BIOLOGICAL MOLECULES- SUMMARY NOTES

1. Explain why an understanding of chemistry is essential to the study of cell biology.

Biology is the science of life which studies the structure, function, behaviour, origin, evolution
and distribution of living things.

Chemistry is the science of the composition, properties, structure, functions and reactions of
matter. It deals with the identification of substances that matter is made of, the study of their
properties and the ways in which they associate, combine and alter.

The principles of chemistry, especially at a molecular level are useful in cell biology simply
because all living cells consist of chemicals and various chemical processes take place in many
living organisms. For example, when an organism takes in food with sugar, the cells in the body
catabolise the sugar into energy which is important in processes such as muscle contraction, active
transport and synthesis of complex substances.

2. Describe the nature of covalent bonds, and why some bonds have unequal
distributions of electrical charge.

3. Identify polar and non-polar molecules and understand the consequences of polarity
in cellular molecules.

Covalent Bonds
Electrons are shared in covalent bonds. The carbon atom in methane (CH4) shares electrons equally
with four hydrogen atoms. The equal sharing of electrons in non-polar covalent bonds in H2 (a
molecule) and CH4 is shown below.

Recall that atoms are most stable when their outer shells are filled and when each electron orbital
is filled (i.e., with a pair of electrons).

Polar covalent bonds form when electrons in a molecule are shared unequally. This
happens if the atomic nuclei in a molecule are very different in size (eg Water).
 -
The paired e s in water are closer to the O atom
because its nucleus is much larger than that of the H
atoms:

Illustration by G.
Bergtrom

The larger nucleus of the oxygen atom in H2O attracts electrons more strongly than do either
of the two H atoms. As a result, the shared electrons spend more of their time orbiting the O
atom, such that the O atom carries a partial negative charge while each of the H atoms carry a
partial positive charge. Note the position of the paired electrons in water with those illustrated
for hydrogen gas or methane.

Ionic Bonds

Atoms that gain or lose electrons to achieve a filled outer shell form ions, acquiring a negative or
a positive charge, respectively. Despite being electrically charged, ions are stable because their
outer electron shells are filled. Common table salt is a good example.

Illustration by G. Bergtrom

Na (sodium) can donate a single electron to Cl (chlorine) atoms, generating Na+ and Cl- ions. The
oppositely charged ions then come together forming an ionic bond, an electrostatic interaction of
opposite charges that holds the Na+ and Cl- ions together in crystal salt.
4. List the type of weak bonds and explain why they are important in cells.

Two weak bonds that occur frequently are hydrogen bonds and van der Waals interactions.

 Hydrogen bonds are a subcategory of electrostatic interaction (i.e., formed by the attraction
of oppositely charges). Water molecules attract one another because of strong electrostatic
interactions that form H-bonds.
 Because of water’s polar covalent nature, it is able to attract positively and negatively
charged groups of solutes, making it a good solvent.
 Solutes (water-soluble molecules) or molecular surfaces attracted to water are hydrophilic.
 Lipids like fats and oils are not polar molecules and therefore do not dissolve in water; they
are hydrophobic (from hydro, water; phobic, fearing).

5. List the properties and explain why water is ideally suited to life.

 Its attraction to polar molecules-

Cohesion, otherwise known as water's attraction to other water molecules, is one of the
major properties of water. Water's polarity lends it to be attracted to other water
molecules. The hydrogen bonds in water hold other water molecules together.
Due to water's cohesiveness:
i. Liquid water has surface tension. This allows for insects, such as Water
Striders, to walk on water.
ii. Water is a liquid at moderate temperatures, and not a gas
 High-specific heat

Water can moderate temperature because of the two properties: high-specific heat and the
high heat of vaporization.
High-specific heat is the amount of energy that is absorbed or lost by one gram of a
substance to change the temperature by 1 degree celsius. Water molecules form a lot of
hydrogen bonds between one another. As such, a lot of energy is needed to break down
those bonds. Breaking the bonds allows individual water molecules to move freely about
and have a higher temperature. In other words: if there are a lot of individual water
molecules moving about, they’ll create more friction and more heat, which means a higher
temperature.
The hydrogen bonds between water molecules absorb the heat when they break and release
heat when they form, which minimizes temperature changes. Water helps maintain a
moderate temperature of organisms and environments.
Water takes a long time to heat up, and holds its temperature longer when heat is not
applied.

 High heat of vaporization

Water's high heat of evaporation is the amount of heat energy needed to change a gram of
liquid into gas. Water also needs a lot of energy in order to break down the hydrogen
bonds. The evaporation of water off a surface causes a cooling effect. Much like among
humans—when we get hot, or energy inside our body is breaking chemical bonds, we
sweat as a cooling effect. In this case, the same process occurs: as the water evaporates
off the surface of the skin, it cools down the surface.

 The lower density of ice

At cooler temperatures, the hydrogen bonds of water molecules form ice crystals. The
hydrogen bonds are more stable and will maintain its crystal-like shape. Ice—the solid
form of water—is less dense than water because of the hydrogen bonds being spaced out
and being relatively apart. The low density is what allows icebergs to float and are the
reason that only the top part of lakes are frozen.
  High polarity

Water is a polar molecule that has a high level of polarity and attraction to ions and other
polar molecules.
Water can form hydrogen bonds, which make it a powerful solvent. Water molecules are
attracted to other molecules that contain a full charge, like an ion, a partial charge, or polar.
Salt (NA+ CL-) dissolves in water. Water molecules surround the salt molecules and
separate the NA+ from the CL- by forming hydration shells around those two individual
ions.

Chemical Properties

• Universal solvent: Water can dissolve hydrophilic (water-loving) substances such as proteins,
gases, salts, and carbohydrates and transport them inside the cell, in and out of cells, and between
different cells. It cannot dissolve hydrophobic (water-fearing) substances.
• Chemically active: It can participate in many chemical reactions.
Physical Properties
• Heat transfer: Water remains liquid over a wide range of temperatures and conducts heat well.
Think of a pot of water on the stove—only the water at the bottom of the pot is in contact with
active heat, but all of the water is heated.

For Consideration: it is easy to dissolve hydrophilic salt in water, but virtually impossible to dissolve
hydrophobic butter. WHY?

Fats can be dissolved in water if detergent is added. Detergents are amphipathic molecules that “bring
together” hydrophilic and hydrophobic substances. Detergents contain hydrophobic areas to interact
with the fat and hydrophilic areas to interact with the water.
6. Consider why some salts are not soluble in water in terms of water’s properties.

Soluble salts like NaCl dissolve because the Cl- and Na+ ions more strongly attract the partial
positive and negative charges (respectively) of water molecules. The result is that the ions separate.
We call this separation of salt ionization. The ionization of NaCl dissolving in water is shown
below.

Illustration by G.

Water is also a good solvent for macromolecules (proteins, nucleic acids) with exposed polar
chemical groups on their surfaces that attract water molecules, as shown below.

Illustration by G.
Bergtrom

Q. Salts like silver chloride and calcium carbonate are virtually insoluble. Since we (and all
cells) need salts and ions, interactions of salts and water are fundamental to life. In chemical
terms, why are some salts insoluble in water?
CARBON

Carbon has a unique role in the cell because of its ability to form strong covalent bonds with other
carbon atoms. Thus carbon atoms can join to form chains, branched structures or rings.

A carbon chain can include double bonds. If these are on alternate carbon atoms, the bonding
electrons move within the molecule, stabilizing the structure by a phenomenon called resonance.
The differences in arrangement of atoms and functional chemical groups around C atom result in
isomerism. Isomers of an organic molecule have the same chemical formula but different shapes
(and so, potentially different chemical properties and biochemical function).

The structural isomers of C4H10 (above left and right) have different shapes. You cannot convert
one structural isomer to the other without breaking covalent bonds. In the geometric isomers of
C4H8 in the lower panel, the H atoms on the double-bonded C atoms can be on the same (cis) or
opposite (trans) side of the planar double bond. Geometric isomers too, cannot be interconverted
without breaking chemical bonds.
 7. Distinguish between chemical “bonds” and “linkages” in polymers.

Monomers to Polymers and Back: Dehydration Synthesis and Hydrolysis

All living things build and break down polymers (macromolecules) by dehydration synthesis
(condensation reactions) and hydrolysis, respectively. Dehydration synthesis and hydrolysis
reactions are essentially the reverse of each other, as illustrated below:

Condensation reactions build macromolecules by removing a water molecule from interacting

monomers. The ‘bond’ that forms in a condensation reaction is not a single bond, but a linkage
involving several bonds. The linkages form by removing an OH from one monomer and an H
group from the other to form a water molecule

Cells perform repeated condensation reactions to build other polymers, including polysaccharides
and polynucleotides (the RNA and DNA nucleic acids) and as shown below between two amino
acids to form the peptide linkages that build polypeptides during translation.
 The condensation reactions shown below link glucose monomers, forming storage and
structural polysaccharides.

Illustration by G.
Bergtrom
Can you spot the error?

The -OH (hydroxyl) groups on the #1 C of α glucose are below the glucose rings. The
condensation reaction removes a water molecule, linking the sugars by an α1,4 glycoside linkage
in the dimer, connecting them by their # 1 and # 4 carbons. Other linkages are possible; diverse
α-glycoside linkages characterize branched storage polysaccharides like glycogen in animals and
the starches in plants. When β glucose enantiomers polymerize, they form rigid structural
polysaccharides such as those of cellulose in plant cell walls. A modified β-glucose called N-
acetyl glucosamine (shown below) polymerizes to form chitin, the principal component of fungal
cell walls and of the tough exoskeleton of arthropods (insects, crustacea).