MCB Exam One

Which term best describes a fatty acid?

Amphipathic

______ is the term used to describe fatty acids that have both hydrophobic and hydrophilic components within the same molecule

Amphipathic

Which type of movement is the least common for lipids in a bilayer?

Flip-flop

Mutations in the nucleic acid sequence of a gene can sometimes direct the substitution of one amino acid for another in the encoded protein. Which amino acid substitution would be most likely to severely disrupt the normal structure of a protein?

Methionine to arginine

If the products of a reaction have more free energy than the reactants, then that reaction is

Not energetically favorable

Which bond term describes a covalent bond in which electrons are shared unequally?

Polar

Protein molecules that have a quaternary structure must have two or more of which of the following?

Polypeptide chains

What determines the specificity an antibody has for its antigen?

Polypeptide loo[s in its variable domains

Which carbohydrates contain hundreds or thousands of sugar subunits?

Polysaccharides

You have developed a promising anti-cancer agent, but it has poor solubility in water. Which of the following changes should improve water solubility?

- Adding a carboxyl group - Adding a hydroxyl group

For a given protein, hydrogen bonds can form between which of the following?

- Atoms in the polypeptide backbone - Atoms of two peptide bonds - Atoms in two side chains - A side chain and water

The plasma membrane is involved in which activities?

- Cell signaling - Import and export of nutrients and wastes - Cell recognition - Cell growth and motility

Your company has developed an organic molecule with commercial potential and you know how to produce it in the lab. You want to increase production and make as much of the molecule as possible, but the reaction has a positive ΔG°. What can you do to try to drive the reaction toward your desired product?

- Continually remove products - Increase the concentration of reactants

Generally speaking, what determines the biological activity of a protein?

Amino acid sequence

Which statements are true about the differences between phospholipids and detergents?

- Detergents are shaped like cones, whereas phospholipids are more cylindrical - Phospholipids have two hydrocarbon tails, whereas detergents have just one - Phospholipids form bilayers in water, whereas detergents tend to form micelles

Chaperone proteins can aid in protein folding by doing which of the following?

- Isolating a polypeptide chain within the crowded cytoplasm to prevent aggregation of proteins - Steering partially folded polypeptide chains along the most energetically favorable folding pathway

What distinguishes the chemistry of life from other types of chemistry?

- It takes place almost exclusively in water - It is dominated by collections of polymers

What function is served by the carbohydrates attached to cell-surface proteins?

- Lubricate cells to keep from sticking together - Protect the cell from mechanical and chemical damage - Promote cell-cell adhesion - Establish a distinctive identity for cell-cell recognition

Which of the following can be a component of cell membranes?

- Protein - Lipid - Cholesterol - Sugar

Which of the following is a function of proteins in the plasma membrane?

- Serve as anchors to attach the cell to the extracellular matrix - Transmit extracellular signals to the cell interior - Allow specific ions to cross the plasma membrane, thereby controlling its electrical properties - Transport molecules across the membrane

Which is a mechanism for restricting the movement of proteins in the plasma membrane?

- Tethering proteins to the surface of another cell - Tethering proteins to the extracellular matrix - Tethering proteins to the cell cortex - Using barriers such as tight junctions

Predict what would happen to the secondary structure of a protein if an alcohol that disrupts hydrogen-bonding were added.

- The B sheets would unfold, disrupting protein structure - The a helices would unfold, disrupting protein structure

In a cytosolic folded protein, what orientation and/or interaction do the hydrophobic amino acids tend to have?

- They are interacting with other nonpolar amino acids - They are tucked away inside the protein

Which is true of prion proteins?

- They are misfolded forms of normal proteins - They can spread from one organism to another

Why do cell biologists study yeast?

- Yeast carries all the basic tasks that a eukaryotic cell must perform - Yeast is as closely related to animals as it is to plants

Carbohydrates on the surface of leukocytes play an important role in responding to infection or inflammation. Place the following steps of the response in the correct order.

1. Cytokines are released at sites of infection or inflammation and stimulate endothelial cells of blood vessels 2. Endothelial cells express selectins on their plasma membrane 3. Selectins bind to carbohydrates on the surface of leukocytes, causing them to stick 4. Leukocytes roll along vessel walls 5. Leukocytes crawl out of vessel into adjacent tissue

Choose the statement that best describes the distribution of amino acid sequence variability in antibody molecules that accounts for the broad antigen-binding repertoire of an antibody, even while the overall structure of the antibody experiences little change.

Amino acid sequence variability is concentrated in the hypervariable loops of both the VH and VL domains, as it is the hypervariable loops that primarily make direct contact with the antigen

Which of these molecules would you least expect to easily dissolve in water?

2-methylpropane

How many different amino acids are commonly used in making proteins?

20

You want to test pentapeptides (short peptides with only five amino acids) for their ability to bind to and inhibit a particular receptor. To do this, you set out to synthesize all possible pentapeptides and test each individually. Assuming you'll use just the 20 common amino acids, how many different pentapeptides will you have to test for receptor binding?

3200000

Sort the following secondary structure characteristics into the correct categories.

A helix only: - Cylindrical structure - One full turn every 3.6 amino acids B sheets only: - Consists of antiparallel or parallel strands - Side chains alternating above and below the structure Both a helix and B sheets: - Can be formed by many sequences - Formed by hydrogen-bonding between backbone atoms

In water, hydrogen bonds can form between which of the following?

A hydrogen atom of one water molecule and an oxygen atom of another

Which membrane would show a more rapid recovery of fluorescence in a FRAP study?

A membrane containing a larger proportion of unsaturated fatty acids

What do eukaryotic cells have that prokaryotes lack?

A nucleus and membrane-bound organelles

When NADH or NADPH transfers electrons to a recipient molecule, the recipient becomes reduced and the activated carriers are oxidized (to NAD+ or NADP+, respectively). What else happens during this reaction?

A proton is taken up by the recipient molecule

Detergent molecules are ___________ in nature and bind with membrane proteins and membrane lipids to disrupt their interactions and release the proteins from the membrane.

Amphipathic

Which term correctly describes the entire phospholipid molecule?

Amphipathic

Margarine is produced from vegetable oil by a process that does which of the following?

Adds hydrogen, which removes the double bonds from their phospholipid tails

Which statement represents the cell theory?

All cells are formed by the growth and division of existing cells

How does binding of GTP to a GTP-binding protein affect its activity?

Always activates the protein

One of the grand challenges in biology is understanding how the first cells formed on Earth. Since all cells are bound by a cell membrane, origin of life researchers are interested in modeling what the first membranes may have been like. What types of molecules might these researchers consider to be the original building blocks of cell membranes?

Amphipathic molecules

All four possible reactions in the animation are energetically favorable; the energy of the four products is lower than the energy of the original starting molecule. Why does the starting molecule not completely and quickly convert to its possible products before the addition of heat or an enzyme?

An activation energy barrier exists that must be overcome for conversion to products

Compared to adding heat to the system, what is the advantage of using an enzyme to overcome an energy barrier?

An enzyme can catalyze a reaction in many different ways

Which statement about enzymes is not true?

An enzyme can force an energetically unfavorable reaction to take place inside the cell

Reactions that use energy to drive the synthesis of molecules inside the cell are most specifically considered.

Anabolic

Reactions that build larger molecules in the cell are called ___________; reactions that break down molecules into smaller ones are called ___________.

Anabolic; catabolic

Actin filaments, microtubules, and the spherical shells of certain virus particles are all structures built from which of the following?

Assemblages of identical proteins

At equilibrium, the free energy of a reaction is which of the following?

At its lowest point

If the backbone of a polypeptide is hydrophilic, how can a transmembrane alpha helix span the hydrophobic portion of the lipid bilayer?

Because amino acid side chains in a transmembrane helix are hydrophobic and interact with the hydrophobic interior of the bilayer

The chemical reactions that take place in a cell, as compared to the chemistry in nonliving matter, primarily occur

Between carbon-based molecules

Mutation in the hemoglobin gene can cause sickle-cell anemia. The defective protein found in sickle-cell anemia causes red blood cells to "sickle"—become a misshapen C shape. These misshapen cells abnormally stick to each other and can become trapped by leukocytes (white blood cells) that are rolling or paused on the endothelial cells lining the vessel. This causes blockages of small blood vessels, causing severe pain and strokes called vaso-occlusive crisis. A new drug that binds and blocks selectin proteins is in phase III clinical trials to test for improvement in patients' symptoms. Why might this be an effective treatment for vaso-occlusive crisis?

Blocking selectins would block the ability of selectin to bind leukocytes, so leukocytes would be less likely to move slowly along the vessel wall and cause a blockage of red blood cells

Why are the oils found in plant seeds and the fat droplets found in the fat (or adipose) cells of animals similar?

Both are hydrophobic

Animals exploit the phospholipid asymmetry of their plasma membrane to distinguish between live cells and dead ones. When animal cells undergo a form of programmed cell death called apoptosis, phosphatidylserine—a phospholipid that is normally confined to the cytosolic monolayer of the plasma membrane—rapidly translocates to the extracellular, outer monolayer. The presence of phosphatidylserine on the cell surface serves as a signal that helps direct the rapid removal of the dead cell. How might a cell actively engineer this phospholipid redistribution?

By activating a scramblase and inactivating a flippase in the plasma membrane

How do protein, nucleic acid, and polysaccharide molecules polymerize (grow in length)?

By condensation reactions

Carbon atoms cycle continuously through the biosphere. What is a by-product of cell respiration, and what does this by-product represent?

CO2; completely oxidized carbon

Which chemical group is found on all amino acids?

Carboxylic acid group

The shape of a cell and the mechanical properties of its plasma membrane are determined by a meshwork of fibrous proteins called what?

Cell cortex

Which statement is not true of chloroplasts?

Chloroplasts are present in essentially all eukaryotic cells and in certain photosynthetic bacteria

Long polymers are made from single subunits in cells using a ___________ reaction, which ___________ water.

Condensation; releases

What type of bond is formed when two atoms share electrons?

Covalent bond

Disulfide bonds stabilize protein shape outside the cell by

Covalent bonds between cysteines

Which method is most suitable for determining the three-dimensional structure of an extremely large integral membrane protein complex?

Cryoelectron microscopy

Which amino acid is involved in the formation of disulfide bonds?

Cysteine

What purpose does NADPH serve in biosynthetic reactions like the one pictured here?

Donating electrons for a reduction reaction

What effect do double bonds have on phospholipid hydrocarbon tails and on the fluidity of the membrane?

Double bonds decrease the ability of hydrocarbon tails to pack together, which makes the bilayer more fluid

Which energy conversion characterizes photosynthesis?

Electromagnetic (light) energy → chemical bond energy

Which is not a function of proteins?

Encoding genetic information

Which of the following organelles is an irregular maze of interconnected spaces enclosed by a membrane and functions as the site where most cell membrane components, as well as materials destined for export from the cell, are made?

Endoplasmic reticulum

Which of the following is INCORRECT regarding how enzymes lower the activation energy of a reactin?

Enzymes reduce the free energy of the products of the reaction

In an α helix, hydrogen bonds form between which of the following?

Every fourth amino acid

What are protein families?

Evolutionarily related proteins that are similar in amino acid sequence and three-dimensional conformation

In a globular protein, where would the amino acid arginine most likely be found?

Exposed at the protein's surface

Determine if the following statement is true or false. To purify a protein from cells or tissues, the protein's amino acid sequence must be known.

False

Is the following statement true, false, or impossible to determine?Because living cells generate order by surviving, growing, and forming complex communities, they defy the second law of thermodynamics.

False

Is the following statement true, false, or impossible to determine?Phosphorylation can only take place in the cell nucleus.

False

Is the following statement true, false, or impossible to determine?Phosphorylation is the only form of covalent modification that can affect a protein's activity or location.

False

Which statement concerning feedback inhibition is false?

Feedback inhibition is difficult to reverse

In 1970, Frye and Edidin published research describing the mobility of plasma membrane proteins. They fused mouse and human cells together, creating a hybrid cell, and then examined the localization of mouse and human proteins over time. Initially mouse and human proteins were each restricted to one-half of the heterokaryon, but over time the mouse and human proteins mixed, with each being present over the entire cell surface. What technique did Frye and Edidin likely use to examine the mouse and human proteins?

Fluorescence microscopy

Intracellular condensates are non-membrane bound biochemical subcompartments that form due to phase separation among networks of weakly interacting molecules. Sabari et al., 2018, proposed that the transcriptional coactivator BRD4 helps form intracellular condensates containing other transcriptional proteins. A prediction of this proposal is that BRD4 should behave as a liquid within the condensate with rapid movement. Which procedure could be used to analyze movement of BRD2 in living cells?

Fluorescence recovery after photobleaching (FRAP)

Which reaction can be driven by the hydrolysis of a molecule of ATP?

Glucose + fructose → sucrose (ΔG = 5.5 kcal/mole)

Which portion of a membrane phospholipid faces the outside of the membrane?

Head

Which of the following correctly describes phosphorylation of a protein?

It can increase or decrease the protein's activity

Which of the following statements is not true?

Hydrogenation reactions are oxidations, and dehydrogenation reactions are reductions

Porin proteins—which form large, water-filled pores in mitochondrial and bacterial outer membranes—fold into β-barrel structures. The amino acids that face the outside of the barrel have what kind of side chains?

Hydrophobic

Which characteristic describes the tails of phospholipids?

Hydrophobic

Which of the following occurs by bringing nonpolar surfaces together to exclude water?

Hydrophobic forces

Which important intramolecular force for polypeptide folding is demonstrated by the clustering of green side chains?

Hydrophobic interaction

What is a drawback to using electron microscopy?

It cannot be used to view living cells

What is a drawback to using light microscopy?

It cannot be used to view structures smaller than a bacterium

When a ligand binds to an allosteric enzyme's regulatory site, it changes the activity of that enzyme by

Inducing a conformational change

How does an allosteric inhibitor work?

It binds to a site other than the active site, causing a conformational change in the enzyme that makes the active site less accommodating to the substrate

Is the following statement true or false, and why? Within a developed multicellular organism, all cells possess the ability to divide and do so regularly.

It is false, because some cells lose the ability to replicate their DNA and divide

How does the inclusion of cholesterol affect animal cell membranes?

It tends to make the lipid bilayer less fluid

What kind of enzyme adds a phosphate group to another protein?

Kinase

________ are the most abundant molecules in the animal cell membrane, whereas ________ make up 50% of the membrane by mass.

Lipids; proteins

Which of the following is a small, irregularly shaped organelle in which intracellular digestion occurs?

Lysosome

A binding site on the surface of a protein interacts specifically with another protein through

Many weak non-covalent interactions

Which of the following statements is true regarding protein structure determination?

Mass spectrometry can be used to determine the amino acid sequences of a complex mixture of different proteins

Which is not evidence for the endosymbiotic origins of mitochondria and chloroplasts?

Mitochondria and chloroplasts have similar DNA

Which statement is not true of mitochondria?

Mitochondria are not present in plant cells

What is the general term for the simplest sugars?

Monosaccharide

A less permeable membrane is likely to have

More cholesterol

Which of the following statements about NADPH and/or NADH is not true?

NADPH is an activated carrier molecule that is used primarily by plants

The epidermal growth factor receptor, HER2, contributes to the development of certain forms of breast cancer when over-expressed in breast tissue because it drives increased cell survival and division. HER2-positive breast cancers can sometimes be treated with monoclonal antibody drugs, which bind to HER2 and block its function. One such drug, pertuzumab (Perjeta), was FDA approved in 2012 for the treatment of advanced HER2-positive cancers. The mechanism of action of pertuzumab has been studied extensively and is dependent on its direct binding to HER2, which requires the interaction of the side chain of tyrosine 99 of the pertuzumab heavy chain with the side chain of histidine 296 of HER2. In rodents, the homolog of human HER2 is called Neu. Even though HER2 and Neu are closely related, pertuzumab does not block the function of Neu in rodents. Which of the following is the most likely hypothesis for why pertuzumab does not inhibit the function of Neu?

Neu has an amino acid substitution at the position equivalent to histidine 296 in HER2, and this amino acid in Neu does not have a side chain capable of forming the hydrogen bond with tyrosine 99 in pertuzumab required for binding

The genome of the bacterium E. coli contains 4.6 million (4.6 × 10^6) nucleotide pairs, whereas the human genome contains some 3200 × 10^6 nucleotide pairs. What can be concluded based on these numbers?

None of the above conclusions are drawn correctly

Chemical reactions proceed spontaneously only in which direction?

One that leads to a release of free energy

In both plants and animals, the process of "controlled burning" extracts energy from food molecules. This is a gradual of what?

Oxidation

Consider an O-H covalent bond in H2O. In H2O, the ______ atom more strongly attracts electrons and acquires a partial negative charge within the molecule itself.

Oxygen

What are the two types of β sheets?

Parallel and antiparallel

Proteins that are associated with the membrane by noncovalent interactions with other membrane proteins are called ___________ proteins.

Peripheral membrane

What kind of enzyme removes a phosphate group from a protein?

Phosphatase

What is the name used for a molecule in which two carbons of glycerol are attached to fatty acid chains, and the third carbon is attached to a phosphate group?

Phospholipid

Which of the following would produce the most fluid lipid bilayer?

Phospholipids with tails of 18 carbon atoms and two double bonds

What provides the information necessary to specify the three-dimensional shape of a protein? Choose the best answer in the context of which generally applies to most proteins.

Protein's amino acid sequence

Consider the thermodynamic properties of chemical reactions. Even though enzymes do not affect the overall energy of the reactants or the products (i.e., the thermodynamics), they alter the speed of the reaction. Enzymes accomplish this by doing which of the following?

Reducing the activation energy of a reaction

Which of the following is NOT a way that cells restrict the lateral movement of membrane proteins?

Reducing the temperature of the membrane

Which of these cannot be resolved with a conventional light microscope?

Ribosome

A cell's plasma membrane with a greater degree of ______ hydrocarbons will exhibit less fluidity at room temperature.

Saturated

Which term describes a hydrocarbon tail of a fatty acid that has no double bonds between its carbon atoms?

Saturated

What type of protein moves randomly selected phospholipids from one monolayer of a lipid bilayer to the other?

Scramblase

The majority of proteins belong to "protein families" that share which attribute?

Sequence patterns and therefore structural domains

Which part of an amino acid gives it its unique properties?

Side chain

Chemical modifications like phosphorylation and acetylation of proteins occur on ___________ of amino acids and can affect interaction of proteins with other cell components or structures.

Side chains

Which of the following does not contain sugars?

Steroids

What is the origin of the energy that animals acquire by eating plants or other animals?

Sunlight

Many proteins are regulated by the binding of GTP or GDP. Which form is the active state of the protein?

The GTP-bound form

Imagine that this experiment uses a mutant version that increases the enzyme's affinity, or ability, to bind its substrate. Using the graph as a comparison, what effect would the mutant version of the enzyme likely have on the KM?

The KM would move to the left (decrease)

Enzymes can have both active and regulatory sites. What is the purpose of these sites?

The binding of CTP at a regulatory site on the protein causes decreased production of carbamoyl aspartate

The Michaelis constant (KM) of an enzyme is a measure of

The binding strength of enzyme to substrate

In eukaryotic cells, phospholipids are synthesized by enzymes bound to which of the following?

The cytosolic face of the endoplasmic reticulum

On what side of the plasma membrane are the carbohydrate chains of glycoproteins, proteoglycans, and glycolipids located?

The extracellular side

Which of the following best describes the stable protein-ligand interaction that is represented in the image? Be sure to use the image as a guide but apply your knowledge regarding how protein and ligand commonly interact with each other. A note of caution though: the red lines in the figure are merely representing interactions and are not meant to be quantified.

The formation of a set of many weak, non-covalent interactions maintains the interaction between protein and ligand

In their search for the molecular basis of cystic fibrosis, researchers identified a chlorine ion channel in which a variety of inherited mutations can precipitate the disease. These studies also showed that people who do not have cystic fibrosis can harbor amino acid substitutions in this protein—even in a critical stretch of amino acids that forms a membrane-spanning α helix. How is it possible for such amino acid substitutions to exist within the population without disrupting the α helical structure of that region of the channel?

The formation of an a helix is governed by hydrogen bonding between atoms that are not in the side chains (R groups) of the amino acids in this region

Why do phospholipids form bilayers in water?

The hydrophilic head is attracted to water, while the hydrophobic tail shuns water

What does the primary structure of a protein refer to?

The linear amino acid sequence of the protein

All of the carbohydrates in the plasma membrane face the cell exterior. Which direction do the carbohydrates on internal cell membranes face?

The lumen of the vesicle or organelle

In a famous experiment, mouse cells and human cells were fused into hybrid cells and the membrane proteins of human origin and mouse origin were specifically tagged and examined. After cell fusion and incubation, what was observed by investigators?

The mouse and human proteins mixed evenly throughout the membrane of the hybrid cell

In the α helices of transmembrane proteins, the hydrophobic side chains face which direction?

The outside of the membrane-spanning helix

How does phosphorylation control protein activity?

The phosphate group induces a change in the protein's confromation

Scientists were studying yeast cells in which a mutation inactivated a gene required for cell division. Without this gene—and the protein it encoded—these mutant yeast cells were unable to divide normally. But the scientists discovered that introducing a related protein from human cells could "rescue" these mutant yeast cells, allowing the cells to resume normal division. Based on this finding, what is the most likely conclusion you could make?

The proteins that control cell division in yeast and humans are functionally equivalent and have been conserved, almost unchanged, for more than a billion years

Which of the following is true of an enzyme that is operating at its maximum rate?

The substrate-binding sites on the enzyme molecules are fully occupied

Which of the following does not occur in cells?

The use of heat to burn foodstuffs and transport glucose

Why do phospholipids aggregate to form cell membranes?

They are amphipathic

What is the role of activated carriers in cells?

They capture energy from energy releasing reactions and transfer it to other reactions

Which of the following is true about amyloid protein structures?

They consist of stacked B sheets

Ras is a GTP-binding protein involved in cell proliferation (division). In its active form, with GTP bound, Ras activates cell signaling pathways that promote cell division. Mutations in the gene that encodes Ras can lead to cancer. How might mutations in the gene encoding Ras lead to the uncontrolled proliferation characteristic of cancer cells?

They decrease the rate at which Ras hydrolyzes GTP

Which statement is true of hydrophilic molecules?

They mix well with water

What is true of human red blood cells?

They possess no internal membranes

All of the following are true concerning enzymes except which statement?

They require an input of energy from ATP for activation

In what way are all cells alike?

They store their genetic instructions in DNA

Inhibitor molecules can block an enzyme's activity. Some inhibitors, called competitive inhibitors, compete directly with the substrate for the enzyme's active site. What effect will such inhibitors have on the reaction?

They will have no effect on the Vmax of the reaction

Determine whether the following statement is true or false: Adenosine triphosphate (ATP) is a crucially important energy carrier in cells.

True

Determine whether the following statement is true or false: Energetically unfavorable reactions can occur if they are coupled to a second reaction with a negative ΔG so large that the net ΔG of the entire process is negative.

True

Determine whether the following statement is true or false: In isolation, the formation of an activated carrier, such as ATP, NADH, or NADPH, is an energetically unfavorable reaction.

True

Determine whether the following statement is true or false: When an enzyme lowers the activation energy for the forward reaction X → Y, it also lowers the activation energy for the reverse reaction Y → X by the same amount.

True

Is the following statement true, false, or impossible to determine? Many protein molecules (not just enzymes) are allosteric.

True

Is the following statement true, false, or impossible to determine? The binding of a regulatory ligand can change the equilibrium between two protein conformations.

True

Antibodies are large proteins with quarternary structure and multiple domains, but only a specific portion of the antibody directly binds to antigen. Which of the following antibody domains directly determine antigen binding?

VH domains and VL domains

Which of these amino acids could be represented by the green side chains that are clustered in the center of the folded protein?

Valine, phenylalanine, and leucine

Which contains the largest number of carbon-carbon double bonds?

Vegetable oil

In an enzyme-catalyzed reaction, a small value of KM indicates that a substrate binds to the enzyme in which manner?

Very tightly

On the basis of weight, which is most abundant in a living bacterial cell?

Water

In a lipid bilayer, where do lipids rapidly diffuse?

Within the plane of their own monolayer

Which of the following is frequently studied as a model vertebrate?

Zebrafish