Biochemistry II Exam I review

a. Triacylglycerols have 3 fatty acyl groups in ester linkage with glycerol; very hydrophobic b/c the carboxyl groups, involved in ester linkages, cannot ionize. Phosphoglycerides have polar region at their head group, where a phosphate in a phosphodiester linage bears a full negative charge. b. These lipid bilayers are stabilized by the energy gained from burying hydrophobic groups out of contact with water. A hydrophobic chain in water forces the formation of a cage of immobilized water molecules around it. When several hydrophobic regions cluster in a bilayer, the surfaces area exposed to water decreases, and the water molecules in the cage are released, accompanied by a gain in entropy that drives the formation of the bilayer.

(a) Explain why phosphoglycerides (or glycerophospholipids) are capable of spontaneously assembling into the bilayer structure found in biological membranes but triacylglycerols are not. (b) what are the forces that drive bilayer formation?

(a) The transition temperature of a membrane is the temperature at which its structure changes from a paracrystalline solid to a liquid state. (b) The two characteristics of fatty acids that directly affect Tt are degree of unsaturation (decrease) and chain length (increase).

(a) What is meant by the transition temperature of a membrane? List the two characteristics of the fatty acids in a biological membrane that affect the transition temperature. Using up or down show in which direction an increase in these characteristic would change the transitions temperature.

a. Forces that hold integral proteins in the membrane are hydrophobic interactions between hydrophobic domains of the protein and the fatty acyl chains of the lipid bilayer interior. b. Peripheral proteins associated with membranes primarily through ionic interactions and hydrogen bonds between charged and polar side chains of the protein and polar head groups of membrane lipids. Some contain covalently bound lipid that anchors them to the bilayer. c. To remove integral proteins, its generally necessary to use detergents, convert membranes into "soluble" micelles. Peripheral proteins required buffers of high or low salt conc., high or low pH, r low concentrations of divalent cations.

(a) What kinds of forces or bonds anchor an integral membrane protein in a biological membrane? (b) What forces hold a peripheral membrane protein to the membrane? (c) What might one do to solubilize each of the two types of membrane proteins?

a. micelles b. bilayers c. Micelles are favored when the polar head groups has a greater cross-sectional area then the nonpolar acyl chain, making the molecule wedge-shaped; bilayers are favored when the cross-sectional area of head group and acyl chain(s) are about the same, so that the molecule is cylindrical.

(a) When relatively high concentrations of fatty acids are suspended in water, they form structures known as ______. (b) When relatively high concentrations of membrane phospholipids are dissolved in water, they form structures known as _____. (c) Why are the structures listed in your answers to (a) and (b) above energetically favored?

More saturated fatty acids will cause an increase in membrane fluidity b/c unsaturated fatty acids contain "kinks" and cannot pack as tightly as saturated fatty acids. At cold temperatures, the fluidity increase from the extra unsaturated fatty acids coutnerbalances the tendency of lipids to solidify at low temperature. At high temperatures, the fluidizing effects of the extra unsaturated fatty acids add to the fluidizing effect of higher temperature, and the membrane of the new plant loses it integrity.

A plant breeder developed new frost resistant variety of tomato that contains higher levels of unsaturated fatty acids in membrane lipids than those found in standard tomato varieties. However, when temperatures climb above 95F, this frost resistant variety dies, whereas the standard variety continues to grow. Provide a likely explanation of the biochemical basis of increased tolerance to cold and increased susceptibility to heat of this new tomato variety.

d. sphingolipids

A polar head group is connected by glycosidic or phosphodiester linkage in which lipid? a. glycerophospholipids b. phosphatidylcholine c. plasmalogen d. sphingolipids

Integral membrane protein associates with the lipid bilayer through hydrophobic interactions between domains containing many hydrophobic amino acids and the fatty acyl chains of membrane lipids. Polar and charged residues are located on portions of the protein that protrude out of either face of the membrane. The protein is free to diffuse laterally in the plane of the membrane, but cannot move across the lipid bilayer.

A protein is found to extend all the way through the membrane of a cell. Describe this protein in terms of the location of particular types of amino side chains in its structure and its ability to move within the membrane.

At pH 7, tryptophan exists as a zwitterion (having a positive and negative charge), whereas indole is uncharged. The movement of the less polar indole through the hydrophobic core of the bilayer is more energetically favorable.

At pH 7, tryptophan crosses a lipid bilayer at about one-thousandth the rate of indole, a closely related compound: Suggest an explanation for this observation.

a. glycosphingolipids

Blood groups are determine in part by the type of sugars located on the head groups in which lipid groups? a. glycosphingolipids b. sphingomyelin c. plasmalogen d. sphingolipids

Hyrdophobic interaction are the driving force for membrane formation. B/c these forces are noncovalent and reversible, membrane can easily anneal after disruption.

Cellular membrane are self-sealing - if they are punctured or disrupted mechanically, they quickly and automatically reseal. What properties of membranes are responsible for this important feature?

Symport and antiport are both types of cotransport systems in which two solutes move through the membrane simultaneously. In symport, both move in the same direction; in antiport, one solute goes in one direction, the other in the opposite direction. The Na+K+ ATPase of the plasma membrane is an antiport system. It moves K+ in and Na+ out in a ratio of 2 K+ per 3 Na+. Neither of the two ions can be transported unless the other is present, which is characteristic of cotransport systems.

Compare and contrast symport and antiport. Which term best describes the transport system mediated by the Na+K+ ATPase?

Both proteins have domains that specifically recognize and bind to their substrates via weak interactions; they both therefore mediate processes that are stereospecific and saturable. The membrane transporter usually spans the membrane, having one or several hydrophobic domains that interact with the hydrophobic acyl chains of fatty acids in the interior of the lipid bilayer. Soluble enzymes tend to have their hydrophobic residues buried within their interiors, and their hydrophilic residues on the surface, where they interact with water.

Compare the structure and activity of a membrane transport protein that transports a polar substance across a membrane with a typical soluble enzyme. How are transporter and enzyme similar? How are they different?

To compensate for the solidifying effect of low temperature on membrane lipids, it can synthesize and place in the membrane (1) a greater proportion of unsaturated fatty acids and (2) shorter-chain fatty acids. Both increase the fluidity of the lipid bilayer.

Describe two different ways a plant can adjust the components of its cell membranes to keep them as fluid as possible on a cold winter morning.

(a) Energy dependent? AT only (b) Need carrier protein(s)? FD and AT (c) Can be saturated by substrate? FD and AT (d) Can establish conc gradient? AT only (e) 5.7 kJ/mol

Distinguish between simple diffusion (SD), facilitated diffusion (FD), and active transport (AT) across a membrane for the following questions. (More than one may be true.) a. Which process are energy dependent? b. Which processes need some kind of carrier protein(s)? c. Which processes can be saturated by substrate? d. Which process can establish a concentration gradient? e. How much energy does it take to trasnsport an uncharged substrate in, if it's starting inside conc is 10-fold greater than outside?

-Modifying a different backbone -changing the fatty acids -modifying the head groups

Diversification of lipids can come from?

-Integral proteins are very firmly associated with the membrane; their hydrophobic domains are associated with the fatty acyl groups in the interior in hydrophobic interactions. -Peripheral proteins are more loosely associated and usually do not penetrate the hydrophobic interior of the bilayer. Conditions that reduce ionic interactions and hydrogen bonds commonly release them.

Explain the difference between integral and peripheral membrane proteins.

A nonpolar compound is more soluble in nonpolar solutes, such as benzene or chloroform, than in polar solvents, such as water. They generally pass through biological membrane unaided b/c it is energetically favorable for them to move from the aqueous solvent into the nonpolar regions of the bilayer interior.

Explain why nonpolar compounds are generally able to diffuse across biological membranes without the aid of a specific transport system.

a. driven by a difference of solute concentration

Facilitated diffusion through a biological membrane is: a. driven by a difference of solute concentration b. driven by ATP c. endergonic d. generally irreversible e. not specific with respect to the substrate

a. long-term, slow

Fats are for ____ energy needs, good storage and ____ delivery. a. long-term, slow b. long-term, quick c. short-term, quick d. short-term, slow

DeltaGt=RTln(C2/C1)+nFdeltaPhi R=8.314 J/K*mol T= 310K C1= 12mM C2= 145mM n= 1mol F= 96,480 J/V*mol DeltaPhi= 0.07V =6.4 KJ/mol + 6.8 KJ/mol=13.2KJ Note that 6.8 KJ/mol is the membrane potential portion.

For a typical vertebrate cell with a membrane potential of 0.070V (inside negative), what is the free-energy change for transporting 1 mol of Na+ out of the cell and into the blood at 37C? Assume the conc of Na+ inside the cell is 12mM, and that in blood plasma is 145mM.

pH=-log [H+], then [H+] = 10^-pH at pH 1.5, [H+]=10^-1.5=3.2x10^-2M. at pH 7.4, [H+]=10^-7.4=4.0x10^-8M. b/c deltaGt=RTln(C2/C1) R=8.314 J/K*mol T=37C+273=310K C1=4.0x10^-8M C2=3.2x10^-2M DeltaGt=35kJ/mol 35kJ/58kJ/mol=0.60mol

Gastric juice (pH 1.5) is produced by pumping HCl from blood plasma (pH 7.4) into the stomach. Calc the amount of free energy required to concentrate the H+ in 1L of gastric juice at 37C. The free-energy change for ATP hydrolysis under cellular conditions is about -58kJ/mol. Ignore the effects of the transmembrane electrical potential.

c. short-term, quick

Glucose and glycogen are for ____ energy needs, _____ delivery. a. long-term, slow b. long-term, quick c. short-term, quick d. short-term, slow

c. alcohol; head group

Glycerophospholipids highly polar phosphate group may be further esterified by an _____; such substituent groups are called the ______. a. amide; head group b. alcohol; tail group c. alcohol; head group d. amide; tail group

"rafts"; ordered; saturated

Glycosphingolipids and cholesterol cluster together in membrane regions known as "_____." These microdomains are more _______ than the surrounding phospholipid-rich membrane due to a high content of _____ fatty acids. Proteins aggregated in this fashion are often functionally related.

b. increase in degree of unsaturation

How do you decrease melting temperature? a. keep degree of unsaturation b. increase in degree of unsaturation c. decrease in degree of unsaturation

b. 3 Na+out, 2 K+ in, and converts 1 ATP to ADP+Pi

In one catalytic cycle the Na+/K+ ATPase transporter transports: a. 2 Na+ out, 3 K+ in, and converts 1 ATP to ADP+Pi b. 3 Na+out, 2 K+ in, and converts 1 ATP to ADP+Pi c. 3 Na+ in, 2 K+ out, and converts 1 ATP to ADP+Pi d. 1 Na+ out, 1 K+ in, and converts 1 ATP to ADP+Pi e. 2 Na+ out, 3 K+ in, and converts 1 ATP to ADP+Pi

-Phospholipids and sterols found on both faces of the lipid bilayer. -Integral membrane proteins penetrate or span the lipid bilayer. -Peripheral membrane proteins associate at the membrane surface with lipid head groups or integral proteins. -Carbohydrates moieties of glycolipids and glycoproteins are invariably on the outside face of the plasma membrane.

Indicate the positions and orientations of phospholipids, cholesterol, integral, and peripheral membrane proteins, and the carbohydrate moieties of glycoproteins and glycolipids. [short answer]

a. complex lipids

Lipids that do contain fatty acids and can be further separated into storage and membrane lipids. a. complex lipids b. cholesterol, hormones, ect. c. unsaturated lipids

b. Cholesterol, hormones, ect.

Lipids that do not contain fatty acids. a. complex lipids b. cholesterol, hormones, ect. c. unsaturated lipids

a. increases

Melting temperature increases and solubility decreases when chain length: a. increases b. decreases c. stays the same

d. tSNARE and vSNARE

Membrane fusion leading to neurotransmitter release requires the action of: a. cadherins b. selectins c. flipases d. tSNARE and vSNARE e. None of the above

The temperature of body tissues at the extremities, such as near the hooves, is generally lower than that of tissues closer to the center of the body. To maintain fluidity, as required by the fluid-mosaic model, membranes at lower temperatures must contain a higher percentage of polyunsaturated fatty acids: a higher content of unsaturated fatty acids lowers the melting point of lipid mixtures.

Membrane lipids in tissue samples obtained from difference parts of the leg of a reindeer have different fatty acid compositions. Membrane lipids from tissue near the hooves contain a larger proportion of unsaturated fatty acids than those from tissue in the upper leg. What is the significance of this observation?

Reagent A will label phosphatidylethanolamine head groups in both the outer and the inner monolayer of the membrane; reagent B will label only the phosphatidylethanolamine molecules on the outer face. If phosphatidylethanolamine is equally distributed on both sides of the bilayer twice as much labeling of phosphatidylethanolamine should be observed with reagent A as with reagent B. Deviations from this ratio indicate asymmetry in the distribution of phosphatidylethanolamine.

Reagents A and B react covalently with primary amino groups such as those of phosphatidylethanolamine. Reagent A permeates erythrocytes, but reagent B is impermeant. Both A and B are available in radioisotopically labeled form. Describe a simple experiment by which you might determine whether the phosphatidylethanolamine of erythrocyte membranes is located in the outside face of the lipid bilayer, the inside face or in both.

No, the symport may be able to transport more than one equivalent of glucose per Na+.

Suppose that you determined experimentally that a cellular transport system for glucose, driven by symport of Na+, could accumulate glucose to conc 25 times greater than in the external medium, while the external [Na+] was only 10 times greater than the intracellular [Na+]. Would this violate the laws of thermodynamics? If not, how could you explain this observation.

d. sphingosine

The backbone of sphingolipids is long chain amino alcohol _______. a. spingoester b. sphingoamine c. sphingoamide d. sphingosine

At 40C, the membrane of E. coli ill contain more saturated fatty acids than at 20C. The cell regulates fatty composition to achieve the same fluidity in its membranes, regardless of growth temperature. Saturated fatty acids counterbalance the fluidizing effect of high temperature.

The bacterium E. coli can grow at 20C to 40C. At which growth temperature would you except the membrane phospholipids to have a higher ratio of saturated to unsaturated fatty acids, and why?

b. amide

The fatty acids in sphingolipids are joined together by which linkages? a. ester b. amide c. ether d. alcohol

Because protein X can be removed by salt treatment, it must be peripheral membrane protein. Inability to digest the protein with proteases unless the membrane has been disrupted indicates that protein X is located internally, bound to the inner surface of the erythrocyte plasma membrane.

The following observations are made on an unknown membrane protein, X. It can be extracted from disrupted erythrocyte membranes into a concentrated salt solution, and it can be cleaved into fragments by proteolytic enzymes. Treatment of erythrocytes with proteolytic enzymes followed by disruption and extraction of membrane components yield intact X. However, treatment of erythrocyte "ghosts" (which consist of just plasma membranes, produced by disrupting the cells and washing out the hemoglobin) with proteolytic enzymes followed by disruption and extraction yields extensively fragmented X. What do these observations indicate about the location of X in the plasma membrane? Do the properties of X resemble those of an integral or peripheral membrane protein?

The energy required to flip a charged polar head group through a hydrophobic lipid bilayer is prohibitively high.

The inner leaflet (monolayer) of the human erythrocyte membrane consists predominantly of phosphatidylethanolamine and phosphatidylserine. The outer leaflet consists predominantly of phosphatidylcholine and sphingomyelin. Although the phospholipid components of the membrane can diffuse in the fluid bilayer, this sidedness is preserved at all times. How?

d. secondary active transport

The type of membrane transport that uses ion gradiants as the energy source is: a. facilitated diffusion b. passive transport c. primary active transport d. secondary active transport e. simple diffusion

The activity of interest is membrane bound. The first mild rinse at pH 6, you "lost" the activity due to a mild rinse, presumably losing a required peripheral membrane protein to the soluble fraction. Next treatment with mild detergent, presumably lost a protein with a lipid anchor to the soluble fraction. Combining the peripheral membrane protein lost in the pH 6 wash with the lipid anchor protein lost in the mild detergent, recovery activity. Therefore, the enzyme requires two components to be active: the peripheral part and lipid anchor part. This not uncommon.

Trying to isolate an enzyme that catalyzes the conversion of A -> B, and have a sensitive assay for this enzyme. After lysing open the cells, results show the activity is associated with membrane fraction, not the soluble fraction (which you throw away). Then follow the procedure shown. Explain the sudden re-occurrence of activity at the end of the protocol.

d. fatty acids carry more energy per carbon and less water per gram.

What are the advantages of fats over polysaccharides? a. fatty acids carry equal amounts of energy and water. b. fatty acids carry more energy per carbon and more water per gram. c. fatty acids carry less energy per carbon and less water per gram. d. fatty acids carry more energy per carbon and less water per gram.

-Lipid bilayer: individual lipids are free to move laterally but not across the bilayer. -Integral membrane proteins: penetrate or span the bilayer, associating with lipid acyl chains by hydrophobic interactions and exhibiting lateral mobility. -Peripheral membrane proteins: associate noncovalently with the lipid head groups and protruding domains of integral protein, and which are sometimes tethered to the membrane by a covalent lipid anchor.

What are the principle features of the fluid mosaic model of membranes? [short answer]

(1) The rate of ion movement through channels is much greater; (2) ion transporters exhibit saturation, whereas ion channels do not; (3) ion channels open and close in response to external stimuli or events such as ligand-binding or changes in electrical potential across the membrane.

What are three differences between ion channels and ion transporters?

An amphipathic compound has hydrophilic and hydrophobic regions. In water, compounds tend to arrange in a way that exposes their hydrophilic regions to the solvent and hides their hydrophobic domains. Example, lipid bilayer, which forms spontaneously with phospholipids in water.

What is an amphipathic compound? Explain how such compounds contribute to the structure of biological membranes. [short answer]

Non-gated channels are always open; gated channels open in response to a signal. Two possible signals are the presence of a ligand or a change in membrane potential.

What is the major difference between gated and non-gated ion channels? Give an example of two different gating signals.

b. head groups

What properties of lipids determine the surface properties of membranes? a. backbones b. head groups c. fatty acids d. tails

d. putting more unsaturated fatty acids into its membranes.

When a bacterium such as E. coli is shifted from a warmer growth temperature to a cooler growth temperature, it compensates by: a. increasing its metabolic rate to generate more heat. b. putting longer-chain fatty acids into its membranes. c. putting more unsaturated fatty acids into it membranes. d. shifting from aerobic to anaerobic metabolism e. synthesizing thicker membranes to insulate the cell.

d. sphingolipids and galactolipids

Which is an example of glycolipids? a. glycerophospholipids and sphingolipids c. sphingolipids and triacylglycerols d. sphingolipids and galactolipids

a. glycerophospholipids and sphingolipids

Which is an example of phospholipids? a. glycerophospholipids and sphingolipids c. sphingolipids and triacylglycerols d. sphingolipids and galactolipids

c. triacylglycerols

Which is an examples of storage lipids (neutral)? a. glycerophospholipids b. sphingolipids c. triacylglycerols d. galactolipids

b. phosphatidylcholine

Which of the following cannot be synthesized by many prokaryotes, such as E. coli? a. glycerophospholipids b. phosphatidylcholine c. plasmalogen d. sphingolipids

d. sphingolipids

Which of the following does not have glycerol as the backbone? a. glycerophospholipids b. phosphatidylcholine c. plasmalogen d. sphingolipids

a. glycerophospholipids

Which of the following has head group that is charged at physiological pH? a. glycerophospholipids b. phosphatidylcholine c. plasmalogen d. sphingolipids

c. sterols

Which of the following has the characteristics of having 4 fused rings, hydroxyl group in the A-ring, and is the derivative of many hormones? a. plasmalogen b. sphingolipids c. sterols d. sphingomyelin

d. cholesterol

Which of the following in low-density lipoproteins tends to deposit and clog arteries? a. sphingolipids b. plasmalogen c. sterols d. cholesterol

c. plasmalogen

Which of the following is a vinyl ether analog of phosphatidylethanolamine? a. glycerophospholipids b. phosphatidylcholine c. plasmalogen d. sphingolipids

b. sphingomyelin

Which of the following is abundant in myelin sheath that surrounds some nerve cells in animals? a. glycerophospholipids b. sphingomyelin c. plasmalogen d. sphingolipids

c. plasmalogen

Which of the following is common in vertebrate heart tissue? a. glycerophospholipids b. phosphatidylcholine c. plasmalogen d. sphingolipids

b. phosphatidylcholine

Which of the following is the major component of most eukaryotic cell membranes? a. glycerophospholipids b. phosphatidylcholine c. plasmalogen d. sphingolipids

a. glycerophospholipids

Which of the following is the primary constituents of cell membranes? a. glycerophospholipids b. phosphatidylcholine c. plasmalogen d. sphingolipids

The similar Kt values for L-leucine and L-valine

You are studying the uptake of L-leucine by epithelial cells of the mouse intestine. Measurements of the rate of uptake of L-leucine and several of its analogs, with and without Na in the assay buffer, yield the results given in the table. What can you conclude about the properties and mechanism of the leucine transporter?

a. phospholipids, sterols, proteins (integral and peripheral) b. Peripheral membrane proteins. Forces = ionic and hydrogen bonds between their charged heads and polar side chains and the charged head groups of phospholipids. c. Integral membrane proteins. Forces = hydrophobic interactions between their nonpolar side chain and the hydrophobic fatty acyl chains of phospholipids.

a. List three major components of eukaryotic membranes. b. Mitochondrial membranes treated with high salt (0.5M NaCl), 40% of total protein in this preparation was solubilized. What kind of membrane proteins are in this soluble extract and what forces normally hold them to membrane? c. What kind of proteins constitute the insoluble 60% and what forces hold these proteins to membrane? [short answer]

a. Lipids that form bilayers are amphipathic molecules. They contain hydrophilic and hydrophobic regions. They want to minimize the hydrophobic areas exposure to water. b. These sheets form the closed membrane surfaces that envelop cells and compartments within cells (organelles).

a. What properties of lipids are responsible for forming bilayer? b. What are the consequences of this property for the structure of biological membranes? [short answer]

(5.4 A/turn)/(3.6 residues/turn) = 1.5 A = 0.15nm 3nm/0.15nm = 10 residues

if the hydrophobic interior of a membrane were about 3 nm thick, what would be the minimum number of amino acids in a stretch of transmembrane alpha helix? (dimensions of an alpha helix are about 5.4 A/turn and there are 3.6 residues/turn)