Nucleic Acids / DNA / RNA

At the core of each cell are molecules that store the blueprint of life,
deoxyribonucleic acid (DNA). DNA is composed of four types of
molecules known as nucleic acids or nucleotides. The four
nucleotides are: adenine (A), guanine (G), cytosine (C), and thymine
(T). These molecules are further classified into two families. Adenine
(A) and guanine (G) are known as purine and cytosine (C) and
thymine (T) are known as pyrimidine. During DNA synthesis,
nucleotides are converted into nucleic acids to so that they can be
linked to form strands of DNA. The assembled strand of DNA takes
on the structure of a double helix.

The chemical structures of the four nucleotides are planar due to the
delocalized electrons in the five- and six-membered rings, each
having a thickness of 3.4 angstroms. When the nucleotides form the  
double helix structure, A-T and G-C are joined together by a The two strands of DNA are held
hydrogen bond to form a base pair. The base pairs are then joined together by hydrogen bonds between
together by sugar bonds to form the helix. X-ray data shows that adjacent complementary nucleotides.
there are 10 base pairs per turn of the helix.

The helical model of DNA also explains the theory of genetic

replication. James Watson once described it as the "pretty molecule"
because the method of replication is so self evident in this structure.
During replication, the hydrogen bonds between nucleotides break
and allow each single strand of DNA to serve as a template for
replication of the other half. The two identical copies of newly
synthesized of DNA are then distributed to two new daughter cells.
Because during each cycle of replication half of the old DNA is
preserved, DNA replication is said to be semi-conservative.

Although DNA contains the genetic blueprint of life, it requires the

assistance of ribonucleic acid (RNA) to be functional. RNA also
consists of strands of nucleic acids joined together by sugar-
phosphate bonds. Unlike DNA, RNA substitutes the nucleotide
thymine (T) with uracil (U) and exists as single strands. After DNA
is converted into strands of RNA, the messenger RNA (mRNA) is
sent to the ribosome to direct the synthesis of proteins.

Amino Acids

Amino acids are the subunits of proteins. Each protein is formed by a chain of amino acids linked together
through peptide bonds. The chain of amino acids takes on different shapes to form different proteins. The
various shapes allow proteins to take on different characteristics in cells. Each amino acid is composed of a
constant (always remain the same) group and a variable amine group as shown below:
There are 20 common amino acids that are responsible for forming proteins. They can be classified into 4
main families based on their chemical characteristics: acidic, basic, uncharged polar, and nonpolar.

Picture showing the 3 different amino acids exhibiting different properties.

How Proteins are Made From DNA

Now that you know what amino acids and proteins are, you might ask what the relationship is between DNA
and amino acids and proteins. While they seem to be unrelated entities, DNA actually plays a crucial role in
protein production. When a cell wants to manufacture a certain protein, it has to go find the recipe for that
protein. The recipe is stored in the form of DNA. Combinations of three nucleotides correspond to different
amino acids. For example, CCT codes for proline and CGT codes for arginine. This way, during protein
synthesis, DNA turns into the instruction for making a protein. For the details of protein synthesis, please
visit Protein Synthesis page.

Amino Acid Codon Table. This is commonly used to identify the DNA sequence for each amino acid.
Proteins

Proteins consist of strands of amino acids folded into a specific shape. The different protein structures can be
classified by four levels of folding, each successive one being constructed from the preceding one.

Primary Structure - The very basic strand of amino acids is the

called the primary structure.

Secondary Structure - The hydrogen-bond interaction among

strands of amino acids gives rise to the first level of folding, alpha-
helices and beta-sheets.

Tertiary - Interaction between alpha-helices and beta-sheets

comprise the second level of folding, protein domains. These protein
domains are then strung together through third level folding to form
small globular proteins. The combination of second and third level
folding yields tertiary structure.

Quaternary Structure - In order to achieve enhanced function,

small globular proteins often come together to form protein
aggregates. This fourth level of protein structure is called the
quaternary structure. A famous example of quaternary structure is
hemoglobin.
Lipids

Lipids serve a diverse array of functions inside the cell, ranging from
being energy sources to constructing the cell membrane. Lipids are
made of fatty acid molecules (e.g. palmitic acid, shown below) that
consist two distinct regions: a long hydrophobic hydrocarbon chain
and a hydrophilic carboxylic acid group.

Fatty acids are a valuable food source. Each molecule of fatty acid
can be converted into twice the number of ATP molecules as
glucose.

The most important function of fatty acid is its ability to combine to

form uniform bilayers of lipid (to prevent the hydrophobic region
from being exposed). These lipid bilayers are used to form the
impermeable cell membrane and helped to define the first cell (see
From Molecules to the First Cell). The hydrophobic property of lipid
membrane also allows the cell to facilitate transport of molecules.

Sugars

Sugars provide the energy resource for cells. The simplest form of sugar, glucose, features a 6-carbon ring
and has the chemical composition of C6H12O2 (shown below).

Glucose is the principal food source for cells. Even larger sugars, called polysaccharides, are digested into
glucose before being converted into ATP. The chemical reaction for converting glucose into energy is as
follows:

C6H12O2 + 6O2 -> 6CO2 + 6H2O + energy (in the form of ATP and NAHD)

Sugar is also used as a form of energy storage in cells. In animal cells, polysaccharides (long repeating
structure containing glucose) in the form of glycogen are used to store energy. Plant cells use starch to store
energy.
Properties of Water

Life would not have existed on earth without water. Water molecules are composed of one oxygen atom and
two hydrogen atoms. Together, the hydrogen and oxygen molecules form a shape that resembles the head of
Mickey Mouse. 

While water molecules seem to be simple compounds, their properties have profound impact on life.
Because of the arrangement of hydrogen and oxygen atoms, water molecules have polarized charges (one
end is positive and the other end is negative). Due to their polarized nature, 2 adjacent water molecules can
form a linkage via a hydrogen bond.

The polarized nature of water causes other molecules to be either hydrophilic (like water) or hydrophobic
(afraid of water). This property allows certain molecules to dissolve in water while preventing others from
entering the cell. For example, hydrophobic interaction can hold molecules together.

Osmosis

Another important property of water is its ability to facilitate the transfer of molecules through osmosis.
When 2 aqueous solutions are separated by a membrane that only allows the passage of water molecules,
water will move from the less concentrated to the more concentrated side (Shown in the diagram below).

Hydrophobic interactions can hold molecules together: 2 or more hydrophobic groups surrounded by water
will tend to coalesce since they thereby cause less disruption to the hydrogen-bonded structure of water
(Shown in the diagram below. Red hexagons represent hydrophobic material and blue dots represent water
molecules.).
Cell Membrane

While the plant cell has a rigid cell wall, an animal cell membrane is a flexible lipid bilayer. The lipid
molecules (mostly phospholipids) that make up the membrane have a polar, hydrophilic head and two
hydrophobic hydrocarbon tails. When the lipids are immersed in an aqueous solution the lipids
spontaneously bury the tails together and leave the hydrophilic heads exposed. Thus this is a handy
membrane to use, because it can automatically fix itself when torn. There are three different major classes of
lipid molecules - phospholipids, cholesterol, and glycolipids. Different membranes have different ratios of
the three lipids. 

What makes the membrane truly special is the presence of different proteins on the surface that are used for
various functions such as cell surface receptors, enzymes, surface antigens, and transporters. Many of the
membrane-associated proteins have hydrophilic and hydrophobic regions. The hydrophilic regions are used
to help anchor the protein inside of the cell membrane. Some proteins extend across the lipid bilayer, others
cross the bilayer several times

Diagram of the cell membrane. The proteins are embedded inside of the cell membrane. The lipid
content of the membrane allows the cell membrane to automatically repair itself when it is torn.

Membrane Transport of Small Molecules

Because of the hydrophobic interior of the lipid bilayer, polar molecules cannot enter the cell. However,
cells devised means of transferring small polar molecules. Transport proteins, each specialized for a certain
molecule, can transport polar molecules across the membrane. There are several types of membrane
transport proteins. Uniports simply move solutes from one side to another. Cotransport systems work by
simultaneously sending two solutes across the lipid bilayer. There are two types of cotransport systems -
symport, in which the solutes are sent in the same direction, or antiport, in which they are sent in opposite
directions. These transport proteins work passively, meaning that the cell doesn't have to expend energy
sending the solute in or out. This is dependent on the solute moving in its natural direction - i.e. moving
from more concentrated solution to less concentrated, or from positive to negative. 

Some specific examples of transport membranes are channel proteins, which allow solutes to cross if they
are the correct size and charge. Carrier proteins bind to the solute and lead it through the bilayer. These are
examples of passive transport. To move a solute against their natural direction - for example higher
concentration to lower concentration, energy (ATP) is needed to pump the solute in or out. 

An example of active transport is the sodium-potassium pump, which in conjunction with the potassium leak
channel, allows the cell the control it's membrane potential. The sodium-potassium-ATPase, which uses the
energy of ATP hydrolysis, pump pumps sodium out and potassium in, which creates a high concentration of
potassium inside the cell, and a low concentration outside. The reverse applies to the sodium. The potassium
leak channel allows the potassium to leak out (so to even out the concentrations), which gives the cell and
negative charge on the inside.

Diagram comparing uniport, symport, and antiport.

Membrane Transport of Macromolecules

Most cells use exocytosis and endocytosis to secrete and ingest macromolecules, respectively. In exocytosis
the contents of special vesicles are released when the vesicle fuses with the cell membrane. In endocytosis
the membrane depresses and pinches off, enclosing the molecule. Two different sizes are formed -
pinocytotic (small) and phagocytic (large).

In receptor-mediated endocytosis, coated pits and vesicles bind to specific receptors on the cell surface,
allowing the cell to select what molecules to take and what to reject.

Membrane Receptors

The cell membrane is pocketed with receptors and antigens. Molecules targeted toward that specific cell will
bind with the cell surface receptor, which binds the signaling molecule and sends a signal that alters the
behavior of the target cell. Antigens are used to tell the cell whether foreign materials are present. If any
foreign materials are detected the immune system will mobilize its killer T-cells to destroy the foreign cell.
Cell Wall

The plant cell wall is a remarkable structure. It provides the most

significant difference between plant cells and other eukaryotic
cells. The cell wall is rigid (up to many micrometers in thickness)
and gives plant cells a very defined shape. While most cells have
a outer membrane, none is comparable in strength to the plant
cell wall. The cell wall is the reason for the difference between
plant and animal cell functions. Because the plant has evolved
this rigid structure, they have lost the opportunity to develop
nervous systems, immune systems, and most importantly,
mobility. Diagram of a cell wall. The different layers of cell wall are shown.
The cell wall is composed of cellulose, polysaccharides, and
The cell wall is composed of cellulose fiber, polysaccharides, and proteins.
proteins. In new cells the cell wall is thin and not very rigid. This
allows the young cell to grow. This first cell wall of these  
growing cells is called the primary cell wall. When the cell is
fully grown, it may retain its primary wall, sometimes thickening
it, or it may deposit new layers of a different material, called the
secondary cell wall.

On the whole, each cell's cell wall interacts with its neighbors to
form a tightly bound plant structure. Despite the rigidity of the
cell wall, chemical signals and cellular excretions are allowed to
pass between cells.

 
Picture of Lily Parenchyma cell. The cell wall which provides a
rigid structure is in green.
Cell Structure

In eukaryotic cells, there are large numbers of organelles which perform specific tasks. Eukaryotic cells
contain a nucleus that is kept separate from the cytoplasm by a double membrane structure. The cytoplasm
contains the rest of the organelles such as the endoplasmic reticulum and the mitochondria, each necessary
for the cell's reproduction and survival.

The area of the cytoplasm outside of the individual organelles is called the cytosol. The cytosol is the largest
structure in the cell. It composes 54% of the cells total volume. The cytosol contains thousands of enzymes
that are responsible for the catalyzation of glycolysis and gluconeogenesis and for the biosynthesis of sugars,
fatty acids, and amino acids. The cytosol takes molecules and breaks them down, so that the individual
organelles can use them. For example, in order for respiration to occur, glucose is ingested and broken down
into pyruvate in the cytosol, for use in the mitochondria.

The cytosol also contains a skeletal structure, called the cytoskeleton. This structure gives the cell its shape
and allows it to organize many of the chemical reactions that occur in the cytoplasm. Additionally, the
cytoskeleton can aid in the movement of the cell.

MitochondrionThe mitochondrion consists of four major sections – the outer membrane, the
intermembrane space, the inner membrane, and the matrix.

 
Left: Diagram of a mitochondrion. Right: Electron Micrograph of a mitochondrion.

The Outer Membrane

This membrane contains a great number of large transport proteins, which allows for large molecules to
enter with ease. This membrane includes proteins that can convert lipid substrates into forms that can be
used by the matrix.

The Intermembrane Space

This space contains enzymes that use ATP to phosphorylate other nucleotides.

The Inner Membrane

This membrane is highly convoluted, forming many folds called cristae. This serves to greatly increase the
surface area, allowing more work to be done is a smaller space. It contains three major proteins - 1. the
proteins that carry out the oxidation reactions of the respiratory chain, 2. an enzyme complex called ATP
synthetase which makes ATP, and 3. transport proteins which regulate the transfer of molecules into and out
of the matrix. This is where the oxidation phosphorylation takes place.

The Matrix

The Kreb Cycle takes place here. It also contains several copies of the mitochondrial DNA genome, special
mitochondrial ribosomes, tRNAs, and various enzymes required for the expression of the mitochondrial
gene.
Chloroplast

The chloroplast, basically, is the organelle responsible for

photosynthesis. Structurally it is very similar to the
mitochondrion. It contains a permeable outer membrane, a less
permeable inner membrane, a intermembrane space, and an
inner section called the stroma. However, the chloroplast is
larger than the mitochondria. It needs to have the larger size
because its membrane is not folded into cristae. Also the inner
membrane is not used for the electron transport chain. Instead
it contains the light-absorbing system, the electron transport
chain, and ATP synthetase in a third membrane that forms a
series of flattened discs, called the thylakoids.

[Diagram of a plant chloroplast. Notice the bi-layer

 

Endoplasmic Reticulum

The endoplasmic reticulum (ER) is repsonible
most of the cell's organelles. The ER contains a
sheet enclosing a single closed sac. This internal
responsible for moving proteins and other
membrane, to the lysosomes, or wherever else
for the production of the protein and lipid components of
great amount of folds - but the membrane forms a single
space is called the ER lumen. The ER is additionally
carbohydrates to the Golgi apparatus, to the plasma
needed.

There are two types of ER - rough, which is coated with ribosomes, and smooth, which isn't. Rough
ER is the site of protein synthesis. The smooth ER is where the vesicles carrying newly synthesized
proteins (from the rough ER) are budded off.
Golgi Apparatus

The Golgi complex is composed of numerous sets of smooth cisternae, which are coated with lipid
membranes. Each disc-shaped cisternae forms a structure that resembles a stack of plates, called a Golgi
stack. The Golgi complex contains a great number of vesicles. These vesicles are used to send molecules to
the cellular membrane, where they are excreted. There are also larger secretory vesicles, which are used for
selective excretion.

The Golgi is principally responsible for directing molecular traffic in the cell - nearly all molecules pass
through the Golgi complex at some point in their existence. The sorting is mediated by the vesicles. When
proteins bind with their appropriate receptor on the vesicle, they are encoated in the vesicle and transported
away.

Lysosomes

The lysosome is a membranous bag which contains hydrolytic enzymes that are used to digest
macromolecules. The lysosome contains over 40 enzymes, some of which are the proteases, nucleases, and
phopholipases. These enzymes optimally work at a pH of 5 (acidic), so should these enzymes leak out they
would cause minimal damage to the cytoplasm. These enzymes, called hydrolases, are made in the ER and
transported to the lysosome by the Golgi complex, using a vesicle.

Should certain hydrolases be missing from the cells, serious illness can occur because of a buildup of
molecules which cannot be digested by the lysosome. These extra molecules can interfere with normal cell
functions, causing problems.

Cytoskeleton
Eukaryotic cells have a wide variety of distinct shapes and internal organizations. Cells are capable of
changing their shape, moving organelles, and in many cases, move from place to place. This requires a
network a protein filaments placed in the cytoplasm known as the cytoskeleton.

The two most important protein filaments are called the actin filaments and the microtubules. The actin is
responsbile for contraction (like in muscles) and the microtubules are for structural strength.

Ribosomes

The ribosome is plays a key role is the synthesis of protein. When the polypeptide chain is growing it must
be kept aligned with the mRNA molecule so that each codon still hooks up with the tRNA molecule. After
the addition of one amino acid the chain is moved down three codons. This is done using a large complex
composed of protein and RNA, called the ribosome.

Ribosomes consist of one large unit and one small unit. Half of the eukaryotic ribosomal weight comes
from RNA. The ribosome contains a groove that guides the polypeptide chain and another groove that
holds the mRNA molecule.

Vacuole

The vacuole is used only in plant cells. It is responsible for maintaining the shape and structure of the cell.
Plant cells don't increase in size by expanding the cytosplasm, rather they increase the size of their
vacuoles. The vacuole is a large vesicle which is also used to store nutrients, metabolites, and waste
products. The pressure applied by the vacuole, called turgor, is necessary to maintain the size of the cell.
If turgor is lost the cell becomes flaccid. The vacuole typically is 50% of the volume of the cell, yet it can
take up to 95% of the cell!

Nucleus

The nucleus is the cellular control center and exists only in eukaryotes. The nucleus contains the genetic
information for the cell, in the form of DNA and RNA. The genetic information is surrounded by a two-
layer nuclear envelope and it is generally found at the center of the cell. The nucleus is responsible for
communicating with other organelles in the cytoplasm (the gel-like space surrounding the nucleus).
Messages from inside the nucleus travel through pores on the nuclear envelope to enter the cytoplasm.

Inside the nucleus, called the nucleoplasm, DNA is bound by histone proteins and organized into chromatin.
During replication, the chromatins are condensed to form highly organized structures called chromosomes.
Besides the genetic information, most nuclei also contain one or more spherical-shaped organelles called the
nucleoli. The nucleolus is where ribosomes are assembled.

Nucleic Acids / DNA / RNA

At the core of each cell are molecules that store the blueprint of life,  
deoxyribonucleic acid (DNA). DNA is composed of four types of Historical Fact: The structure of DNA was
molecules known as nucleic acids or nucleotides. The four not resolved until the early 1950's when
nucleotides are: adenine (A), guanine (G), cytosine (C), and thymine James Watson and Francis Crick assembled
all of the previously known information about
(T). These molecules are further classified into two families. DNA to construct a model of DNA. Their
Adenine (A) and guanine (G) are known as purine and cytosine (C) result was published as a letter to the
and thymine (T) are known as pyrimidine. During DNA synthesis, prominent scientific journal Nature and was
nucleotides are converted into nucleic acids to so that they can be later recognized by the Nobel Foundation.
linked to form strands of DNA. The assembled strand of DNA takes
on the structure of a double helix.

The chemical structures of the four nucleotides are planar due to the
delocalized electrons in the five- and six-membered rings, each
having a thickness of 3.4 angstroms. When the nucleotides form the
double helix structure, A-T and G-C are joined together by a
hydrogen bond to form a base pair. The base pairs are then joined
together by sugar bonds to form the helix. X-ray data shows that
there are 10 base pairs per turn of the helix.

The helical model of DNA also explains the theory of genetic

replication. James Watson once described it as the "pretty molecule"
because the method of replication is so self evident in this structure.
During replication, the hydrogen bonds between nucleotides break
and allow each single strand of DNA to serve as a template for
replication of the other half. The two identical copies of newly  
synthesized of DNA are then distributed to two new daughter cells. The two strands of DNA are held
Because during each cycle of replication half of the old DNA is together by hydrogen bonds between
preserved, DNA replication is said to be semi-conservative. adjacent complementary nucleotides.

Although DNA contains the genetic blueprint of life, it requires the

assistance of ribonucleic acid (RNA) to be functional. RNA also
consists of strands of nucleic acids joined together by sugar-
phosphate bonds. Unlike DNA, RNA substitutes the nucleotide
thymine (T) with uracil (U) and exists as single strands. After DNA
is converted into strands of RNA, the messenger RNA (mRNA) is
sent to the ribosome to direct the synthesis of proteins.

Chromosome

A cell's genetic information, in the form of DNA, is stored in the nucleus. The space inside the nucleus is
limited and has to contain billions of nucleotides that compose the cell's DNA. Therefore, the DNA has to
be highly organized. There are several levels to the DNA packaging.

At the finest level, the nucleotides are organized in the form of linear strands of double helices. As you
zoom out, the DNA strand is wrapped around histones, a form of DNA binding proteins. Each unit of DNA
wrapped around a histone molecule is called a nucleosome. The nucleosomes are linked together by the
long strand of DNA.

To further condense the DNA material, nucleosomes are compacted together to form chromatin fibers. The
chromatin fibers then fold together into large looped domain. During the mitotic cycle, the looped domains
are organized into distinct structures called the chromosomes.
Chromosomes are also used as a way of referring to the genetic basis of an organism as either diploid or
haploid. Many eukaryotic cells have two sets of the chromosomes and are called diploid. Other cells that
only contain one set of the chromosomes are called haploid.

The chromosome also plays an important role in cell death-related aging phenomena. At the tips of
chromosomes are segments called telomeres. As a cell's DNA is damaged, the telomeres are shortened. Once
the telomeres have been reduced to a level, the cell decides that it can no longer repair itself and initiates
apoptosis, the cellular death process. Today, much research efforts have been devoted to elucidating the
specific mechanisms by which telomeres cause cell death.