CONCEPT OF CELL STRUCTURES AND FUNCTIONS assist in the creation of proteins when they come together with
messenger RNA.
The cell structure is defined by the cell membrane, the
cytoplasm, and the nucleus. A cell is the smallest unit of life and its
structure helps it to work as the basic building block of biology.
The cell function is to keep all of the functions of the
body performing as intended. This includes keeping toxins out of
the body, help to break down waste, make nutrients and act as
barriers within organelles.
Four Key Parts of a Cell: Cell Membrane, Cytoplasm, DNA and
Ribosomes
CELL MEMBRANE
Cells have a plasma membrane, cell membrane, or cell
wall that surrounds the cell and acts as their skin. It makes up the
boundary between the cell and their environment and controls
what can move in and out of the cell. The cell membrane is
constructed out of a phospholipid bilayer, two layers of lipids
facing opposite directions. The lipid layers are made out of
building blocks of fatty acids and consist of a head and body. The
body of the lipid is hydrophobic, meaning it repels water while the
heads of the lipids are hydrophilic meaning that it likes water.
In addition to the cell membrane found in animal cells,
plant cells also have a cell wall. The cell wall is made out of
cellulose and it helps give the cell extra protection and support. A
crucial difference is that unlike cell membranes cells walls do not
allow for the passage of materials through them. To get around
this problem cell walls have unique structures called
plasmodesmata, special holes that allow the material to move in
and out.
CYTOPLASM
The cell membrane holds in a cell’s cytoplasm. The
cytoplasm is a jelly-like substance, made up of mostly water, that
keeps the various organelles within the cell separate from each
other. Many of the cell’s biochemical reactions, like metabolic
processes, occur within the cytoplasm. There are gaps in a cell’s
plasma membrane referred to as pores or channels.
These pores or channels are made out of proteins and
they control what chemicals, like water and food, are able to
move into the cell.
DNA
Deoxyribonucleic Acid, or DNA, is frequently referred to
as “the blueprints for life” and it contains the generic information
that allows cells to reproduce and perform their respective
functions. The DNA of a cell is held within the nucleus of the cells,
specifically within the nucleolus.
The cell’s nucleus is often referred to as the “brain” of
the cell, or the control center. It is the largest part of the cell
within the cytoplasm. Cells that have nuclei are found in plants,
animals, algae, protozoa, and fungi. Bacterial cells do not have a
nucleus. The nucleus is home to a smaller structure within it called
the nucleolus. The nucleolus is an organelle which creates
ribosomes. The nucleus has nuclear pores that allow the
ribosomes to exit the nucleus and for other materials to move in.
RIBOSOMES
Ribosomes themselves are organelles which assist in the
creation of proteins. Proteins are necessary for the cell to carry
out their essential functions. Ribosomes are made out of one large
piece and one smaller unit. Both of the subunits in the ribosomes
OTHER IMPORTANT PARTS OF CELL:
ENDOPLASCMIC RETICULUM
The endoplasmic reticulum (ER) is made out of various
membranes, and it synthesizes proteins and for the cell. The
endoplasmic reticulum is referred to “rough ER” when it has the
ribosomes attached to it, and it is called “smooth ER” when there
are no ribosomes attached to it. The rough endoplasmic reticulum
synthesizes the proteins, while the smooth endoplasmic reticulum
performs two functions. The smooth ER synthesizes lipids for use
in the cell, but it also detoxifies harmful substances.
GOLGI COMPLEX
Golgi complex sorts the proteins out and then sends them to the
area that they are needed in. In this respect the Golgi complex is
like a post office, distributing packages to their destinations.
MITOCHONDRIA
Mitochondria are organelles which are responsible for converting
the food eaten by an organism into energy. Food is converted into
units of energy called ATP by the mitochondria and every cell has
differing amounts of mitochondria depending on the cell’s
function and needs. Cells that do more work, like heart cells, need
more mitochondria than other cells.
CHLOROPLASTS (IN PLANTS)
Chloroplasts in a plant cell are where photosynthesis happens,
converting the energy from the sun into chemical energy that the
plant cells can use. Plant cells also have a vacuole or seemingly
large empty space in the middle of the cell. However, the vacuole
of a plant cell actually contains important chemicals like sugar and
water.
VESICLES
Vesicles are responsible for carrying materials in, out, and around
the cell. The vesicles carry material from one part of the cell to
another, but they also transport waste products outside the cell in
a process called exocytosis.
PEROXISOMES
Peroxisomes are responsible for collecting toxic chemicals and
breaking them down into harmless byproducts, while centrioles
are unique to animal cells and they guide the division and
organization of chromosomes as cells divide.
LYSOSOMES
Lysosomes are structures secreted by the Golgi apparatus which
can take large molecules and break them apart into smaller
chunks the cell can utilize.
 PHOTOSYNTHESIS
Photosynthesis is the process by which plants, some
bacteria and some protistans use the energy from sunlight to
produce glucose from carbon dioxide and water. This glucose can
be converted into pyruvate which releases adenosine
triphosphate (ATP) by cellular respiration. Oxygen is also formed.
Photosynthesis may be summarised by the word equation:
carbon dioxide + water glucose + oxygen
Stages of photosynthesis
When chlorophyll a absorbs light energy, an electron gains energy
and is 'excited'. The excited electron is transferred to another
molecule (called a primary electron acceptor). The chlorophyll
molecule is oxidized (loss of electron) and has a positive charge.
Photoactivation of chlorophyll a result in the splitting of water
molecules and the transfer of energy to ATP and reduced
nicotinamide adenine dinucleotide phosphate (NADP).
The chemical reactions involved include:
 condensation reactions - responsible for water
molecules splitting out, including phosphorylation (the
addition of a phosphate group to an organic compound)
 oxidation/reduction (redox) reactions involving electron
transfer
Photosynthesis is a two stage process.
The Light dependent reactions, a light-dependent series of
reactions which occur in the grana, and require the direct energy
of light to make energy-carrier molecules that are used in the
second process:
 light energy is trapped by chlorophyll to make ATP
(photophosphorylation)
 at the same time water is split into oxygen, hydrogen
ions and free electrons:
2H2O     4H+ + O2 + 4e- (photolysis)
 the electrons then react with a carrier molecule
nicotinamide adenine dinucleotide phosphate (NADP),
changing it from its oxidised state (NADP+) to its reduced
state (NADPH):
NADP+ + 2e- + 2H+     NADPH + H+
The light-independent reactions, a light-independent series of
reactions which occur in the stroma of the chloroplasts, when the
products of the light reaction, ATP and NADPH, are used to make
carbohydrates from carbon dioxide (reduction); initially
glyceraldehyde 3-phosphate (a 3-carbon atom molecule) is
formed.
The light-dependent reactions
When light energy is absorbed by a chlorophyll molecule
its electrons gain energy and move to higher energy levels in the
molecule (photoexcitation). Sufficient energy ionises the
molecule, with the electron being 'freed' leaving a positively
charged chlorophyll ion. This is called photoionisation.
In whole chloroplasts each chlorophyll molecule is
associated with an electron acceptor and an electron donor. These
three molecules make up the core of a photosystem. Two
electrons from a photoionised chlorophyll molecule are
transferred to the electron acceptor. The positively charged
chlorophyll ion then takes a pair of electrons from a neighbouring
electron donor such as water.
An electron transfer system (a series of chemical reactions) carries
the two electrons to and from across the thylakoid membrane.
The energy to drive these processes comes from two
photosystems:
 Photosystem II (PSII) (P680)
 Photosystem I (PSI) (P700)
It may seem confusing, but PSII occurs before PSI. It is named
because it was the second to be discovered and hence named
second.
The light-independent reactions
In the Light-Independent Process (the Dark reaction)
carbon dioxide from the atmosphere (or water for aquatic/marine
organisms) is captured and modified by the addition of hydrogen
to form carbohydrates. The incorporation of carbon dioxide into
organic compounds is known as carbon fixation. The energy for
this comes from the first phase of the photosynthetic process.
Living systems cannot directly utilize light energy, but can, through
a complicated series of reactions, convert it into C-C bond energy
that can be released by glycolysis and other metabolic processes.
 Carbon dioxide combines with a five-carbon sugar,
ribulose 1,5-biphosphate (RuBP). A six-carbon sugar
forms but is unstable. Each molecule breaks down to
form two glycerate 3-phosphate (GP) molecules.
 These glycerate 3-phosphate (GP) molecules are
phosphorylated by ATP into glycerate diphosphate
molecules.
 These are reduced by NADPH to two molecules of
glyceraldehyde 3-phosphate (GALP).
 Of each pair of GALP molecules produced:
o one molecule is the initial end product of
photosynthesis; it is quickly converted to
glucose and other carbohydrates, lipids or
amino acids
o one molecule forms RuBP through a series of
chemical reactions
The first steps in the Calvin cycle
The first stable product of the Calvin Cycle is
phosphoglycerate (PGA), a 3-C chemical. The energy from ATP and
NADPH energy carriers generated by the photosystems is used to
phosphorylate the PGA. Eventually there are 12 molecules of
glyceraldehyde phosphate (also known as phosphoglyceraldehyde
or PGAL, a 3-C), two of which are removed from the cycle to make
a glucose. The remaining PGAL molecules are converted by ATP
energy to reform six RuBP molecules, and thus start the cycle
again.
CELLULAR RESPIRATION
Cellular respiration can be an anaerobic or aerobic
respiration, depending on whether or not oxygen is present.
Anaerobic respiration makes a total of 2 ATP. Aerobic respiration
is much more efficient and can produce up to 38 ATP with a single
molecule of glucose.
Anaerobic respiration consists of two steps.
               1. Glycolysis (2 ATP)
This is the process of taking one glucose (sugar)
molecule and breaking it down into pyruvate and energy (2 ATP).
We will discuss this in depth during aerobic respiration.
               2. Fermentation  ELECTRON TRANSPORT CHAIN
               Total = 2 ATP
Fermentation starts with pyruvate (the end product of
glycolysis). Depending on the organism, pyruvate can either be
fermented into ethanol (a fancy name for alcohol) or lactate (lactic
acid). Fermentation releases CO2, but does not make any ATP
Aerobic respiration consists of three steps.
               1. Glycolysis (2 ATP)
               2. Krebs Cycle (2 ATP) 
               3. Electron Transport Chain (34 ATP)
               Total = 38 ATP
GLYCOLYSIS
The first step in cellular respiration is glycolysis, or the
breakdown of glucose. The naming of this process is actually very
logical. Glycolysis literally means the breakdown of glucose. If we
know that ‘glycose’ is an older term for ‘glucose’ and if we
remember ‘lysis’ means to breakdown, then we can understand
that glycolysis = glycose + lysis, or the breakdown of glucose.
Glycolysis is the first step in cellular respiration for both
anaerobic and aerobic processes. Glycolysis takes place in the
cytosol of a cell. In the cytosol we convert 1 molecule of glucose
into 2 molecules of pyruvate. Of course glucose can’t be
converted into pyruvate without a little bit of help. This
conversion requires 2 NAD+ and some energy, in the form of 2
ATP. Once glycolysis is completed, we are left with 2 pyruvate, 2
NADH, and 4 ATPs as products. Since glycolysis yields 4 ATP, but
we had to use 2 ATP in the beginning of the process, the total Net
Gain of energy is 2 ATP. The cell will use the 2 ATP for energy.
NADH will be recycled back to NAD+ in a future process so that it
can be used in glycolysis again. The 2 pyruvate molecules will be
used for the second step of cellular respiration.
KREB CYCLE / CITRIC ACID CYCLE / TCA CYCLE
The Krebs cycle is the second step in aerobic respiration
and takes place in the matrix of the mitochondria (middle of the
mitochondria). This is a multi-step process, but don’t worry, we
don’t have to memorize all of the compounds or each enzyme
involved. Here, we will only focus on the key players.
We start with one of the two pyruvate molecules that
were made in the cytosol of the cell during glycolysis. The
pyruvate molecule enters the matrix of the mitochondria where it
is converted to acetyl CoA. Acetyl CoA is responsible for initiating
a cyclical series of reactions. Acetyl CoA creates the first
compound in the Krebs cycle (Citrate) by enzymatically
transforming the very last product formed in Krebs cycle,
Oxaloacetate, into Citrate. The names of these specific
compounds are not important, however, it is important to
understand why it is referred to as a cycle.
Every time through the Krebs cycle, 1 ATP molecule is
created and 3 molecules of carbon dioxide, CO2, are released.
Since only 1 pyruvate is needed to circle through the Krebs cycle
and 2 pyruvate molecules were formed during glycolysis, the
Krebs cycle is repeated. This means during cellular respiration, six
carbon dioxide molecules are release and the Krebs cycle forms 2
additional ATP. Through the first two steps of cellular respiration
there is a net gain of 4 ATP. Although the Krebs cycle doesn’t
provide much energy, it does yield several molecules of NADH and
FADH2. These two molecules will be the key to producing many
more ATPs in the third step of cellular respiration, the electron
transport chain.
The ETC takes place within the innermost membrane. Often the
term oxidative phosphorylation is used interchangeably with the
electron transport chain; however, oxidative phosphorylation is
the series of reaction that takes place during the ETC.
Oxygen comes into play during this third process. This is also the
step where the most energy is made. Since this third step makes
the majority of ATP and it takes place within the mitochondria, we
refer to the mighty mitochondria as the ‘power house of the cell’
because it supplies most of the cell’s energy.
NADH and FADH2, which are made during the Krebs cycle, initiate
the electron transport chain. Both NADH and FADH2 transport
electrons down a chain of reactions. NADH or FADH2, whichever is
present at the time, will work with electrons and oxygen to
convert ADP to ATP. In the process NADH loses its hydrogen and
creates a hydrogen concentration gradient across the inner
mitochondria membrane. This hydrogen concentration gradient
drives the production of more ATP. Since NADH lost its hydrogen,
it is now NAD+. Do you remember why this is important? This
process recycles NADH to NAD+ so that NAD+ can be reused in
glycolysis.
At the end of the ETC, water (H2O) and ATP is made. Depending
on how many NADH molecules are available, the electron
transport chain makes a total of 32 or 34 ATP. These 32-34 ATP
combined with 2 ATP from glycolysis and 2 ATP from the Krebs
cycle means that one molecule of glucose (sugar) can make a total
of 36-38 ATP.
 CENTRAL DOGMA OF LIFE CELL THEORY

The central dogma of life is the basis of life on earth and required Cell Theory is one of the basic principles of biology. Credit for the
to control the biological processes. Following this hierarchical flow formulation of this theory is given to German scientists Theodor
of information from DNA to protein allows nucleus to control all Schwann, Matthias Schleiden, and Rudolph Virchow.
biological activities in a cell. Under normal conditions, the flow of
information sequence-to-sequence requires 3 process. The three- The Cell Theory states:
process required for flow of information is as follows: 
 All living organisms are composed of cells. They may be
(1) Sequence dependent synthesis of DNA from pre-exisitng unicellular or multicellular.
DNA [Replication].  The cell is the basic unit of life.
 Cells arise from pre-existing cells. (They are not derived
(2) Sequence dependent synthesis of RNA from
from spontaneous generation.)
DNA [Transcription].

(3) Sequence dependent synthesis of DNA from pre-exisitng
DNA [Translation]. 
The underlying process to flow the information in
proposed central dogma of life is as follows:  
The modern version of the Cell Theory includes the ideas that:
 Energy flow occurs within cells.
 Heredity information (DNA) is passed on from cell to
cell.
 All cells have the same basic chemical composition.

1. Replication: Genomic content in an organism needs to be

duplicated during S phase of cell-cycle. Duplication of DNA is
done by replication utilizing the sequence information of parent
DNA. The enzyme used for this purpose is DNA dependent DNA
polymerase. 

2. Transcription: The DNA is present in nucleus whereas the

protein synthesis machinery is present in cytosol. Hence the
information present in DNA is used to synthesize RNA which has
ability to transport outside the nucleus to participate into protein
synthesis. Synthesis of RNA from DNA is done by transcription
utilizing the sequence information of DNA. The enzyme used for
this purpose is DNA dependent RNA polymerase. 

3. Translation: The RNA present in cytosol is utilized by translation

machinery to synthesize protein in a sequence dependent manner
through a process known as translation.