The Chemistry of Life II: The larger biomolecules
Reading
OpenStax book: Ch. 2 - "Chemistry of Life" section 2.3 to the end
BJU: 2B - "Organic chemistry"
AP students additional reading: Princeton Review ""Chemistry of Life" from Organic Molecules to the end.
OpenStax book: Ch. 2 - "Chemistry of Life" section 2.3 to the end
BJU: 2B - "Organic chemistry"
AP students additional reading: Princeton Review ""Chemistry of Life" from Organic Molecules to the end.
Topics
Labs
Memo: 2020-2021 labs will include hands-on and virtual, and may vary as the Covid-19 situation changes. Some of you want more hands-on than others. We will do what we can do.
There are many good "chemistry of life" labs, we can choose from the list below.
DNA (left) and Sucrose (right): two examples of "macromolecules"
- Proteins, carbohydrates (sugars), lipids (fats & oils)
- Nucleic acids (DNA and RNA)
- Enzymes
Labs
Memo: 2020-2021 labs will include hands-on and virtual, and may vary as the Covid-19 situation changes. Some of you want more hands-on than others. We will do what we can do.
There are many good "chemistry of life" labs, we can choose from the list below.
- Make and test O2 and CO2
- Measure pH
- Food chemistry lab
- DNA extraction lab
- Enzyme lab using H2O2 and peroxidase (fulfills AP "dirty dozen lab" #12)
- There are virtual lab versions of these, as well
DNA (left) and Sucrose (right): two examples of "macromolecules"
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Lecture outline
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:
Carbohydrates:
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: James Watson explains how they worked out the structure of DNA (2 min)
Below: DNA winding and replication (3 min)
Below: Journey Inside the Cell (3 min)
Print out "The DNA Double Helix" and have it with you during the lecture. We will review this together in class. You will have some homework questions taken from this paper, so it's important to have in front of you so you can circle key portions.
| "The DNA Double Helix" |
LABS & HOMEWORK BELOW: There are numerous labs, projects, presentations, and homework exercises posted on this portal. Don't panic. Some of these are current, some are left over from prior years, and some are just "parked" here for future use. DO NOT WORK ON A LAB OR HOMEWORK EXERCISE unless it has been assigned in your weekly class email! Due to the 2020-2021 Covid-19 situation, I will assign labs and homework as we go along based on what we are able to do.
Homework
Homework will be posted here with instructions....
You will have something due every Monday - either a homework assignment or a lab report. You will always be given a week to complete the assignment, and you will usually turn it in on Canvas. Instructions will be given in your weekly class emails - usually emailed on Mondays. Make sure I have your correct email address(es)!
Homework will be posted here with instructions....
You will have something due every Monday - either a homework assignment or a lab report. You will always be given a week to complete the assignment, and you will usually turn it in on Canvas. Instructions will be given in your weekly class emails - usually emailed on Mondays. Make sure I have your correct email address(es)!
DNA Extraction Lab
| DNA_extraction_from_kiwi_strawberry_1 page_simple_protocol.pdf |
| DNA_extraction_explaining_all_the_steps_22slides.pptx |
| DNA_extraction_long_version_58_slides.pdf |