Unit 1: The Chemistry of Life
Reading:
- BJU Biology: Ch. 2
- OpenStax Biology: Ch. 2 & 3
Homework
Various handouts are posted near the bottom. Not all of them will be assigned, so see Canvas for due dates.
Various handouts are posted near the bottom. Not all of them will be assigned, so see Canvas for due dates.
Labs
Note: When I assign a hand-written lab report in this class, follow the format in "Lab Report Requirements" posted on the Policies/Handouts tab. You will find several student examples posted there.
These are the possible labs for this Unit. We will do what we have time to do.
Note: When I assign a hand-written lab report in this class, follow the format in "Lab Report Requirements" posted on the Policies/Handouts tab. You will find several student examples posted there.
These are the possible labs for this Unit. We will do what we have time to do.
- Make and test O2 and CO2
- pH, Acids & Bases Weblab
- Food chemistry lab
- DNA extraction lab
- Enzyme lab
- Water's polarity
- Carbon lab
| 1._biology_lecture_notes_-_inorganic_chemistry.docx |
| biomolecules lecture slides.pptx |
Lecture outline
Atoms and molecules:
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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There are four (4) biochemical groups: Proteins, Carbohydrates, Lipids, and Nucleic Acids. We obtain these molecules through what we eat (dietary uptake) and what our cells manufacture.
Proteins:
- Protein molecules are constructed from long chains of amino acids. There are 20 different amino acids; your body can manufacture about half of them, and you need to obtain the other half in your food (these are known as "essential amino acids" - because it's 'essential' that they are in your diet).
- Protein molecules are the ‘workhorses’ of the cell. They function as the structural parts of the cell, the chemical messengers of the cell, and the numerous enzymes which enable the cell’s metabolism to proceed.
- There are around 100,000 different types of specific proteins in our bodies. No doubt you have heard of some - collagen, keratin, insulin, amylase, and so on. Discovering new proteins, and what they do, is a major focus of research in biomedicine and other areas.
Carbohydrates:
- Carbohydrates are made of carbon, hydrogen, and oxygen, always in a C1H2O1 ratio.
- Simple carbohydrates are the sugars such as glucose, sucrose, and fructose.
- Complex carbohydrates include starch, cellulose, and glycogen.
- Carbohydrates perform many functions in the cell. They form the structural elements of plants (cellulose), they function as intermediate energy storage for the body (glycogen) as well as quick energy (glucose), and perform many ‘packaging and shipping’ functions in the cell by serving as chemical markers
Lipids:
Nucleic acids:
- Lipids (fats & oils) are the long term energy storage source in the body.
- Lipids also provide insulation, padding/protection, and lubrication functions
- Lipids also provide the membranes of the cell. Cell membranes are constructed of phospholipids arranged in a double layer, called a “phospholipid bilayer”.
- In the body, fats consist of three long carbon-hydrogen chains bonded at one end to a glycerin molecule, from where they get the name ‘triglycerides’.
- Lipids contain 9 kcals/gram of energy, compared to just 4 kcals/gram for proteins and carbohydrates. This is because they are more ‘reduced’; i.e. there are more C:H chemical bonds which can be oxidized to produce energy
Nucleic acids:
- The nucleic acids, DNA and RNA, contain the coded information necessary for all life.
- DNA is a 'parts list' for proteins. In other words, DNA contains the information needed to build the various protein molecules. We will cover this topic later in the course.
- RNA is the "Post-It Note" that carries the instructions from the nucleus out to the cell factory. We will cover this later.
Enzymes:
- Enzymes are in the protein family of molecules
- Enzymes act as catalysts which enable chemical reactions. An example is amylase, an enzyme in saliva which breaks down carbohydrates into sugars as you chew your food.
- Enzymes can also be very complex nano-machines which perform complicated tasks. An example is ATP Synthase, a rotary turbine in the Mitochondria which spins very fast and charges ATP molecules (we will look at a video of this).
DNA and Cell videos
At this point, we need to start forming a "visual picture" of what goes on in a typical cell. The biomolecules we have been discussing all play important functions in the cell, and it's necessary to start building a mental picture of what is actually going on. We will watch these and discuss them in class...
Below: "Inside the Cell".
At this point, we need to start forming a "visual picture" of what goes on in a typical cell. The biomolecules we have been discussing all play important functions in the cell, and it's necessary to start building a mental picture of what is actually going on. We will watch these and discuss them in class...
Below: "Inside the Cell".
Below: Journey Inside the Cell (3 min)
Below: DNA winding and replication (3 min)
Below: James Watson explains how they worked out the structure of DNA (2 min)
Homework handouts
| 1._inorganic_chemistry_questions (for biology).docx |
| client_report_for_hans_spielman__2021_.docx |
| "The DNA Double Helix" |
| 2._dna_double_helix_homework_questions.docx |
Food Tests Lab
| 2._food_tests_lab_handout_for_starch_sugar_proteins_lipids.docx |
O2 and CO2 Lab
| o2_lab_handout.pdf |
| co2_lab_handout.pdf |
pH, Acids & Bases Weblab
| ph_acids_and_bases_weblab.docx |
DNA Extraction Lab
| Lab handout: DNA_extraction_from_kiwi_strawberry_1 page_handout.pdf |
| DNA_extraction_explaining_all_the_steps_22slides.pptx |
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