biol 203

Mad cow disease is an infectious disease where one misfolded protein causes all other copies of the protein to begin misfolding. This is an example of a disease impacting _ structure.

tertiary (3°)

Which categories of amino acid would you expect to find on the surface of a soluble protein and which categories would you expect to find in the interior? What distribution of amino acids would you expect to find in a protein embedded in a lipid bilayer?

Surface of a soluble protein (i.e. antibody) would contain polar and charged amino acids to interact with water and interior of a soluble protein could contain nonpolar, polar and charged amino acids. Surface of a protein embedded in the lipid bilayer (i.e. porin) would contain nonpolar amino acids where it interacts with the phospholipid fatty acid tails and polar and charged amino acids where it interacts with the cytosol or extracellular fluid. The interior would contain polar and charged amino acids needed to transport polar solutes.

What are prions?
a. Viruses that infect animal cells.
b. Viruses that infect bacteria.
c. Misfolded, infectious proteins.
d. Infectious bacteria.

c. Misfolded, infectious proteins.

PrPc has more α-helices than the infectious prion protein. What type of bond is directly involved in the formation of an α-helix?
a. Hydrogen bonds between amino acid residues
b. Peptide bonds between amino acid residues
c. Van der Waals interactions between nonpolar residues
d. Disulfide bonds that form between cysteine residues

a. Hydrogen bonds between amino acid residues

Gerstmann-Sträussler-Scheinker disease (GSS) is a rare inherited disease in humans associated with mutations in the PrPc protein gene that change amino acids within the protein, and make the GSS protein more prone to misfolding and aggregation. When researchers changed six histidines for tyrosines, PrPc lost its ability to bind copper. The structural formula of histidine and tyrosine are shown below. The R-groups highlighted in gray are.
a. Nonpolar for both histidine and tyrosine
b. Polar (partial charges can form with hydrogen bonds) for tyrosine and electrically charged/basic for histidine
c. Nonpolar for tyrosine due to the ring structure and electrically charged/acidic for histidine
d. Electrically charged/basic for histidine and electrically charged/acidic for tyrosine

b. Polar (partial charges can form with hydrogen bonds) for tyrosine and electrically charged/basic for histidine

In a cellular protein that resides in the cytosol, where would you expect to find an amino acid like valine?
a. on the exterior surface, interacting with water
b. in the interior, protected by the sugar-phosphate backbone
c. on the interior of the double helix, away from water
d. in the interior of the folded polypeptide, away from water

d. in the interior of the folded polypeptide, away from water

Prions are unusually resistant to an enzyme called proteinase K which breaks proteins into their monomer building blocks. Which bonds are being broken by the enzymatic action of proteinase K?
a. peptide bonds between amino acids
b. phosphodiester linkages between nucleotides
c. disulfide bonds between amino acids
d. peptide bonds between nucleotides

a. peptide bonds between amino acids

Which structural formula depicts a ribonucleotide?
a. A.
b. B.
c. C.
d. D.

b. B
(look for pentose sugar, phosphate group = two O's and an OH, and a nucleotide base)

Proteins that interact with DNA often interact with the phosphates that are part of this molecule. Which of the following types of amino acids would you predict to be present in the part of the protein that interacts with the phosphates in DNA?
a. Electrically charged/acidic amino acids
b. Polar amino acids (partial charges can form with hydrogen bonds)
c. Nonpolar amino acids
d. Electrically charged/basic amino acids

d. Electrically charged/basic amino acids

If one strand of a DNA molecule has the sequence of bases 5'-ATTGCA-3', the other complementary strand would have the sequence _.
a. 5'-TAACGT-3'
b. 3'-UAACGU-5'
c. 5'-UAACGU-3'
d. 5'-TGCAAT-3'

d. 5'-TGCAAT-3'

This table gives the results of assays of percentages of bases from nucleic acids isolated from different sources. The nucleic acid from source 3 is and _.
A. DNA; double stranded
B. RNA; double stranded
C. DNA; single stranded
D. RNA; single stranded

C. DNA; single stranded
(has T instead of U, complementary base pairs don't match up so single stranded)

Muscle contraction is initiated when a section of a DHPR protein moves, allowing calcium ions to flow into a cell. The protein is said to act as a gate for calcium ions. This is an example of ___.
A. protein evolution
B. the flexible nature of proteins
C. the complex nature of proteins
D. the quaternary structure of proteins

B. the flexible nature of proteins

The molecule below is ___ and this is its ___ structure.
5'- A C U A A A U C G A U A U A U A A G G A A -3'
a. a protein; 1o
b. DNA; 2o
c. RNA; 1o
d. a ribozyme; 3o

c. RNA; 1o

A mutation occurs in this portion of a DNA molecule, where an adenine replaces a cytosine. What impact do you think this will have on the DNA structure?
A. Adenine is larger than cytosine and will not be able to base pair properly with the guanine on the opposing strand. This will cause the phosphodiester bonds to break, and the DNA will hydrolyze.
B. Adenine is larger than cytosine and will not be able to base pair properly with the guanine on the opposing strand. This will cause the DNA to denature or unzip.
C. Adenine is larger than cytosine and will not be able to base pair properly with the guanine on the opposing strand. This will cause the DNA to bulge.
D. Since adenine is still a nitrogenous base, this mutation will have no impact on the DNA structure.

C. Adenine is larger than cytosine and will not be able to base pair properly with the guanine on the opposing strand. This will cause the DNA to bulge.

A solution with a hydrogen ion concentration of 0.0015 M has a pH of , and is therefore _.
A. 3.5, acidic
B. 2.82, acidic
C. 15, basic
D. 1 × 10-1.5, basic

B. 2.82, acidic

Why can some insects walk on water?
A. Because of the high heat capacity of water, requiring more energy for it to evaporate, thus allowing insects to walk.
B. Because of the surface tension of water, resulting from the attraction between water molecules (cohesion) at the surface of the body of water (the liquid-air/gas interface).
C. Because liquid water is more dense than ice, it is therefore more dense than insects, allowing them to walk.
D. Because water ionizes which give rise to pH, the neutral pH of water allows insects to walk.

B. Because of the surface tension of water, resulting from the attraction between water molecules (cohesion) at the surface of the body of water (the liquid-air/gas interface).

Read the following sentences, and then choose one option below.
I. "In this study, we tested the hypothesis that the cause of muscle mass loss after nerve damage is an increase in the protein TRB3."
II. "In this study, we tested the hypothesis that treatment with an antibody that blocks the enzymatic activity of protein PAPP-A will reduce atherosclerotic plaque progression."
A. Both I and II are hypotheses.
B. I is a hypothesis, but II is a prediction.
C. I is a prediction, but II is a hypothesis.
D. Both I and II are predictions.

B. I is a hypothesis, but II is a prediction.

Data show that copper binding stabilizes the structure of PrPc. In 2019, researchers hypothesized that copper binding plays a role in PrPc's ability to promote the growth of neurons. To test this hypothesis, they disrupted copper-binding sites on PrPc, by changing histidines to tyrosines (PrP-H→Y). Neurons were isolated from mouse brains and cultured in the lab in a physiological buffer (PBS, mock) or in the presence of wild-type (normal) PrPc in PBS, or the mutant PrP-H→Y in PBS. The growth of neurites (projections from the neuron cell body) was measured in microns (Max growth, µm) by microscopy in replicate samples. A graph of the results is shown below (standard error bars indicate the uncertainty in the mean). A statistical test was performed to determine whether there was a statistically significant difference between the groups.
a. What are the results of this experiment? (1 pt)
b. What can you conclude fr

a. Neurites grown in the presence of PrPc grew on average ~11.5 μm, compared with ~4 μm for neurites grown in the presence of the mock solution and only ~3 μm for neurites grown in the presence of PrP‐H→Y.
b. The results suggest that copper‐binding by PrPc is required for neurite growth and that the difference between histidine (being electrically charged basic) and tyrosine (being uncharged polar) might lead to a disruption of copper‐binding. When comparing PrPc to the mock trial and PrP‐H→Y, the error bars are nonoverlapping, suggesting a difference, and the four asterisks indicate a P value that is highly significant (P<0.0001), confirming that there is a statistically significant difference between PrPc and mock, and PrPc and PrP‐H→Y. When comparing PrP‐H→Y to mock trial, the error bars overlap, suggesting there is not a difference. The absence of asterisks confirm that there is no statistically significant difference between PrP‐H→Y and mock.
c. The "mock" treatment served as a "negative" control. The mock group included only PBS, the buffer that acted as the solvent for the proteins (PrPc and PrP‐H→Y). Measuring neurite growth in the presence of PBS confirmed that buffer alone did not promote neurite growth. Stimulation of neurite growth was dependent on the presence of the wild‐type protein.

Glycosidic linkages are common to , whereas __ are found in fats (triglycerides).
A. proteins; phosphodiester linkages
B. DNA; ester linkages
C. glycogen; peptide bonds
D. carbohydrates; ester linkages

D. carbohydrates; ester linkages

What holds the quaternary (4o) structure of cellulose molecules together in bundles large enough to form fibers?
A. glycosidic linkages
B. hydrogen bonds
C. the cell wall
D. peptide bonds

B. hydrogen bonds

What physical property is associated with the chemical differences between saturated and unsaturated fats?
A. C=C bonds normally result in a more compact structure that decreases the spacing between fats and thus makes unsaturated fats less fluid than saturated fats.
B. C=C bonds normally form less hydrogen linkages, which increases the spacing between fats and thus make unsaturated fats more fluid than saturated fats.
C. C=C bonds normally result in kinks that increase the spacing between fats and thus make unsaturated fats more fluid than saturated fats.
D. C=C bonds normally form more hydrogen linkages, which decreases the spacing between fats and thus make unsaturated fats less fluid than saturated fats.

C. C=C bonds normally result in kinks that increase the spacing between fats and thus make unsaturated fats more fluid than saturated fats.

Enzymes that readily break starch apart cannot hydrolyze the glycosidic linkages found in cellulose. Why is this logical?
A. Starch is held together by hydrogen bonding, not covalent bonding.
B. Cellulose molecules are highly branched, and enzymes are too bulky to fit.
C. The geometry of the bonds is different, and the shapes of enzyme active sites are highly specific.
D. Starch is held together by peptide bonds, not glycosidic linkages.

C. The geometry of the bonds is different, and the shapes of enzyme active sites are highly specific.

Cells use the sodium electrical gradient to perform many activities. What membrane protein is used to establish the sodium electrochemical gradient and how does it work?
A. The sodium electrical gradient would be established by the voltage-gated sodium channel through facilitated diffusion.
B. The sodium-potassium pump (Na+/K+-ATPase) establishes the sodium electrical gradient by using ATP to undergo conformational changes that result in moving three sodium ions out of the cell and two potassium ions into the cell.
C. The sodium-potassium pump (Na+/K+-ATPase) establishes the sodium electrical gradient by using ATP to undergo conformational changes that result in moving two potassium ions out of the cell and three sodium ions into the cell.
D. No membrane protein is required because lipid bilayers are highly permeable to sodium ions.

B. The sodium-potassium pump (Na+/K+-ATPase) establishes the sodium electrical gradient by using ATP to undergo conformational changes that result in moving three sodium ions out of the cell and two potassium ions into the cell.

After a sodium gradient is established, which side of the plasma membrane would you expect to be more positively charged?
A. There will be no difference in charge between the extracellular and intracellular sides of the membrane.
B. The extracellular side of the membrane will be more negatively charged
C. The intracellular side of the membrane will be more positively charged.
D. The extracellular side of the membrane will be more positively charged.

D. The extracellular side of the membrane will be more positively charged.

The figure below shows the activated and deactivated conformations of the voltage-gated sodium channel. Changes in conformation are based on a regulatory alpha-helix (represented by the gray cylinder on each side of the channel) that slides closer to the cytoplasm in the deactivated state and closer to the exterior of the cell in the activated state. What type of amino acids would you expect to be included in the regulatory alpha helix based on its change in position?
A. The helix would contain basic (positively charged) amino acids, such as lysine, arginine, and histidine.
B. The helix would contain acidic (negatively charged) amino acids, such as aspartate and glutamate.
C. Any type of amino acid could be present in the helix without a change in function.
D. The part of the helix that extends into the exterior of the cell would contain hydrophobic amino acids.

A. The helix would contain basic (positively charged) amino acids, such as lysine, arginine, and histidine.

A doctor injects a patient with what the doctor thinks is an isotonic saline solution. The patient dies, and an autopsy reveals that many red blood cells have been destroyed, leaving membrane fragments. Do you think the solution the doctor injected was really isotonic?
A. Yes, because an isotonic solution would cause water to leave cells, thereby making them shrink.
B. Yes, because an isotonic solution would cause water to enter the cells, thereby making them burst.
C. No, it must have been hypertonic because a hypertonic solution would cause water to leave the cells, thereby making them shrink.
D. No, it must have been hypotonic because a hypotonic solution would cause water to enter the cells, thereby making them burst.

D. No, it must have been hypotonic because a hypotonic solution would cause water to enter the cells, thereby making them burst.

Injecting a dose of a solution containing potassium ions (K+) into a person's blood can cause the heart to stop beating. This method is often used during open heart surgery. Using what you know about the Na+/K+-ATPase and electochemical gradients, why do you think an injection containing K+ ions leads to cardiac arrest?
A. Cells typically have a high concentration of Na+ in the cytoplasm and a high concentration of K+ in the extracellular fluid. A potassium solution would disrupt the gradient and cause the cells to not function properly.
B. Cells typically have a high concentration of K+ in the cytoplasm and a high concentration of Na+ in the extracellular fluid. A potassium solution would disrupt the gradient and cause the cells to not function properly.
C. Cells typically have equal concentrations of Na+ and K+ in the cytoplasm and in the extracellular fluid. A potassium solution would disrupt the gradient and caus

B. Cells typically have a high concentration of K+ in the cytoplasm and a high concentration of Na+ in the extracellular fluid. A potassium solution would disrupt the gradient and cause the cells to not function properly.

According to the diagram below, which substance is experiencing passive transport?
Na+
Glucose
Plasma membrane
Molecule A

Na+
(look for substance going from high to low concentration)

According to the diagram below, which substance is experiencing secondary active transport?
Na+
Glucose
Plasma membrane
Molecule A

Glucose
(look for substance going from low to high concentration)

Which of the following is not an extracellular role of carbohydrates?
A. protect an insect's internal organs from external trauma
B. prevent plant cells from lysing after the plant is watered
C. maintain the shape of a fungal spore
D. provide energy for muscle movement

D. provide energy for muscle movement

You have a planar bilayer with equal amounts of saturated and unsaturated phospholipids. After recording the degree of permeability of this membrane to glucose (there was some permeability), you increase the proportion of saturated phospholipids in the bilayer. This bilayer .
A. has changed, but glucose permeability has not
B. is more permeable to glucose now
C. is less permeable to glucose now
D. is less permeable to glucose but more permeable to Na+ ions now

C. is less permeable to glucose now

Aquaporins are proteins embedded in the plasma membrane that allow water molecules to move between the extracellular matrix and the intracellular space. Based on its function and location, describe the key features of the protein's shape and the chemical characteristics of its amino acids.
A. The protein must form an amphipathic carrier protein in the plasma membrane that allows water to enter and exit the cell down its concentration gradient.
B. The protein must form an amphipathic pump in the plasma membrane that allows water to enter and exit the cell against its concentration gradient.
C. The protein must form an amphipathic channel in the plasma membrane that allows water to enter and exit the cell down its concentration gradient.
D. The protein must form an amphipathic pump in the plasma membrane that binds water molecules and transports them across the plasma membrane down its concentration gradient.

C. The protein must form an amphipathic channel in the plasma membrane that allows water to enter and exit the cell down its concentration gradient.

Cell walls are used by many different organisms for protection from their environment and structural support. These cell walls must be insoluble in water; otherwise, they would dissolve the first time an organism got wet. Which of the following carbohydrates would you expect to be most soluble in water?
A. chitin
B. starch
C. cellulose
D. peptidoglycan

B. starch

Draw a simple representation of a plasma membrane. Then, for each of the following membrane activities, (1) add a clearly-labeled drawing of the process to your membrane (include any proteins, other molecules involved, symbols, etc.), (2) indicate whether ATP is required or not, and (3) indicate the specific type of transport.
(2 pts) movement of water into and out of a cell (hint: don't forget about aquaporins)
(1 pt) movement of carbon dioxide into and out of a cell
(2 pts) movement of glucose molecules into a cell from the extracellular fluid, which contains a higher concentration of glucose than the concentration inside the cell

a) Show water molecules moving from high to low concentration directly across the lipid bilayer, but moving relatively slowly (by a wavy or thin arrow; or show at equilibrium with bidirectional arrow), and also show them moving more rapidly through aquaporin (protein shape should span membrane and have a channel). No ATP required. Osmosis. (2 pts)
b) Show carbon dioxide molecules moving from high to low concentration directly across the lipid bilayer (or show at equilibrium with bidirectional arrow). No ATP required. Diffusion. (1 pts)
c) Show glucose moving from high to low concentration through the carrier protein GLUT1, which changes shape upon binding glucose, allowing glucose to enter the cell. No ATP required. Facilated diffusion. (2 pts)

The human stomach contains a natural, carbohydrate-based antibiotic that probably protects a large portion of the population from various diseases caused by the bacterium Helicobacter pylori. This bacterium has been linked to peptic ulcers, gastritis, and stomach cancer. This naturally occurring antibiotic is described by researchers as having a terminal α-1, 4-linked N-acetylglucosamine (NAG), and it acts by inhibiting the biosynthesis of a major component of the cell wall in H. pylori. Researchers created a glycoprotein with a terminal NAG (that is, a protein with NAG attached to its end). Their hypothesis is that the terminal NAG, and not the protein component, is responsible for the damage to the cell wall in H. pylori. What would be the most appropriate control for testing this hypothesis?

B. Grow H. pylori in a test tube with a glycoprotein that has its terminal NAG removed.

Using the pH scale on the right, pure water has ____ H+ in solution than tomatoes.
A. 1000 times more
B. 1000 times less
C. 100 times more
D. 100 times less

B. 1000 times less

If a double-stranded DNA sample was composed of 10 percent thymine, what would be the percentage of guanine?
A. 10
B. 20
C. 40
D. 80

C. 40

The molecule to the right, which is frequently found in the stomach, is best categorized as a __ having a(n) ___ bond/linkage.
A. lipid; ester
B. protein; peptide
C. carbohydrate; glycosidic
D. lipid; phosphodiester
E. None of the above

C. carbohydrate; glycosidic

What would happen to the function of this chymotrypsin if all other proteins were already broken down into individual amino acids?
A. Fewer proteins will be torn apart
B. More proteins will be torn apart
C. Chymotrypsin will start working on substrates made of carbohydrates
D. The bonds that create the tertiary structure of chymotrypsin change

A. Fewer proteins will be torn apart

The amino acid residues at the active site are highly acidic. In designing a drug that would bind to the active site and jam it, researchers should use a molecule that is .
A. hydrophobic
B. polar
C. charged
D. acidic

C. charged
(if site is hydrophobic --> hydrophobic molecule)

Both proteins and DNA can be denatured and undergo hydrolysis. These processes involve disrupting specific interactions and breaking bonds, which can require enzymes. What would happen to DNA molecules treated with these enzymes?

A. the phosphodiester linkages of the polynucleotide backbone would be broken

The chemical reaction illustrated in the accompanying figure ___.
a. links two polymers to form a monomer
b. joins two fatty acids together
c. is a hydrolysis reaction
d. results in a peptide bond

d. results in a peptide bond

In class we stated that ribosomal RNA is a type of ribozyme, catalyzing the formation of a peptide bond. Which of the following best describes the tertiary structure of RNA molecules, such as ribozymes?

A single nucleotide strand where multiple "stem and loop" structures begin to interact

Which of the following is not dependent upon hydrogen bonding interactions?

C. Primary structure of a protein

How do the alpha and beta forms of glucose differ?

Their ring structures differ in the location of a hydroxyl group

A student has drawn this model to study for her exam. Which statement is TRUE about her model?
A. The shape with the dark area represents a barrier preventing substances from entering.
B. The shape with the dark area represents a pore to transport substances.
C. The phospholipids are drawn with their heds and tails in the wrong orientation in the bilayer.
D. Only two different types of macromolecules are represented in this model.
E. All statements are true.

B. The shape with the dark area represents a pore to transport substances.

The membrane protein labeled "A" in the image on the right is carrier protein GLUT-1. What might you expect about the movement of Na+ and/or glucose across the cell membrane?

D. Glucose would likely move from the outside of the cell to the inside.

Membrane protein B in the diagram below is the pore-like channel protein, aquaporin. Where would you expect to find the amino acids alanine and valine?

D. Both would be in the exterior of the channel protein interacting with the phospholipid tails.

If molecule X is C2H6, what does the above diagram indicate is happening?
A. Simple diffusion out of the cell
B. Facilitated diffusion out of the cell
C. Active transport out of the cell
D. Active transport into the cell
E. Neither of the above, because molecule X cannot cross the membrane

A. Simple diffusion out of the cell

Read the following:
I. "We tested the hypothesis that the level of vitamin D in blood serum correlates to the expansion of endothelium-dependent blood vessels."
II. "We tested the hypothesis that PINK1 and Parkin promote mitochondrial loss by producing targeted destruction of core proteins of mitochondrial development."

C. I is a prediction, but II is a hypothesis

The partial negative charge at one end of a water molecular is attracted to the partial positive charge of another water molecule. What is this attraction called?
A. a hydrogen bond
B. a covalent bond
C. an ionic bond
D. A van der Waals interaction

A. a hydrogen bond

A mutation occurs in this portion of a chromosome where thymine replaces guanine. What impact do you think this will have on the DNA structure below?
A. This will cause the phosphodiester bonds to break, and the DNA will hydrolyze.
B. This will cause the DNA secondary structure to denature or unzip.
C. This will cause a bulge in the DNA secondary structure.
D. This will cause a slight distortion in the DNA secondary structure.

D. This will cause a slight distortion in the DNA secondary structure.

electrophoresis gel:
What can you conclude about samples, A and B?

A. RNA sequence A is larger and longer than sample B.
(didn't travel as far = not as fast = bigger)

electrophoresis gel:
Assume that both samples A and B are purified functional proteins. An extra band appears in sample B at the same location on the gel as sample A. What might you conclude from this result?

C. Sample B has quaternary structure

Normal b-hexosaminidase A (HexA) is a heterodimer, consisting of an a-subunit and a bsubunit. In Tay-Sachs disease, a single amino acid is changed in the a-subunit causing the formation of two mutants. Mutant 1, E482K, has the amino acid E replaced with K at residue number 482 and Mutant 2, G269S, has the amino acid G replaced with S at residue 269. Both mutants are defective in enzymatic activity and exhibit altered folding pathways compared with wild-type a-subunit. Mutant E482K is more severely misfolded than G269S, as observed by its aggregation and inability to associate with the HexA β-subunit.
A) What family of macromolecules does b-hexosaminidase A (HexA) belong?
B) We discussed levels of structures (1o , 2o , 3o , 4o ) for macromolecules. Based on the information in the prompt alone, what levels of structure are altered in HexA? For each structural level chosen, briefly support your selection with evidence

A) proteins
B) Primary structure (1o ): a single amino acid is changed in the a-subunit (any mention of amino acid)
Secondary is not altered
Tertiary structure (3o ): exhibit altered folding pathways (any mention of folding); aggregation
Quaternary (4o ): heterodimer; inability to associate with the HexA β-subunit
C) Mutant 1 has a change in charges from a negatively charged acidic amino acid (glutamic acid) to a positively charged basic amino acid (lysine). This could seriously disrupt the ionic bonds which may be formed in the 3o structure. Mutant 2 has a change from a mildly nonpolar H (glycine) to a polar hydroxyl (serine) which may create unintended new hydrogen bonds in the 3o structure, which is not as severe as disrupting ionic bonds.

Lysozyme, an enzyme found in human saliva, tears, and other secretions, catalyzes the hydrolysis of the β-1,4-glycosidic linkages in peptidoglycan.
A) What family of macromolecules does the substrate of this enzyme belong?
B) Name two other molecules this enzyme may be able to hydrolyze.
C) Predict the effect of this enzyme on bacteria and how it may be involved in human health.

A) carbohydrates
B) chitin and cellulose (lactose also acceptable)
C) When bacteria contact lysozyme, the peptidoglycan in their cell walls begins to degrade, leading to the death of the bacteria. Lysozyme therefore helps protect humans against bacterial infections.

Determine if the following reaction is spontaneous or not, addressing both potential energy and entropy. Explain how this obeys the 1st Law of Thermodynamics.
CH4 + 2 O2 --> CO2 + 2 H2O

The entropy of the reaction is unchanged as there are an equal number of molecules on the products' and reactants' sides. However, the products side has lower potential energy due to less nonpolar, high potential energy C-H bonds and more polar bonds than the reactants. Therefore, the reaction is spontaneous as ΔH < 0. As this is a balanced equation, it demonstrates the 1st Law of Thermodynamics as no energy is created nor destroyed, it is only converted.

Compare and contrast competitive inhibition and allosteric regulation.

Both competitive inhibition and allosteric regulation are a form of enzyme activity regulation. However, competitive inhibition involves a substance that is able to bind to an active site, preventing the intended substrate from binding and generally stopping the chemical reaction. Allosteric regulation, on the other hand, involves a substance binding to the allosteric site, and this can either activate or inhibit an enzyme.

Using the metabolic pathway below, predict how inactivating enzyme 2 would affect the concentration of molecules A, B, C, and D relative to what they would be if the pathway was fully functional.
A-->B-->C-->D

If enzyme 2 is inactivated, molecules C and D would not be produced because the pathway would be cut off. The concentration of molecule B would increase as it would no longer be converted into molecule C, and the concentration of molecule A would also slightly increase due to the build-up of B.

Compare and contrast (2 each) the three cytoskeletal motor proteins and provide a distinct cellular role for each.

Compare: all require ATP; all made of amino acids Contrast: myosin walks on actin to + end, kinesin walks on microtubules to + end, dynein walks on microtubules to - end; myosin cause muscle contraction, kinesin carries vesicles, dynein moves flagella.

If a cell receives a vesicle by endocytosis containing macromolecules to be digested, explain where it is going and how it gets there?

Plasma membrane pinches in to form a vesicle containing macromolecules to be digested. Dynein transports vesicle to lysosome by walking on microtubules towards the minus (-) end.

Predict the final location of a protein that was experimentally modified to include a nuclear localization signal, an ER signal sequence, and a mannose-6-phosphate tag. Justify your answer by addressing the impact of each signal on its transport.

The ER signal sequence indicates that the protein is synthesized in the lumen of the ER, and since the protein will not be in the cytosol, the NLS will not be expressed. The protein will then move from the ER to the Golgi apparatus for further processing, and since the protein also has the mannose-6-phosphate tag, it will then travel to a lysosome via a vesicle.

Analyze the flow of electrons in chloroplasts.
a. Draw a flowchart showing the flow of electrons.
b. What are the primary electron donors?
c. What are the terminal electron acceptors?
d. Are the final electrons at a high energy or low energy state?

a. H2O → PSII → Pheophytin → ETS (PQ → Cyt complex → PC) → PSI → Ferredoxin → NADP+ → NADPH
b. Primary electron donor: H2O
c. Terminal electron acceptor: NADP+
d. Final electrons at high energy state

Predict how the following conditions would affect the production of O2, ATP, and NADPH and state whether noncyclic or cyclic electron flow would occur in each:
a. What if only blue photons hit a chloroplast?
b. What if blue and red photons hit a chloroplast, but no NADP+ is available?

a) Blue photons are high-energy photons, and O2, ATP, and NADPH would be formed via noncyclic electron flow.
b) Since there is no NADP+ available, no NADPH would be produced and photosynthesis will occur in cyclic electron flow (meaning also no O2).

Predict the relative concentration of starch in leaves at the start of the day versus the end of the day.

The concentration of starch would be highest at the end of the day and lowest at the start of the day. Starch is made and stored in the chloroplasts of leaves during periods of high photosynthetic activity during the day. At night, it is broken down to make sucrose, which is transported throughout the plant to drive cellular respiration.

What is the role of PEP carboxylase in C4 and CAM plants?
a. It fixes CO2 into an organic acid.
b. It produces ATP for the Calvin cycle.
c. It replaces Rubisco in the Calvin cycle.
d. It releases CO2 from organic acids

a. It fixes CO2 into an organic acid.

An investigator exposes chloroplasts to 700-nm photons and observes low O2 production, but high ATP production. What is a plausible explanation for this observation?

Photosystem II is not splitting water, and the ATP is being produced by cycling electrons via photosystem I.

Which molecule becomes reduced in the following chemical reaction?
3-Phosphoglycerate (3PGA) + NADPH → Glyceraldehyde-3-phosphate (G3P) + NADP+ + H+
A. 3PGA
B. G3P
C. NADP+
D. NADPH

A. 3PGA

When electrons flow along the electron transport chain of thylakoid membranes, which of the following changes occurs?
a. The pH of the stroma increases
b. ATP synthase pumps protons by active transport
c. NADP+ is oxidized.
d. The pH of the lumen increases

a. The pH of the stroma increases

A solution of starch at room temperature does NOT readily decompose to form a solution of simple sugars because __ .
A. the starch solution has less free energy than the sugar solution
B. the activation energy barrier for this reaction cannot easily be surmounted at room temperature
C. the hydrolysis of starch to sugar is endergonic
D. starch cannot be hydrolyzed in the presence of so much water

B. the activation energy barrier for this reaction cannot easily be surmounted at room temperature

What can you infer about a high-molecular-weight protein that cannot be transported into the nucleus?
a. It is too large
b. It lacks a nuclear localization signal (NLS)
c. It lacks a mannose-6-phosphate tag
d. It lacks an ER signal sequence

b. It lacks a nuclear localization signal (NLS)

Enzymatic activity can be controlled by whereas when and where the enzyme functions can be regulated by .
A. the active site; substrate
B. time; allosteric molecules
C. pH; substrate
D. temperature; allosteric molecules

D. temperature; allosteric molecules

Which of the following correctly matches a component of the cytoskeleton to one of its functions?
a. Microtubules help animal cells divide into two
b. Actin filaments cause bending of cilia
c. Intermediate filaments anchor the nucleus
d. Microfilaments move chromosomes

c. Intermediate filaments anchor the nucleus

What wavelength of light in the accompanying figure is most effective in driving photosynthesis?
a. 420 mm
b. 475 mm
c. 575 mm
d. 625 mm

a. 420 mm

Recall from the "Mystery of the Newt" that a single rough-skinned newt killed three hunters after it got into their coffee pot. As the newt was boiled over the campfire, a substance on its skin called tetrodotoxin (TTX) contaminated the water to make a lethal brew. The newts store TTX in secretory vesicles inside gland cells, and secrete the toxin as a defense mechanism. When newts are stimulated to secrete TTX, predict which motor protein would deliver the vesicle to its destination in the cell and how?
A. Kinesin walking towards the minus end of the microtubule will deliver vesicle to the lysosome.
B. Kinesin walking towards the plus end of the microtubule will deliver vesicle to the plasma membrane.
C. Dynein walking towards the minus end of the microtubule will deliver vesicle to the lysosome.
D. Myosin walking towards the plus end of the microtubule will deliver vesicle to the plasma membrane.

B. Kinesin walking towards the plus end of the microtubule will deliver vesicle to the plasma membrane.

CAM plants keep stomata closed in the daytime, thus reducing loss of water. They can do this because they .
a. Fix CO2 into organic acids during the night
b. Fix CO2 into sugars in the bundle-sheath cells
c. Fix CO2 into pyruvate in the mesophyll cells
d. Use the enzyme PEP carboxylase, which outcompetes Rubisco for CO2 in the bundle sheath cells.

a. Fix CO2 into organic acids during the night

Reactions that require CO2 take place in .
a. The light reactions alone
b. The Calvin cycle alone
c. The C4 cycle alone
d. Both the Calvin cycle and the C4 cycle.

d. Both the Calvin cycle and the C4 cycle.

Inhibitors of microtubule assembly, vinblastine for example, are used for cancer chemotherapy. What function of microtubules might this inhibitor block to affect cancer cells?
A. The inhibitors prevent the separation of chromosomes, thereby stopping cell division.
B. The inhibition of microtubules interferes with the synthesis of proteins.
C. The inhibitors disrupts the endomembrane system, stopping cell division.
D. The inhibitor interferes with energy production.

A. The inhibitors prevent the separation of chromosomes, thereby stopping cell division.

In a 'pulse-chase' experiment, radioactively labeled amino acids are fed to a culture of bacteria, and then the bacteria are added to a culture of neutrophils (white blood cells). From earliest to latest, where would radioactive materials appear?
A. Endoplasmic reticulum, Golgi, vesicles near the Golgi, vesicles near the cell surface.
B. Vesicles near the cell surface, vesicles deeper in the cell, lysosomes, cytoplasm.
C. Vesicles near the cell surface, vesicles deeper in the cell, Golgi, endoplasmic reticulum.
D. None of the above

B. Vesicles near the cell surface, vesicles deeper in the cell, lysosomes, cytoplasm.

Assume a thylakoid is somehow punctured so that the interior of the thylakoid is no longer separated from the stroma. This damage will most directly affect the .
a. Splitting of water
b. Absorption of light energy by chlorophyll
c. Flow of electrons from photosystem II to photosystem I
d. Synthesis of ATP

d. Synthesis of ATP

Which of the following would halt the light capturing reactions in photosynthesis?
A. Lack of O2
B. Lack of CO2
C. Lack of H2O
D. Lack of Ferredoxin

D. Lack of Ferredoxin

Rubisco binds to CO2 and catalyzes a chemical reaction that fixes CO2 to RuBP. Once this reaction occurs, Rubisco _.
A. has been converted to 3-phosphoglycerate (3PGA)
B. is the product of the reaction
C. cannot be used again
D. is unchanged

D. is unchanged

In a series of enzyme catalyzed reactions of A + B → C → D → E, we find that increasing the concentration of A & B to 10 M steadily increases the rate of production of E. When A & B are raised to 11 M or more, the rate of increase in C continues to rise, but the rate of production of D & E does not change. What might be occurring?
A. Saturation of the enzyme that catalyzes C → D.
B. Competitive inhibition of the enzyme that catalyzes A + B → C.
C. Feedback allosteric inhibition of E on the enzyme that catalyzes A + B → C.
D. Competitive inhibition of the enzyme that catalyzes D → E.

A. Saturation of the enzyme that catalyzes C → D.

Explain why many different molecules—including lipids, amino acids, and CO2—end up radiolabeled when cells are fed glucose with radioactive carbons (14C).

Products formed during glucose catabolism are used to make lipids, amino acids. CO2 is a direct product formed during pyruvate processing & Citric Acid Cycle.
Examples:
Glucose → Pyruvate → Acetyl CoA → Fatty Acids → Phospholipids
Glucose → Pyruvate → Acetyl CoA → Citric Acid Cycle → Amino Acid synthesis
Glucose → Pyruvate → Acetyl CoA → Citric Acid Cycle → CO2

Explain the role of ATP in the energy-investment phase. Why is it not necessary for the energy-payoff phase?

Early reactions are endergonic; need ATP coupling to make exergonic. Later reactions are already exergonic.

What if the regulatory site in phosphofructokinase (PFK) had a higher affinity for ATP than the active site. Show how the rate would change by drawing a graph of rate of ATP production vs ATP concentration.

normal - start of high and go down as ATP concentration increases
changed - will be constantly low (ATP binding to regulatory stopping production)

Compare and contrast (a) substrate-level phosphorylation, (b) oxidative phosphorylation, and (c) photophosphorylation.

Similar: All require enzymes; all produce ATP from ADP
Different:

• SLP uses an enzyme to transfer a phosphate from a substrate to ADP, whereas OP & PP forms ATP from ADP and Pi.
• SLP uses the energy in a phosphorylated substrate to drive the reaction, whereas OP & PP use a proton-motive force (H+ electrochemical gradient) generated by the ETC to supply the energy for ATP synthase to make ATP.
• The initial energy source in OP is from NADH/FADH2 (or glucose) oxidation, whereas the initial energy source in PP is light energy.
• The number of ATP molecules made in each process: more in OP

What if cyanide (C=N- ) blocks complex IV in the ETC. Write a hypothesis for what happens to the ETC when complex IV stops working. Explain why cyanide poisoning in humans is fatal.

Cyanide-blocking complex IV in ETC would mean that the electrons wouldn't be transported to the final electron acceptor (O2), greatly inhibiting cellular respiration as a whole. ATP production would drop dramatically and cells would no longer be able to have the energy resources to perform vital functions, eventually leading to cell death. Therefore, cyanide poisoning would be fatal as it would prevent energy production and lead to eventual death in cells impacted by it.

Compare and contrast the flow of electrons in the chloroplast and mitochondria. Identify the primary electron donors and terminal electron acceptors, and their energy levels.

In mitochondria, electrons begin with high energy (in forms of NADH and FADH2) and eventually go through the electron transport chain. They gradually decrease in energy and are finally accepted by O2 to form H2O. In contrast, H2O is the primary donor of electrons in chloroplasts, which are then excited to higher energy levels due to photon energy and end up in a high-energy electron carrier, converting NADP+ into NADPH.

Explain how each signal deactivation method turns off the signal?
a. GTP hydrolysis
b. Phosphatase activity
c. Phosphodiesterase activity

a. inactivates the G-protein by converting GTP to GDP which causes a shape change, and stops activation of its downstream target
b. removal of phosphate groups from molecules involved in the phosphorylation cascade
c. hydrolysis of the second messengers cAMP & cGMP

The chemical EDTA binds with high affinity to Ca2+ ions. What if you added EDTA to a cell culture, what effect would this have on cell signaling.

This will block signal transduction and amplification when Ca2+ ions are produced as second messengers.

What if Ras has a GTP analog bound to it that cannot be hydrolyzed, what effect would this have on the cell?

Ras would remain active and continue stimulating the phosphorylation cascade even when no signal molecule is bound to the RTK. This would cause cells to continue dividing, leading to cancer.

When actively growing cells are treated with Taxol, a chemical isolated from plant cells that prevents microtubule depolymerization, they often are unable to complete the cell cycle. Based on what you have learned about cell-cycle checkpoints, which checkpoint likely causes these cells to arrest? Why?

When treated with Taxol, the cells would arrest in the M phase (which involves mitosis and cytokinesis). Taxol causes the inhibition of microtubule depolymerization, so there would not be complete separation of chromosomes in anaphase (part of M phase), meaning that the cells would then arrest.

What if the following condition existed in a cell, could it lead to uncontrolled cell growth resulting in cancer? Justify your response.
a. Overexpression of MPF activity
b. Rb being underproduced
c. Overproduction of BRCA1
d. Ras with a nonhydrolyzable GTP
e. Nonfunctional E2F
f. Nonfunctional phosphatase

a. No; MPF activity must decrease in order for cells to proceed thru mitosis (anaphase to telophase).
b. Yes; underproduced Rb cannot control E2F expression, therefore E2F would drive cell into S-phase.
c. No; BRCA1 is tumor suppressor, halting cell in G1.
d. Yes; can't turn off phosphorylation cascade to stop signaling
e. No; E2F needed to drive cell into S-phase
f. No; can't activate G1 cyclin-Cdk; Yes; can't turn off phosphorylation cascade

When electrons flow along the electron transport chains of mitochondria, which of the following changes occurs?
a. The pH of the matrix increases
b. ATP synthase pumps protons by active transport
c. NAD+ is oxidized.
d. The cytochromes phosphorylate ADP to form ATP

a. The pH of the matrix increases

The ATP made during the fermentation process is generated by .
a. The electron transport chain
b. Substrate-level phosphorylation
c. Chemiosmosis
d. Oxidative phosphorylation

b. Substrate-level phosphorylation

Canine phosphofructokinase (PFK) deficiency afflicts Springer spaniels, affecting an estimated 10 percent of the breed. Given its critical role in glycolysis, one implication of the genetic defect resulting in PFK deficiency in dogs is .
a. Early embryonic mortality
b. Elevated glucose levels in the dog's blood
c. An intolerance for exercise
d. A reduced life span

c. An intolerance for exercise

What if NADH competitive inhibition occurs, what will happen to the levels of succinate and isocitrate in the citric acid cycle shown in the accompanying figure?
a. Succinate will decrease, and isocitrate will accumulate
b. Both succinate and isocitrate will decrease
c. Succinate will accumulate, and isocitrate will decrease
d. Both succinate and isocitrate will accumulate

a. Succinate will decrease, and isocitrate will accumulate

Which of the following would halt glycolysis:
A. Lack of O2
B. Lack of CO2
C. Lack of NAD+
D. Both A and C

C. Lack of NAD+

Chondrocytes are cells found in the cartilage in our joints. In some forms of osteoarthritis, destruction of the chondrocyte extracellular matrix is associated with a diseased endoplasmic reticulum. This finding supports the idea that _.
A. extracellular matrix material is easily damaged
B. endoplasmic reticulum is involved in the synthesis of extracellular matrix
C. Golgi apparatus is not involved with the synthesis of the extracellular matrix
D. the extracellular matrix is a complex structure

B. endoplasmic reticulum is involved in the synthesis of extracellular matrix