Chapter 4 Homework

Which amino acid is the smallest and least chemically active?

glycine

Indicate whether the amino acids are hydrophilic or hydrophobic by dragging them into the appropriate categories: methionine, aspartate, isoleucine, valine, lysine, and phenylaline

hydrophobic: methionine, isoleucine, valine, and phenylaline hydrophilic: aspartate, lysine

When a protein folds, transitioning from denatured to native state, the change in free energy is favorable (ΔG < 0). In general, the entropic change is _________ due to the more limited number of conformations. The enthalpic change is ___________favorable due to the many weak interactions that are formed. With the exception of disulfide bonds, weak interactions include the formation of ___________hydrogen bonds and numerous _______________ van der Waals interactions in the native state.

unfavorable; favorable; hydrogen; Van der Waals

The various chemical properties of the amino acid side chains determine the chemical properties and the three-dimensional structures of proteins. What are the four groups that amino acids can be divided into? A. charged; aromatic; hydrophilic or polar uncharged; hydrophobic or aliphatic B. polar; nonpolar; aerobic; hydrophobic or aliphatic C. short-chain Polar; long-chain aliphatic; aromatic; unreactive D. charged; aromatic; lipophilic; sulfur-containing

A. charged; aromatic; hydrophilic or polar uncharged; hydrophobic or aliphatic

From the partial nucleotide sequence given below, what peptides could be encoded?5'-GCCUCCAAACCCCUCCA-3' Choose one or more: A.Ala-Ser-Lys-Pro-Leu B.Leu-Gln-Thr-Pro-Pro C.Met-Arg-His-Asp-Pro D.Pro-Pro-Asn-Pro-Ser E.Lys-Pro-Ser-Gly-Met

A.Ala-Ser-Lys-Pro-Leu B.Leu-Gln-Thr-Pro-Pro D.Pro-Pro-Asn-Pro-Ser

Many diseases, including Alzheimer's disease, are associated withChoose one: A. high ATP levels in the liver. B. protein aggregation. C. antibodies. D. dietary deficiencies. E. buildup of uric acid.

B. protein aggregation.

The core biochemical principle that protein structure determines protein function is illustrated by green fluorescent protein (GFP), which is an autofluorescent protein isolated from the Pacific Northwest jellyfish Aequorea victoria. GFP is a β-barrel protein containing in its interior its own chromophore (part of a molecule responsible for producing color). The chromophore forms spontaneously through a chemical reaction involving three amino acid residues. Expression of the cloned GFP gene in most cells results in the emission of green light (∼510 nm) after excitation with blue light (∼470 nm). In other words, as long as the protein maintains its structure, it performs the same function, regardless of the organism from which it originates. GFP is frequently used as a reporter of expression, being added as a fusion tag to other proteins of interest. What would you expect to observe if you overexpressed a GFP fusion protein in E. coli? Choose one: A. The E. coli would have a blue appearance when observed in white light. B. The E. coli would have a green appearance when observed in white light. C. The E. coli would not grow unless they were in a dark environment. D. The E. coli would be no different than a control expressing just the protein of interest without the GFP tag. Multiple sea creatures utilize proteins that interact with light. Why would GFP not be a good choice of light-interacting protein for a creature that lives exclusively in a cold, dark sea cave? Choose one: A. GFP requires many other genes to synthesize the chromophore, making it poorly suited for use in organisms other than jellyfish. B. GFP would not emit green light since there is no blue light for it to absorb and re-emit. C. The environment is too cold for GFP to fold. D. The β barrel of GFP would not fold without light.

B. The E. coli would have a green appearance when observed in white light. B. GFP would not emit green light since there is no blue light for it to absorb and re-emit.

Fibrous proteins are multi-subunit complexes that constitute some of the most abundant proteins in nature, including keratin, silk fiber, and collagen. Keratin is a homodimer of two helical polypeptides that are wrapped around each other to form what is called a coiled coil. The keratin helix itself is right-handed; however, the coiled coil dimer is formed from the helices wrapping around each other in a left-handed direction. The ∼300-amino-acid core polypeptide of each keratin subunit consists of a 7-amino-acid repeating unit, in which the first, and usually the fourth, amino acid is hydrophobic. This repeat provides a hydrophobic strip that rotates anticlockwise around the surface of the helix. Two helices have to twist around each other in order to line up those two hydrophobic strips. Thus, the helices pack together with an extensive hydrophobic interface. The strength of keratin comes from covalent cross-linking between coiled coil dimers as a result of disulfide bridge formation between cysteine residues. Many different types of keratins are found in nature, which differ primarily in the number of cysteine residues. Given the nature of hair and fingernails, and knowing both have high levels of keratin, which of the following is true?Choose one: A. Keratin in hair has more cysteines and therefore fewer disulfide bonds than keratin in fingernails. B. Keratin in hair has more cysteines and therefore more disulfide bonds than keratin in fingernails. C. Keratin in hair has fewer cysteines and therefore fewer disulfide bonds than keratin in fingernails. D. Keratin in hair has fewer cysteines and therefore more disulfide bonds than keratin in fingernails. Getting your hair permed must involve which of the following?Choose one: A. reduction of disulfide bonds, reshaping, and then oxidation of disulfide bonds B. proteolytic digestions of keratin C. irreversible denaturation of keratin D. oxidation of disulfide bonds, reshaping, and then reduction of disulfide bonds

C. Keratin in hair has fewer cysteines and therefore fewer disulfide bonds than keratin in fingernails. A. reduction of disulfide bonds, reshaping, and then oxidation of disulfide bonds

Based on the hydrophobic collapse model for protein folding, which of the following conditions can denature a protein? Choose one or more: A. Exposing the protein to white light causes the hydrophobic residues to cluster in the core. B. Adding glycerol stabilizes hydrophobic residues on the protein surface. C. Changes in pH break salt bridge interactions that stabilize the sequesteration of hydrophobic residues into the protected core of the protein. D. Heating proteins leads to exposure of the hydrophobic core, disrupting folding. E. Lowering the protein concentration changes the hydration surface, altering residues that partition into the hydrophobic core.

C.Changes in pH break salt bridge interactions that stabilize the sequesteration of hydrophobic residues into the protected core of the protein. D.Heating proteins leads to exposure of the hydrophobic core, disrupting folding.

What level of protein structure describes the spatial location of every atom in a protein? A. 1° B. 4° C. 2° D. 3°

D. 3°