Chapter Questions
wqwqwqwqDenaturation is usually associated with transitions from helical structures to random coils. If an imaginary process were to transform the keratin in your hair from an $\alpha$ -helix to a $\beta$ -pleated sheet structure, would you call the process denaturation? Explain.
Show how to form the dipeptide valylphenylalanine (Val-Phe).
What is the oxidation number (the charge) on the platinum atom in cisplatin, $\left[\mathrm{Pt}\left(\mathrm{NH}_{3}\right)_{2} \mathrm{Cl}_{2}\right] ?$
Describe the bonding in the complex ion $\left[\mathrm{Co}\left(\mathrm{NH}_{3}\right)_{5} \mathrm{Cl}\right]^{2+}$
What kind of noncovalent interaction occurs between the side chains ofarginine and glutamic acid?
What are the functions of (a) ovalbumin and(b) myosin?
The members of which class of proteins are insoluble in water and can serve as structural materials?
What is the function of an immunoglobulin?
What are the two basic types of proteins?
What is the difference in structure between tyrosine and phenylalanine?
Classify the following amino acids as nonpolar, polar but neutral, acidic, or basic.(a) Arginine(b) Leucine(c) Glutamic acid(d) Asparagine(e) Tyrosine(f) Phenylalanine$(g)$ Glycine
Which amino acid has the highest percentage of nitrogen $(\mathrm{g} \mathrm{N} / 100 \mathrm{g} \text { amino acid }) ?$
Why does glycine have no D or L form?
Draw the structure of proline. To which class of heterocyclic compounds does this molecule belong? (See Section 16.1.)
Which amino acid is also a thiol?
Why is it necessary to have proteins in our diets?
Which amino acids in Table 22.1 have more than one stereocenter?
What are the similarities and differences in the structures of alanine and phenylalanine?
Draw the structures of $L$ - and n-valine.
Why are all amino acids solids at room temperature?
Show how alanine, in solution at its isoelectric point, acts as a buffer (write equations to show why the pH does not change much if we add an acid or a base
Explain why an amino acid cannot exist in an un-ionized form at any pH.
Draw the structure of valine at pH 1 and at $\mathrm{pH} 12$
Draw the most predominant form of aspartic acid at its isoelectric point.
Draw the most predominant form of histidine at its isoelectric point.
Draw the most predominant form of lysine at its isoelectric point.
Draw the sequential transition of glutamic acid as it passes from its fully protonated form to its fully deprotonated form as the pH rises.
Which of the three functional groups on histidine is the most unique?
How are aromatic amino acids related to neurotransmitters?
Why is histidine considered a basic amino acid when the $\mathrm{p} K_{\mathrm{a}}$ of its side chain is $6.0 ?$
Which are the acidic amino acids?
Which are the basic amino acids?
Why does proline not absorb light at 280 nm?
Two of the 20 amino acids listed in Table 22.1 can be obtained by hydroxylation of other amino acids. What are those two, and what are their precursor amino acids?
When a protein contains hydroxyproline, at what point in the production of the protein is the proline hydroxylated?
What is the effect of thyroxine on metabolism?
How is thyroxine made?
Show by chemical equations how alanine and glutamine can be combined to give two different dipeptides.
A tetrapeptide is abbreviated as DPKH. Which amino acid is at the N-terminal, and which is at the C-terminal?
Draw the structure of a tripeptide made of threonine, arginine, and methionine.
(a) Use the three-letter abbreviations to write a representation of the following tripeptide:(b) Which amino acid is at the C-terminal end, and which is at the N-terminal end?
A polypeptide chain is made of alternating valine and phenylalanine. Which part of the polypeptide is polar (hydrophilic)?
(a) How many atoms of the peptide bond lie in the same plane?(b) Which atoms are they?
(a) Draw the structural formula of the tripeptide met-ser-cys.(b) Draw the different ionic structures of this tripeptide at $\mathrm{pH} 2.0,7.0,$ and 10.0
How can a protein act as a buffer?
Proteins are least soluble at their isoelectric points. What would happen to a protein precipitated at its isoelectric point if a few drops of dilute HCl were added?
How many different tripeptides can be made(a) using one, two, or three residues each of leucine, threonine, and valine and (b) using all 20 amino acids?
How many different tetrapeptides can be made(a) if the peptides contain the residues of asparagine, proline, serine, and methionine and (b) if all 20 amino acids can be used?
How many amino acid residues in the A chain of insulin are the same in insulin from humans, cattle (bovine), hogs, and sheep?
Based on your knowledge of the chemical properties of amino acid side chains, suggest a substitution for leucine in the primary structure of a protein that would probably not change the character of the protein very much.
Is a random coil a (a) primary, (b) secondary,(c) tertiary, or (d) quaternary structure?? Explain.
Decide whether the following structures that exist in collagen are primary, secondary, tertiary, or quaternary.(a) Tropocollagen(b) Collagen fibril(c) Collagen fiber(d) The proline- hydroxyproline- glycine repeating sequence
Proline is often called an $\alpha$ -helix terminator; that is, it is usually in the random-coil secondary structure following an $\alpha$ -helical portion of a protein chain. Why does proline not fit easily into an $\alpha$ -helix structure?
Consider the coordination compound $\mathrm{Fe}(\mathrm{CO})_{5}$ and show that in forming this compound, the 18 -electron rule is satisfied for iron.
Consider the molecule carbon monoxide, CO.(a) Explain why the following is not an acceptable Lewis structure for CO. (Chapter 3)(b) Write an acceptable structure for CO. (Chapter 3 )(c) Propose which electron pair of $\mathrm{CO}$ is donated to iron to form the coordinate covalent bond $\mathrm{Fe}(\mathrm{CO})_{5}$ (Chapter 3 )(d) Draw a Lewis structure for an oxygen molecule, $\mathrm{O}_{2}$ and suggest how an oxygen molecule might form a coordinate covalent bond with an $\mathrm{Fe}^{2+}$ ion that is present in hemoglobin and myoglobin. (Chapter 3 )
Consider the coordination compound $\left[\mathrm{Zn}\left(\mathrm{NH}_{3}\right)_{2} \mathrm{Cl}_{2}\right]$ which contains $\mathrm{Zn}\left(\mathrm{NH}_{3}\right)_{2}^{2+}$ and $\mathrm{Cl}^{-}$ ions. Show that in forming this coordination compound, the 18 -electron rule is satisfied for zinc.
Knowing what you do about VSEPR, predict the shape (geometry) of the cobalt binding site in vitamin $\mathrm{B}_{12}$
Polyglutamic acid (a polypeptide chain made only of glutamic acid residues) has an $\alpha$ -helix conformation below pH 6.0 and a random-coil conformation above pH $6.0 .$ What is the reason for this conformational change?
Distinguish between intermolecular and intramolecular hydrogen bonding between backbone groups. Where in protein structures do you find one, and where do you find the other?
Identify the primary, secondary, and tertiary structures in the numbered boxes:
If both cysteine residues on the $\mathrm{B}$ chain of insulin were changed to alanine residues, how would it affect the quaternary structure of insulin?
(a) What is the difference in the quaternary structure between fetal hemoglobin and adult hemoglobin?(b) Which can carry more oxygen?(c) What would the oxygen saturation curve of fetal hemoglobin look like compared to that of mygoglobin and regular adult hemoglobin?
Where are the nonpolar side chains of proteins located in an integral membrane protein?
The cytochrome $c$ protein is important in producing energy from food. It contains a heme surrounded by a polypeptide chain. What kind of structure do these two entities form? To which group of proteins does cytochrome $c$ belong?
Hemoglobin is an important protein for many reasons and has interesting physical characteristics. How would you classify hemoglobin?
In a $6 M$ urea solution, a protein that contained mostly antiparallel $\beta$ -sheets became a random coil. Which groups and bonds were affected by urea?
What kind of changes are necessary to transform a protein having a predominantly $\alpha$ -helical structure into one having a $\beta$ -pleated sheet structure?
Which amino acid side chain is most frequently involved in denaturation by reduction?
What does the reducing agent do in straightening curly hair?
Silver nitrate is sometimes put into the eyes of newborn infants as a preventive measure against gonorrhea. Silver is a heavy metal. Explain how this treatment may work against bacteria.
Why do nurses and physicians use $70 \%$ alcohol to wipe the skin before giving injections?
(Chemical Connections 22 A) Why must some people avoid drinking diet sodas with Nutrasweet?
(Chemical Connections 22 B) AGE products become disturbing only in elderly people, even though they also form in younger people. Why don't they harm younger people?
(Chemical Connections $22 \mathrm{C}$ ) Define hypoglycemicawareness.
(Chemical Connections 22 D) How does hydroxyurea therapy alleviate the symptoms of sickle cell anemia?
(Chemical Connections $22 \mathrm{E}$ ) What is the difference in the conformation between normal prion protein and the amyloid prion that causes mad cow disease?
(Chemical Connections $22 \mathrm{F}$ ) What is the aim of proteomics?
(Chemical Connections $22 \mathrm{G}$ ) Explain the difference in oxygen-binding behavior of myoglobin and hemoglobin.
(Chemical Connections $22 \mathrm{H}$ ) How does the fiberscope help to heal bleeding ulcers?
Which diseases are associated with amyloid plaques?
How many different dipeptides can be made(a) using only alanine, tryptophan, glutamic acid, and arginine and(b) using all 20 amino acids?
Draw the structure of lysine (a) above,(b) below, and(c) at its isoelectric point.
In collagen, some of the chains of the triple helices in tropocollagen are cross-linked by covalent bonds between two lysine residues. What kind of structure is formed by these cross-links? Explain.
Considering the vast number of animal and plant species on Earth (including those now extinct) and the large variety of protein molecules in each organism, have all possible protein molecules been used already by some species or other? Explain.
What kind of noncovalent interaction occurs between the following amino acids?(a) Valine and isoleucine(b) Glutamic acid and lysine(c) Tyrosine and threonine(d) Alanine and alanine
How many different decapeptides (peptides containing 10 amino acids each can be made from the 20 amino acids?
Which amino acid does not rotate the plane of polarized light?
Write the expected products of the acid hydrolysis of the following tetrapeptide:
What charges are on aspartic acid at pH $2.0 ?$
How many ways can you link the two amino acids lysine and valine in a dipeptide? Which of these peptide bonds will you find in proteins?
Enzymes are biological catalysts and usually proteins. They catalyze common organic reactions. Why are amino acids such as histidine, aspartic acid, and serine found more often near the reaction catalysis site than amino acids such as leucine and valine?
Hormones are molecules that are released from one tissue but have their effect in another tissue. Give an example of a hormone encountered in this chapter that would be ineffective if taken orally. Give an example of one that could be effective if taken orally.
Using what you know about protein denaturation, what is one reason you must maintain a body temperature in a strict range?
What is the difference between genomics and proteomics?
Why does knowing the complete genome of an organism not necessarily tell you about the nature of all the proteins in the organism?
Why is collagen not a very good source of dietary protein?
A recent diet supplement advertised that it would repair your muscles while allowing you to burn fat because the product had collagen protein. Evaluate this claim.