College of Science

Cell Biology
Theoretical Lecture 2
2023-2024

What is the chemical composition of the cell?

Organisms are made up of a lot of different chemicals. These vary in size, from small
molecules like water to large molecules like DNA, and interact and associate in
many different ways to generate the processes of life.

Water is the most abundant substance in organisms. Cells are rich in water.
Cytoplasm consists of organelles floating in a watery medium called cytosol that
also contains proteins.

Organization of living things

Atom: the building blocks of all matter, (the smallest unit of an element)
Element: the simplest form of matter. They cannot be broken down chemically
Molecule: two or more atoms combined chemically (the smallest unit of compound)
Organelles: structures within cells that perform specific functions.
Cell: the smallest unit of a living thing.
Tissue: a group of similar cells that perform a similar function. (muscle tissue, bone tissue, skin tissue.
Organ: a group of tissues that work together to perform a specific task. (brain, stomach, heart, etc.)
System: a group of organs that work together to perform a specific task. (skeletal system, digestive system,
etc.)

Organism: complete, entire living things may exist as single cells, as simple organisms with tissues but no
organs, or they may have organs that are not organized into organ systems. However if multicellular,
then organisms are made up of several organ systems.

Cell Organization:
There are three levels of organization to describe the molecules that make up
living organisms:
1. The simplest level is the individual elements such as carbon, nitrogen, or
oxygen.
2. The basic elements can be arranged into a series of small molecules known as
Building Blocks. Building blocks include compounds such as amino acids and
nucleic acids.
Elements, Irons and Trace minerals that make up living organisms
Elements Ions Trace minerals
Oxygen Sodium Manganese, Iron, Cobalt, Copper,
Carbon Potassium Zinc, Aluminum, Iodine, Nickel,
Nitrogen Magnesium Chromium, Selenium, Boron,
Hydrogen Calcium Vanadium, Molybdenum, Silicon,
Phosphorus Chloride Tin and Fluorine
Sulfur

3. The building blocks are organized into larger compounds, known as

Macromolecules. Macromolecules comprise the different structures that are
 found in cells. Four different types of macromolecules are used to construct a
cell: • Nucleic acids • Proteins • Lipids • Carbohydrates.

Three levels of organization describe the compounds that make up living organisms.
I Elements
Phosphate
Pyrimidines Fatty acids
Amino
II Purines Glycerol Sugars
acids
Ribose Other components
Deoxyribose
Carbohydrates or
III Nucleic acids Proteins Lipids
Polysaccharides

Nucleic acids:
It can be subdivided into DNA and RNA.
DNA is composed of two kinds of building blocks,
1-The bases (adenine, guanine, cytosine, and thymine).
2- a sugar phosphate backbone.
DNA is used by the cell as a repository for all of the information necessary to
direct synthesis of the macromolecules and to produce energy for this synthesis.
DNA is also used to transmit information from one generation to the next.
RNA has a very similar composition to DNA. The two major differences between
DNA and RNA are:
 1- The sugar used in the sugar phosphate backbone (ribose for RNA and
deoxyribose for DNA)
2- In one of the bases (uracil for RNA and thymine for DNA).

The RNA in the cell has at least four different functions:

A. Messenger RNA (mRNA) is used to direct the synthesis of specific proteins.
B. Transfer RNA (tRNA) is used as an adapter molecule between the mRNA and
the amino acids in the process of making the proteins.
C. Ribosomal RNA (rRNA) is a structural component of a large complex of
proteins and RNA known as the ribosome. The ribosome is responsible for
binding to the mRNA and directing the synthesis of proteins.
The fourth class of RNA is a catch-all class. There are small, stable RNAs whose
functions remain a mystery.

In general, RNA is used to convey information from the DNA into proteins.
Proteins :
Proteins are composed of amino acids. Most proteins are made from a unique
combination of 20 different amino acids . The order in which amino acids appear
in a protein are specified by the mRNA used to direct synthesis of the protein.
The amino acids can be grouped together and described by physical properties
such as charge (acid or basic), size, interactions with water (hydrophobic water
“hating” or hydrophilic water “loving”), a specific element (sulfur containing) or
structure they contain (aromatic rings).
Proteins perform many duties in the cell
Including functioning as structural and motor components, enzymes, signaling
molecules, and regulatory molecules. Some proteins perform only one function
while others are multifunctional.
Lipids :
They are an unusual group of molecules that, in bacteria, are used to make the
membranes that surround a cell. One type of lipid, known as a fatty acid, is composed
of long chains of carbon molecules attached to a smaller head group (Fig. below).
The small head group is known as the polar head group.

Saturated fatty acids are flexible and can be tightly packed.

If the fatty acids contain any double bonds they are known as unsaturated fatty
acids.
Unsaturated fatty acids have a kink in them and cannot be packed as closely.
Membranes usually contain a mixture of fatty acids to maintain the right packing
density and fluidity.
Carbohydrates
It was composed of simple sugars . They can be used as:
1- Immediate source of energy.
2- Stored source of energy.
3- Structural components of the cell. In bacteria, carbohydrates that are used as
immediate.
The fatty acid attached carbohydrates
help protect the cell from detergents
and antibiotics. A complex mixture of
carbohydrates is used to make the cell
wall. Cell walls maintain the shape of
the cell.

Lipid molecules. (a) The general structure of a saturated fatty acid. (b)
The structure of membranes with two leaflets. (c) The general
structure of an unsaturated fatty acid.
Carbohydrate Function:
➢Production and storage of energy (glycogen)

➢Mechanical support (cellulose, chitin)

➢Integration in the membranes (glycolipids)

➢Signaling (glycosaminoglycans)
Each of the four types of macromolecules provides unique functions to the
cell. For some of the cell’s requirements, a single type of macromolecule suffices

Types and general structures of carbohydrates. The polymerizing of

galactose with glucose results in the formation of lactose upon
liberation of one H2O molecule.
 Four major classes of biomolecules and their essential features: carbohydrates, lipids, amino acids/proteins and
nucleotides/nucleic acids.
Proteins… are long chains of subunits, called amino acids.
Carbohydrates…
are highly polar molecules composed of “carbon atoms and water”.

Monosaccharide Disaccharide

Glucose Fructose
GLUCOSE
SUCROSE
1. Are highly polar, well soluble in water.
Polysaccharide
2. Exist as monomers, dimers and polymers.
3. Important sources of energy, components of cell
All amino acids have the same
membranes and the backbone of nucleic acids backbone but different side
4. Glucose is the ONLY source of energy for the brain. chains. It is the side chains
5. Glycogen is abundant most abundant in liver but is which actually make all the
also present in muscles. The only brain cells which difference!
GLYCOGEN contain glycogen are called astrocytes.
6. There are about 10 “glycogen storage diseases” due
to various mutations in enzymes involved in its
synthesis and degradation.

Four major classes of biomolecules and their essential features: carbohydrates, lipids, amino acids/proteins and
nucleotides and nucleic acids.
Amino acids get connected together and form
Lipids… are composed largely of carbon and hydrogen atoms and
therefore are nonpolar. long chains (sometimes > 1000 amino acids).
These chains are called PROTEINS

1 Fatty acid
Glycerol
1. Fatty acids are nonpolar, water-
insoluble molecules. They are used
to store energy.
2. Phospholipids have a polar “head”
and nonpolar fatty acid “tails”.
They are amphipathic. In water
2 Triglycerol (fat) 3 Phospholipid they form clusters. In the cells
they are the essential component
of all membranes.
3. Steroids have 4 cycles of carbon
atoms and are important
components of plasma membrane
and also act as signalling
4 Steroid molecules.

Phospholipids: the building blocks of cellular membrane

Macro-molecular complex protein haemoglobin

consists of 4 individual protein chains

Phospholipid bi-layer is
the key component of all
cellular membranes

The structure and function of proteins are determined

by the amino acid composition.
Structural and functional blocks/parts of a protein is often referred to as
“domains” (e.g. “catalytic domain” or “regulatory domain”).
The key aminoacids which are responsible for the function of a domain are
usually conserved throughout evolution. We can trace some of the domains in
our proteins back to the yeast cells.

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 Nucleic Acids (DNA and RNA) contain and The plasma membrane of a cell consists of the
handle the information in the cell. phospholipid bi-layer and numerous proteins embedded
H in it.
RNA = ribonucleic acid
DNA = deoxyribonucleic acid REMINDER: polar molecules solve well in water. And non-polar … in what?

DNA is built of numerous

nucleotides connected via
phosphoric acid residues

In order for a molecule to be inside the lipid bi-layer it needs to …

Nucleic Acids (DNA and RNA) contain and
handle the information in the cell.

1. DNA and RNA are polymer molecules. Their subunits are called = non-polar,
nucleotides. hydrophobic
2. Four different nucleotides are found in DNA and RNA (3 are the same in COOH
NH2
both)
= polar or
3. Sequence of nucleotides is the genetic code of the cell as it determines charged,
the sequence of amino acids in the proteins hydrophilic

Some Functions of (INTEGRAL) Membrane proteins

Other interesting facts about nucleic acids:
Receptor – detects chemical signals A channel (leak)

1. RNA can not only carry information but also perform functions,
similar to proteins: in the ribosome where the proteins are Anchoring/connecting

made it is the RNA which obviously joins the amino acids

together. There are also “rybozymes” – species of RNA which
can attack and destroy other RNAs.
2. Nucleotides give rise to ATP. ATP is the universal energy effect
currency of the cell but also perhaps the most archaic cell-to
cell signalling molecule. A gated channel
Carriers
3. Viruses have genomes encoded in either DNA or RNA form.
4. Some viruses can use RNA as a template to generate DNA (e.g. Chemical reactions
information flows in reverse direction).
5. DNA is almost always double-stranded while RNA is usually
single-stranded. Because of that RNA often folds on itself
forming hairpin-like structures.
6. NOT all the DNA in the cell is located in the nucleus,
mitochondria have their own genomes which are different from
the main one.

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The Key Points:
1. Polar & charged molecules dissolve in water while non-polar dissolve in
oil/fat/lipid media
2. Carbohydrates (sugars) exist as monomers, dimers or polymers. They are
polar molecules and are serve as sources of energy and components of
other molecules, such as nucleic acids.
3. There are 4 main classes of lipids (fatty acids, triglycerides,
phospholipids and steroids). Most lipids are water-insoluble but
phospholipids are amphipathic (= have hydrophobic “tails” and hydrophilic
“heads”). They are the essential components of all membranes.
4. Proteins are long stretches of amino acids. Their structure and function is
determined by the sequence of amino acids. They are responsible for all
cellular activities / functions.
5. Nucleic acids (RNA and DNA) are long stretches of nucleotides. There are
4 kinds of nucleotides in RNA and DNA. DNA encodes all the information
in the cell and encodes all the proteins while RNA is responsible for the
transfer of this information to the places where the proteins are being
produced.
6. Some proteins are embedded into the cell membrane. This is possible
because their sequences have parts enriched in hydrophobic (non-polar)
amino acids. These parts form “membrane-spanning domains”.