Biology
Biochemistry

Biochemistry

Standards

SB1. Students will analyze the nature of the relationships between structures and functions in living cells. 


Learning Tasks

 


Key Terms

Click here to download a list of key terms for this module. 

 



Pre-Assessment Water and Macromolecules

This activity is not for a grade and will not be considered as part of your course requirement.  However, it will give you an idea of what you already know and topics where you need additional instruction. Please choose true or false for the following statements.

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When you are ready, go to the navigation bar for the course and click on QUIZZES. Choose the quiz titled Pre-Assessment: Water and Macromolecules 


Notes: Chemistry of Water

Image of Earth landing in a drop of water  

According to data from NASA, water covers 75% of the Earth's surface. It is the single most abundant compound in living organisms. Water has several important physical properties:

Image of water molecule

The Water Molecule

Overall, water is a neutral molecule.  In other words, it has the same number of protons as electrons.  However, the electrons are unequally distributed.  The oxygen atom, with its eight positively charged protons, has a strong pull on the negative electrons which makes the probability of finding those electrons near the oxygen greater than finding them near the hydrogen atoms.  This gives the oxygen end of the water molecule a slightly negative charge and the hydrogen ends of the water molecule slightly positive charges.
 
For a better understanding of water, click here to see how water molecules are connected by hydrogen bonds.

 

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The unequal distribution of charges on a molecule results in polarity (having a positive pole on one end and negative on the other). Water molecules' positive and negative charges cause opposite ends of water molecules to attract each other like tiny magnets.

 

Another representation of a water molecule

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If a water bug can walk across the water, why can't a frog? It's an interesting question. In order to answer this question, you need to know a lot more about the properties of water.

Get some answers by viewing the following animation, A Closer Look At Water from Northland College and reading about surface tension from Boise State.

 

 

Hydrogen bonds (intermolecular or between the molecules) exist between water molecules.  Hydrogen bonding is weaker than most other types of chemical bonds, allowing them to be broken by other charged substances.  The bonding of water molecules due to their polarity allows for several unique chemical properties: 

The forces of cohesion and adhesion work together to produce capillary action, the force of water rising in a thin tube.  This force makes it possible for water to travel up the thin tubes inside plants from roots to leaves.  Adhesive forces cause the water molecules to be attracted to the insides of the tubes.  The cohesive forces cause the water molecules to cling to each other.

 

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Hydrogen molecules bonding between water molecules To learn more about the chemical behavior of water, visit and complete the tutorial, the Chemistry of Water.

Note that water often is found in nature as a mixture.  A mixture is a material that is composed of two or more substances that are physically combined. Examples of combining two substances physically include mixing iron filings with sulfur or dissolving sugar into hot tea. There are two types of mixtures that can be made with water.

 

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Solutions and Suspensions: 

Bloodbag

 

What is blood? Blood is an example of a biological fluid that is both a solution and suspension.  There are some molecules that are evenly distributed throughout the plasma and others that are not evenly distributed.

 

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Acids, Bases and pH

Water molecules can dissociate, or come apart, into two ions:

H2O → H+ + OH-

water → hydrogen ion + hydroxide ion

 

Scientists have devised a scale to measure the concentration of hydrogen ions (H+) and hydroxide ions (OH-) that exist in solutions.  The scale is called the pH scale.  The pH scale ranges from 0 to 14.

 

When a solution such as water has equal amounts of H+ and OH- ions, the solution has a neutral pH.  The pH scale is based on 7 as the reading for neutral.

When a solution has a greater amount of H+, then it is assigned an acidic pH which is a number below 7 on the pH scale.

When a solution has a greater amount of OH, then it is assigned a basic pH which is a number greater than 7 on the pH scale.

 

The image below from the Environmental Protection Agency webpage about Acid Rain shows the pH of some common substances:

pH scale and link to EPA information about pH related facts  

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All living organisms have a set range of pH levels that are optimal for their growth and development.  Sudden changes in pH levels can harm organisms.

The pH inside human cells must be kept close to neutral in the range of 6.5 to 7.5.  If a chemical with a lower or higher pH enters the cell, it could disrupt chemical reactions and disrupt the cells' homeostasis.  Therefore, cells contain weak acids and weak bases called buffers which work to neutralize substances inside cells that are too acidic or too basic.

 


BrainPOP Video: Water

View the BrainPOP movie entitled Water.

Screenshot of and link to BrainPop movie about the properties of water

 

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After viewing the movie Water, click on the QUIZZES link in the navigation bar. Choose the quiz titled Water, BrainPOP.

 

To really gain some insight into how impressive water is, use a 3D interactive simulation of water molecules condensing into a hydrogen-bonded droplet. Clicking on the controls at the bottom of the window allows you to rotate and zoom in and out. You can also use your mouse to drag and rotate the 3D model of the water atoms.

Image of and link to an interactive simulation of water molecules condensing into a hydrogen-bonded droplet

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If that seems intriguing, you might also want to check out a similar simulation of intermolecular hydrogen bonds in liquid water and in ice. Both of these engaging simulations and others are available by way of Molecular Visualization Resources (all free and open source) collected by Eric Martz.

 


Properties of Water and pH Study Guide

Answer the questions listed below. You can click here to download a word processing document with the questions. Your notes on water will be helpful as you complete this assignment. Place the completed assignment in your notebook.

 

The Water Molecule

image of water molecule

 

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1. Is the following sentence true or false? A water molecule is neutral. 

2. Why is a water molecule polar?
3.
Write the letter of each sentence that is true about hydrogen bonds. 

a. A hydrogen bond is stronger than an ionic bond.

b. The attraction between the hydrogen atom on one water molecule and the oxygen atom on another water molecule is an example.

c. A hydrogen bond is stronger than a covalent bond.

d. They are the strongest bonds that form between molecules.

  

FORMS OF ATTRACTION

image of beads of water on grass blade

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4.
Complete the table about forms of attraction.

Form of Attraction

Definition

Cohesion

 ?

Adhesion

 ?

  

5. Why is water extremely cohesive? 
6.
What is the rise of water in a narrow tube against the force of gravity called?
7.
How does capillary action affect plants? 

 

Solutions and Suspensions

8. What is a mixture?
9.
What is a mixture of two or more substances in which the molecules of the substances are evenly mixed called?
10.
The greatest solvent in the world is what? (Hint: It's also known as a universal solvent.)
11.
What is a suspension? 
12.
Complete the table about substances in solutions.

 

SUBSTANCES IN SOLUTIONS

Substance

Definition

Saltwater Solution

Solute

 ?

 ?

 ?

 ?

Water

 

 

Acids, Bases, and pH

pH scale and link to EPA information about pH related facts

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13. Water molecules can dissociate to form what?
14.
Why is water neutral despite the production of hydrogen ions and hydroxide ions? 
15.
What does the pH scale indicate?
16.
On the pH scale, in which direction do solutions become increasingly acidic and in which direction do they become basic?
17.
How many more H+ ions does a solution with a pH of 4 have than a solution with a pH of 5?


18.
List the letter of each sentence that is true about acids. 

a. Acidic solutions have pH values below 7.

b. An acid is any compound that forms H+ ions in solution.

c. Strong acids have pH values ranging from 11 to 14.

d. Acidic solutions contain higher concentrations of H+ ions than pure water.


19.
List the letter of each sentence that is true about bases. 

a. Alkaline solutions have pH values below 7.

b. A base is a compound that produces OH ions in solution.

c. Strong bases have pH values ranging from 11 to 14.

d. Basic solutions contain lower concentrations of H + ions than pure water.


20.
What are buffers? 

 


Properties of Water Assignment Check

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You should have your Properties of Water and pH Study Guide finished and with you as you complete this assignment check. You will have 10 minutes to complete this assignment check.

When your are ready to start, go to the navigation bar, click on QUIZZES and choose Properties of Water Study Guide AC.

 


Build It!

Visit the MolviZ website where you can examine the three dimensional structure of molecules that are very important to living organisms.

Screenshot of and link to Molviz,org--a site with 3 dimensional models of molecules

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Three Dimensional Models of Molecules

image of girl building molecules

Using common household objects or materials, build a couple of 3D models.

 

Create ONE of these:

 

Create ONE of these:

 

Ideas for materials:

 

If you can take a digital photo of your creation, please e-mail it to your instructor. Photos may be posted for other students to see!

 


Biochemistry - Virtual Lab: pH of Common Substances

Click here to download a word processing document of the data table below.

 

After that, visit John Kyrk's interactive Power of Hydrogen (pH scale) resource. You'll need to click on the button in the lower left hand side of the screen to advance to the interactive pH scale. The button looks like this:

Image of a button

Once you get to the interactive pH scale, complete the data table below for each substance by moving the slider VERY SLOWLY to the correct pH. The pH of each item and if the item is an acid or a base. When you have found the correct pH, the substance and the pH will be listed on the top of the screen. Take your time.

Table and link to word processing document that asks participants to ascertain whether given substances are acids or bases

 

Kyrk, a San Francisco biologist and artist, also has a number of stunning Cell Biology animations that will prove useful to you later in this course.

 

After completing the table, visit some or all of the additional sites listed below. Doing so will help you gain a better understanding of what pH is and how we categorize substances as either acids or bases.

 

The interactive simulation below from PhET allows you to test the pH of substances such as coffee, saliva, and soap to determine whether each is acidic, basic, or neutral. The simulation visualizes the relative number of hydroxide ions and hydronium ions in solution. It can be used to investigate whether changing the volume or diluting with water affects the pH. You can also design your own liquid.

pH simulation screenshot

Additional web-based resources:


 

Notes: Macromolecules


Assortment of macromolecules

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There are 4 classes of large molecules that make up the majority of living things. They are called Macromolecules.  Since macromolecules are generally made up of many smaller molecules and atoms, they are referred to as polymers.  Polymers are made up of smaller units known as monomers.

The macromolecules of life are:

We will look at each to determine the make-up, functions and examples as found in living things.

Ever wonder where life's molecular building blocks come from? If so, take a look at the Molecular Logic Project's nifty concept map. The Molecular Logic Project's mission is to improve the ability of all students to understand fundamental biological phenomena in terms of the interactions of atoms and molecules.

Image of and link to a graphic organizer from the Molecular Logic Project.

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In order to gain a better understanding of macromolecules and the molecular building blocks that comprise them, you may want to visit and use MolviZ.Orgwhich contains a number of molecular visualization resources initiated and authored or managed by Eric Martz (University of Massachusetts, Amherst).

Screenshot and link to MolviZ.org

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CARBON CHEMISTRY

Carbon compounds are found in all living things and are called organic compounds. Several properties of carbon contribute to its versatility:

 

Inorganic compounds are those that do not contain carbon; many are also essential to life.  Water, nitrate and phosphate compounds are required, but are not organic. Exceptions to the 'carbon' rule are Carbon Dioxide and Carbon monoxide. They contain carbon, but are not considered organic.

 

Just to make sure you get the idea: Carbon (solid), Hydrogen (gas), Oxygen (gas), and Nitrogen (gas) are among the four most common elements found in living organisms (just remember CHON). These four elements are also notable for being the least massive (and having the lowest atomic number) in their group in the periodic table.


CARBOHYDRATES

Carbohydrates - macromolecules composed of carbon, hydrogen and oxygen in a ratio of 1:2:1.     

Ex:  glucose, C6H12O6

Carbohydrates are sugars; sugars can be simple monomers, such as glucose or fructose, or complex polymers, such as starch.

 

Polysaccharides are large sugar molecules composed of many smaller units, linked together in complex arrangements.  Starch and cellulose (as depicted in the 3D model below), made by plants and glycogen found in animals are types of polysaccharides.  Starches and glycogen are used to store energy; cellulose is the structural component of cell walls.

Image and link to model of polysaccharide known as cellulose
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Disaccharides are sugar molecules with only two monomers; table sugar is an example of a disaccharide.  These types of sugars are generally used as a source of energy.

 

This is sucrose, a common disaccharide.

image of sucrose or Saccharose  

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Here's another representation of sucrose as well.

Image and link to a 3D model of sucrose.

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Monosaccharides are the monomer units of carbohydrates; they are glucose, fructose and galactose.

Representation of glucose and fructose

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LIPIDS

Lipids are macromolecules composed of mostly carbon and hydrogen chains; primarily fats, waxes oils and steroids

Monomers (single) units of lipids are made of fatty acids attached to a glycerol molecule.  They usually combine in a ratio of 1 glycerol to 3 fatty acids. What you see below is ball and stick model of glycerol. Glycerol is a type of alcohol with a hydroxyl group on each of its three carbons.

 

Image of glycerol molecule

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Glycerol along with 3 fatty acids make a monomer of lipid.

 

Add a few things to glycerol (like fatty acids) and you have the ingredients for substances that are extremely useful to living things. For example, triglyceride is glyceride in which the glycerol is esterified with three fatty acids. You'll find it in stuff like vegetable oil and animal fats.

 

Image of and link to informationa about triglyceride

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Examples of lipids are fats, oils, waxes and steroids. Lipids are not soluble in water. The fatty acids can be saturated or unsaturated.

Lipids have a lot of important jobs in living things. Some of these are:

They form waterproofing (waxes) act as

To learn more about lipids, click here to visit J. Stein Carter's webpage devoted to the topic.

Screenshot of and link to a webpage about lipids


NUCLEIC ACIDS

Nucleic acids - macromolecules containing hydrogen, oxygen, nitrogen, carbon and phosphorus and are associated with organism's genetic code.

Monomer (single) units of nucleic acids are called nucleotides.  One nucleotide consists of a 5-carbon sugar, a phosphate group and a nitrogen base.

 

Two examples of nucleic acids are deoxyribonucleic acid (DNA), and ribonucleic acid (RNA).  

Image depicting how the process of transcription is carried out by RNA polymerase, using DNA as a template to produce RNA

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The function of nucleic acids is to store and transmit genetic information (chemical instructions about how living things should form and operate).  You will learn much more about nucleic acids in a future unit of study.

PROTEINS

Proteins - macromolecules containing carbon, hydrogen, oxygen and nitrogen; proteins are considered the building blocks of tissue

Monomer units of proteins are called amino acids.
Amino acids can link together and form molecules called proteins.

Proteins perform several critical jobs in cells. Functions of proteins include:

 One of the most important types of proteins is called an enzyme:

Enzymes can be synthetic (they can build up) or hydrolytic (they can breakdown or digest). They are very specific for their substrates. Most end in -ase .

SUBSTRATE... ENZYME ... PRODUCTS

 

Enzymes must have the best environmental conditions to operate most efficiently. This is called their optimum enzyme activity.

The three (3) conditions that limit enzyme activity are:


Click here to visit Chem4Kids and read more about enzymes.

 


Body Chemistry BrainPOP

 

View the BrainPOP movie entitled Body Chemistry.

Screenshot of and link to BrainPop Body Chemistry video

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After viewing the movie, click on the QUIZZES link in the navigation bar. Choose the quiz titled Body Chemistry, BrainPOP.

 


Macromolecules Video and Questions

Here are a few questions and concepts that you should be familiar with as you explore what living things need. All of the questions are related to macromolecules.

  1. All organic chemical compounds possess one thing in common.-all of them contain the element ____________.
  2. Carbohydrates are made up of three different elements in a ratio of 1:2:1.  In order, these elements are __________, ________, and _______________.
  3. A simple sugar called _____________, whose chemical formula is C6H12O6 is broken down during glycolysis.
  4. Creating larger molecules from smaller molecules is called__________________.
  5. What three elements make up lipids?
  6. What is stored in the chemical bonds of lipids?
  7. Proteins are made up of chains of simple molecules called__________.
  8. What is the job of an enzyme?
  9. Nucleic Acids are made up of chains of simple molecules called__________.
  10. What holds your master set of instructions that control both the day to day operations and the reproduction of cells?

 

In order to find answers to these and other related questions consider watching the following video clips. Each clip reveals important information about macromolecules.

Watch the videos in the video showcase below. You can move from one video to the next by using the arrow in the upper right hand corner.

Macromolecules Video Clips:


Macromolecules Video and Questions Assignment Check

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You should have your Macromolecules Video and Questions finished and with you as you complete this assignment check. You will have 10 minutes to complete this assignment check. Go to the navigation bar, click on QUIZZES and choose Macromolecules Video and Questions Assignment Check.

 


Macromolecules Organized

In this assignment, you will organize your information about the macromolecules in a form that will illustrate all the important facts in a neat and brief format. The following information must be included for carbohydrates, proteins, and lipids:

 

You may use a concept map or some other outline or other presentation format. You may:

For example, by using a simple tool such as Text2Mindmap (it's free!) and following a few instructions, you can turn an outline like this...

simple outline about carbohydrates

into a simple mindmap like this...

 concept map about carbohydrates

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If you need a few ideas to get you started, take a look at concept maps other people have created.

This macromolecule concept map was created with CMap.

Use this rubric to assess your work before submitting it.

 

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Submit your finished work to the DROPBOX titled Macromolecules Organized.

 



Recorded Lecture Notes: The 4 Macromolecules

The following recorded lecture accompanies the notes that are provided in this unit.

Screenshot of and link to a presentation that accompanies notes about macromolecules that have been provided in this unit

 


Virtual Macromolecule Labs

Read and or download the questions listed below. Answering the questions below will help you practice using what you know about macromolecules. Visit the Oklahoma Community College website Biology Labs Online's Organic Molecules website. Once there carefully read and follow instructions to test substances for the presence of the four macromolecules. When you have completed your work, submit it to the dropbox entitled Virtual Macromolecule Labs

screenshot of and link to a virtual macromolecule lab activity

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Carbohydrates Lab:

1.  List the steps and reagent used to test for simple sugars: What does a positive test reaction look like?
2.  List the steps and reagent used to test for starch: What does a positive test reaction look like?

Protein Lab:

List the steps and reagent used to test for protein:

What does a positive test reaction look like?

Lipids Lab:

List the steps and reagent used to test for lipids:

What does a positive test reaction look like?

Foods:

Perform the carbohydrate, protein and lipids tests on the foods shown and record the positive test results below:

Potatoes are a ___?

Orange juice is a ___?

Almonds___?

Eggs___?

Salmon___?

Milk___?

 

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Submit your work to the DROPBOX entitled Virtual Macromolecule Labs.

 


Ingredients for Life: Carbon

Star Trek: The Motion Picture was a movie produced in 1979 that was based on the idea that an artificial life form comes to earth looking for carbon-based units.  With all the carbon, hydrogen and other substances in the universe, could it be possible? Is life without carbon really possible?

Such ideas aren't new and have intrigued speculative scientists and artists alike. In the trailer for the 1957 film The Monolith Monsters, movie-goers imagined the results of relentless silicon life-forms ravaging our planet in a horrific, systematic fashion.

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Watch the following short video Ingredients for Life: Carbon from Teacher's Domain and learn why carbon is vital to life (at least, on our planet, Earth).

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After viewing the video, write a paragraph expressing your opinion about the possibility of life somewhere out there in space. You might also want to consult other resources about hypothetical types of biochemistry such as speculations on ammonia-based life and silicon-based organisms.

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Submit your completed work to the DROPBOX titled Ingredients for Life.

 


Protein Structure Animation

 

Image of a protein structure

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Proteins are composed of chains of amino acids arranged in a specific sequence.  That sequence is referred to as its Primary Structure.  The way it bends, twists, bonds, folds and groups with other chains make up its Secondary, Tertiary and Quaternary structures. View a protein structure animation and watch for these four protein structures. There is no assignment but you should be familiar with these structures for future quizzes or tests.

Proteins are made in the process of translation, where RNA is translated on ribosomes to synthesize proteins from amino acids. RNA is synthesized from DNA, and enters the ribosome where protein translation and synthesis occurs. Watch the video below to gain a better understanding of the process.

 

You might also want to watch a Learner.org video about the three-dimensional structure of a protein. Afterward, consider examining an Introduction to Protein Structure which is part of the Rediscovering Biology series also made available from Learner.org.

Screenshot and link to Annenberg video about the structure of proteins

Understanding the structure of proteins is extremely important. When proteins behave properly, they assemble and fold into shapes that help them carry out their important tasks. However, when proteins do not fold properly, there are numerous tragic consequences. For example, many well known diseases, such as Alzheimer's, Mad Cow (BSE), CJD, ALS, Huntington's, Parkinson's disease, and many Cancers and cancer-related syndromes are related to proteins that have not folded properly.

 

Folding@home is a distributed computing project that studies protein folding and misfolding. The webpage for the science behind Folding@home project has rich and useful information about:

Screenshot of and link to the Folding@Home protein folding website

 


Biochemistry of Water Discussion

Water, water, everywhere!  Water plays an important role in our world. The water we use on earth today is exactly the same water that existed billions of years ago. Water is a finite resource. There is no more and no less. Continually recycled and refreshed in its various forms as liquid, vapor, and ice, water is an incredible substance. Living things need water for life. In this discussion we are going to play the "What If?" game.  You will use your notes or a website you have found that describes the properties of water.
image showing water in different forms

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You will:

 

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Post your work to the DISCUSSION titled Water Discussion. You must comment on at least two other person's discussions.

 


Resources on Macromolecules

Macromolecules Review


For a review of the macromolecules covered in this unit, visit the Macromolecules tutorial below and do the following:

1. Read the Introduction

2. Click on the Animation Tab and choose the Narrated button at the bottom.  

3. Select one of the molecule categories and click Play (multiple times to watch the entire tutorial).  Repeat for the other categories.

4. Click the Quiz tab and test yourself to see how much you have learned!

 



Assignments

Before continuing on to the Unit Test, be sure the following graded items have been completed. Click on a link below to return to the page in the module containing the assignment.

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Water BrainPop Quiz

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Properties of Water Study Guide AC

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Body Chemistry, BrainPOP

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Macromolecules Video and Questions Assignment Check

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Macromolecules Organized

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Virtual Macromolecule Labs (counts as lab)

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Ingredients for Life

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Water Discussion

 

 


Biochemistry Unit Test

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Go to the navigation bar and click on QUIZZES. Choose the selection titled Biochemistry Unit Test.