The chemistry of life

1. To understand the mechanism of life, or how living organisms manage to

reproduce, grow, move, think, eat and do whatever it is that they are doing,
biologists can apply chemistry and physics to the study of life.
2. The important foundation for any biologist who wants to understand
molecular mechanisms underlying all life are based on understanding
following observations:
3. Six elements - carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur -
make up 96% of all molecules of life. The remaining elements constitute
essential minerals.
4. Molecules show a tremendous variation in structure based on the ability of
carbon atoms to link up as chains of various length, branching points,
double and single bonds and forming ring shaped molecules.
5. These basic carbon based molecules can be combined as polymers of
various length and combination creating an additional level of diversity of
structure among the biological macromolecules.
6. Understanding the physics and chemistry of biologically important
molecules allows insight into the structure and function of cells. The
20th century has made great progress in molecular biology and
biochemistry. The 21st century will make great progress in putting the
molecular pieces together and reconnect classical biology with molecular
biology and the whole with its parts, a science called systems biology.
7. Biological macromolecules are defining the properties of cells. These
molecules include proteins, nucleic acids, carbohydrates and lipids. The
properties they convey are enzymatic activity (metabolism), genetic
inheritance, reproduction, cell growth, energy storage and conversion,
signaling and adhesion, and interaction with the environment.
 8. All living organisms use the same four types of macromolecules for cellular
metabolism and reproduction. Together, they illustrate the commonalities of
life on earth. The way they are used in different forms and combinations
explains today's variety or biodiversity. Both aspects, sameness and
variety, are the result of biological evolution.
9. An interesting link between hierarchical organization and chemistry is the
combinatorial nature of living things. With this I mean that cells are made of
macromolecules, macromolecules of molecules and molecules of
elements. In living things we find a 'language' or information system that is
used to make the next higher level of organization. Six select elements
make the majority of biological molecules, select molecules are the building
blocks of macromolecules, select macromolecules are the building blocks
of cells. We can see them as letters, words and sentences - an alphabet to
create information used to make structures with specific functions.
10. For instance, biological molecules are made of carbon (C), hydrogen
(H), oxygen (O), nitrogen (N), sulfur (S) and phosphor (P) plus many ionic
species (e.g. sodium, potassium, chloride, calcium, magnesium, iron,
copper, cobalt, manganese, selenium). So how does the molecular
alphabet of life work? The table shows the basic elements found in the four
classes of macromolecules.

Macromolecules Elements* KEGG structures

of building blocks
Lipids C, H, O Fatty acids
Carbohydrates C, H, O Monosaccharides
Proteins C, H, O, N, S Amino acids
Nucleic acids C, H, O, N, P Nucleotides
*These combinations show the most common types and there are of course
lipids and carbohydrates that have N, P and S. Examples are phospho-, sulfo-
and sphingolipids, and glucosamines. Hydrocarbons, however, are very rare and
are either waste products or energy sources (e.g. methane) or secondary
metabolites (e.g. carotenes).

The origin of structural variability

Looking at this table, how then can lipids and carbohydrates be different? This, of
course, comes from the way the elements are put together. Lipids have higher
proportions of hydrogen bound to carbons (they are hydrocarbons), while
carbohydrates have one equivalent of water (H2O) for every carbon (C), i.e., they
are carbohydrates. Variability comes also in form of carbon backbone structures.
With this we mean the modes of connection between neighboring carbon atoms
via chemical bonds. What is found in nature is that carbon backbones vary in the
following four modes:

linear
branched
cyclic
double bonds

In addition, the number of carbon atoms that can be built into these backbone
structures seem unlimited, creating the foundation of an incredibly diverse three
dimensional diversity. All bonds not used for carbon-carbon linkage is used to
add either hydrogen, oxygen, nitrogen, sulfur or phosphorus atoms. Now we get
a good impression of the ability to create very large numbers of different
molecular structures using only six different elements.
Cell structures

There are two basic forms of cells found in nature; the prokaryotic and eukaryotic
cell type. The prokaryotic cell type is a cell with just one intracellular
compartment that contains all the DNA and proteins necessary for reproduction
and growth. They all have a polymer based rigid cell wall. Prokaryotic cells are
found in to domains of life, the bacteria and archaea. The eukaryotic cell type is
a much larger cell and contains multiple internal organelles that divide these
larger cells into specialized compartments. These subcellular compartments
include the nucleus (containing genes) and endomembrane systems (secreting,
importing and redistribution cellular components) for biosynthesis, the
mitochondria and chloroplasts for producing energy, and lysosomes, peroxisome
and vacuoles for break down and storage. In addition, eukaryotic cells contain a
cytoskeleton structure important for internal movement and overall structure. The
table below summarizes cell structure characteristics as determined by domain of
life.

Domain Bacteria Archaea Eukarya

Cell type prokaryotic prokaryotic eukayrotic
Ribosomal RNA unique* unique; some unique; some
match eukarya match archaea
RNA polymerase one type several types several types
Chromosome circular linear linear
structure
Introns rare some common
Histones in
no rare yes
chromosomes
Responds to
yes no no
antibiotics
Peptidoglycan in
yes no no
cell wall
Membrane lipids unbranched; branched, unbranched; fatty
fatty acids isoprenes acids
Membrane bound
no no yes
organelles
Multi cellular
no no yes
organisms

* Note that the original split of all forms of life into three domains, with
prokaryotes composing two domains, came from sequence comparison of
ribosomal RNA. Multiple sequence alignment showed that these RNA types
come in three large clusters largely congruent with genetic and biochemical
features of bacteria, archaea and eukarya listed here. This comparison shows
that archaea and eukarya or genetically more closely related to each other and
differ from bacteria, considered the oldest form of life on earth.

Multicellular organisms

Multicellular organisms contain only eukaryotic cells. These cells also need
surface junctions that allow them to connect and communicate with each other to
provide proper stability and physiological integration into the often very large
body structures (animals, plants).
For biological macromolecules and cells, and for any hierarchical level for that
matter, the basic principle is function follows form (*). This means that over
evolutionary time, the structure of proteins, DNA, cells and shape of organisms
have evolved altering specific functions which may or may not improve the
chance for survival of the organism ('survival of the fittest').

* Note: most biology textbooks introduce the notion of 'form follows function', a
paradigm of design first articulated by the American architect Louis Sullivan
(1856 - 1924). Evolution is not design of a structure for a purpose (e.g. use
windows to have natural light inside a house), the rational behind Sullivan's
dictum. Rather, evolution is design by trial and error. Evolution does not plan
ahead, but tinkers with changes in structures (mutations) subject to selection
('trial') allowing novel functions (an 'error') to propagate to the next generation
(see our discussion of intelligent design theory and why it is not a scientific
theory, but theistic belief).

No life without energy

All life depends on the continuous input of energy. Many chemical reactions in
our bodies are tuned to extract energy from food and use this energy to make
new cells and keep cells already made alive. In this process food molecules play
two roles; first, they contain energy that can be converted to forms generally
useful for biological reaction; second, they contain molecular structures that can
be used to make macromolecules.
The energy for all life originates from the sun. Light energy is converted into
chemical energy (organic molecules) in the presence of water and minerals.
Some of the captured energy is used to make more biomass (plants) to sustain
animal life, provide energy to grow and do work (animals walk around), while
some energy is lost as heat and waste molecules. The most effective way of
converting chemical energy into useful energy to sustain life is respiration. Warm
blooded animals have found ways to use the heat to maintain a relatively high
body temperature which gives them an advantage in colder environments.

No life without enzymes

In biological processes like photosynthesis that converts sunlight energy into

sugar and respiration that converts sugar into useful cellular energy to sustain
life, proteins have evolved that catalyze chemical reactions in very specific and
very efficient ways. These proteins are called enzymes. Enzymes interact with
reactants converting them into products. This conversion step may need input of
energy to proceed or it can release energy to do work. Enzymes are the catalysts
that control every biological process of life, with one exception; RNA molecules
control and make proteins.

Many enzymes are membrane proteins. This means they are part of the natural
barrier that separates the content of a cell from its surroundings. They control
transport of molecules in and out of cells, receive and produce signals that cells
use to communicate with each other, even if they are physically distant, convert
light energy into chemical, and chemical energy into work, and they catalyze
synthesis and degradation of many cellular structures making sure that old parts
are replaced by new ones, or that invading microorganisms are destroyed before
they can destroy the cell.

Life operates in small steps

The generations of mutations for natural selection, the breakdown of organic food
molecules to generate energy to do work are all examples of small steps that
together form stable cellular structure and functions. For instance, respiration is a
process where sugar is oxidized to generate the energy currency ATP in cells to
be used as fuel for almost all cellular processes. To avoid releasing too much
energy in one step (like the heat of a burning fire), cellular respiration divides the
oxidation into three dozen steps, each step extracting a minuscule portion of the
available energy from a sugar (or fat or protein) molecule. Cellular respiration
comprises only a small portion of all cellular reactions (metabolism) and it is the
thousands of small steps that together constitute a stable cell.

Similarly, evolution proceeds in small steps and the number of trails (mutations)
and time available is literally enormous allowing for successful adaptation of a
species to changes in the environment.
All cells come from cells

The most distinguishing feature of life is the ability of organisms to reproduce. A

central feature of reproduction is the capacity of cells to grow and divide (cell
division) and make two almost identical copies (daughter cells) of themselves.
While single cells reproduce through cell division called asexual reproduction,
larger multicellular organisms use cell fusion or sexual reproduction to produce
offspring. Both processes are related but differ in their way of reproducing the
complete set of genetic material (genome) from generation to generation. Both
processes demand a faithful copying of genetic material. However, sexually
reproducing species use a mechanism to randomly shuffle existing genetic
variations from one generation to the next, thus maintaining diversity. Genetic
variations are important because they are the only way life can evolve, i.e., adapt
to changes in the environment.

Asexual reproduction and mitosis

Asexual reproduction is used by all single-celled organisms and all somatic cells
(e.g. skin cell) of a multicellular organism during growth and wound healing.
Simple cell division involves growing the size of a cell, duplicating the genetic
material and separating it in equal amounts into the two ensuing daughter cells.
This process is known as mitosis in eukaryotic cells, and binary fission in
prokaryotic cells. The result is two genetically identical cells, with the exception of
random mutations, or errors in copying during cell division. Most asexually
reproducing cells come in large numbers (i.e. population) and have a relatively
short generation time, the time elapsed between two generations. For
prokaryotes and simple cells the generation time can be measured in hours. This
allows for a very large number of offspring in a matter of days or month which is
often a time frame during which environmental changes occur only slowly or not
at all.

Sexual reproduction and meiosis

Animals and plants, however, have generation times that are measured in days,
month and usually years. The environment can change drastically over this time
period and random mutations cannot provide for adequate changes to adapt.
Thus, sexual reproduction of these organisms makes use of enhanced mixing up
of genetic variation from generation to generation by using multiple copies of
each gene (e.g. diploid if two copies) that can be randomly assorted before and
mixed during fertilization of a male and female gamete (egg and sperm cells). For
this purpose, sexually reproducing organisms depend on two parents, rather then
one, allowing mixing of genetic material causing random distributing of the of
genetic variability through out a population. The resulting gene pool is
characteristic of a species. As a result, each individual is genetically unique
unlike descendant of a single bacterial cell (a clonal population).

The process of sexual reproduction much like asexual reproduction strives to

maintain the number of genes (or chromosomes which contain the genes) of the
organism from generation to generation. Since sexual reproduction involves
fusion of gametes from two parents, the number of genes or chromosome sets
first has to be reduced. Otherwise, the number of the copies of genes would
increase exponentially from generation to generation. For this mechanism to
work, each gene (and chromosome) must be present in two copies. Sexually
reproducing organisms contain two full genetic complements (genomes). They
are said to be diploid. During reproduction the reproductive organs of males and
females produce single copy genomes (haploid cells) from diploid cells in a
process called meiosis. Unlike mitosis which consists of one round of duplication
and separation of sister chromatides followed by a single cell division
(cytokinesis), meiosis adds two additional features: first, after duplication, the
sister chromatids of homologous pairs of chromosomes are joined in a tetrad
(synapsis formation) where homologous chromatids exchange portions of their
structures (recombination or crossing-over); second, after recombination the cell
undergoes two rounds of cell divisions (cytokinesis) without further duplication of
chromosomes, separating first homologous chromosome pairs forming haploid
cells where recombined sister chromatides are still joined, followed by separation
of these sister chromatides into single copy cells (sperm or egg). These gametes
contain one set of chromosomes composed of randomly assorted chromosomes
inherited from both parents. Random fusion of one egg and one sperm from two
different individuals during fertilization produces a diploid zygote, the first step in
the life cycle of a new individual.

Because of this random mixing of two parental chromosome sets into a new
single set of chromosomes during mitosis, each gamete is genetically different
from any other gamete decreasing the probability of subsequent fertilization
events producing genetically identical offspring. The only exception in sexual
reproduction, where genetically identical offspring (not identical with parents) are
formed are twins (and triplets etc. ) that are the result of early separation of
single cells after a few rounds of cell division by mitosis of the zygote into an
embryo (see embryonic stem cells).

The ultimate source of diversity are mutations

Mutations are also the source of genetic variability in mitosis and prokaryotic
binary fission. Mutations can be a simple as errors in replication substituting the
wrong nucleotide, inserting an additional building block or deleting a building
block. Mutations, however, can also affect large segments of chromosomes
through insertion, deletion or duplication. The rate of mutations depends on the
mechanism of replication, but is heavily influenced by environmental factors such
as radiation and unstable molecules (radicals) that randomly attach nucleic acids
on other molecules in cells.

The rate at which mutations accumulate effects the fate of a cell or population.
Many microorganisms, particularly viruses, often show a high rate of mutation,
which helps them change their surface structure and evading the defense
mechanisms of their hosts. Larger, sexually reproducing organisms have low
mutation rates, but use sexual reproduction to maintain a high variability of
already existing mutations within a population. While for most instances the
parental chromosomes (homologous chromosomes) are largely identical, they
always differ somewhat, because some of the genes are mutated in one parent,
but not the other. These genes are referred to as alleles and sexual reproduction
ensures random distribution of acquired mutations throughout a population. The
distribution of such mutations or alleles in a population of a species can be
tracked by Mendelian genetics.

Different mutations affect organisms in different ways. Mutations sometimes have

no immediate effect on the functioning of an organisms. These are called silent
mutations. Other mutations, those that affect protein coding genes, or the
regulatory elements on chromosomes, do affect the functioning of organisms,
often in a detrimental effect, causing diseases or even death (lethal mutations).

Atoms are the "basic building block" of molecules.

The materials that make up cells - macromolecules, molecules, and even water - are
made of atoms. All molecules are assembled from two or more atoms.

o At the atomic level, a person consists of nothing more than carbon, hydrogen,
oxygen, nitrogen, phosphorus, sulfur, and small amounts of other elements.

Atoms are made of smaller particles. Each atom has:

o an atomic nucleus, consisting of one or

more protons (positive charge). Most atoms
 also have one or more neutrons (no charge).

o an electron cloud, which surrounds the

atomic nucleus. Each atom has one or
more electrons (negatively charged); the
electrons are in constant motion.

There are more than 100 different kinds of atoms, also called the elements.

o Examples of elements include carbon, hydrogen, oxygen, nitrogen, sulfur,

phosphorus, iron, aluminum, gold, silver, lead, potassium, sodium, magnesium,
and zinc.

o Different elements have different chemical properties. The chemical properties

of a molecule (a molecule consists of two or more atoms) are determined by
the atomic make-up of the molecule - which atoms are present and in what
amounts.

The Periodic Table of the Elements lists the different kinds of

atoms - the elements.

Many molecules are made of more than one kind of element. This kind of molecule is
called a compound.

o Water is a compound In this ball-and-stick model of the water

containing two hydrogen molecule, the balls represent individual atoms of
atoms and one oxygen atom hydrogen and oxygen; the sticks
represent covalent bonds.
(H20).
 o Glucose, a
simple sugar, contains 6 This structural formula of glucose represents
the atoms as letters (carbons, hydrogens,
carbons, 12 hydrogens, and 6 and oxygens). The lines connecting the
oxygens (C6H12O6). letters are covalent bonds.

The atoms are held together in molecules by chemical bonds.

o Covalent Bonds involve shared electrons between atoms. In cells, covalent

bonds are strong attachments between atoms and are the most important kind of
bond that holds molecules together.

Covalent bonds involve shared electrons between two atoms. When the
single electron of hydrogen pairs up with one of the electrons of carbon, a
covalent bond forms, represented here by the pair of electrons between the
two atoms.

o Hydrogen Bonds form when a molecule with a weak partial positive

charge associates with a molecule with a weak partial negative charge.
Individually, hydrogen bonds are not as strong as covalent bonds. Hydrogen
bonds readily break and re-form in cells (in the presence of water).
 In some covalent bonds, the electrons stay closer to one atom than the other.
This gives the atom that is "hogging" the electrons a weak, "partial" negative
charge; the other atom has a corresponding weak, partial positive charge. Th
weak negative charge on one atom can bind to the weak positive charge on
another molecule; this is called a hydrogen bond.Water is an example of a
chemical compound that readily forms covalent bonds.

o Ionic Bonds form when an atom with a positive charge associates with an atom
with a negative charge. Ionic bonds readily break in cells (in the presence of
water).

A positively charged atom (here, sodium is positively charged - Na+) is

strongly attracted to a negatively charged atom (here, chloride is negativel
charged - Cl-). This association based on the attraction of opposite charges
an ionic bond. Ionic bonds are less stable in the presence of water, becau
the partially charged water molecules can bind to the charged ions.

Molecules = combination of two or more connected atoms.

The material that makes up cells is mostly molecules (and large molecules called
macromolecules. All molecules are made of atoms. Atoms can be attached
by chemical bonds.

o The bond that is most commonly used to hold together molecules in cells is
the covalent bond.
Water - Ball and Glucose - structural Methane - two representations. At bottom is a simple structura
Stick representation. formula. The diagram formula. The upper figure illustrates the electrons that are shar
Each ball is an atom indicates the location of to form the covalent bonds between each hydrogen and the
- water contains two the different atoms and carbon.
hydrogens and an their connections. Each
oxygen.The lines line represents a covalent
connecting the bond. There are 6
atoms represent carbons, 12 hydrogens,
covalent bonds. and 6 oxygens; the
chemical formula of
glucose is C6H12O6.
 The chemical properties of a
particular molecule are
determined by the atoms that
are present, as well as their
arrangement - the way they
are attached to each other.

o For Example, Glucose

and Fructose are
both sugars, and both
consist of 6 carbons, 12
hydrogens, and 6
oxygens (C6H12O6).
However, they taste
very different - fructose
is a much sweeter
sugar.

The molecules of cells usually contain carbon, hydrogen and oxygen.

o Typical sugars are C6H12O6.

o Nucleotides, DNA, and RNA also contain nitrogen and phosphorus.

o Amino acids and proteins also contain nitrogen and sometimes sulfur.

Nucleotides are found free in the cytoplasm of cells, and are also p
The amino acid cysteine. All amino acids of DNA and RNA. In addition to the carbons, hydrogens, and
contain at least one nitrogen (N). Some oxygens, there is nitrogen in the "nitrogenous base" and phosphor
amino acids also contain sulfur (S) (P) (1, 2, or 3 of them) at the other end of the molecule.
 Some Molecules are charged (positive or negative
charge).

o Atoms consist of positively

charged protons and uncharged neutrons in
the atomic nucleus and negatively
charged electrons in the electron cloud.

o Atoms can sometimes gain or lose an electron.

o A molecule can get a negative charge if one of

its atoms gains an electron, because electrons
have a negative charge.

o A molecule can get a positive charge if one of

its atoms loses an electron.

Some Molecules have partial charges.

o Some covalent bonds involve equally shared electrons between the two atoms

o Some atoms can "hog" the electrons - the electrons stay closer to one atom than
to the other in the covalent bond. When this happens, the atom that is attracting
the electrons becomes weakly negatively charged, and the atom that is losing
the electrons becomes weakly positively charged. These weak positive and
negative charges are called partial charges.

o These partial charges are the basis for hydrogen bonding.

In some covalent bonds (such as the ones in water), unequal sharing

of electrons gives part of the molecule a partial negative charge and part of th
molecule a partial positive charge. The molecule as a whole is NOT charged
does not have a net positive or net negative charge - but it DOES have positiv
and negative regions within the molecule. These partial charges can interact
with each other. For example, water molecules bind to each other using these
partial charges. This kind of interaction is called a hydrogen bond.

Molecules with charges or partial charges mix readily with water.

 o Water molecules have partial positive and partial negative charges.

o Water molecules interact with each other and other molecules that have charge
or partial charge.

o Molecules with charge or partial charge mix in water (are soluble in water).
This property is called hydrophilic.

o Molecules without any charge do not mix well with water and are
called hydrophobic.

Think of a simple oil-and-vinegar

salad dressing: The vinegar molecules
(chemical name = acetic acid), which
are charged, are found in the water
layer, but the oil rapidly separates into
another layer, on top. Oil is hydrophobic
due to the absence of charge.

Chemical bonds = attachments between atoms.

Cells are composed mostly of molecules - chemicals formed by connecting two or
more atoms.

Covalent bonds are one of the most important kind of bond in cells.

o Covalent bonds involve the "sharing" of electrons between two atoms.

o In cells, covalent bonds are very strong and stable. Forming or breaking a
covalent bond usually requires the help of an enzyme - a protein that exists for
this purpose.

o Most molecules in cells are held together by covalent bonds.

 This diagram of methane (CH4) shows the sharing of electrons In this "ball-and-stick" representation of th
between the carbon atom and each of the four hydrogen atoms. The water molecule, the covalent bonds betwe
shared electrons are the small black circles; there are a pair of the oxygen atom (O) and each hydrogen
shared electrons in each of these covalent bonds. atom (H) are symbolized by a line; the line
represents the pair of shared electrons.

Hydrogen bonds are also important in cells.

o Hydrogen bonds are much weaker than covalent bonds

o Hydrogen bonds form when a molecule with a partial positive charge interacts
with a molecule that has a partial negative charge.

Water molecules form hydrogen bonds between the oxygen atom of one water molecule and the hydrogen atom
of another water molecule. This occurs because the hydrogen atoms and the oxygen atom of each water
molecule have a "partial charge." The electrons of the covalent bond are not shared equally between hydrogen
and oxygen, but are closer to the oxygen. As a result, the negative electrons make oxygen slightly negative, an
the lack of electrons make hydrogen slightly positive. The partially positive hydrogen of one water molecule is
attracted to the partially negative oxygen of another water molecule. Liquid water consists of a network of
individual water molecules connected to each other by hydrogen bonds. Because the individual hydrogen bond
are weak, they can break and re-form with different water molecules. As a result, individual water molecules ca
freely move around in a glass of water, making and breaking connections with nearby water molecules as they
so.

o In cells, individual hydrogen bonds are readily formed and broken, even
without the help of enzymes.
 o In some molecules, such as DNA and protein, a large number of hydrogen
bonds are present. In these molecules, hydrogen bonds are important for the
overall structure of the molecule. The large number of hydrogen bonds creates
strength, but at the same time, the individual hydrogen bonds can be readily
broken, allowing DNA to "unzip," for example.

Have you ever looked closely at a strip

of Velcro? One side consists of many
little hooks that catch on many little
loops on the other side. The individual
hooks and loops are like hydrogen
bonds - weak individually, but strong
when present in large numbers. A
person wearing an outfit covered with
Velcro can stick to the side of a wall,
above the ground.

Ionic bonds form between an atom with a positive charge and an atom with a
negative charge.

o Ionic bonds readily break in the presence of water, and are therefore not stable
in cells.

Cells are mostly made of molecules. Important molecules in

biology include:
Water - All cells contain water, and the properties of water set the rules for how
molecules interact with each other in cells.

Proteins - are large molecules formed from long chains of amino acids. Different
proteins may be:
 o Enzymes - proteins that enable specific chemical reactions to occur, such as
conversion of starch to glucose.

o Transporters - Proteins that help other molecules move into or out of cells.

o Movement - Proteins move molecules within cells, and help cells and
organisms move through the world.

o Structural - Proteins give cells their shape, and help the cells of multicellular
organisms stay attached. In humans, hair and nails are mostly protein.

o Other Proteins - have specialized functions. Many hormones are small

proteins. Many bacterial toxins (molecules that are released by the bacteria,
causing disease symptoms) are also proteins.

Sugars and Polysaccharides - You probably know that sugars are an important
source of calories - energy for cells. Did you know that sugars can be connected into
long chains (called polysaccharides) that can be used for energy storage? Did you
know that polysaccharides are also important structural molecules in everything from
bacteria to humans?

Nucleic Acids and Nucleotides - The nucleic acids are DNA and RNA. DNA is the
genetic material in chromosomes that stores all of the instructions required to make a
cell. The main function of RNA is to produce proteins. DNA and RNA are both
polymers (long chains) made from smaller subunits called nucleotides. Nucleotides
are used as components of DNA or RNA, and are ALSO used as molecules that
provide energy to cells.

Water is the most abundant molecule in cells.

This means that almost all biological processes
in cells involve water.

The properties of water determine the

nature of chemical reactions within cells.

Each water molecule consists of three atoms - 2 hydrogen and one oxygen
(H2O). The hydrogens are connected to the oxygen by covalent bonds.

Water molecules have a partial charge because the electrons in each

covalent bond between the oxygen and each hydrogen are unequally
shared - the electrons are closer to the oxygen. This means that each
water molecule has a partial negative charge on the oxygen and
partial positive charges on the hydrogens.

Water molecules bind to each other using the partial

charges.
This process is called hydrogen bonding.
Have you ever noticed that water can be poured into a glass
higher than the rim? This is because the water molecules are
bonded to each other. If you try to pour a liquid that does NOT
hydrogen-bond higher than the rim of the glass, you'll make a
mess.

If you'd like to learn more about properties of water such as surface tension, try
this link. Pictured at right is a bug called a water strider.

Other molecules that are charged or partially charged dissolve readily in water. These
molecules can interact with the water molecules due to the attraction of charged
molecules to each other.
 In water, negatively charged molecules interact with the
positively charged part of the water molecule, and
positively charged molecules interact with the negativel
charged part of the water molecule.

o Molecules with a charge or a partial charge that readily interact with water are
sometimes called hydrophilic.

Molecules that do not have charges or partial charges on their surface do NOT mix
readily with water; these molecules cannot hydrogen bond with water. As a result,
they get pushed away from the water by the strength of the hydrogen bonds that form
when the water molecules bind to each other.

This figure shows the water

molecules (red and white circles)
connected by hydrogen bonds
(dotted red lines). The hydrophobic
molecule, represented by a green
blob, cannot form hydrogen bonds
with the water molecules.

o Molecules that are uncharged and that do not associate well with water are
referred to as hydrophobic.
 Oil is hydrophobic because it cannot
form hydrogen bonds with water. This
is why the oil and vinegar (which is
acetic acid and water) separate in
salad dressing, or in a test tube.

Proteins are chains of amino acids.

Proteins have many important functions in cells.

Proteins are made of amino acids, in long chains (polymers).

A chain of amino acids; each amino acid

A structural representation of a chain of amino acids. Actual proteins
is represented by a red ball. The different
are considerably larger, typically consisting of hundreds or thousands
amino acids shown are Proline (Pro),
of amino acids.
Lysine (Lys), Phenylalanine (Phe), etc.

o A short chain of amino acids is referred to as a peptide (or oligopeptide); a

long chain of many (hundreds or thousands) amino acids is referred to as
a polypeptide.
 o Each cell makes thousands of different KINDS of proteins.

o Different kinds of proteins are composed of a different sequence of amino

acids.

For example, the first six amino acids in actin (a protein involved in
muscle contraction and the cytoskeleton) are: Methionine, then cysteine,
then aspartic acid, then asparagine, then asparagine, then valine.

The first six amino acids in beta-globin (part of hemoglobin, the protein
that transports oxygen in our blood) are: Methionine, then valine, then
glutamine, then leucine, then serine, then serine.

o Proteins typically consist of MANY amino acids. For example, actin consists of
more than 300 amino acids. A complete hemoglobin molecule has around 600
amino acids. A single antibody molecule (part of the immune system) contains
about 1,400 amino acids or more.

o The SAME protein consists of the SAME sequence of amino acids. For
example, if actin is a protein consisting of a chain of 376 amino acids, then
EVERY actin protein will be 376 amino acids long, and EVERY actin protein
will have the same amino acid sequence, starting with methionine, cysteine,
aspartic acid, asparagine, asparagine, and valine.

Amino acids are the subunit that are extended in a long chain to become proteins.

o There are 20 different amino acids. All cells in all organisms (bacteria,
protozoa, fungi, plants, and animals) use these 20 amino acids to make proteins.

o The names of the 20 amino acids are:

Alanine Arginine Asparagine Aspartic Acid Cysteine

Glutamine Glutamic Acid Glycine Histidine Isoleucine
Leucine Lysine Methionine Phenylalanine Proline
Serine Threonine Tryptophan Tryrosine Valine

o Different amino acids have different chemical structures. For example:

 Structure of the amino acid Aspartic Acid. Structure of the amino acid Tryptophan.

o As a result, different amino acids have different chemical properties. Each kind
of protein is a unique combination of different amino acids, and the properties
of a protein are determined by the amino acids used to make it.

For example, proteins that are found

in membranes contain many hydrophobic amino
acids, because the interior of membranes is a
hydrophobic environment.

These two diagrams of transport proteins show the

location of the protein IN the cell membrane. Here, This structural diagram of a transport protein (in red)
the protein is a blue oval/cylinder. shows its close association with the membrane lipids
(green).

Proteins have up to four levels of structure.

o Part of what makes a protein function the way it does is its particular three-
dimensional structure (shape).

o The amino acid sequence of a particular protein determines its shape (also
called conformation.
o The organization of protein structure is divided into four levels, called primary,
secondary, tertiary, and quaternary.

The primary structure of a protein is

simply the sequence of amino acids.

o The secondary structure of a protein is the initial arrangement of the primary

structure.

Sometimes part of the amino acid sequence folds into a

coil called a helix. The diagram shows a model of the
structure of a protein that contains many helices (coils).
The line (red and green) represents the amino acid chain;
it is coiled into numerous separate helices. EACH coil
shown is a separate unit of secondary structure.

Sometimes part of the amino acid sequence folds into a

sheet of parallel strands. This diagrammed protein (a
snake venom molecule) illustrates how a long chain of
amino acids (the grey and blue line) can form back-and-
forth rows called a sheet. Unlike the helices, the amino
acid chain does NOT form coils here.

The complete protein may have some parts where the

secondary structure is a helix, and other parts where the
secondary structure is a sheet. There may also be sections
where the secondary structure is neither helix nor sheet
(these sections are sometimes called random coil). Shown
here is a diagram of a special receptor on the surface of
most human cells. The protein has a "floor" of sheet
structure and "sides" of alpha helix. The shapes of the
different parts of the protein form a groove (like a hot dog
bun); small molecules can bind within the groove. NOTE
that each coil and sheet is a separate region of secondary
structure.
In most proteins, once the secondary structure has formed, the secondary structure is further arranged
into clumps called tertiary structure. Several examples of tertiary structure are visible above . Tertia
 structure is simply the grouping of different separate secondary structures, such as multiple helices or
multiple sheets or a combination of helices and sheets.
Quaternary Stucture: Some complete proteins actually consist of more than one separate polypeptid
(long chain of amino acids). For example, hemoglobin consists of FOUR separate polypeptide chains
two alpha-globin polypeptides plus two beta-globin polypeptide chains. When multiple separate
polypeptide chains are required to make the complete protein, the protein has quaternary structure.

o In summary, there are up to four levels of protein structure:

Primary Structure The amino acid sequence.

Secondary Structure Initial folding of the amino acid sequence into helixes and sheets.
Tertiary Structure Arrangements and groupings of the secondary structure into clumps.
Arrangement of separate tertiary structures, when multiple amino acid c
Quaternary Structure
required to make a single protein.

Protein structure can change.

o Protein primary structure is strong and stable, because the amino acids are
connected to each other by covalent bonds.

o Secondary, Tertiary, and Quaternary structure in proteins are held together

primarily by hydrogen bondsand other weak interactions.

Small changes in structure often happen during protein functioning. In

other words, proteins can change shape. In fact, this is how many
proteins do their jobs: by moving and changing shape. For example,
some enzymes attach two substrate molecules by flexing and literally
smashing the two substrate molecules together to make a product. The
particular shape of a protein is sometimes called its conformation.

If all of the hydrogen bonds break at the same time, the protein can
completely unravel. If this happens, the protein will lose all structure
except for the primary structure. When a protein loses its structure, it
is denatured.

You've probably conducted experiments in protein denaturation at

home. When eggs cook, the proteins denature, and because they
are unable to re-form the correct secondary and tertiary structure,
the process is irreversible (cooked eggs don't revert back to the
liquid state when they cool). Some proteins CAN correctly reverse
the denaturation process by themselves. An example is gelatin:
 you can melt Jello, let it solidify, remelt it, and re-solidify it as
many times as you want.

o Allosteric Modification: The function of some proteins is regulated by

causing a conformation change - causing a change in the three-dimensional
shape of the protein. For example, sometimes an enzyme is activated (or
inactivated) if some regulatory molecule binds to the enzyme. When the
regulatory molecule binds, it causes the enzyme to change shape, causing it to
gain (or sometimes to lose) its function. Sometimes a protein can be turned
"off" or turned "on" when a molecule binds and causes a change in shape.

Types of Proteins: There are many different kinds of proteins in cells. They perform a
variety of functions in cells. All proteins, however, consist of chains of amino acids
arranged into secondary, tertiary, and perhaps quaternary structure.

o Enzymes - proteins that enable specific chemical reactions to occur, such as

conversion of starch to glucose. Most enzymes only catalyze ONE kind of
chemical reaction. For example, the eight chemical reactions
of glycolysis (breakdown of glucose to pyruvate) each require a different kind
of enzyme.

o Transporters - Proteins that help other molecules move into or out of cells.

o Movement - Proteins move molecules within cells, and help cells and
organisms move through the world.

o Structural - Proteins give cells their shape, and help the cells of multicellular
organisms stay attached. In humans, hair and nails are mostly protein.

o Other Proteins - have specialized functions. Many hormones are small

proteins. Many bacterial toxins (molecules that are released by the bacteria,
causing disease symptoms) are also proteins. Some proteins, such as receptors,
are involved in transmitting information into the cell from the outside.

Where do proteins come from?

o Proteins are made by ribosomes, in the process of protein synthesis, also

called translation.

o The instructions for protein synthesis - the code for the correct order and
number of amino acids for each protein - is contained in the DNA (in the genes,
 on the chromosomes). In fact, this is a main function of the genetic material - to
store the instructions that allow the cell to make proteins.

Sugars are present in cells individually, in pairs, or in longer

chains. Sugars provide energy and structure to organisms.

Simple Sugars: Individual sugar molecules, also

called monosaccharides, are a ring or chain. Sugars consist
of carbon, hydrogen, and oxygen atoms. The composition of a
glucose, a typical sugar, is C6H12O6. Sugars such as glucose
can exist in linear or ring forms.

Glucose in the linear Glucose in the ring

(or "open-chain") form. In nature,
form. sugars are more
commonly found in
the ring form.

Number of Carbons: Many monosaccharides,

including glucose are six-carbon sugars, but cells also
use sugars that have other numbers of sugars. Two
other important sugars are ribose, (a five-carbon sugar)
and glycerol (a three-carbon sugar). Ribose is an
important component of nucleotides. Glycerol is an
important part of lipids.

o Functions of monosaccharides:
 Energy source - many sugars are readily metabolized by cells to
make ATP, one of the main molecule used to power cells.

Component of larger molecules. For example, ribose is a component of

nucleotides (which themselves are components of nucleic acids such
as DNAand RNA). Glycerol is a component of lipids.

Disaccharides are covalently attached pairs of monosaccharides. For example:

Sucrose (table = Glucose +

sugar) Fructose

= Glucose +
Lactose
Galactose

= Glucose +
Maltose
Glucose

o Function of disaccharides:

Energy source - many disaccharides are easily broken down into

monosaccharides, which are readily metabolized by cells to make ATP,
one of the main molecule used to power cells.
 Polysaccharides are long chains of sugar molecules.

Starch, Glycogen (animal

starch), and Cellulose
(plant structure) are all
long chains of
glucose.Small
differences in the
chemical structure at the
covalent bond
attachment between the
sugars account for the
different properties of
these polysaccharides.

o Functions of polysaccharides:

Storage of Energy - polysaccharides such as starch and glycogen (both

are long chains of glucose) are used to store glucose. When needed,
glucose can be released and then metabolized to make ATP, one of the
main molecule used to power cells.

Structure - polysaccharides are important components of cells. Cellulose

(a long chain of glucose) forms the cell wall of plants. Chitin (a polymer
of a sugar called N-acetyl-glucosamine) forms the cell wall of fungi.
Polysaccharides help "glue" the cells of multicellular animals (including
humans) together. Polysaccharides are also found on the surface of
bacteria, where they help the bacteria to cause disease.

Nucleic acids contain genetic information and enable synthesis of

proteins. Nucleotides are used to make Nucleic Acids.
Nucleotides are the subunit that is
polymerized (connected into a long
chain) to make nucleic acids (DNA and
RNA). Nucleotides consist of three
smaller components: a ribose sugar, a
nitrogenous base, and phosphate
group(s).
Generic nucleotide structure. The
"nitrogenous
base" varies in different nucleotides.

Ribose is the sugar component of nucleotides.

One of the main chemical differences between
DNA and RNA is that in RNA, the sugar is
ribose, but in DNA, the sugar is deoxyribose, in
which an oxygen has been removed. (compare
the bottom right corners of the two structures -
you'll see that the "OH" side group of ribose has
been replaced with an "H" ).

o Nitrogenous Bases are Adenine, Guanine, Cytosine, and Thymine in DNA. One of the
chemical differences between DNA and RNA is that in RNA, the nitrogenous base Uracil
is used instead of Thymine.

o Phosphate group(s):

Nucleotides may have one, two, or three phosphate groups attached.

 If there is one phosphate, the nucleotide is a monophosphate
If there are two phosphates, the nucleotide is a diphosphate
If there are three phosphates, the nucleotide is a triphosphate

Click to enlarge.

If there are NO phosphate groups, the molecule is called a nucleoside, not a

nucleotide.

Naming Nucleotides: Nucleotide names are a three letter abbreviation. The first letter refers to
the nitrogenous base, the third letter refers to the phosphate, and the second letter refers to the
number of phosphates. For example:

ATP Adenosine Tri-Phosphate

AMP Adenosine Mono-Phosphate
TTP Thymidine Tri-Phosphate
GDP Guanosine Di-Phosphate
NOTE: If you're paying attention, you probably noticed that the nitrogenous bases have
names like Adenine, Thymine, and Guanine. Are you wondering why the nucleotides are
called Adenosine, Thymidine, and Guanosine? "Adenosine" is the name for a nucleoside
of adenine + ribose. Likewise, "thymidine" and "guanosine" refer to the nucleosides - the
combination of ribose sugar and nitrogenous base.

Nucleotides can be connected to make nucleic acids.

 The connection that
forms between nucleotides is
between the sugar of the first
nucleotide and the phosphate
group of the second.
Each connection between
nucleotides is a covalent
bond, so the nucleic acids
have a covalently
attached sugar-phosphate
backbone.

In this figure, the nitrogenous

bases are representated as
squares labeled T, C, and G,
respectively.

o Nucleic Acid Synthesis: Connecting nucleotides to make nucleic acids requires:

Specific enzymes - DNA polymerase connects nucleotides to make DNA, and

RNA polymerase connects nucleotides to make RNA.

A pre-existing nucleic acid molecule to serve as a template - a model or mold that

determines the sequence of the strand being made. Nucleotides are added based
on complementary base-pairing (discussed below).

o RNA is a long single chain of nucleotides.

Each sugar is ribose.

The nitrogenous bases are Adenine, Cytosine, Guanine, and Uracil.

 The process of RNA synthesis is called transcription.

RNA, like DNA (see below) is a long chain

of individual nucleotides. Unlike DNA,
RNA is a single strand of nucleotides. In
nature, parts of an RNA molecule often
base-pair with other parts of the same RNA
molecule, as depicted in the diagram (red
lines indicating hydrogen bonds between
the base pairs C-G, A-U, and U-A).

To see an enlarged version of this

figure, click here.

o DNA is a pair of long chains of nucleotides.

Each sugar is deoxyribose.

The nitrogenous bases are Adenine, Cytosine, Guanine, and Thymine.

The process of DNA synthesis is called replication.

 DNA Structure. At left is an "unfolded" view of
a double-stranded DNA molecule, showing
the two chains of nucleotides, connected in
the center by a series of hydrogen bonds
between nitrogenous bases. At right, a
schematic illustration showing the
arrangement of the two strands in the double- DNA structure. The two strands of DNA
helix configuration. The "backbone" on the backbone are visible as red and grey balls;
outside is the sugar-phosphate chain, and the the nitrogenous bases are the blue and grey
nitrogenous bases form the bridges across regions in the center of the double helix.
the middle. For an enlarged version, click
here.
For more on DNA structure, scroll down or click here.

Nitrogenous bases can form hydrogen bonds.

o Adenine, Thymine, and Uracil can form TWO hydrogen bonds

o Guanine and Cytosine can form THREE hydrogen bonds.

o In nucleic acids (DNA and RNA), nitrogenous bases can bind to each other by hydrogen
bonding.

Guanine binds to Cytosine, and Cytosine binds to Guanine

In DNA, Adenine binds to Thymine. In RNA, Adenine binds to Uracil.

 These hydrogen-bond interactions between nucleotides C-G and A-T or A-U are referred to
as base-pairing or complementary base-pairing.

o Base-pairing holds the double-stranded DNA molecule together.

o Base-pairing is necessary for DNA synthesis, RNA synthesis, and Protein synthesis to
occur.

o Base-pairing can occur between two strands of DNA, between two strands of RNA, or
between one strand of DNA and one strand of RNA.

Some Nucleic Acids are RNA, which stands for ribonucleic acid. RNA contains the nitrogenous
bases Adenine, Cytosine, Guanine, and Uracil.

o All RNA is single-stranded (a single long chain of nucleotides). However, one section of
the RNA molecule can base-pair with another section.

This molecule, called tRNA base-pairs with
itself to form a cloveleaf structure. Each circle
represents a single nucleotide (A, U, c, or G).
Lines that connect different nucleotides
represent the hydrogen bonds of base-pairing.
In nature, the cloverleaf folds up into a "L"
shape. This is the same molecule
represented in the figure at left. The inset is
another kind of depiction of the structure of
tRNA, called a space-filling model.

o There are three kinds of RNA; the main purpose of all of these is protein synthesis.

rRNA = ribosomal RNA - part of the ribosome. Ribosomes are large complexes
consisting of multiple different RNA molecules and many different protein
molecules.

mRNA = messenger RNA - This long RNA molecule is an RNA copy of a gene (a
region of DNA that contains the instructions for synthesis of a particular kind of
protein).

tRNA = transfer RNA - during protein synthesis, carries amino acids to the
ribosome, where the amino acids are attached in a growing chain that becomes the
new protein. tRNA binds to mRNA by complementary base-pairing, so tRNA also
serves as a "bridge" between the information code of DNA and RNA (the order of
the nucleotides) and the code of protein (the order of amino acids). To learn more
about this process, read about protein synthesis.

Some Nucleic Acids are DNA, which stands for deoxyribonucleic acid. Nitrogenous bases in
DNA are Adenine, Cytosine, Guanine, and Thymine.
o All DNA is double-stranded. The two strands are antiparallel (pointing in
opposite directions). The backbone of each strand is the chain of sugars and phosphates. The
nitrogenous bases of each strand are in the center, pointing toward the other strand. Each
nitrogenous base forms hydrogen bonds with the complementary base pair on the opposite
strand. Because the double-stranded DNA molecule twists around, it actually looks more like
a spiral staircase than like a ladder. DNA is referred to as the "double-helix" because of this
twist.

Click Here for an enlarged DNA structure image.

o DNA is the genetic material in cells - the essential part of the chromosomes.

Chromosomes are very long double-helixes of DNA - a long pair of

chains of nucleotides. The number of nucleotides in each strand is
different for each chromosome, but is generally MILLIONS of
nucleotides long. More on chromosomes.

Chromosomes in eukaryotic cells are linear - they have two ends.

Chromosomes in bacteria are circular - the two ends are attached.

Genes are regions of the DNA on chromosomes. DNA is simply a long

chain of A, T, C, and G nucleotides in a particular order. Genes are
particular regions of DNA (A, T, C, and G nucleotides in a particular
order) that contain the instructions for making RNA and protein
molecules. For example, human genes contain thousands of genes,
including the gene for beta-globin (part of the hemoglobin protein,
which transports oxygen in the blood) and the gene for insulin (a
hormone involved in regulation of glucose levels). On a specific part of
one human chromosome, the gene for beta-globin is found: a specific
sequence of A, T, C, and G nucleotides that contains the information
required for the cell to make beta-globin. On another chromosome is a
specific site where the sequence of nucleotides that encodes insulin is
found.
Lipids have water-friendly and water-hating parts. Lipids form
membranes, which enclose cells or regions of cells.
Lipids include fats, steroids, and phospholipids. Most or all of a
lipid molecule ishydrophobic - uncharged and therefore insoluble in (unable to mix
with) water. Some lipids include a charged or partially charged region that
is hydrophilic - readily mixes with water.

For example, this

phospholipid has both
hydrophobic AND
hydrophilic regions (in
other words, it
is amphipathic).

Amphipathic lipids such as phospholipids can spontaneously form membranes if

added to water. A biological membrane is a double-layer of phospholipids (a
phospholipid bilayer) which usually also contains other lipids as well as many
proteins.

The phospholipid bilayer is a stable arrangement of

amphipathic molecules, which have a hydrophilic,
water-loving end and a hydrophobic, water-avoiding
end.

The hydrophobic fatty acid tails (wiggly orange lines)

are on the inside. The hydrophilic polar (charged)
heads are on the outside. Water is found on the
outside but NOT on the inside. Both parts of the
molecule are in the right chemical environment.

Phospholipid bilayers are a stable structure that can

form spontaneously when water is added to
phospholipids.
 Biological membranes consist of a phospholipid
bilayer with other associated molecules. Other lipids,
such as cholesterol, are found in membranes. Many
different proteins are found IN (the blue blobs and
lines passing through) or ATTACHED to biological
membranes.

The properties of biological membranes:

o The membrane consists of a double-layer (a phospholipid bilayer) of

amphipathic lipids. The hydrophobic ends face each other on the inside, and the
hydrophilic ends are on the outsides of the membrane. That way, the
hydrophobic regions do not interact with water, and the hydrophilic regions do.
Both parts of each phospholipid molecule are "happy."

o Other molecules are also found in the membrane. For example, other lipids,
such as cholesterol, may be present. Many proteins are found in the membrane,
or else are attached to lipids in the membrane.

o The lipids, proteins, and other molecules found in biological membranes can
freely move laterally (sideways). The proteins can move from one side of the
cell to another (like driftwood floating in a lipid sea). Membrane proteins can
move towards or away from each other. Sometimes this happens randomly, and
sometimes the cell controls movement of membrane proteins.

o The proteins and lipids do NOT normally move from one side of the membrane
to the other. For example, in the cell membrane, proteins facing the outside of
the cell (on the external side of the membrane) do NOT flip around and face
into the cell (to the cytoplasmic side of the membrane). This is important: if a
protein that normally pumps glucose INTO the cell flipped around into the
opposite orientation, perhaps it would pump glucose OUT of the cell.

The membrane is sometimes called a "fluid-mosaic phospholipid bilayer" because it

consists of many separate molecules that move around in a double-layer lipid sea.
Does EACH word in the phrase "fluid-mosaic phospholipid bilayer" make sense to
you?

The function of biological membranes:

 o Membranes are selectively permeable. This means that some molecules can
freely cross membranes and others cannot. Membranes are used by cells to
enclose and contain certain areas.

The cell membrane serves as a boundary of the internal cell environment

(the cytoplasm), and restricts the movement of molecules into or out of
the cell.

The membranes surrounding organelles and vesicles (such as

the mitochondria, the nucleus, and the lysosomes) separate these parts of
the cell and allow them to have different internal chemical environments
compared to the cytoplasm. For example, lysosomes can be highly acidic
and contain enzymes that could destroy the cytoplasm if they escaped
out of their membrane enclosures.

o Membranes can regulate the contents of cells. Transport proteins located within
membranes can move ions and molecules across the membrane. Cells can
pump IN food molecules such as glucose and pump OUT toxic metabolic waste
products.

o Learn MORE about biological membranes: read about the cell membrane.

All living things are made of one or more cells.

The cell is the basic building block of all organisms.

o Some organisms are single cells = unicellular. Examples include bacteria,

yeasts, and protozoa such as amoebas.
 Bacteria Yeast Amoeba

o Some organisms are consist of many cells = multicellular. Examples include

plants, animals, and some fungi such as mushrooms and molds.

Cells are small.

o The size of a typical bacterium is about 1 - 4 micrometers (one millionth of a

meter) in diameter. This means that a million bacterial cells take up about as
much space as a large grain of sand.

o The cells of multicellular organisms, such as people, are larger than bacterial
cells, but are also very small - 10 micrometers in diameter or larger.

How many bacteria can fit on the head of a pin? Each of the tiny yellow spots is one
bacterial cell. The larger yellow regions are clumps of many bacteria.

Large organisms contain more cells.

o As a general rule, larger organisms are larger because they have more cells,
NOT because their cells are larger.

o A typical adult human consists of approximately 10 trillion

(10,000,000,000,000) human cells. A mouse consists of a mere 3 billion
(3,000,000,000) cells. Many insects have a mere million (1,000,000) cells.
 Cells have the ability to reproduce (produce more cells), grow, digest food, produce
and use energy, and manufacture biological molecules.

All cells contain a cell membrane, one or more chromosomes,

ribosomes, and cytoplasm.
The Cell Membrane forms a boundary between the interior of the cell and the
external environment (however, there ARE cell components beyond the cell
membrane, and some important cellular processes occur OUTSIDE of the cell
membrane).

Like all biological membranes, the cell membrane consists of a

fluid phospholipid bilayercontaining proteins and other molecules.
 Biological membranes are selectively permeable, which means that although
some molecules can diffuse across the membrane, many molecules cannot. This
means that the cell membrane can form a barrier - keeping some molecules,
such as poisons, OUTSIDE the cell, and keeping other molecules, such as
nutrients, INSIDE the cell.

The cell membrane (like other biological membranes)

contains transport proteins that help move molecules INTO the cell or OUT of
the cell. This means that the cell membrane helps regulate the contents of the
cell. For example, some transport proteins move IN food molecules such as
sugars or amino acids. Other transport proteins move OUT waste products.

Two representations of a transportprotein in a

cell membrane. The transport protein,
embedded in the cell membrane, allows a
specific molecule to enter or exit the cell -
perhaps an ion like sodium, perhaps a sugar
like glucose.
 Cytoplasm is the water-based
material found within the cell
membrane - the inside of the
cell. All of the sugars, enzymes,
proteins, amino acids, salts and
other molecules are either
contained in the cytoplasm, or
else are contained in other
structures found within the
cytoplasm. The cytoplasm,
although mostly (75 - 80%)
water, is so densely packed with
these other molecules and
structures that it has the
consistency of a gel.

In this artistic rendition of the

cross-section of a bacterial cell,
the bacterial chromosome is
shown at lower left (long red line
wrapped around blue disks).
Ribosomes, proteins, and other
molecules are shown in the
middle. Outer layers of the cell
(this bacterial cell has a cell
membrane, a cell wall, and an
outer membrane) are shown at
the top of the figure.

Key to Figure
External environment - outside of cell

Cell Membrane and external structures.

Cytoplasmic matrix: Upper part of diagram contains ribosomes (large pink

blobs). Lower part of diagram contains chromosome (long pink lines, wrapped
around blue discs).
 Chromosome or Chromosomes are the structures in cells where genetic information
is stored. The chromosomes consist of DNA (which contains the genetic information)
and protein (which protects the DNA).

Photo of Human X and Y chromosomes as

they appear microscopically (the chromosomes
are in condensed form like this for mitosis and
meiosis - cell division). Each chromosome is a
long double-stranded DNA molecule. To see
how the double-stranded DNA gets bundled
and packaged to make the condensed
chromosome form shown, click here.

Electron Micrograph of a bacterial cell that has

been lysed. The yellow rod is E. coli, and the
stringy material surrounding it is its
chromosome. In bacteria, there is only one
chromosome, and it is circular, rather than
linear.

o In prokaryotic organisms (bacteria) there is normally ONE chromosome. It is

a single DNA molecule arranged in a circle (no ends). This single DNA
molecule can contain ALL of the genetic information the cell needs. In bacteria,
the chromosome is found in a region of the cytoplasm called the nuclear region,
but the chromosome is NOT contained within a nucleus.

o In Eukaryotic chromosomes, there are normally two or more kinds of

chromosomes. Each chromosome contains SOME genetic information -
different genes on the different chromosomes. In at least one stage of the life
cycle of eukaryotic organisms, the cells have two copies of each kind of
chromosome. To have two copies of each kind of chromosome is to be diploid.
 For example, humans are diploid throughout our life cycle (except as
egg and sperm cells). Humans have 23 different sets of chromosomes,
and since we are diploid, our total number of chromosomes is 46. Each
cell has 46 chromosomes = two sets of 23. To see a complete set of
human chromosomes, click here.

In Eukaryotic cells, the chromosomes are found in a special structure called

the nucleus.

o Chromosomes store genetic information in genes. Genes contain the

information required for the cell to make either proteins or to
make RNA molecules such as tRNA or rRNA.

Ribosomes are the structures in cells where protein synthesis occurs.

Protein Synthesis: This illustration of a ribosome in Structural model of ribosomal

action shows the messenger RNA (mRNA; long strand subunit. Separate protein and RNA
with short side-chains) and growing chain of amino components are visible when a full
acids (circular blobs). The large irregular structure in size image is viewed.
the center is the ribosome. It actually consists of two
subunits, and each subunit is assembled from a
number of different proteins plus one or
more ribosomal RNA (rRNA) molecules.

o Ribosomes are large complexes of several different RNA molecules plus many
different proteins.
 o Each ribosome consists of two subunits that join together
to form the complete ribosome only when a particular
protein is being made. After the protein is completed, the
two subunits of the ribosome separate again.

o In prokaryotic cells, ribosomes are found in the

cytoplasm. In eukaryoticcells, some ribosomes are found in the cytoplasm, and
others are found attached to the endoplasmic reticulum (specifically, at
the rough ER).

o A single cell may have thousands of ribosomes.

o Prokaryotic ribosomes are smaller and less complex than eukaryotic ribosomes.

The Cell Wall is a structure found outside the cell membrane.

The cell wall is located beyond (outside) the cell membrane. In this In this electron micrograph of pine wood,
diagram, the cell membrane is shown at the bottom the network of cell walls is visible. The cells
(the phospholipid bilayer). The white space below the cell membrane were found within the open regions.
is cytoplasm. Above the cell membrane is the cell wall, and above
the cell wall is the external environment. This is an illustration of a
bacterial cell wall.

o Many kinds of cells in ALL of the taxonomic groups (most prokaryotic cells,
including both Eubacteria and Archaebacteria, as well as some groups
of Eukaryotes - the plants and fungi - produce cell wall.

o NOT ALL organisms have cell walls. Members of the Animal and Protozoan
kingdoms lack cell walls. Some bacteria also lack cell walls.

o Different organisms use different molecules to make the cell wall. For example,
in plants and some fungi, the cell wall consists mainly of cellulose,
a polysaccharide made of glucose. In bacteria (Eubacteria), the cell wall
consists of a substance called peptidoglycan, which contains both amino acids
and sugars.

o The cell wall helps provide shape and structure to the cell, and also protects the
cell from bursting due to osmosis - movement of water by diffusion.

If a cell is in pure water or water that has few other kinds of molecule in
it, then water will diffuse INTO the cell. As water accumulates in the
cell, it will expand. Eventually, the cell will burst if a cell wall is not
present to restrict the expansion.

To view animations of the effects of osmosis on cells, click here.

Or click here for a more technical discussion, with more animations.