Chapter 20

In living cells, amino acids combine to make peptides and proteins. Are these processes accompanied by increases or decreases in the entropy of the reaction system?

What is the difference between a peptide bond and an amide bond?

What does the alpha mean in \(\alpha\) -amino acid?

In 1806 French scientists were the first to isolate an amino acid. The source was asparagus shoots. The compound forms an anion in neutral aqueous solutions. Can you identify it?

Meteorites contain more L-amino acids, which are the forms that make up the proteins in our bodies, than D-amino acids. What do the prefixes \(\mathrm{L}\) - and \(\mathrm{D}\) - mean?

Why do most amino acids exist in the zwitterionic form at physiological \(\mathrm{pH}(\mathrm{pH} \approx 7.4) ?\)

A simple organic acid with no functional groups other than an alkyl chain and a carboxylic acid typically has a \(\mathrm{p} K_{\mathrm{a}}\) between 4 and \(5 .\) The \(\mathrm{p} K_{\mathrm{a}}\) values of amino acids are all between 1.7 and \(2.4 .\) Why are amino acids more acidic than simple carboxylic acids?

Draw all possible structures of the peptides produced from condensation reactions of the following L-amino acids: a. Alanine \(+\) serine b. Alanine \(+\) phenylalanine c. Alanine \(+\) valine

Draw all possible structures of the peptides produced from condensation reactions of the following L-amino acids: a. Methionine \(+\) alanine \(+\) glycine b. Methionine \(+\) valine \(+\) alanine c. Serine \(+\) glycine \(+\) tyrosine

Which of the four levels of protein structure is most closely associated with the sequence of amino acids in a protein?

Which type of intermolecular interaction plays the dominant role in holding strands of proteins together in \(\beta\)-pleated sheets and stabilizing \(\alpha\) helices?

Which level of protein structure is associated with ion-ion interactions and disulfide bond formation?

Hard-Boiled Eggs The protein in egg whites is ovalbumin. When an egg is hard- boiled, which is least affected in ovalbumin: its primary, secondary, tertiary, or quaternary structure? Explain your answer.

Describe the induced-fit theory of enzyme activity.

What will happen if an enzyme is added to a solution in which the substrate and product are in equilibrium?

Describe the role that molecular structure plays in the specificity of enzyme activity.

The rates of most reactions increase with increasing temperature, but above a critical temperature the rate of an enzyme-mediated reaction decreases with increasing temperature. Explain why.

When protein strands fold back onto themselves in forming stable tertiary structures, lysine residues are often paired up with glutamic acid residues. Why?

What are the structural differences between starch and cellulose?

Is the fuel value of glucose in the linear form the same as that in the cyclic form?

Without doing the actual calculation, estimate the fuel values of glucose and starch by considering average bond energies. Do you predict the fuel values of the two substances to be the same or different?

Describe in your own words the function of carbohydrates in the diet.

Do polysaccharides have a quaternary structure? Explain your answer.

How do we calculate the overall free-energy change of a process consisting of two steps?

During glycolysis, a monosaccharide is converted to pyruvate. Do you think this process produces an increase or decrease in the entropy of the system? Explain your answer.

When \(5.00 \mathrm{g}\) of glucose \(\left(\mathrm{C}_{6} \mathrm{H}_{12} \mathrm{O}_{6}\right)\) was burned in a bomb calorimeter, the temperature of \(1.750 \mathrm{kg}\) of water was raised from \(19^{\circ} \mathrm{C}\) to \(39^{\circ} \mathrm{C} .\) The specific heat of water is \(4.184 \mathrm{J} / \mathrm{g} \cdot^{\circ} \mathrm{C}\) a. Calculate the fuel value (energy) of the glucose. b. Fructose \(\left(\mathrm{C}_{6} \mathrm{H}_{12} \mathrm{O}_{6}\right)\) has the same energy value as glucose when measured in a calorimeter, but dietarily, 1 oz of fructose provides 104 Calories of energy, while 1 oz of glucose provides 110 Calories. Explain why these values differ.

What is the difference between a saturated and an unsaturated fatty acid?

Why are the average fuel values of fats higher than those of carbohydrates and proteins?

Polar Exploration Some Arctic explorers have eaten sticks of butter on their explorations. Give a nutritional reason for this unusual cuisine.

Salad Dressing Salad dressings containing oil and vinegar quickly separate on standing. Explain the observed separation of layers based on the structure and properties of aqueous vinegar and oil.

Do triglycerides have a chiral center? Explain your answer.

Using your knowledge of molecular geometry and intermolecular forces, explain why polyunsaturated triglycerides are more likely to be liquids and not solids than saturated triglycerides?

Draw the structures of the three fats formed by the reaction of glycerol with (a) octanoic acid (C \(_{7} \mathrm{H}_{15} \mathrm{COOH}\) ), (b) decanoic acid \(\left(\mathrm{C}_{9} \mathrm{H}_{19} \mathrm{COOH}\right),\) and \((\mathrm{c})\) dodecanoic acid \(\left(\mathrm{C}_{11} \mathrm{H}_{23} \mathrm{COOH}\right).\)

What are the three kinds of molecular subunits in DNA? Which two form the "backbone" of DNA strands?

Why does a codon consist of a sequence of three, and not two, ribonucleotides?

What kind of intermolecular force holds together the strands of DNA in the double-helix configuration?

Draw the structure of adenosine \(5^{\prime}\) -monophosphate, one of the four ribonucleotides in a strand of RNA.

During the replication of DNA, a segment of an original strand has the sequence T-C-G-G-T-A. What is the sequence of the double-stranded helix formed in replication?

During transcription, a segment of the strand of DNA that is transcribed has the sequence T-C-G-G-T-A. What is the corresponding sequence of nucleotides on the messenger RNA that is produced in transcription?

Cytochrome \(\mathrm{c}\) is an enzyme involved in oxidationreduction reactions and is an intermediate in apoptosis, a controlled form of killing cells in response to infection or DNA damage. An elemental analysis of cytochrome c determined that it is \(0.43 \%\) iron and \(1.48 \%\) sulfur by mass. What is the minimum molecular weight of cytochrome c, and what is the minimum number of sulfur atoms per molecule?

The addition of ethanol to an aqueous solution of a globular protein causes the protein to denature. Ethanol also disrupts the structure of cell membranes. What interactions could be responsible for both of these effects?

Without doing the actual calculation, estimate the fuel values of leucine and isoleucine by considering average bond energies. Should the fuel values of the two amino acids be the same? Actual calorimetric measurements show that isoleucine has a lower fuel value than leucine. Explain why.