Chapter 3: (51-64) Chemistry of cellular components
Diversity lies in the variation of chemistry and arrangement cellular components.
3.1-Strong and weak chemical bonds:
Major components in living things: Hydrogen, Oxygen, Carbon, Nitrogen, Phosphorus, and Sulfur.
The molecule consists of two and more atoms chemically bonded to each other.
They are strong bonds formed between chemical elements in which electrons are shared more or less
equally between atoms. Single, double and triple covalent bonds can form.
Monomers: Chemical elements bond to form them. They associate to form polymers. Covalently bonded
polymers in living cells are called macromolecules.
Hydrogen bonding and polarity
Hydrogen bonds: They form as a result of weak electro-static interactions between hydrogen atoms and
more electronegative atoms such as nitrogen and oxygen. Because the other atoms will be more
electronegative than the hydrogen, this will create a shift in the shared electrons closer to that atom,
creating a slight charge separation. An individual hydrogen bond by itself is very weak but many
hydrogen bonds together will achieve stability. Water is polar and its molecules tend to associate with one
another and remain apart from nonpolar (hydrophobic) molecules. Water is extensively made of hydrogen
bonds. Also hydrogen bonds are found in protein which assures its stability.
Other weak bonds
-Van der Walls forces are weak attractive forces that occur between atoms when they become closer
than about 3-4 angstroms; they play an important in binding the substrate to enzymes and in protein-
nucleic acid interactions.
- Ionic bonds, such as Na+ and Cl- in NaCl are weak electrostatic interactions that support ionization in
-Hydrophobic interactions are also considered weak bonds. They occur when non-polar molecules or
non-polar regions of molecules associate tightly in a polar environment. Like Van der Walls forces,
hydrophobic interactions help in binding substrates to enzymes, folding of proteins and controlling how
different subunits in a multi-subunit protein associate with one another (quaternary structure) to form the
biologically active molecule. They also help stabilize RNA.
3.2- An overview of macromolecules and water as the solvent of life
Carbons are the major components in all macromolecules. Water on the other hand is the major
constituent. 95% of the dry weigh of a cell consists of macromolecules. Carbon can bind to each other and
also to other subunits. Different organic compounds have different bonding patterns. Each of these
patterns is called a functional group:
- Proteins are polymers of monomers called amino acids. They are the most abundant class in the
cell dry mass; they play both a structural and an enzymatic role.
- Nucleic acids are polymers of nucleotides and are found in two forms, RNA and DNA. RNAs
are the next most abundant macromolecule in an actively growing cell. RNA is abundant because there are many types of ribosomes and RNA (mRNA, tRNA). Ribosomes are composed of a
mixture of RNAs and protein. DNA is less abundant.
- Lipids are formed of both hydrophilic and hydrophobic properties and play a crucial role in the
cells such as membranes and storage depots for excess carbon.
- Polysaccharides are polymers of sugars, and they are present in the cell, especially in the cell
wall. They can exist like glycogen, in the form of a carbon and energy storage in the cell.
Water as a Biological solvent
Water has two important features that make it an ideal biological solvent. The first feature is the
polarity of water which facilitates the dissolving of many macromolecules which are already
polar. This also promotes the stability of large molecules because of the increased opportunities
for hydrogen bonding. Water also forces the non-polar molecules to aggregate and remain
together. The hydrogen bonding gives the water cohesiveness. Water molecules have a big
affinity for one another and form arrangements in which hydrogen bonds are constantly forming,
breaking and reforming. The cohesiveness of water is responsible for important properties such as
high surface tension, and high specific heat. Water expands on freezing to yield a less dense solid
Play an important role as structural and reserve of water.
Carbohydrates: they are organic compounds that contain carbon, hydrogen, and oxygen in ratio
of 1:2:1. Glucose (C H O ) is the most abundant sugar on earth .Pentose (C5) are important
6 12 6
because their role as structural backbones of nucleic acids. Hexoses (C6) are the monomeric
constituents of cell wall polymers and energy reserves.
Derivatives of simple carbohydrates are formed when the hydroxyl group on the sugar is
replaced. For example, the important cell wall polymer peptidoglycan contains the glucose
Polysaccharides are carbohydrates containing up to 100 or 1000 monosaccharides. These are
connected by covalent bonds called glycosidic bonds. 2 monosaccharides: disaccharide, 3
monosaccharides: trisaccharide, several more monosaccharides: oligosaccharide, long chain of
Glycosidic bonds can form in two different geometric orientation, a and b.
The 1-4 a orientation functions as important carbon and energy reserves in bacteria, plants and
animals. The 1-4 b orientation are present in stiff plant and algal cell wall component.
Polysaccharides can also combine with other classes of macromolecules such as proteins and
lipids to form polysaccharides, glycoproteins and glycolipids. They play an important role as
cell-surface receptors. They reside on the external surface where they are in contact with external
environment of cells. Glycolipids are and important compound of the cell wall of gram negative
bacteria. 3.4- Lipids
Lipids are amphipathic which means that they both show hydrophilic and hydrophobic properties.
Fatty acids are major constituents of Bacteria and Eukarya lipids.
By contrast, lipids of Aarchaea contain a hydrocarbon side chain not composed of fatty acids.
Fatty acids contain both hydrophobic and hydrophilic components.
Fatty acids consist of fatty acids bonded to C3 alcohol glycerol.
Triglycerides and complex lipids
Simple lipids are also called triglyceride because three fatty acids are bonded to a glycerol unit.
Complex lipids are simple lipids that contain additional elements such as phosphorus, nitrogen,
sulphur or small hydrophilic organic compounds such as sugars.
Ex: phospholipids, they play an important role in the cytoplasmic membrane.
Lipids aggregate to form membranes. The hydrophilic glycerol portion is in contact with external
environment and cytoplasm while hydrophobic region remains imbedded inside the membrane.
This makes the membrane an ideal permeability barrier.
The sequence of monomers in nucleic acids carries genetic information and the sequence of monomers in
proteins carries structural and functional information. Nucleic acids and proteins are thus informational
3.5- nucleic acids
RNA= Ribonucleic acid
They are macromolecules composed of monomers called nucleoids. DNA and RNA are polynucleotides.
A nucleotide is composed of three components:
- A pentose sugar: Ribose in RNA or Deoxyribose in DNA.
- A Nitrogen base
- A molecule of phosphate, PO 43-
The nitrogen bases of nucleic acids belong to two classes:
- Purine bases: adenine (A) and guanine (G). They contain two fused heterocyclic rings.
- Pyrimidine bases: thymine (T), cytosine (C), and uracil (U). They contain a single six-
membered heterocyclic ring.
- G, A, C are present only in DNA. T is only present in DNA and U only in RNA.
Nucleotides consist of a nitrogen base attached to a pentose sugar by a glycosidic linkage
between carbon atom 1 of the sugar and nitrogen of the base, either the nitrogen atom labeled 1(in
a pyrimidine base) or 9(in purine base). Without the phosphate the molecule is called nucleoside.
Nucleotides are thus nucleosides containing one or more phosphates.
Nucleotides also play a role in energy production in ATP and in metabolism by inhibiting or
simulating the activities of certain enzymes or metabolic events. Nucleic acids
Polynucleotides consist of nucleotides covalently bonded via phosphate from carbon 3- called the
3 (3 prime) carbon of one sugar to 5 carbon of the adjacent sugar. The phosphate linkage is
called a phosphodiester bond because a phosphate connects 2 sugar molecules by ester linkage.
The sequence of nucleotides in a DNA or RNA is called its primary structure.
It is double stranded. Each chromosome consists of two strands of DNA. Hydrogen bonds play a
role in linking the two strands. Hydrogen bonding is most stable when adenine bonds with
thymine (A-T) by two hydrogen bonds and (C-G) with 3 hydrogen bonds.
They are single stranded molecules but can fold upon themselves in regions where
complementary base pairing is possible to form folded structures called secondary structures.
Four classes of RNA exist:
1. Messenger RNA: carries the genetic information of DNA in a single stranded molecule
complementary in base sequence to that of a DNA.
2. Transfer RNA; tRNA: converts the genetic information found in the mRNA