1
Name: ________________________
Date: ______________
Unit 2: Ecological Biochemistry
Unit 2B Biochemistry Part 2
NOTES
D. Proteins
Of all the organic compounds, proteins are the largest, most
complex, and most diverse.
While 70% of the body is water, most of the other 30%
is protein!
• Made of elements C, H, O, N
One
amino
acid
Many linked
amino acids is
a _________
• Made of _____________________ (the
monomer)
• ______________ bonds link amino acids together to
make polypeptides
• One or more polypeptides “fold” into a
___________
Proteins are Diverse
• __________ amino acids are used to make proteins
• Different combos of amino acids lead to different
functioning proteins
• DNA tells the proteins how to assemble.
Summary/Additional Notes:
One or more
polypeptides
folds into a
_________
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Amino Acids
Amino acids are compounds with an ____________ group (-NH2) on one end and
a _____________ (-COOH) group on the other end.
Each amino acid consists of one of each of the following, connected to each other
by covalent bonds.
1) central carbon atom (-C-)
Central Carbon
Lone Hydrogen
2) carboxyl group (-COOH)
3) amino group (-NH2)
4) one lone hydrogen atom (-H)
5) 'R' (variable) group - one of 20 different side chains
Because of their uniform structure, any amino acid can bond to any other amino
acid using a covalent bond called a ________________________.
 What process will link together two individual amino acids?
________________________________________
Summary/Additional Notes:
3
Examples of Specific Amino Acids

Circle each amino group, box each carboxyl group and label each R group (-R).
 On the two amino acids below, circle the atoms that must be removed in
order to create a peptide bond.
Hint: These atoms create a _______________ molecule, which is a product of the
reaction.
Glycine
Valine
Summary/Additional Notes:
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Polypeptides
Segments of amino acids are called polypeptides
When they are first assembled, polypeptides are _____________ (straight) chains.
They are not yet functioning proteins!
R groups on the amino acids ______________ with each
other causing the polypeptide to __________ into a specific
3-dimentional shape or structure.
Once it is completely and correctly folded, it is considered a
protein.
(other small changes or ___________________ may also occur before the protein
is completely functional)
The structure of each protein in unique; Structure leads to function!
 How many amino acids are shown in the polypeptide below?
_______________ (Hint: count the R groups)
 How many peptide bonds are shown in the polypeptide below?
______________ (Hint: peptide bonds are between which two atoms?)
 How many water molecules were released as this polypeptide was
formed?______________ (Hint: one for each bond made!)
Summary/Additional Notes:
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Chemical Reactions and Energy
Everything that happens in an organism is based on a chemical reaction.
A chemical reaction:
- Changes one set of chemicals into another
- Changes chemical bonds
- Reactants- elements/compounds that enter the reaction
- Products- are produced by the reaction
When bonds are made or broken…
Energy is ________________ (taken in) or ____________________ (given off)
- Reactions releasing energy can (but not always)
occur on their own, or__________________________
- Reactions absorbing energy will not occur without a
_________________ of energy
*Example of a chemical reaction that releases energy:
Paper is made of cellulose which burns in the presence of oxygen, and releases
energy in the form of heat and light. But this packet is not spontaneously
bursting into flames right now.
 Why not? What is missing?
_______________________________________________
 Where does your body get energy for chemical reactions? __________
Plants: ____________________________________________________________
__________________________________________________________________
Animals: __________________________________________________________
__________________________________________________________________
Summary/Additional Notes:
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Activation Energy: Is the amount of ______________ that a reaction needs to
_________________________.
Every reaction requires a certain amount of activation energy to get started,
regardless of whether it is an energy-absorbing or energy-releasing reaction.
ENERGY ABSORBING REACTIONS
(Endergonic)
- _________________ have more energy than
the reactants
- Products larger less stable, and more complex
than reactants
- It takes more energy to break bonds in the
reactants than is released by making new bonds
in the products
Examples: dehydration synthesis;
photosynthesis
Dehydration
Synthesis
__________
__________
ENERGY RELEASING REACTIONS
(Exergonic)
- _________________ have more energy than
the products
- Reactants are larger, less stable, and more
complex than products
- More energy is released when new bonds are
formed in the products than was needed to
break the old bonds in the reactants
Examples: hydrolysis; cellular respiration
Summary/Additional Notes:
Hydrolysis
__________
__________
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Enzymes
Some chemical reactions would be too slow or have too high of an activation
energy without a little help.
Catalyst- a substance that speeds up a chemical reaction
- works by _______________ the activation energy
Cells make special proteins called enzymes to act as
catalysts for chemical reactions.
- There is __________ type of enzyme for each type of
chemical reaction (its shape makes it _________ for its
job)
Would the hill be higher or lower with an enzyme
present? __________
How do Enzymes Work?
1. They provide a site for the reactants to be brought together to react.
2. They help to break the bonds of the reactants.
- This ___________ the energy needed for the reaction.
“Enzyme Catalyzed Reaction”- a reaction sped up by an enzyme
Substrates- what the _________________ are called in an enzyme catalyzed
reaction.
Substrates bind to a place on the enzyme called the active site which has a specific
shape.
Summary/Additional Notes:
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Two Models Help Explain How Enzymes Work
1. "Lock and Key Model": The substrates fit the enzymes like a key fits into a lock.
A very _______________ interaction!
 This provides the site for the reactants to come together.
2. “Induced-fit Model”: The enzyme binds the substrate(s) and slightly changes its
shape to “hug” the substrate(s) tightly (like a handshake).
 This places “strain” on existing
bonds, allowing bonds to break and
the chemical reaction to go
______________.
Example of an enzyme-catalyzed reaction: ____________ is formed by combining
___________________ and water in the
presence of the enzyme
“_______________________”.
 WHY aren’t enzymes considered a
reactant or a product? (analyze the
reaction to the right for a hint)
__________________________________________________________________
Enzymes are _________________!
Some enzymes help to synthesize larger molecules, other help to break them down
(hydrolysis)
Summary/Additional Notes:
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Examples of some types of biologically-important hydrolytic enzymes
The suffix "–ase" commonly indicates that a protein is an enzyme.
1. protease- any enzyme that speeds hydrolysis or breakdown of proteins
2. sucrase (a disaccharidease) - an enzyme which speeds the breakdown of
___________________
3. lipase - any enzyme which speeds the breakdown of
_________________________
4. nuclease - any enzyme which speeds the breakdown of
_______________________
5. amylase - an enzyme which speeds the breakdown of amylose (=starch!)
Factors Affecting Enzyme Activity
Temperature, pH, and regulatory molecules affect enzyme activity
An ____________ in temperature will increase the rate of a reaction to a certain
point
After that point, the enzyme will no longer work
Denaturation - when a protein
____________ and loses its
overall shape (and thus function)
due to increased temp or changes
in pH.
A denatured enzyme loses the
shape of its active site and will no longer function.
Think! Why are temperature and pH important factors in maintaining homeostasis?
__________________________________________________________________
__________________________________________________________________
Summary/Additional Notes:
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pH
Water is one of the most important inorganic substances in living organisms.
Sometime water molecules will break apart (___________________) to form ions.
Ion- a positively or negatively charged atom (set of atoms) due to loss or gain of
electrons
About 1 water molecule in 550 million splits in this way.
Because the number of positive H+ ions is equal to the number of negative OHions, water is _____________.
The pH scale- measures the concentration of ________ ions [H+] in a particular
solution.
•
•
•
•
•
Measured 0-14
Each step represents a factor of ________.
7 is _____________ (like water- has equal amounts of H+ and OH-)
Lower from 7 becomes more _________________ (has more H+)
Higher from 7 becomes more _________________________ (has less H+)
Summary/Additional Notes:
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 Order these substances in order of increasing acidity:
human blood, acid rain, bleach, seawater, stomach acid.
1. ____________________
2. ____________________
3. ____________________
4. ____________________
5. ____________________
 Label as Acid, Base, or Neutral. Strong or weak?
pH 7:___________ pH 13.5:___________
pH 8:___________ pH 2:____________
 Which one is more acidic?(circle one)
pH of 2
-or-
pH of 4
 How many times more?___________
 Which one is more basic? (circle one) Tomato juice
-or-
Soap
 How many times more?________
Definitions of acids and bases
ACID- compound that forms H+ ions in solution
BASE- compounds that forms OH- ions in solution
• Study the reaction below. Is this substance an ACID or BASE? (circle)
HCl
Hydrogen Chloride
Dissociation In Water
→
H+
+
Hydrogen ion
ClChloride ion
• Study the reaction below. Is this substance an ACID or BASE?(Circle)
NaOH
Sodium Hydroxide
Summary/Additional Notes:
Dissociation In Water
→
Na+
Sodium ion
+
OHhydroxide ion
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Sample Acids and Bases:
ACIDS
BASES
Solutions have a
pH_______7
Solutions have a pH
______ 7
Taste sour
Taste bitter
Can corrode metals
Can denature
proteins (feel
"slippery")
In solution: [H+]
_____ [OH-]
In solution: [H+]
_____ [OH-]
ACID
Draw a solution
with more H+
than OHRange of pH
______________
[H+] ______
[OH-] in this
type of solution.
NEUTRAL
Draw solution
with equal
numbers of H+
and OHRange of pH
______________
[H+] ______
[OH-] in this
type of solution.
Summary/Additional Notes:
BASE
Draw solution
with more OHthan H+
Range of pH
______________
[H+] ______
[OH-] in this
type of solution.
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Buffers
Controlling pH is important for
______________________ in cells.
maintaining
The pH of most cells in the human body must be kept
between ___________ and ___________.
Buffers- Weak acids or bases that react with strong
acids or bases to ___________________ sharp, sudden
_____________________ of pH.
Example: Sudden pH changes in ______ are prevented
by buffers such as bicarbonate and phosphate ions.
Summary/Additional Notes: