LS 2 Midterm 1 Questions

Which of the following describes what you would expect to observe in cells treated with a compound that prevents the recognition of signal sequence by SRP?

An accumulation of insulin in the cytosol

Why do cells need membranes?

Distinguish itself from surroundings, be selective about what gets in/out, keep internal environment constant

Which of the following reactions would you predict could be coupled to ATP synthesis from ADP + Pi? Choose all that apply. 1. phosphoenolpyruvate + H2O ? Pyruvate + Pi, delta G -14.8 kcal/mol 2. glutamic acid + NH3 ? glutamine, delta G +3.4 kcal/mol 3. creatine phosphate + H2O ? creatine + Pi, delta G -10.3 kcal/mol 4. glucose 6-phosphate + H2O ? glucose + Pi, delta G -3.3 kcal/mol 5. glucose 1-phosphate + H2O ? glucose + Pi, delta G -5.0 kcal/mol

#1 and #3; If the hydrolysis of ATP into ADP + Pi releases 7.3 kcal/mol of energy, then the reverse reaction (synthesizing ATP from ADP + Pi) will require 7.3 kcal/mol of energy. This reaction is endergonic and therefore will need to be coupled to an exergonic reaction that has a change in free energy that is less than -7.3 kcal/mol in order for the coupled reaction to have an overall negative change in free energy.

What is the formula for the change in potential energy?

(total energy of bonds broken) - (total energy of bonds formed)

Enzymes accelerate the rxn of a substrate by...(3 things)

1. Aligning two substrates closely together 2. Donation/removal of electrons 3. Stressing the substrate

How, when, or where are enzymes regulated?

1. Cells regulate when/where enzymes function (for example if enough ATP is supplied the different complexes in cellular respiration will tell one another to stop) 2. External factors like drugs can activate/inhibit enzyme function

The overall reaction rate of a catalyzed reaction is determined by what two things?

1. How quickly the enzyme and substrate "find" each other 2. How fast the active site can catalyze the rxn and lower the activation energy

What's actually going on at the enzyme's active site for a rxn coupling? (3 steps)

1. Phosphate group removed from ATP in an exergonic reaction, releasing energy 2. Substrate gets "activated" upon addition of phosphate group 3. Phosphate group is removed from activated substrate to complete the rxn ---> ADP-P, A+B // A + B-P + ADP // A-B + P + ADP

What are the two ways in which an endergonic reaction may become favorable?

1. Reaction coupling to a more exergonic rxn (to make delta G negative) 2. Changing the concentration/ratio of reactants vs. products

How an enzyme aids a reaction...(4 steps)

1. enzyme and substrate are available 2. Substrate binds to enzyme, forming enzyme-substrate complex (enzyme normally forms non-covalent bonds with substrate) 3. Substrate is converted into products (often with addition of H2O) 4. Products are released and enzyme is ready for new substrate

Which of the following is TRUE of lysosomes? (Select all that apply.) 1. The pH is often higher inside the lysosome than in the cytoplasm. 2. Lysosomes fuse with other vesicles that contain macromolecules targeted for breakdown. 3. Lysosomal membranes often contain proteins that transport amino acids, simple sugars, and nucleotides. 4. Proton pumps are sometimes found in the lysosomal membranes. 5. The concentration of protons in the lysosome is often higher than in the cytoplasm.

2, 4, and 5

Imagine that you are investigating the production of insulin in normal cells. You are using these cells to help determine the cause of faulty insulin production in other cells where insulin appears to be synthesized but fails to be secreted from the cell. You design an experiment using a pharmaceutical compound that blocks the SRP release from the ribosome and mRNA. Which of the following describes what you would expect to observe in cells treated with the inhibitor of SRP release from the ribosome and mRNA? 1. an accumulation of insulin at the plasma membrane 2. a lack of insulin in the cell 3. an accumulation of insulin in the cytosol 4. an accumulation of insulin in the cytosol

2; a lack of insulin in the cell

Which of the following statements violates the first law of thermodynamics? 1. Endergonic reactions store energy. 2. The conversion of energy from one form to another is 100% efficient. 3. The universe contains a constant amount of energy. 4. Cells make energy when they produce ATP.

4; The first law of thermodynamics states that energy cannot be created or destroyed; therefore, cells do not "make" energy when they produce ATP, but rather take one form of energy and convert it into a type of energy that may be used by the cell (in this case, ATP).

Which of the following sequences of events correctly describes the progress of a protein that will be secreted from the cell? 1. SRP binds to the growing polypeptide chain and to the ribosome. 2. Translation resumes. 3. SRP binds to its receptor. 4. The signal sequence is cleaved. 5. Protein synthesis begins in the cytosol. 6. Translation pauses.

5 → 1 → 6 → 3 → 2 → 4

I-Cell Disease is a genetic condition that leads to incorrect protein sorting. Proteins destined for the lysosome are instead secreted from the cell. Which of the following protein defects would most likely cause this problem?

A defective enzyme in the Golgi

Weak covalent bonds, such as ones in carbohydrates and lipids, have:

A lot of potential energy

Insulin is a secreted protein. Which of the following describes what you would expect to observe in cells treated with an inhibitor of transport vesicle formation?

An accumulation of insulin in the ER

What happens to the reaction rate at very high substrate concentrations?

All of the enzymes are bound to substrate. (and thus the reaction rate plateaus)

If a mutation rendered the signal recognition particle nonfunctional, what would be the most obvious effect on the cell?

All proteins normally secreted by the cell would remain in the cytosol.

Secondary structure

Alpha helix (hydrogen bonds between the backbone atoms of amino acids) and beta sheets (side by side carbon chains with hydrogen bonds on opposing amino acids)

Breaking a chemical bond... (Always requires energy, never requires energy, or depends)

Always requires energy

When delta G = 0, the rate of reaction is...

Both reactions are occurring at roughly the same rate

If ∆G of ATP to ADP conversion is -7.3 kCal/mole, what could be the ∆G of combining HCO3 and Acetyl CoA? a. -8.0 kCal/mole b. -7.0 kCal/mole c. +7.0 kCal/mole d. +8.0kCal/mole

C

Which one of the following molecules would MOST likely require a transport protein to cross the plasma membrane of a red blood cell?

C6H12O6

What would happen if glucose carriers were present on both surfaces of the intestine cell?

Carrier A and Carrier B would move glucose out of the intestine cell.

What does a cell need?

Communication with its environment, organization/transportation of cellular components, a barrier between itself and its surroundings, waste removal, movement (some cells) ---->a way to capture, store, and use energy

What is the most precise general description of the role of enzymes in catalyzing biochemical reactions?

Enzymes stabilize the transition state by decreasing its free energy.

Why doesn't ATP spontaneously hydrolyze in the cell?

Even though the hydrolysis of ATP has a negative delta G, the rxn has an activation energy, or a certain energy barrier must be overcome in order to drive the reaction forward (thermodynamics vs. kinetics)

Consider the reversible formation of carbonic acid: CO2 + H2O = H2CO3, delta Gnaught = -2 kcal/mol, RT = 0.6 Which reaction (forward or reverse) will be exergonic when the concentration of reactants is 100x higher than the concentration of products?

Forward

Given a sodium/potassium pump, K+ ions should be _______inside the cell as outside

Higher (to minimize the concentration of Na+)

Tertiary structure

Hydrophobic chains wrapped inside to protect from surrounding water (has to do with 3D shape of protein, which determines function)

How to distinguish hypotonic and hypertonic

HypOtonic makes an O, or will swell; hypertonic will not swell, or will shrivel

Way of memorizing Anabolic v. Catabolic rxns

I have two friends, Ana and Cat. Ana goes to 'SC and Cat is a CS major.

To initiate translation of mRNA into protein, a ribosome must first locate and bind to an mRNA transcript. Where in the cell does this initial ribosome-mRNA binding take place?

In the cytosol; Binding occurs in the cytosol. If a signal peptide is synthesized, then the ribosome/mRNA complex relocates.

A car engine transforms fuel (chemical energy) into mechanical energy (movement to drive the car). But not even the most efficient can transform 100% of the fuel energy into movement. What happens to the rest of the fuel energy?

It is transformed into another form of energy entirely

If membrane fluidity needs to be maintained, which of the following would be most important in an animal cell as a response to a decrease in temperature?

Introducing more double bonds into the fatty acid chains in the phospholipid bilayer.

How does cholesterol affect membrane fluidity?

It increases fluidity at low temperatures and decreases fluidity at physiological temperatures

Imagine a cell with equal concentrations of oxygen inside and outside of the cell at 10 micromolar. You observe the cell for a few minutes. How will the free energy change within this time frame?

It will not change since the concentration of oxygen is already in equilibrium

What would happen to the surface area of the cell if you blocked exocytosis but allowed endocytosis?

It would decrease

Cells can internalize and secrete material through the processes of endocytosis and exocytosis, respectively. As shown in the figure below, endocytosis involves the formation of vesicles at the cell membrane and exocytosis involves the fusion of vesicles with the cell membrane. What would happen to the surface area of a cell if you blocked exocytosis but allowed endocytosis?

It would decrease; Every time a vesicle fuses with the cell membrane via exocytosis, lipids are added and the surface area increases a tiny bit. Every time a vesicle forms from the cell membrane via endocytosis, lipids are removed and the surface area decreases a tiny bit. Only allowing endocytosis would cause the surface area of the cell membrane to become smaller over time.

If lysosome proteins are sorted incorrectly, what do you expect to observe in the cells affected by I-Cell Disease?

Larger-than-usual lysosomes

Enzymes and Reaction Rates have a ____________ relationship

Linear

Primary Structure

Linear sequence of amino acids that make DNA; amino acids are bonded w/ polypeptide bonds; protein backbone = carbon chain; H2O molecules are released each time a bond is formed.

When is the entropy of a system the lowest? The highest?

Lowest when there is the most order (least disorder); the highest when there is the least order (most disorder)

Fick's first Law of Diffusion

Net movement = DA (C2-C1)/X

Consider two chambers of equal volumes. The chambers are separated by a selectively permeable membrane that only allows water through. The concentration of solute is higher on the right than on the left. What will happen to the water molecules?

Net movement to the right.

Are enzymes "all or nothing"? Meaning, do they only work at specific temperatures/pHs?

No; Enzyme activity is not "all-or-nothing" and enzymes can catalyze their respective reactions at varying temperatures. However, it must be said that with varying temperature comes varying rate of reaction, so their may be an "ideal temperature" where the enzyme catalyzes the reaction the most quickly.

In a metabolic pathway, a series of enzymatic reactions catalyzes the conversion of molecule A to molecule E. Several intermediate steps are involved in which the product of one reaction becomes the substrate for the next. If given a graph illustrating the free energy of the each intermediate at each point in the reaction, can you determine which step will be the fastest?

No; The rate of the reaction is related to the activation energy, which will depend on the activity of the enzymes responsible for catalyzing each step in the pathway.

Does the size of the molecules on either side of the membrane matter?

No; even if the solute molecules are larger on one side of the membrane, is the concentration of solute is higher on the other side, the net movement will still be to the right.

What happens when the O2 concentration is the same inside and outside of the cell?

O2 will enter and leave at roughly the same rate

What is the difference between diffusion and osmosis?

Osmosis refers specifically to the movement of water, whereas diffusion is the movement of any molecules

Which one of the following statements BEST represents the relationship between cellular respiration and photosynthesis?

Photosynthesis stores energy in organic molecules, while respiration releases it.

Electrons from water are transported through the photosystems and photosynthetic electron transport chain and are ultimately used to reduce NADP⁺ to NADPH. At what point do the electrons have the greatest amount of potential energy?

Photosystem I

What variable could we change in the Van't Hoff equation to transform an endergonic process into an exergonic process?

Q

What will happen to the reaction rate when the substrate concentration is much lower?

Reaction rate will decrease

Consider the reversible formation of carbonic acid: CO2 + H2O = H2CO3, delta Gnaught = -2 kcal/mol, RT = 0.6 Which reaction (forward or reverse) will be exergonic when the concentration of reactants is 10x higher than the concentration of products?

Reverse

α-helices and β-strands are an example of ___________ structure

Secondary

Which level of protein structure is important for producing the active site of an enzyme?

Tertiary

Consider two membranes. The inside of both cells has the same concentration of oxygen molecules. However, cell membrane #1 has a higher concentration of oxygen on the outside of the membrane than membrane #2 does. Which cell will initially have a greater net movement of oxygen molecules across the cell membrane?

The cell with the higher concentration outside of the cell membrane (in this case cell membrane #1)

From the First Law of Thermodynamics, what must be true about the energy used by our muscles?

The energy consumed equals the energy used to contract the muscle plus the heat dissipated.

It is often stated that the phosphate bonds in ATP are "high energy," but in fact, they are not notably high in energy. Rather, they are easy to break, and the delta G of hydrolysis is a "useful" quantity of energy. What makes the phosphate bonds easy to break?

The negative charges on the phosphate groups repel each other.

Which of the following statements must be true in order for mitochondrial ATP synthase to function properly?

The pH of the intermembrane space must be lower than the pH of the mitochondrial matrix.

Consider three reactions with three unique activation energies. Which reaction will occur the fastest, or will they all be equally fast?

The reaction with the lowest activation energy.

Imagine a cell with equal concentrations of oxygen inside and outside of the cell at 10 micromolar. You observe the cell for a few minutes. What will be the rate of the oxygen cells coming in and out of the cell, respectively?

They will be the same; the oxygen molecules will enter and leave the cell at the same rate (rxn is at equilibrium, delta G = 0); According to Fick's Law of Diffusion, when the concentration gradient is zero (as is the case in this example), the net movement of molecules is also zero. This does not mean that molecules stop moving, but rather that the number of molecules moving into the cell is equal to the number of molecules moving out of the cell so that the overall concentrations of molecules inside and outside do not change.

In a metabolic pathway, a series of enzymatic reactions catalyzes the conversion of molecule A to molecule E. Several intermediate steps are involved in which the product of one reaction becomes the substrate for the next. If one of the steps is endergonic, how might the reaction proceed in the forward direction?

Through reaction coupling or through changing the ratio of the concentration of products and reactants (according to the Van't Hoff equation)

Amino acids with hydrophobic R groups are most often found buried in the interior of folded proteins. (T/F)

True

Even though the full oxidation of glucose is exergonic, some of the reactions in cellular respiration are endergonic. (T/F)

True

Mitochondria and chloroplasts both have inner and outer membranes. (T/F)

True

In what state carbonic anhydrase be able to catalyze the reaction shown below?

When it is folded in its native state

In what state will carbonic anhydrase be able to catalyze the reaction that converts carbon dioxide to carbonic acid?

When it is folded in its native state; proteins only do their "proper function" when they are properly folded and everything falls into place just right.

We get energy from our food by digesting molecules. Where does the energy come from?

When the molecule is digested, new molecules are formed that have an overall lower potential energy.

Can Enzymes catalyze endergonic reactions?

Yes

May exergonic reactions still require enzymes to proceed?

Yes, enzymes lower activation energy, not free energy. Thus, exergonic reactions with high or even low activation energies may use an enzyme

Suppose that a kinase regulates a pathway by adding a phosphate group to (i.e, "phosphorylating") the enzyme that catalyzes the reaction in which A is converted to B. If the phosphorlyation lowers the activation energy of a given reaction, the enzyme is acting as a(n) ____________________

allosteric activator; We can see from the free energy diagram that the reaction with the phosphorylated enzyme has the lowest activation energy and will therefore be the fastest reaction. This means that the enzyme catalyzes the reaction fast (i.e., is more active) when it is phosphorylated, so phosphorylation of this enzyme is acting as an allosteric activator. The answer can't be competitive activation because blocking the enzyme's active site can only inhibit the enzyme by preventing the substrate from binding (aka competitive activation does not exist).

Which of the following would be expected to decrease the fluidity of a membrane?

an increase in phospholipid fatty acid chain length and an increase in chain saturation

The assembly of glucose molecules into polysaccharides is a(n) _____ process.

anabolic (Ana goes to 'SC and Cat is a CS major)

Two faces of the membrane are ___________

asymmetrical

Oxygen molecules will diffuse down the concentration gradient and enter the cell. Is this process exergonic or endergonic?

exergonic

Is diffusion an endergonic or exergonic process?

exergonic (releases energy, occurs spontaneously)

Reactions in which there is a negative change in free energy (-deltaG) are:

exergonic and spontaneous

You are studying a protein that you call Protein X. There is an aspartic acid at a key position in Protein X that is important in the folding and stabilization of that protein. If this aspartic acid is changed to a different amino acid, which one of the following amino acid substitutions is MOST likely to allow the protein to fold normally?

glutamic acid

In chemical reactions, MOST of the entropy increase occurs as:

heat

Which way does the water move if the cell is in a hypotonic environment?

into the cell

Lipid bilayers spontaneously form to orient the _____ tails _____ to minimize their contact with water.

hydrophobic; inside

Where are ribosomes found inside a cell?

in the cytosol, mitochondria, and attached to the rough endoplasmic reticulum

Rank the following molecules in order of least permeable to most permeable based on their ability to pass through a pure (synthetic) lipid bilayer: oxygen, sodium ion, urea, and glucose

least permeable --> most permeable: Sodium ion Glucose Urea Oxygen

In general, a faster rate of reaction corresponds to a ___________ activation energy

lower

The chemical bonds of carbohydrates and lipids have high potential energy because:

many of these bonds are C-C and C-H bonds.

Individuals with a condition known as exercise intolerance suffer extreme fatigue from minimal exertion. Choose the organelle that, if defective, is most likely to cause this condition.

mitochondrion (since mitochondria are responsible for converting chemical energy in the form of fuel molecules s/a glucose, carbs, and proteins, to a form that the cell can use (ATP)

Facilitated diffusion

molecules move down their concentration gradient through a channel, forms a passage way for molecules like ions to cross the plasma membranes; carries can bind to molecules and carry them across the plasma membrane

The energy in organic molecules is released in a series of steps because:

more energy can be harvested for cellular use in multiple steps than from a single step.

Fluid Mosaic Model

plasma membrane is not rigid, but fluid, and contains phospho-heads, proteins, etc, like a mosaic. Theorized by Frye and Edidin.

The unique properties of water are due to the _____ of water molecules and the ability of water to form _____ with other water molecules and with other polar molecules.

polarity; hydrogen bonds

Peptide bonds form between the amino acids stabilize the __________ structure of a protein.

primary

Enzymes are a special class of _____________

protein

Which of the following eukaryotic cell structures plays a role in protein trafficking and sorting?

the Golgi apparatus

Many environmental factors influence the structure of biological membranes. Which one of the following could permanently disrupt phospholipid bilayers in an aqueous solution?

the addition of acid to change the pH (since this can change the relative charge of the hydrophilic heads and thus change its shape)

Phospholipase is an enzyme that cleaves the phosphate head group off a phospholipid molecule. The plasma membrane is not, however, permeable to the enzyme. Imagine a cell where phospholipid A is present in the monolayer facing the exterior of the cell, and phospholipid B is present in the monolayer facing the interior of the cell. After adding phospholipase to the medium in which the cell is growing, what would you expect to find in the fluid surrounding the cell?

the phosphate head group from phospholipid A only

The tendency of nonpolar molecules to self-associate in water instead of dissolve individually is called the hydrophobic effect. (T/F)

true

Quaternary structure

two or more polypeptide chains bound together