Unit 1: The Chemistry of Life I: Atoms and molecules
Reading: (weeks 1 & 2)
- OpenStax orange book: Ch. 2 - "Chemistry of life", sections 2.1 & 2.2
- BJU: 2A - "Basic chemistry"
- AP: Green book: Ch. 2 "The Chemical Foundation of Life"
Topics
- Atoms and molecules
- Chemical bonding
- Water
- Oxygen (O2) and carbon dioxide (CO2)
- pH, acids and bases, buffers
Homework
Handouts are posted near the bottom of page. (see weekly class email for instructions and due dates)
Handouts are posted near the bottom of page. (see weekly class email for instructions and due dates)
Labs
Our Chemistry/Biochemistry lab is described in Unit 2.
Our Chemistry/Biochemistry lab is described in Unit 2.
Below: The carbon atom is the backbone for the molecules of life - proteins, carbohydrates, lipids, and nucleic acids
| 1._biology_lecture_notes_-_inorganic_chemistry.docx |
| biomolecules lecture slides.pptx |
Lecture outline
Atoms and molecules:
- All matter in the universe is made up of one or more of the 'elements' on the Periodic Table - shown below.
- Any element by itself - Oxygen (O), Carbon (C), or Nitrogen (N) - is called an atom. The atom is the smallest unit of an element.
- When atoms combine, they form molecules. Examples are water (H2O), oxygen gas (O2), and carbon dioxide gas (CO2).
- Atoms and molecules are very small! Even the simplest living cell is made from trillions and trillions of atoms and molecules.
Chemical bonding:
- Ionic bonds are common in salts. Sodium (Na) will stick to Chlorine (Cl) to form sodium chloride, or table salt (NaCl), with an ionic bond. When dissolved in water, the sodium and chlorine break apart to form charged particles known as ions. The positive ion, sodium, is then known as a cation, while the negative ion, chloride, is known as an anion.
- Covalent bonds are the result of 'electron sharing', and occur in molecules. Examples are water, protein molecules, sugars and carbohydrates, DNA, RNA, and the fats & oils.
- Hydrogen bonds are intermediate attractive forces between certain molecules. A hydrogen bond will form between a hydrogen atom (H) on one molecule, and a nitrogen (N), oxygen (O), or fluorine (F) atom on an adjacent molecule. Examples: the hydrogen bonding between water molecules make it an excellent solvent, and the two strands of the DNA 'double helix' are held together by hydrogen bonding.
- Van der Waals forces are weak attractive forces between molecules, caused by uneven distributions of electrons.
- The sometimes-confusing term, compound, is a more generic term to describe molecules and ionic substances. For example, sodium chloride (NaCl), an ionic salt, is technically not a molecule - so we can use the term 'compound' in a broad sense to describe all ionic substances and molecules with more than one atom.
Covalent bonding between two atoms
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Ionic bonding between two atoms
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Water:
- Water is the most important and abundant chemical compound in living things.
- Most of the body's chemical reactions occur in a watery medium. Plants and animals need water to keep minerals in solution, and transport things around.
- The water molecule (H2O) is polar; thus, it is an excellent solvent for polar substances such as minerals and sugars. (in other words, it keeps these in solution very well)
- On the other hand, water is not a suitable solvent for fats and oils, because these are non-polar substances.
- Interestingly, fats and oils dissolve quite well in non-polar solvents like other oils and hydrocarbon substances.
Oxygen and carbon dioxide:
- Two oxygen (O) atoms will bond together to form the gaseous molecule we call oxygen (O2). Oxygen is known as the 'great attacker', because it supports combustion. In your body, the oxygen you breathe-in is used to carry out 'cellular respiration' - the process of breaking down your food/fuel into usable energy. Your body is quite literally a 'furnace' which burns your food very slowly and produces energy and body-heat. We will be discussing this in more detail later in the course...
- One carbon atom (C) will bond with two oxygen atoms (O) to form a gaseous molecule known as carbon dioxide (CO2). You breathe-out carbon dioxide as a waste product. The plant kingdom, on the other hand, uses carbon dioxide to build the sugars and carbohydrates needed to construct their leaves, stems, branches, fruit, etc - in a process known as Photosynthesis. More on that later in the course...
- Thus, the animal and plant kingdoms are mutually dependent. One uses oxygen and throws away carbon dioxide, and the other does the opposite.
- If you bubble CO2 into water, it will lower the pH (it will become more acidic).
- If you lower a glowing broomstraw into a test tube of pure O2, it will burst into bright flame. If you lower-in a red-hot piece of steel wool, it will also burst into bright flame!
- If you lower a lit candle into a jar of pure CO2, it will instantly go out. You can also 'pour' CO2 out of a jar on top of a lit candle, and it will instantly go out!
Acids, bases, and the pH scale:
- Acids will dissolve metals, and will donate hydrogen ions into a solution. Examples are citric acid (lemons), acetic acid (vinegar), and carbonic acid (soda pop). Strong industrial acids include hydrochloric acid and sulfuric acid.
- Bases will neutralize acids (and vice versa), and most will donate hydroxide ions into a solution. Examples are calcium hydroxide (lime, Tums), sodium hydroxide (drain cleaner), and ammonium hydroxide (household ammonia).
- Buffers are substances that absorb excess acidity or basicity, and balance out (buffer) a system. Your body uses "bicarbonate" and "phosphate" buffers to maintain the pH of your blood and bodily fluids at an optimal level. An example of a buffer in your kitchen is sodium bicarbonate - also known as "baking soda".
- pH is how we measure acidity and basicity. The pH scale goes from 1 to 14. Anything below 7 is acidic; above 7 is basic; and right at 7 is neutral.
- You can measure the pH of something using colored pH paper, or a digital pH meter
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Homework handouts
| 1._inorganic_chemistry_questions.docx |
| main_chemical_elements_in_the_body_1p.pdf |
| ph_scale.pdf |
| glucose_fructose_sucrose.pdf |