Structural Biochemistry/Cell Organelles

Pictorial representation of organelles in a typical animal cell

Cell

Structural biochemistry plays a vital role in the functions of an organism's cell through
various means, one of them being the organelles in a cell. It is through the structure and
functions of living molecules (and some non-living), such as nucleic acids, amino
acids, purine, and lipids that life is even possible.
Some properties of living organisms include high degree of chemical complexity and
microscopic organization, systems to extract, transform and use energy from the
environment, self-replication and self-assembly, sensing and responding to changes in
the environment, define functions for each component and regulation among them, and
history of evolutionary change.
Organelles are the components of the cell that synthesize new materials, recycle old
materials, transport molecules, and anything else that is essential to ensure the proper
survival of the cell and its propagation. Organelles incorporate all broad ranges of
organic molecules including nucleic acids, amino acids, carbohydrates, and lipids to
produce a viable cell.
As discussed before, the "lipid bilayer" that forms the cell membrane contains
membrane protein and cholesterol. The membrane protein plays a vital role in the
membrane functions while the cholesterol performs the structural role within the
membrane.
There are two types of protein membranes:

• Integral membrane protein: lies within the membrane

• Peripheral membrane protein: bound to membrane
The cell membrane is often referred to as a mosaic. Proteins in the membrane
determine most of the membranes specific function. These proteins are categorized as
integral and peripheral proteins. Integral proteins can perform a number of functions
such as being transport proteins that provide a hydrophilic channel across the
membrane. Integral proteins can also act a receptor sites for chemical messengers like
hormones. Enzymes can also be found in the lipid bilayer with its active site exposed to
substances in adjacent solutions. Elements of the cytoskeleton may also be bonded to
the membrane proteins; a function that helps maintain cell structure. The structure of
these membrane protein can also be either alpha helices or beta sheets. Due to
the hydrophobic interactions, the hydrophobic residues of the alpha helices will not
exposed to the aqueous environment. The beta sheet forms a hollow cylindrical
configuration where the inside is hydrophilic. The cylindrical structure is driven by the
unsatisfied hydrogen bonding at the ends of the beta sheet. Wrapping around itself, the
beta sheet is able to satisfy all hydrogen bonding.

The major functions performed by proteins of the plasma membrane are:

1. Transport: Some membrane proteins provide selective hydrophilic channels for

exchange of substances.
2. Enzymatic activity: Membrane proteins may also be enzymes with their active
sites exposed to the surrounding solutions.
3. Signal transduction: Membrane proteins may act as receptors with specific
binding sites that allows perfect fit with chemical messengers, which can cause
the protein to change shape and allow it to relay the message to the inside of the
cell.
4. Cell-cell recognition: Some glycoproteins allow specific identification by
membrane protein of other cells.
5. Intercellular joining: Membrane proteins of adjacent cells may join together in
different junctions.
6. Attachment to the cytoskeleton and extracellular matrix (ECM): Membrane
proteins can be non-covalently bound with elements of the cytoskeleton in order
to maintain cell shape and stabilize the location of certain membrane proteins.

Cholesterol regulates the fluidity of the membrane in eukaryotic cells. The ability to
incorporate cholesterol into the cell membrane with hydrophobic and hydrophilic
interactions allows the cholesterol to disrupt the phospholipid interaction within the bi-
layer. Since prokaryotic cells do not have cholesterol to regulate fluidity, these cells
depend on the variation in the saturation level and length of the fatty acid chain. The
shorter and more saturated the chain the more rigid the membrane will become (due to
the fact that the longer and saturated chains can interact more closely with one another)
Fluid Mosaic Model
This model claims that the lipid layer has an important role in cell membrane. The cell
membrane serves as the solvent for the integral membrane proteins, and it also serves
as a barrier that separates the cellular activities within the cell from the extracellular
space. The permeable barrier regulates what enters the cell. This Fluid Mosaic Model is
regulated by the concentration of cholesterol and fatty acid chain mentioned above.
The Properties of Membrane

• Sheet-like structure
• Formed by lipid bilayers and proteins
• The different ratio of lipids to proteins will correspond to the different cell types and
organelles which gives it the amphiphatic properties
• Non-covalent assemblies include van deer Waals, hydrogen bonding, and
hydrophobic interactions
• Asymmetric
• The orientation of the proteins are fixed and will not interchange between the inner
or outer layers
• Fluid Structures
• Electrically polarized because of the charged head groups

Major Organelles
1. Ribosome
Ribosomes are the sites by which nucleic acids are translated and proteins are
synthesized. Ribosomes are about 20 nm in diameter and are composed of ribosomal
RNA and proteins. They can be found freely floating in the cytosol and not attached to
any organelles in prokaryote cells. In eukaryote, ribosomes may be found on the rough
endoplasmic reticulum. The rough ER earns its name because of ribosomes on its
surface, giving a studding appearance. The proteins produced by the ribosomes of the
rough ER are sent through the lumen of the ER, where they are modified. The protein is
then transported in a vesicle to the Golgi Apparatus, where the protein undergoes
further modification.
First, the genetic code from DNA is transcribed into a complementary strand called
messenger RNA (mRNA) (mRNA) by DNA polymerase. In prokaryotes, the mRNA
moves away from the nucleoid and is bounded to free-floating ribosomes in the cytosol.
However, in eukaryotes, mRNA is made in the nucleus and transported across the
nuclear membrane and into the cytoplasm. This is called translocation. In the next step,
known as translation, the mRNA is attached to the ribosome, and codons on the mRNA
are matched with the complementary nucleotide bases (anticodons) located on a
transfer RNA (tRNA) molecule. The enzyme aminoacyl tRNA synthetase matches the
tRNA codons with the appropriate amino acids through a series of esterification
reactions. Ribosomal RNA synthesizes the protein through use of RNA polymerase.
This elongates the protein until a stop codon terminates the protein synthesis chain. The
synthesis of proteins always moves in the direction of the N-terminus to the C-terminus.
DNA replication is also go from the 5' to 3' direction.
2. Cell Membrane
The cell membrane, as explained above, is a selectively permeable barrier of ions and
molecules that move into and out of the cell. In other words, not all molecules are able
to pass through the cell membrane. During the division of the cell, none of the
membrane integrity is lost. As the cell grows, new lipid and protein molecules are placed
into the cell’s plasma membrane.

Prokaryotes Organelles
Prokaryotes typically have no compartmentalized organelles. The cell's DNA and
ribosomes are free-floating with the cytosol, which is surrounded by a cell membrane. A
prokaryotic cell is generally one hundred times smaller than a eukaryotic cell.
1. Nucleoid
In the nucleoid, the chromosomal DNA is wrapped around binding proteins. "Replication
by DNA polymerase and transcription by RNA polymerase occur at the same time within
the nucleoid."
2. Pili
Pili (Fimbriae)is a thin structure that stick out from the surface. They are made out of a
single protein called pilin. Pili's functions include DNA transfer, binding to surfaces, and
motility. Pili has the ability to attach to a substrate. One type of pili called sex pili, it
attaches a "male" donor cell to a "female" recipient cell for transfer of DNA. This process
is called conjugation.

Eukaryotes Organelles
Eukaryotes include animals, plants, fungi, and protists. They are typically more complex
than prokaryotic cells. There are many compartmentalized organelles enclosed in
membranes within the cell which allow for various reactions to take place. The
eukaryotic cell is typically much larger than the prokaryotic cell, usually by a factor of
around 100. Each organelle in Eukaryotes has their own function in the cell.
1. Nucleus
The nucleus is one of the primary organelles that distinguish eukaryotic cells from
prokaryotic cells. It is an organelle that enclosed compartment with a specific function. It
contains chromatin. Nuclei contains nucleolus (where ribosome assembly is).
Ribosomal RNA get together with ribosomal proteins to form the ribosomal subunits.
The nucleus contains DNA that house the genes coding for the synthesis of proteins,
antibodies and molecules that perform the basic functions of the cell. The nuclear
membrane contains nuclear pore conplexes that allow for transport of material into and
out of membrane. They also export mRNAs out of the nucleus. [2]
2. Endoplasmic Reticulum
There are two types of endoplasmic reticulum: smooth ER and rough ER. The smooth
ER is the site of lipid synthesis and some detoxification of noxious compounds. The
rough ER is the site where transmembrane proteins or secreted proteins are
translocated. Ribosomes are located in the rough ER instead of smooth ER because
the protein has a hydrophobic signal sequence on its amino terminus. Endoplasmic
Reticulum is where proteins can be modified too.
3. Mitochondrion
Mitochondria (Singular: Mitochondrion) involved in cellular energy production. It has a
function in performing oxidative respiration and are found in nearly all eukaryotes.
Mitochondria also produces ATP by oxidative respiration. It also has an outer and an
inner membrane. Both DNA and ribosomes of mitochondria show similarities with DNA
and ribosomes of bacteria.
4. Golgi Apparatus
Proteins that are not part of ER now move to the Golgi. Golgi complex has membrane
stacks (cisternae) that each contain unique enzymes. Carbohydrates may be modified
as proteins pass through the cisternae. Vesicles leaving the Golgi complex may fuse
with the cell membrane.
5. Centriole
Centrioles are involved in a process called nuclear division. They are small, self-
replicating, and are located in the cytoplasm near the nucleus. organelles present near
nucleus of animal cells.
6. Cell Wall
The cell wall, located outside the cell membrane, is a tough layer that provides the rest
of the cell with structure support and protection. Cell walls are present in plants, fungi,
algae, some archaea, and bacteria cells, but not in animal cells. The cell wall confers
the shape and rigidity to bacterial cell and helps it withstand the intracellular turgor
pressure that can build up as a result of osmotic pressure.
7. Chloroplasts
Chloroplasts are only found in photosynthetic eukaryotes. They convert Sun-derived
light energy to ATP and reduced NADPH. Ancient cyanobacteria gave rise to
chloroplasts. In other words, cyanobacteria are the ancestor of chloroplasts.
Chloroplasts have an outer membrane, an inner membrane, and the thylakoid
membrane. Some algal chloroplasts have more membranes outside these. Chloroplasts
are typically found within the mesophyll cells, or the inner tissues of a leaf. Chloroplasts
are discs that are typically somewhere between 2-7 micrometers in diameter and 1
micrometer thick. Chlorophylls a and b, which are the green pigments located within
plant chloroplasts, give plants their typical green color. During photosynthesis, carbon
dioxide enters the leaf through microscopic pores known as the stomata, and oxygen
leaves as a byproduct through the stomata. The dense fluid found within the chloroplast
is known as the stroma, and amongst this are several interconnected membranous sacs
shaped in flat discs with their own compartments, known as the thylakoids. In plants,
thylakoids are arranged in a stacked conformation known as grana. Most other
photosynthetic organisms and some plant chloroplasts have unstacked thylakoids. The
space within these compartments are called the thylakoid space. The membranes of the
thylakoids hold the cell's chlorophyll.
8. Vacuole
Vacuoles serve as the cell's storage centers of food and other necessary materials. The
vacuole further functions in the removal of unwanted structural materials, the containing
of several waste products and small molecules (which could involve the isolation of
potentially harmful products in the cell), the exportation of unwanted materials from the
cell, and the maintenance of an acidic internal pH and constant internal pressure. In
plants, the central vacuole is typically the largest compartment of all the cell's
organelles, occupying in itself the majority of the cell volume. This large compartment is
enclosed by a membrane called the tonoplast, which is selectively permeable to certain
solutes within the cytosol. The solution inside the vacuole is referred to as cell sap,
which is of different composition from the cytosol. Some plant vacuoles contain
pigments that color the cells, such as during pollination season by which the plant must
attract different organisms to carry out its fertilization. Plants maintain its structure
through the maintenance of internal pressure through the manipulation of water into and
out of the vacuole. Through water osmosis, water diffuses into the vacuole, which
places pressure onto the cell wall. If too much water were to be lost, this pressure
against the cell wall would be lacking, and the cell would collapse onto itself. Thus, cells
also serve to maintain the cell's size. Another important feature of the vacuole in plants
is that an enlarged central vacuole may add a specific amount of pressure against the
other compartments in the cell and push them towards the cell membrane, thereby
giving a type of conformation that permits the absorbance of more solar energy.
9. Lysosome
Lysosomes are membrane enclosed organelles that help eukaryotic cells obtain
nourishment from macromolecular nutrients. They contain hydrolytic enzymes.
Lysosomal and phagocytosis digestion help the eukaryotic cell because they increase
the membrane surface area. In eukaryotes, lysosomes allow intracellular digestion
crosses the lysosomal membrane into cytoplasm. Lysosomes are the 'garbage bin' of
the cell.
10. Peroxisome
Peroxisomes are the centers by which the cell may be rid of potential toxins. The
peroxisomes are in itself a receptacle of oxidative enzymes that remove hydrogen
atoms from certain organic substances to produce peroxides, which in itself is harmful.
This peroxide serves to oxidate the potentially harmful substances, such as alcohol.

Cell Compartment
1. Evolution[
During evolution, cells start to develop into two compartments: the outer and inner
aqueous compartment. The advantage of having an inner aqueous compartment allows
the better segregation of cellular organelles from the external environment. Thus, each
organelle is able to develop and refine its structural and functional distinction inside this
aqueous compartment throughout the course of evolution. The "lipid bilayer" (further
discussed) existed as a protective wall that allows hydrophilic interaction in the external
and internal compartment of the cells while maintain proficient rigidity with its
hydrophobic interior structure. The inner aqueous compartment ultimately becomes the
cytoplasm which serves the same purpose as it has been during evolution.
2. Liposomes
Liposomes are essentially lipid vesicles that are surrounded by a circular
phospholipid bilayer. They form identical structure as other phospholipids vesicles:
interior hydrophobic tails away from the aqueous solution, and external hydrophilic
heads towards the aqueous solution. Liposomes are formed through the process called
sonification that results in ions and solutes inside the enclosed compartments. They can
be used to study the permeability of certain membranes and transportation of ions or
solutes found in different cells.
3. Lipid Bilayer
Lipid bilayers form in a spontaneous and self-assembled manner in aqueous
environment. Its unique properties allow the formation of enclosed compartments. The
sheet-like bimolecular structure called lipid bilayers or energetically favored because of
the hydrophobic interactions. As mentioned previously, phospholipids, an amphiphlic
moiety as a major class of membrane lipids, exist in an aqueous solution. The
hydrophobic tails from two phospholipid bilayers interact with each other to form a
hydrophobic center. Meanwhile, the hydrophilic heads line up with each other, form a
hydrophilic coating on each side of the bilayer, and isolate the inner compartment from
the outer environment.
Membrane Movement
A. Lateral Diffusion
The lateral diffusion, or the motion of moving laterally, of the biological membranes
illustrates the fact that the membranes are not rigid and static. In fact, the membrane is
not stable. There is a technique known as Fluorescence Recovery After
Photobleaching (FRAP)assists to visualize the lateral diffusion of membrane proteins.
An example of the experiment is as follow: 1) Label a specific cell component with
fluorescence. 2) Use a intense beam of laser light to bleach, or destroy, the small part of
the florescence labeled cell surface. 3) The intensity of bleaching recovers as the lateral
diffusion of unbleached membrane proteins move into the region that has been
bleached.
B. Transverse Diffusion
Transverse Diffusion describes the movement of molecules from one side the
membrane to the opposite side. In comparison to the rapid movement of lateral
diffusion, the speed of transverse diffusion is rather slow. The reason for the
preservation of membrane structural asymmetry is due to the greater energy barriers
formed in order to travel across membrane from one side to the other.
The Cycling Process of Cells
Endocytosis
Endocytosis is the creation of internal membranes from the cell's plasma membrane
lipid bilayer. It is a way for plasma membrane lipids and integral proteins to be brought
inside the cell. It is thus the opposite of exocytosis. This allows cells to do things like
regulate the sensitivity of cells to ligands since receptors can be removed from the cell
surface by endocytosis. Plasma membrane buds, called caveolae, are on little creices
on the surface of many mammalian cells. These can make up almost a third of a cells
surface area. Given their structure, they are often involved in endocytic events. Another
way of internalizing in cells is called phagocytosis. In this method, material can be take
in when 'invaginations' are formed around particles to be engulfed while using or not
using the growth of surrounding membrane extensions.