Exam 3 study guide

redox potential: Reduced ubiquinone ↔ oxidized ubiquinone + 2H+ + 2 e-

+ 30 mV

redox potential: H2O ↔ 1/2O2 + 2H+ + 2 e-

+ 820 mV

redox potential: Reduced cytochrome c ↔ oxidized cytochrome c + e-

+230 mV

In a resting muscle, the concentrations of ATP, ADP, and Pi are approximately 0.005 M, 0.001 M, and 0.010 M, respectively. What is the DG for ATP synthesis in resting muscle?

-11.1 kcal/mole

redox potential: NADH ↔ NAD+ + H+ + 2 e

-320 mV

Glycolysis generates more stored energy than it expends. What is the net number of activated carrier molecules produced in this process (number and type of molecules produced minus the number of those molecules used as input)?

2 ATP, 2 NADH

How many molecules of ATP are "invested" in activating glucose to form fructose-1,6-bis-phosphate (a.k.a. fructose-1,6-diphosphate)? How many ATP molecules are produced in glycolysis and what is the net gain

2/4/2

what is the substrate for the enzyme phosphoglycerate?

3-phophoglycerate

The classical point of view is that, during mitochondrial respiration, three ATP molecules can be generated from one molecule of NADH + H+ and only two from FADH2. When factoring in the cytosolic NADH + H+, the maximum number of molecules of ATP per glucose generated by the electron transport system is _____.

38

In a resting muscle, the concentrations of ATP, ADP, and Pi are approximately 0.005 M, 0.001 M, and 0.010 M, respectively. At [Pi] = 0.010 M, what will be the ratio [ATP]/[ADP] at equilibrium?

7.2 x 10-8

Porin proteins form large, barrel-like channels in the membrane. Which of the following is not true about these channels? a) They are made primarily of a-helices. b) They are made primarily of b-pleated sheets. c) Proteins cannot form narrow channels. d) They have alternating hydrophobic and hydrophilic amino acids.

A

Predict which of the following organisms will have the highest percentage of unsaturated phospholipids in their membranes. Explain your answer. a) Antarctic fish b) Desert snake c) Humans living in a temperate forest d) Thermophilic bacterium that lives in hot springs near 100°C

A

Which of the following statements is false? a) Phospholipids will spontaneously form liposomes in polar solvents such as water. b) In eukaryotes, all membrane-enclosed organelles are surrounded by one lipid bilayer. c) Membrane lipids diffuse within the plane of the membrane. d) Membrane lipids do not frequently flip-flop between one monolayer ("membrane leaf") and the other

B

Experimental evidence supporting the chemiosmotic hypothesis was gathered by using artificial vesicles containing a protein that can pump protons in one direction across the vesicle membrane to create a proton gradient. Which protein was used to generate the gradient in a highly controlled manner?

Bacteriorhodopsin

Which of the following reactions is catalyzed by ribozymes? a) DNA synthesis b) transcription c) RNA splicing d) protein hydrolysis

C

Although the extracellular environment in some animal tissues has a high sodium ion concentration and the intracellular environment exhibits a high potassium ion concentration, both must be neutralized by negatively charged molecules. What is the principal anion counteracting the charges of Na+ and K+?

Cl-

Which of the following antibiotics targets RNA polymerase? a) Bacitracin b) Streptomycin c) Ampicillin d) Rifamycin

D

You are examining the DNA sequences that code for the enzyme phosphofructokinase in lizards of the family Scincidae (skinks) and Komodo dragons, which can grow to 3 m or longer and are classified in the family Varanidae. You notice that the nucleotidyl sequence that directs the sequence of amino acyl residues (open reading frame or ORF) in the enzyme is very similar in the two organisms but that the surrounding sequences (untranslated regions or UTRs) vary to a large extent. What is the most likely explanation for this phenomenon? a) Coding sequences are repaired more efficiently after DNA damage. b) Coding sequences are replicated more accurately. c) Coding sequences are packaged more tightly in the chromosomes to protect them from DNA damage. d) Mutations in coding sequences are more likely to be damaging to the organism than mutations in noncoding sequences.

D

The bacterium Brucella abortus can utilize the tetrose erythritol as a carbon source. The concentration of erythritol within a B. abortus cell is 10 mM, while the external erythritol concentration is at levels as low as 0.20 mM. What is the energy requirement for the inward transport of erythritol at 37°C under these conditions? Hint: You may use the equation below. Hint: In this case, T = 37 °C = 310 K.

DGinward = -2,409.7 cal/mol·°

T OR F: Number 1 and number 6 point to the 3'- and 5'-untranslated regions, respectively.

F; 5-3

T OR F: . In order to function, all extracellular signal molecules must be transported by their receptor across the plasma membrane into the cytosol.

FALSE

T OR F: . Some signal molecules can bind directly to intracellular proteins that bind DNA and regulate gene transcription

FALSE

T OR F: A cell-surface receptor capable of binding only one type of signal molecule can mediate only one kind of cell response.

FALSE

T OR F: A ribosome binds one tRNA at a time

FALSE

T OR F: During glycolysis, glucose molecules are broken down to ultimately yield CO2 and H2O.

FALSE

T OR F: Gluconeogenesis is a linear reaction pathway the cell employs to generate glucose from pyruvate and uses the same enzymes in what is exactly the reverse of glycolysis

FALSE

T OR F: In the generation of ATP by oxidative phosphorylation inorganic phosphate (Pi) binds directly to ADP via a dehydration reaction (i.e., ADP + Pi ⇌ ATP).

FALSE

T OR F: Ribosomes are large RNA structures composed solely of rRNA

FALSE

T OR F: Ribosomes are synthesized entirely in the cytoplasm.

FALSE

T OR F: The cleavage of fructose 1,6-bisphosphate yields two molecules of glyceraldehyde 3-phosphate.

FALSE

T OR F: The human DNA was inserted in the bacterial DNA next to a bacterial promoter and in its normal orientation.

FALSE

T OR F: The proteins of the electron transport chain remove a pair of electrons from the reductant molecules NADH + H+ and FADH2, after which the electrons move across the inner mitochondrial membrane to maintain the voltage gradient.

FALSE

T OR F: When subjected to anaerobic conditions, glycolysis in mammalian cells continues and causes a buildup of pyruvate in the cytosol.

FALSE

T OR F: Triplets indicated with the number 2 are termination codons

FALSE; START CODON

We can estimate the relative mobility of a population of molecules along the surface of a living cell by fluorescently labeling the molecules of interest, bleaching the label in one small area using laser, and then measuring the speed of signal recovery as molecules migrate back into the bleached area. What is this method called?

FRAP

In mammals, glycogen is a more useful food storage molecule than fat because:

Glycogen can be used to produce ATP under anaerobic conditions whereas fat cannot

Unfortunately, the grape juice is contaminated with proteases that attack some of the transport proteins in the yeast cell membrane, and the yeast cell dies. Which of the following could account for the yeast cell's demise?

Inability to import sugar into the cell

What purpose does the phosphorylation of glucose to glucose 6-phosphate by the enzyme hexokinase serve as the first step in glycolysis?

It helps drive the uptake of glucose from outside the cell

A poison isolated from an Amazonian fungus was added to an in vitro translation mixture containing mRNA molecules with the sequence 5¢-AUGAAAAAAAAAAAAUAA-3¢ and it had the following effect: The only product made is a Met-Lys dipeptide that remains attached to the ribosome. What is the most likely way in which this poison acts to inhibit protein synthesis?

It inhibits movement of the small subunit relative to the large subunit.

Where does oxidative phosphorylation take place in the animal cell and what other processes are required for this to occur?

It takes place in the mitochondrion and follows the production of NADH + H+ and FADH2.

NADH and FADH2 carry high-energy electrons that are used to power the production of ATP in the mitochondria. These cofactors are generated during glycolysis, the citric acid cycle, and the fatty acid cycle. Which of the options below represents the cofactor that will help produce the largest number of ATP molecules?

NADH from the citric acid cycle

Thus, oxidative phosphorylation refers to the oxidation of __________________ and __________________ molecules and the phosphorylation of __________________. Without this process, the yield of ATP from each glucose molecule would be __________________ decreased.

NADH, FADH2, ADP, severly

Cells make use of H+ electrochemical gradients (DpH) in many ways. Which of the following proton transporters is used to regulate pH in animal cells?

Na+/H+ exchanger

more likely to diffuse: H2O or O2

O2

In oxidative phosphorylation, ATP production is coupled to the events in the electron-transport chain. What is accomplished in the final electron transfer event in the electron-transport chain?

O2 is reduced to H2O

A bacterium is suddenly expelled from a warm human intestine into the cold world outside (hey, it's been a cold spring!). Which of the following adjustments might the bacterium make to maintain the same level of membrane fluidity?

Produce lipids with hydrocarbon tails that are shorter and have more double bonds

Transcription in bacteria differs from transcription in a eukaryotic cell in that

RNA polymerase (along with its sigma subunit) can initiate transcription on its own.

In eukaryotic cells, general transcription factors are required for the activity of all promoters transcribed by RNA polymerase II. The assembly of the general transcription factors begins with the binding of the factor __________________ to DNA, causing a dramatic local distortion in the DNA. This factor binds at the DNA sequence called the ___________, which is typically located 25 nucleotides upstream from the transcription start site.

TFIID, TATA box

T OR F: Extracellular signal molecules that are hydrophilic must bind to a cell-surface receptor in order to signal a target cell to change its behavior.

TRUE

T OR F: Number 5 points to open reading frames (protein-coding regions).

TRUE

T OR F: Sectors marked with the number 3 are ribosomal binding sites.

TRUE

T OR F: The figure represents a eukaryotic message.

TRUE

T OR F: The human DNA contained an intron.

TRUE

T OR F: The human DNA underwent a deletion while in the bacterium

TRUE

T OR F: The human DNA was inserted in the bacterial DNA next to a bacterial promoter but in an opposite orientation (compared to the normal orientation).

TRUE

T OR F: Triplets indicated with the number 4 are termination codons.

TRUE

T OR F: rRNA contains the catalytic activity that joins amino acids together

TRUE

Which type of defect described below is the most likely to cause the redistribution of that protein around the entire cell?

The deletion of a junctional protein

In the final stage of the oxidation of food molecules, a gradient of protons is formed across the inner mitochondrial membrane, which is normally impermeable to protons. If cells were exposed to an agent that causes the membrane to become freely permeable to protons, which of the following effects would you expect to observe?

The ratio of ATP to ADP in the cytoplasm would fall.

Cystic fibrosis is a term that describes a syndrome produced by defective Cl- channels in humans or their lack of intracellular transport from the ER to the plasma membrane. Why would a cystic fibrosis patient have mucus accumulation in the lungs?

Water molecules that keep the interior of the lungs wet leave cells as solvation spheres for Cl-.

Three phospholipids X, Y, and Z are distributed in the plasma membrane as indicated in the figure on the left. For which of these phospholipids does a flippase probably exist?

X and Y

Cholesterol serves several essential functions in mammalian cells. Which of the following properties of the membrane is not influenced by cholesterol? a) Membrane thickness. b) Membrane rigidity. c) Membrane fluidity. d) Membrane permeability

a

Which of the following are secondary messengers? a) Ca2+, GTP, cAMP b) hormones c) growth factors d) neurotransmitters e) None of the above

a

Which of the following does not occur before a eukaryotic mRNA is exported from the nucleus? a) The ribosome binds to the mRNA. b) The mRNA is polyadenylated at its 3' end. c) methyl-G is added in a 5¢ to 5¢ linkage to the mRNA. d) RNA polymerase dissociates.

a

A strain of yeast translates mRNA into protein inaccurately. Individual molecules of a particular protein isolated from this yeast have variations in the first 11 amino acids compared with the sequence of the same protein isolated from normal yeast cells, as listed in the table below. What is the most likely cause of this variation in protein sequence?

a mutation in the isoleucyl-tRNA synthetase that decreases its ability to distinguish between different amino acids

The molecule that enters the Krebs cycle to regenerate citric acid by reacting with malate is

acetyl CoA

Depending on the enzymes present in particular organisms, two common pathways for fermentation convert pyruvate to

acetyl CoA or lactate

The final metabolite produced by -oxidation of fatty acids is

acetyl-CoA

In eukaryotes, the general transcription factors and RNA polymerase are not sufficient to initiate transcription in the cell and are affected by proteins bound thousands of nucleotides away from the promoter. Proteins that link the distantly bound gene regulatory proteins to RNA polymerase and the general transcription factors include the large complex of proteins called ________________.

activator

Pumps are transporters that are able to harness energy provided by other components in the cells to drive the movement of solutes across membranes, against their concentration gradient. This type of transport is called

active transport

more likely to diffuse: adenosine or ATP

adenosine

A metabolic pathway that replenishes an intermediate that has been used up is called

anaplerotic

The figure below shows the pathway through which nitric oxide (NO) triggers smooth muscle relaxation in a blood-vessel wall. Which of the following situations would lead to relaxation of the smooth muscle cells in the absence of acetylcholine? a) A smooth muscle cell that has a defect in guanylyl cyclase such that it cannot bind NO b) A muscle cell that has a defect in guanylyl cyclase such that it constitutively converts GTP to cyclic GMP c) A muscle cell that has cyclic GMP phosphodiesterase constitutively active d) A drug that blocks an enzyme involved in the metabolic pathway from arginine to NO e) None of the above

b

You have generated antibodies that recognize the extracellular domain of the Ca2+ pump. Adding these antibodies to animal cells blocks the active transport of Ca2+ from the cytosol into the extracellular environment. What do you expect to observe with respect to intracellular Ca2+?

b) Ca2+ pumps in the endoplasmic reticulum membrane keep cytosolic calcium levels low.

more likely to diffuse: amino acid or benzene

benzene

Find the mismatched pair a) Reductant (reducing equivalent) utilized in anabolic pathways—NADPH + H+ b) Produced under anaerobic conditions in mammalian muscle tissue—lactate c) Produced under anaerobic conditions by several microbial groups—cholesterol d) Product of pyruvate reduction; entry point to the Krebs cycle— acetyl-S-CoA e) Reductant produced in catabolic reactions—NADH + H+

c

Which of the following steps or processes in aerobic respiration include the production of carbon dioxide? a) Breakdown of glycogen b) Glycolysis c) Conversion of pyruvate to acetyl CoA d) Oxidative phosphorylatio

c

As pyruvate is completely broken down in the TCA (Krebs) cycle, some of its energy is

conserved in NADH + H+ and FADH2.

In eukaryotic cells the TCA takes place in the mitochondrial matrix, whereas in bacteria, it takes place in the

cytoplasm

New membrane phospholipids are synthesized by enzymes bound to the _____________ side of the _________________ membrane

cytosolic, endoplasmic reticulum

The following is incorrect regarding the statement "A small amount of ATP is made in glycolysis": a) The process takes place through substrate-level phosphorylation. b) Enzymes producing ATP from ADP + Pi, coupled with DG < 0 reactions, are called kinases. c) A total investment of 2 ATPs renders a total of 4 ATPs with a net gain of 2 ATPs. d) Substrate-level phosphorylation depends on a DpH and a voltage gradient. e) ATP is formed by phosphoglycerate kinase and pyruvate kinase.

d

There are several reasons why the primase used to make the RNA primer for DNA replication is not suitable for gene transcription. Which of the statements below is not one of those reasons? a) Primase initiates RNA synthesis on a single-stranded DNA template. b) Primase can initiate RNA synthesis without the need for a base-paired primer. c) Primase synthesizes only RNAs of around 5 to 20 nucleotides in length. d) The RNA synthesized by primase remains base-paired to the DNA template.

d

Which of the following membrane lipids does not contain fatty acid tails? a) Phosphatidylcholine b) A glycolipid c) Phosphatidylserine d) Cholesterol

d

Which of the following might decrease the transcription of a single specific gene in a bacterial cell? a) A decrease in the amount of sigma factor. b) A decrease in the amount of RNA polymerase. c) A mutation that introduced a stop codon into the DNA that precedes the gene's coding sequence. d) A mutation that introduced extensive sequence changes into the DNA that precedes the gene's transcription start site.

d

Which of the following processes do not take place in the mitochondrion? a) Citric acid cycle b) Conversion of pyruvate to activated acetyl groups c) Oxidation of fatty acids to acetyl CoA d) Glycogen breakdow

d

Which of the following statements is false? a) A constitutively active (i.e., always expressed) mutant form of PKA (cyclic AMP-dependent phosphorylase kinase) in skeletal muscle cells would lead to a decrease in the amount of unphosphorylated phosphorylase kinase. b) A constitutively active mutant form of PKA in skeletal muscle cells would not increase the affinity of adrenaline for the adrenergic receptor. c) A constitutively active mutant form of PKA in skeletal muscle cells would lead to an excess in the amount of glucose available. d) A constitutively active mutant form of PKA in skeletal muscle cells would lead to an excess in the amount of glycogen available.

d

The following is correct regarding calmodulin: a) It is a widespread calcium-responsive protein. b) It is present in all eukaryotic groups (animals, plants, fungi, protistans, etc.). c) It is a cytoplasmic protein that alters the activities of a broad range of other proteins. d) A homodimer, a holoprotein of calmodulin will bind a total of four Ca2+ ions. e) All of the above

e

Which of the following is not true of glycolysis? a) it splits glucose to form two molecules of pyruvate b) it begins the oxidation of glucose c) it produces a small amount of ATP d) it generates NADH + H+ e) it oxidizes glucose to carbon dioxide

e

The advantage to the cell of the gradual oxidation of glucose during cellular respiration compared with its combustion to CO2 and H2O in a single step is:

energy can be extracted in usable amounts.

more likely to diffuse: Cl- or ethanol

ethanol

T OR F: Facilitated diffusion can be described as the favorable movement of one solute down its concentration gradient being coupled with the unfavorable movement of a second solute up its concentration gradient

false

for the enzyme aldolase, what is the substrate and product?

fructose-1,6 bisphosphate; dihydroxyacetone phosphate and glyceraldehyde-3-phosphate

Which one of the following is the main reason that a typical eukaryotic gene is able to respond to a far greater variety of regulatory signals than a typical prokaryotic gene or operon? e) Eukaryotes have three types of RNA polymerase. f) Eukaryotic RNA polymerases require general transcription factors. g) The transcription of a eukaryotic gene can be influenced by proteins that bind far from the promoter. h) Prokaryotic genes are packaged into nucleosomes.

g

more likely to diffuse: glycerol or RNA

glycerol

What is the enzyme for the substrate glucose?

hexokinase

Since their concentration is much __________________ outside than inside the mitochondria, the flow of __________________ down the concentration gradient is energetically very __________________ and can thus be coupled to the production of _______ from ______.

higher, protons, favorable, ATP, ADP

When a primary signal needs to be sent to most cells throughout a multicellular organism, the signal most suited for this is a ___________.

hormone

A biochemist has synthesized a drug that blocks phosphofructokinase. This drug would not be a good antibacterial treatment for human use because

human cells also perform glycolysis so the drug might also poison them

Where is the mitochondrial genome and the citric acid cycle enzymes located?

in the matrix

Where are proteins of the electron transport chain, ATP synthase, and membrane transport protein for pyruvate located in the mitochondria?

inner membrane

Oxidative phosphorylation is a process that occurs in the _______________ of mitochondria. It requires an electron-transport chain that operates on the high-energy electrons taken from the activated carrier molecules+ _____________ and _______________ that are produced by glycolysis and the citric acid cycle.

inner membrane, NADH, FADH2

During strenuous exercise, hypoxic (low oxygen) muscle cells convert pyruvate to:

lactate

In anaerobic conditions, skeletal muscle produces:

lactate only

Cell membranes are fluid and thus proteins can diffuse laterally within the lipid bilayer most likely accompanied by specific lipids. This association of protein and lipids is called

lipid raft

Total nucleic acids are extracted from a culture of yeast cells and are then mixed with resin beads to which the polynucleotide 5¢-TTTTTTTTTTTTTTTTTTTTTTTTT-3¢ has been covalently attached. After a short incubation, the beads are then extracted from the mixture. When you analyze the cellular nucleic acids that have stuck to the beads, which of the following is most abundant?

mRNA

Where is porin located in the mitochondria?

outer membrane

You have a protein that is easily extracted from a cell membrane preparation, without any associated lipids, by washing with a buffer containing a salt (e.g. 2M NaBr) without the need to treat the membrane with detergents. What type of protein do you have?

peripheral (extrinsic)

These electrons are transferred through a series of molecules, and the energy released during these transfers is used to generate a gradient of _____________.

protons [H+]

The final metabolite produced by glycolysis is:

pyruvate

The sigma subunit of bacterial RNA polymerase:

recognizes promoter sites in the DNA.

Hydrophobic primary messengers usually cause molecular changes leading to modifications in metabolism. Examples of hydrophobic primary messengers are ______________

steroid hormones

Photosynthesis is a process that takes place in chloroplasts and uses light energy to generate high-energy electrons, which are passed along an electron transport chain. Where are the proteins of the electron transport chain located in chloroplasts?

thylakoid membrane

The ATP synthase found in chloroplasts is structurally similar to the ATP synthase in mitochondria. Knowing that ATP is being synthesized in the stroma, where will the Fo portion" of the ATP synthase be located?

thylakoid membrane

In the initial stage of photosynthesis, a proton gradient is generated and ATP is synthesized. Where do protons become concentrated in the chloroplast?

thylakoid space

There are several ways that membrane proteins can associate with the cell membrane. Membrane proteins that extend through the lipid bilayer are called __________________ proteins and have __________________ regions that are exposed to the interior of the bilayer. On the other hand, membraneassociated proteins do not span the bilayer and instead associate with the membrane through an a-helix that is __________________. Other proteins are __________________ attached to lipid molecules that are inserted in the membrane. __________________ membrane proteins are linked to the membrane through noncovalent interactions with other membrane-bound proteins.

transmembrane, hydrophobic, amphipathic, covalently, peripheral

T OR F: Anaerobically growing yeast further metabolizes the pyruvate produced by glycolysis to CO2 and ethanol as part of a series of fermentation reactions. A physiological role of fermentation, other than the production of small amounts of ATP, is to regenerate NAD+.

true

true or false: Transporters transition between different conformations, depending upon whether the substrate-binding pocket is empty or occupied.

true

Membranes undergo spontaneous rearrangement if torn. Which of the following would happen if a cell membrane had a large tear?

vesicles form