Modern Biology - Exam 1 - Answer Key

1. Molecules (25 pts)

For each of the following structures:

(a) Name the type of compound.

(b) Classify the compound as hydrophobic or Hydrophilic.

(c) Circle all sites on each molecule that can hydrogen bond with water and draw a water hydrogen bonded to one site on each molecule

(d) Name a cellular structure for which each molecule is the major component.

(e) Label one methyl group, one hydroxyl group, one amino group and one carboxyl group on any of these structures.

2. Cell Outer Surface (25 pts)

(a) (15 pts) Illustrate the fluid mosaic model of the plasma membrane. Label the integral membrane proteins, peripheral membrane proteins, carbohydrate signals and phospholipids.

see figure 5-2 for typical illustration of fluid mosaic membrane

(c) (5) Why is this structure described as a semi-permeable barrier? What are two functions of the plasma membrane

It is a continuous hydrophobic barrier between two hydrophilic solvents. It can act as a solubility barrier with only hydrophobic molecules able to penetrate the bilayer.

Functions: (1) provide structure to the cell, protective barrier.

(2) control passage of molecules/particles into and outof the cell

(3) communication (signal transduction)

(d) (5 pts) Describe how the electronegativity of oxygen affects the properties of water and of the biological molecules of which it is a part. The absence of electronegative atoms contributes to formation of special interactions with water, describe them.

It makes a molecule polar, thus making that portion of any molcule in which it is included water soluble due to potential for hydrogen bonding

The special interaction is the hydrophobic interaction that excludes water. Examples are the lipid bilayer formed from phospholipids and the interior of proteins formed by the interaction of hydrophobic side chains on amino acids.

3. Transport/Communication (25 pts)

(a) (6 pts) What is the difference between diffusion and osmosis? Applying each together to a cell define the relationship between isotonic and hypertonic solutions. State a rule for predicting the movement of particles in facilitated diffusion.

Diffusion (dialysis) is the movement of the solute while osmosis is the movement of the solvent.

Isotonic olutions are those for which the ion concentrations are equal while a hypertonic solution has a higher ion concentration than a hypotonic solution or is higher relative to the original isotonic solution.

The general rule is that molecules will move spontaneously from an area of high concentration to one of low concentration.

(b) (6 pts)Define the difference between pinocytosis and phagocytosis. Describe the process of phagocytosis and the fate of an external membrane marker during the process.

The process involves the contacting of a particle with the surface of a cell and the enclosure of the plasma membrane around the particle. Eventually the particle is completely surrounded by the plasma membrane and the enclosed particle is budded into an internal vesicle within the cell.

Any marker that was on the outside surface of the plasma membrane will be on the inner surface of the enclosed vesicle.

(c) (7 pts) Biological systems are distinguished by the fact that they have mechanisms that discriminate between molecules and structures. Give three examples of this principle from the material we have discussed thusfar. One of the mechanisms should involve transport of materials into a cell.

D and L amino acids

D and L carbohydrates

receptor recognition for receptor mediated endocytosis

(d) (6 pts) Gap junctions and transmembrane ion channels have features in common and clear differences. Give a similarity and a difference between each. What secondary protein structure dominates the formation of these structures and why is that structure particularly suited to the functioning of a channel?

Similarity: both provide means for transfer of materials across the lipid bilayer. They are both made of protein.

Differences: Gap junctions join two cells and provide channel for ions to pass directly between cells while transmembrane proteins provide channels for molecules and ions to pass from the inside to the outside of individual cells.

These structures are dominated generally by transmembrane alpha helices that align in such a way as to create a pore through the center. The description would be that of a rain barrel where the sides of the barrel are made of helices and the inside is characterized by a complementary property to that which is to go through the pore while the outside is hydrophobic to interact stabily with the lipid portion of the lipid bilayer. Helices are particularly suited for this structure because the side chains radiate from the center of the helix like spokes on a wheel and thus can be arranged in the sequence (primary structure) such that specific side chains with specific properties are pointed toward the area needed.

4. Structure and Function (25 pts)

(a) (5 pts) Liposome structure is dominated by what feature (illustrate or describe). Describe the structure and a characteristic of the building block of a liposome that results in the regular structure of the liposome.

Liposome is dominated by the lipid bilayer (see illustration in figure 5-3. The building block of the liposome is the phospholipid which is amphipathic with hydrocarbon chains of 18-22 carbons in length thus giving the structure uniform length. The hydrocarbon chains are extended toward the center of the bilayer where there is minimal overlap of the ends of the chains. The glycerol phosphate polar ends are aligned toward the polar solvent area.

(b) (5 pts) Describe (illustrate) a transmembrane protein used for facilitated diffusion of a simple carbohydrate. What are the building blocks of this protein (by general category) and how would they be distributed in the sequence (internal and external features) of this structure.

A transmembrane protein for carbohydrates would be characterized by the fact that the outside would be hydrophobic to interact with the lipid of the membrane while the inside would be polar to hydrogen bond with the hydroxyls of the carbohydrate. The building blocks of this protein are amino acids which would be aligned in the sequence such that the hydrophbic amino acids would face the outside and the polar amino acids would face the inside in the final tertiary structure of the protein.

(c) (5 pts) Describe the structure of a plant cell wall. What are the building blocks that form this structure and what characteristic of the building blocks make them particularly suitable to this structure. How does the structure of a bacterial cell wall differ from the plant cell wall?

A plant cell wall is made of a linear polymer of glucose molecules that form strands of cellulose. Parallel strands of cellulose are linked by hydrogen bonding to form a network of fibers that give the cell structure. The glucose molecules are particularly well suited for this structure because of the maximum use of the hydroxyl groups on every carbon that form hydrogen bonds.

The bacterial cell wall is a peptidoglycan that has linear polysaccharide chains linked by short peptide fragments linked by covalent bonds. Thus the matrix of cellulose is held together by hydrogen bonding while the peptidoglycan is held together by covalent bonds.

(d) (5 pts) Cells have complex carbohydrates that are used as signals. Proteins recognize these signals. What type of bonding would dominate the recognition of these signals by proteins? Two signals differ only by the fact that one has 4 glucose molecules linked together and the other has seven glucose molecules linked together. Without knowing anything else about the structure, which signal would you predict to bond more tightly to a protein. Why?

The dominant bonding would be hydrogen bonding which makes use of the many hydroxyls on the carbohydrates and the variety of amino acid side chains on proteins that can undergo hydrogen bonding.

The signal with 7 glucose molecules would probably be favored because of the greater number of hydrogen bonds that can be formed. Strength comes from the sum of the number of possible interactions.

(e) (5 pts) The tertiary structure of protein is a combination of what secondary structures? These secondary structures interact through what four types of bonding?

Secondary structures in proteins are alpha helix, beta sheet and beta turns. The secondary structures interact through hydrogen bonding, ionic bonding, covalent disulfide bonds, and hydrophobic interactions invoving primarily the variety of side chain functional groups to form the final tertiary structure of the protein.