Biology dictionary

A
Abdomen
Abdomen Definition
The abdomen refers to the region between the pelvis (pelvic brim) and the thorax
(thoracic diaphragm) in vertebrates, including humans. The space constituting the
abdomen is termed the abdominal cavity. The borders of the abdominal cavity are
comprised of the posterior peritoneal surface, the anterior abdominal wall, the inferior
pelvic inlet, and the superior thoracic diaphragm. The abdomen functions to house the
digestive system and provides muscles essential for posture, balance, and breathing.

Abdomen Anatomy
The abdomen is comprised primarily of the digestive tract and other accessory organs
which assist in digestion, the urinary system, spleen, and the abdominal muscles
(shown below). The majority of these organs are encased in a protective membrane
termed the peritoneum. While the digestive organs and assessor organs are located
within the peritoneum, the kidneys, ureters and urinary bladder are located outsider of
the peritoneum, and thus, are considered by some scientists to be pelvic organs.

Acetic Acid
Acetic acid structure is that of a simple carboxylic acid and consists of a methyl group
attached to a carboxyl group as seen in the image below. Acetic acid or ethanoic acid
is a

protic solvent; it is able to donate protons in the form of hydrons (positively charged
hydrogen atoms). This characteristic means it is a member of the Brønsted acid group
where protons are donated to acceptor molecules known as Brønsted bases. The
donated hydrogen is dissociated from the carboxyl group. Vinegar is a solution of
acetic acid and water where approximately 0.4% of acetic acid molecules give up their
H+ atoms leading to an acidic solution of approximately 2.4 pH. In comparison with
the world’s strongest acid – carborane acid (H(CHB11Cl11)) – with a pH value of -18,
acetic acid is mildly acidic in comparison.

It should be made clear that it is not the presence of a single hydrogen atom that
changes the pH of a solution. Neutral solutions (neither acid nor alkaline) contain a
balanced number of hydronium ions (H30+) and hydroxyl ions (OH–). Two molecules
of water (H20) are formed when a hydronium and hydroxyl ion bind and the positive
and negative charges are canceled out. When acetic acid is added to water, it splits
into a negatively charged acetate ion (CH3COO–) and H+. It is, therefore, possible to
understand the alternative name of acetic acid – hydrogen acetate. A small percentage
of positively charged hydrogen ions bind to the water molecules and turn them into
H30+. This means there are more hydronium ions and, therefore, create a positively
charged (or acidic) solution. The pH of a solution is, therefore, dependent upon the
balance of hydronium and hydroxyl and not the number of hydrogen ions, although
these will affect this balance. A pH value is also only given to a solution. A solution
always contains water; even modern superacids such as carborane are dissolved in
concentrated aqueous solutions of other acids. Even glacial acetic acid has a small
quantity of water.

The following image shows the dissociation of acetic acid to acetate in water. To the
left are a single acetic acid molecule and a single water molecule. Acetic acid passes
on a hydrogen ion to the water molecule to produce a hydronium ion. We say that the
water molecule is protonated or has had a proton (hydron) donated to it.

As a solvent, liquid acetic acid dissolves polar (hydrophilic) compounds such as salts
and sugars and non-polar compounds which include fats and oils. This means it has
many uses in industrial chemical production but has also gained a reputation as a
weight-loss supplement as it affects fat and sugar metabolism. More information
pertaining to acetic acid uses will be discussed later on in this article. In crystalline
form, two acetic acid molecules join together with hydrogen bonds to form a dimer.
When water is added, these bonds are broken and the crystalline form dissolves.
Acetic Acid Formula

The acetic acid formula is a simple one and the result of a methyl group and a
carboxyl group. Methyl groups are one of the most common organic
compounds on the planet but are rarely found as single entities. They are
composed of three hydrogen atoms and one carbon atom (CH 3). As carbon
has four electrons, the free electron usually bonds with other molecules by
way of a covalent bond. The simplest carbon molecule is methane (CH4), well
known for its contribution to global warming. With a free electron, methane
reacts with ozone (O3) to produce carbon dioxide and water in the following
reaction: (3)CH4 + (4)O3 = (3)CO2 + (6)H2O. The picture shows a methane
molecule composed of a methyl group and an extra hydrogen atom.

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.

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.”
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.
Adenosine Triphosphate (ATP)
Adenosine Triphosphate Definition
Adenosine triphosphate, also known as ATP, is a molecule that carries energy
within cells. It is the main energy currency of the cell, and it is an end product
of the processes of photophosphorylation (adding a phosphate group to a
molecule using energy from light), cellular respiration, and fermentation. All
living things use ATP. In addition to being used as an energy source, it is also
used in signal transduction pathways for cell communication and is
incorporated into deoxyribonucleic acid (DNA) during DNA synthesis.

Structure of ATP

This is a structural diagram of ATP. It is made up of the molecule adenosine

(which itself is made up of adenine and a ribose sugar) and three phosphate
groups. It is soluble in water and has a high energy content due to having
two phosphoanhydride bonds connecting the three phosphate groups.

Functions of ATP
Energy Source

ATP is the main carrier of energy that is used for all cellular activities. When
ATP is hydrolyzed and converted to adenosine diphosphate (ADP), energy is
released. The removal of one phosphate group releases 7.3 kilocalories per
mole, or 30.6 kilojoules per mole, under standard conditions. This energy
powers all reactions that take place inside the cell. ADP can also be converted
back into ATP so that the energy is available for other cellular reactions.

ATP is produced through several different methods. Photophosphorylation is a

method specific to plants and cyanobacteria. It is the creation of ATP from
ADP using energy from sunlight, and occurs during photosynthesis. ATP is
also formed from the process of cellular respiration in the mitochondria of a
cell. This can be through aerobic respiration, which requires oxygen, or
anaerobic respiration, which does not. Aerobic respiration produces ATP
(along with carbon dioxide and water) from glucose and oxygen. Anaerobic
respiration uses chemicals other than oxygen, and this process is primarily
used by archaea and bacteria that live in anaerobic environments.
Fermentation is another way of producing ATP that does not require oxygen;
it is different from anaerobic respiration because it does not use an electron
transport chain. Yeast and bacteria are examples of organisms that use
fermentation to generate ATP.

Signal Transduction

ATP is a signaling molecule used for cell communication. Kinases, which are
enzymes that phosphorylate molecules, use ATP as a source of phosphate
groups. Kinases are important for signal transduction, which is how a physical
or chemical signal is transmitted from receptors on the outside of the cell to
the inside of the cell. Once the signal is inside the cell, the cell can respond
appropriately. Cells may be given signals to grow, metabolize, differentiate
into specific types, or even die.

DNA Synthesis

The nucleobase adenine is part of adenosine, a molecule that is formed from

ATP and put directly into RNA. The other nucleobases in RNA, cytosine,
guanine, and uracil, are similarly formed from CTP, GTP, and UTP. Adenine is
also found in DNA, and its incorporation is very similar, except ATP is
converted into the form deoxyadenosine triphosphate (dATP) before
becoming part of a DNA strand.

ATP, ADP, AMP, cAMP

Other molecules are related to ATP and have similar names, such as
adenosine diphosphate (ADP), adenosine monophosphate (AMP), and cyclic
AMP (cAMP). In order to avoid confusion, it is important to know some
differences between these molecules.

ADP

Adenosine diphosphate (ADP), which is sometimes also known as adenosine

pyrophosphate (APP), especially in chemistry, has already been mentioned in
this article. It differs from ATP because it has two phosphate groups. ATP
becomes ADP with the loss of a phosphate group, and this reaction releases
energy. ADP itself is formed from AMP. Cycling between ADP and ATP during
cellular respiration gives cells the energy needed to carry out cellular
activities.

AMP

Adenosine monophosphate (AMP), also called 5’-adenylic acid, has only one
phosphate group. This molecule is found in RNA and contains adenine, which
is part of the genetic code. It can be produced along with ATP from two ADP
molecules, or by hydrolysis of ATP. It is also formed when RNA is broken
down. It can be converted into uric acid, which is a component of urine, and
excreted via the bladder.
cAMP

Cyclic adenosine monophosphate (cAMP) is derived from ATP and is another

messenger used for signal transduction and activating certain protein kinases.
It can be broken down into AMP. cAMP pathways may play a role in certain
cancers such as carcinoma. In bacteria, it has a role in metabolism. When a
bacterial cell is not producing enough energy (from insufficient glucose, for
example), high cAMP levels occur, and this turns on genes that use energy
sources other than glucose.

Adrenal Gland
Definition:
The adrenal gland has several metabolic roles in the human body, which it
completes by releasing hormones. The two adrenal glands within the body
release hormones that help control the metabolism, undergo sexual
maturation as we grow, and respond to stress.

Overview
The stress response is known to us as the primal “fight or flight” response.
It is the knee-jerk reaction we get upon seeing a life-endangering stimulus.
Cortisol is the key hormone coordinating the processes that allow us to fight
or run from this perceived danger. There is obvious evolutionary value in
being able to do this.

Anything that shortens the time in which we can engage our muscles and run
will likely increase our chance of survival. But even more low key
scenarios trigger the release of cortisol from the adrenal gland. A
feeling we may be familiar with is the intense focus we feel when studying for
an exam the night before we have it. Cortisol is largely responsible for this
newfound focus. In spite of all of the negative connotations associated with
stress, in normal amounts the stress hormones allow us to focus better to
perform the tasks at hand.

Thus, the adrenal glands play a functional role in our alertness, growth, and
more. The main products released by the adrenal glands are cortisol,
epinephrine, aldosterone, and adrenal androgens, precursors of sex
hormones. We will discuss each in more detail.

Adrenal Gland Function

The most unique function of the adrenal glands is their ability to orchestrate
responses to stressors. This has the most primal purpose of helping us
evade danger and, therefore, of prolonging our lifespan. However, the adrenal
gland is also involved in more mundane, but equally important, aspects of our
everyday life.

Adrenal Gland Location

Our two adrenal glands can be found lying on top of each of our
kidneys. Here, they can release hormones into the bloodstream which
stimulate various aspects of the stress response.
The image above depicts a simple illustration of the adrenal glands and
surrounding structures.

Aldosterone
Definition:

Aldosterone (C21H28O5) is a mineralocorticoid hormone compound secreted by

the adrenal gland cortex. It is part of the renin angiotensin aldosterone
system or RAAS and is an integral part of the complex mechanisms that
control water and electrolyte balance within the body. Its action affects
sodium, potassium and water levels via the excretory and circulatory systems.

Aldosterone Function
The main function of aldosterone is to increase reabsorption within
the latter portion of the distal tubule of the nephron and the
collecting ducts. When working specifically at this location the hormone
binds to mineralocorticoid receptors on the membrane of the distal tubule.
Once bound, distal tubule membrane permeability increases. This makes it
easier for potassium and sodium to pass through. Aldosterone also activates
the mechanism of hydrogen ion secretion in the collecting ducts. This
regulates the pH of the plasma and therefore is important in the acid-base
balance. It is also understood that aldosterone has a further role in
antidiuretic hormone (vasopressin or ADH) release from the pituitary gland
whereby more water is reabsorbed into the body via the nephron.
However, aldosterone only affects approximately 3% of total water
reabsorption. It is therefore considered to be a fine-tuning mechanism
which is more appropriate for small, regular changes in blood volumes rather
than a saving measure in acute blood loss.
Aldosterone in the RAAS

The renin-angiotensin-aldosterone system or RAAS regulates blood pressure

by way of a single pathway composed of various hormones.
These hormones – renin, angiotensin, and aldosterone – work together to
produce the enzymes responsible for vasoconstriction and regulate secretion
and excretion in the kidneys. The RAAS works alongside the RAS or renin-
angiotensin system to rapidly control blood pressure whenever required.

Amino Acids
Definition:

Amino acids are the building blocks of polypeptides and proteins and play
important roles in metabolic pathway, gene expression, and cell signal
transduction regulation. A single organic amino acid molecule contains two
functional groups – amine and carboxyl – and a unique side chain. Humans
require twenty different amino acids; eleven are synthesized in the body and
nine obtained from dietary sources.

Amino Acids Benefits

Amino acid benefits are simple to name because, without amino acids, we
cannot exist. Every anatomical and physiological feature of a living organism
is made possible through the existence of amino acids. The synthesis of
nutritionally non-essential amino acids in the human body – alanine, arginine,
asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline,
serine, and tyrosine – occurs through the de novo construction of their carbon
skeletons. However, recent studies show that we can still benefit from the
ingestion of non-essential amino acids to promote optimal health and well-
being. Only when quantities of essential amino acids and glucose are
sufficient and available can the rate of non-essential amino acid
synthesis increase. It is, therefore, important to consume both types of
amino acid in the diet in order to benefit from their many positive, if not
absolutely essential, effects.
Allele
Allele Definition
An allele is specific variation of a gene. Bacteria, because they have a single
ring of DNA, have one allele per gene per organism. In sexually reproducing
organisms, each parent gives an allele for each gene, giving the offspring two
alleles per gene. Because alleles are just variants of specific genes, different
alleles are found on the same locations on the chromosomes of different
individuals. This is important because it gives organisms to be incredibly
varied in the functions of their various alleles, while at the same time being
able to reproduce. This create variety caused by mutations in specific genes
gives rise to a wide number of alleles for any trait in a given population.

Some areas of the genome are more protected against mutation than other
areas. For instance, the ends of chromosomes are often broken and changed
chemically because of the interactions with the surrounding cytosol and
membranes it may come into contact with. This breakage or damage
necessitates DNA repair. While the enzymes that repair DNA are extremely
efficient, they sometimes make mistakes.

The repair of DNA molecules is carried out by a variety of enzymes, one of the
most important of which is DNA polymerase. DNA polymerase uses free
floating nucleic acid bases to “rebuild” the DNA, one nucleic acid at a time.
After the DNA is unwound by another enzyme, helicase, DNA polymerase goes
to work on each strand of the two-stranded DNA molecule. By “reading” one
strand and adding nucleic acid bases together, it creates a brand new strand
that can couple to the first strand. DNA bases have counterparts that always
go together. Guanine (G) is the base pair of cytosine (C). Thymine (T) is
always the base pair of adenine (A).
Sometimes, the polymerase makes a mistake, and the wrong base pairs are
put together. Other enzymes are designed to “check” the DNA after it has
been synthesized to find these errors. The enzyme runs along the DNA,
checking for bumps that signify two base pairs are not properly bonded. If all
these mechanisms fail to catch the mutation, it will be replicated the next time
the cell divides. In bacteria this can give rise to whole colonies that have
novel mutations and can be easily studied. In sexually reproducing organisms,
a beneficial mutation is only valuable if it happens early in development or in
the production of gametes. A mutation in a single skin cell, for instance, will
not be able to help the organism in a large way. The cell may give rise to a
few thousand “good” skin cells, but compared to the trillions on your body,
they wouldn’t matter. In early development, or in the production of gametes
however, the mutations of a gene into different alleles can be passed onto
entire organisms, which can then reproduce the allele to its full benefit.

Other mutations, known as deleterious mutations, cause a disruption of

cellular function. These mutations cause non-functional alleles to arise, as is
the case in cancers. Some cancers are caused by mutations in tumor-
suppressing genes, which regulate the size, shape, and growth of individual
cells. A non-functional allele at this gene means the cell will continue to grow
and divide, regardless of the signals it receives. As part of a functioning body
of trillions of cells, this can cause a terrible amount of damage if the
cancerous cells are in a sensitive or vital area.

Examples of Allele
Flower Color in Peas

The founder of the field of genetics, Gregor Mendel, was a friar who studied
peas. One of the traits that he studied was flower color. Mendel’s peas
produced two different colors of flower, purple and white. Although he did not
know it at the time, these two colors represented the interactions of different
alleles in the genomes of the plants. Plants are sexually reproducing, meaning
they receive two alleles for each trait. The trait for flower color is determined
by a gene that creates an enzyme responsible for creating the pigment we
see as purple. Plants that received even one functioning allele produce purple
flowers, while plants that receive two non-functioning alleles produce white
flowers. Because one functioning allele can completely mask the effects of the
non-functioning allele, the former is said to be the dominant allele, while the
non-functioning allele is the recessive.

The interactions between these alleles produces important variability in the

flowers. While the recessive allele can be masked by the dominant allele, it
does not mean that the dominant allele is better for the plant. It could be true
that white flowers attract more pollinators, and are therefore more successful
at reproducing. If this were true, the allele frequency of the non-functioning
allele would increase in the population, even though it is not functioning.
Sometimes the most adaptable function of an enzyme is to not have the
enzyme functioning at all.

Amino Acids
Definition:
Amino acids are the building blocks of polypeptides and proteins and play
important roles in metabolic pathway, gene expression, and cell signal
transduction regulation. A single organic amino acid molecule contains two
functional groups – amine and carboxyl – and a unique side chain. Humans
require twenty different amino acids; eleven are synthesized in the body and
nine obtained from dietary sources.

Amoeba
Amoeba Definition
An amoeba is a highly motile eukaryotic, unicellular organism. Typically
belonging to the kingdom protozoa, it moves in an “amoeboid” fashion. As
such, microbiologists often use the term “amoeboid”, to refer to a specific
type of movement and amoebae interchangeably. Interestingly, amoebae are
not a distinct taxonomic group and are, instead, characterized based on their
“amoeboid” movement rather than distinct morphological characteristics.
Moreover, even members of the same species can appear dissimilar. Amebae
species can be found in all major eukaryotic lineages, including fungi, algae,
and even animals.

Amoebae contain an endoplasm that is granular in nature. This granular

endoplasm contains the nucleus and various engulfed food vacuoles. In
addition, amoebae are eukaryotic by definition and possess a unique nucleus
that contains a central karyosome with a thin layer of beaded chromatin
coating the inner nuclear membrane; however, unlike many eukaryotes,
amoebae are anaerobic. Thus, amoebae contain no mitochondria and
generate ATP exclusively via anaerobic means.

Amoebas can be classified as free-living and parasitic. Parasitic amoebas are

ubiquitous and often parasitize higher vertebrates and invertebrates alike.
Only a limited number of amoeba species are capable of infecting humans,
and typically invade the intestine. Specifically,
only Entamoebahistolytica represents a true human pathogen, which infects
the gastrointestinal tract. A second gut pathogen, Dientamoeba fragilis, is
commonly mistaken as an amoeba owing to its similar morphology under a
light microscope. Indeed, D. fragilis was originally misclassified as an amoeba;
however, modern methods have identified it as a nonflagellate trichomonad
parasite. Interestingly, some free-living amoebas can cause opportunistic
infections in humans, leading to eye infections, as well as various
neurological, and cutaneous (skin) infections.

Anatomy
Anatomy Definition
Anatomy is the branch of biology which studies how various parts of an
organism are connected, and how they are related to other body parts both
spatially and functionally. Anatomy has many sub-disciplines, and is used in
many different fields. In general, there are two main types of
anatomy: gross or macroscopic anatomy, and microscopic anatomy. However,
most biology specialties require knowledge of both types of anatomy.

Animal Cell
Definition
Animal cells are the basic unit of life in organisms of the kingdom Animalia.
They are eukaryotic cells, meaning that they have a true nucleus and
specialized structures called organelles that carry out different functions.
Animal cells do not have plant-specific organelles like cell walls, which support
the plant cell, or chloroplasts, the organelle that carries out photosynthesis.

Atrophy
Atrophy Definition
Atrophy is a term that describes the wasting away of cell tissue. On a larger
scale, atrophy can see a reduction in the size and function of a muscle or
limb. This process if often gradual and chronic, if not permanent. However,
atrophy is not exclusively a pathologic state. Atrophy is actually a part of our
natural, homeostatic development. The wrinkles that appear on our faces as
we age is atrophy, as is our thinning hair and the loss of teeth. There are
many reasons for why a tissue may atrophy. It can be caused by age or
genetics, such as inheriting a faulty set of genes that signal cell lysing or
inhibit a crucial protein from assembling. Another factor is environmental
change. Depending on our health or income status, we may experience
nutritional deficits. Or a physical injury may pierce our tissues or damage the
nerves innervating our muscles. Likewise, chronic illness can impact our
tissues permanently.

The inevitable consequence of tissue atrophy is that it diminishes the

impacted limb’s ability to perform its functions. However, the actual degree of
damage depends on its partial or complete effect and on the subject of
atrophy. Atrophy that targets nerves or a wide-spread muscle will systemically
affect the body. This kind of effect would result in pronounced deficits (i.e.
multiple sclerosis). In fact, sufferers of atrophy often show two clinical signs:
shortened limbs and bodily weakness.

Atrophy Types
While atrophy can describe a wide array of conditions, it can arise either
naturally or from disease. In fact, some presentations can occur for either
reason. For example, Disuse atrophy is a progressive withering of bone and
muscle that results from prolonged inactivity. In the event that a patient
develops a chronic illness like cancer or HIV, bone density and muscle mass
whittle down considerably. Cachexia is a clinical name for a non-intentional
muscle loss that follows illness or precedes death. Hence, it’s colloquial name,
“muscle wasting.” The same applies to bed-ridden patients with spinal
injuries, paraplegia, or sudden disabilities. However, disuse atrophy can also
take place in healthy individuals. For instance, a student athlete may
experience some disuse atrophy during their off-season from the sport they
play in face of a reduced work load.