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Test #2 Notes: Biochemistry
I. Biochemistry
A. Atoms – The smallest unit of matter that retains its chemical property.
1. Protons (p+) Neutrons (n0 ) are found in the nucleus or center of an atom
a) Atomic # -# of protons found in the nucleus of an element. The atomic # determines an element’s
identity.
Atomic #1 = _____ protons = the element _________
Atomic #6 = _____ protons = the element _________
Atomic #7 = _____ protons = the element _________
Atomic #8 = _____ protons = the element _________
b) Mass # - The total number of protons and neutrons in the nucleus.
Mass # 12 = the element ______________, which has _______ protons and ________ neutrons.
Mass # 16 = the element ______________, which has _______ protons and ________ neutrons.
 Element - A pure substance that consists entirely of one type of atom.
 Isotopes – Atoms of the same element that contain a different number of neutrons.
C-12 = _____ p+ and _____ n0
C-13 = _____ p+ and _____ n0
C-14 = _____ p+ and _____ n0
 Radioisotopes – Radioactive/ unstable isotopes.

What causes some isotopes to become unstable?

What are some biological uses of radioisotopes?
pg. 1
2. Electrons (e-) are found traveling at specific distances
(orbitals, energy levels, shells) from the nucleus

The first and closest energy level, orbital, or shell
can hold a maximum of 2 e- and the rest of the shells
can hold a maximum of 8 e-. The electrons farthest
from the nucleus, located in the outer energy level shell, are called valence electrons.
*Complete the following diagrams by drawing the electrons in the correct positions.
Carbon
Sodium
Oxygen
Nitrogen

Atoms/ elements want full shells and will share, give, or take valence electrons to become full.

In an electrically neutral atom, the number of protons (+) equals the number of electrons (-).
An atom that has an imbalance in the number of protons and electrons is called an ion.
Chemical Reaction: The process of making or breaking bonds between atoms.
O
Example: Water  Chemical formula2= H O, Structural formula =H
H
? Why are valence electrons essential for life? ________________________________________
B. Molecules – A combination of 2 or more bonded atoms.

Ionic Bonds – One atom ________or _____________
an electron (becoming a cation/ +), and the other
atom accepts or gains an electron (becoming an
anion/ -). As opposite charges attract, they form
an ionic bond.

Covalent Bonds – Form when electrons are ___________
between atoms to fill the outer energy level/ shell.
Most organic molecules (contain carbon and are
essential to life) are formed from covalent bonds.
pg. 2

Hydrogen Bonds – Are the result of weak electrical attractions involving hydrogen atoms
Inorganic Molecules

Molecules that do not contain the element Carbon (except carbon dioxide). The most common and most
important inorganic molecule is WATER.
 Water: a unique inorganic molecule essential for life.

Acts as a solvent to break up other molecules into
ions which are used for biological reactions.
Water acts as a solvent because it is a polar
molecule: _____________________________
***Draw a water molecule, show how it is polar.***

Water has the ability to travel through small pores or to move upward through narrow vessels against
the force of gravity
___________________ – Water molecules and the molecules of solid surfaces are attracted to each
other.

Water heats up and cools down at a slow rate, which keeps an organism’s body temperature steady.
___________________ – The uneven electrical charge within each water molecule causes them to be
attracted to each other, the positively charged H+ is attracted to the
negatively charge O-.

Water molecules can react with other elements to form ions ( H2O
H+
+
OH- )
pH Scale - A range from 0-14 that indicates the ___________________________________________



Pure water has a pH of 7, the concentration
of H+ and OH- are equal, and it is neutral.
A solution with a pH above 7, has more OHions than H+ ions, and is basic.
A solution with a pH below 7, has more H+
ions than OH- ions, and is acidic.
Buffer - Weak acids or bases that can react with strong
acids or bases to prevent sharp, sudden changes in
pH.
*This helps humans maintain homeostasis by keeping
our pH level at 7.4. If the pH changes more
than .5, then many chemical reactions in our cells will
be negatively affected. We cannot survive more than
a few hours if our pH level moves too far in either direction.
pg. 3
Organic Molecules

Molecules from living things that contain ___________

Carbon possesses four valence electrons
Three reasons carbon molecules are so complex:
a) The four valence electrons allow carbon to form four bonds.
b) Carbon can bond to other carbon atoms as well as different atoms.
c) Carbon can bond in many different positions creating different shaped molecules (remember shape
determines function)
Straight Chain
Branched Chain
Rings

Organic Macromolecule – A __________ molecule containing ___________. There are 4 types: lipids,
carbohydrates, proteins, nucleic acids
* Macromolecules are made up of many smaller molecules (______________), which are made up of
smaller units (_________________).
Monomer (1 unit) = M
(BRICK)
Polymer (many monomers) = M-M-M-M-M-M-M-M
(ROOM)
M-M-M-M-M
Macromolecule (multiple polymers)
(FHC)
M-M-M-M-M-M
M-M-M
M-M-M-M-M-M-M-M-M-M-M-M-M
The Making and Breaking of Organic Molecules
 Dehydration Synthesis – The process of making a larger molecule
from 2 or more small molecules/ monomers.
- One monomer loses a hydrogen ion (H+) and
another loses a hydroxide ion (OH-).
- The loss of H+ and OH- (H2O – water) makes
valence electrons available for bonds to form.
pg. 4
- As a result of dehydration synthesis, the monomers
lose or give off energy.

- Also referred to as a condensation reaction, because water condenses as a product
Hydration Synthesis – The process of making 2 or more smaller molecules
from a larger molecule.
- One product will gain a hydrogen ion (H+) and the
other gains a hydroxide ion (OH-).
- As a result of hydration synthesis monomers
gain or store energy.
- Also referred to as a hydrolysis reaction, because
water is added and then broken apart during
the reaction
Reaction
Water
(lost or gained?)
Energy
(lost or gained?)
Purpose
(end result)
Dehydration Synthesis
Hydration Synthesis
(Hydrolysis)
C. Energy in Reactions- In the two reactions above, energy is either stored or released as a result of the
reaction. Chemical reactions do not always occur spontaneously; often energy is
needed to start.
 Activation Energy – The energy that is needed to get a reaction started.
 Enzymes – A type of protein molecule that acts as a catalyst to speed up a reaction by lowering
the amount of activation energy needed to start a reaction.
How enzymes work:
1. Substrates are the reactants in a chemical reaction that are catalyzed/changed by the enzyme.
2. Enzymes bind to the substrates. This is determined by their shape; they fit like “lock and key.”
3. Rate of chemical reaction is increased. (Happens faster because less activation energy is needed.)
4. Enzymes can be reused because they are not changed as a result of the reaction.
pg. 5
Enzymes can be used 1000’s of times because they are not changed as a result of the reaction.
There are four steps in the process of an enzyme working.
1. An enzyme and a substrate are in the same area. The
substrate is the biological molecule that the enzyme will
attack.
2. The enzyme grabs onto the substrate with a special
area called the active site The active site is a specially
shaped area of the enzyme that fits around the
substrate. The active site is the keyhole of the lock.
3. A process called catalysis happens. Catalysis is when
the substrate is changed. It could be broken down or
combined with another molecule to make something new.
4. The enzyme lets go. Big idea: When the enzyme lets go,
it returns to normal, ready to do another reaction. The
substrate is no longer the same. The substrate is now
called the product.
Cellular Respiration
Q: Enzymes must function properly for
organisms to stay alive and healthy.
What determines the enzyme’s
function? _______________________
Q: What factors can cause an enzyme’s
shape to change, thus affecting its
function?

___________________________

___________________________

___________________________
The Four Macromolecules
1) Lipids
 Atoms = __________________

Monomers = ___________________

Functions = long term energy storage & is a structural component
of cell membranes

Examples = oils (liquids at room temperature), fats (solid at
room temperature), waxes, and the
cell membrane.
pg. 6
2) Carbohydrates (most end in –ose)

Atoms = __________________

Monomer = ___________________
*Some Monosaccharide Examples:
 glucose – monosaccharide made by plants during
photosynthesis
 fructose – monosaccharide found in fruits.
 galactose – monosaccharide found in milk
 Isomers – Molecules that share the same molecular
formula, but their structural formula’s
differ. For example, in the preceding diagram, glucose and fructose have the same molecular
formula (C6H12O6), but different structures.

Examples of carbohydrates with their functions:

Disaccharides – A combination of 2 monosaccharides by the process of _______________________.
Sucrose = fructose + glucose

Lactose = galactose + glucose
Macromolecules
Glycogen – Made up of hundreds of glucose molecules bonded in a highly branched chain.
- Animals store their glucose in this form, and it is used for short-term energy.
Starch – Made up of thousands of glucose molecules in straight or branched chains.
- Plants store their glucose in this form.
Cellulose – Made up of thousands of glucose molecules in long straight chains.
- Cellulose, located in plant cell walls, gives plants strength and rigidity for support. Is fiber
in some animal diets.
Chitin – Structural component in animals (shells) & Fungi (cell walls)
3) Protein
 Atoms = _________________
 Monomers = ____________________________,
(twenty exist in nature.)

Amino Acid Structure: Each of the 20 amino acids have the same chemical make-up with one exception
(see below).
General structure
Alanine
Serine
pg. 7

The sequence and number of bonded amino acids will determine the shape and size of the protein, thus its
_____________.


Examples of proteins with their functions
 Structural Proteins – collagen found in tendons & ligaments, keratin in horns, feathers & nails for
protection & support

Transport Proteins – hemoglobin transports oxygen by blood, other proteins transport molecules across
cell membranes.

Hormonal Proteins – Regulation of bodily activities, Insulin is a hormonal protein that regulates blood
sugar levels.

Contractile Proteins – actin & myosin are proteins found in muscle that allows for muscle movement and
contraction

Antibodies – chemically defend the body against pathogens like bacteria, viruses, and fungi.

Enzymes – Enzymes act as catalysts to regulate the chemistry of cells by selectively speeding up
chemical reactions.
Protein Structure: Protein shapes and functions are based on
amino acids undergoing condensation and forming peptide bonds.
4) Nucleic Acids

Atoms =

Monomer =

Examples of nucleic acids with their functions:
 DNA (Deoxyribose Nucleic Acid) –
______________________________
______________________________
 RNA (Ribose Nucleic Acid) –
______________________________
______________________________
pg. 8
pg. 9
Biology Review Sheet Test #2: Biochemistry
Test Date: September 29, 2010
I. Multiple choice questions (1-22)
A. Know the following terms:
 Atomic # and Mass # (p. 1)
 Radioisotopes (Definition & uses) (p. 1)
 Covalent and ionic bonds (Notes p. 2-3)
 Buffer (Definition & importance of) (p. 3)
 Polar, Cohesion and Adhesion (p. 4)
 What properties of carbon make it a unique element found in all living things? (p. 4)
 Dehydration Synthesis, Hydration Synthesis (p. 4-5)
 Activation Energy (p. 5)
 Enzymes (p. 5)
 Isomers (p. 6)
 Organic molecules vs. inorganic molecules (definition & examples) (p. 6-8)
 Catalyst (p. 8)
B. Be able to distinguish acids and bases by their concentrations of OH - and H+ ions, and be able to read a pH scale
and determine which direction is more acidic v. basic. (p. 3)
C. Building molecules and breaking them down
 Compare and contrast Dehydration Synthesis and Hydration Synthesis (Hydrolysis) (p. 4 - 5)
 Know that energy is absorbed or released in the breakdown or synthesis of organic compounds (p. 5)
D. Enzymes
 Know the relationship between enzymes and their substrates. (p. 5)
 Explain how protein enzymes affect chemical reactions. (p. 5)
 Interpret data for the effect of enzymes on a biochemical reaction. (p. 5, see text book)
 Identify factors that effect the function of enzymes and why (they change their shape). (p. 5)
E. Carbohydrates
 How do plants store their carbohydrates? Animals? (p. 7)
II. Matching (23-30)

Match the 4 macromolecules to their elements, monomers, examples, and functions. Study your Macrobox!
III. Constructed Response (31-36)







Draw a water molecule (structural) and state why it is considered a polar molecule.
Why are valence electrons essential for life?
Identify two internal environmental factors that directly influence the rate of enzyme action.
Explain how an enzyme can have its shape changed/altered (into abnormal structure).
Explain why changing the shape of an enzyme could affect the ability of the enzyme to function.
Draw and/or explain the relationship between monomers, polymers, and macromolecules.
Draw and label an electrically neutral atom (for example – carbon, oxygen, etc.). You do NOT need to
memorize atomic number.
pg. 10
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