Biochemistry
It can be argued that life itself is a spontaneous chemical reaction. From this perspective it is no wonder that the beginning of our biology course focuses on the fundamental principles of chemistry. As this course unfolds you will gain an increasingly deeper understanding of the interconnectedness between biology and chemistry. This link is so strong that an entire subdivision of biology called biochemistry has emerged to study it. Consequently biochemistry is also the title of our first unit of study. What follows is a summary of some key principles of chemistry that will lay the foundations for your understanding of subsequent topics throughout this course.
What are living things made of?
For all of their complexity, 96% of the mass of all living things is composed of just four elements. They are carbon, oxygen, hydrogen and nitrogen.The atomic structure of these elements is important for understanding how they form molecules. The valence (outer most) electrons are the most important for bonding. Using a periodic table, let us analyse the composition of these 4 elements.
Recall how to use the periodic table:
/ Standard atomicnotation
/ Protons = 15
Electrons = 15
Neutrons = 31-15 = 16 / Lewis Diagram
P / able to make
3Bonds
Periodic table highlighting the most common elements in the human body / Element / Lewis diagram / # of bonds it can form
Carbon
Nitrogen
Oxygen
Hydrogen
Radioisotopes
The number of protons determines the characteristics of an atom. By changing the number of neutrons present, the chemical properties of the atom remain identical, however the atoms mass and/or stability of the nucleus will be altered. Unstable nuclei decay and produce detectable radiation at a steady rate. These radioisotopes are used by scientists for a variety of functions including determining the age of organic material and fossils, as radioactive tracers to map biochemical processes and as part of medical diagnosis and treatments.
Since organic compounds are mostly composed of carbon and hydrogen, it is their isotopes that are most commonly used to study biochemical processes.
Chemical Bonds
Atoms often form stable interactions known as chemical bonds by allowing their valence electrons to interact. Electrons may either be transferred from one element to another (ionic bonding), or shared between atoms (covalent / molecular bonding).
Ionic Bonding / Covalent / Molecular BondingBetween: / Metal and Non-metal / Two or more non-metals
Mechanism: / Metal loses e- cation
Non-metal gains e- anion / Valence electrons are shared
(up to three shared pairs)
Example: / lithium + chlorine lithium chloride
Li + Cl LiCl
Li + Cl [ Li ]+ + [ Cl ]- / bromine + chlorine bromine chloride
Br + Cl BrCl
Br + Cl Br Cl
Force of Attraction: / Electrostatic interaction
(attraction between positively
and negatively charged ions) / Physically shared eletron pair(s)
Conceptual Diagram: / /
Structure: / Crystal Lattice / Individual molecules.
Structures vary greatly depending on how individual molecules interact with each other.
Depends mostly on:
polarity, size and 3D shape
Polarity
Not all covalent bonds behave the same way. Every element has its own characteristic electronegativity. This is an assigned value used to describean element’s overall pull for electrons. When one element in a covalent bond has a stronger electronegativity than the other, then the electrons will not be shared evenly. If one side of a molecule holds electrons closer, it will gain a slight negative charge. The side with a weaker hold on its electrons will become positively charged. A molecule with an uneven distribution of charge is referred to as a polar molecule.
Intermolecular Forces
If a molecule is polar, or if it is particularly large, forces between different molecules play an important role in their behaviour. The most important intermolecular forces in biology are hydrogen bonds.
Hydrogen bonds:Hydrogen often forms strongly polar bonds with electronegative elements like oxygen and nitrogen. The positively charge hydrogen atoms in these bonds will attract any nearby negative charges. These may be charges on a different molecule or a different region of the same molecule.
van der Waal:Intermolecular forces are collectively known as van der Waal forces. Most are extremely weak, however their cumulative effect becomes important for increasingly larger molecules.
Water
More than 65% of your body is composed of water. Reactions in your body take place in aqueous solution. This means that in order for a substance to be used by your cells, it must be able to dissolve in water. Water is a polar solvent.
In the context of dissolving:“LIKES DISSOLVE LIKES”
i.e. Polar solutes dissolve in polar solvents. Nonpolar solutes dissolve in nonpolar solvents
Polar moleculesdissolve in water “water loving”HYDROPHYLLIC
Non-polardoes not dissolve in water“water fearing”HYDROPHOBIC
Ionic usually dissolve in water to form aqueous ions
Acids and Bases
Some molecular compounds not only dissolve in water, but they also partially dissociate into ions. If they produce hydrogen ions (H+), then they are referred to as acidic. An acid can be neutralized using a base. These are hydrogen acceptors which often produce OH- in solution.
The pH Scale
The concentration of H+ ions (may also indicated as the hydronium ion, H3O+) in a solution determines its level of acidity. Acidity is assigned a numerical value on a 14 point scale. This value is calculated using the concentration of hydrogen ions [H+] in solution according to the following formula:
pH = − log[H+]
The strength of an acid is independent of its concentration and pH. The strength of an acid refers to the degree to which it dissociates into ions in water. A strong acid completely dissociates in water (there are only 6 of them), whereas a weak acid only partially dissociates. Organic acids are weak acids.
The dissociation of acetic acid (vinegar) in waterCH3COOH + H2O CH3COO− + H3O+
Types of Reactions
Summarize the four most common types of reactions in biology in the table below.
Dehydration /Condensation
Hydrolysis
Neutralization
Redox