Blog Archives

August 21 - 31, 2017

8/20/2017

Housekeeping: So we're done with biochemistry. You have the lab on Friday and a quiz next week (Aug. 30). We will move now into pure chemistry, beginning with an introduction to chemistry and the nature of matter.

Content Review:
Weebly Links: Matter
Link: Substances & Mixtures Elements & Compounds Matter, Elements & Atoms

Student Missions:
Mission 1: The Beginning of All Things.
Mission Objectives. You should be able to...
1. Explain the necessity of studying chemistry.
2. Describe the benefits of chemistry in modern research.
3. Describe the basic procedures at the core of scientific methodology.
4. List the skills used in problem solving.
5. Name the five major areas of study in chemistry

We will do an extensive, exhaustive overview of the nature of chemistry. The good news is that there is a supplemental handout to help you organize your notes. Bear in mind that this is only a smidge of the information you need to know for this unit. Make sure you reference the mission objectives.

Mission 2: What's the Matter?
Mission Objectives. You should be able to...
1. Define "matter" and list its states.
2. Describe matter in terms of physical and chemical properties.
3. Describe matter in terms of physical and chemical changes.

Paul Anderson of Bozeman Science (I met him; he is a REALLY COOL dude) introduces the enormous concept of matter. Need some help organizing it? Look here.

When I was a kid, there were only THREE states of matter. Now we have FIVE. How did we go from three to five? Do you think that, in the future, there will be more states of matter? Can you conceptualize what they may be and how they might be discovered? Use your imagination.

Physical or Chemical? What's the difference and why should we give a hoot? Mr. Anderson continues his series on introductory chemical with this somewhat slightly thrilling podcast. Can you describe what happens to your food as you eat it? What is another name for a chemical change?

Mission 3: Stuff!! What About All This Stuff??
Mission Objectives. You should be able to...
1. Differentiate between substances, mixtures, elements and compounds.
2. List and describe the ways mixtures can be separated.
3. Provide examples of substances and mixtures.

Substances & Mixtures. What's the main difference between substances and mixtures?

Here's a matter packet for you guys to use: http://www.sfponline.org/Uploads/71/matter%20packet.pdf

At some point, you guys will do a lab where you separate mixtures. Watch this video as part of your prep. Download this handout to use for the lab.

Student Missions:
Mission 1: Elements & Compounds. Come on and sing along with me.

Last year, period 7 of the PT was completed with the discovery of four new elements. Scientists everywhere rejoiced (well, some of them) because the predictions came true. Let's learn all about nihonium, moscovium, tennessine, and oganesson.

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Macromolecules Lab Prep

8/17/2017

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You will do a lab next week experimenting with macromolecules. You will be testing for lipids, carbohydrates and proteins.

Go here and download this lab writeup. You should have it read by Wednesday, Aug. 23.

Different foods change color when indicators were added to denote the presence of macromolecules. Why does this happen? To understand this phenomenon, you need to be able to describe the structures of carbohydrates, lipids and proteins and explain why they behave in the way that they do when exposed to certain indicators.

You will have at least three (3) hypotheses. The hypotheses need to be tailored into "if...then" statements that are derived from the information presented in the Introduction. For example, "If nucleic acids are present in a sample, then adding phenolphthalein will turn the sample pink." You will complete three tests, so you should have three hypotheses.

Background Knowledge. Take a look at this interactive link. It describes the six functional groups. What is important for you to understand is what happens during the complementary processes of hydrolysis and dehydration. Another important fact is to understand what happens when electrons are donated by one molecule and received by another. Molecules that donate electrons are called reducing agents and molecules that receive electrons are reduced.

We will be working with three specific reagents: Benedict's reagent, Biuret's reagent, and iodine solution. To test for lipids, we will put the samples in water.

Benedict’s reagent changes color when exposed to a reducing agent, and all monosaccharides are reducing agents. Some disaccharides (like sucrose) have no free carbonyl groups and thus are non-reducing agents.

Biuret's reagent changes color in the presence of proteins because the copper II ions form a complex with the nitrogen atoms. The color change ranges from blue to violet, and the more peptide bonds present, the more violet the change.

Iodine solution is good for identifying the presence of starch because iodine atoms can fit inside the helical structure of starch compounds and change the color from dark blue to black.

If you want to know more (including the overwhelming biochemistry of it all, go here and here.

You need to create a chart for data collection. Remember that you will have three hypotheses. I expect you to run three trials. After you have collected your data, you need to determine if your hypotheses were supported by the data. I strongly suggest you show me your conclusions before you submit your work.

You will turn in your hypotheses, your data table, and your conclusion for a lab grade. Each person will submit their own report.

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August 14 - 18, 2017

8/14/2017

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Housekeeping: It's my understanding that Thursday is a holiday. That means I'll see you guys today and Wednesday. It throws off my plans to have you do a lab this week, so we're pushing it to next week.

Agenda:
1. Macromolecules Review
2. Water
3. Chemical Reactions

Content Review:
Links: Biochem Basics Macromolecules
Textbook Readings:

Student Missions:
Mission 1: Well, It's What We're Made Of, Right?
Mission Objectives. You should be able to...
1. List and describe the essential properties of water.
2. Explain the necessity of hydrogen bonding.
3. Explain the solubility of water and its relationship to transporting molecules in organisms.

Water is the medium of life. Understanding why it is so important requires understanding of its structure. There are two hydrogen ions sharing electrons with an oxygen ion. Sharing of electrons results in a covalent bond. The water molecule is polar, meaning that it has a net charge on one end (the oxygen end). As a result, water can interact with itself and other molecules in different ways. Water has many different properties which makes it so important in living organisms.

Just to make sure you have a handle on what's going on with water, here's a link to help you understand.

Mission 2: Enzymes...Real & True Speed Demons!
Mission Objectives. You should be able to...
1. Describe the function of an enzyme.
2. Explain how an enzyme/substrate is a chemical reaction.
3. List and describe the factors that affect enzyme-catalyzed reactions.

Enzymes are biological catalysts that have specific functions. The reactants for this chemical reaction are called substrates. They bind to the enzyme on the active site, matching up according to their shapes. Once this process occurs, the active site changes shape and the bonds in the reactants are broken down and new bonds are formed into products.

Take a look at this animation. And here is the Amoeba Sisters' take on it.

Factors that affect enzyme-catalyzed reactions:

Temperature. Increasing temperature increases the speed at which molecules move and thus collide. This happens with or without enzymes. However, there is an upper limit to which enzymes can affect reaction rates. This is based on the temperature at which the enzyme denatures and loses its 3D shape.

pH. Negative and positive areas of a substrate must match the opposite charge when the substrate hits the active site of the enzyme in order for the catalytic properties to work. Solutions that are too acidic (that have more H+) cause the H ions to bond to the negative charge on the enzyme or substrate and prevent proper charge matching. Same thing happens with solutions that are too basic (more OH-). Either situation causes the enzymes to be less efficient and possibly denature or be ineffective. Most enzymes work best at a pH of near 7 (neutral) with the exception of stomach digestive enzymes. The stomach is highly acidic.

Concentration of the substrate. Increasing concentration increases reaction rates because of the number of collisions increase. However, like temperature effects, there is an upper limit because when the enzymes are working at optimal levels, adding more substrate won't increase collisions.

Activity: Get to know enzymes on an interactive level with Bioman's Enzymatic Game. Complete the interactive and take the quiz. You only get one chance. Screen-shot your quiz score and send it to me at [email protected]

Mission 3: Chemical Reactions
Mission Objectives. You should be able to...
1. Explain what happens in a simple chemical reaction.
2. Describe the processes of photosynthesis and respiration.
3. Differentiate between endothermic and exothermic reactions.
4. Identify parts of a chemical reaction graph.

Chemical reactions are the process by which elements and/or compounds change into new substances. Chemical equations are written representations of chemical reactions and you can see that the atoms are rearranged. The substances on the left are called reactants and the substances on the right are called products.

In biology, there are two key chemical reactions that you need to be aware of: photosynthesis & respiration. They are complementary processes. Photosynthesis takes place in chloroplasts and respiration takes place in mitochondria. Photosynthesis requires carbon dioxide, water and energy (in the form of sunlight) to produce glucose (a simple sugar) and oxygen. Respiration requires glucose and oxygen and transforms it into carbon dioxide, water and energy (in the form of ATP).

As you can see, both equations are balanced. Any chemical equation must be balanced because mass is always conserved.

Chemical reactions require energy. The minimum amount of energy needed for reactants to form products is called activation energy. (Ea) Once this threshold is reached, no further input of energy is required. If you are looking at an energy curve, the peak represents activation energy. Exothermic reactions are reactions where energy is released because the energy of the reactants is higher than the energy of the products. Endothermic reactions are reactions where energy is absorbed because the energy of the products is higher than the energy of the reactants.

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August 11 - 18, 2017

8/10/2017

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Housekeeping: Well, we've made it through the first week!!!

Agenda:
1. Review
2. Macromolecules
3. Water

Lesson Objectives. By the end of this lesson, you will be able to:
1. Define and distinguish between the four classes of macromolecules
2. Compare and contrast the structure of macromolecules.
3. Name two kinds of each macromolecule (except nucleic acids).
4. Explain why carbon is an essential element in organic chemistry.

Content Review:
Links: Biochem Basics Macromolecules
Textbook Readings:

Student Missions:
Mission 1: Atoms & Molecules Review
Mission Objectives: You should be able to...
1. Recall the structure of the atom
2. Explain the difference between ionic bonding and covalent bonding.

Let's go here and watch a short video.

I'm giving you a handout to work on as we move through this unit.

Mission 2: Big Little Things.
Mission Objectives. You should be able to...
1. Define and distinguish between the four classes of macromolecules
2. Compare and contrast the structure of macromolecules.
3. Name three kinds of each macromolecule.
4. Explain why carbon is an essential element in organic chemistry.

Carbon atoms can form four covalent bonds, which allows a diversity of stable compounds to exist. As a result, carbon-containing organic molecules can form chains, rings, and branched chains. This allows for the assembly of macromolecules.

There are four classes of macromolecules that make up living organisms: carbohydrates, lipids, proteins & nucleic acids. Each macromolecule has its own building blocks. Carbohydrates are composed of monosaccharides (simple sugars), proteins are composed of amino acids, lipids are composed of glycerol, fatty acids, and phosphate groups, and nucleic acids are formed from nucleotides.

The Amoeba Sisters break down the nitty gritty. You need to create a chart or some sort of table that compares and contrasts macromolecules. We will pause at certain points to make sure you understand what you need to know. One thing is to know the structures of each type. What is a functional group? Which macromolecules contain amino groups? Which macromolecules contain carboxyl groups? What are the properties of the functional groups?

Mission 3: Well, It's What We're Made Of, Right?
Mission Objectives. You should be able to...
1. List and describe the essential properties of water.
2. Explain the necessity of hydrogen bonding.
3. Explain the solubility of water and its relationship to transporting molecules in organisms.

Water is the medium of life. Understanding why it is so important requires understanding of its structure. There are two hydrogen ions sharing electrons with an oxygen ion. Sharing of electrons results in a covalent bond. The water molecule is polar, meaning that it has a net charge on one end (the oxygen end). As a result, water can interact with itself and other molecules in different ways. Water has many different properties which makes it so important in living organisms.

For the next class, please come in with construction paper, glue, scissors, colored markers, etc. We will be making macromolecule models and personalized enzymes.

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August 8 - 11, 2017

8/7/2017

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Housekeeping: Good morning! Welcome to the Mad!Lab!

Agenda:
Welcome
Introduction to the course
Class procedures
Housekeeping (5 min)
Warmup & review (10 min)
Missions (20-25 min)
Wrap-up/homework (5 min)
Navigating the website (Where to find…?)

Student Missions
Mission 1: Science SMART!!!
Mission Objectives: You should be able to...
1. Generate at least five lab safety rules.
2. Develop a reasonable method for doing science.
3. Distinguish between research questions, hypotheses and variables.
4. Practice with significant figures and scientific notation.

Sig Figs & Scientific Notation

Mission 2: Thinking and Writing
Mission Objectives. You should be able to...
1. Generate a hypothesis.
2. Identify the independent and dependent variables.
3. Write a research question.

Write a hypothesis for the following statements. Identify the independent and dependent variables.

a. What effect does studying with music have on test scores?
b. What effect does light have on plant growth?

Write a research question for the following. Identify the independent and dependent variables.

c. If plants are watered, then growth will increase.
d. If chocolate is given to teachers, then the amount of assigned homework will decrease.

Let's practice!!!

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