Chapter 24

(a) Draw the Lewis structure for the amino acid valine, showing the amino group and the carboxylic acid group in their un-ionized forms. (b) Draw the Lewis structure for the zwitterionic form of valine. (c) Which of these structures will be the predominant form at physiological pH?

Consider the amino acids alanine, leucine, serine, phenylalanine, lysine, and aspartic acid. Which have polar R groups, and which have nonpolar R groups?

Do the amino acid sequences: valine-asparagine and asparagine-valine represent the same compound? Explain.

Identify the type of structure (primary, secondary, tertiary, or quaternary) that corresponds to the following statements. (a) This type of structure is the amino acid sequence in the protein. (b) This type of structure indicates how different peptide chains in the overall protein are arranged with respect to one another. (c) This type of structure refers to how the polypeptide chain is folded, including how amino acids that are far apart in the sequence end up in the overall molecule. (d) This type of structure deals with structures that arise from hydrogen bonding between amide groups in the protein's backbone.

The \(\beta\) -pleated sheet is a structure that commonly arises in proteins. Part of a \(\beta\) -pleated sheet is shown in the following figure. This type of structure is an example of which level of protein structure: primary, secondary, tertiary, or quaternary?

Draw the structural formulas for \(\alpha\) -D-glucose and \(\beta\) -D-glucose.

(a) Draw the structural formula for the sugar \(\beta\) -D-ribose. (b) Draw the structural formula for the nucleoside adenosine (it consists of \(\beta\) -D-ribose and adenine). (c) Draw the structural formula for the nucleotide adenosine \(5^{\prime}\) -monophosphate.

(a) Draw the structural formula for the sugar \(\beta\) -p-2-deoxyribose. (b) Draw the structural formula for the nucleoside deoxyadenosine (it consists of \(\beta\) -D-2-deoxyribose and adenine). (c) Draw the structural formula for the nucleotide deoxyadenosine \(5^{\prime}\) -monophosphate.

Draw the structural formula for the tetradeoxynucleotide CGTA.

Sketch a section of a phospholipid bilayer in which you let a circle represent the polar head group and curvy lines represent the hydrocarbon tails. Label the regions of the bilayer as being polar or nonpolar.

What structure do all steroids have in common?

Consider the following reaction: $$\mathrm{NADH}+\mathrm{H}^{+}+1 / 2 \mathrm{O}_{2} \rightarrow \mathrm{NAD}^{+}+\mathrm{H}_{2} \mathrm{O}$$ (a) Which species (NADH, H \(^{+}\), or \(\mathbf{O}_{2}\) ) undergoes oxidation? (b) Which species undergoes reduction? (c) Which species is the oxidizing agent? (d) Which species is the reducing agent?

The body processes ethanol by first converting it to acetaldehyde in a reaction catalyzed by the enzyme alcohol dehydrogenase. $$\mathrm{CH}_{3} \mathrm{CH}_{2} \mathrm{OH}+\mathrm{NAD}^{+} \stackrel{\text { alcohol dehydrogenase }}{\longrightarrow} \mathrm{CH}_{3} \mathrm{CHO}+\mathrm{NADH}+\mathrm{H}^{+}$$ In the body, acetaldehyde can cause headaches and nausea and is one of the causes of hangovers. Eventually, the acetaldehyde is oxidized to the acetate ion and then converted to carbon dioxide and water. In the reaction of ethanol with \(\mathrm{NAD}^{+},\) which species (ethanol or \(\mathrm{NAD}^{+}\) ) undergoes oxidation? Which species undergoes reduction?

How many codons are possible? All of these codons are used in molecules of mRNA and there are only 20 amino acids normally encoded (plus start codons and stop codons). Is there exactly one codon per amino acid, must some codons select for more than one amino acid, or must there be some amino acids for which there is more than one codon?

There are \(4^{1}=4\) mononucleotides of DNA, there are \(4^{2}=16\) possible dinucleotides, and so on. If a segment of DNA were completely random, how many nucleotides long would it need to be in order to have one possible sequence for each person on Earth (currently about 7.5 billion people)?

In the process of respiration $$\mathrm{C}_{6} \mathrm{H}_{12} \mathrm{O}_{6}(\mathrm{s})+6 \mathrm{O}_{2}(\mathrm{g}) \rightarrow 6 \mathrm{CO}_{2}(\mathrm{g})+6 \mathrm{H}_{2} \mathrm{O}(\ell)$$ which molecule undergoes oxidation? Which molecule undergoes reduction?

The first step of the metabolic process known as glycolysis is the conversion of glucose to glucose6-phosphate. This process has a positive value for \(\Delta_{\mathrm{r}} G^{\circ \prime}\). Glucose \(+P_{i} \rightarrow\) Glucose-6-phosphate \(+\mathrm{H}_{2} \mathrm{O}\) \(\Delta_{\mathrm{r}} G^{\circ \prime}=+13.8 \mathrm{kJ} / \mathrm{mol}-\mathrm{rxn}\) This reaction is coupled to the hydrolysis of ATP \(\mathrm{ATP}+\mathrm{H}_{2} \mathrm{O} \rightarrow \mathrm{ADP}+\mathrm{P}_{\mathrm{i}} \quad \Delta_{\mathrm{r}} G^{\circ \prime}=-30.5 \mathrm{kJ} / \mathrm{mol}-\mathrm{rxn}\) What is the sum of these two equations and the value of \(\Delta_{\mathrm{r}} G^{\circ}\) ' for the coupled reaction? Is the coupled reaction product-favored at equilibrium?

Insulin is a protein important in the metabolism of sugar. Its molar mass can be determined by means of an osmotic pressure experiment. A \(50.0-\mathrm{mg}\) sample of insulin was dissolved in enough water to make 100. mL of solution. This solution was determined to have an osmotic pressure of \(21.8 \mathrm{mm}\) \(\mathrm{H}_{2} \mathrm{O} .\) What is the molar mass of insulin? (Hint: The density of mercury is \(13.6 \mathrm{g} / \mathrm{mL} .\) )

(a) What type of interaction holds DNA's doublehelical strands together? (b) Why would it not be good for DNA's doublehelical strands to be held together by covalent bonds?

For many chemical reactions in the laboratory, a percent yield of the correct product of \(95 \%\) is considered very good. Many biochemical reactions, however, require a much greater percent yield of the correct product. (a) Assume that there is a process that replicates DNA with only \(95 \%\) accuracy for each nucleotide added and that we wish to make complementary copies of identical strands of DNA 10 nucleotides long. What fraction of the molecules produced would have the correct sequence of nucleotides? (b) Many naturally occurring DNA polymerases, enzymes that catalyze the replication of DNA, have an accuracy much greater, often being \(99.999999 \%\) accurate. If an enzyme with this accuracy constructed a 10 -nucleotide sequence of DNA, what fraction of the molecules would have the correct sequence?

(a) Describe what occurs in the process of transcription. (b) Describe what occurs in the process of translation.

Which of the following statements is/are true? (a) Breaking the \(P-\) O bond in ATP is an exothermic process. (b) Making a new bond between the phosphorus atom in the phosphate group being cleaved off ATP and the OH group of water is an exothermic process. (c) Breaking bonds is an endothermic process. (d) The energy released in the hydrolysis of ATP may be used to run endothermic reactions in a cell.