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Chemistry for Biologists 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 atomic notation Lewis Diagram Protons = 15 Electrons = 15 Neutrons = 31-15 = 16 Element P Lewis diagram able to make 3 Bonds # of bonds it can form Carbon Nitrogen Oxygen Periodic table highlighting the most common elements in the human body 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). Between: Mechanism: Ionic Bonding Covalent / Molecular Bonding Metal and Non-metal Two or more non-metals Metal loses e- cation Valence electrons are shared (up to three shared pairs) - Non-metal gains e anion lithium + chlorine lithium chloride Example: Force of Attraction: Li + Cl Li + Cl LiCl [ Li ]+ + [ Cl ]- bromine + chlorine bromine chloride Br Br + + Cl Cl BrCl Br Cl Electrostatic interaction (attraction between positively and negatively charged ions) Physically shared eletron pair(s) Crystal Lattice Individual molecules. Structures vary greatly depending on how individual molecules interact with each other. Depends mostly on: polarity, size and 3D shape Conceptual Diagram: Structure: Polarity Not all covalent bonds behave the same way. Every element has its own characteristic electronegativity. This is an assigned value used to describe an 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 molecules “water loving” HYDROPHYLLIC Non-polar does not dissolve in water “water fearing” HYDROPHOBIC Ionic usually dissolve in water to form aqueous ions dissolve in water 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 (which may also be 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. Another word for a weak acid is a buffer. This is because solutions containing weak acids are able to resist small changes in pH by either producing H+ or consuming H+ in response to changes in H+ concentration. A common buffer (weak acid) in human blood is bicarbonate H2CO3 HCO3− + H+ Types of Reactions Summarize the four most common types of reactions in biology in the table below. Dehydration / Condensation Hydrolysis Neutralization Redox Practice! Answer the following questions on a separate page. 1) Living things are made mostly from just 4 elements. Based on the number of bonds each of them is able to make, propose an explanation for why only these 4 elements are needed to make all of the molecules necessary for life. 2) a) Describe the differences between stable isotopes and radioisotopes. b) Explain how isotopes can be used to study biochemical reactions 3) a) Based on the properties of molecular compounds explain why they are the main components of living things rather than ionic compounds. b) Why are molecular compounds so much more varied than ionic compounds? 4) The molecules that make up organisms seem to obey the same laws of chemistry and physics as all other molecules. How do these molecules fold into complex 3D shapes and self assemble into complex arrangements as is required for living things? In your answer focus on the two most important intermolecular forces we discussed. 5) Explain what is meant by hydrophilic and hydrophobic molecules. Which type would you expect to find more of in living cells and why? 6) What is a buffer and how are they helpful to living things? Textbook Work Pg 18 # 4-10 Pg. 24 # 4, 8, 10 Sample Communication Answers For Question #1 Example #1 Though living things are complex, they are composed almost entirely of just four elements. It is mostly the 3D shape a molecule that determines its function and 3D shape depends on the number of bonds made by the elements in the molecule. Hydrogen, oxygen, nitrogen and carbon represent the full spectrum of potential bond numbers. The minimum number of bonds that an element can make is one and the maximum is four. Hydrogen makes one bond, oxygen makes two, nitrogen makes three and carbon makes four. By combining just these four elements you can make molecules that represent nearly all of the possible 3D shapes that exist in chemistry. Furthermore, these are the simplest, most abundant elements that can form their respective number of bonds. Example #2 It may seem surprising that for all of life’s complexity, organisms are almost exclusively composed of just four elements. These elements are hydrogen, oxygen, nitrogen and carbon. A likely reason for this is that these four elements are the simplest elements that can form a full range of bond numbers. Hydrogen forms just one bond, oxygen forms two, nitrogen forms three and carbon forms the maximum of 4 bonds. By combining these elements, you can form nearly all possible shapes in chemistry. Ultimately it is the 3D shape of biological molecules that determines their function.