Download BiochemTargetPracticeKEY2014 - Self

UNIT 2 BIOCHEMISTRY
TARGET PRACTICE ANSWER KEY
1
Practice Questions Related to Biochemistry Unit Targets
TARGET VII. Using one or more macromolecules, either monomer or polymers, state at least three
specific examples that reinforce the relationship between structure of a molecule and its function.
Describe possible biological consequences of improper molecular shape for each example.
Carbohydrate—polymer glycogen is very branched making it easy for glucose molecules to be broken
off for energy. Glycogen is used for energy when glucose levels are low in animals. If this were not
branched, animals could not utilize the stored glucose as easily and thus not have energy needed
to make ATP.
Proteins—enzymes are long chains of amino acids that fold into secondary and tertiary structures due
to interactions between R groups on individual amino acids. If the wrong amino acid is in place,
the folding may not be correct which could change the structure of the active site, not allowing it
to catalyze the reaction it normally does. This would prohibit a metabolic function from occurring.
For example, in NKH, a disorder that causes brain damage in infants due to build up of glycine,
Mutations lead to the production of a nonfunctional version of glycine dehydrogenase. Many of
these genetic changes alter single amino acids in glycine dehydrogenase. For example, the most
common GLDC mutation in the Finnish population replaces the amino acid serine with the amino
acid isoleucine at position 564 in the enzyme which. When an altered version of this enzyme is
incorporated into the glycine cleavage enzyme complex, it prevents the complex from breaking
down glycine properly. As a result, excess glycine can build up to toxic levels in the body's organs
and tissues. Damage caused by harmful amounts of this molecule in the brain and spinal cord is
responsible for the intellectual disability, seizures, and breathing difficulties characteristic of
glycine encephalopathy.
Phospholipids – Have a hydrophilic ‘head’ region and a hydrophobic ‘tail’ region that allows the
molecule to form a lipid bilayer characteristic of a cell membrane. Without the amphipathic
structure of the phospholipid, the molecule would not form a bilayer nor be useful as a cell or
organelle boundary.
TARGET XIII. Cite specific examples to describe the relationship between enzyme function and
metabolism. How are enzymes involved in general metabolic processes? How is enzyme action
regulated, thereby regulating metabolism?
Enzymes control when and where metabolic reactions take place. In many cases, the molecules
that naturally regulate enzyme activity in a cell behave similarily to noncompetitive inhibitors
These regulatory molecules change an enzyme’s shape and the functioning of its active site. This
allosteric regulation is when a proteins function at the active site is affected by the binding of a
regulatory molecule to a separate site. This may cause either activation or stimulation.
TARGETS XI & XII. How do effects of increased temperature, increased or decreased pH cause
denaturation of a protein. Be sure to address protein structure in your answer.
To a point, the rate of an enzymatic reaction increases with increasing temperature, partly
because substrates collide with active sites more frequently when the molecules move rapidly.
However, the heat disrupts the hydrogen bonds, ionic bonds and other weak interactions that
stabilize the active shape of the enzyme(secondary and tertiary structure). This denatures the
enzyme, Each enzyme has an optimal temperature at which the reaction rate is greatest. In
humans, that temperature is 35-40 degrees celcius. There are, however, bacteria living in 70
degree celcius hot springs.
2
Each enzyme also has an optimal pH. Most are between 6 and 8. Some are lower, like pepsin in
the stomach. Since it operates in an environment of a pH of 2, it has a lower optimal pH. The pH of
a solution can have several effects of the structure and activity of enzymes. For example, pH can have
an effect of the state of ionization of acidic or basic amino acids. Acidic amino acids have carboxyl
functional groups in their side chains. Basic amino acids have amine functional groups in their side
chains. If the state of ionization of amino acids in a protein is altered then the ionic bonds that help to
determine the tertiary shape of the protein can be altered. This can lead to altered protein recognition or
an enzyme might become inactive. Changes in pH may not only affect the shape of an enzyme but it
may also change the shape or charge properties of the substrate so that either the substrate cannot bind to
the active site or it cannot undergo catalysis.
TARGET XI. How do the “lock and key” model and the “induced fit” model for enzyme mechanics differ?
How are they similar? Provide an example for each model.
Lock and Key Model--The specific action of an enzyme with a single substrate can be explained using a
Lock and Key analogy. In this analogy, the lock is the enzyme and the key is the substrate. Only the
correctly sized key (substrate) fits into the key hole (active site) of the lock (enzyme). Smaller keys,
larger keys, or incorrectly positioned teeth on keys (incorrectly shaped or sized substrate molecules)
do not fit into the lock (enzyme). Only the correctly shaped key opens a particular lock. Examples of
enzyme/substrate pairs that exhibit lock and key include: polyphenoloxidase & catechol, sucrase &
sucrose, pepsin & proteins
Induced-fit Model--Not all experimental evidence can be adequately explained by using the lock and
key model. For this reason, a modification called the induced-fit model has been proposed. The
induced-fit model assumes that the substrate plays a role in determining the final shape of the
enzyme and that the enzyme is partially flexible. This explains why certain compounds can bind to the
enzyme but do not react because the enzyme has been distorted too much. Other molecules may be
too small to induce the proper alignment and therefore cannot react. Only the proper substrate is
capable of inducing the proper alignment of the active site.
“Active sites in the uninduced enzyme are shown schematically with rounded contours. Binding of the
first substrate (gold) induces a physical conformational shift (angular contours) in the protein that
facilitates binding of the second substrate (blue), with far lower energy than otherwise required.
When catalysis is complete, the product is released, and the enzyme returns to its uninduced state.
The induced fit model has been compared to a hand-in-glove model, wherein it may be difficult to
insert the first finger into the proper place, but once done, the other fingers go in easily because the
glove is now properly aligned.”
(from: http://www.mun.ca/biology/scarr/Induced-Fit_Model.html )
3
TARGET XI. How do enzymes actually lower the activation energy of the reaction they catalyze. What are
the benefits to having reactions proceed at lower activation energy levels?
Enzymes bind temporarily to one or more of the reactants of the reaction they catalyze. In doing so,
they lower the amount of activation energy needed and thus speed up the reaction. This allows for
organisms to exist at lower temperatures. For example, 451degrees F (232 degrees Celcius) is the
temperature at which paper (cellulose) combusts. You know this from English class. Carbohydrate
combusts in us too, but at a lower temperature due to enzymes. Humans and other organisms could
not survive at such high temperatures. Organisms also conserve energy by enzymes being able to
lower the energy required for reactions.
TARGET III. Describe the polarity of the water molecule. Relate water polarity to four characteristic
properties of water and to biological examples where properties are beneficial to life.
Water is a "polar" molecule, meaning that there is an uneven distribution of electron density. Water
has a partial negative charge ( ) near the oxygen atom due the unshared pairs of electrons, and
partial positive charges ( ) near the hydrogen atoms. An electrostatic attraction between the
partial positive charge near the hydrogen atoms and the partial negative charge near the oxygen
results in the formation of hydrogen bonds.
Cohesion—Water molecules stay close to each other –causes transport of water and dissolved
minerals against gravity in plants. It also causes surface tension which allows some insects to walk on
the surface of the water.
Moderation of Temperature—Water can absorb and release a relatively large amount of heat with
only a slight change in its own temperature. This is because temperature is a measure of the average
kinetic energy of molecules. Increasing heat will increase the temperature (motion of molecules)
only after the heat has disrupted the hydrogen bonds to allow the molecules to move. Thus water has
a high specific heat (the amount of heat that must be absorbed or lost for 1g of a substance to be
raised by 1 degree celcius) and also a high heat of vaporization (the amount of heat a liquid must
absorb for 1g of it to be converted from the liquid to the gaseous state. This allows for air
temperature near large bodies of water does not change as much. Also, the ocean’s temperature
remains relatively constant. In addition, much heat can be carried from a human body when water
absorbs the heat and evaporates into the air.
Very good Solvent—Water is highly polar, thus it can dissolve many polar molecules . This occurs
because the sides of the water molecules are attracted to the oppositely charged sides of the solute
molecules. Water is thus the solvent of life because many different kinds of polar compound are
dissolved in water based substances like blood, plant sap and cytoplasm.
Water is less dense as a solid than as a liquid. At temperatures lower than 4 degrees celcius, water
forms a crystalline structure because the hydrogen bonds keep the molecules apart. This gives the
molecules more space and thus makes the solid more dense than the liquid. This allows ice to float in
bodies of water. This provides liquid underneath for organisms to live. If it didn’t float, the body of
water would freeze solid.
4
TARGET VI. Each type of macromolecule is composed of specific functional groups. Explain three (or
more) examples of how a functional group determines the structure and function of a particular
macromolecule.
Many answers possible.
TARGET IV. How do buffers regulate the pH of solutions? Provide and explain an example of a biological
buffering system.
Buffers minimize the changes in the concentration of hydrogen and hydroxide ions in a solution by
accepting hydrogen ions from the solution when they are in excess and donating hydrogen ions to
the solution when they have been depleted. In blood, carbonic acid acts as a buffer. Carbonic acid
dissociates to yield a bicarbonate ion and a hydrogen ion. When hydrogen ions are high, (pH
lowered) bicarbonate will accept the H+, raising the pH. Of course, this buffering capacity has
limits.
TARGET V. Distinguish between the three types isomers. How are isomers related to enzymes? How are
isomers related to macromolecules?
Isomers are slightly different shapes. Enzymes typically CANNOT catalyze both isomers because of the
difference in shape. They do not fit the same active site. Cellulose and Starch are isomers, but the same
enzyme cannot breakdown each of them because of the slightly different shape.
5
TARGET VIII. Distinguish between the five types of polysaccharides. Which are produced by plants or by
animals? Which are branched? Why? Which have structural versus energetic functions?
5 Types: Amylose & Amylopectin (make up “starch”), Chitin, Cellulose, Glycogen
Plants: Amylose, Amyloopectin, Cellulose
Animals: Chitin, Glycogen
Structural: Chitin, Cellulose
Branched: Amylopectin and Glycogen-more bonds per area, more energy storage
Energetic: Amylose, Amylopectin, Glycogen
TARGET I. Give an example of a Van der Waals interaction and a hydrogen bond. Which is
stronger/weaker? Which is between polar molecules and non polar? When would it be beneficial for
molecules to have weaker attractions? Give an example. Stronger? Give an example.
Van der Waals interactions are weak and occur only when atoms and molecules are close together
due to electrons not being distributed equally in any molecules. These can be between polar and
non-polar molecules. This is due to differences in electronegativity. Van der Waals forces between
hairs on a gecko’s toe allow for the hairs to together hold the gecko up.
Hydrogen bonds are between a hydrogen atom covalently bonded to one electronegative atom is
also attracted to an electronegative atom of another molecule. These are usually between polar
molecules. The attraction between the positive end of one water molecule and the negative end of
another is an example of this.
Hydrogen bonds are types of Van der Waals forces, but hydrogen bonds are stronger than other
Van der Waals forces like dipole-dipole interactions.
Weak interactions are good in organisms when the connection must be broken and reformed
often. The weaker this attraction, the less energy this will require. The 2 sides of the DNA ladder
are held together by hydrogen bonds. They are often broken in order for DNA to replicate and be
transcribed.
6
TARGET III. Fill in the table below that summarizes the properties of water that contribute to the fitness
of the environment for life:
PROPERTY
EXPLANATION OF PROPERTY
a. Cohesion & Adhesion
Hydrogen bonds hold molecules
together and enable them to
adhere to hydrophilic surfaces.
High Specific Heat
c. Before water can change
temperature, energy must be
used to break or form
hydrogen bonds
d. High Heat of
Vaporization
Hydrogen bonds must be broken
for water to evaporate.
f. Evaporative cooling
Water molecules with high
kinetic energy evaporate;
remaining molecules are cooler.
Ice floats
j. Very good solvent
h. Hydrogen bonds keep water
molecules apart as they
freeze—water less dense as a
solid
k. water is highly polar
EXAMPLE OF BENEFIT TO LIFE
b.Transpiration—water
molecules are drawn up a plant
by cohesion to each other and
adhesion to the xylem (transport
tube) walls
Temperature changes in
environment and organisms are
moderated.
e. Much heat can be released
from humans when sweat
evaporates
g. Evaporation of water from the
leaves of a plant helps keep the
tissues in the leaves from
becoming too warm
i. Bodies of water do not freeze
through—ice stays on top
allowing organisms to live
underneath
Most chemical reactions in life
involve solutes dissolved in water.
TARGET IV. Explain the basis for the pH scale. How do acids and bases directly (or indirectly) affect the
hydrogen ion concentration of a solution? The concentration of hydrogen ions is commonly expressed in
terms of the pH scale. The pH scale measures how acidic or basic a substance is. The pH scale ranges from
0 to 14. A pH of 7 is neutral. A pH less than 7 is acidic. A pH greater than 7 is basic. The pH scale is
logarithmic and as a result, each whole pH value below 7 is ten times more acidic than the next higher
value. For example, pH 4 is ten times more acidic than pH 5 and 100 times (10 times 10) more acidic than
pH 6. The same holds true for pH values above 7, each of which is ten times more alkaline (another way
to say basic) than the next lower whole value. For example, pH 10 is ten times more alkaline than pH 9
and 100 times (10 times 10) more alkaline than pH 8.Low pH corresponds to high hydrogen ion
concentration and vice versa. A substance that when added to water increases the concentration of
hydrogen ions(lowers the pH) is called an acid. A substance that reduces the concentration of hydrogen
ions(raises the pH) is called a base.
TARGET IV. What is the pH of a solution that has a hydrogen ion concentration of 10-3moles/liter?
Would such a solution be acidic or basic? pH of 3 –it is acidic
7
TARGET V. Why is the carbon atom considered the most versatile building block in molecules? What are
some of the ways that the feature of carbon-to-carbon bonds influence the stability and threedimensional structure of organic molecules? Carbon atoms are the smallest element with 4 valence
electrons meaning 4 strong covalent bonds can be formed. These bonds involve the sharing of electrons
and are very stable. The bonds can be single, double, or triple, so there is great diversity to the shape they
can have.
TARGET VII. What types of molecules are formed by dehydration synthesis (also called condensation)
reactions? What types of molecules are formed by hydrolysis? Dehydration synthesis involves
monomers combining to form larger molecules (like monosaccharides forming disachharides or
polysachharides) Hydrolysis involves breaking the macromolecules into their monomers. For example,
breaking a protein down to its amino acids. Dehydration sytnthesis produces water in the process, while
hydrolysis needs water to proceed.
TARGETS V & VIII. Compare the structures and functions of starch, chitin and cellulose; what, in specific,
about the structures of these molecules allows humans to digest starch, but not cellulose? Cellulose is
composed of beta-glucose monomers; starch and glycogen are composed of alpha-glucose. The bond
orientation between the glucose subunits of starch and glycogen allows the polymers to form compact
spirals. The monomers of cellulose and chitin are bonded together in such a way that the molecule is
straight and un-branched. The molecule remains straight because every other glucose is twisted to an
upside-down position compared to the two monomers on each side. The enzymes that digest starch in
humans do not have an active site to match this arrangement.
TARGET IX. What are the two kinds of subunits that make up a fat molecule, and how are they arranged
in the molecule? How do phospholipids and steroids differ from triglycerides? Triglycerides are formed
by combining glycerol with three molecules of fatty acid. The glycerol molecule has three hydroxyl (HO-)
groups. Each fatty acid has a carboxyl group (HOOC-). In triglycerides, the hydroxyl groups of the glycerol
join the carboxyl groups of the fatty acid to form ester bonds. For phospholipids, the structure is similar,
but instead of 3 fatty acids and a glycerol, there are 2 fatty acids and a phosphate group. Steroids are
composed of 4 carbon rings. They are non-polar like the other lipids.
TARGET IX. Describe the differences between a saturated fat and an unsaturated fat; why are saturated
fats considered less healthy to consume? A saturated fat has fatty acid chains that lack carbon double
bonds. These fats are ‘saturated’ with the maximum # of hydrogen atoms per carbon. Unsaturated fats
have fatty acids that have one (monounsaturated) or many (polyunsaturated) double bonds in the chain.
These double bonds cause the fatty acids to be ‘kinky’ (not linear). Saturated fats are used in the
production of LDL cholesterol (low-density lipoproteins). These LDLs are stored in blood vessels
including the arterties of the heart and over time, can harden into plaque that increase blood pressure
and decrease elasticity and diameter of vessels.
TARGET IX. Food labels now include the % of cis and trans fats. Distinguish between these two types of
fats and explain which type should be avoided. Both of these fats are unsaturated. Unsaturated fat is a fat
molecule containing one or more double bonds between the carbon atoms. Since the carbons are doublebonded to each other, there are fewer bonds connected to hydrogen, so there are fewer hydrogen atoms,
hence "unsaturated". Cis and trans are terms that refer to the arrangement of chains of carbon atoms
across the double bond. In the cis arrangement, the chains are on the same side of the double bond,
resulting in a kink. In the trans arrangement, the chains are on opposite sides of the double bond, and the
chain is straight. The process of hydrogenation adds hydrogen atoms to cis-unsaturated fats, eliminating
double bonds and making them into partially or completely saturated fats. However, partial
8
hydrogenation converts a part of cis-isomers into trans-unsaturated fats instead of hydrogenating them
completely. Some neat info about the history(not needed to answer the target, but interesting:
Prior to 1910, dietary fats consisted primarily of butterfat, beef tallow, and lard. During Napoleon’s
reign in France in the early 1800s, a type of margarine was invented to feed the troops using tallow and
buttermilk; it did not gain acceptance in the U.S. In the early 1900s, soybeans began to be imported into
the U.S. as a source of protein; soybean oil was a by-product. What to do with that oil became an issue.
At the same time, there was not enough butterfat available for consumers. The method of
hydrogenating fat and turning a liquid fat into a solid one had been discovered, and now the ingredients
(soybeans) and the “need” (shortage of butter) were there. Later, the means for storage, the
refrigerator, was a factor in trans fat development. The fat industry found that hydrogenated fats
provided some special features to margarines, which, unlike butter, allowed margarine to be taken out
of the refrigerator and immediately spread on a slice of bread. By some minor changes to the chemical
composition of hydrogenated fat, such hydrogenated fat was found to provide superior baking
properties compared to lard. Margarine made from hydrogenated soybean oil began to replace
butterfat. Hydrogenated fat such as Crisco and Spry, sold in England, began to replace lard in the baking
of bread, pies, cookies, and cakes in 1920.[12]
Cis Configuration
Trans Configuration
Trans fats should be avoided as they have been shown to increase risks of coronary artery disease.
TARGET X. What is meant by the primary, secondary, tertiary and quaternary structure of a protein?
Explain how the primary structure of a polypeptide influences its secondary and tertiary structure.
Primary structure of a protein is the straight chain of amino acids. Each amino acid has an amino
group and a carboxyl group as well as a hydrogen and an R group that varies. There are 20 different R
groups, thus 20 amino acids. The order of the amino acids is determined by DNA. Glycine has just a
hydrogen atom in place of an R-group. At physiological pH, some amino acid R-groups are charged,
because of dissociation or association of a proton by, e.g., a carboxyl or amino group. Some side-chain
groups that are uncharged at the near-neutral pH of the cytosol or extracellular space, may dissociate or
gain a proton in the microenvironment of an enzyme active site.
Secondary Structure: Primary structures fold upon themselves. These are usually shapes called a-helix
and beta pleated sheets. In an a-helix, the amino acid R-groups protrude out from the helically coiled
polypeptide backbone. The surface of an a-helix largely consists of the R-groups of amino acid residues
An a-helix is stabilized by hydrogen bonds between backbone amino and carbonyl groups and those in
the next turn of the helix. The hydrogen and oxygen atoms are attracted to one another because the H
atom carries a partial positive charge and the O atom carries a partial negative charge, due to unequal
sharing of electrons in N-H and O=C bonds.
In a b sheet, strands of protein lie adjacent to one another, interacting laterally via H bonds between
backbone carbonyl oxygen and amino H atoms. The strands may be parallel (N-termini of both strands at
the same end) or antiparallel. Because of the tetrahedral nature of carbon bonds, a B-sheet is puckered,
leading to the designation pleated sheet. R groups of amino acids in a b-strand alternately point to one
side or the other of a b-strand. Hence every other amino acid is exposed on one side or the other of a bsheet.
9
Tertiary protein structure refers to the complete three dimensional folding of a protein. Stabilization of
a protein's tertiary structure may involve interactions between amino acids located far apart along the
primary sequence. These may include:



weak interactions such as hydrogen bonds and Van der Waals interactions.
ionic bonds involving negatively charged and positively charged amino acid side-chain groups.
disulfide bonds, covalent linkages that may form as the thiol groups of two cysteine residues are
oxidized to a disulfide: 2 R-SH ® R-S-S-R.
Interactions with the aqueous solvent, known as the hydrophobic effect results in residues with nonpolar side-chains typically being buried in the interior of a protein. Conversely, polar amino acid sidechains tend to on the surface of a protein where they are exposed to the water environment..
Quaternary protein structure refers to the regular association of two or more polypeptide chains to
form a complex. A multi-subunit protein may be composed of two or more identical polypeptides, or it
may include different polypeptides. Quaternary structure tends to be stabilized mainly by weak
interactions between residues exposed on surfaces polypeptides within a complex.
TARGET IX. Describe the differences between a saturated fat and an unsaturated fat; why are saturated
fats considered less healthy to consume?
Saturated fats- no carbon-to-carbon double bonds, straight, no “kinks”, higher melting point, solid at
room temperature
Unsaturated fats- at least one carbon-to-carbon double bond, more “kinks”, lower melting point, liquid at
room temperature
Saturated fats form LDL cholesterol which tend clog arteries. Unsaturated fats form HDL cholesterol
which tend to clear arteries of plaque.
10
TARGETS VII, VI, X. Draw a structural formula of a simple amino acid and identify the carboxyl group,
amino group and R group. Diagram the formation of a dipeptide.
TARGET X, XII. Explain the relationship between the conformation of a protein and its function. What
might disrupt (denature) the conformation of a protein? Give a specific example. All the levels of protein
structure (1o, 2 o, 3 o, 4o ) will determine if the protein performs its proper function. A deviation in ANY
level or protein structure alters the shape and therefore alters the function of the protein.
TARGET VII, IX, X. From this list, identify the carbohydrate, fatty acid, amino acid and polypeptide:
A) +NH3-CHR-COO- ____amino acid______________________
B) C12H22O11 ______carbohydrate__________________
C) (glycine)20 __________polypeptide_____________________
D) CH3(CH2)16COOH _____fatty acid_____________________
TARGETS I, II, & VI. You are studying a cellular enzyme involved in breaking down fatty acids for energy.
Looking at the R groups of the amino acids, what amino acids would you predict to occur in the parts of
the enzyme that interact with the fatty acids? Why might this region of the enzyme need to be
sequestered (hidden) in a pocket rather than on the enzyme’s surface? Enzymes that interact with fatty
acids are probably non-polar & hydrophilic (from figure 5.17) including: glycine, alanine, valine, leucine...
The portion of the enzyme involved in hydrolysis of fatty acids would be sequestered deep within the
protein because of the van der Waals forces and hydrophilic nature of these amino acids in this region
11
TARGET VI. Complete the following table:
Example(s) of
molecules containing
the group
(circle group in a
drawing)
Functional Group
Name of Group
Chemical
properties of the
group
-OH
hydroxyl
polar & hydrophillic
alcohol
-C=O
carbonyl
polar & hydrophillic
monosaccharides:
ketones & aldehydes
-COOH
carboxyl
polar “acid” group
& hydrophillic
amino acids, organic
acids, fatty acids
-NH2
amino
polar & hydrophillic
amino acids, nucleotides
sulfhydryl
polar & hydrophillic
amino acid cysteine –
forms disulfide bridges in
tertiary structure of
proteins
-CH3
methyl
non-polar
(hydrophobic)
hydrocarbons,
methylated (inactive)
DNA
-PO43-
phosphate
polar & hydrophillic
energy molecules
including ATP, ADP, AMP
-SH
12