Chemistry of Life
Matter is anything that occupies space. Matter is made of one or more elements.
An element is the most pure form of matter. Elements are made of atoms.
There are 111 elements and of these 92 are naturally occurring.
Essential Elements
About 25 elements are essential to life. These are called ‘essential elements’.
4 essential elements make up 96% of the human body. These are O, C, H and N. The other elements account for the remaining 4%.
Trace Elements
Certain elements are needed in trace amounts. These are also essential to life.
Eg. The human body needs trace amounts of boron, chromium, iron, iodine, etc.
Humans need 0.15 mg of iodine each day. If iodine is deficient or in excess, a goiter develops – due to malfunctioning of the thyroid gland.
Properties of Atoms
All atom have a neutral charge because of the following:
In nucleus of atom are protons that have a positive charge (p+)
and neutrons that have a neutral charge.
Outside of the nucleus are the electrons.
Electrons have a negative charge.
The number of electrons is equal to
the number of protons:
so negative charges cancel out the positive charges.
Atomic Number= number of protons (also number of electrons)
Atomic Weight = number of protons + number of neutrons
Atomic weight is the average weight number of isotopes for one elements. Atoms for one element have different numbers of neutrons and are called isotopes.
Isotopes = different isotopes of an element have the same atomic # but different atomic weights. Example: Carbon – 12, Carbon – 13 and Carbon – 14 all have the same # of protons (i.e. 6 protons), but, # of neutrons vary. C12 has 6 neutrons, C13has 7 neutrons and C14 has 8 neutrons. Hence they all have the same molecular number, ie. 6, but different atomic weights: viz. 12, 13 and 14, respectively.
Radioactive Isotopes
Whereas C12 and C13 are stable isotopes, C14 is an unstable isotope, also called a radioactive isotope.
Radioactive isotopes constantly emit energy and particles due to nuclear decay.
There are both benefits and dangers to radioactive isotopes.
Radio-isotopes – Benefits
Radio-isotopes can be used beneficially as ‘tracers’ for scientific research (for example, C14 was used to label CO2 to find out what molecules the plants make during photosynthesis) and medical diagnosis eg. PET scan helps in diagnosing cancer. Also radio-isotopes can detect kidney disorders.
Radio-isotopes - Dangers
Dangers: Radio-isotopes are damaging to DNA on continuous exposure.
There were many deaths from the explosion of the nuclear reactor at Chernobyl, Ukraine in 1930. The survivors have had increased risks of birth-defects and thyroid cancer and general risk of cancer.
Radon – a radioactive gas is a causative agent for lung-cancer.
Outside the nucleus are electron clouds or orbits. Electrons are found in these orbits in fixed number depending on the orbit.
S orbit holds a maximum of 2 electrons
P orbits hold a maximum of 8 electrons
Other orbits are not discussed in this class
An atom is considered stable or inert if the outer orbit has the maximum number of electrons. A stable atom does not form molecules or compounds. When the outer orbit of an atom is not filled it is unstable and can form chemical bonds. Atoms bond to complete their outer orbit with electrons and to form molecules and compounds.
Determine whether or not each of the following atoms is stable. If the atom is not stable, how many more electrons are needed to fill the outer electron shell?
Neon (Atomic Number = 10)
Argon (Atomic Number = 18)
Carbon (Atomic Number = 6)
Nitrogen (Atomic Number = 7)
Oxygen (Atomic Number = 8)
Compounds
Compounds are made up of 2 or more elements or molecules in a fixed ratio.
Elements are rarely found as such in nature. They are generally found as compounds.
Many compounds are made up of only 2 elements. Eg. Table salt (NaCl).
In living organisms, compounds are made up of 3 – 4 different elements. Eg. Proteins are made up of C, H, O and N.
Three type of bonds
Ionic Bonds form between atoms that have formed ions. An ion forms when an atom looses or gains an electron.
1. Ionic bonds form polar molecules that can dissolve in water. They are considered hydrophilic in nature, meaning water loving.
- Covalent Bonds form when two atoms share electrons to complete the outer complete orbit. Covalent bonds can be polar or non-polar
Polar covalent bonds when sharing in unequal (oxygen
and two hydrogen atoms form water, the sharing is
unequal).This creates a polar compound with unique
properties. One end is slightly negative the other
slightly positive.
Non-Polar covalent bond forms when sharing is equal, the molecule has no charge (i.e. hydrocarbons are components of fats). These compounds are hydrophobic, or water fearing. When oxygen bond to another oxygen. Electrons are shared equally.
3. Hydrogen Bonds occur when polar covalent bonds produce slightly negative and slightly positive charges that attract one another.
Unusual Properties of Water
The partial negative charge of the oxygen atom on one water molecule forms a hydrogen-bond with two hydrogen atoms of adjacent water molecules, each water molecule can hydrogen-bond with up to 4 partner water molecules.
Due to its polarity and hydrogen bonding, water has several unusual properties:
Water can exist in three different states of matter – viz. solid (ice),liquid (water) and gas (water-vapor).
Water has also a high surface tension. Hence, it acts as an unbroken film to water insects.
Water is adhesive: it is attracted to different substances.
Water is highly cohesive. Cohesion is the attraction of water to itself. Hence the tree-sap rises up in an uninterrupted flow from the roots to the leaves.
Water conducts heat and is a great evaporative cooler due to two properties:
It has a high specific heat which allows it to absorb a lot of heat
It has a high heat of vaporization which allows it to moderate temperature.
Water is a universal solvent; Hence, just about anything can dissolve in water.
Ice is less dense than liquid water. Ice crystals have a much more spaceous arrangement of water molecules compared to the structure of liquid water. (See photo).
Solutions:
Equation (Eq): Solution = Solute + Solvent
Hydrophobic Solutes are water-fearing and cannot dissolve in H2O or aqueous solutions. They dissolve in hydrophobic solvents.
Hydrophylic Solutions are aqueous and. Polar solutes are soluble in water. Ionic solutes are charged and polar.
The Acidity or Basicity of a Solution or pH
Pure water can dissociate into an equal amount of H and OH ions.
H2O H+ + OH-
Solutes dissolved in water affect this equilibrium. The pH represents the relative amount of H+ in a solution. pH by definition is a measure of the hydrogen ion concentration in a solution.
When the concentration of H+ = concentration of OH- then the pH is neutral = 7
When the concentration of H+ > concentration of OH- then the pH is acidic < 7
When the concentration of H+ < concentration of OH- then the pH is basic > 7
The pH ranges from 0-14
The pH is important for cell function.
Buffer are substances that help to maintain a constant pH. All cells are buffered. Human blood is buffered with carbon dioxide and stays at approximately 7.3.
The pH can affect the shape of a molecule and will change its function or activity.
A change of 1 pH unit results in a 10 fold change in the concentration of the H+.
SHAPE DETERMINES FUNCTION
Life’s Processes are Sensitive to pH
pH = the chemical potential hydrogen.
This is a measure for acidity or basicity.
An acid is a substance which donates hydrogen (H+) ions.
A base is a substance which accepts hydrogen ions or donates (OH)- ions.
The pH scale ranges from 0 (most acidic) to 14 (most basic).
A buffer is a substance which resists changes in pH by accepting (H+) ions when in excess and donating (H+) ions when they are depleted.
Chemical Reactions
Chemical reactions rearrange matter.
Example: Two molecules hydrogen react with one molecule of oxygen to give two molecules of water.
A reaction consists of the starting molecules called ‘reactants’ and the resulting ‘products’.
Macromolecules in Cells
Many large molecules are essential to living systems. The following 4 are polymers; they are composed of repeating units called monomers. The monomers are joined or linked together by the removal of water. This is known as dehydration synthesis.
The 4 common macromolecules are:
1. Carbohydrates are polymers of sugars (saccharides). They have a carbon:hydrogen:oxygen ratio of 1:2:1
2. Lipids
3. Proteins
4. Nucleic Acids
Plants Have Primary & Secondary Metabolism
Primary Metabolism includes
Photosynthesis
Cell Respiration
Metabolism that involves the making of the 4 macromolecules
Secondary metabolism produces secondary compounds such as:
Terpenes like carotenoid pigments that give rise to vitamin A, sage and mint oils, various fragrances . Citronella used to repel insects, rubber, turpentine , resins on the trunks of pines
Phenolics found in grape, blueberries may have health benefits. Tannins are toxic to herbivorous animals, stop microbial growth. Tannins give astringent flavor to tea and red wine. Phenolics include cinnamin, nutmeg, genger, vanilla and capsaicin's in chilies. Lignin gives wood its strength. Few organisms can breakdown wood.
Flavonoids: Anthocyanin pigments produce the orange pink and red colors in flowers and fruit.
Alkoloids
all contain N
include nicotine, caffeine and others commonly used in medicines,
STRYCHNINEA poison found in hemlock , theobromine inchocolate
quinine an antimalarial. The highly addictive pain killers morphine and cocaine