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Checked and edited by your instructor:
Unit 1 Objectives: Chapter 1
1. List the AP Themes and explain what they are.
The AP themes are:
a) Science as a process—the scientific method is a universal process every scientist
goes through during an experiment.
b) Evolution—“you have to do a lot of running to stay in same place”. Evolution is
always happening, because everything is changing.
c) Energy transfer—energy and matter is constantly cycling (Basic photosynthesis)
d) Structure and Function—every structure is formed by evolution to maximize their
purpose
e) Regulation—keeping homeostasis, or an even “state of being”. Genes and
hormones are initiated or shut down to keep this.
f) Interdependence—animals evolved together because energy is transferred that
way
g) Science and Technology—technology is furthering biological advancement
Chapter 2
1. Name the levels into which life can be organized.
Atomic to molecular to organelle to cellular to tissue to organ to organ system to
organism.
2. Name the important elements that make up life.
Carbon, Oxygen, Hydrogen, Nitrogen, Sulfur (CHONS) Do you remember CHOPKINS
CaFé (has) Mighty Good Salt? – these are ALL the elements of life.
3. Name some important trace elements and state why they are needed in living beings.
Iron is important because it keeps blood normal. Not enough iron in the blood is called
anemia. Without iodine, the thyroid gland swells up – goiter results.
4. Define Atomic Number, Atomic Weight, Isotopes.
Atomic number is the number of protons. Atomic Weight is the number of protons and
neutrons. Isotopes are the same atoms but with different numbers of neutrons.
5. How are isotopes useful in carbon dating?
The proportion of C14 and C12 identifies the age of a fossil. The longer an organism is
dead, the lower number of C14 atoms because it gets constantly degraded.
6. What are covalent bonds? Give an example. Are they weak or strong bonds?
When two atoms share valence electrons, it is called a covalent bond. O2 is an example.
They are strong bonds.
7. What are polar covalent bonds? Draw the polar bonds in water molecules.
Unequal sharing of valence electrons because one of the atoms is large ( like oxygen) and
electronegative and pulls the electrons towards its own nucleus (from Hydrogen atoms) is
called polar covalent bonds.
8. What are hydrogen bonds? Are they weak or strong bonds? Draw the hydrogen bonds
between water molecules.
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A hydrogen bond occurs between two polar molecules with strong electronegative atoms
( 2 sides of DNA are held together by Hydrogen bonds between the bases). They are weak
bonds.
9. What are ionic bonds?
Ionic bonds are the strongest bonds. One atom takes an electron. Not observed much in
biology as everything is dynamic in life!
10. Why is the shape of a molecule important for its function?
The shape of a molecule defines its function.
11. What is chemical equilibrium—why is it important in living systems?
Chemical equilibrium is a reaction that can go forwards and backwards. It is important
because as life changes it may need more of a substrate than of a product, or vice versa.
Chapter 3 -Water – Objectives:
1) How much of your cell is made up of water?
A cell is made up of about 70-95% water.
2) What is the single most important chemical property of water that makes it behave in
incredibly versatile ways?
Water is versatile because it is polar from the high electro negativity from the oxygen
atoms, which results in the ability to form hydrogen bonds with the act of cohesion.
3) What is cohesion and when does this property of water become useful in living
organisms?
Cohesion is the act of a water molecule sticking to another water molecule. This is
important for hydrogen bonding because the hydrogen atoms need to stick to the hydrogen
atoms in the other water molecules to form a bond, which is an important factor in the uses of
living organisms.
4) What is adhesion and when does this property of water become useful in living
organisms?
Adhesion is when water sticks to something else that is not water, and this is important in
living organisms because water is an important part in all aspects of the way of life.
5) What is surface tension and when does this property of water become useful?
Surface tension is when water behaves as if it has a thin layer of invisible film on the
surface and this is useful in many aspects such as the bug that can “walk on water” and when
leaves float, etc.
6) How does the density of liquid water compare with its solid form – ice? When does this
property of water become useful?
The density of ice is less than the density of water which results in ice floating in water.
This is because the molecular structure of ice is more spread out and has more open space
which causes it to float. This is useful because when the winter season comes around, the
animals in the water are able to still survive under the layer of ice.
7) How does the high specific heat of water and the high heat of vaporization become useful
properties in living systems?
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Specific heat is how well a substance resists temperature change when it is releasing and
absorbing heat. This is important to living systems because they are made up of mostly water
and give off and absorb heat slowly. Heat of vaporization is the amount of heat needed to
change a substance from liquid to vapor form. This is important in living systems because
this is essentially what perspiration and transpiration are in animals and plants.
8) Why is water considered a universal solvent?
Water is considered a universal solvent because it is versatile and because it uses a
hydration shell which is when the water molecules surround an ion.
9) What happens when water dissociates?
When water dissociates it changes from its original H2O form to an ion form such as H+
(hydrogen ion) or –OH (hydroxide ion) or sometimes even H3O+ (hydronium ion). Only
about 1/554 water molecules are dissociated.
10) A pH of 0 to 6 is acidic, while a pH of 8 to 14 is increasingly basic.
11) A difference of 1 pH unit is representative of a difference of 10 times in concentration of
the acid or base.
12) How is pH important in humans?
The pH level in humans is about 7.35 – 7. 45. When the levels of pH change in
organisms, they are very sensitive to it. A buffer is the action of resistance in change of pH
by adding H+ or –OH to the solution. pH is an important part of humans and biology in
general because if out pH gets out of a normal range there could be very bad consequences.
Our body does a good job regulating our pH because out pH changes with little things such
as exercise and breathing.
Chapter 4 – Carbon - Objectives:
1) What is the Abiotic Synthesis Theory for the origin of life?
The theory is that life originated from inorganic compounds.
2) What is Stanley Miller’s evidence for the Abiotic Synthesis Theory? Why is this theory
questioned today?
Miller simulated the conditions on the primitive Earth and was able to create amino acids,
purines, and pyrimidines, which are life ‘matter’. His theory is questioned today because it is
thought that life originated in the abyssal zone in the hydrothermal vents - but his experiment
was on the top layer of the oceans.
3) What types of bond does carbon make with surrounding atoms?
Carbon makes covalent bonds.
4) Illustrate the following with examples - Carbon compounds are highly varied due to
differences in:
a) Length of carbon skeleton
b) Arrangement of atoms around the carbon atoms
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c) Functional groups
5) What are Isomers? What are the 3 kinds of Isomers?
Isomers are compounds that have the same molecular formula but different structures and
therefore different chemical properties. There are structural isomers, geometric isomers, and
enantiomers.
6) What are Structural Isomers – give an example.
Structural isomers are molecules with the same molecular formula but differ in the
covalent arrangement of atoms. An example would be Butane and Isobutane:
7) What are Geometric Isomers? Give an example. What is one important characteristic to
look for before you decide if a CARBON compound is a geometric isomer?
Geometric Isomers are compounds with the same covalent partnerships that differ in their
spatial arrangements around a carbon-carbon double bond. We always need to look for a
C=C double bond.
8) What are Enantiomers? Give an example.
Enantiomers are molecules that are mirror images of each other.
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9) What are functional groups?
Functional groups are attachments that replace one or more hydrogen atoms to the carbon
skeleton of the hydrocarbon.
10) Identify the chemical structure of the following functional groups:
a) Hydroxyl/Alcohol
b) Carbonyl – both types namely aldehyde and ketone
c) Carboxyl acid
d) Sulfhydryl
e) Amino
f) Phosphate
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Chapter 5 Macromolecules - Objectives:
1) What are macromolecules?
They are biological molecules (many of them polymers) - thousands of atoms in size that
weigh over 100,000 Daltons.
2) What are the 4 important types of macromolecules?
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The four kinds of macromolecules are proteins, lipids, carbohydrates, and nucleic acids.
3) What are monomers and polymers?
Monomers are the repeated units and sequences of elements to make things such as
macromolecules. Polymers are chains made up of many monomers.
4) What reaction makes polymers from monomers? Describe the process
Condensation and dehydration reactions make polymers from monomers. By using ATP
and energy, one monomer connects its –OH to another monomer’s H- to form water. This
water molecule then detaches from the chain which is now a polymer. (Water leaving =
dehydration).
5) Give an example of an anabolic (building polymers) reaction
An anabolic reaction is how people, such as our ‘governor’, build macromolecules – ex:
myosin and actin proteins in muscle with the use of steroids or ATP! Here free energy is
positive
6) What reaction makes monomers from polymers? Describe the process
This process is the breaking apart of polymers into monomers, called Hydrolysis reaction.
This is when water is added to break the bond up, the exact opposite of dehydration
reactions. It uses enzymes and provides ATP to do this.
7) Give an example of a catabolic (breaking down polymers) reaction
A catabolic reaction would be digestion within our bodies or cell respiration – it breaks
down macromolecules (opposite of anabolic reaction). Here free energy is negative.
8) The common biochemical name for sugars is saccharides.
9) The monomer of sugars is called monosaccharide. Give examples
Fructose, glucose, and ribose are all monosaccharides as they have only one sugar.
Monsaccharides can of many types based on the number and arrangement of carbons,
functional groups, and ring structure.
10) The polymer of sugars is called polysaccharide. Give examples
Polysaccharides are many monosaccharides linked together such as chitin (exoskeleton of
arthopods) and glycogen.
11) What is a disaccharide? Give some examples and sources of these sugars
A disaccharide is when two monosaccharides are linked together by dehydration reaction.
Such sugars are sucrose (glucose and fructose), lactose (glucose and galactose), and maltose.
12) Sugars end with the letters –ose.
13) What is the difference between a ketose and an aldose?
What type of macromolecule are they?: C=O represents both a ketose and an aldose. The
difference is the placement in the structure and the other atoms surrounding it. Ketoses are in
the middle while aldoses are on the end. Aldose is a –H-C=O (-CHO) group while ketose is –
C=O. They are in the monosaccharide groups- sugars and therefore make up the functional
groups in all carbohydrates!
14) Identify the number of carbon atoms in the Hexose sugar – glucose and the Pentose sugar
– Ribose. Why is ribose an important sugar to remember?
Hexose- 6C, Pentose- 5C. Ribose is important to remember because it is in RNA.
15) How many forms can glucose take chemically?
Glucose can bein a strainght chain form or a ring structure
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16) What reaction makes disaccharides from monosacharrides?
Dehydration reaction makes monosaccharides into disaccharides.
17) What is a glycosidic linkage? In what macromolecule can you see this?
Glycosidic linkage is between two sugar monomers. They are connected by an oxygen
atom and found in carbohydrates.
18) What are the 2 types of polysaccharides? Give examples of each in plant and animals
Polysaccharides in plants are cellulose and starch while in animals there are glycogen and
chitin. They are all made of repeating units of monomers – the glucose rings connected by
glycosidic linkages.
19) What reaction makes a polysaccharide from a monosaccharide?
This reaction is called condensation.
20) What are lipids? Are they made of monomers?
Lipids are mostly hydrocarbons that are hydrophobic and are not polymers.
21) What are some important types of lipids?
Fats, phospholipids, and steroids make up the lipid groups.
22) What are the two parts of a fat molecule? What reaction puts those two parts together to
make a fat?
Fats are made up of glycerol and fatty acids. Ester linkage connects these two parts.
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23) What is the difference between a saturated fat and an unsaturated fat?
Saturated fats are solids at room temperature while unsaturated fats are liquid. Saturated
also means that all the carbon bonds are taken and hold their maximum number of atoms
while the unsaturated fats have double bonds because they can still hold more atoms.
24) What is a trans fat? Why is it unhealthful?
Trans fat is when a saturated and unsaturated fat come together as one. It’s unhealthy
because it clogs arteries easily which is also referred to as carcinogenic because it can cause
heart problems and cancer.
25) Should you avoid eating ALL fats? What is the function of fats in the body?
Not eating any fats would kill you because your body stores fats for energy, uses it as
insulation, and also helps with the absorption of Vitamins K, E, D, and A.
26) What are phospholipids? Where can you find them?
Phospholipids are made up of fatty acids, a phosphate group, a polar group, and a
glycerol. They are also both hydrophobic and hydrophilic. They are found in cell membranes.
27) What are steroids? What is their function in the body?
Steroids are lipids such as sex hormones and cholesterol and consist of four fused rings.
They are found naturally in the body and each have specific roles such as defining whether
you are male or female.
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28) What are proteins? Name some important proteins in the body
Proteins are polymers made up of amino acids monomers such as enzymes and
cytoskeleton.
29) What is the monomer in proteins? Draw the structure of a
monomer with the functional groups indicated clearly
QuickTime™ and a
TIFF (Uncompress ed) dec ompres sor
Amino acids are the monomers in proteins.
are needed to s ee this pic ture.
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30) What are the amino acids made of? How many amino acids make up ALL the proteins in
our body? How can so many different proteins be composed from just a few amino
acids?
All amino acids have a carboxyl and amino group, a center alpha carbon, and an R group.
There are 20 amino acids and they can make up so many proteins because the combinations
of them are endless.
31) What is different in the structures of the 20 amino acids found in the body? Elaborate on
how this difference is critical to the functioning of the protein they make up: The
difference in these amino acids is the R group. This makes a difference of its function
because some are acidic, basic, polar and nonpolar which affect how it reacts to its
surroundings.
32) What is a peptide bond – draw one
A peptide bond is made by dehydration reaction, which connects two amino acid
monomers together to form a bond.
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33) What is the primary structure of a protein?
If there is a change in the primary structure,
how will the functions of the protein
change?
The primary structure of a protein is the
sequence of the amino acid chain (the order). If
there is any change in the sequence, the function
QuickTime™ and a
of the protein will change (i.e.- Sickle Cell).
TIFF (Uncompressed) decompressor
are needed to see this picture.
34) What is the secondary structure of a
protein? If there is a change in the
secondary structure, how will the function of
the protein change?
Secondary structure is the result of hydrogen
bonding between O=C and N-H (polypeptide
backbone). They are in the forms of the alpha
helix and beta pleated sheets. With a change of the structure the protein will act differently,
such as hydrogen bonds breaking, etc.
35) What is the tertiary structure of a protein? If there is a change in the tertiary structure,
how will the functions of the protein change?
This structure is the result of hydrogen bonding between the R groups. It is unique
because of the disulfide bridges it forms. If there was any change it could change the function
of the protein.
36) What is the quaternary structure of a protein? If there is a change in the quaternary
structure, how will the functions of the protein change?
This structure is made up of tertiary structures and if they aren’t exactly right they aren’t
going to function right.
37) What will happen to a protein when it is heated or when an acid is added to it?
With changes such as temperature, pH, or salt concentration, proteins can denaturize
(lose biological activity).
38) What is a nucleic acid – is it the same as an amino acid?
A nucleic acid is made up of nucleotides (monomer), which is itself made up of sugarphosphate-nitrogen base (subunit of monomer).
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39) What is the monomer in Nucleic Acids? What are these monomers made up of?
Nucleotides are the monomers in nucleic acids. They are made of a pentose sugar, a
nitrogen base, and a phosphate group.
40) What are the two important types of Nucleic Acids? Where are they found in the cell?
DNA and RNA are important nucleic acids. DNA is found in the nucleus and RNA in the
cytoplasm and nucleus.
41) Describe the way the monomers link up to make these Nucleic Acids
Purines and Pyrimidines (nucleotides) link together to form a bond in nucleic acids.
Adenine, Guanine, Uracil, Cytosine, and Thymine are nucleotides that make up DNA and
RNA. A = T; G=C
42) Name a really important nucleotide that is involved in energy transfer in cells
Adenosine Triphosphate or ATP
Chapter 6 Enzymes - Objectives:
1) What is Metabolism?
The sum of an organism’s chemical reactions is called metabolism.
2) What is an anabolic reaction? Is it energy yielding or energy consuming reaction? Give
an example.
Anabolic pathways consume energy to build complicated molecules from simpler
compounds. This process consumes energy. An example of this would be when a baby grows. At
this time these molecules form organs and organ systems.
3) What is a catabolic reaction? Is it energy yielding or energy consuming reaction? Give an
example.
Catabolic reaction is breaking down complex molecules to simpler compounds. This is an
energy releasing process. An example of this is when polysaccharides are broken down to form
monosaccharides.
4) Is an anabolic reaction an exergonic or endergonic reaction? Why?
Anabolic reaction is an endergonic reaction because it consumes the energy.
5) Is an catabolic reaction an exergonic or endergonic reaction? Why?
Catabolic reaction is an exergonic reaction because it releases energy.
6) What is the energy molecule of the cell? What type of macromolecule is it?
Energy molecule of the cell is ATP, which is a nucleotide.
7) How does the energy released in a catabolic reaction get harnessed and utilized in an
anabolic reaction?
Bonds between PO4 groups are broken to release energy and then the PO4 group is tagged
to the reactant, which gets phosphorylated and is able to undergo the chemical reaction.
8) What ‘activities’ need energy inside a cell?
Mechanical work (movement), transport of macromolecules into and out of cells, and
chemical work (drive endergonic reactions in anabolic pathways).
9) What is Activation energy?
Activation energy is needed by reactants to make the products.
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10) What do enzymes do inside our cells?
Enzymes lower the activation energy and thus drive most chemical reactions.
11) What class of macromolecule do enzymes belong to?
Enzymes are proteins.
12) Explain the following statement: Enzymes are specific and recyclable.
This means that specific enzymes work for only specific substrates and they can be
reused many times.
13) Illustrate and explain the way an enzyme works – be sure to include the following
concepts: Active site – site where an enzyme binds, Enzyme Substrate complex – formed
when enzyme binds to substrate – it is not a permanent structure as the products break off
and enzyme is reused, Induced Fit Hypothesis – enzyme shape is not a lock – a fixed
structure, BUT it is like a hand that catches a ball – the enzyme active site shapes itself to
fit the substrate, Activation Energy – see before.
What happens to the enzyme at the end of a reaction?
The catalyst gets back to its original form at the end of reaction.
14) What is the overall effect of adding an enzyme on the rate/speed of a reaction?
It increases the rate/speed of reaction.
15) How can you make this above enzyme-catalyzed reaction go faster?
Increase the temperature or pressure.
16) Draw graphs showing the effect of changing the following factors on the speed of an
enzyme catalyzed reaction:
a) Substrate concentration – like density dependent population graph – 4 parts (see chp52)
Rate
of
Reaction
Substrate concentration
b) Temperature
Rate
of
Reaction
Temperature
c) pH
Depends on an enzyme
Rate
of
Reaction
pH
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17) What is feedback inhibition – illustrate with an example.
Feedback inhibition is when a metabolic pathway is turned off by its end product.
18) Complete the following table:
Factor
Effect on Enzyme
Catalyzed reaction
Substrate
concentration
Increase the reaction rate
until enzyme is saturated
Temperature
Increase the reaction rate
until enzyme denatures
pH
Increases or decreases
based on type
Cofactors/co
enzymes
Salt
Increases until there are
too many cofactors
Increases or decreases
based on type
Competitive
Inhibitor
Noncompetiti
ve Inhibitor
Allosteric
Activator
Decrease
Does not affect the rate
Increases the rate of
reaction
Biochemical
Reason For
This Effect
Increase the
chance of
collisions
Increase the
number of
collisions
R-groups’
charge changes
which alter
structure
Activates the
site
R-groups’
ionization
changes which
alters structure
Occupies the
active site
Occupies the
allosteric site
Stabilizes
activity of the
enzyme
Is there a limit
to this effect?
What is it?
Saturation of
enzyme
Example
Too acidic or
too basic
More milk =
more milk
broken down
Lactase works
best at 37.5
degrees Celsius
Human enzyme
pH is 6-8
Too many
Vitamins
Denaturation
Too much
More inhibitors
=less catalyzing
More inhibitors
=less catalyzing
Activator
increases;
inhibitor
decreases
Alcohol
Nerve gas
Anti-anxiety
drugs