Unit 5

Question 1

Given the total number of carbons, draw the structure of a straight-chain fatty acid (16 C)

Answer 1

• You always have to make sure to draw the carboxylic acid (deprotonated) first
• If you need you can also draw out the chemical formula (remember, one will be a CH3 group while the other will be included in the carboxylic acid so subtract two from your CH2s)
  *Draw

Question 2

Given the total number of carbons, draw the structure of a straight-chain fatty acid (14 C)

Answer 2

*Draw

Question 3

Given the total number of carbons, draw the structure of a straight-chain fatty acid (18 C)

Answer 3

*Draw

Question 4

Representing the structure of a fatty acid as shown below, draw the structure of diacylglycerol 3-phosphate)

Answer 4

*Draw
diacylglycerol 3-phosphate is the same as phosphatidate

Question 5

What kind of linkage joins the fatty acid to the glycerol part of the molecule?

Answer 5

Ester linkage

Question 6

What kind of linkage joins the phosphate to the glycerol part of the molecule?

Answer 6

A phosphodiester linkage

Question 7

Draw structure of phosphatidic acid

Answer 7

• H

Question 8

Draw structure for phosphatidylethanolamine

Answer 8

-NH3

Question 9

Draw structure for phosphatidylcholine

Answer 9

N(Ch3)3

Question 10

Draw structure for phosphatidylserine

Answer 10

• Nh3 (carboxylic acid no H) (and separate H)

Question 11

Draw structure for phosphatidylglycerol

Answer 11

• Glycerol upside down with OH instead of O

Question 12

Draw structure for phosphatidylinositol-4,5-bisphosphate

Question 13

Draw structure for Cardiolipin

Question 14

Give a general description of the structure of cholesterol

Answer 14

Has a polar hydroxyl head group ,and a nonpolar steroid nucleus, and a nonpolar alykl side chain

It’s amphipathic

Question 15

Is cholesterol present in eukaryotic or prokaryotic membranes?

Answer 15

Eukaryotes have cholesterol, prokaryotes do not

Question 16

Identify the eukaryotic membrane in which cholesterol is the most prominent

Answer 16

Plasma membrane

Question 17

Micelle

Answer 17

• Individual units are wedge-shaped (cross-section of head is greater than that of side chain)

Spherical structures that contain amphipathic molecules, which are arranged with hydrophobic regions in the core’s hydrophilic head so it contacts water. There is no water in the interior

Question 18

Lipid bilayer

Answer 18

• Individual units are cylindrically shaped (cross section of head equals that of side chain)

Two lipid monolayers that forms a 2D sheet. Hydrophobic on the inside while hydrophilic on the outside

Question 19

Vesicle

Answer 19

• Folded, closed bilayer that forms a 3D hollow sphere liposome, enclosing an aqueous cavity (the vesicle lumen). Hydrophobic on the inside, hydrophilic on teh outside
• In a 2D monolayer, the hydrophobic regions at the end are unstable since they are exposed to water, so the bilayer will fold back on itself to form a hollow sphere.

Question 20

What is the major driving force for the formation of micelles, lipid bilayers, and vesicles?

Answer 20

The hydrophobic effect

Question 21

Detergents, including soaps (i.e. ionized fatty acids), form micelles and phospholipids form bilayers. Discuss the difference in structure that could account for the formation of micelles vs bilayers

Answer 21

• Micelle formation is favored when the cross-section area of the head is greater than the fatty acid (wedge shaped)
• Phospholipids can’t form micelles because their 2 fatty acid tails are too bulky to fit the interior of a micelle so it prefers a bilayer, when the cross-section of the head is equal to that of its tails

Question 22

True or false: liposomes, which can be made by several methods, such as sonication, have a wide variety of sizes. They have been used extensively to study transporters and receptors, lipid permeability, and lipid interactions

Answer 22

True

Question 23

How does cholesterol impact the bilayer at low temp?

Answer 23

At low temp there is tight packing so cholesterol binding interrupts the tight packing to increase membrane fluidity

Question 24

How does cholesterol impact the bilayer at high temp?

Answer 24

At high temp, there is loose packing so cholesterol can fill in the holes and create more of a rigid structure

Question 25

Integral membrane proteins

Answer 25

- Protein embedded within the bilayer because it is amphipathic - Can only be removed by agents like detergent that can overcome the hydrophobic effect (a type of noncovalent interaction) Types: - Polytopic - Monotopic - Biotopic

Question 26

Polytopic integral membrane protein

Answer 26

Protein that crosses the membrane several times. As a result they have multiple hydrophobic sequences, each of which is in a alpha-helical conformation

Question 27

Monotopic integral membrane protein

Answer 27

Protein in only one layer of the bilayer (most likely only has one alpha helix). Have small hydrophobic domains that interact with only a leaflet of the membrane

Question 28

Biotopic integral membrane protein

Answer 28

Protein spans the bilayer once, extending on either surface

Question 29

Peripheral membrane proteins

Answer 29

Protein associates with the bilayer through electrostatic interactions and hydrogen bonding --> can be released with a mild treatment like pH change, ionic strength (salt), removal of Ca2+, or adding urea Can interact electrostatically with a integral protein or it can interact with the head groups on the membrane

Question 30

Amphitropic membrane protein

Answer 30

Associates reversibly with the bilayer - Found on both the membrane and in the cytosol - affinity for membrane comes from noncovalent interactions with another membrane protein or lipid (head group), and in other cases one or more covalently attached lipids

Question 31

How do detergents "solubilize" membranes and membrane protein ?

Answer 31

- Detergents are amphipathic so when added to a bilayer, they insert their hydrophobic tails into the hydrophobic interior of the membrane disrupting the lipid-lipid interaction which makes the bilayer more fluid - Similarly, detergents interact with their hydrophobic tails with the hydrophobic region of the membrane proteins, disrupting the lipid-protein interaction. This allows the detergent to surround the hydrophobic regions of the protein, forming protein-detergent complex

Question 32

The structure of many integral membrane proteins have been determined. Make some generalizations about these structures in terms of alpha-helices and beta-sheets

Answer 32

1. alpha helices exist as integral membrane proteins because they can span the bilayer and are oriented not quite perpendicular to the bilayer plane. This makes sense because if you are going to bring a protein into a hydrophobic environment and shield its polar backbone from water, it must have enough hydrogen bonds to compensate for what it is not getting from the water 2. Beta-barrels are Beta-sheets that form a cylinder. 3. Tyr and Trp residues: possess hydrophobic characteristics in their side chains. These hydrophobic side chains enable them to interact favorably with the hydrophobic lipid core of the membrane, anchoring the protein within the lipid bilayer. They also have. apolar or charged group which helps them interact with the aqueous phase. This interaction allows these residues to serve as "membrane interface anchors," meaning they help stabilize the protein within the membrane. 4. Positive-inside rule: the positively charged Lys and Arg residues in the extra membrane loop of a membrane protein occur more commonly on the cytoplasmic face of plasma membranes

Question 33

When the primary sequence but not the structure of a membrane is known, how can a model of the structure be made

Answer 33

1) You can do X-ray crystallography; however, this is very time consuming and it's difficult to get proteins out of the bilayer without disrupting them 2) You can use the hydropathy index. You can ONLY use the hydropathy index on alpha helices. Alpha helices take about 20 amino acids to go through the bilayer. Therefore, if you give the hydropathy index your primary structure, it will create windows, each having 20 amino acids, and scans them for the hydrophobicity. The higher up on the hydropathy index, the more hydrophobic and the more negative, the more hydrophilic. Each window will count as one point on the plot. The windows are sliding, therefore the next window is 2-21, then 3-22 etc. When you have found a hydrophobic region (which should be at least 20 amino acids long), this is how you know you have a integral membrane protein. If you have multiple, that means you have a polytopic integral membrane protein and you can count how many alpha helices they have due to how many hydrophobic regions they have. This is all the information can tell you, not anything else.

Question 34

What is the effect of unsaturated fatty acids on the fluidity of the membrane?

Answer 34

Makes the membrane more fluid

Question 35

What is the relationship between fatty acid length and fluidity?

Answer 35

The longer the fatty acid, the more fluid. The shorter the fatty acid, the more rigid

Question 36

Liquid Ordered State

Answer 36

Below normal temperature, all types of lipid movement is restricted

Question 37

Liquid Disordered State

Answer 37

Above physiological temperature, individual hydrocarbon chains or fatty acids are in constant motion

Question 38

What is the major barrier to movement of phospholipids and proteins from one side of the membrane to the other?

Answer 38

Flip flop requires that a polar charged head group laeve its aqueous environment and move into the hydrophobic interior of the bilayer, a process that requires a large amount of energy

Question 39

Flippase

Answer 39

(P-Type ATPase - means ATP powered pump that can phosphorylate itself) moves phosphatidylethanolamine (PE) and phosphatidylserine (PS) from the outer leaflet to the cytoplasmic leaflet * PS cannot be on the outer leaflet or else it will trigger apoptosis

Question 40

Floppase

Answer 40

(ABC transporter) - moves phospholipids from cytosolic side to outer leaflet ATP dependent

Question 41

Scramblase

Answer 41

Moves lipids in either direction towards equilibrium (from the leaflet where it has a higher concentration to the leaflet where it has a lower concentration). Their activity is not ATP dependent but some require Ca2+

Question 42

If scramblases are trying to promote equilibrium, what is leading to the asymmetric distribution of lipids between the two sides of the bilayer.?

Answer 42

Flipasses

Question 43

FRAP

Answer 43

- A small region of the cell surface with fluorescence-tagged lipids is bleached by intense laser radiation so that it no longer fluoresces - WIthin milliseconds, the region recovers its fluorescence as unbleached lipid molecules diffuse away from it - The rate of fluorescence recovery after photobleaching, or FRAP, is a measure of the rate of lateral diffusion of the lipids

Question 44

Discuss how the two components of the electrochemical potential affect the movement of a permeant ion across the membrane

Answer 44

- The concentration directs movement of ion across the the membrane from high to low in order to reach equilibrium - The negatives move towards the positive side to neutralize it and the positives move towards the negative side to neutralize until it reaches equilibrium and there is an equal number of positive and negative charges on both sides

Question 45

Simple diffusion

Answer 45

Molecule diffuses across membrane, down concentration gradient

Question 46

Facilitated diffusion

Answer 46

Passive transport, protein mediated passage through the membrane adn down the electrochemical gradient ex. ion channels (holes specific to an ion) and transporters (very specific, slower than ion channel and saturatable) (uniport)

Question 47

Active Transport and what are the types

Answer 47

Driving substrate across membrane up the electrochemical gradient - Primary active transport - Secondary active transport

Question 48

Primary active transport

Answer 48

Use energy freed by chemical reaction (hydrolysis of ATP)

Question 49

Secondary active transport

Answer 49

Couple one molecule going down teh gradient to one molecule going up the gradient (symport and antiport)

Question 50

Is phosphatidic acid the same as phosphatidate?

Answer 50

Yes