Download 22. Think of two different proteins: both are enzymes. a) What

22. Think of two different proteins: both are enzymes.
a) What landmark (feature) of conformation (overall structure) will be found in both enzymes?
(Name it and tell its function).
Active sites for binding substrates to catalyze chemical reactions.
b) If one of the enzymes is an allosteric protein, what structural feature will it have that the
other protein does not have?
Allosteric protein has a second binding site for an allosteric effector that binds noncovalently.
(Regulatory site)
c) What type of regulation of protein activity is similar to allosteric control?
Phosphorylation/Dephosphorylation: requires donor of phosphate group (ATP=P1+energy)
d) What is the main difference between the mechanism in c) and allosteric control?
Two enzymes are needed to regulate for covalent binding in phosphorylation/de. and no
enzymes are used for non covalent allosteric binding
23. a) Cells must regulate all functions (chemical, transport, mechanical). Proteins carry out
most functions. Overall, how can protein function be controlled in cells (this is not about
allosteric vs. phosphorylation yet, but more general)?
b) If protein activity is controlled, what are two very common choices (just their names)?
c) Mark each description in the following list with A for allosteric regulation and/or P for
regulation by phosphorylation/dephosphorylation. Mark N if it doesn’t apply to either:
·
A depends on the concentration of the effector
·
P requires an enzyme to activate or inactivate the protein
·
N uses a single enzyme for activation and inactivation of the protein
·
A involves non-covalent bonding of regulating a molecule a
·
P involves covalent bonding (which always requires enzymes)
·
N is always positive (always activating)
·
AP involve binding of something to a site different from the functional (active) site
·
AP both cause conformational changes in the protein affecting the functional (active) site
24. Answer the questions below with reference to the following diagram, which represents
energy levels relative to molecules X and Y.
a) Which energy difference (a-f) represents the free energy change for the reaction X-->Y?
E (from where x starts to where y flat lines)
b) Which energy difference represents the activation energy for the uncatalyzed reaction?
F
c) Which energy difference represents the activation energy for the catalyzed reaction?
A
25. a) Why does a molecule such as ATP remain ATP, and not spontaneously break down to
ADP and phosphate, even though such a reaction would release energy? (What does it take
to get it to react?)
A molecule like ATP is chemically stable in that it requires energy to be able to react.
b) How do enzymes increase rates of chemical reactions, from immeasurably slow to
extremely fast?
Enzymes binding to substrate provides a reaction mechanism that has a lower requirement for
activation energy compared to an uncatalyzed reaction.
26. Why do enzyme-catalyzed reactions have saturation kinetics, where the rate of the
process reaches a maximum and levels off with increasing substrate concentration?
Reaction increases with substrate concentration, but any more substrate added has to wait
in line to get in to the active site of the enzyme for the one on one interaction between the
protein and its ligand. The v max is reached because the enzymes are full due to the time that
it takes the enzyme to react with the substrate.
27. a) What is the general meaning of the phrase "optimum conditions"?
Optimum conditions generally mean conditions that provide the maximum function of the
system.
b) Why do enzymes have optimum conditions of pH, temperature, and salt concentration?
Enzymes are proteins whose working conformations are held by noncovalent bonds
Changes in pH, temperature or [salt] can disrupt these bonds, reducing activity of the
Enzyme. Optimum conditions come from the best the working conformation disrupting the
best working conformation disrupts the activity of the enzyme. Optimum conditions provides
the specific environment that maintains the working conformation of the protein allowing the
enzyme to have the maximum function.
28. a) Diagram the basic lipid structure of a cell membrane.
0= =0
0= =0
0= =0
b) Describe the specific bonds or interactions, including molecules or parts of molecules
involved that hold a phospholipid bilayer together.
Hydrophilic head faces water to single phospholipid either faces inside the cell or outside
And has hydrogen-ionic bonds to water. Hydrophobic tail faces another phospholipid’s
Tail inside the membrane or the middle and is held by hydrophobic forces to the other tails.
29. a) Define diffusion.
Diffusion is the movement of any substance from an area of higher concentration to an area
of Lower concentration.
b) Define osmosis.
Diffusion of water across a semi-permeable membrane.
c) With regard to membrane transport, what characteristics do simple diffusion and facilitated
diffusion have in common?
Both are passive transport which means energy is released both are going down the
concentration gradient.
d) How do simple diffusion and facilitated diffusion differ?
Simple diffusion requires no protein and facilitated diffusion requires a transport protein
e) With regard to membrane transport, what characteristics do facilitated diffusion and active
transport have in common?
Both require transport proteins
f) How do facilitated diffusion and active transport differ?
Facilitated diffusion releases energy and active transport moves substances in the opposite
Direction of diffusion and thus requires energy.
g) List two substances commonly transported by each of the three types of movement across
membranes: simple diffusion, facilitated diffusion, and active transport.
simple: gases
facilitated: amino acids/ glucose
active: ions (sodium, potassium, calcium)
30. a) What are the relative concentrations of sodium (Na+) and potassium (K+) ions inside
and outside of animal cells?
There is a double concentration: [Na+] > outside than [Na+] inside. [K+] > inside than [K+]
outside.
b) How does the cell maintain these different concentrations?
Na+/K+ pump (sodium potassium pump) (ATPase), a simple protein complex pulls K+ into the
cell and pushes Na+ out the cell.
31. a) What is the difference between a chemical reaction and a metabolic pathway?
Chemical RXN= process where a reactant changes in to a product. Substance changes to
another.
Metabolic pathway= sequence of connected chemical RXN where the product
Of one reaction becomes the reactant of the next reaction. Serious of chemical rxns that are
connected where the product of one is the reactant of another.
b) Give an example of a catabolic pathway by naming the starting molecule and end
product. Do the same for an anabolic pathway.
Catabolic pathways are food molecule breakdown processes that release energy
Overall. Anabolic pathways are biosynthesis and requires energy overall.
catabolic pathway: food breakdown; glucose --> CO2 (respiration overall)
anabolic pathway: biosynthesis; acetate ---> fatty acid
photosynthesis: CO2 ----> glucose
c) What is the term that describes the molecules between starting molecule and end product
in a metabolic pathway?
Intermediates
32. a) In the following reaction, ATP synthesis is coupled to the conversion of R-P to R.
ADP ATP
R-P R
If the coupling is direct, how many enzymes and how many steps are required, and how is
coupling accomplished?
One enzyme is required and it takes one step. The enzyme has R and ATP has substrates
Binding them at the same time and taking P from ATP and putting it on R. It takes the P from
the R and binds it to ATP.
b) What would it mean if the coupling of the two reactions in a) were indirect?
This means that the two reactions are not physically linked. They may not occur
In the same space and they maybe separate by one or more steps.
c) Explain the differences between the energy coupling that goes on for respiration overall
(C6H12O6 + 6O2 6 CO2 + 6H20 coupled to 36 ADP + 36 Pi --> 36 ATP) and the energy coupling
that goes on when Glucose + ATP --> Glucose-P + ADP is catalyzed by hexokinase. (Give a
name to the type of coupling in each case, and explain what that means.)
Indirect coupling and it doesn’t happen in the same place and one or more steps.
Direct coupling hexokinase bindes glucose and atp to make adp in the same place.
33. The reaction below is an oxidation-reduction reaction:
AH + B ----> A + BH
a) If it is an oxidation-reduction, why are no electrons shown (or are they)?
H is carrying the electron we are following
b) Which molecule gets reduced, and which gets oxidized, and how can you tell?
B is being reduced because it is gaining an electron from h, A is being oxidized because it is
losing the hydrogen electron
c) Suppose the redox coupling is not direct. Using NAD as the electron carrier, write the two
reactions (simplified) needed to get to the products shown above.
AH + NAD --> A + NADH
B + NADH --> BH + NAD
d) Explain (in terms of chemical characteristics of the molecules involved) how both reactions
in c) could release energy (without any energy assistance, e.g. from ATP).
NAD's (electron acceptor) electronegativity is greater than the electronegativity of electron
donor A
34. Glucose + 6 Oxygen ---> 6 Carbon dioxide + 6 Water is the overall reaction of respiration,
and is an oxidation-reduction.
a) Which atoms in which molecules get reduced and which get oxidized in the reaction and
why is energy released overall?
Carbons in glucose are being oxidized and oxygen is being reduced. Oxygen has higher
electronegativity than carbon so when carbon gives its electrons to oxygen there is a release
of energy.
b) Can you think of a way to easily demonstrate that respiration overall releases energy?
Burning of paper which contains glucose and oxygen to be available to demonstrate energy
being released In the form of heat and light.
35. Glucose + 6 Oxygen ---> 6 Carbon dioxide + 6 Water
a) Break the above overall reaction down into 3 overall “third reactions” that occur in the 3
parts of cellular respiration: Glycolysis, Citric Acid Cycle, Oxidative phosphorylation. Add one
molecule that is needed to write 3 reactions. (Assume the CAC begins with the product of
glycolysis.) Equations do not need to be balanced, and electron carriers and ATP do not
need to be included.
Glycolysis= glucosepyruvate
Citrus acid cycle= pyruvateCarbon dioxide
Oxidative phosphorylation= Oxygenwater
b) Name the exact cell location of each of the 3 processes.
Glycolysis= cytosol.
Citrus acid cycle=mitochondrial matrix.
Oxidative phosphorylation= inner mitochondrial membrane
c) For each of the processes, tell which of the following compounds is produced (net): ADP,
ATP, NAD, NADH
Glycolysis=ATP, NADH
Citrus acid cycle= NADH, ATP
Oxidative phosphorylation= ATP, NAD
d) At the end of a complete round of all 3 processes above, which of the following
compounds has the cell netted: ADP, ATP, NAD, NADH?
ATP
36. a)Is fermentation part of respiration or a complete alternative? Explain your answer.
Fermentation is an anaerobic energy-yielding pathway and therefore is an alternative to
respiration, which uptakes molecular oxygen to be coupled with the production of carbon
dioxide. Fermentation uses glycolysis in the beginning process which is part of respiration but
a few steps are just added to it.
b) In what conditions, and why, do cells do fermentation?
For anaerobic organisms, which do not use molecular oxygen and can grow and divide
without it, glycolysis is the principal source of the cell's ATP. So, fermentations allow ATP to
be produced in the absence of oxygen. Fermentation is done to produce ATP since cells need it
to survive.
c) In fermentation, what function is served by conversion of pyruvate to lactate?
The pyruvate is converted into products that are excreted from the cell, lactate
in muscle. In this process, the NADH gives up its electrons and is converted back
to NAD+. The regeneration of NAD+ is required to continue the reactions of
glycolysis.
37. What do NAD, ATP and Coenzyme A have in common, in terms of structure and function?
Coenzyme A is similar to ATP and NAD in that it carries small packages and is an
adenine nucleotide derivative.
38. Explain why the following statement is true or false: Energy capture from carbohydrate
Catabolism occurs in totally different pathways than energy capture from lipid catabolism.
False. Carbohydrate and lipid catabolism start in separate pathways but both uses citric
Acid cycle and oxidative phosphorylation to generate ATP.
39. Answer the following questions with regard to oxidative phosphorylation:
a) What is the first donor of electrons to the electron transport chain?
NADH
b) What is the last recipient of electrons from the electron transport chain?
Oxygen
c) What gradient (what chemical substance, across which membrane) is produced as a
result of electron transport?
A proton gradient across the inner mitochondria membrane is produced as a result of
electron transport.
d) What does the gradient in c) do for the cell, and what is the process/mechanism?
The energy releases by the electron transport is used to pump protons across the
membrane, creating a concentration gradient. The process involved is diffusion. Provides
energy to make ATP. ATP synthase is a diffusion channel for protons. The protons are going to diffuse
to cause it to make ATP.
40. a) When oxygen is present, purified mitochondria cause the pH of the medium in which
they are suspended to decrease. What mechanism or model is supported by this observation,
and what part of #39 does it relate to?
When the pH level of the medium goes down when oxygen is present, it shows that
mitochondria release protons. This supports the chemiosmotic mechanism (the link between
electron transport and ATP synthesis= proton gradient). It helps to demonstrate the
movement of protons across membranes.
b) Mitochondrial vesicles (submitochondrial particles) can make ATP in the absence of
oxygen, pyruvate and NADH. What, in addition to ADP + inorganic phosphate, is required for
them to make ATP? What mechanism is supported by this observation, and what part of #39
does it relate to?
Acid(low pH solution) must be put in the medium (outside the vesicles). The energy released
during electron transport is used to create a proton gradient across the inner mitochondrial
membrane. (The experiment uses an artificial protein gradient to demonstrate its role in the
mechanism of ATP synthesis in respiration. It supports the chemiosmotic mechanism which is
c in number 39.
41. Enz1 Enz2 Enz3 Enz4
A-------> B---------> C--------> D---------->E
a) Explain what feedback inhibition means by referring to the metabolic pathway shown.
The end product E shuts down (inhibits) the first step in the pathway of (A->B).
b) If the mechanism of feedback inhibition is allosteric regulation, how does it work (what does
the effector do, and what is the result)?
42.
Enz1
Enz2
Enz3
Enz4
A-------> B---------> C--------> D---------->E
Enz5
Enz6
Enz7
--------> L -----------> M---------> N
(Draw in a line diagonally from B to the arrow going to L).
If feedback inhibition occurs in the above metabolic pathway, list the two most likely enzymes
affected, and the molecules most likely to control them.
Both molecules (E & N) in this case are negative effectors/allosteric inhibitors.
Molecule N will inhibit Enz5, but because Enz1 is more of a secondary step,
molecule E will have the most effect on Enz2 because it is the first step in the
pathway that is unique.
43. PFK is an enzyme that catalyzes an early step in glycolysis.
a) Name the molecule that is a negative effector/allosteric inhibitor of PFK.
ATP is a negative effector/allosteric inhibitor of PFK
b) Name the molecule that is a positive effector/allosteric activator of PFK.
ADP is a positive effector/ allosteric activator of PFK.
c) Describe one way, and a specific case (it involves allosteric regulation), that cells use to “measure”
relative amounts of ATP and ADP present.
Since ATP is a negative effector/allosteric inhibitor of PFK and ADP is a positive effector/
allosteric activator of PFK. A cell's energy quotient is the ratio of ATP to ADP. Glycolysis one a
specific case where the end product is ATP and by inhibiting PFK, ATP provides feedback
inhibition of respiration. Glycolysis is the beginning of respiration. The end product of
respiration is ATP. Once ATP has been made it returns to the beginning of the glycolysis to stop
production of more ATP.