BCHM 307 Exam 1 Purdue

Name the four types of small biological molecules. Which three are capable of forming polymeric structures? What are the names of the polymeric structures that are formed?

4 types of biological molecules: amino acids, nucleotides, monosaccharides, lipids

3 capable of forming polymeric strucures: amino acids, monosccharides, and nucleotides

Names of polymeric structures formed: proteins, carbohydrates, nucleic acids

A healthy diet must include some protein. Assuming you had a way to measure the amount of each element in a sample of food, which element would you measure in order to tell whether the food contained protein?

Assuming you had a way to measure each element in a food sample, you should measure for the element nitrogen if determining the amount of protein. Protein is the only macronutrient that contains nitrogen.

Which has the greater entropy, a polymeric molecule or a mixture of its constituent monomers?

The polymeric molecule is much more ordered compared to a mixture of its constituent monomers. This order results in less entropy. A constituent monomer may have multiple arrangements which results in greater entropy.

A soccer coach keeps a couple of instant cold packs in her bag in case one of her players suffers a muscle injury. Instant cold packs are composed of a plastic bag containing a smaller water bag and solid ammonium nitrate. In order to activate the cold pack, the bag is kneaded until the smaller water bag breaks, which allows the released water to dissolve the ammonium nitrate. the equation for the dissolution of ammonium nitrate in water is shown below. How does the cold pack work.

The positive charge indicates that the dissolution of ammonium nitrate is an endothermic process. When the ammonium nitrates dissolves in water, it absorbs heat from its surroundings, making its surroundings cooler, making it useable is a cold pack for injuries.

Which compound has a higher boiling point, H2O or H2S? Explain.

Although both have the same geometry and can form H bonds, the H bonds of water are stronger. The electronegativity between H and O is greater than between H and S, resulting in a greater difference in partial charges on the atoms in the water molecule.

Explain why water forms nearly spherical droplets on the surface of a freshly waxed car. Why doesn't water bead on a clean windshield.

Water is hydrophilic, so when exposed to a hydrophobic surface, water will try minimize its exposure to that surface, which is why it beads in the shape of a spherical droplet on a waxed car. However when a water is exposed to a hydrophilic surface in which it can interact, such as a clean windshield, it will spread out.

Several hours after a meal, partially digested food leaves the stomach and enters the small intestine, where pancreatic juice is added. How does the pH of the partially digested mixture change as it passes from the stomach into the intestine?

The partially digested food has a low pH until the pancreatic juices are added. The pancreatic juice is nearly alkaline and therefore will increase the pH of the partially digested food.

In 1952, Alfred Hershey and Martha Chase carried out experiments using bacteriophages, which consist of nucleic acid enclosed by a protein capsid (coat). They first labeled the bacteriophages with the radioactive isotopes and . Because proteins contain sulfur but not phosphorus, and DNA contains phosphorus but not sulfur, each type of molecule was separately labeled. The radio labeled bacteriophages were allowed to infect the bacteria, and then the preparation was treated to separate the empty capsids (ghosts) from the bacterial cells. The ghosts were found to contain most of the label, whereas 30% of the was found in the new bacteriophages produced by the infected cells. What does this experiment reveal about the roles of bacteriophage DNA and protein?

Some of the labeled "parent" DNA appears in the progeny, but none of the labeled protein appears in the progeny. This indicates that the bacteriophage DNA is involved in the production of progeny bacteriophages, but bacteriophage protein is not required.

A diploid organism with 30,000 kb haploid genome contains 19% T residues. Calculate the the number of A, C, G, and T residues in the DNA of each cell in this organism.

A, T= (.19) (6x10^7) = 1.14x10^7

C,G= (.31) (6x10^7) = 1.86 x 10^7

Explain whether the following statement is true or false: Because a G:C base pair is stabilized by three hydrogen bonds, whereas an A:T base pair is stabilized by only two hydrogen bonds, GC-rich DNA is harder to melt than AT-rich DNA.

False.

The G:C base pair doesn't solely have to rely on hydrogen bonds for stability because it has stronger stacking interactions.

What might you find in comparing the GC content of DNA from Thermus aquaticus or Pyrococcus furiosus and DNA from bacteria in a typical backyard bond?

The DNA of thermus aquaticus or Pyrococcus which thrive in hot environments would have more G and C therefore it is better suited for heat exposure compared to DNA from bacteria in a typical backyard bond

Discuss the shortcomings of the following definitions for a gene:

a. A gene is the information that determines an inherited characteristic such as flower color.

b. A gene is a segment of DNA that encodes a protein.

c. A gene is a segment of DNA that is transcribed in all cells

a. an inherited characteristic could be determined by more than one gene

b. Some sequences of DNA encode RNA molecules that are not translated into protein

c. Some genes are not transcribed during a cell's lifetime. This can occur if the gene is expressed only under certain environmental conditions or in certain specialized cells in a multicellular organism.

An Asp residue in the RNase T1 enzyme is protonated. Does this make the side chain more or less likely to form hydrogen bonds with neighboring amino acid side chains in the enzyme.

The Asp residue is more likely to form hydrogen bonds when protonated. The carboxylic acid side chain can participate in three hydrogen bonds, whereas the carboxylate group can participate in only two

Certain bacteria synthesize cyclic tetrapeptides.

a. Estimate the net charge at pH 7.0 of such a compound that consists of two Pro and two Tyr residues.

b. If the peptide were linear rather than cyclic, what would be the net charge

The net charge is 0

If the molecule were linear, it would contain a free amino group (+1 charge) and a free carboxylate group (-1 charge) but its net charge would still be 0

Read the following sentences and identify each statement as describing the primary, secondary, tertiary, or quaternary structure of the protein:

a. the shape of myoglobin is roughly spherical

b. Hemoglobin consists of four polypeptide chains

c. about one third of the amino acid residues in collagen are glycine

d. the lysozyme molecule contains regions of helical structure

a. tertiary

b. quaternary

c. primary

d. secondary

Proline is known as a helix disrupter; it sometimes appears at the beginning or the end of an alpha helix but never in the middle. Explain

The amino group of pro is linked to its side chain, which limits the conformational flexibility of a peptide bond involving the amino group. The geometry of this peptide bond is incompatible with the bond angles required for a polypeptide to form an alpha helix.

A Glu residue in a receptor protein is altered to Ala in a site-directed mutagensis experiment. Binding of the ligand to the mutant receptor decreases 100 fold. What does this tell you about the interaction between the ligand and the receptor.

Its possible that the ligand has a positive charge and forms in an ion pair with the negatively charged GLu on the receptor. When the Glu is mutated to Ala, the negative charge on the receptor is lost and the ion pair between the receptor and the ligand can no longer form.

In the mid-1980s, scientists noted that if cells were incubated at 42°C instead of the normal 37°C, the synthesis of a group of proteins dramatically increased. For lack of a better name, the scientists called these heat-shock proteins. It was later determined that the heat-shock proteins were chaperones. Why do you think that the cell would increase its synthesis of chaperones when the temperature increases?

When the temperature increases, the vibrational and rotational energy of the atoms making up the protein molecules also increases, which increases the chance that the proteins will denature. Increasing the synthesis of chaperones under these conditions allows the cell to renature, or refold, proteins denatured by heat.

The microtubules involved in cell division are less stable than microtubules found in axon extensions of nerve cells. why is this?

Cell division is a temporary state for a cell and the microtubules used in separating chromosomes must be disassembled after they have pulled the chromosomes to opposite ends of the dividing cell. In contrast, the axonal structures of neurons are relatively permanent, so a more stable tubulin structure is advantageous.

Why is the sequence Ile-Gln-Glu-Val-Glu-Arg-Asp more likely than the sequence Trp-Gln-Glu-Tyr-Glu-Arg-Asp to appear in a coiled coil of keratin?

Although amino acids 1 and 4 are hydrophobic in both sequences, the Trp and Tyr residues are much more than Ile and Val, and therefore would not fit as well in the contact area between the peptide strands of the coiled coil

Straight hair can be curled and curly hair can be straightened by exposing wet hair to a reducing agent, repositioning the hair with rollers, then exposing the hair to an oxidizing agent. Explain how this procedure alters the shape of the hair.

The reducing agent breaks the disulfide bonds between keratin molecules. Setting the hair brings the reduced Cys residues closer to new partners on other keratin chains. When the hair is the exposed to an oxidizing agent, new disulfide bonds form between the Cys residues and the hair retains the shape of the rollers.

A cook decides to flavor a gelatin dessert with fresh papaya and pineapple. The fruits are added to a solution of gelatin in hot water, then the mixture is allowed to cool. What is the result and how could the cook have avoided this? (Hint: Gelatin is a food product obtained from the thermal degradation of collagen.)

-adding papaya or pineapple means the proteolytic enzymes present in the fruit will degrade the collagen/gelatin and prevent it form setting

-if the enzymes in the fruit and heated prior to adding to the gelatin, then the gelatin would set as expected. Using canned fruit wouldn't cause a problem due to being heated during the canning process

Is myosin a fibrous or globular protein? explain

It is both a fibrous and globular protein. Its two heads are globular with several layers of secondary structure. Its tail however consists of a single fibrous coiled coil

Explain why the movement of myosin along an actin filament is "hopping" whereas the movement of kinesin along a microtubule is "walking"

Although each myosin molecule is composed of two globular heads and a fibrous tail, similar to kinesin, the action of the heads is different for each molecule. The myosin heads release and re-attach to the actin microfilamet in synchrony meaning theres a stage when the individual myosin molecule is not attached to the actin, hence the reference to "hopping". In contrast, each of kinesin's two heads detach and reattach to the microtuble sequentially, meaing one of the heads is always in contact with the microtubule as it moves or "walks" along

Explain why a one headed kinesin motor would be ineffective

If kinesin only had one head it wouldn't be able to maintain a connection with the microtubule and the kinesin molecule and its cargo would "float" away. This doesn't happen with the myosin, because many myosin molecules act together; an attached myosin can always compensate for an unattached myosin.

Why is rigor mortis of concern to those in the meat industry

It may require that there be a delay between animal slaughter and butchering.

How could a forensic pathologist use the concept of the rigor mortis to investigate the circumstances of an individuals death?

Following death, rigor mortis iwll occur in a particular time frame depending on the environment in which the body was found. Certain factors, especially temperature, will affect the length of time after death that rigor mortis will occur, and how long it will last. If the environment the body was exposed to after death is known, the occurrence of rigor mortis will help to estimate the time of death.

Why are most enzymes globular rather than fibrous proteins

A globular protein can bind substrates in a sheltered active site and can support an arrangement of functional groups that facilitates the reaction and stabilizes the transition state. Most fibrous proteins are rigid and extended and therefore cannot surround the substrate to sequester it or promote its chemical transformation.

Amino acids such as glycine, alanine, and valine are not known to particiapte directly in acid-base or covalent catalysis.

a. Explain why this is the case.

b. Mutating a glycine, alanine, or valine residue in an enzymes active site can still have dramatic effects on catalysis. Why?

a. Gly, Ala, and Val have side chains that lack the functional groups required for acid-base or covalent catalysis

b. mutating one of these residues may alter the conformation at the active site enough to disrupt the arrangement of other groups that are involved in catalysis

Daniel Koshland has noted that hexokinase undergoes a large conformational change on substrate binding, which apparently prevents water from entering the active site and participating in hydrolysis. However, the serine proteases do not undergo large conformational changes on substrate binding. Explain.

In a serine protease, there is no need to exclude water from the active site, since it is a reactant for the hydrolysis reaction catalyzed by the enzyme

You are attempting to determine KM by measuring the reaction velocity at different concentrations, but you do not realize that the substrate tends to precipitate under the experimental conditions you have chosen. How would this affect your measurement of KM?

The apparent KM would be greater than the true KM because the experimental substrate concentration would be less than expected if some of the substrate has precipitated out of solution during the reaction

Which of the flycerophospholipids have hydrogen bonding head groups?

All except phosphatidylcholine have hydrogen bonding head groups

In some autoimmune diseases, an individual develops antibodies that recognize cell constituents such as DNA and phospholipids. Some of the antibodies actually react with both DNA and phospho-lipids. What is the biochemical basis for this cross-reactivity?

Both DNA and phospholipids have exposed phosphate groups that are recognized by the antibodies

Spicy Indian dishes flavored with hot peppers are often served with a side dish made from whole-milk yogurt. Why is a spoonful of yogurt preferable to a drink of water after a mouthful of spicy food?

The spicy ingredient in the food is a powder made from peppers that contains the hydrophobic compund capsaicin. Yogurt containing whole milk also contains hydrophobic ingredient that cal cleanse the palate of the irritating capsaicin. Water is polar so it does not dissolve the capsaicin and cannot cleanse the palate.

In a nutrition study, volunteers consumed salads with and without added avocado (a rich source of monounsaturated lipids). Blood samples drawn from the volunteers showed a dramatic increase in β-carotene (an orange pigment found in plants that is processed by cells to yield vitamin A) following the consumption of salad containing avocado. Explain these findings.

Vitamin A, and the compound from which it is derived, beta carotene, are lipid soluble molecules. The vegetables in a typical salad do not contain large amounts of lipid. The addition of the lipid rich avocado provides a means to solubilize the beta carotene and thus increase its absorption

Does the vitamin D fit the definition of a vitamin as a substance that an organism requires but cannot synthesize?

The traditional definition of a vitamin (a substance that an organism requires but cannot synthesize) implies that vitamins must be obtained in the diet. Because vitamin D3 can be produced form cholesterol, it is not strictly a vitamin. However, its production does require ultraviolet light, which an individual must obtain through exposure to the sun and which may not always be available.

Explain why long-term use of antibiotics may lead to a vitamin K deficiency

Bacteria provide about half of an individuals daily vitamin K requirement. Prolonged use of antibiotics may kill these beneficial Vit.K producing bacteria as well as the disease causing bacteria, resulting in a Vitamin K deficiency

Why can't triacyglycerols form a lipid bilayer?

Lipids that form bilayers are amphipathic, whereas tricylglycerols are nonpolar. Amphipathic molecules orient themselves so that their polar head groups face the aqeous medium on the inside and outside of the cell. Also, triacylglycerols, which lack a large head group, are cone-shaped rather than cylindrical and thus would not fit well in a bilayer structure.

The triacylglycerols of animals tend to be solids (fats), whereas the triacylglycerols of plants tend to be liquids (oils) at room temperature. What can you conclude about the nature of the fatty acyl chains in animal and plant triacylglycerols?

In general animal triaclylglycerols contain longer and/or more saturated acyl chains than plant triacylglycerols since these chains have higher melting points and are more likely to be in the crystalline phase at room temperature. The plant triacylglycerols contain shorter and\or less saturated acyl chains in order to remain fluid at room temperature.

Purification of transmembrane proteins requires the addition of detergents to the buffers in order to solubilize the proteins.

a. Why would transmembrane proteins be insoluble in the absence of detergent?

b. Draw a schematic diagram that shows how the detergent sodium dodecyl sulfate interacts with a transmembrane protein.

a. Detergents are required to solubilize a transmembrane protein because the protein domains that interact with the non polar acyl chains are highly hydrophobic and would not form favorable interactions with water

Peptide hormones must bind to receptors on the extracellular surface of their target cells before their effects are communicated to the cell interior. In contrast, receptors for steroid hormones such as estrogen are intracellular proteins. Why is this possible?

A steroid is a hydrohobic lipid that can easily cross a membrane to enter the cell. It does not require a cell surface receptor as does a polar molecule such as a peptide

Identify the monosaccharides preesent in coenzyme A, NAD, and FAD

Coenzyme A, NAD, and FAD all contain ribose residues

Explain why lactose is a reducing sugar, whereas sucrose is not.

Lactose is a reducing sugar because it has a free anomeric carbon (C1 of the glucose residue). Sucrose is not a reducing sugar because the anomeric carbons of both glucose and fructose are involved in the glycosidic bond

The sugar alcohol sorbitol (see Solution 17c) is sometimes used instead of sucrose to sweeten processed foods. Unfortunately, the consumption of large amounts of sorbitol may lead to gastrointestinal distress in susceptible individuals, especially children. Sorbitol-sweetened foods have a lower calorie count than sucrose-sweetened foods. Explain why.

In order for sorbitol to be catabolized to yield energy it would need to enter the same catabolic pathway as glucose. The enzymes that catalyze glucose catabolism are specific for glucose and do not bind to sorbitol, so the sugar alcohol is not metabolized and passes through the body undigested. In this manner, sorbitol contributes no calories to the food containing it, but it is nearly identical to its parent monosaccharide in taste and sweetness.

A friend tells you that she plans to eat a lot of celery because she heard that the digestion of celery consumes more calories than the food contains, and this will help her to lose weight. How do you respond?

Celery is mainly cellulose and water, neither of which provides nutritive calories. Humans do not have beta glucosidase enzymes and cannot hydrolyze the beta glycosidic bonds linking the glucose residues in cellulose. Since cellulose is not digested, the body does not spend any energy to further the process it. Foods like celery contribute roughage, or fiber to the diet but these foods neither provide nor cost the body much in the way of energy.

Explain why a growing plant cell which produces cellulose must also produce cellulase

The cellulose based plat cell wall is strong and rigid but it must be remodeled as the plant cell grows. The cell uses cellulase to weaken the cell wall so that the cell can expland