AP Biology

Protein Structure and Enzymes

Connection to the Nitrogen-cycle
• Amino acids (protein)
• Nucleic acids (RNA and DNA)
• ATP
78%
1. Assimilation of
nitrate by
photosynthetic
eukaryotes
2. Nitrogen
fixation by
prokaryotes
3. Denitrification
by anaerobic
prokaryotes
1. Assimilation of
nitrate by
photosynthetic
eukaryotes D
2. Nitrogen
fixation by
prokaryotes A
3. Denitrification
by anaerobic
prokaryotes E
•Amino acids (a.a.) are
monomers of polypeptides
(protein polymer)
•Amino group has Nitrogen
•R-groups have different
properties: hydrophilic,
hydrophobic, etc.
Why are these amino acids hydrophobic?
Why are these amino acids hydrophilic?
• Two a.a. join with a peptide bond
• Dehydration synthesis: H2O is released
R-group R-group

Carboxyl Amine

Peptide Bond
1. Label the amino groups.
2. Label the carboxyl groups.
3. Label the R-groups.
4. Show how the two molecules would join together
to form a peptide bond:
5. Show the molecule that would be released?
1. Label the amino groups.
2. Label the carboxyl groups.
3. Label the R-groups.
4. Show how the two molecules would join together
to form a peptide bond:
5. Which molecule would be released? H2O
Primary Structure
• The unique a.a. sequence

• This model of the enzyme

lysozyme is 129 a.a. long

• If left to chance, there are

20129 different ways to
arrange the 20 a.a. into a
chain this long

• The ordering is “spelled”

out in the DNA of a gene
 Secondary Structure
Coils = alpha helix Folds = beta pleated sheet
Result of H-bonding Result of H-bonding
What is responsible for the secondary structure of
proteins?
Tertiary Structure
Irregular
contortions
(tweaking) caused
by interactions
between R-groups
 1
2
3

Match the terms to the #s:

hydrophobic interactions, hydrogen-bonding, ionic
interactions, disulfide bridge
 Quaternary Structure
Two or more polypeptide subunits combine
Ex. Collagen has 3 subunits, Hemoglobin 4
1. Specific order of amino acids

2: H-bonding resulting in alpha

helix and beta pleated sheets

3. Other chemical bonds result in

complex pattern of folding

4. 2 or more subunits come together

to form finished product
1. ___________ energy is
added, then:
2. Bonds become ________
3. Bonds ___________
4. Atoms ___________
5. New bonds _______
6. Matter is ____________

7. Enzymes _________
activation energy (see
graph to the right)
1. Activation energy is added, then:
2. Bonds become _unstable__
3. Bonds _break____
4. Atoms __rearrange___
5. New bonds _form__
6. Matter is __conserved_____
1. Which number represents the amount of activation
energy required without an enzyme?
2. With an enzyme?
3. Summarize the effect of an enzyme on activation
energy?

2 3
reactants

1
4

products
Label your graph with the following:
• Reactants
• Products
• Activation energy without an enzyme
• Activation energy with an enzyme
• Change in free energy reactants → products
 Without enzyme
With enzyme

Reactants

Change in free
energy
reactants →
products
Products
1. Is this an exergonic or endergonic reaction?
2. Is this a catabolic or anabolic reaction?
3. Would ∆G be positive or negative?
A catalyst is a substance that speeds up a
chemical reaction without being consumed in
the reaction.

Enzymes are biological catalysts they lower

activation energy.

Enzymes are proteins, having a complex 3-D

shape (4-levels of structure).
 Sucrose

Catabolic Enzyme: Sucrase

Enzyme
Enzyme
1. Where, specifically, in the body does sucrose (table
sugar) digestion take place?
2. Describe how the structures called the villi and
microvilli affect the surface area for nutrient
Enzyme Sucrase
absorption:
3. Describe the action of the enzyme sucrase on sucrose:
4. Explain how the enzyme (sucrase) and substrate
(sucrose) fit together, using the vocabulary terms:
lock-and-key, and induced fit.

https://www.youtube.com/watch?v=q_fZtJMMLPE
 The complex 3-D shape of the enzyme is critical
to its function because of the lock-key-fit that is
necessary for the enzyme’s function

Induced fit is like a clasping

handshake – the enzyme
changes shape to grip the
substrate
Enzyme-Cycle Diagram
1. Calculate the rate of reaction 0 – 10 min.

2. Calculate the rate of reaction 10 – 20 min.

3. Make a claim with justification for which represents Vmax:

1. Calculate the rate of reaction 0 – 10 min.
(5.1 μM – 0 μM)/(10 min. – 0min.) = 0.51 μM/min.
2. Calculate the rate of reaction 10 – 20 min.
(8.6 μM – 5.1 μM)/(20 min. – 10min.) = 0.35 μM/min.
3. Make a claim with justification for which represents Vmax:
0 – 10 min. because the rate of 0.51 μM/min. is larger
than 0.35 for 10 – 20 min.
 1. Describe the rate at A - D
2. Explain the rate at A – D
3. Calculate Vmax D

Amount of Product Formed

C

A
 Slow rate Rate zero because enzyme
due to lag-time ran out of substrate

Amount of Product Formed

substrate must
be transported
in, processed, Rate slows as substrate
and product starts to run out
transported out Highest rate (Vmax)
is steepest slope, between
5 and 20 min. because
substrate is abundant:
rate = 17.3 µmol/mL ∙ min.
Enzymes are _______, they speed up chemical reactions
in biological systems.

They lower _________, that is needed for molecules to

react with one another.

Catabolic enzymes act on substrates such that they:

________. For example lactase _____________.

Anabolic enzymes act on substrates such that they:

________. For example ATP synthase ____________.
 Enzyme Peroxidase Investigation
• Enzyme = peroxidase
• Found in peroxisomes – membranous sack that
buds off the ER and is full of digestive enzymes
(the liver is rich in peroxisomes)
• Peroxidase performs the following chemical
reaction:
2 H2O2 → 2 H2O + O2
• Hydrogen peroxide is a byproduct of metabolism
and it is highly-reactive and is thus a toxin that
cells must eliminate.
We will use an indicator called guaiacol
Guaiacol has a high affinity for oxygen in solution, it
binds instantly to form tetraguaiacol, which is brownish,
as O2 ↑, the darker the color
 Time Observed Color
(Min.) (1 – 10)
0 1
1 3
2 4
3 5
4 5
5 5

Baseline is used to establish a reference so we can

compare treatments to infer an increase, decrease, or no
change in rate.
1. Which time will serve as your baseline? Why?
2. Which variables could you manipulate to change the
rate of reaction? Which would you hold constant?
 Take one color
measurement at
baseline time for
each of six test-tubes
(pH 3, 4, 6, 7, 8, 10)

The color chart can be used to infer

increase, decrease, or no change in
rate; this inference is called the
relative rate of the reaction.
The darker (brown) the sample the more light is
absorbed (absorbency goes up)
pH above or below
optimal will break
Hydrogen and ionic
bonds, causing the
enzyme to denature.
1. Describe the relationship between pH and reaction
rate for pepsin
2. What is the optimal pH for each enzyme?
3. Suggest why there is this difference:
Describe & explain how the reaction rate is
changing form A, to B, to C:
A B C
1. What is the optimal temp. for humans enzymes?
2. Why is this the optimal temperature?
3. What is the optimal temperature for heat-tolerant
bacteria?
4. Why is this the optimal temperature?
5. Why is there a difference in optimal temp. between
the two organisms shown?
 Substrate was
exhausted

This scenario does not assume

a large excess of substrate
• Cofactor = nonprotein enzyme-helpers
• Some are inorganic such as metal atoms: zinc,
iron, copper
• Some are organic (called coenzymes) – most
vitamins are examples of coenzymes
 Enzyme Inhibitors

Resembles
substrate

• Toxins & poisons often act as irreversible enzyme

inhibitors: sarin gas, DDT, penicillin
• But, inhibition also helps to regulate (control)
enzyme activity (which is good)
Allosteric enzymes
(protein) can
experience a 3-D
shape change

May be turned on
(active) or off
(inactive) in this way
Regulation of Enzyme Activity
• Tryptophan = a.a.
• After meal, supply ↑
(demand for construction ↓)
• Rapid response by feedback
inhibition
• Tryptophan inhibits the first
enzyme in the pathway
• Between meals: supply ↓ &
demand ↑ and the pathway
is active – making Tryptophan