Biokimia

Problem 1: Recognition of the peptide bond
Tutorial to help answer the question

Which arrow points to a peptide bond?
Tutorial
Amino acids
The polypeptide chains of proteins are linear
polymers of amino acids linked by peptide bonds.
Each amino acid has an amino group (-NH2) and a
carboxyl group (-COOH) that are used for peptide
bond formation.
Peptide bonds
As shown in the diagram, the peptide bond forms between the carbon atom (C) of the
carboxyl group and the nitrogen atom (N) of the amino group. The elements of water are
removed as a by product of this reaction. Water (HOH) forms from the -OH of the carboxyl
group of one amino acid and a hydrogen from the -NH2 group of the other amino acid.
Polypeptide chains
In this diagram, we visually separate the individual amino acids at the peptide bonds. Note
that the backbone of the peptide is formed from a repeating pattern of the atoms N-C-C,
corresponding respectively to the amino nitrogen-alpha carbon-carbonyl carbon of the
individual amino acids. The groups shown as R1, R2, R3, etc represent the side chains of
different amino acids.
Which arrow points to a peptide bond?
A.
B.
C.
D.
E.
1
2
2 and 3
3
4 and 5
Arrow 4 denotes the peptide bond between the first and second amino acid, and arrow 5
marks the peptide bond joining the fourth and fifth amino acid.
Problem 2: Identification of biological molecules

The structure on the left is a(n) _________________, and the structure on the right
is a(n)_________________.
Tutorial
There are four major classes of small biological molecules found in cells. These are
carbohydrates, lipids, amino acids, nucleotides. The different classes of compounds
can be identified by their characteristic structural features.
Carbohydrates
1. Carbohydrates can be either a single sugar (monosaccharide) like

glucose, a disaccharide like sucrose, or a series of monosaccharides
linked together by glycosidic bonds.
2. Common monosaccharides in cells have 4, 5, or 6 carbon atoms, and
multiple, polar -OH groups.
3. In common sugars, the ratio of C, H, and O is 1:2:1.
4. Common 5 and 6 carbons sugars usually exist as 5- or 6-membered

ring structures in cells, with one oxygen atom in the ring.
5. The abundance of -OH groups, the 1:2:1 ration of C:H:O, and the ring
structure with an O atom in the ring are key features to use in
identifying carbohydrates.
Lipids
1. Lipids or fats are characterized by their insolubility in water and

solubility in organic solvents or detergents.
2. Lipids are the most efficient energy storage molecules in cells.
3. Most of the structure of lipids is very non-polar, formed almost
exclusively of carbon and hydrogen atoms.
4. Triglycerides, used for energy storage in adipose (fat) tissue, are
composed of a glycerol molecule condensed with three fatty acids.
Fatty acids have long, hydrophobic tails consisting mostly of repeats
of -CH2- groups.
5. Diglycerides, which occur in cell membranes, are composed of a
glycerol, usually two long fatty acid chains, and a more hydrophilic
"head" group.
6. The presence of long, hydrophobic fatty acid chains is a key feature
to use in identifying many important lipids.
Amino Acids
1. Amino acids are the building blocks of proteins.
2. As shown in the diagram, amino acids have a generalized structure,

including an amino group, carboxyl group, and variable side chain
designated as the R-group.
3. There are 20 different amino acids used to make proteins. They differ from
each other in the structure and property of the R-groups, which may be polar
and charged, polar and uncharged, or hydrophobic.
4. To identify an amino acid, look for the generalized structural features.
Nucleotides
1. Nucleotides are the building blocks of RNA and DNA.

2. They are formed from a 5-carbon sugar (ribose or deoxyribose), a
phosphate group, and a nitrogenous pyrimidine or purine base. The
pyrimidines are 6 membered rings with 2 nitrogen atoms in the ring.
The purines are a 6 and a 5 membered ring fused together, with 4 ring
nitrogen atoms.
3. To identify a nucleotide, look for the sugar-phosphate portion linked
to a complex ring containing nitrogen atoms in the ring.
4. Problem 2: Identification of biological molecules
5.
2. The structure on the left is a(n) _________________, and the structure on

the right is a(n)_________________.
6.
7.
A. lipid, polypeptide
B. carbohydrate, lipid
C.
carbohydrate, amino acid
Carbohydrates have the general formula of C(H2O), with abundant
hydroxyl groups (-OH); amino acids have conserved amino and
carboxyl groups, and variable R-groups all attached to the alpha carbon.
Valine is the amino acid illustrated.
D. nucleotide, amino acid
E. nucleotide, carbohydrate
Problem 3: Tertiary structure of a protein

The tertiary structure of a protein refers to the:
A. Sequence of amino acids
B. Presence of alpha-helices or beta-sheets
C. Unique three dimensional folding of the molecule
D. Interactions of a protein with other subunits of enzymes
E. Interaction of a protein with a nucleic acid
Tutorial
It is convenient to describe protein structure in terms of 4 different aspects of covalent
structure and folding patterns. The different levels of protein structure are known as primary,
secondary, tertiary, and quaternary structure.
Primary Structure of Proteins

The primary structure is the sequence of amino acids that
make up a polypeptide chain. 20 different amino acids are
found in proteins. The exact order of the amino acids in a
specific protein is the primary sequence for that protein.
Secondary Structure of Proteins

Protein secondary structure refers to regular, repeated patterns of folding of the protein
backbone. The two most common folding patterns are the alpha helix and the beta sheet.
Alpha Helix
In an alpha helix, the polypeptide backbone coils around an
imaginary helix axis in clockwise direction.
In this illustration, only the N-C-CO backbone atoms are
shown. Note the coiling of the backbone around an
imaginary axis down the center of the helix.
Beta sheet
In the beta sheet secondary structure, the polypeptide
backbone is nearly fully extended. The R-groups (not shown)
are alternately pointed above and then below the extended
backbone.
Tertiary Structure of Proteins

Tertiary structure refers to the overall folding of the entire
polypeptide chain into a specific 3D shape. The tertiary
structure of enzymes is often a compact, globular shape.
Tertiary structure of the triose phosphate isomerase (TPI) molecule.
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Quaternary Structure of Proteins

Many proteins are formed from more than one polypeptide chain. The quaternary structure
describes the way in which the different subunits are packed together to form the overall
structure of the protein. For example, the human hemoglobin molecule shown below is made
of four subunits.
Problem 3: Tertiary structure of a protein

The tertiary structure of a protein refers to the:
A. Sequence of amino acids
B. Presence of alpha-helices or beta-sheets
C. Unique three dimensional folding of the molecule
Tertiary structure refers to the overall 3D folding of the polypeptide chain.
D. Interactions of a protein with other subunits of enzymes
E. Interaction of a protein with a nucleic acid
Problem 4: Identification of another biological molecule

The structure shown in the diagram is an example of a lipid.
Tutorial
If necessary, review the tutorial for question 2 with information on the
characteristic properties of different classes of biological molecules.
The feature of this molecule that can be most easily recognized is the three fatty
acids with long, hydrophobic tails consisting mostly of repeats of -CH 2- groups.
The three fatty acids are covalently linked to a glycerol. This compound is a
neutral fat of the type used to store reserves of energy in our fatty (adipose) tissues.

The structure shown in the diagram is an example of:
A. RNA.
B. a protein.
C. a polysaccharide.
D. DNA.
E. a lipid.

A. RNA.
B. a protein.
C. a polysaccharide.
D. DNA.
E. a lipid.
The long hydrophobic tails of this triglyceride are characteristic of a lipid.
Problem 5: Elements of protein structure
Which statement is true concerning the structure of proteins?

A.
B.
C.
D.
E.
The primary structure is the sequence of amino acids.

Alpha helices and beta sheets are examples of secondary structure.
Side chains (R-groups) of amino acids can be hydrophilic or hydrophobic.
Proteins made of two or more polypeptide chains have quaternary structure.
All statements are true.

Tutorial
Here is a review of features of protein structure that can be used to analyze the different
answer choices. You may discover that all of the answer choices are correct!
Protein structures
Primary structure
Proteins are composed of 20 different kinds of amino acids joined in a linear polypeptide
chain by peptide bonds. The primary structure is the sequence of the amino acids.
Secondary structure
Protein secondary structure refers to regular, repeated patters of folding of the protein
backbone. The two most common folding patterns are the alpha helix and the beta sheet.
Tertiary structure
Tertiary structure refers to the overall folding of the entire polypeptide chain into a specific
3D shape.
Quaternary structure
The quaternary structure describes the way in which the different subunits are packed
together to form the overall structure of the protein. Proteins made of two or more
polypeptide chains have quaternary structure.
(For more information on structures, refer to the tutorial for problem 3)
Amino Acid Side Chains (R-groups)

There are 20 different amino acids found in proteins. The side chains (R-groups) differ in
chemical properties. Some are polar, but uncharged. Some are polar and normally have a
positive or negative charge in solution.
Amino acids with polar side chains are said to be hydrophilic (water loving) because they
form weak interactions with water molecules. The R-groups of hydrophilic amino acids
contain electronegative atoms like O and N. Some amino acids are non-polar (hydrophobic)
because their side chains are made up mostly of hydrocarbon chains.
Examples of different categories of amino acids:
Different proteins have different structures and properties due to the

specific locations of hydrophilic and hydrophobic amino acids.

A. The primary structure is the sequence of amino acids.
B. Alpha helices and beta sheets are examples of secondary structure.
C. Side chains (R-groups) of amino acids can be hydrophilic or hydrophobic.
D. Proteins made of two or more polypeptide chains have quaternary structure.
E. All statements are true.
This is a good summary of important features to know about protein structure.
The structure shown in the diagram is an example of a monomer unit used in the
formation of:
A. RNA
B. protein
C. DNA
D. polysaccharides
E. lipids
Tutorial
Nucleotides
The molecule illustrated in the question is a nucleotide.
Nucleotides, the monomer units of RNA and DNA, consist
of a pentose sugar, either ribose in RNA or deoxyribose in
DNA, a phosphate group, and a nitrogenous base.
As the name implies, a pentose is a 5-membered, puckered
ring. Attached to the ring is the phosphate group, which is
a phosphorous atom with 4 covalently attached oxygen
atoms. Nucleotides also have either a pyrimidine or purine
base, attached to the pentose sugar.
Nitrogenous bases: purines and pyrimidines

Pyrimidines are planar, six-membered rings of 5 carbon and 1 nitrogen atom. Purines are
planar, fused N-containing rings. The purine and pyrimidine bases of RNA and DNA are
shown below.
DNA and RNA

RNA and DNA are polymers of nucleotides. The backbone of the polymer is a repeating
chain of sugar-phosphate-sugar-phosphate- etc. These polymers have "polarity", meaning
having a directionality. The phosphate of the 5'-end of one nucleotide is linked to the 3'position of the next nucleotide. In the model of DNA (left), the left strand has a polarity of 5'
(top) to 3' (bottom), and the other DNA strand has the opposite polarity. The two DNA
strands are said to be "antiparallel".
In the RNA model, note the extra -OH of the pentose sugar, and the use of the uracil base (U)
rather than the thymine (T) base of DNA.
Problem 6:Identification of a monomer unit of a biological macromolecule
The structure shown in the diagram is an example of a monomer unit used in the
formation of:
A. RNA
The compound, UMP or uridine monophosphate, is found internal to RNA chains.
The 2'-OH group on the sugar ring is the best indicator that it is from RNA and not
DNA.
B. protein
C. DNA
D. polysaccharides
E. lipids
Problem 7: Weak forces involved in interactions between macromolecules
Two macromolecules, such as proteins, can adhere tightly and specifically to each
other. How can weak forces such as electrostatic attraction, van der Waals bonds,
hydrogen bonds, and hydrophobic forces lead to such strong adherence?
Tutorial
Non-covalent bonds and other weak forces are important in biological structures.
Electrostatic bonds (ionic) result from the electrostatic attraction between two ionized
groups of opposite charge, such as carboxyl (-COO-) and amino (-NH3+). In water, these
bonds are very weak, but in a hydrophobic environment such as a protein-protein contact,
they are stronger.
Hydrogen bonds result from electrostatic attraction between an electronegative atom (O or
N) and a hydrogen atom that is bonded covalently to a second electronegative atom.
(N-H ----- O=C-) or (-O-H----- O=C-)
Van Der Waals bonds are short range attractive forces between chemical groups in contact.
They are caused by slight charge displacements that allow the electrons of one atom to be
attracted by the protons of another atom.
Hydrophobic attractions cause non-polar groups such as hydrocarbon chains to associate
with each other in an aqueous environment.
Multiple weak bonds or forces can cause strong interactions Biological recognition results
from a three dimensional structure that allows multiple weak forces between molecules.
Problem 7: Weak forces involved in interactions between macromolecules
Two macromolecules, such as proteins, can adhere tightly and specifically to each
other. How can weak forces such as electrostatic attraction, van der Waals bonds,
hydrogen bonds, and hydrophobic forces lead to such strong adherence?
A. adherence can be quite strong by having many weak forces involved in molecular
adhesion.
The additive effect of many weak forces, including hydrogen bonds, hydrophobic
interactions, van der Waals forces, and ionic bonds provide significant energy for
biological structure.
B. the weak forces can become very strong once non-polar groups are excluded from the
inside of the molecules.
C. the weak forces are readily converted to covalent bonds, thus leading to strong adherence
between molecules.
D. if the weak forces are correctly aligned they can become as strong as covalent bonds.
E. adhesion is strong because the weak forces can be involved in condensation reactions.
Problem 8: Identification of a macromolecule

A. a polysaccharide.
B. DNA.
C. RNA.
D. a protein.
E. a lipid.
Tutorial
The polymer shown in the structural diagram can be identified as a nucleic acid because the
covalent backbone is an alternating polymer of sugar and phosphate.
Which nucleic acid?

Is it DNA or RNA? There are two major differences in the covalent structure on a DNA
strand compared to an RNA strand.
1. The sugar in the DNA backbone lacks a hydroxyl group (-OH) at the 2'-position.
RNA has a 2'-hydroxyl group;
2. The bases of DNA are A, G, C, and T.
The bases of RNA are A, G, C, and U.
Problem 8: Identification of a macromolecule

A. a polysaccharide.
B. DNA.
The alternating sugar-phosphate backbone tells us that this is
either DNA or RNA. The characteristic identifying features of
DNA, but not RNA, include the absence of a hydroxyl group at
the 2'-position on the sugar and the presence of the T base.
C. RNA.
D. a protein.
E. a lipid.
Problem 9: Identification of a hydrophobic amino acid
Which amino acid has a hydrophobic side chain?
Tutorial
The hydrophobic amino acids
There are 20 different amino acids found in proteins. The side chains (R-groups) differ in
chemical properties. Some are polar, but uncharged. Some are polar and normally have a
positive or negative charge in solution.
The eight amino acids shown below have distinctly hydrophobic side chains. Note that the
side chains are composed almost entirely of C-C and C-H chemical bonds, being either
entirely hydrocarbons, or mostly hydrocarbons with a single polar atom.
Problem 10 Tutorial: Protein-protein interactions

Proteins 1 and 2 interact strongly. A significant part of the interaction is
between the amino acid side chains shown below.
Assume that a mutation occurs in protein 2 that changes the amino acid
shown above to one of the amino acids shown below.
What change should disrupt the interaction between proteins 1 and 2 the most? the
least?
Tutorial
Attractive force
The arginine amino acid side chain of protein 1 has a positive charge. The glutamic acid
amino acid side chain of protein 2 has a negative charge. The most likely interaction between
these two amino acids is an ionic bond, i.e. an attractive force between the positive and
negative charge.
Most disruptive
If the amino acid of protein 2 were mutated to an amino acid with a positive charge, such as
lysine, then the positive charges of the arginine of protein 1 and the lysine of protein 2 would
repel each other. Lysine would be the most disruptive to protein-protein interaction.
Least disruptive
If the amino acid of protein 2 were mutated to another amino acid with a negative charge,
such as aspartic acid, the positive charge of the arginine of protein 1 and the negative charge
of aspartic acid of protein 2 might still form an ionic bond. Aspartic acid would be the least
disruptive to protein-protein interaction.
Problem 10: Protein-protein interactions
Proteins 1 and 2 interact strongly. A significant part of the interaction is

between the amino acid side chains shown below.
Assume that a mutation occurs in protein 2 that changes the amino acid
shown above to one of the amino acids shown below.
What change should disrupt the interaction between proteins 1 and 2 the most? the
least?
A. The most: aspartic acid; the least: leucine

B. The most: lysine; the least: serine
C. The most: Serine; the least: aspartic acid
D. The most: lysine; the least: aspartic acid
The two amino acids are involved in an ionic interaction
E. The most: aspartic acid; the least: serine
Problem 11: Sequence of a polypeptide
A polypeptide 5 amino acids long is split into various smaller fragments and the
amino acid sequences of some of the fragments are determined. The identified
fragments include: his-gly-ser, ala-his, and ala-ala. Predict the primary sequence
of the polypeptide.
Tutorial
Amino acids of a polypeptide
The amino acids of a polypeptide are linked together like the links of a chain. A polypeptide
of 5 amino acids is analogous to a chain with five links. It has two end amino acids, and three
internal links. Breaking our chain into smaller pieces is similar to cutting links of a chain and
producing smaller chains. The amino acids that are adjacent to each other in the smaller
fragments were also adjacent in the larger chain.
Amino acid composition

A good starting point for a problem like this is to try to determine the amino acid
composition of the unknown. What are the five amino acids that are combined to form the
peptide? If we examine the sequences of the three fragments, we see that:
One fragment has the sequence his-gly-ser, so each of these three amino acids is present.
Another fragment has the sequence ala-ala, meaning that there are 2 alanines present.
From these two fragments alone, we can unambiguously define the amino acid composition
of the 5 amino acid long peptide as (his-gly-ser, and ala-ala). Note that the two other
combination of two fragments (either ala-ala and ala-his or ala-his and his-gly-ser would
only have been sufficient to define 3 or 4 of the 5 amino acids.
Overlapping pieces
From the two fragments used to determine amino acid composition, you
can also deduce that the sequence must be either his-gly-ser-alaala or ala-ala-his-gly-ser. The overlapping fragment of ala-his is used to
distinguish these two possibilities.
The final sequence of the polypeptide with 5 amino acids is ala-ala-hisgly-ser.
Problem 11: Sequence of a polypeptide
A polypeptide 5 amino acids long is split into various smaller fragments, and the
fragments include: his-gly-ser,ala-his, and ala-ala. Predict the primary sequence
of the polypeptide.
A. his-gly-ser-ala-ala
B. ala-his-gly-ser-ala
C. ala-ala-his-gly-ser
You have correctly interpreted the source of the fragments.
D. his-gly-ser-ala-ala
E. cannot be determined without more information.
Problem 12: Sequence of a longer polypeptide
fragments include: ala-gly-ser-gln, lys-trp-arg-pro, gln-his-lys, asp-ala-gly.
What is the primary sequence of the polypeptide?
Tutorial
Amino acids of a polypeptide
As with the previous question, a key piece of information is that the length of the unknown
polypeptide is 10 amino acids. What are the 10 amino acids that make up the unknown? This
is determined by examining the sequences of the three fragments. Note that there are 10
different amino acids present in the three fragments. They are, in alphabetical order:
ala, arg, asp, gly, gln, his, lys, pro, ser, trp
Overlapping pieces
Since no amino acids are duplicated in this example, any amino acid found in two fragments
identify an overlap. The four fragments overlapped as follows:
The original peptide must have the sequence of:

asp-ala-gly-ser-gln-his-lys-trp-arg-pro
Problem 12: Sequence of a longer polypeptide
fragments include: ala-gly-ser-gln, lys-trp-arg-pro, gln-his-lys, asp-ala-gly.
What is the primary sequence of the polypeptide?
A. ala-gly-ser-gln-lys-trp-arg-pro-gln-his
B. asp-ala-gly-ser-gln-his-lys-trp-arg-pro
The four fragments have been assembled into the correct sequence.
C. ala-gly-ser-gln-his-lys-trp-arg-pro-asp
D. lys-trp-arg-pro-gln-his-lys-asp-ala-gly
E. none of these
Which statement about enzyme catalyzed reactions is NOT true?
A.
B.
C.
D.
E.
enzymes form complexes with their substrates.

enzymes lower the activation energy for chemical reactions.
enzymes change the Keq for chemical reactions.
many enzymes change shape slightly when substrate binds.
reactions occur at the "active site" of enzymes, where a precise 3D orientation of amino
acids is an important feature of catalysis.
Features of Enzyme Catalyzed Reactions
Enzymes are biological catalysts. Catalysts lower the activation energy for
reactions. The lower the activation energy for a reaction, the faster the rate. Thus
enzymes speed up reactions by lowering activation energy. Many enzymes change
shape when substrates bind. This is termed "induced fit", meaning that the precise
orientation of the enzyme required for catalytic activity can be induced by the
binding of the substrate.
Enzymes have active sites. The enzyme active site is the location on the enzyme
surface where substrates bind, and where the chemical reaction catalyzed by the
enzyme occurs. There is a precise substrate interaction that occurs at the active site
stabilized by numerous weak interactions (hydrogen bonds, electrostatic
interactions, hydrophobic contacts, and van der Waals forces).
Enzymes form complexes with their substrates. The binding of a substrate to an
enzyme active site is termed the "enzyme-substrate complex." A generic equation
for complex formation is as follows:
Enzymes do not:
Change the equilibrium constant for a reaction. Keq depends only on the
difference in energy level between reactants and products.
Change G for a reaction. As shown in the graphs above, enzymes only
lower activation energy, but do not change the difference in energy levels
between reactants and products.
Convert a nonspontaneous reaction into a spontaneous reaction.
Problem 1: Features of enzyme catalyzed reactions.
Which statement about enzyme catalyzed reactions is NOT true?
A.
B.
C.
D.
E.
enzymes form complexes with their substrates.

enzymes lower the activation energy for chemical reactions.
enzymes change the Keq for chemical reactions.
many enzymes change shape slightly when substrate binds.
reactions occur at the "active site" of enzymes, where a precise 3D orientation of amino
acids is an important feature of catalysis.
The equilibrium constant for the conversion of the disaccharide sucrose to the
simple sugars glucose and fructose is 140,000. What can you conclude about the
reaction: sucrose + H2O glucose + fructose?
Reaction equations
The equation for the chemical reaction described in this problem is as follows:
This is a hydrolysis reaction. The disaccharide glucose is hydrolyzed to the two

monosaccharides glucose and fructose. Biological hydrolysis reactions are almost
always spontaneous (exergonic).
The balance between the forward and reverse reactions is known as the chemical
equilibrium, which is defined as the ratio of the concentration of products and
reactants at equilibrium when there is no further change in concentrations.
For this reaction,
Free energy and chemical equilibrium
This chemical reaction can run in both the forward and reverse directions, but the
products glucose and fructose are at a lower energy level than the reactant sucrose.
The difference between a spontaneous and nonspontaneous reaction can be
distinguished by the following relationships:
Spontaneous Reaction
Keq > 1
G<0
Exergonic
Forward reaction favored
Nonspontaneous Reaction
Keq < 1
G>0
Endergonic
Reverse reaction favored
The hydrolysis of sucrose
This is a spontaneous reaction beginning with sucrose because K eq > 1.

Problem 2: Equilibrium constant for sucrose hydrolysis.
The equilibrium constant for the conversion of the disaccharide sucrose to the
simple sugars glucose and fructose is 140,000. What can you conclude about the
reaction: sucrose + H2O glucose + fructose?
A.
B.
C.
D.
It is a closed system.
It never reaches equilibrium.
It is spontaneous, starting with sucrose.
The equilibrium constant increases when the starting concentration of sucrose is
increased.
E. At equilibrium, the concentration of sucrose is much higher than the concentrations of
glucose and fructose.
Problem 3 Tutorial: Kinetics of an allosteric enzyme.

Which of the following graphs shows the results of reaction rate vs substrate
concentration for an allosteric enzyme in the absence and presence of an allosteric
inhibitor?
Allosteric enzymes
Enzymes with multiple subunits have quaternary structure. One consequence of
multiple subunits is that individual catalytic subunits each have their own active
site. This means that an enzyme with quaternary structure can bind more than one
substrate molecule. Allostery means "different shape." Allosteric enzymes change
shape between active and inactive shapes as a result of the binding of substrates at
the active site, and of regulatory molecules at other sites. In the simple case of an
allosteric enzyme with an active and inactive form, the change in reaction rate with
increasing substrate concentration is typically an "S-shaped" curve. For more
information on allosteric enzyme, see the tutorial for question 14.
Binding of effectors to regulatory subunits
Allosteric enzymes may also have regulatory subunits that bind either activators or
inhibitors. Activators and inhibitors are termed "effectors." Inhibitors cause the
allosteric enzyme to adopt the inactive shape. Activators promote the active shape.
An equilibrium exists between the active and inactive shapes. The amount of active
and inactive enzyme is dependent on the relative concentrations of substrate and
inhibitor, as suggested by the diagram:
The binding of an allosteric inhibitor causes the enzyme to adopt the inactive
conformation, and promotes the cooperative binding of a second inhibitor.
An excess of substrate can overcome the inhibitor effect. Substrate binding causes
the enzyme to assume the active conformation, and promotes the cooperative
binding of additional substrate, leading to product formation.
The meaning of the S-shaped Curves with and without inhibitor
The shape of the curve minus inhibitor is described in more
detail in the tutorial to question 14. As the substrate
concentration is increased, substrate binds to enzyme and
triggers a conformation change to the active shape of the
enzyme.
In the presence of inhibitor (plus inhibitor), higher
concentration of substrate is required to shift the enzyme to the
active conformation. However once a high enough
concentration of substrate is reached to promote active shape,
the substrate binds cooperatively (S-shaped curve), and the
same maximum rate is achieved as without inhibitor.
Problem 3: Kinetics of an allosteric enzyme.

concentration for an allosteric enzyme in the absence and presence of an allosteric
inhibitor?
A. 1
B. 2
C. 3
D. 4
E. none of the graphs.
Problem 4 Tutorial: An energy barrier separating reactions and products in a
chemical reaction.
To overcome an energy barrier between reactants and products, energy must be
provided to get the reaction started. This energy, which is recovered as the reaction
proceeds, is called:
Activation energy
There is an energy barrier that separates the energy levels of the
reactants and products. Energy must be added to the reactants
to overcome the energy barrier, which is recovered when
products are formed. The energy barrier is known as Ea, the
activation energy. The activation energy is distinct from the G,
or free energy difference between the reactants and products.
Problem 5 Tutorial: Why do enzymes reach a maximum rate at high substrate

concentration?
In the presence of alcohol dehydrogenase, the rate of reduction of acetaldehyde to
ethanol increases as you increase the concentration of acetaldehyde. Eventually the
rate of the reaction reaches a maximum, where further increases in the

concentration of acetaldehyde have no effect. Why?
The reduction of acetaldehyde to ethanol is an oxidation-reduction reaction.
Acetaldehyde is reduced by the addition of 2 electrons and 2 hydrogen ions
supplied by NADH, which is reduced to NAD+.
The equation for this reaction is:
In the presence of alcohol dehydrogenase, the rate of

the production of ethanol increases as the concentration
of acetaldehyde is increased as shown in the rate curve
to the right.
An enzyme catalyzed reaction may be written as:
E is the enzyme, S is the substrate (acetaldehyde), ES is the enzyme-substrate

complex and P is the product (ethanol).
The substrate binds to a specific site on the surface of the enzyme known as the
active site. The reaction occurs on the enzyme surface, after which product and
enzyme are released. The enzyme can then bind another substrate, and continue to
catalyze the reduction of acetaldehyde many, many times per minute.
An explanation for the shape of the enzyme kinetics curve
At low substrate concentration the rate of ethanol production increases sharply

with increasing concentration of acetaldehyde because there is lots of free enzyme
available (E). At high substrate concentration, the rate of ethanol production
reaches a plateau as the enzyme active sites of alcohol dehydrogenase are saturated
with substrate (ES complex).
Problem 5: Why do enzymes reach a maximum rate at high substrate
concentration?
In the presence of alcohol dehydrogenase, the rate of reduction of acetaldehyde to
ethanol increases as you increase the concentration of acetaldehyde. Eventually the
rate of the reaction reaches a maximum, where further increases in the

concentration of acetaldehyde have no effect. Why?
A.
B.
C.
D.
all of the alcohol dehydrogenase molecules are bound to acetaldehyde molecules

at high concentrations of acetaldehyde, the activation energy of the reaction decreases
the enzyme is no longer specific for acetaldehyde
at high concentrations of acetaldehyde, the change in free energy of the reaction decreases
Problem 6: Equilibrium constant for ionization of acetic acid.

The equilibrium constant for the ionization of acetic acid,
,
is 0.00002. What can you conclude about this reaction?
A. It is a closed system.
B. At equilibrium, the concentration of CH3COOH is much higher than the concentrations of
CH3COO- + H+.
C. It never reaches equilibrium.
D. It is spontaneous, starting with CH3COOH.
E. The equilibrium constant increases when the starting concentration of CH3COOH is
increased.
Problem 6 Tutorial: Equilibrium constant for ionization of acetic acid

,
Chemical equilibrium
The equation for the chemical reaction in this problem describes the ionization of
acetic acid. Acetic acid (CH3COOH) can ionize to the acetate (CH 3COO-) and
hydrogen (H+) ions.
For this reaction,
Because the equilibrium constant is very, very small we can conclude that almost
all of the acetic acid remains unionized, and that ionization of acetic acid is
nonspontaneous.
Below is a summary of the important relationships between free energy,

spontaneous vs nonspontaneous reactions, and chemical equilibria:
Spontaneous Reaction
Keq > 1
G<0
Exergonic
Forward reaction favored
Nonspontaneous Reaction
Keq< 1
G>0
Endergonic
Reverse reaction favored
The ionization of acetic acid
This is a non-spontaneous reaction beginning with acetic acid.

,
A. It is a closed system.
B. At equilibrium, the concentration of CH3COOH is much higher than the concentrations of
CH3COO- + H+.
C. It never reaches equilibrium.
D. It is spontaneous, starting with CH3COOH.
E. The equilibrium constant increases when the starting concentration of CH3COOH is
increased.
Problem 7 Tutorial: Describing the reaction rate for a chemical reaction.

Which of the following statements about reaction rate is NOT true?
A.
B.
C.
D.
E.
Reaction rate is the speed at which the reaction proceeds toward equilibrium.
Reaction rate is governed by the energy barrier between reactions and products.
Enzymes can accelerate the rate of a reaction.
Reaction rates are not sensitive to temperature.
None of these.
General information about reaction rates
Reaction rate is the speed at which the reaction proceeds toward equilibrium. For
an enzyme catalyzed reaction, the rate is usually expressed in the amount of
product produced per minute.
Reaction rate is governed by the energy barrier between reactions and products. In
general, energy must be added to the reactants to overcome the energy barrier. This
added energy is termed "activation energy," and is recovered as the reactants pass
over the barrier and descend to the energy level of the products.
Enzymes can accelerate the rate of a reaction. Enzymes are biological catalysts.
Catalysts accelerate the rates of reactions by lowering the activation energy barrier
between reactants and products. For a diagram comparing the energy barrier of a
noncatalyzed reaction to a catalyzed reaction, see the tutorial for problem 1.
Temperature can have an important effect on enzyme activity and reaction rates. At
low temperature, warming usually increases the rate of an enzyme catalyzed
reaction because the reactants have more energy, and can more readily achieve the
activation energy level. However if the temperature is raised too high, it is possible
to denature the enzyme, causing a disruption of tertiary structure and loss of
catalytic activity.
Problem 7: Describing the reaction rate for a chemical reaction.
Which of the following statements about reaction rate is NOT true?
A.
B.
C.
D.
E.
Reaction rate is the speed at which the reaction proceeds toward equilibrium.
Reaction rate is governed by the energy barrier between reactions and products.
Enzymes can accelerate the rate of a reaction.
Reaction rates are not sensitive to temperature.
None of these.
Problem 8 Tutorial: Features of an exergonic reaction.

Exergonic reactions:
A. release energy
B. are spontaneous reactions
C. have an equilibrium constant greater than 1
D. can be coupled to energonic reactions
E. All statements are true
Exergonic reactions release energy
An energy diagram for an exergonic or spontaneous

reaction is shown to the right. The energy level of the
products is lower than the energy level of the reactants.
Energy is released in this reaction. The amount of
energy released during the reaction is termed G,
which is less than zero.
Exergonic reactions are also termed "spontaneous" reactions

The equilibrium constant for an exergonic reaction is greater than 1, meaning that
the concentration of products is greater than the concentration of reactants at
equilibrium.
Exergonic reactions can be coupled to endergonic reactions. Oxidation-reduction

(redox) reactions are examples of the coupling of exergonic and endergonic
reactions. Enzymes often act by coupling an endergonic reaction to the exergonic
hydrolysis of ATP.
Problem 8: Features of an exergonic reaction.
Exergonic reactions:
A. release energy
B. are spontaneous reactions
C. have an equilibruim constant greater than 1
D. can be coupled to energonic reactions
E. All statements are true
Problem 9: Kinetics of an enzyme reaction with a non-competitive inhibitor.
concentration for an non-allosteric enzyme in the absence and presence of a noncompetitive inhibitor (non-competitive inhibitors bind to an enzyme at a site
different than the active site)?
A. 1
B. 2
C. 3
D. 4
Problem 9 Tutorial: Kinetics of an enzyme reaction with a non-competitive
inhibitor.
concentration for an non-allosteric enzyme in the absence and presence of a
noncompetitive inhibitor (noncompetitive inhibitors bind to an enzyme at a site
Noncompetitive inhibition of an enzyme can occur when an inhibitor binds to an

enzyme at a site other than the active site. The noncompetitive inhibitor slows
down the reaction rate, i.e. the rate of the product formation is less with inhibitor
present than with inhibitor absent. This means that the active site is modified, but
not disabled, by the presence of the inhibitor.
As shown in graph #2, the effect of noncompetitive inhibitor cannot be overcome
with high substrate concentration. Since the inhibitor and substrate are not
competing for the same binding site on the enzyme, a noncompetitive inhibitor
reduces the reaction rate at all substrate concentrations.
Problem 9: Kinetics of an enzyme reaction with a non-competitive inhibitor.
concentration for an non-allosteric enzyme in the absence and presence of a noncompetitive inhibitor (non-competitive inhibitors bind to an enzyme at a site
A. 1
B. 2
C. 3
D. 4
Problem 10 Tutorial: Enzyme features
Enzymes:
A.
B.
C.
D.
E.
are composed primarily of polypeptides, which are polymers of amino acids.

can bind prosthetic groups such as metal ions that participate in enzyme reactions.
have defined structures.
bind their substrates at active sites.
all statements are true.
Features of enzymes and enzyme structure

Enzymes are composed primarily of proteins, which are polymers of amino acids. Enzymes
can bind prosthetic groups that participate in enzyme reactions. Prosthetic are not part of the
enzyme polypeptide chain. Prosthetic groups can be metal ions or various types of organic
compounds. Enzymes fold into defined, 3D conformations. The three dimensional structure
of many enzymes has been determined. As an example, the defined structure of the enzyme
lysozyme with a carbohydrate substrate bound to the active site is shown in the left panel of
the figure.
Enzymes bind their substrates at active sites. The active
site is the location on the surface of the enzyme where
the catalyzed reaction takes place. In the two views of
lysozyme shown above, the left panel shows a
carbohydrate colored green bound to the active site of
lysozyme. The right panel shows the empty active site.
Notice that the active site forms a cleft on the enzyme
surface designed to specifically interact with the
substrate.
Problem 10: Enzyme features

Enzymes:
A.
B.
C.
D.
E.
are composed primarily of polypeptides, which are polymers of amino acids.

can bind prosthetic groups such as metal ions that participate in enzyme reactions.
have defined structures.
bind their substrates at active sites.
all statements are true.
Problem 11: Understanding activation energy

Activation energy is
A. energy that must be added to get a reaction started, which is recovered as the reaction
proceeds
B. difference in energy between reactants and products
C. energy that is lost as heat
D. free energy
E. equal to the entropy times the absolute temperature
Problem 11 Tutorial: Understanding activation energy

proceeds
D. free energy
Activation energy
There is an energy barrier that separates the energy levels of the
reactants and products. Energy must be added to the reactants
to overcome the energy barrier, which is recovered when
products are formed. The energy barrier is known as Ea, the
activation energy. The activation energy is distinct from the G,
or free energy difference between the reactants and products.
Problem 11: Understanding activation energy

proceeds
D. free energy
Problem 12 Tutorial: Energy requiring reactions in biological systems

Coupled Reactions
Enzymes can couple exergonic reactions with endergonic reactions to result in a
coupled reaction that is exergonic overall. An exergonic reaction is one in which
the energy level of the products is lower than the energy level of the reactants (a
spontaneous reaction).
Consider the coupled reaction described in Problem 5 of this problem set. This is a
redox reaction. All redox reactions are coupled reactions, since an oxidation
reaction is coupled to a reduction reaction. The dehydrogenase enzyme reduces
acetaldehyde to ethanol, which is an endergonic (energy-requiring) reaction:
The reduction of acetaldehyde is coupled to the oxidation of NADH to NAD +,

which is an exergonic reaction. The oxidized NAD + has a lower energy level than
NADH.
The sum of these two reactions is the coupled reaction catalyzed by acetaldehyde
dehydrogenase, shown on the bottom line in the figure above.
Problem 12: Energy requiring reactions in biological systems
Energy-requiring reactions can occur in biological systems because enzymes allow
their coupling to other reactions with:
A. an increase in entropy
B. a low activation energy
C. no inhibitors
D. products of lower free energy than the reactants
E. oxidation-reduction
Problem 13 Tutorial: Equilibrium constant for hydrolysis of glucose-6-phosphate
The equilibrium constant for the reaction, glucose 6-phosphate + water

+ phosphate, is 260. What can you conclude about this reaction:
glucose
The equation for the chemical reaction described in this problem is:
This is a hydrolysis reaction. The glucose-6-phosphate is hydrolyzed to the glucose

and phosphate. Biological hydrolysis reactions are almost always spontaneous
(exergonic).
For this reaction, equilibrium favors product formation.
The products of glucose and phosphate are at a lower energy level than the
reactants. Since Keq > 1, this is a spontaneous (exergonic) reaction starting with
glucose-6-phosphate.
Problem 13: Equilibruim constant for hydrolysis of glucose-6-phosphate
The equilibrium constant for the reaction, glucose 6-phosphate + water
+ phosphate, is 260. What can you conclude about this reaction:
glucose
A. It is a closed system
B. It never reaches equilibrium.
C. Starting with glucose 6-phosphate, it is not spontaneous.
D. At equilibrium, the concentration of glucose is much higher than the concentrations of
glucose 6-phosphate.
E. The equilibrium constant increases when the starting concentration of glucose 6phosphate is increased.
Problem 14 Tutorial: Interpreting an "S-shaped" enzyme kinetics curve
The graph shows the results of reaction rate vs substrate

concentration for a(n):
Allosteric Enzymes
Enzymes with multiple subunits have quaternary structure. One consequence of

multiple subunits is that individual catalytic subunits each have their own active
site. This means that an enzyme with quaternary structure can bind more than one
substrate molecule. Allostery means "different shape." Allosteric enzymes change
shape between active and inactive shapes as a result of the binding of substrates at
the active site, and of regulatory molecules at other sites. In the simple case of an
allosteric enzyme with an active and inactive form, the change in reaction rate with
increasing substrate concentration is typically an "S-shaped" curve.
The meaning of the S-shaped curve for allosteric enzyme

At low substrate concentration, the enzyme is in the inactive shape (inactive
conformation). As the substrate concentration is increased, substrate binds to
enzyme and triggers a conformation change to the active shape of the enzyme.
After the first substrate is bound, the second and subsequent substrates all bind
more readily. This is termed "cooperativity," and the S-shaped curve indicates
cooperative binding of substrate. The result of the change to the active shape is a
steep increase in both substrate binding, and as a result, in reaction rate over a
narrow range of substrate concentration. When all active sites on the allosteric
enzyme are occupied with substrate, a plateau is reached.
The importance of allosteric enzymes to cellular regulation
Allosteric enzymes can be regulated between very low and very high reaction rates
with only small changes in substrate concentration. Allosteric enzymes are used by
cells to regulate metabolic pathways where the concentration of cellular substrates
fluctuate over narrow concentration ranges.
Energy, Enzymes, and Catalysis Problem Set

Problem 14: Interpreting an "S-shaped" enzyme kinetics curve
The graph shows the results of reaction rate vs substrate

concentration for a(n):
A. enzyme plus a competitive inhibitor

B. enzyme plus a non-competitive inhibitor
C. allosteric enzyme
D. enzyme plus an un-competitive inhibitor
E. two enzymes competing for the same substrate
Problem 15 Tutorial: Interpreting the plateau of an enzyme kinetics curve
In the graph reaction rate vs substrate concentration,

the reason that the curve reaches a plateau, and does
not increase any further at high substrate concentration
is that:
Enzyme catalyzed reactions

An enzyme catalyzed reaction may be written as:
E is the enzyme, S is the substrate, ES is the enzyme-substrate complex and P is
the product.
The substrate binds to a specific site on the surface of the enzyme known as the
active site. The reaction occurs on the enzyme surface, after which product and
enzyme are released. The enzyme can then bind another substrate.
An illustration of an enzyme-substrate complex
The enzyme lysozyme is shown with a hexose sugar bound to the active
site. The substrate hexose is colored green, and it occupies the active site.
The study of the rates of enzyme catalyzed reactions is called enzyme
kinetics.
A typical enzyme kinetics curve for a non-allosteric enzyme is shown in the
graph:
An explanation for the shape of the enzyme kinetics curve
At low substrate concentration the reaction rate increases sharply with increasing
substrate concentration because there abundant free enzyme available (E) to bind
added substrate. At high substrate concentration, the reaction rate reaches a plateau
as the enzyme active sites become saturated with substrate (ES complex), and no
free
Problem 15: Interpreting the plateau of an enzyme kinetics curves
In the graph reaction rate vs substrate concentration,

the reason that the curve reaches a plateau, and does
not increase any further at high substrate concentration
is that:
A. the active site is saturated with substrate

B. there is a competitive inhibitor present
C. there is a non-competitive inhibitor present
D. the allosteric enzyme is locked in an inactive conformation
E. all substrate has been converted to product
Problem 16 Tutorial: Energy requiring and energy yielding reactions
Endergonic Reaction
An energy diagram for an endergonic or

nonspontaneous reaction is shown to the right. The
energy level of the products is higher than the energy
level of the reactants. Energy must be added for this
reaction to proceed. The amount of energy required is
termed G, which is greater than zero. The equilibrium
constant for an endergonic reaction is less than 1.
The result of a(n) __________ reaction is that energy is released. Energy must be
added for a(n) __________ reaction to proceed.
A. enzyme catalyzed, non-spontaneous

B. exergonic, endergonic
C. endergonic, spontaneous
D. catalytic, non-catalytic
E. oxidative, hydrolysis
Metabolism Problem Set

Problem 1 Tutorial: Glucose conversion
Glycolysis leads to the production of ____________ and two molecules of ATP. In
the absence of oxygen, fermentation leads to the production of ______________.
Glycolysis plus the citric acid cycle can convert the carbons of glucose to
_________ , storing the energy as ATP, _____________ and ___________.
Products of glycolysis
In glycolysis, glucose with six carbons is converted into two molecules of

pyruvate, each with three carbons. In the summary of glycolysis below, glucose
converts to two molecules of pyruvate,yielding 2 ATP and 2 NADH.
Products of fermentation
In fermentation, pyruvate is decarboxylated to acetaldehyde, and acetaldehyde is

reduced by NAD+ producing lactic acid. Fermentation occurs in the absence of
oxygen, and is designed to regenerate NAD+ to allow glycolysis to continue. Note
that you can't use NADH for energy unless oxygen is present.
Products of fermentation
In fermentation, pyruvate is decarboxylated to acetaldehyde, and acetaldehyde is

reduced by NAD+ producing lactic acid. Fermentation occurs in the absence of
oxygen, and is designed to regenerate NAD+ to allow glycolysis to continue. Note
that you can't use NADH for energy unless oxygen is present.
Products of glycolysis + the citric acid cycle
Glycolysis produces two molecules of pyruvate for each molecule of glucose. In in

the presence of oxygen (aerobic), the pyruvate enters the mitochondria and is
metabolized to CO2 and H2O in the citric acid cycle. A combination of glycolysis
and the citric acid cycle oxidizes glucose to CO 2producing ATP and the reduced
electron carriers NADH and FADH2. The reaction below summarizes the actions
of glycolysis and the citric acid cycle.
Problem 1:Glucose conversion

Glycolysis leads to the production of ____________ and two molecules of ATP. In
the absence of oxygen, fermentation leads to the production of ______________.
Glycolysis plus the citric acid cycle can convert the carbons of glucose to
_________ , storing the energy as ATP, _____________ and ___________.
A. lactic acid, pyruvate, CO2, NADH, FADH2
B. pyruvate, lactic acid, CO2, NADH, FADH2
In glycolysis, glucose with six carbons is converted into two molecules of
pyruvate, each with three carbons.
In fermentation, pyruvate is reduced by NAD+ producing lactic acid.
In the citric acid cycle, the carbons of glucose are converted to CO 2and the H
atoms used to reduce NAD+ and FAD forming NADH and FADH2.
C. CO2, NADH, FADH2, lactic acid, pyruvate
D. O2, lactic acid, pyruvate, FADH2
E. glucose, lactic acid, CO2, NADH, FADH2

Problem 2 Tutorial: Products of Glycolysis
At the end of glycolysis, each molecule of glucose has yielded 2 molecules of
_______, 2 molecules of ________, and a net of 2 molecules of _________.
Molecules converted in glycolysis
Glycolysis is a series of 10 reactions requiring two molecules of ATP to convert

glucose to activated intermediates, followed by cleavage and conversions to two
molecules of pyruvate. The summary below of glycolysis shows that the process
produces two molecules of NADH and four molecules of ATP for a net yield of 2
ATP.
Problem 2:Products of Glycolysis

At the end of glycolysis, each molecule of glucose has yielded 2 molecules of
_______, 2 molecules of ________, and a net of 2 molecules of _________.
A. FAD; NAD+; ADP
B. CO2; NAD+; ADP
C. lactic acid; ethanol; CO2
D. pyruvate; NADH; ATP
Glycolysis is the conversion of glucose to two molecules of pyruvate, yielding a
net 2 ATP and 2 NADH. Recall that 2 ATP were needed to initiate glycolysis and 4
ATP were produced in the pathway, for a net gain of 2 ATP.
E. H2O; CO2; ATP
Problem 3 Tutorial: Trematol
Trematol is a metabolic poison derived from the white snake root. Cows eating this
plant concentrate the poison in their milk. The poison inhibits liver enzymes that
convert lactic acid to other compounds for metabolism. Why does physical
exertion increase symptoms of poisoning by trematol? Why does the pH of the
blood decrease in a person who has digested trematol?
Fermentation and blood pH
Lactic acid is produced in our cells in the absence of sufficient oxygen in a process
called fermentation. Our muscles in particular use the conversion of pyruvate
produced in glycolysis to lactic acid to regenerate NAD + from NADH, allowing
continued ATP production from glycolysis.
Lactic acid build up leads to the symptoms of trematol poisoning. Exertion would
increase lactic acid production by our muscles, and an inability to metabolize lactic
acid in our liver due to tremetol would result in a build up of lactic acid in our
blood, decreasing the pH.
Problem 3: Trematol
Trematol is a metabolic poison derived from the white snake root. Cows eating this
plant concentrate the poison in their milk. The poison inhibits liver enzymes that
convert lactic acid to other compounds for metabolism. Why does physical
exertion increase symptoms of poisoning by trematol? Why does the pH of the
blood decrease in a person who has digested trematol?
A. Physical exertion would increase the production of latic acid by fermentation, and the
build up of lactic acid decreases blood pH when liver enzymes are blocked.
During exertion, our muscles produce lactic acid from pyruvate by fermentation, allowing
the regeneration of NAD+ for continued ATP production by glycolysis. Because lactic
acid metabolism is blocked by tremetol, the acid would build up in our blood, decreasing
the pH.
B. Physical exertion increases metabolism, and the electron transport chain, pumping H+ out
of mitochondria increases blood pH.
Metabolism Problem Set

Problem 4: Dinitrophenol
Dinitrophenol (DNP) is an uncoupler, or has the ability to separate the flow of electrons and
the pumping of H+ ions for ATP synthesis. This means that the energy from electron transfer
cannot be used for ATP synthesis. Fifty years ago, DNP was given as a drug to help patients
lose weight. Why does this work? Why would this be dangerous?
A. Uncoupling the electron transport chain would inhibit fermentation and decrease ATP
production, a potentially dangerous situation.
B. If electron transport doesn't produce ATP, then much more sugar must be metabolized for
energy needs. Very low production of ATP would be lethal.
Problem 4 Tutorial: Dinitrophenol
Dinitrophenol (DNP) is an uncoupler, or has the ability to separate the flow of

electrons and the pumping of H+ ions for ATP synthesis. This means that the energy
from electron transfer cannot be used for ATP synthesis. Fifty years ago, DNP was
given as a drug to help patients lose weight. Why does this work? Why would this
be dangerous?
Dinitrophenal's effects on metabolism

In oxidative phosphorylation, the flow of electrons from NADH and FADH 2 to
oxygen results in the pumping of H+ from the matrix to the intermembrane space.
This gradient of H+ can produce ATP by flowing through ATP synthetase in the
mitochondrial inner membrane.
Dinitrophenol disrupts the H+ gradient reducing ATP synthesis. Under these

conditions, much of our food that we eat could not be used for ATP synthesis are
we lose weight. However, too much inhibitor and we could make too little ATP for
life. The difference between weight loss and death is only a small concentration
change in dinitrophenol, making the drug dangerous.
Dinitrophenol (DNP) is an uncoupler, or has the ability to separate the flow of
electrons and the pumping of H+ ions for ATP synthesis. This means that the energy
from electron transfer cannot be used for ATP synthesis. Fifty years ago, DNP was
given as a drug to help patients lose weight. Why does this work? Why would this
be dangerous?
A. Uncoupling the electron transport chain would inhibit fermentation and decrease ATP
production, a potentially dangerous situation.
B. If electron transport doesn't produce ATP, then much more sugar must be metabolized for
energy needs. Very low production of ATP would be lethal.

In oxidative phosphorylation, the flow of electrons from NADH and FADH2 to oxygen
results in the pumping of H+ from the matrix to the inner membrane space. This gradient
of H+ can produce ATP by flowing through ATP synthetase in the mitochondrial inner
membrane. Dinitrophenol disrupts the H+ gradient reducing ATP synthesis. Under these
conditions, much of our food that we eat could not be used for ATP synthesis are we lose
weight. However, too much inhibitor and we could make too little ATP for life. The
difference between weight loss and death is only a small concentration change in
dinitrophenol, making the drug dangerous.
Problem 5 Tutorial: Effect of pH on Mitochondria

If you isolate mitochondria and place them in buffer with a low pH they begin to
manufacture ATP. Why?
Permeability of outer membrane
Mitochondrial production of ATP requires a concentration gradient of H +, with a

high concentration at the inter membrane space and a low concentration in the
matrix. The inner membrane is is impermeable to H +, but the outer membrane of
the mitochondria will allow H+ to pass through.
Thus, placing mitochondria in a low pH buffer produces a H + gradient that can
generate ATP through ATP synthetase.
If you isolate mitochondria and place them in buffer with a low pH they begin to
manufacture ATP. Why?
A. Low pH increases the concentration of base causing mitochondria to pump outH+ to the
inter membrane space leading to ATP production.
B. The high external acid concentration causes an increase in H+ in the inter membrane
space leading to increased ATP production by ATP synthetase.
Mitochondrial production of ATP requires a concentration gradient of H+ with a high
concentration at the inter membrane space and a low concentration in the matrix. The
inner membrane is impermeable to H+, but the outer membrane of the mitochondria will
allow H+ to pass through. Thus, placing mitochondria in a low pH buffer produces
a H+ gradient that can generate ATP through ATP synthetase.
C. Low pH increases the acid concentration in the mitochondrial matrix, a condition that
normally causes ATP production.
D. Low pH increases the OH- concentration in the matrix resulting in ATP production by ATP
synthetase.
Problem 6 Tutorial: Lactic Acid Production

A new drug was found to decrease hepatitis B virus. The drug is an analogue of
one of the nucleic acid bases of DNA and probably works by being incorporated
into the virus and disrupting viral genes during viral DNA replication. However,
patients in a clinical trial of the drug began to experience drastic overproduction of
lactic acid and liver failure leading to death. The most likely explanation for the
problem:
Why did fermentation occur?
The overproduction of lactic acid is evidence that fermentation is occurring on a

large scale. Knowing that the drug can interfere with DNA replication, it makes
sense to conclude that it has interfered with mitochondrial DNA and affected
normal ATP production.
If the mitochondria's ability to produce ATP were disrupted, the ATP would have to
be produced outside the mitochondria, by fermentation taking place in the cytosol.
Though it is normal for the body to use fermentation, especially by muscle cells
during hard exercise, fermentation is a temporary response that cannot be sustained
in humans.
In the case of patients in this clinical trial, ongoing exposure to the drug would
disrupt mitochondrial DNA as use continued, rendering more mitochondria unable
to produce ATP. Lactic acid production as a by-product of fermentation would
continue, and eventually overwhelm the liver
Problem 6: Lactic Acid Production
A new drug was found to decrease Hepatitis B virus. The drug is an analogue of
one of the nucleic acid bases of DNA and probably works by being incorporated
into the virus and disrupting viral genes during viral DNA replication. However,
patients in a clinical trial of the drug began to experience drastic overproduction of
lactic acid and liver failure leading to death. The most likely explanation for the
problem:
A. Incorporation of the drug into mitochondrial DNA disrupts the ability of mitochondria to
make ATP.
The key concept is that lactic acid is produced only when there is exertion for the muscles
or when mitochondrial function is inhibited. The drastic overproduction of lactic acid and
liver failure due to a drug that acts like a nucleotide would only occur if this analogue was
incorporated into mitochondrial DNA, disrupting mitochondria function. Tragically, that
is exactly what happened in this case.
B. The virus with mutations must overproduce lactic acid.
Problem 7 Tutorial: Pyruvate / Lactate Ratio

Explain why in anaerobic cells the ratio of pyruvate/lactate is much less than 1
while under aerobic conditions the ratio of pyruvate/ acetate is much greater than 1.
Anaerobic conditions and lactic acid production
The glycolytic pathway produces pyruvate, which in the presence of oxygen will
be further metabolized in the citric acid cycle to produce NADH and FADH 2 for
oxidative phosphorylation in the mitochondria. Normally, lactic acid will be low
under these conditions.
In the absence of oxygen (anaerobic), pyruvate must be converted to lactic acid,

the only reaction that can regenerate NAD+ allowing further glycolysis. The
production of lactic acid only under anaerobic conditions explains why
pyruvate/lactate is much less than 1 in anaerobic cells and much greater than one in
aerobic cells.
Problem 7: Pyruvate/ Lactate Ratio

Explain why in anaerobic cells the ratio of pyruvate/ lactate is much less than 1
while under aerobic conditions the ratio of pyruvate/ lactate is much greater than 1.
A. Lactate is produced from pyruvate only under anaerobic conditions.

The glycolytic pathway produces pyruvate, which in the presence of oxygen will
be further metabolized in the citric acid cycle to produce NADH and FADH 2 for
oxidative phosphorylation in the mitochondria. Normally, lactic acid will be low
under these conditions. In the absence of oxygen (anaerobic), pyruvate must be
converted to lactic acid, the only reaction that can regenerate NAD + allowing
further glycolysis. The production of lactic acid only under anaerobic conditions
explains why pyruvate/lactate is much less than 1 in anaerobic cells and much
greater than one in aerobic cells.
B. Under anaerobic conditions pyruvate is converted to carbon dioxide.
C. In anaerobic conditions, pyruvate is converted to glucose using the energy of
light.
D. Lactate is the terminal electron acceptor under aerobic conditions.
E. Pyruvate is transported into mitochondria under anaerobic conditions.
Problem 8 Tutorial: Mitochondria
Which of the following statements about mitochondria is false?
A. They contain an inner and an outer membrane.
B. The region enclosed by the inner membrane is termed the matrix.
C. They contain DNA and ribosomes.
D. They are an important site for energy production in cells.
E. They contain stacked internal thylakoid membranes.
Characteristics of mitochondria
Mitochondria have both an inner and outer membrane.

The inner membrane is folded into cristae, and contains
electron transport systems and oxidative
phosphorylation. This is where ATP synthesis occurs.
The region enclosed by the inner membrane is termed
the matrix. This is where pyruvate is dehydrated,
forming acetyl CoA, and where the citric acid cycle
takes place.
Ribosomes are located in three places in the cell, one
of which is the mitochondria. They are also present on
the surface of the endoplasmic reticulum, and in the
cytoplasm.
Stacked thylakoid membranes are not present in
mitochondria. They make up the granum within
plastids, such as plant chloroplasts, and are involved in
photosynthesis. Here they have a similar function to
the inner mitochondrial membrane. This is where the
ATP synthase is located in plants.
Problem 8: Mitochondria
Which of the following statements about mitochondria is false?
A. They contain an inner and an outer membrane.
B. The region enclosed by the inner membrane is termed the matrix.
C. They contain DNA and ribosomes.
D. They are an important site for energy production in cells.
E. They contain stacked internal thylakoid membranes.
Stacked thylakoid membranes (granum), exist only in plastids, such as plant
chloroplasts, not in mitochondria.
Problem 9 Tutorial: Electron Transport Chain
The electron transport chain is located predominantly in the:
Inner membrane of the mitochondria
The inner membrane of mitochondria contains the proteins of the electron transport
chain, and is the barrier allowing the formation of a H + gradient for ATP production
through ATP synthetase.
Problem 9: Electron Transport Chain

The electron transport chain is located predominantly in the:
A. Outer membrane of the mitochondria
B. Intermembrane space of the mitochondria
C. Inner membrane of the mitochondria
The inner membrane of mitochondria contains the proteins of the electron transport
chain, and is the barrier allowing the formation of a H+ gradient for ATP
production through ATP synthetase.
D. Matrix of the mitochondria
E. Cytoplasm of the cell
Problem 10 Tutorial: Acidity During Electron Transport
What cellular compartment becomes acidic (high concentration of hydrogen ions)
during mitochondrial electron transport?
Intermembrane space of mitochondria
Electron transport results when NADH and FADH2 donate electrons to complexes
in the inner mitochondrial membrane. The electrons flow through the complexes
and are eventually donated to oxygen forming water.
This process pumps protons (H+) into the intermembrane space. The gradient
created (high concentration of protons in the intermembrane space and low
concentration in the matrix) causes protons to flow through ATP synthetase in the
inner membrane resulting in production of ATP.
Problem 10: Acidity During Electron Transport

What cellular compartment becomes acidic (high concentration of hydrogen ions)
during mitochondrial electron transport?
A. mitochondrial stroma
B. cytoplasm
C. endoplasmic reticulum
D. space between inner and outer mitochondrial membranes
Electron transport produces a high concentration of H + (protons) in the inner
membrane space of the mitochondria.
E. thylakoid membranes
Problem 11 Tutorial: Fermentation
In the absence of oxygen, the primary purpose of fermentation is to:
The purpose of fermentation
Fermentation allows continued glycolysis by regenerating NAD + from NADH.

NAD+ is limiting, and must be reformed to allow the continuation of the glycolytic
degradation of glucose producing
Problem 11: Fermentation
In the absence of oxygen, the primary purpose of fermentation is to:
A. produce amino acids for protein synthesis
B. generate a proton gradient for ATP synthesis
C. oxidize glucose to generate reduce electron carriers
D. generate alcohol for beverages
E. regenerate NAD+ from NADH allowing glycolysis to continue
Fermentation allows continued glycolysis by regenerating NAD + from NADH.
NAD+ is limiting, and must be reformed to allow the continuation of the glycolytic
degradation of glucose producing ATP.
Problem 12 Tutorial: Hexokinase
In the first step of glycolysis, the enzyme hexokinase uses ATP to transfer a
phosphate to glucose to form glucose-6-phosphate. The product continues to be
oxidized forming pyryvate in glycolysis and is a precursor to acetyl-CoA for the
citric acid cycle. Suppose that a cell has only glucose available for energy and that
the activity of hexokinase is suddenly stopped in this cell. Which of the following
conditions will occur?
Hexokinase's role in ATP production
Glycolysis must occur before ATP is produced, regardless of whether it is

fermentation or the citric acid cycle that follows. Because hexokinase is involved
in this preliminary step, if its activity were stopped, the cell could not continue to
produce ATP by either pathway.
Problem 12: Hexokinase
In the first step of glycolysis, the enzyme hexokinase uses ATP to transfer a
phosphate to glucose to form glucose-6-phosphate. The product continues to be
oxidized forming pyryvate in glycolysis and is a precursor to acetyl-CoA for the
citric acid cycle. Suppose that a cell has only glucose available for energy and that
the activity of hexokinase is suddenly stopped in this cell. Which of the following
conditions will occur?
A. The cell will continue to produce energy from mitochondrial electron transport
B. The cell will continue to produce ATP using the citric acid cycle.
C. The cell will ultimately be unable to produce ATP
Because energy production requires that glucose first be metabolized in glycolysis,
the loss of hexokinase would block ATP production in the cell.
D. The cell will be forced to switch to fermentation to produce ATP.
E. The use of oxygen by the cell will increase.
Problem 13 Tutorial: Storing Usable Energy
As a result of glycolysis, pyruvate oxidation and the citric acid cycle, only a small
portion of the energy of glucose has been converted to ATP. At this point, the
majority of the usable energy is contained in:
Usable energy after the citric acid cycle
Oxidative phosphorylation produces the majority of the energy generated in the

cell. The combination of glycolysis and the citric acid cycle alone yield only 4 ATP.
The majority of the energy is stored in the electron carriers NADH and FADH 2.
Oxidative phosphorylation can produce 3 ATP for each NADH and 2 ATP for each
FADH2.
Problem 13: Storing Usable Energy

As a result of glycolysis, pyruvate oxidation and the citric acid cycle, only a small
portion of the energy of glucose has been converted to ATP. At this point, the
majority of the usable energy is contained in:
A. oxidized electron carriers NAD+ and FAD
B. carbon dioxide
C. pyruvate
D. acetyl coenzyme A
E. reduced electron carriers NADH and FADH2
Oxidative phosphorylation produces the majority of the energy generated in the
cell. The combination of glycolysis and the citric acid cycle alone yield only 4 ATP.
The majority of the energy is stored in the electron carriers NADH and FADH 2.
Problem 14 Tutorial: Terminal Electron Acceptor
The terminal electron acceptor during mitochondrial respiration:
Electron transport in the inner mitochondrial membrane
The electron transport in the inner membrane of the mitochondria is a series of

protein complexes that receive electrons from NADH and FADH 2. Transferring
electrons through the protein complexes results in the pumping of protons into the
inner membrane space, and the final acceptor is oxygen, generating water.
The significance of O2 as the terminal electron acceptor
Our main reason for breathing is to provide oxygen as the terminal electron
acceptor. The water produced represents about 1/3 of our needed water for each
day. The rest must be provided by eating and drinking. Any reduction in oxygen to
our bodies severely restricts our ability to produce ATP. Our brains, lacking the
pathway for fermentation, are particularly sensitive to oxygen depletion.
The terminal electron acceptor during mitochondrial respiration:
A. H2O
B. NAD+
C. FAD
D. ATP
E. O2
The electron transport in the inner membrane of the mitochondria is a series of
protein complexes that receive electrons from NADH and FADH 2. Transferring
electrons through the protein complexes results in the pumping of protons into the
inner membrane space, and the final acceptor is oxygen, generating water.
Problem 15 Tutorial: Metabolism During Heart Attack
During a heart attack, blood flowing to the heart muscle is interrupted by blockage of a
coronary artery. How would you expect the metabolism in the heart to change?:
Effects of a heart attack on heart metabolism
Reducing blood flow to the heart restricts oxygen delivery. This slows oxidative
phosphorylation in mitochondria requiring the cell to resort to fermentation, producing lactic
acid to regenerate NAD+for glycolysis. Since glycolysis can only product ATP, the amount of
glucose needed for energy increases exhausting stores of glycogen. Water is produced when
oxygen serves as the terminal electron acceptor. Thus, without oxygen the production of
water from electron transport is severely inhibited.
Problem 15: Metabolism During Heart Attack

During a heart attack, blood flowing to the heart muscle is interrupted by blockage
of a coronary artery. How would you expect the metabolism in the heart to change?
A. oxidative phosphorylation would slow down in the mitochondria
B. the rate of production of lactic acid would be stimulated
C. the use of glucose by the muscle tissue would increase
D. the production of water by mitochondria would be inhibited
E. all are expected metabolic changes
Arteries carry oxygenated blood. If the flow of blood through the coronary artery
to the heart is blocked, the heart is being deprived of oxygen. All of the above
answers are expected effects of an insufficient oxygen supply to the cells, and
resulting fermentation.
Problem 16 Tutorial: ATP Production
The major production of ATP during aerobic metabolism occurs when electrons
from __________ and _____________ are transferred to _______________.
Electron transfer and ATP production
After the citric acid cycle, the majority of energy is stored in the reduced electron
carriers NADH and FADH2. Electrons from the carriers are donated to the electron
transport chain in the mitochondrial inner membrane and are ultimately transferred
to oxygen to produce water. The proton gradient that is produced during this
process can generate ATP by passing through the inner mitochondria membrane
associated ATP synthetase.
Problem 16: ATP Production
The major production of ATP during aerobic metabolism occurs when electrons
from __________ and _____________ are transferred to _______________.
A. FADH2, NADH, H20
B. O2, FADH2, NADH
C. FADH2, O2, NADH

D. NADH, O2, FADH2
E. FADH2, NADH, O2
After the citric acid cycle, the majority of energy is stored in the reduced electron
carriers NADH and FADH2. Electrons from the carriers are donated to the electron
transport chain in the mitochondrial inner membrane and are ultimately transferred
to oxygen to produce water. The proton gradient that is produced during this
process can generate ATP by passing through the inner mitochondrial membrane
associated ATP synthetase.
Problem 17 Tutorial: ATP synthase
ATP synthase can produce ATP using as a direct energy source:
Production of ATP by ATP synthase
The electrons from from NADH and FADH2 flow through the electron transport
chain in the inner mitochondrial membrane generating a H + buildup in the inner
membrane space.
This proton gradient (gradient of H+) flowing through the membrane enzyme
complex ATP synthetase is the direct energy source for producing ATP.
Problem 17: ATP synthase

ATP synthase can produce ATP using as a direct energy source:
A. energy from the conversion of glucose to pyruvate
B. energy from the oxidation of pyruvate producing CO 2 and H20
C. energy from a proton gradient established in mitochondria
The electrons from from NADH and FADH2 flow through the electron transport
chain in the inner mitochondrial membrane generating a H+ buildup in the inner
membrane space. This proton gradient (gradient of H+) flowing through the
membrane enzyme complex ATP synthetase is the direct energy source for
producing ATP.
D. energy derived from the breakdown of NADH and FADH2
E. energy from the metabolism of amino acids
Regulation of Carbohydrate Metabolism Problem Set

Question 1: Liver Enzymes Affected by Insulin
Insulin facilitates energy storage in liver. Which enzymes of carbohydrate

metabolism are coordinately regulated in liver in response to insulin signaling?
1. Glycogen synthase
2. Glycogen phosphorylase
3. Phosphofructokinase-1 (PFK-1)
5. Pyruvate kinase
Tutorial
Six enzymes shown in red (including all five listed in question) are affected by
insulin, via three different mechanisms. All but glycogen phosphorylase are
stimulated. However, note that PFK-2 is one activity of a bifunctional enzyme - the
other "half" of this two-headed beast will come up later in this tutorial.
Insulin facilitates energy storage in liver. Which enzymes of carbohydrate
metabolism are coordinately regulated in liver in response to insulin signaling?
5. Pyruvate kinase
Yes, all of these enzymes are affected by insulin action. Regulation of
all five enzymes can be logically explained as promoting glucose
utilization and storage, either in the form of glycogen (liver), fatty
acids (adipose tissue) or cholesterol (liver and other peripheral
tissues). Intuitively, these processes seem appropriate during times of
insulin secretion (i.e., high blood glucose).
Question 2: Enzymes Dephosphorylated by Insulin Action
Of the enzymes of carbohydrate metabolism listed below, which are
(de)phosphorylated in liver in response to insulin signaling?
5. Pyruvate kinase
Tutorial
Four of the six enzymes named in the above figure are dephosphorylated in
response to insulin. These enzymes are denoted by a red -OH, signifying that the
phosphate group has been removed from the serine or threonine residue in the
enzyme, leaving a free hydroxyl. Recall that enzyme dephosphorylation is often
the way in which enzymes are ultimately regulated by insulin (don't worry about
the exact mechanism for now - there are too many steps between insulin binding
and activation of the protein phosphatase).
In three of the four cases, the enzyme is activated by dephosphorylation. The
exception is found in the glycogen synthase/phosphorylase pair, which obviously
cannot both be activated at the same time. However, you don't necessarily have to
memorize which one is inhibited by insulin - this can be reasoned through by
considering which way the reaction should go in times of high blood glucose. You
guessed it, toward glucose storage (i.e., glycogen synthesis).
Question 2: Enzyme Dephosphorylaton by Insulin Action
Of the enzymes of carbohydrate metabolism listed below, which are
(de)phosphorylated in liver in response to insulin signaling?
5. Pyruvate kinase
Four of these enzymes are directly modified via dephosphorylation
(1, 2, 4, and 5). Three of the dephosphorylation events activate the
affected enzyme, but one (glycogen phosphorylase) is inhibited by
this modification. Again, this makes sense in view of insulin's role to
store, not mobilize glucose. The remaining enzyme is
affected indirectly by insulin, but how?
Question 3: PFK-1 Regulation in Liver
Given that the phosphofructokinase-1 (PFK-1) enzyme is regulated by insulin, but
not via (de)phosphorylation, how is this regulation accomplished?
A. Via increased transcription of the gene encoding this enzyme
B. By recruitment of pre-existing enzyme from the Golgi
C. Via allosteric regulation by fructose-2,6-bisphosphate

D. Activation by association with IRS-1
E. An inhibitory subunit of the enzyme dissociates after binding cAMP
Tutorial
This regulatory loop is a liver specialty. PFK-2, which exists mainly in liver, is part
of a bifunctional enzyme. In the presence of insulin, this activity is activated via
dephosphorylation and produces small amounts of fructose-2,6-bisphosphate (note
the correspondence between PFK-2 and F-2,6-bisP, versus the more common
enzyme PFK-1 and its product F-1,6-bisP).
Anyway, this small amount of F-2,6-bisP is enough to switch on PFK-1 in liver,
leading to eventual conversion of glucose to pyruvate and thence to fatty acids,
lipids and other goodies. Again, memorization of this whole scenario can be
minimized (but unfortunately not eliminated) by always keeping in mind the
purpose of insulin, namely to promote glucose uptake/storage. Or at least you
could check yourself by remembering this.
Question 3: PFK-1 Regulation in Liver
Given that the phosphofructokinase-1 (PFK-1) enzyme is regulated by insulin, but
not via (de)phosphorylation, how is this regulation accomplished?
Activation of PFK-1 in liver is indirect, and occurs as follows: dephosphorylation of the
bifunctional PFK-2/Fructose-bisphosphatase enzyme places this enzyme in the PFK-2
mode, producing fructose-2,6-bisP, which then allosterically activates PFK-1 (the tutorial
for this question provides a diagram of this). A bit complicated, but when placed in the
context of insulin's role to promote glucose utilization/storage, it fits nicely into the big
picture.
Question 4: Insulin Regulation of Glucokinase

Glucokinase is also regulated by insulin in liver, but not via phosphorylation. How
is this regulation accomplished?
A.
B.
C.
D.
E.
Via increased transcription of the gene encoding this enzyme

By recruitment of pre-existing enzyme from the Golgi
Via allosteric regulation by fructose-2,6-bisphosphate
Activation by association with IRS-1
An inhibitory subunit of the enzyme dissociates after binding cAMP
Tutorial
When glucose concentrations become very high or are chronically high, insulin has
another card to play in order to clear glucose from the blood. Recall that
glucokinase, a liver enzyme, has a relatively high K m for glucose, and therefore
only really comes into action when glucose concentrations are high. This enzyme
is well suited for removing glucose from the blood for two reasons.
1. First, it is located in liver, a major storage site for excess glucose.
2. Second, its high Km will allow it to perform this function without removing
too much glucose from the blood (thus depriving other tissues), even if
enzyme concentrations are high.
So, it makes sense that insulin would upregulate this enzyme, and it does so by
increasing gene transcription (again, do not worry about the mechanism).
Now, before we move on to consider glucagon action, this is a good time to take a
last look at the whole picture of insulin action in liver, which includes coordinated
regulation of six enzymes in order to achieve glucose uptake and storage (just
follow the green arrows!).
Question 4: Insulin Regulation of Glucokinase

Glucokinase is also regulated by insulin in liver, but not via phosphorylation. How
is this regulation accomplished?
This is a different type of regulation from the more rapid (de)phosphorylation mechanism,
but is by no means unusual in metabolic systems. The actual mechanism of this insulininitiated regulation is beyond the scope of this course. However, recall that glucokinase is
the "high Km" kinase for glucose, so there is really no reason for it to even be around if
glucose concentrations stay low most of the time.
Question 5: Enzyme Phosphorylation Induced by Glucagon

Tutorial to help answer the question.
The same enzymes that are (de)phosphorylated by insulin action (namely glycogen
synthase, glycogen phosphorylase, the PFK-2/FBPase-2 bifunctional enzyme and
pyruvate kinase) are phosphorylated via glucagon and/or epinephrine action.
Which kinase is responsible for these phosphorylation events?
A.
B.
C.
D.
E.
Protein kinase C
Calmodulin-dependent kinase
Protein kinase A
Receptor tyrosine kinase
beta-ARK
Tutorial
Glucagon Acts via cAMP
Even though glucagon is a peptide, not a catecholamine, the glucagon receptor can
almost be considered to be an adrenergic receptor, in that it is linked via G s to
adenylate cyclase. The cAMP second messenger that results from this linkage
activates a kinase, very imaginatively named "cAMP-dependent protein kinase" or
protein kinase A. This enzyme then phosphorylates all of the enzymes that insulin
may have previously dephosphorylated. Thus, the concept that insulin and
glucagon have opposite actions has a definite biochemical basis!
Question 5: Enzyme Phosphorylation Induced by Glucagon
The same enzymes that are (de)phosphorylated by insulin action (namely glycogen
synthase, glycogen phosphorylase, the PFK-2/FBPase-2 bifunctional enzyme and
pyruvate kinase) are phosphorylated via glucagon and/or epinephrine action.
Which kinase is responsible for these phosphorylation events?
A. Protein kinase C
B. Calmodulin-dependent kinase
C. Protein kinase A
This is a very clear example of how glucagon and epinephrine oppose the actions of
insulin. Also, the general rule that insulin promotes dephosphorylation, while glucagon
promotes phosphorylation via cAMP/protein kinase A, will hold up very well throughout
the course.
D. Receptor tyrosine kinase
E. beta-ARK
Question 6: Epinephrine Action to Mobilize Glycogen

To which receptor does epinephrine bind in order to stimulate phosphorylation of
glycogen synthase, glycogen phosphorylase, PFK-2/FBPase-2 bifunctional
enzyme, and pyruvate kinase?
A.
B.
C.
D.
alpha-1
alpha-2
glucagon
beta
Tutorial
We are dealing here with the major action of epinephrine to mobilize glycogen
from liver (shown), and also muscle (which lacks PFK-2 and glucose-6phosphatase). The context is acute stress, so the liver's role is to release fuel into
the blood, while muscle would then use the fuel, from either the liver or from its
own glycogen stores, for the "fight or flight response".
The coordinate regulation of glucose metabolism is via phosphorylation, the
opposite of insulin's action via dephosphorylation. As you will recall, the
Gs/cAMP/protein kinase A pathway is involved in many important phosphorylation
events, including the ones here. Recall also that epinephrine, unlike the peptide
hormone glucagon,is a catecholamine and thus must bind to an adrenergic receptor.
Which adrenergic receptor subtype(s) act via G s?
Primary Action of Epinephrine in a Liver Cell
Question 6: Epinephrine Action to Mobilize Glycogen

To which receptor does epinephrine bind in order to stimulate phosphorylation of
glycogen synthase, glycogen phosphorylase, PFK-2/FBPase-2 bifunctional
enzyme, and pyruvate kinase?
A.
B.
C.
D.
alpha-1
alpha-2
glucagon
beta
One way to arrive at the correct answer is to recall that the actions of epinephrine
resemble that of glucagon in opposing insulin. However, since epinephrine is a
catecholamine, its receptor must be distinct from the glucagon receptor, which binds a
polypeptide ligand. Otherwise, the similarity with glucagon holds, in that both agents
exert their effects on the liver (or muscle) cell by raising cAMP to activate protein kinase
A. For the purposes of the Biochemistry course (but not necessarily Physiology!), do not
worry about the distinction between beta-1 and beta-2. But there is more to the
epinephrine story...
Question 7: A Secondary Action of Epinephrine in Liver

To which additional adrenergic receptor subtype does epinephrine bind in order to
further activate glycogen phosphorylase in liver?
A.
B.
C.
alpha-1
alpha-2
beta-1
D.
a novel beta-3 subtype
Tutorial
Think of this as an auxiliary action of epinephrine to boost the action of glycogen
phosphorylase in a true emergency. Recall that phosphorylase kinase is the enzyme
that phosphorylates and activates glycogen phosphorylase, and that phosphorylase
kinase b, the inactive form, can be phosphorylated to phosphorylase kinase "a"
(active) as part of a phosphorylation cascade initiated by cAMP and protein kinase
A.
A part of the regulation you may have forgotten is that intracellular calcium can
activate phosphorylase kinase b even in the absence of the phosphorylation signal.
This effect would then activate even those molecules of phosphorylase kinase that
did not become phosphorylated in the cascade, creating an additive effect to boost
glycogen hydrolysis.
Intracellular calcium would be naturally released in muscle with "fight or flight"
contractions to accomplish this additive activation, but how can this happen in
liver? The answer is a second type of adrenergic receptor to which epinephrine can
bind to boost intracellular calcium. This occurs via the G q/phospholipase
C/IP3 pathway. The only remaining issue: which adrenergic receptor type is linked
to Gq?
Secondary Action of Epinephrine in Liver
Question 7: A Secondary Action of Epinephrine in Liver
To which additional adrenergic receptor subtype does epinephrine bind in order to

further activate glycogen phosphorylase in liver?
A. alpha-1
This seems like a picky question, but recall that the liver is one of the main sources of
quick fuel in the "fight or flight" response, and so it needs a second pathway for
maximum responsiveness. Having already dispensed with the beta adrenergic receptors in
the previous question, we can also eliminate the alpha-2 receptor, which would actually
work against glycogenolysis by lowering cAMP and thus shutting down the protein kinase
A-initiated cascade.
The only receptor left is alpha-1, the correct answer. Alpha-1 receptors act by generating
DAG/IP3 signals and mobilizing intracellular Ca++. Elevated intracellular Ca++ then
allosterically activates phosphorylase kinase in the absence of phosphorylation, which
then can activate glycogen phosphorylase via an abbreviated phosphorylation pathway.
(There is one other allosteric activator besides Ca++ that can activate glycogen
phosphorylase by bypassing the normal PKA step - the (non-cyclic!) AMP "cellular
distress signal", which acts to directly activate glycogen phosphorylase b in the absence of
a phosphorylation signal.)
B. alpha-2
C. beta-1
D. a novel beta-3 subtype
Question 8: Insulin action in skeletal muscle

Insulin regulates all of the following enzymes in liver. Which of these enzymes are
also regulated by insulin in muscle?
5. Glucokinase
Tutorial
This is essentially the same figure as for insulin action in liver (question 1 of this
module), and the five enzymes in question are denoted with question marks. The
key for arriving at the correct answer is to determine which enzymes are missing in
muscle.
Question 8: Insulin action in (skeletal) muscle

Insulin regulates all of the following enzymes in liver. Which of these enzymes are
also regulated by insulin in muscle?
Recall that glucokinase and PFK-2 are liver specialties. Since PFK-1 is
regulated indirectly via PFK-2, that also eliminates PFK-1. The only ones
left are two enzymes controlling glycogen metabolism. Muscle does not
contain glucokinase but instead contains hexokinase (which is not regulated
by insulin).
5. Glucokinase

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Problem 1: Recognition of the peptide bond

Tutorial to help answer the question

Which arrow points to a peptide bond?

Problem 2: Identification of biological molecules

1. Carbohydrates can be either a single sugar (monosaccharide) like

4. Common 5 and 6 carbons sugars usually exist as 5- or 6-membered

1. Lipids or fats are characterized by their insolubility in water and

2. As shown in the diagram, amino acids have a generalized structure,

1. Nucleotides are the building blocks of RNA and DNA.

2. The structure on the left is a(n) _________________, and the structure on

Problem 3: Tertiary structure of a protein

Primary Structure of Proteins

Secondary Structure of Proteins

Tertiary Structure of Proteins

Tertiary structure of the triose phosphate isomerase (TPI) molecule.

Quaternary Structure of Proteins

Problem 3: Tertiary structure of a protein

Problem 4: Identification of another biological molecule

Problem 4: Identification of another biological molecule

The structure shown in the diagram is an example of:

The structure shown in the diagram is an example of:

Which statement is true concerning the structure of proteins?

The primary structure is the sequence of amino acids.

Problem 5: Elements of protein structure

Amino Acid Side Chains (R-groups)

Examples of different categories of amino acids:

Different proteins have different structures and properties due to the

Problem 5: Elements of protein structure

Which statement is true concerning the structure of proteins?

Nitrogenous bases: purines and pyrimidines

DNA and RNA

Problem 6:Identification of a monomer unit of a biological macromolecule

Problem 7: Weak forces involved in interactions between macromolecules

Problem 8: Identification of a macromolecule

Which nucleic acid?

Problem 8: Identification of a macromolecule

The structure shown in the diagram is an example of:

Problem 9: Identification of a hydrophobic amino acid

Tutorial to help answer the question

Which amino acid has a hydrophobic side chain?

Problem 10 Tutorial: Protein-protein interactions

Problem 10: Protein-protein interactions

Proteins 1 and 2 interact strongly. A significant part of the interaction is

A. The most: aspartic acid; the least: leucine

Amino acid composition

The final sequence of the polypeptide with 5 amino acids is ala-ala-hisgly-ser.

Problem 11: Sequence of a polypeptide

The original peptide must have the sequence of:

Problem 12: Sequence of a longer polypeptide

enzymes form complexes with their substrates.

Features of Enzyme Catalyzed Reactions

enzymes form complexes with their substrates.

This is a hydrolysis reaction. The disaccharide glucose is hydrolyzed to the two

Free energy and chemical equilibrium

The hydrolysis of sucrose

This is a spontaneous reaction beginning with sucrose because K eq > 1.

Problem 3 Tutorial: Kinetics of an allosteric enzyme.

Problem 3: Kinetics of an allosteric enzyme.

Problem 5 Tutorial: Why do enzymes reach a maximum rate at high substrate

rate of the reaction reaches a maximum, where further increases in the

In the presence of alcohol dehydrogenase, the rate of

An enzyme catalyzed reaction may be written as:

E is the enzyme, S is the substrate (acetaldehyde), ES is the enzyme-substrate

At low substrate concentration the rate of ethanol production increases sharply