Cell Biology Chapter 4

You wish to produce a human enzyme, protein A, by introducing its gene into bacteria. The genetically engineered bacteria make large amounts of protein A, but it is in the form of an insoluble aggregate with no enzymatic activity. Which of the following procedures might help you to obtain soluble, enzymatically active protein.

A. Make the bacteria synthesize protein A in smaller amounts. B. Dissolve the protein aggregate in urea, then dilute the solution and gradually remove the urea. D. Make the bacteria overproduce chaperone proteins in addition to protein A.

Instead of studying one or two proteins or protein complexes present in the cell at any given time, we can now look at a snapshot of all proteins being expressed in cells being grown in specific conditions. This large scale, systematic approach to the study of proteins is called ___.

A. Proteomics

For some proteins, small molecules are integral to their structure and function. Enzymes can synthesize some of these small molecules, whereas others, called vitamins, must be ingested in the food we eat. Which of the following molecules is NOT classified as a vitamin but does require the ingestion of a vitamin for it's production?

A. Retinal

The three-dimensional coordinates of atoms within a folded protein are determined experimentally. After researchers obtain a protein's structural details, they can use different techniques to highlight particular aspects of the structure. What visual model best displays a protein's secondary structures ( alpha helices, and Beta sheets)?

A. Ribbon

You have two purified samples of protein Y: the wild-type (nonmutated) protein and a mutant version with a single amino acid substitution. When washed through the same gel-filtration column, mutant protein Y runs through the column more slowly than the normal protein. Which of the following changes in the mutant protein is most likely to explain this result?

A. The loss of a binding site on the mutant protein surface through which protein Y normally forms dimers.

Studies conducted with a lysozyme mutant that contains an Asp-->Asn change at position 52 and a Glu-->Gln change at position 35 exhibited almost a complete loss in enzymatic activity. What is the most likely explanation for the decrease in enzyme activity in the mutant?

B. Absense of negative charges in the active site

Which of the following is NOT a feature commonly observed in Beta sheets?

B. Coiled-coil patterns

Proteins bind selectively to small molecule targets called ligands. The selection of one ligand out of a mixture of possible ligands depends on the number of weak, noncovalent interactions in the protein's ligand-binding site. Where is the binding site typically located in the protein structure?

B. Inside a cavity on the protein surface

The phosphorylation of a protein is typically associated with a change in activity, the assembly of a protein complex, or the triggering of a downstream signaling cascade. The addition of ubiquitin, a small polypeptide, is another type of covalent modification that can affect the protein function. Ubiquitylation often results in ___.

B. Protein degradation

To study how proteins fold, scientists must be able to purify the protein of interest, use solvents to denature the folded protein, and observe the process of refolding at successive time points. What is the effect of the solvents used in the denaturation process?

B. The solvents break all noncovalent interactions.

The human immune system produces ___ of different immunoglobins, also called ___, which enable the immune system to recognize and fight germs by specifically binding one or a few related ___. The hypervariable structural element that forms the ligand-binding site is comprised of several ___. Purified antibodies are useful for a variety of experimental purposes, including protein purification using ___ chromatography.

Billions; Antibodies; Antigens; Loops; affinity

Fully folded proteins typically have polar side chains on their surfaces, where electrostatic attractions and hydrogen bonds can form between the polar group on the amino acid and the polar molecules in the solvent. In contrast, some proteins have a polar side chain in their hydrophobic interior. Which of the following would NOT occur to help accomodate an internal, polar side chain?

C. A hydrogen bond forms between a polar side chain and an aromatic side chain.

Which of the following mechanisms best describes the manner in which lysozyme lowers the energy required for its substrate to reach its transition state conformation?

C. By speeding up the rate at which water molecules collide with the substrate.

The biosynthetic pathway for the two amino acids E and H is shown schematically in Figure Q4-41. You are able to show that E inhibits enzyme V, and H inhibits enzyme X. Enzyme T is most likely to be subject to feedback inhibition by ___ alone.

C. C

Which of the following statements is true?

C. Disulfide bonds stabilize but do not change a protein's final conformation.

Which of the following states is true?

C. Nonpolar amino acids tend to be found in the interior of proteins.

Which of the following methods used to study proteins is limited to proteins with a molecular weight of 50 kD or less?

C. Nuclear Magnetic Resonance

Cysteine

Cys; C; Nonpolar

The Ras protein is a GTPase that functions in many growth-factor signaling pathways. In its active form, with GTP bound, it transmits a downstream signal that leads to cell proliferation; in its inactive form, with GDP bound, the signal is not transmitted. Mutations in the gene for Ras are found in many cancers. Of the choices below, which alteration of Ras activity is most likely to contribute to the uncontrolled growth of cancer cells?

D. A change that decreases the rate of hydrolysis of GTP by Ras

Motor proteins use the energy in ATP to transport organelles, rearrange elements of the cytoskeleton during cell migration, and move chromosomes during cell division. Which of the following mechanisms is sufficient to ensure the unidirectional movement of a motor protein along its substrate?

D. A conformational change is linked to ATP hydrolysis.

Protein structures have several different levels of organization. The primary structure of a protein is its amino acid sequence. The secondary and tertiary structures are more complicated. COnsider the definitions below and select the one that best fits the term "protein domain."

D. A protein segment that folds independently

Although all protein structures are unique, there are common structural building blocks that are referred to as regular secondary structures. Some have alpha helices, some have Beta sheets, and still others have a combination of both. What makes it possible for proteins to have these common structural elements?

D. Hydrogen Bonds along the protein backbone

Lysozyme is an enzyme that specifically recognizes bacterial polysaccharides, which renders it an effective antibacterial agent. Into what classification of enzymes does lysozyme fall?

D. Hydrolase

Energy required by the cell is generated in the form of ATP. ATP is hydrolyzed to power many of the cellular processes, increasing the pool of ADP. ADP molecules then bind to glycolytic enzymes, which will lead to the production of more ATP. The best way to describe how oxidation energy is converted to ATP energy during glycolysis is by ___.

D. Substrate-level phosphorylation

The correct folding of proteins is necessary to maintain healthy cells and tissues. Unfolded proteins are responsible for such neurodegenerative disorders as Alzheimer's, Huntington's, and Creutzfeld-Jacob disease (the specific faulty protein is different for each disease). What is the ultimate fate of these disease-causing, unfolded proteins?

D. They form protein aggregates.

Carboxylase

Enzyme

Feedback inhibition is defined as a mechanism of down-regulating enzyme activity by the accumulation of a product earlier in the pathway.

False

Generally, the total number of nonpolar amino acids has a greater effect on protein structure than the exact order of amino acids in a polypeptide chain.

False

Protein phosphorylation is another way to alter the conformation of an enzyme and serves exclusively as a mechanism to increase enzyme activity.

False

The "polypeptide backbone" refers to all atoms in a polypeptide chain, except for those that form the peptide bonds.

False

Antibodies are Y shaped and are composed of six different polypeptide chains.

False; Composed of 4 polypeptide chains.

The amino acids in the interior of a protein do not interact with the ligand and do not play a role in selective binding.

False; Directly interacts with ligand.

Homeodomain Proteins

Gene Regulatory

Glutamine

Gln; Q; Polar

Glutamic Acid

Glu; E; Acidic, Negative

Glycine

Gly; G; Nonpolar

Histidine

His; H; Positive Charge

ATPases generate ATP for the cell.

Hydrolyzes ATP, do not produce it.

Myosin

Motor

Green Fluorescent Protein

Special Purpose

A newly synthesized protein generally folds up into a ___ conformation. All the information required to determine a protein's conformation is contained in its amino acid ___. On being heated, a protein molecule will become ___ as a result of breakage of ___ bonds. On removal of urea, an unfolded protein can become ___. The final folded conformation adopted by a protein is that of ___ energy.

Stable; Sequence; Denatured; Noncovalent; Renatured; Lowest.

Ferritin

Storage

Tubulin

Structural

Threonine

Thr; T; Polar

Hemoglobin

Transport

Tryptophan

Trp; W; Nonpolar

GTP binding proteins typically have GTPase activity, and the hydrolysis of GTP transforms them to the "off" conformation.

True

Hexokinase recognizes and phosphorylates only one of the glucose stereoisomers.

True

If an enzyme's allosteric binding site is occupied, the enzyme may adopt an alternative conformation that is not optimal for catalysis.

True

The chemical properties of amino acids side chains include charged, uncharged polar, and nonpolar.

True

The relative distribution of polar and nonpolar amino acids in a folded protein is determined largely by hydrophobic interactions, which favor the clustering of nonpolar side chains in the interior.

True

Tyrosine

Tyr; Y; Polar

Valine

Val; V; Nonpolar

Methionine

Met; M; Nonpolar

Arginine

Arg; R; Positive Charge

Asparagine

Asn; N; Uncharged Polar

Aspartic Acid

Asp; D; Acidic, Negative

Calculate how many different amino acid sequences there are for a polypeptide chain 10 amino acids long.

20^10= 10,240,000,000,000

The process of generating monoclonal antibodies is labor-intensive and expensive. An alternative is to use polyclonal antibodies. A subpopulation of purified polyclonal antibodies that recognize a particular antigen can be isolated by chromatography. Which type of chromatography is used for this purpose?

A. Affinity

Globular proteins fold up into compact, spherical structures that have uneven surfaces. They tend to form multisubunit complexes, which also have a rounded shape. Fibrous proteins, in contrast, span relatively large distances within the cell and in the extracellular space. Which of the proteins below is NOT classified as a fibrous protein?

A. Elastase

In an attempt to define the protein domains of protein X, you treat it with a ptoease and use polyacrylamide gel electrophoresis to analyze the peptides produced. In the past, you have used chymotrypsin to perform this experiment, but the stock of this enzyme has been used up. You find a stock of elastase and decide to use it instead of waiting for a new stock of chymotrypsin to arrive. A. Give two reasons why elastase is a good substitute for chymotrypsin in this assay. B. Why might proteolysis of the same substrate by chymotrypsin or elastase yield different results?

A. Elastase is a protease. B. High degree of structural similiarity.

For each of the following indicate whether the individual folded polypeptide chain forms a globular (G) or fibrous (F) protein molecule. A. Keratin B. Lysozyme C. Elastin D. Collagen E. Hemoglobin F. Actin

A. Keratin- Fibrous B. Lysozyme- Globular C. Elastin- Fibrous D. Collagen- Fibrous E. Hemoglobin- Globular F. Actin- Globular

Which of the following is NOT a feature commonly observed in alpha helices?

A. Left-Handedness

Alanine

Ala; A; nonpolar

Isoleucine

Ile; I; Nonpolar

Leucine

Leu; L; Nonpolar

Any substance that will bind to a protein is known as it's ___. Enzymes bind their ___ at the ___. The enzyme hexokinase is so specific that it reacts with only one of the two ___ of glucose. Enzymes catalyze a chemical reaction by lowering the ___, because they provide conditions favorable for the formation of a ___ intermediate called the ___. Once the reaction is completed, the enzyme releases the ___ of the reaction.

Ligand; Substrates; Active Site; Isomers; Activation Energy; High-energy; Transition State; Products

Lysine

Lys; K; Positive Charge

Phenylalanine

Phe; F; Nonpolar

Proline

Pro; P; Nonpolar

Rhodopsin

Receptor

The alpha helices and Beta sheets are examples of protein ___ structure. A protein such as hemoglobin, which is composed of more than one protein ___, has ___ structure. A protein's amino acid sequence is known as its ___ structure. A protein ___ is the modular unit from which many larger single-chain proteins are constructed. The three-dimensional conformation of a protein is its ___ structure.

Secondary; Subunit; Quaternary; Primary; Domain; Tertiary

Serine

Ser; S; Polar

Insulin

Signal Protein