BIO-002 MT2

What is an enzyme

An enzyme is a protein that acts as a catalyst for ONE specific reaction

How do enzymes catalyze reactions?

Enzymes lower the activation energy required for a reaction by holding their substrate in a way that makes the high energy transition state acquirable at lower energy levels, WITHOUT changing the temperature.
- DONT change the energy of the reactants or the products of the reaction. (i.e. DONT change the temperature of the cell)

Do enzymes form temporary covalent bonds with substrates?

Yes

Are enzymes changed after catalyzing a reaction?

No

What is a metabolic pathway?

A metabolic pathway is a series of reactions in which the products of one are the reactants of the next, where each reaction can be catalyzed by a different enzyme.

Metabolism

All of the chemical reactions that occur in an organism

What are the 2 types of metabolism and how are they different?

Anabolism and Catabolism

Catabolism = Complex -> Simple

* Releases usable energy while some energy is lost as heat
* Energetically favorable (spontaneous)

Anabolism = Simple -> Complex

* Uses energy to create bonds between two molecules
* Energetically unfavorable (nonspontaneous)

What is the second law of thermodynamics?

The entropy of an isolated system always increases

How do cells create order when entropy must always increase?

Cells create order inside themselves by making its environment more disordered leading to an overall increase in entropy in the isolated system (cell + environment)

When cells break chemical bonds some of the energy is captured as \_______ energy while the rest is lost as \__________.

chemical; heat

What is the ultimate/ primary source of energy?

The Sun because plants convert the energy from the sun to chemical energy which animals consume.

Oxidation reactions

Loss of electrons; Gain of Oxygen; Loss of Hydrogen
- Dehydrogenation

Reduction reactions

Gain of electrons; Loss of Oxygen; Gain of Hydrogen
- Hydrogenation ( when molecules pick up electrons, they also pick up H+ or protons from the environment resulting in hydrogenation)
A + e- + H+ -\> AH

Redox reactions

Reactions that involve the transfer of electrons
- Can be a complete transfer of electrons or can exist in a covalent bond where electrons are only partially transferred

Spontaneous Reaction

Reaction in which there is a loss of free energy (ΔG < 0) and once started, proceeds without any additional input of energy.
- Energetically favorable

Nonspontaneous Reaction

Reaction in which there is a gain in free energy (ΔG \> 0) and requires a constant input of energy to proceed.
- Energetically unfavorable

What is the behavior of ΔG throughout a reaction?

ΔG tends to decrease in a reaction until it hits 0 at which the reaction is at equilibrium
- Reactions tend to proceed until reaching equilibrium.

What is metabolic disequilibrium and why is it important?

Metabolic disequilibrium refers to the ability of cells to keep themselves in a state of constant disequilibrium by either removing products or adding reactants. If cells reach equilibrium they will die as there is no input of energy.

Standard free energy change allows what to be calculated? what is the equation used?

Allows the calculation of free energy change for a reaction with different concentrations of product and reactant.

ΔG \= ΔG° + RT ln [Product]/[Reactant]

What is equilibrium constant K?

The ratio of product to reactant concentration for a particular reaction at equilibrium.
- The HIGHER the K, the MORE NEGATIVE ΔG

For reactions with only 1 reactant K \= [product]/[reactant]
For reactions with 2 substrates, K \= [Product]/([reactant_1][reactant_2])

What equation can you use to calculate the concentration of products to reactants at equilibrium for a reaction with only 1 reactant?

ΔG° \= -1.42 log K

- where 1.42 \= RT in kcal/mole
- For every 1.42 kcal/mol diff in free energy, K is changed by a factor of 10.

What are association and disassociation rates equal to?

association rate is equal to the concentration of reactant 1 MULTIPLIED by the concentration of reactant 2 because the reactant molecules must collide in order to react.

The larger the values of K, the \__________ the binding b/w 2 substrates by \___________ bonds.

stronger, noncovalent

At higher value of K, the shape of the 2 substrates are \___________ complementary, because they have \_____________ binding.

more; stronger

The more 2 substrates bind together complementarily, the \___________ negative the value of ΔG for the reaction.

more

Similarly to Hess's Law for Changes in enthalpy, changes in free energy for sequential reactions are \_______________.

additive

How can sequential reactions allow unfavorable reactions to occur?

Unfavorable reactions can occur when there is a favorable reaction right after it that uses the products as its reactants and has a negative enough ΔG that it makes the overall ΔG negative.
- "Siphons" the products of the unfavorable reaction by quickly converting the products of the unfavorable reaction to products of the favorable reaction, making the amount of reactant concentration of the unfavorable reaction always higher than the product concentration, therefore lowering the ΔG of the unfavorable reaction.

What does Enzyme catalyzation rate depend on?

How fast and how often enzyme collides with its substrate
- Increase in substrate concentration increases catalyzation rate
- Increase in temperature increases catalyzation rate

How fast the products form and diffuse away

How is the rate of catalysis of enzymes measured?

Michaelis Constant

What is Vmax?

V max refers to the rate of catalysis by an enzyme at which enzymes are fully saturated with substrate molecules
- No real way to determine this value

What is Michaelis Constant?

KM \= The concentration of substrate at which the enzyme is functioning at half its maximum speed.

Concentration at 1/2 Vmax

What is the relationship between KM and the strength of binding b/w substrate and enzyme?

Large KM \= Weak binding because it take a larger concentration of the substrate to reach half of the enzymes max saturation

Small KM \= Strong binding because it takes less concentration of substrate to reach half of the enzymes max saturation

Enzymes catalyze the forward and backward reactions the same amount

T/F

True

The net distance a molecule travels through the cytosol via diffusion is relatively short in comparison with the total distance it may need to travel. This is because movement governed by diffusion alone is a \__________ process that is most effective for the dispersion of small molecules over short distances.

slow

Seed oils are often dehydrogenated and added back into processed foods. The new fatty acids have an increased number of carbon-carbon double bonds. The dehydrogenation reaction could also be described as a/an \__________ reaction.

Oxidation

When there is an excess of nutrients available in the human body, insulin is released to stimulate the synthesis of glycogen from glucose. This is a specific example of a/an \__________ process, a general process in which larger molecules are made from smaller molecules.

Anabolic

The energy used by the cell to generate specific biological molecules and highly ordered structures is not stored in the form of \______________. (choose all that apply).
- Brownian Movement
- Heat
- Light Waves
- Chemical Bonds

Brownian Movement, Heat, Light Waves

The study of enzymes also includes an examination of how the activity is regulated. Molecules that can act as competitive inhibitors for a specific reaction are often similar in shape and size to the enzyme's substrate. Which variable or variables used to describe enzyme activity will remain the same in the presence and absence of a competitive inhibitor?

Vmax

Chemical reactions carried out by living systems depend on the ability of some organisms to capture and use atoms from nonliving sources in the environment. The specific subset of these reactions that use protein to build muscle is

Anabolic

What is the name of the catalysts used by cells to lower the activation energy of a given reaction?

Enzymes

The equilibrium constant for complex formation between molecules A and B will depend on their relative concentrations, as well as the rates at which the molecules associate and dissociate. The association rate will be larger than the dissociation rate when complex formation is favorable. The energy that drives this process is referred to as \__________ energy.

Binding

Your body extracts energy from the food you ingest by catalyzing reactions that essentially "burn" the food molecules in a stepwise fashion. What is another way to describe this process?

Oxidation

Oxidation is a favorable process in an aerobic environment, which is the reason cells are able to derive energy from the oxidation of macromolecules. Once carbon has been oxidized to \__________, its most stable form, it can only cycle back into the organic portion of the carbon cycle through \__________.

CO2; Photosynthesis

Activated carriers (such as ATP and NADH/NADPH) serve as sources of what for biosynthetic reactions?

Energy and Chemical Groups

Plants can produce O2 from H2O despite it being an unfavorable chemical reaction. How are plants able to do this?

Plants absorb light which provides energy to convert H2O into O2

What is a common method for cells drive a reaction with a positive ΔG?

Couple the reaction to another reaction with a negative ΔG

If the reaction X-\> Y is followed by the sequential energetically favorable reaction Y-\> Z, is the equilibrium constant for the X-\> Y reaction changed? Why or why not?

It is not because the equilibrium concentrations is kept constant since as the Y disappears, more X is converted to Y keeping the concentration ratio of product to reactant constant.

The only chemical reactions that are possible are those that \___________ the disorder of the UNIVERSE

increase

What molecule is often hydrolyzed in an energetically favorable reaction, to power unfavorable reactions?

ATP

What are activated carriers?

Organic molecules that can contain READILY TRANSFERRABLE high energy bonds or high energy electrons, that store chemical energy used to power nonfavorable reactions

Activated carrier activation is an energetically \______________ process that is often coupled with an energetically \______________ process that powers it

unfavorable; favorable
- Such as the oxidation of food molecules.

The most widely used activated carrier is

ATP

ATP hydrolysis can be coupled with a \__________ reaction through 2 steps: activation and condensation.

condensation reaction

1st step:
OH group on the molecule that will undergo condensation is replaced by the phosphate group released upon hydrolysis of ATP

2nd Step:
Phosphoanhydride bond holding the phosphate to the molecule is broken and the energy released is used to replace the phosphate group with some other moelcule.

How is the amino acid glutamate formed?

First, the OH on glutamic acid is replaced with a phosphate group, then the phosphate group is replaced by an NH3 group.

What are the two popular activated carriers that transfer electrons

NADH and NADPH

How do NADH and NADPH differ in structure and function?

NADH and NADPH differ in the presence of a phosphate group, which NADPH has and NADH does not.

NAD+ in the body is used as an oxidizing agent for many catabolic reactions (breaking down food molecules) while NADPH is used as a reducing agent for many anabolic reactions (building molecules)

The cell wants to keep (more/less) of NAD+ than NADH and (more/less) of NADPH than NADP+.

The cell wants to keep MORE of NAD+ and MORE of NADPH

Activated carriers are made up of what 2 parts?

Transferrable group and the handle

What do handles often contain and what is a theory for why this is?

Handles often contain nucleotides and a theory that explains this is that the early catalysts were RNA molecules (ribozymes)

The condensation reaction that connects monomers to make macromolecules is coupled with the hydrolysis of ATP by first converting the monomer to a \________________.

high energy intermediate
- Similar to synthesis of glutamine

Hydrolysis of ATP has approximately what free energy change?

-13 kcal/mol

When the hydrolysis of ATP does not produce enough energy to power an unfavorable reaction, ATP can be hydrolyzed into \_____________ and \___________ instead.

AMP and Pyrophosphate
- The pyrophosphate is then hydrolyzed into two inorganic phosphates.

The hydrolysis of ATP to AMP and Pyrophosphate produces \__________ as much energy as hydrolysis of ATP to ADP and P.

twice

The rule that oxidation reactions release energy and reduction reactions require energy is true of all reactions.
T/F

False. This is only true for cells because the unique environment of cells permits this.

High energy electrons in activated carriers are (tightly/loosely) associated with the atomic nucleus.

loosely, because they are readily transferable

Are all biological enzymes proteins?

No

Vmax (is/is not) changed in the presence of competitive inhibitors and (is/is not) changed in the presence of noncompetitive inhibitors

is not; is

What is the difference between competitive and noncompetitive inhibition?

Noncompetitive inhibition cannot be overcome by increasing substrate concentration while competitive inhibition can be.

Changes in Free energy are\_______

additive

Biosynthesis

Energy requiring reactions -\> building molecules ("synthesis)

Which of the following are possible functions of plasma membrane proteins?

All of these are true.
Transporters
Anchors
Receptors
Enzymes

All of these are true.

A prokaryotic organism is isolated from a glacier, where it was thriving. Based on your knowledge of the plasma membrane, you would expect to find a predominance of

- largely saturated fatty acids.
- cell wall to define the cell because the cell membrane would not be present.
- largely unsaturated fatty acids.
- equal amounts of saturated and unsaturated fatty acids, as long as the chain was close to 12 carbons in length.
- none of the above
- excessive amounts of cholesterol

largely unsaturated fatty acids

Which of the following molecules would not readily cross an intact cell membrane by simple diffusion, but would require a facilitator protein?

oxygen
water
thyroid hormone
glucose
fatty acids

Glucose

THINK BEYOND: A colleague gives you two membrane fractions from a plant cell lysate. One contains the plasma membrane fraction, the other the mitochondrial fraction. The tubes are not labeled, but you run the samples anyway, looking at the macromolecule composition of the samples. You know for certain that the second sample contains the mitochondrial fraction simply because it contains insignificant amounts of,

carbohydrates.
specifically phospholipids.
lipids.
protein.
None of the above

Carbohydrates

Membranes contain several classes of lipids, such as phospholipids, sphingolipids, sterols, etc. In spite of their many differences, they all

easily react with bases but not with acids.
can be easily hydrolyzed.
are readily soluble in water at 37C.
are soluble in nonpolar solvents.
can be reduced by strong reducing agents such as sodium.

are soluble in nonpolar solvents

Which of the following is the most common phospholipid in cell membranes?

Phosphatidylcholine
Phosphatidylethanolamine
Phosphatidylinositol
Phosphatidylserine
None of the above

Phosphatidylcholine

Evaluate the ways in which proteins work to keep a membrane selectively permeable.

- All of the these are true
- Many membrane bound proteins are transporters, each with a specific mechanism to allow for entrance of a molecule into the cell
- Many membrane bound proteins are channels, each with a hydrophobic pore across the membrane which allows for diffusion across the membrane
- Certain cells can immobilize certain membrane proteins by attaching them to intracellular or extracellular macro molecules
- The attached sugar chains on some proteins that are attached to lipids not only act to lubricate the cells, but are also involved in cell-cell recognitions

All of these are true

Cell-cell communication in plants takes place via specialized structures called

cell wall pores.
desmids.
gap junctions.
connexons.
plasmodesmata.

plasmodesmata

The most common number of carbons in fatty acid hydrocarbon chains of membrane phospholipids is: (closest answer)

16.
1.
4.
27.
10.

16

Which of the following statements is false regarding the protein Bacteriorhodopsin?

- Bacteriorhodopsin is a very large protein.
- Bacteriorhodopsin acts as a proton pump.
- The polypeptide chain crosses the lipid bilayer at 7 alpha helices.
- This protein contains polar amino acid side chains at strategic locations to help guide the movement of the proton.
- This protein is found in the plasma membrane of Halobacterium halobium, which lives in salt marshes.

Bacteriohodopsin is a very large protein

TECHNIQUE: Inactivation of a fluorescent dye in a very concentrated spot on a cell so that the fluidity of membranes can be subsequently visualized is called,

liposome formation.
ferritin-conjugated lectins.
the freeze-fracture technique.
SDS-PAGE.
photobleaching.

photobleaching

Two cells with different cell-surface markers are fused in the presence of polyethylene glycol (PEG). The cells are then placed at 0°C. What do you expect to observe about the individual cell markers?

- Only one marker will disperse, while the other remains stationary.
- The markers will be endocytosed by the fused cell and then redistributed as fused markers.
- The markers will evenly disperse throughout both membranes.
- Both sets of markers will not mix but will migrate to opposite poles from one another.
- The markers will essentially remain where they are, with little migration.

The markers will essentially remain where they are with little migration

A glycolipid molecule may do which of the following?

Lateral diffusion on the plane of the membrane
Flexion of its fatty acid tails
Rotation about its axis
All of the these
None of the these

All of these

Localized regions of membrane lipids that contain proteins involved in cell signaling are known as,
\[These are also known by other names too]

homeoviscous adaptations.
membrane leaflets.
islands of hydropathy.
hopanoids.
lipid rafts.

Lipid rafts

The flexibility of the membrane and its capacity for expansion allow the cell to do which of the following?

All of the these
None of the these
Grow
Change shape
Move

All of these

(Q002) Which of the following functions of the plasma membrane is possible without membrane proteins?

intercellular communication
selective permeability
cellular movement
import/export of molecules

selective permeability

Since the cell membrane is packed with lipids, in order for nutrients to cross the membrane and reach the cytoplasm, what kinds of macromolecules facilitate such processes that are located in the membrane?

- Transporter proteins.
- Water molecules bound to nutrients through hydrogen bonds.
- Glucose molecules that provide the energy for transportation.

Transporter proteins

(Q015) Which of the following would yield the most highly mobile phospholipid (listed as number of carbons and number of double bonds, respectively)?

24 carbons with one double bond
15 carbons with two double bonds
20 carbons with two double bonds
16 carbons with no double bonds

15 carbons with two double bonds

(Q034) Which mechanism best describes the process by which an antigen-presenting cell triggers an adaptive immune response?

Proteins are tethered to the cell cortex.
Proteins are tethered to the extracellular matrix.
Proteins interact with the proteins on the surface of another cell.
Protein movement is limited by the presence of a diffusion barrier.

Proteins interact with the proteins on the surface of another cell

(Q006) Which of the following statements is TRUE?

Phospholipids will spontaneously form liposomes in nonpolar solvents.
In eukaryotes, all membrane-enclosed organelles are surrounded by one lipid bilayer.
Membrane lipids diffuse within the plane of the membrane.
Membrane lipids frequently flip-flop between one monolayer and the other.

Membrane lipids diffuse within the plane of the membrane.

Which of the following molecules would enter the cell only via a specialized transmembrane receptor?

ethanol
cholesterol
carbon dioxide
fatty acids
water

ethanol

Many integral membrane proteins have not been analyzed by X-ray crystallography.However, transmembrane segments can be inferred using computer analysis of the aminoacid sequence of the protein. This technique is known as

lipid rafting.
lipid analysis.
SDS-PAGE.
hydropathic analysis.
homeoviscous adaptation.

hydropathic analysis

Of the following lipids, which is found in approximately equal amounts in both the outer and inner portions of the lipid bilayer?
\[Review Figures in your textbook]

glycolipid
phosphatidylserine
phophatidylethanolamine
cholesterol
phophatidylinositol

cholesterol

With respect to the outer and inner faces of the lipid bilayer of the cell membrane, the composition of proteins is, [Kaltura Video segment explains all]

highly random and varies throughout the cell.
a mirror image.
identical.
asymmetrical.
not identical but symmetrical.

asymmetrical

Which of the following are ways in which protein lateral mobility can be restricted in the plasma membrane?
\[Multiple answers]

Proteins can be tethered to the cell cortex inside the cell.
Proteins can be tethered to the extracellular matrix molecules outside the cell.
Proteins can be tethered to proteins on the surface of another cell.
Diffusion barriers can restrict proteins to a particular membrane domain.
None of the above

Proteins can be tethered to the cell cortex inside the cell.
Proteins can be tethered to the extracellular matrix molecules outside the cell.
Proteins can be tethered to proteins on the surface of another cell.
Diffusion barriers can restrict proteins to a particular membrane domain.

The likely number of and locations of transmembrane segments of integral membrane proteins is inferred by

hydropathic analysis.
western blot.
affinity labeling.
X-ray crystallography.
SDS-PAGE.

hydropathic analysis

Which of the following molecules would not readily cross an intact cell membrane by simple diffusion, but would require a facilitator protein?
oxygen
water
thyroid hormone
glucose
fatty acids

glucose

Starting with shredded spinach leaves, you follow a procedure that allows for separation of cellular organelles. You are specifically looking for the fraction that contains the mitochondria. To identify this fraction, you should test for the

phospholipids unique to the mitochondrial membrane.
polysaccharides that specifically surround the mitochondria.
phospholipids unique to intracellular membranes.
presence of enzymes associated with cellular respiration.
general presence of enzymes that fix carbon.

presence of enzymes associated with cellular respiration.

A prokaryotic organism is isolated from a hydrothermal vent, where it has been observed to be thriving. Based on your knowledge of the plasma membrane, what would you not expect to find
Long-tail fatty acids.
Saturated fatty acids.
cholesterol.
fatty acids with polar heads.
none of the these answers

Cholesterol

Which of the following is a major class of membrane lipid molecules?
All of the these.
phospholipids
sterols
glycolipids
None of the above

All of these