Name: ___________________________________________ Block: ______ A / B
Unit 2: Biochemistry
Atoms, Elements and Compounds
Read This!
We know that all living things are made of at least 1 or more cells. Inside of all cells there are organelles that
have specific functions that allow the cell to function as a whole. We know that living things create proteins,
reproduce, create energy, and some cells can even produce their own food! Finally, we understand that even
within the same organism, cells look and behave differently depending on what their function is (cell
specialization).
For cells to perform all of their functions, they require materials from their external environment. Our goal in
this unit is to understand what materials living things need from their environment AND why those materials
are so essential for survival. Next unit we will look at HOW the cells obtain those materials.
I. What does a cell need from its environment?
A. Brainstorm with your group to create a list of materials that a cell needs from its environment.
✔ ✔
✔ ✔
✔ ✔ .
B. Many of the materials you listed above are molecules formed when 2 or more atoms join together.
1. What is an atom?
C. Molecules that are made up of 2 or more different atoms are called compounds.
2. Circle the materials above that you think are compounds.
D. Read This! There are four unique characteristics of compounds:
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II. What holds molecules & compounds together?
Read This!
Chemical bonds hold atoms together to create molecules.
As mentioned, if two or more different types of atoms are bonded,
they form a compound. You will learn much more about chemical
bonds in chemistry next year. This year, only one of type of bond is
really essential: Covalent Bonds.
A. Review of atom structure
Parts of the atom- Using Figure 2-1 at right,
fill in the table below (IDENTIFY and indicate the charge & location of each)
Subatomic Particle Charge Inside the nucleus? Or outside?
1.
2.
3.
B. Covalent Bonding
1. Observe the pictures at the right. Which subatomic particle is involved
in the attraction or bond that is occurring between the atoms? What
makes you say that?
2. Describe what holds 2 or more atoms together when they are covalently
bonded.
3. Covalent bonds are usually represented by lines connecting atoms in
a picture of a molecule.
For example – glucose is C6H12O6 or
Read This!
Covalent bonding makes up nearly all of the biologically important molecules that we will learn about
throughout this year including water, glucose, DNA, proteins, carbohydrates, carbon dioxide, oxygen, etc.
Cells are made of (and rely on) many complex molecules made of hundreds of atoms all attached to each other
by covalent bonds. The complexity and size of these molecules is possible because they all contain atoms of
carbon.
Why carbon? Each atom of carbon can form 4 covalent bonds - meaning each atom of carbon can be linked to
4 other atoms simultaneously, making it very versatile in creating molecules of different sizes & functions.
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III. Water is a very important molecular compound!
Read This!
Water covers about 70% of Earth’s surface and it makes up 65-90% of our bodies. It is found inside our blood,
sweat, tears, saliva and other digestive juices, as well as in between and inside our cells. Water is essential for
all life; without it every living thing would die. What makes water so important?
I. Cohesion:
Insects, spiders, & even some lizards ‘walk’ or ‘stand’ on water
a. What is the advantage of water being cohesive?
SEE IT: Slide a small paper clip onto the surface of the water in the beaker
II. Adhesion:
Water can form attractions with other polar substances.
This allows water to cling to surfaces such as the
inside of a plant as water “climbs up” the
narrow channels called xylem.
SEE IT: Place drops of water onto the surface of a penny.
Notice how the water does not spill over the side – this is both due to cohesion & adhesion.
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III. Thermal Energy:
Water is mostly in its liquid form on Earth because water can absorb
a lot of heat energy before it changes temperature and before it evaporates.
This means when water does evaporate, it removes heat energy
from living things which cools them down!
SEE IT: Place a drop of rubbing alcohol in the petri dish labeled ‘alcohol’ WHILE another classmate places a
drop of water in the petri dish labeled ‘water’
Use a paper plate to wave back and forth on top of the dishes while the timer is going.
Time how long it takes for each drop to evaporate
IV. Polarity and Nonpolarity:
Although water is able to form attractions with lots of molecules
(sugars, salt, ions, etc), water does not interact with oils & waxes.
This is a huge benefit for living things that use oils & waxes to repel water.
a. Why would a plant or duck want to repel water?
SEE IT: Place a drop of water on a piece of wax paper. Roll it side to side.
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More interesting “droplets” about water!
Read This!
😊
The ability of insects to walk on water, water defying gravity by climbing up plants, water resisting phase
change and water floating when it freezes can all be explained by the chemistry of water
A. Water’s Molecular Structure
1. What type of bond holds the 2 hydrogen atoms to the
1 oxygen atom?
2. The bonds (lines) seen between the oxygen and
hydrogen atoms in this picture represent where
_________________are being shared.
3. The shading around the molecule represents the density or distribution of electrons. How does the
density of electrons around the oxygen atom compare to that around the hydrogen atoms?
4. Knowing what you know about the charge on an electron, around which atom (the oxygen or the
hydrogens) would you find the majority of the negative charge on a water molecule? ___________
5. What do each of these symbols represent? = _______________ = ______________
6. Recall that electrons in water molecules are located mostly around the oxygen atom compared to
the 2 hydrogen atoms. Circle the correct word in bold to complete each statement below:
a. Because there are more electrons around the oxygen atom of a water molecule, the oxygen end of a
water molecule is slightly more (negative / positive)
b. Because there are fewer electrons around the hydrogen atoms of a water molecule, each hydrogen
end of a water molecule are slightly more (negative / positive)
7. The dotted lines indicate weak attractions that occur between water molecules. Describe the cause
of the attractions between molecules of water.
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Read This!
In some covalently bonded compounds, the electrons are not equally shared between
the atoms. These molecules with a difference of charge across the molecule are called
polar molecules. In a water molecule, the hydrogen molecules are slightly positive,
while the oxygen is slightly negative. The positive area (hydrogen) of one water
molecule is attracted to the negative area (oxygen) of a different water molecule. This
weak attraction is referred to as hydrogen bonding.
B. Hydrogen Bonding
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IV. Macromolecules
Read This!
Macromolecules are large molecules made of smaller molecules linked together. There are 4 macromolecules
essential for life: carbohydrates, lipids, proteins, and nucleic acids. We will study nucleic acids (DNA and RNA)
later on this year. Organic chemistry is the study of molecules based around the element carbon.
A. Carbohydrates
Monosaccharides Disaccharides
1. “Saccharide” is another name for sugar. Explain why the prefixes mono-, di-, and poly- are used to
distinguish between the different types of carbohydrates (sugars) above.
2. Terms such as “simple sugars” or “complex sugars” are used in our everyday lives. Which of the
above carbohydrates do you think would be considered “simple”? Which would be “complex”?
3. What are carbohydrates used for (in all living things)?
4. Predict how the energy content differs between a simple and a complex sugar. Explain your answer
5. Plants create glucose (a simple sugar) during photosynthesis.
a. Which plant cell organelle is used to create glucose? ______________
b. Challenge – suggest what materials would a plant need to take in for creating glucose?
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c. When plants make a lot of glucose, they can change it into starch. Describe, in a simple way, how a
plant can transform glucose into starch.
d. Plants can also build another polysaccharide (by putting together many glucose molecules).
Cellulose is a polysaccharide found in the cell walls of plant cells. Starch is used for energy storage.
Suggest what cellulose might be used for.
Read This!
You might know cellulose by a different name – fiber. Humans cannot break down fiber but it is helpful in
digestion (more on this later). Cellulose can only be digested by some animals like cows, sheep, & goats.
6. Animals eat in order to obtain carbohydrates (both simple and complex).
a. List 2-3 foods that we eat that contain simple carbs:
b. List 2-3 foods that we eat that contain complex carbs:
c. Suggest if it is easier for animal cells to absorb simple or complex carbohydrates.
What makes you say that?
Read This!
Animal digestive systems work to break down the carbohydrates we eat so that they are small enough to enter
our cells (across the cell membrane).
a. Do you think it is easier for digestive systems to break down simple or complex
carbohydrates? Explain your answer.
e. Once carbohydrates are small enough to enter our cells, suggest which organelle inside of
eukaryotic cells are used to transform carbohydrates to energy. ____________________
Read This!
Just like plants have the ability to store excess glucose that we eat as a complex (polysaccharide) carbohydrate
called glycogen. More on this later…
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B. Lipids (Fats)
Read This!
Lipids (fats) are another important biological molecule. Lipid structure is similar to that of a carbohydrate (made of H, C,
and O atoms) though different in that it is not made of hundreds of repeating building blocks linking one after the other.
Instead it is made of saturated and/or unsaturated fatty acids linked together in a trio. Observe the structure of the lipid
below and answer the questions that follow.
1. Suggest what the function of a lipid (fat) is.
2a. What do you notice is different about the fat molecules above?
2b. Suggest - Why are there differences in the molecular structure of the fats above?
What else can fats be used for?
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C.Proteins
Read This!
Proteins are also based around the elements carbon, oxygen, and hydrogen but also contain nitrogen and also can
contain sulfur. Proteins are the most diverse of the macromolecules. It is estimated that our human body can produce
2 million different types of proteins. If you include all living things, there are over 10 million different types of protein.
Proteins therefore perform a wide range of functions. Here are just a few examples:
Hemoglobin (made by red blood cells) = carries oxygen throughout the body
Spider silk = one of the strongest proteins in the world!
Collagen = structural protein that exists between cells, holding them together and providing flexibility
Insulin (made by the pancreas) = hormone that regulates blood glucose levels (more on this later!)
Melanin = protective protein gives coloration to the skin, hair, and iris of the eyes
How can proteins be so diverse? What are some of the functions of these various proteins in our bodies?
The building blocks of proteins are amino acids. There are only 20 different amino acids however they can be arranged
in any combination AND the length of the amino acid chain can vary greatly. Some proteins contain hundreds of amino
acids!!
1. Recall: What organelle(s) in the cell help create
protein (See how many structures you can
identify from this image)
2. Why do you think it is essential to have
protein in your diet?
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V. Making and Breaking Macromolecules
Read This!
Chemical bonds are constantly being formed and being broken apart by living things during chemical reactions.
A chemical reaction is the process by which atoms or groups of atoms in substances (reactants) are
reorganized into different substances (products).
The TOTAL of all the chemical reactions that occur inside a living organism is called metabolism.
There are 1x109chemical reactions per second in each cell in the human body and there are at least 100
trillion cells in the body.
o Chemical reactions that create, synthesize or build large molecules are called anabolic reactions.
o Chemical reactions that break down complex molecules are called catabolic reactions.
Our bodies cannot begin to use the proteins, carbohydrates, and lipids in our diets until they are broken down
small enough to be absorbed into our bloodstream and into our cells. The food we eat undergoes a series of
chemical reactions in our digestive system. This system in our body is just ONE place where chemical
reactions occur. Once inside our cells, our organelles like mitochondria and ribosomes will perform further
chemical reactions.
A. Example 1: H2 + O2 → H2O Read as: “Hydrogen gas and Oxygen gas yields water”
1. Identify the reactants in the chemical equation above: ___________________
Reactants (define) –
2. Identify the products in the chemical equation above: ___________________
Products (define) –
B. Example 2:
1. What do you think this chemical reaction might be? (hint: it happens in plants)
2. Would you say this reaction is anabolic or catabolic? Why?
3. What organelle performs this chemical reaction in plant cells? _____________________
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C. Example 3:
1. Above is the chemical reaction that occurs inside of our cells to release energy. Would you say this
reaction is anabolic or catabolic? Why?
2. What organelle performs this chemical reaction in all eukaryotic cells? ____________________
3. Notice how oxygen is a reactant in this reaction. What happens to your ability to perform this
chemical reaction if you are not breathing properly?
D. Example 4: Digestive System breaking down carbohydrates.
Are the reactions above anabolic or catabolic? How do you know?
Suggest which of these reactions releases more energy over a longer period of time.
What makes you say that?
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VI. Enzymes (proteins) Speed up chemical reactions
Read This!
All biological chemical reactions occur with the help of enzymes. Enzymes are a specific type of
protein found inside of cells (inside lysosomes, cytoplasm, and mitochondria especially) , in our blood,
tears, as well as in our mouth, stomach, and small intestine. Other living things create enzymes too!!
Enzymes are also used to create many products such as baby food, fruit juice, wine, lactose-free dairy
products, laundry detergent, and other cleaning products.
Enzymes can be used to perform both catabolic and anabolic reactions. The same enzyme molecule
can be used over and over again, binding to reactants and releasing products
Enzymes are specific – they only work on ONE type of reactant
The stomach enzyme (pepsin) only worked to digest certain food items.
Enzymes work best at certain temperatures!
The stomachs were sitting in warm temp
because that is the temperature of the human body!
Enzymes work best at certain pHs!
Pepsin works at acidic pHs but other
enzymes (like those in our mouth)
work at different pHs
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VII. Maintaining homeostasis – keeping our levels of materials regulated
Read This!
Homeostasis maintains the internal environment between limits. This includes maintaining the pH of body
fluids (for proper enzyme activity, carbon dioxide concentration, blood glucose concentration, body
temperature, and water balance. Homeostasis is achieved with use of the brain, nerves, and hormones.
Hormones are chemical messengers that are secreted directly into the blood, which carries them to organs
and tissues of the body to perform their functions (note: not all hormones are proteins)
Use the picture below to discover how the body regulates (controls) the amount of glucose in the blood –
making sure it doesn’t get too high or too low.
1. Is glucose a simple or a complex carbohydrate?
2. What organ of the body detects if blood glucose
levels get too high or too low? ____________
3. After you have a big meal, the level of glucose in
your blood increases. When that happens, the
pancreas releases the hormone (insulin / glucagon)
into the blood. What does this tell your cells to do?
4. Your liver also responds to insulin and will convert
the excess glucose to a complex carbohydrate called
glycogen. This lowers the level of glucose in your
blood, storing it for later.
5. If you don’t eat for a while, the level of glucose in
your blood starts to fall below normal. When that
happens, the pancreas releases the hormone (insulin
/ glucagon) into the blood.
What does this tell your liver to do?
6. Diabetes occurs when a person cannot regulate the level of glucose in their blood. Diabetes can cause all of
the following symptoms:
o Excessive thirst o Infections of the skin and gums
o Tiredness o Inability to heal cuts and bruises effectively
o Blurred vision o Itchy skin
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Biochemistry Test Review
WATER REVIEW
1. Define covalent bond.
2. Because of the unequal distribution of charge in a water molecule, it is called a __________ molecule.
3. Draw a dotted line to show the attraction that would exist between these water molecules below.
4. What is the name of the attraction that occurs between polar water molecules? ___________________
5. CIRCLE the word to complete the sentence:
a. In water molecules, the (oxygen / hydrogen) end of the molecule is slightly (negative / positive)
b. While the (oxygen / hydrogen) end of the molecule is slightly (negative / positive)
c. Therefore, positive & negative ends of two different water molecules attract
6. The ability of water molecules to form hydrogen bond attractions with each other is a major benefit to
living things. Two of those benefits are listed below:
a. Water molecules move up plants in one continuous stream – why is this important for plant survival?
b. Some animals (like insects) can “walk” on water – why is this important for their survival?
7. Why is it beneficial to living things that solid water (ice) floats in liquid water?
8. Why is it beneficial to living things that water resists changes in temperature & changes in phase?
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CARBOHYDRATE, LIPID & PROTEIN REVIEW!!
11. When you put MANY monosaccharides together, you form a ___________________.
12. Identify TWO differences between simple and complex carbohydrates.
(HINT: Think size of molecule, ease of breaking it down in our digestive system, or amount of energy)
13. Fill in the chart below to compare and contrast the three macromolecules:
Made up of (smallest unit)
Macromolecule (monosaccharide / amino Function Examples
acid / fatty acid)
Sugars (glucose & sucrose),
Carbohydrate Starch, Glycogen,
Fiber (cellulose)
Lipid Fats, oils & waxes
LOTS of functions including Enzymes and hormones like
Protein structure, transport, insulin & melatonin
transforming matter by (and many more things that give the body
structure and functions)
assisting chemical reactions
14. State the difference between how we use carbohydrates and lipids for energy.
15. Circle the correct answer:
a. Carbohydrates are made by plants during photosynthesis. First, a plant will build (glucose / starch),
then, if it needs to store up excess carbs, it will build (glucose / starch). Chemical reactions that BUILD
smaller molecules into larger molecules are (catabolic / anabolic)
b. We eat carbohydrates. Carbohydrate digestion starts in the mouth with the enzyme salivary
amylase. Complex carbohydrates (starch) get broken down into (monosaccharides / fatty acids /
amino acids)
c. We eat lipids. Lipid digestion starts in the small intestine with the enzyme lipase. Lipids like
saturated & unsaturated fats get broken down into (monosaccharides / fatty acids / amino acids)
d. Digestion is the breakdown of large molecules into simpler ones. Digestion using enzymes is
therefore a (catabolic / anabolic) chemical reaction.
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CHEMICAL REACTION REVIEW!!
16. T/F Chemical reactions ONLY occur when materials are broken down by the body. If false - WHY?
17. T/F Chemical reactions are the only way that compounds can be broken. If false - WHY?
18. Label the reactants and products in this chemical reaction:
C6H12O6 + O2 → CO2 + H2O
19. Distinguish between a reactant and a product.
ENZYME REVIEW!!
20. Enzymes are classified as which type of macromolecule? (carb, lipid, or protein?) ___________________
21. What is the function of an enzyme?
22. (True or False ) Enzymes are very specific – they only work on one type of molecule.
23. Why do we need enzymes in our digestive system? What do they help our digestive system do?
24. Circle the correct answer: The enzyme in our stomach works best at a (lower / higher) pH.
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Practice DATA Analysis Questions
There are a variety of different types of prokaryotic (bacteria) cells on Earth living in a wide variety of environments
including human intestines, arctic lakes, hot springs, and hydrothermal vents. The graph below shows how well each
type of bacteria grows (meaning divides) at various temperatures. Answer the questions that follow:
1. Identify the independent variable in the data above. (1) _______________________________
2. State the optimum temperature for the mesophile bacteria. (1) _____________________________
3. Describe how the growth rate of psychrophiles changes as temperature increases. (2)
__________________________________________________________________________________________________
__________________________________________________________________________________________________
4. Compare and contrast the growth rate of thermophiles and hyperthermophiles. (2)
__________________________________________________________________________________________________
__________________________________________________________________________________________________
__________________________________________________________________________________________________
5. Suggest, with a reason, which of the groups of bacteria is the one found in the human body. (2)
__________________________________________________________________________________________________
__________________________________________________________________________________________________
6. Suggest why there are differences in the growth rates of these different bacteria. In other words, how do these
graphs connect with our learning this unit? (1)
__________________________________________________________________________________________________
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