limited class of molecules.
They must be small in size, and non-polar. While this allows molecules like
water, oxygen and carbon dioxide to diffuse across membranes, it precludes
practically every biopolymer, most nutrients and many important small
molecules.
For instance, glucose is a relatively large molecule that cannot diffuse directly
through the lipid bilayer. Similarly, important ions like sodium, potassium or
calcium ions are charged and therefore repelled by the lipophilic core of cell
membranes. Amino acids and nucleic acids are polar, often charged and too
large to use simple diffusion to enter and exit cells. Occasionally, even the bulk
movement of water across membranes cannot occur quickly through the lipid
bilayer.
In these situations, facilitated diffusion, through integral membrane proteins,
becomes important. These transmembrane proteins are usually of two types –
those that act like carriers and those that form channels across the membrane.
Carriers and Channels
The study of integral membrane proteins is always difficult, since they are made
of long hydrophobic stretches interspersed with hydrophilic regions. Crystallizing
these proteins in order to understand their structure is fraught with difficulty.
However, many of these proteins have been characterized through ingenious
methods and we have some understanding of their activity.
Carrier proteins involved in facilitated diffusion often have two conformations.

The binding of a molecule on one side of the membrane induces a change in the
three-dimensional structure of the protein, which allows the passage of the
molecule through to the other side.
The image shows how a specific molecule (represented as a green ovoid particle)
can induce binding-related conformational change in the carrier protein, creating
a passage into the cell.
Proteins that form channels, on the other hand, have minute pores that
selectively allow certain molecules to pass through. There are a number of
mechanisms that determine the fit between a molecule and its channel proteins
– from size, to charge and the ability to interact with the amino acid side chains
lining the pore. Some channel proteins can show a thousand-fold preference for
one molecule over other biochemically similar substances.
The image is a representation of an aquaporin molecule – protein channels that

allow the quick bulk movement of water.
Examples of Facilitated Diffusion

A number of important molecules undergo facilitated diffusion to move between
cells and subcellular organelles.
Glucose Transporter
When food is digested, there is a high concentration of glucose within the small

intestine. This is transported through the membranes of the cells of
the alimentary canal, towards the endothelial cells lining blood capillaries.
Thereafter, glucose is transported throughout the body by the circulatory
system. When blood flows through tissues that need energy, glucose traverses
the endothelial cell membranes again and enters cells with low glucose
concentration. Occasionally, when blood sugar levels drop, the movement can
occur in reverse – from body tissues into blood circulation. For instance, hepatic
cells can generate glucose even from non-carbohydrate sources to maintain a
basal blood sugar concentration and prevent hypoglycemia.
The glucose transporter that facilitates this movement is a carrier protein that
has two major conformational structures. While the exact three-dimensional
structure is not known, the binding of glucose probably causes a conformational
change that makes the binding site face the interior of the cell. When glucose is
released into the cell, the transporter returns to its original conformation.
Ion Channels
Ion channels have been extensively studied in excitatory cells like neurons
and muscle fibers since the movement of ions across the membrane is an
integral part of their function. These channel proteins form pores on the lipid
bilayer that can be either in the open or closed conformation, depending on the
electrical potential of the cell and the binding of ligands. In this sense, these
proteins are called ‘gated’ channels.
The presence of ion pumps in most cells ensures that the ionic composition of
the extracellular fluid is different from the cytosol. The resting potential of any
cell is driven by this process, with an excess of sodium ions in the extracellular
region and an excess of potassium ions within the cell. The electrical and
concentration gradient generated in this manner is used for the propagation of
action potentials along neurons and the contractility of muscle cells.
When a small change in the voltage of a cell occurs, sodium ion channels open
and allow the rapid ingress of sodium ions into the cell. This, in turn, induces the
opening of potassium ion channels, allowing these ions to move outward,
demonstrating that the diffusion of one substance can occur independently of
another. In a few milliseconds, a region in the cell membrane can undergo large
changes in voltage – from -75 mV to +30 mV.
The binding of neurotransmitters like acetylcholine to receptors on muscle cells

changes the permeability of ligand-gated ion channels. The transmembrane
channel is made of multiple subunits arranged like a closed cylinder. The binding
of the ligand (acetylcholine) alters the conformation of the hydrophobic side
chains that block the central passage. This leads to the rapid influx of sodium
ions into the muscle cell. The change in the electric potential of the cell further
results in the opening of calcium ion channels, which then lead to the contraction
of the muscle fiber.
Aquaporins
Like other transmembrane proteins, aquaporins have not been fully

characterized. However, it is known that there are many such channels for the
rapid passage of water molecules in nearly every cell. These highly conserved
proteins are present in bacteria, plants, fungi and animals. Mutations in the
proteins forming aquaporins can lead to diseases like diabetes insipidus.

 Brownian Motion – Random fluctuations in the velocity of particles in
a fluid medium usually arising from intermolecular collisions.
 Hypoglycemia – Condition characterized by low blood glucose levels.
 Integral Membrane Protein – Proteins that are structurally and
functionally an integral part of a biological membrane. Can traverse the
entire width of the membrane or be attached through a small linker
region.
 Partial Pressure – Hypothetical measure of the concentration of one
gas in a mixture of gases.
Quiz
1. Which of these statements about facilitated diffusion of molecules is
true?
A. Does not directly involve ATP
B. Needs the presence of another molecule
C. Necessary for the diffusion of polar molecules across a membrane
D. All of the above
D is correct. Since diffusion occurs along the concentration gradient, there is no
direct input of energy needed. When polar, charged or large molecules need to
be transported across a membrane, another membrane protein, either a carrier
or a channel, is needed.
2. Which of these factors affects the rate of diffusion?

A. Temperature
B. Viscosity of medium
C. Size of particles
D. All of the above
D is correct. Temperature increases the kinetic energy of molecules and hence
enhances the rate of diffusion. Diffusion slows down in viscous media, since the
molecules of the medium resist the movement of particles. Larger molecules are,
in general, slower to diffuse than smaller ones.
3. Which of these statements is NOT true?

A. Glucose undergoes facilitated diffusion through a transmembrane channel
B. Water can move across a membrane even in the absence of aquaporins
C. The potassium ion transporter has a thousand-fold greater affinity for
potassium ions over sodium ions
D. All of the above
A is correct. Glucose is transported through a transmembrane carrier protein.
Water, as a small, non-charged molecule can diffuse across membranes even in
the absence of aquaporins. The potassium ion channel does have a remarkable
sensitivity towards its carrier molecule, likely mediated by charge density.

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