CHAPTER 7 TEXTBOOK

From chemistry, we know that each methylene (CH2) group in a straight chain hydrocarbon advances the chain length about .13nm. And from studies of protein structure, we know that one turn of an alpha helix included 3.6 aa residues and extends the long axis of the helix by about 0.56nm. use this information to answer the following. How long is a single molecule of palmitate (16 carbon atoms) in its fully extended form? What about molecules of laurate (12 carbon atoms) and arachidate (20 carbon atoms)?

palmitate = 2.08nm; laurate = 1.56nm; and arachidate = 2.6nm

For each of the following statements, specify which one of the five general membrane functions (permeability barrier, localization of function, regulation of transport, detection of signals, or intercellular communication) the statement illustrates. Ions and large polar molecules cannot cross he membrane without the aid of a transport protein

permeability barrier

We know that exposed regions of membrane proteins can be labeled with 125I by the lactoperoxidase (LP) reaction. Similarly, carbohydrate side chains of membrane glycoproteins can be labeled with 3H by oxidation of galactose groups by galactose oxidase (GO) followed by reduction with titrated borohydride (3H---BH4). Noting that both LP and GO are too large to penetrate into the interior of an intact cell, explain each of the following observations made with intact erythrocytes If the erythrocytes are ruptured before the labeling procedure, the LP procedure labeled virtually all of the major membrane proteins

the LP is able to reach the inside of the cell without having to incubate them in an isotonic media, meaning they do not have to be permeable for the LP to reach the proteins on the inside so they are all easily labeled.

Acholeplasma laidlawii is a small bacterium that cannot synthesize its own fatty acids and must therefore construct its plasms membrane from whatever fatty acids are available in the environment. As a result, the acholeplasma membrane takes on the physical characteristics of the fatty acids available at the time If you give acholeplasma cells access to a mixture of saturated and unsaturated fatty acids, they will thrive at room temperature. Can you explain why?

the acholeplasma cells will incorporate an appropriate combination of saturated and unsaturated fatty acids into their membranes to provide the cell with optimum level of membrane fluidity.

For each of the following statements, specify which one of the five general membrane functions (permeability barrier, localization of function, regulation of transport, detection of signals, or intercellular communication) the statement illustrates. Insulin does not enter a target cell but instead binds to a specific membrane receptor on the external surface of the membrane, thereby activating the enzyme adenylyl cyclase on the inner membrane surface

detection of signals

We know that exposed regions of membrane proteins can be labeled with 125I by the lactoperoxidase (LP) reaction. Similarly, carbohydrate side chains of membrane glycoproteins can be labeled with 3H by oxidation of galactose groups by galactose oxidase (GO) followed by reduction with titrated borohydride (3H---BH4). Noting that both LP and GO are too large to penetrate into the interior of an intact cell, explain each of the following observations made with intact erythrocytes All of the proteins of the plasma membrane that are known to contain carbohydrates are labeled with the GO/3H---BH4 method

glycoproteins can be labeled with this method which contain carbohydrates. Membrane proteins so not contain carbohydrates so they must be labeled by the other method.

For each of the following statements, specify which one of the five general membrane functions (permeability barrier, localization of function, regulation of transport, detection of signals, or intercellular communication) the statement illustrates. Adjacent plant cells frequently exchange cytoplasmic components though membrane-like channels called plasmodesmata

intercellular communication

For each of the following statements, specify which one of the five general membrane functions (permeability barrier, localization of function, regulation of transport, detection of signals, or intercellular communication) the statement illustrates. On their outer surface, cells of multicellular organisms carry specific glycoproteins that are responsible for cell-cell adhesion

intercellular communication

Listed below are 4 aa and 4 hydrophobicity vales. Match the hydrophobicity values with the correct aa and explain your reasoning.

A. alanine = 1.0; arginine = -7.5; isoleucine = 4.0; serine = -1.1; isoleucine is the most hydrophobic because has a longer side chain than alanine and is nonpolar. Arginine is the most hydrophilic because it contains an electrically charged side chain (acidic-polar) while serine has a polar neutral side chain so it is not as hydrophilic.

For each of the following false statements, change the statement to make it true and explain your reasoning O-linked and N-linked glycoproteins are formed when sugar chains are attached to the oxygen and nitrogen atoms of the peptide bonds in the proteins

O-linked and N-linked glycoproteins are formed when sugar chains are attached to the oxygen and nitrogen atoms of the side chains in amino acid residues

A hydropathy plot can be used to predict the structure of a membrane protein based on its amino acids sequence and the hydrophobicity values of the amino acids. Hydrophobicity is measured as the standard free energy change delta G not, for the transfer of a given amino acid residue from a hydrophobic solvent into water, in KJ/mol. The hydropathy index is calculated by averaging the hydrophobicity values for a series of short segments of the polypeptide, witch each segment displaced one amino acids farther from N-terminus. The hydropathy index of each successive segment is them plotted as a function of the location of the segment in the aa sequence, and the plot is examined for regions of high hydropathy index. given the way it is defined, would you expect the hydrophobicity index of a hydrophobic residue such as valine or isoleucine to be positive or negative? What about hydrophilic residue such as aspartic acid or arginine?

a hydrophobic aa has a positive hydropathy index, whereas a hydrophilic residue has a negative hydropathy index.

What results would you expect if such inside-out vesicles were subjected to the LP/125I procedure?

all of the membrane proteins on from the inside of the membrane would then be labeled, as they are on the outside of the cell now

From chemistry, we know that each methylene (CH2) group in a straight chain hydrocarbon advances the chain length about .13nm. And from studies of protein structure, we know that one turn of an alpha helix included 3.6 aa residues and extends the long axis of the helix by about 0.56nm. use this information to answer the following. Approximately hoy many amino acids must a helical transmembrane segment of an integral membrane protein have if the segment is to span the lipid bilayer defined by two palmitate molecules end to end?

approximately 27 amino acids (26.74)

From chemistry, we know that each methylene (CH2) group in a straight chain hydrocarbon advances the chain length about .13nm. And from studies of protein structure, we know that one turn of an alpha helix included 3.6 aa residues and extends the long axis of the helix by about 0.56nm. use this information to answer the following. The protein bacteriorhodopsin has 248 amino acids and seven transmembrane segments. Approximately what portion of the amino acids are part of the transmembrane segments? Assuming that most of the remaining amino acids are present in the hydrophilic loops linking the transmembrane segments together, approximately how many amino acids are present in each of these loops, on average?

approximately 56% of the amino acids are part of the transmembrane segment. There are about 18 amino acids in each loop.

We know that exposed regions of membrane proteins can be labeled with 125I by the lactoperoxidase (LP) reaction. Similarly, carbohydrate side chains of membrane glycoproteins can be labeled with 3H by oxidation of galactose groups by galactose oxidase (GO) followed by reduction with titrated borohydride (3H---BH4). Noting that both LP and GO are too large to penetrate into the interior of an intact cell, explain each of the following observations made with intact erythrocytes When intact cells are incubated by LP in the presence of 125I and the membrane proteins are then extracted and analyzed on SDS-polyacrylamide gels, several of the bands on the gel are found to be radioactive

because LP cannot enter the cell it can only label proteins on the outside of the cell. Therefore, radioactive bands contain loops on the extracellular side of the lipid bilayer and can be labeled with 125I.

We know that exposed regions of membrane proteins can be labeled with 125I by the lactoperoxidase (LP) reaction. Similarly, carbohydrate side chains of membrane glycoproteins can be labeled with 3H by oxidation of galactose groups by galactose oxidase (GO) followed by reduction with titrated borohydride (3H---BH4). Noting that both LP and GO are too large to penetrate into the interior of an intact cell, explain each of the following observations made with intact erythrocytes When intact cells are incubated with GO and then reduced with 3H---BH4, several of the bands on the gel are found radioactive

because it was reduced with this, it caused the GO to be able to enter the cell so the radioactive 3H can label the inside and cause it to become radioactive

For each of the following false statements, change the statement to make it true and explain your reasoning Because membranes have a hydrophobic interior, polar and charged molecules cannot pass through the membrane

because membranes have a hydrophobic interior, polar charged molecules can pass though membranes only with the help of a protein transporter

Imagine that a new type of cell was discovered on mars in an organism growing in benzene, a nonpolar liquid. The cell has a lipid bilayer made of phospholipids, but the bilayer's structure is very different from that of our cells membranes How might you isolate and visualize these unusual membranes?

it could require hydrophilic solvents to solubilize these membranes and release embedded proteins prior to visualization by conventional means.

Knowing that it is possible to prepare inside-out vesicles from erythrocyte plasma membranes, can you think of a way to label a transmembrane protein with 3H on one side of the membrane and with 125I on the other side?

label membrane proteins of intact cells with one of the techniques described, then prepare inside-out vesicles and use the second labeling technique

For each of the following statements, specify which one of the five general membrane functions (permeability barrier, localization of function, regulation of transport, detection of signals, or intercellular communication) the statement illustrates. All of the acid phosphatase in a mammalian cell is found within lysosomes

localization of function

For each of the following statements, specify which one of the five general membrane functions (permeability barrier, localization of function, regulation of transport, detection of signals, or intercellular communication) the statement illustrates. Photosystems I and II are embedded in the thylakoid membrane of the chloroplast

localization of function

For each of the following statements, specify which one of the five general membrane functions (permeability barrier, localization of function, regulation of transport, detection of signals, or intercellular communication) the statement illustrates. When cells are disrupted and fractionated into subcellular components, the enzyme cytochrome P-450 is recovered with the endoplasmic reticulum fraction

localization of function

A hydropathy plot can be used to predict the structure of a membrane protein based on its amino acids sequence and the hydrophobicity values of the amino acids. Hydrophobicity is measured as the standard free energy change delta G not, for the transfer of a given amino acid residue from a hydrophobic solvent into water, in KJ/mol. The hydropathy index is calculated by averaging the hydrophobicity values for a series of short segments of the polypeptide, witch each segment displaced one amino acids farther from N-terminus. The hydropathy index of each successive segment is them plotted as a function of the location of the segment in the aa sequence, and the plot is examined for regions of high hydropathy index. why do scientists try to predict the structure of a membrane protein by this indirect means when the technique of X-ray crystallography would reveal the structure directly?

producing samples suitable for X-ray crystallography is difficult; proteins must be purified from cells without denaturation, and then they must be submitted to a large screen to find conditions that are suitable to produce X-ray quality crystals

For each of the following false statements, change the statement to make it true and explain your reasoning Proteins typically transmit signals from the outside of the cell to the cytoplasm by flip flopping from the outer membrane monolayer to the inner monolayer

proteins typically transmit signals from the outside of the cell to the cytoplasm by a change in conformation induced by a molecule binding to the extracellular portion of the protein

For each of the following statements, specify which one of the five general membrane functions (permeability barrier, localization of function, regulation of transport, detection of signals, or intercellular communication) the statement illustrates. The interior of a membrane consists of primarily of the hydrophobic portions of phospholipids and amphipathic proteins

regulation of transport

For each of the following statements, specify which one of the five general membrane functions (permeability barrier, localization of function, regulation of transport, detection of signals, or intercellular communication) the statement illustrates. The membrane of a plant root cell has a ion pump that exchanges phosphate inward for bicarbonate outward

regulation of transport

Acholeplasma laidlawii is a small bacterium that cannot synthesize its own fatty acids and must therefore construct its plasms membrane from whatever fatty acids are available in the environment. As a result, the acholeplasma membrane takes on the physical characteristics of the fatty acids available at the time If you transfer the bacteria of part a to a medium containing only saturated fatty acids but make no other changes in culture conditions, they will stop growing shortly after change in the medium. Propose an explanation

saturated fatty acids make a membrane less fluid; if only saturated fatty acids are available, the transition temperature of the membrane increases until the transition temp is equal to the ambient temperature, at which point the membrane will become a gel

Imagine that a new type of cell was discovered on mars in an organism growing in benzene, a nonpolar liquid. The cell has a lipid bilayer made of phospholipids, but the bilayer's structure is very different from that of our cells membranes Draw what might be a possible structure for the new type of membrane. What might be characteristic features of the phospholipid head groups?

since water is polar, the cells that we are used to have the polar heads of the lipid bilayer facing out because they want to interact with the polar water. However, if the cell was in a nonpolar liquid, the phospholipids would turn to where their nonpolar tails face outward instead.

Imagine that a new type of cell was discovered on mars in an organism growing in benzene, a nonpolar liquid. The cell has a lipid bilayer made of phospholipids, but the bilayer's structure is very different from that of our cells membranes What properties would you expect to find in membrane proteins embedded in this membrane?

the integral membrane proteins would have their polar regions in the middle and nonpolar regions on the external surface. Peripheral membrane proteins would wither have to be embedded into the interior of the membrane because they are held to it by covalent bonds due to their polarity. The lipid anchored proteins would also be flipped to where they are also embedded on the inside of the membrane with the anchor facing out. These are all true given that everything keeps the same properties on mars

From chemistry, we know that each methylene (CH2) group in a straight chain hydrocarbon advances the chain length about .13nm. And from studies of protein structure, we know that one turn of an alpha helix included 3.6 aa residues and extends the long axis of the helix by about 0.56nm. use this information to answer the following. How does the thickness of the hydrophobic inter of a typical membrane compare with the length of two palmitate molecules laid end to end? What about two molecules of laurate or arachidate?

the interior of the membrane for palmitate would be 4.16nm, 3.13nm for laurate, and 5.2nm for arachidate

How long is the average transmembrane segment? How well does it compare to the number you calculated in a previous problem? How many transmembrane segments do you think the protein has? Can you guess which protein this might be?

the segment is 20-30 aa long; this is accurate to what was calculated above, which was 27; the protein should have 4 transmembrane segments; this should be the protein tetraspanins because that one has 4 transmembrane segments

For each of the following false statements, change the statement to make it true and explain your reasoning The three-dimensional structure of a protein cannot be determined unless the protein can be isolated from cells in pure form

the three-dimensional structure of a protein can be determined in part even if the protein cannot be isolated from cells in pure form by comparing its nucleotide sequence to that of other genes encoding proteins of known structure

Which of the following responded are not likely to be seen when a bacterial culture growing at 37 degrees C is transferred to a culture room maintained at 25 degrees C? explain your reasoning. Initial decrease in membrane fluidity

this is likely because the membrane fluidity decreases as temperature is lowered

Which of the following responded are not likely to be seen when a bacterial culture growing at 37 degrees C is transferred to a culture room maintained at 25 degrees C? explain your reasoning. Gradual replacement of stearate by oleate in the membrane phospholipids

this is likely because unsaturated fatty acids (oleate) will increase membrane fluidity

Which of the following responded are not likely to be seen when a bacterial culture growing at 37 degrees C is transferred to a culture room maintained at 25 degrees C? explain your reasoning. Enhance rate of synthesis of unsaturated fatty acids

this is likely because unsaturated fatty acids will increase membrane fluidity

Which of the following responded are not likely to be seen when a bacterial culture growing at 37 degrees C is transferred to a culture room maintained at 25 degrees C? explain your reasoning. Gradual replacement of shorter-chain fatty acids by longer-chain fatty acids in the membrane phospholipids

this is not likely because longer-chain fatty acids decrease membrane fluidity

Which of the following responded are not likely to be seen when a bacterial culture growing at 37 degrees C is transferred to a culture room maintained at 25 degrees C? explain your reasoning. Incorporation of more cholesterol into membrane

this is unlikely because bacteria do not contain cholesterol under any conditions

We know that exposed regions of membrane proteins can be labeled with 125I by the lactoperoxidase (LP) reaction. Similarly, carbohydrate side chains of membrane glycoproteins can be labeled with 3H by oxidation of galactose groups by galactose oxidase (GO) followed by reduction with titrated borohydride (3H---BH4). Noting that both LP and GO are too large to penetrate into the interior of an intact cell, explain each of the following observations made with intact erythrocytes None of the proteins in the erythrocyte plasma membrane that are know to be devoid of carbohydrate is labeled by the LP/125I method

this means that there are no membrane proteins on the outside of the cell

Acholeplasma laidlawii is a small bacterium that cannot synthesize its own fatty acids and must therefore construct its plasms membrane from whatever fatty acids are available in the environment. As a result, the acholeplasma membrane takes on the physical characteristics of the fatty acids available at the time What is one way you could get the bacteria of part b growing again without changing the medium. Explain your reasoning

unsaturated fatty acids increase membrane fluidity, thus increasing the permeability of the membrane to ions and other solutes and making it impossible to maintain concentration gradients that are vital to life.

What conclusion would you draw if some of the proteins that became labeled by the LP/125I method of part b where among those that has been labeled when intact cells were treated in the same way?

we would conclude that they were integral membrane proteins because they were labeled on both sides of the membrane.

What results would you expect is such inside out vesicles were subjected of the GO/3H---BH4 procedure?

you would expect all of the side chains of the glycoproteins of the inner part of the membrane to be labeled

For each of the following false statements, change the statement to make it true and explain your reasoning You would expect membrane lipids from tropical plants such as palm and coconut to have short-chain fatty acids with multiple c=c double bonds

you would expect membrane lipids from tropical plants such as palm and coconut to have long-chain fatty acids without multiple C=C double bonds

1. The effects of temperature and liquid composition on membrane fluidity are often studied by using artificial membranes containing only one or fewer kinds of lipids and no proteins. Assume that you and your lab partner have made the following artificial membranes: · Membrane 1: made entirely from phosphatidylcholine with saturated 16-carbon fatty acids · Membrane 2: same as membrane 1, except that each of the 16-carbon fatty acids has a single cis double bond · Membrane 3: same as membrane 1, except that each of the saturated fatty acids has only 14 carbon atoms After determining the transition temperatures of samples representing each of the membranes, you discover that your lab partner failed to record which membranes the samples corresponded to. The three values you determined are -36 degrees C, 23 degrees C, and 41 degrees C. assign each of these transition temperatures to the correct artificial membrane. And explain your reasoning

~the -36 will go to membrane 2 because having cis double bonds will significantly drop the transition temp ~the 23 will go to membrane 3 because it has fewer carbon atoms ~the 41 will go to membrane 1 because it has the most carbon atoms which increases transition temp and it also has to double bonds to it is the highest.