Unit 2: Biochemistry Review: Honors Bio
MATTER / WATER
a) element
ENZYMES – ORGANIC CATALYSTS
b) atom
a) catalyst
c) ion
b) enzyme
d) molecule
c) reactant vs. product
e) bond
d) how an enzyme works
f)
e) substrate
energy
g) hydrogen bonds
f)
active site
h) polarity: polar vs. nonpolar
g) enzyme-substrate complex
i)
cohesion vs. adhesion
h) shape
j)
surface tension
i)
enzyme specificity
k) capillary action
j)
effect of temperature
k) effect of pH
THE CONCEPT OF PH
l)
effect of concentration
a) pH
m) optimum
b) acid vs. base
n) amylase
c) indicator
o) pepsin
d) pH scale
p) trypsin
e) acidic and basic substances
q) digestion: functions of enzymes
f)
r)
pH of blood, cells, stomach
denaturation
g) neutralization reaction
h) buffer
MACROMOLECULES
i)
alkalosis vs. acidosis
a) monomer units & polymer units
j)
3 causes of acidosis
b) Enery storage
c) Structure and function of molecules
FROM PREVIOUS UNITS
d) sugar homeostasis!
e) IV, DV, control
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Structure of MatterChapter 2.1, 2.2

Define the term matter.

Distinguish among elements, atoms, ions and molecules.

List the main elements that compose organisms.

Create a model of the structure of an atom with labels.

Contrast covalent and ionic bonds.

Define oxidation-reduction (redox) reactions
The Characteristics of Water
Chapter 2.3

Construct the structure of a water molecule.

Differentiate between polar and nonpolar molecules.

Summarize hydrogen bonds.

Draw conclusions how the structure of water is related to its various properties.

Compare and contrast adhesion and cohesion as related to surface tension and capillary action.
The Concept of pH
Chapter 2.3

Use pH indicators to determine the pH of various substances.

Differentiate between acids and bases and their position on the pH scale.

Draw conclusions regarding the role of buffers in maintaining pH homeostasis.
Building Blocks of Life: Macromolecules
Chapters 3.1, 3.2

Analyze the structure of carbon and its importance to living organisms.

Identify the 4 macromolecules of life & their monomer units.

Construct macromolecules.

Compare and contrast properties of the macromolecules.

Analyze the importance of carbon to the structure of biological macromolecules.
Enzymes: Organic Catalysts
Chapter 2.2/3.2

Explain the cause & effect relationship between enzymes and activation energy.

Summarize the reaction of peroxidase/hydrogen peroxide & its importance in the body.

Relate how an enzyme’s shape is important to its function.

Compare & contrast the effect of pH, temperature and concentration on enzyme activity.

Summarize how an enzyme interacts with its substrate.

Illustrate the importance of enzymes.

Investigate and summarize the concept of enzyme specificity.

Interpret how denaturation affects enzyme activity.
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Structure of Matter
Chapter 2: pp. 31-34
Option 1:
After reading the section, write a paragraph using all the words. Try your best to guess the relationship among
the words and the meaning of any unfamiliar words.
Option 2:
After reading the section, create a concept map using the website: www.text2mindmap.com
ELEMENT
CARBON
HYDROGEN
NITROGEN
OXYGEN
SYMBOL
ATOM
PROTON
NEUTRON
ELECTRON
ORBITAL
ISOTOPE
ION
BOND
MOLECULE
IONIC
COVALENT
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PROPERTIES OF WATER: Chapter 2: pp. 39-42
POLAR
NONPOLAR
HYDROGEN
BOND
COHESION
ADHESION
CAPILLARY
ACTION
SOLUTE
SOLVENT
SOLUBILITY
OF WATER
TEMPERATURE
MODERATION
SPECIFIC HEAT
ICE DENSITY
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Reviewing the Properties of Water
Water is a very important molecule to living things. Answer each set of questions based on your observations.
Water in a beaker and graduated cylinder
1. Observe the water in the beaker and the graduated cylinder. Draw the shape of the water at the top of the
beaker and in the graduated cylinder.
Explain your observations using the terms cohesion, adhesion, polar and hydrogen bonds
Drop Shape on Glass and Wax Paper
1. Observe the water on the wax paper and glass slide. Move each and notice how the water moves. Which
substance, wax or glass, is polar? Which is non-polar? How can you tell?
Capillary Action
1. Observe the chromatography paper with ink on it. Is paper polar or nonpolar? Explain. Is the ink polar or
nonpolar? Explain.
2. Observe the chromatography paper with the crayon on it. Is the crayon polar or nonpolar? Explain.
Water and Oil
1. Observe the beaker of water and oil that has already been set up for you. Which is less dense?
2. Explain the mechanism that causes water molecules and oil molecules to separate from one another including
the following terms: polar, nonpolar, hydrogen bond
Density of Ice
1. What property of water is being shown in this beaker? Why is this important to living things?
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Acid alkaline balance in the human body
Name: _____________________
http://www.essortment.com/all/acidalkalineba_rkci.htm retrieved 19February2009
Approximately 50 to 60 percent of a human’s body weight is from water. The percentage varies based on several factors.
For instance, fat holds very little water while muscle is about 75 to 77 percent water. The obese couch potato may contain
50 percent or less in water weight. On the other hand, a fit muscular person may have 60 to 65 percent of water in body
weight. The water in the body can be compared to swimming pool water. Swimming pools are strictly monitored to
keep the water at a certain pH balance. The water should not be too acidic nor too alkalitic. The fluid in the human body
must stay within normal ranges also. Th normal pH balance in the human body is 7.35 to 7.45, (which is basically
neutral). If the pH gets low (acidosis) or high (alkalosis) there will be specific problems that could be life threatening.
The water in the human body is further broken down into specific categories. Intracellular fluid (ICF) is water actually
contained inside cells. Extracellular fluid (ECF) is water outside the cells. Combined, ICF and ECF equal 60 percent on
average of the total body weight. Extracellular fluid is further broken down into interstitial fluid, plasma, bone,
connective tissue, and transcellular fluid. Interstitial fluid, primarily located in the lymphatic system, equals about 12
percent of body weight. Plasma, basically the liquid portion of the blood, equals about 4.5 percent of body weight.
Connective tissue accounts for about 4.5 percent, with the smallest amount of 1.5 percent being composed of transcellular
fluid. The body has several different ways to ensure that the pH balance stays in the normal range of 7.35 to 7.45. These
are referred to as buffer systems. Through normal day to day activity in the body, acids are formed as waste products
that need to be neutralized or eliminated. Some of the acids are released with CO2 from exhaling; others are excreted
via the kidneys. These systems work together in the healthy human body to keep the pH level within normal ranges. If
for some reason the buffering systems fail or are hindered, the pH balance will be upset. Either too much or too little of
the acids will be neutralized. The causes of this can be as simple as the flu or as complications from trauma, disease or
serious illness. Once the body senses the pH is out of kilter, it will attempt to compensate to correct the problem. The
conditions for when this happens are known as acidosis or alkalosis. These are further broken down into either metabolic
or respiratory in nature. This includes metabolic acidosis, respiratory acidosis, metabolic alkalosis, and respiratory
alkalosis.
One of the chief buffers in the blood is bicarbonate, which helps neutralize acids. This is like taking an antacid for
heartburn. Metabolic acidosis is caused by the loss of bicarbonates or an increased production of acids. Some causes for
bicarbonate loss can be severe diarrhea, drug intoxication or abuse, or severe illness. Some causes for increased acid
production include serious illness or injuries, and decreased blood flow. An example of this is when you leg "falls
asleep". Blood flow is decreased allowing acid to build up. Upon standing, blood flow is restored. The tingly pin and
needle sensation is caused from the excess acid in the tissues. The acid is then neutralized resulting in the pin and needle
sensation subsiding.
Respiratory acidosis is usually caused by insufficient respirations or air exchange. This can be caused by head or chest
trauma and respiratory diseases such as emphysema. In cases of emphysema, the lungs cannot perform normally due to
an increase of dead air space. Acidosis develops slowly over a period of time. These are usually treated with
bronchodilators and small amounts of oxygen to increase air exchange in the lungs. With a severe decrease in breathing
caused by trauma or respiratory arrest, the amount of acid quickly increases. Adequate measures need to be taken to treat
the cause. Metabolic alkalosis occurs when too much acid is excreted from the body. This can be caused by eliminating
too much fluid by frequent urination, by excessive vomiting, or various diseases. If the body becomes too alkalitic, the
nervous system and the heart can be affected. The heart may speed up and become irritable while breathing slows in
order to compensate. By slowing respirations, less acid is "blown off" from the lungs. This is in contrast to
hyperventilation often seen in metabolic acidosis. Metabolic alkalosis is treated based on findings from laboratory tests.
Respiratory alkalosis is caused when the body is stressed. Some of the causes include shock, sepsis, trauma and asthma.
Too much acid is "blown off" from increased respirations or hyperventilation. In cases of hyperventilation of
psychogenic origin, the increase in alkalosis causes the tingly sensation around the mouth and in the fingertips. Because
of hyperventilation, blood is slowed to the brain so the respiratory center tells the body to increase respirations. In
psychogenic hyperventilation, the symptoms of tingling and feeling of smothering continue to worsen. Treatment of
respiratory alkalosis is basically to treat the cause. This can include the simple paper bag method for psychogenic
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hyperventilation, to using sedation to slow respiration. By slowing the breathing, the blood flow is returned to the brain.
This allows the respiratory center to regulate itself and get the levels back to normal. Interesting, in psychogenic
hyperventilation, if the person continues to hyperventilate, they often pass out. Respirations slow and return to normal,
in turn the body gets back to normal.
Please answer the following questions below and underline the answers in the above reading.
1. How can water in our body be compared to swimming pools?
2. What is acidosis?
3. What is alkalosis?
4. How does the body ensure that our pH stays between 7.35 & 7.45?
5. What are 2 ways the body releases the acids that build up from day to day activities?
6. What is the primary buffer in the blood system?
7. What are 3 causes for acidosis to occur in our bodies?
8. Explain what occurs when our legs ‘fall asleep,’ using the word acidosis, acid, and blood flow.
9. What are 3 causes for alkalosis to occur in our bodies?
10. How can our bodies be affected by alkalosis?
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Chapter 3: Biochemistry
Biology-H
Section 1: Carbon Compounds
1. Distinguish between organic and inorganic molecules.
2. How many electrons does carbon have? How does this affect its bonding ability?
3.
What shapes can carbon molecules make?
4. Why are functional groups important in organic compounds? Name four common functional groups and
their structural formulas.
5. How are monomers, polymers and macromolecules related to one another?
6. Explain a condensation reaction and hydrolysis reaction.
7. Describe what ATP is and what it is composed of. Briefly explain why ATP is important to living things.
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Section 2: Molecules of Life
1. What are carbohydrates and list 3 different types.
2. What are the 3 most common monosaccharides? Where are they found? How are the similar? Different?
Monosaccharide name
Uses/found
Similar
Different
3. Define disaccharide and give an example.
4. Define polysaccharide and give examples.
5. What makes up a protein? Is it a monomer or a polymer?
6. How many different amino acids are there? How are they similar? How are they different? (Draw this)
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7. What is a lipid? How are they different than carbohydrates? What is the significance of this difference?
8. Describe a fatty acid. Distinguish between hydrophobic, hydrophilic, saturated and unsaturated as they
pertain to fatty acids.
9. Describe the 3 classes of lipids and characteristics of each.
10. How are steroids different than other lipids? Give some examples.
11. Define nucleic acids and describe the two major types.
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Macromolecules: Review
Biology-H
Complete the following chart:
Name of
Macromolecule
Proteins
Monomers
Examples
Lipids
Phospholipid
Triglyceride
Carbohydrates
Polysaccharide
Starch
Glycogen
Cellulose
Nucleic Acids
DNA
RNA
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Elements
Functions/Uses
Enzymes: The Essential Info
…
Enzymes are protein molecules that are essential to all the chemical reactions we’ve learned about in this unit. Let’s
find out how.
1. Define catalyst in your own words.
2. Define enzyme in your own words.
3. How are the two terms in #1&2 connected?
4. Explain the role of activation energy in a reaction. How does an enzyme affect activation energy? What is the
result?
5. Use these terms as you explain how an enzyme specifically works: enzyme, substrate, active site, enzymesubstrate complex, products
6. What is the difference (if any) between reactants and substrates?
7. Most enzyme names end in _________. Give 1-2 examples.
8. Simple cells may have as many as 2000 different enzymes, each one catalyzing a different reaction!
a. How is shape important to an enzyme’s function?
b. Describe enzyme specificity in your own words:
c. DRAW an example of this phenomenon.
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Enzyme Action … A Visual Overview
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Factors Affecting Enzyme Action
Temperature, pH and concentrations of both enzyme and substrate concentrations affect enzyme action in cells.
TEMPERATURE
In general, chemical reactions are slowed down by lowering
the temperature because lower temperatures cause molecules
move slower… therefore they bump into each other less and
react less. Oppositely, heating a substance will cause the
molecules to move faster and therefore speed up the reaction
rate. The temperature that an enzyme works best at is called
its optimum temperature. The same is true of enzymes and
their substrates. At very high temperatures, however, enzymes
stop catalyzing reactions. This happens because the high
temperature breaks the hydrogen bonds that give the enzyme
its shape. The changing of an enzymes shape is called
denaturation. The result of this is that the enzyme and
substrate can’t fit together anymore and therefore there will be
no reaction.
1.
In general, lowering temperature __________________ the rate of enzyme action. Raising the temperature
_________________________ the rate of enzyme action.
2.
The temperature in which an enzyme works best is called its _________________________ temperature.
3.
What is enzyme denaturation?
_________________________________________________________________________
____________________________________________________________________________
4.
What causes denaturation? Why?
_________________________________________________________________
___________________________________________________________________________
5.
What is the result of denaturation?
_________________________________________________________________
__________________________________________________________________________________________
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pH
The effectiveness of an enzyme depends on the pH of its surrounding
environment. Different enzymes work best at different pH levels
depending on where they are found. The pH at which an enzyme
works best is called its optimum pH. The pH of stomach, for
example, is acidic. The enzyme pepsin is found in the stomach. So,
it is made to work in this acidic environment. This is its optimum
pH level. Trypsin is an enzyme found in our intestines (which are
slightly basic). By looking at the graph, you can conclude that
trypsin’s optimum pH is basic.
6.
Pepsin is located in the ________________________ and has a(n) _______________________ optimum pH.
7.
Trypsin is located in the _______________________ and has a(n) _________________________ optimum pH.
8.
Based on the graph, what happens to the rate of enzyme action if the pH is goes above or below from the
optimum? _________________________________________________________________________________
concentration
Concentration is the amount of substance in a given area. The rate
of a reaction depends on how often enzyme and substrate molecules
bump into each other. So, if concentration of either enzyme or
substrate is increased, they will obviously bump into one another
more often – and as a result the reaction rate will increase. Enzymes
can continue to be added to a substrate and they will speed up the
rate of chemical reaction. However, when more substrate is added
to the enzymes there is a point in which the solution is saturated.
This means that all enzymes are occupied by substrate – the reaction
rate plateaus at this point.
9.
What is concentration?
_________________________________________________________________________________
10. When the concentration of enzyme or substrate is increased, what happens to the reaction rate?
15
Independent Investigation: Factors Affecting Enzyme Action
Question:
How do temperature, pH and concentrations of both enzyme and substrate
concentrations affect enzyme action in cells?
Review of Literature:
Read page 19-20 in your packet as background research. Then, find at least one
independent source that provides further support. Include this cited source in your
final poster presentation.
Guided Investigation:
This lab requires the use of Vernier Handheld computers with pressure sensors, as
well as LoggerPro software. As the reaction between hydrogen peroxide and
peroxidase occurs, the gas release will increase the pressure in a closed system. This
pressure change should correlate to the amount of gas being release from the reaction.
By measuring the rate of the pressure change, we can use that correlation to view the
relative rate of reaction. You will first obtain a control by measuring the rate of
reaction between the H2O2 and peroxide at room temperature, standard pH, and a
standard concentration. You will then design an experiment to test one of the factors
in the lab question.
Procedure - Guided:
1. You first need to set up your Vernier handheld. Obtain one sensor kit and one
handheld. Plug the sensor into the “CH 1” opening. Turn on the handheld.
2. Plug the handheld into a laptop using the connection cable. Open the LoggerPro
software under “Vernier software”.
3. On the computer, set up the sensor by clicking “Experiment” => “Set-up
Sensor”=> “labquest 1” =>“channel 1” => “pressure sensor”. This should allow
the computer to read the pressure sensor in kPa.
4. To have the computer take the proper readings, press “Ctrl + D”. Change the
duration to “25 seconds” and change the sampling rate to “10 samples/second”.
Click “done”
5. Connect the sensor kit to the sensor. Make sure all valves are open between the
sensor and the stopper.
6. Obtain a large test tube. Use the provided syringe to fill it with 1mL of chicken
liver blood.
7. Place the stopper on the test tube.
8. Draw exactly 3 mL of hydrogen peroxide using second syringe syringe. Attach
the syringe to the stopper.
9. Simultaneously, have one person press the green “play” button on the computer
while the second person depresses the plunger on the syringe. It is important that
you hold down the plunger and stopper for the duration of the reaction.
10. After the 25 seconds, you may allow the stopper to release from the tube.
11. Click on “Experiment”=> “store latest run”. Double click where it says “run 1”
above the data and change the name to “Control run”.
12. Save your file to your network folder.
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13. The computer is now ready for another run. Each time you perform an
experiment, follow the same procedures.
Procedure- Independent
1. Determine which factor you would like to investigate.
2. Develop a hypothesis based on your background knowledge.
3. Use your experience from the above investigation to design an investigation that
will answer your question.
4. Be specific in your investigation. It is important that you:
a. Identify as many experimental controls as possible. Remember, pressure is
linked to volume and temperature. You want as many things to be the
same with your first run as possible.
b. Write down any procedures you use that are different from the above
investigation. Take careful notes of your results.
c. Ask questions; if it’s something you need to figure out I will let you know.
5. You can export your data to a .csv file, where you can analyze it a little more
easily. You can also copy and paste your graph straight from LoggerPro into a
word document.
Conclusion:
1. Your group will create a poster sharing your investigation.
a. Remember to have the important parts of a lab investigation labeled (see
your first lab).
b. The parts should be typed up and neatly displayed.
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