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Biochem > Unit 5 > Flashcards

Unit 5 Flashcards

1
Q

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

A
  • 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
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2
Q

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

A

*Draw

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3
Q

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

A

*Draw

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4
Q

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

A

*Draw
diacylglycerol 3-phosphate is the same as phosphatidate

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5
Q

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

A

Ester linkage

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6
Q

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

A

A phosphodiester linkage

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7
Q

Draw structure of phosphatidic acid

A
  • H
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8
Q

Draw structure for phosphatidylethanolamine

A

-NH3

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9
Q

Draw structure for phosphatidylcholine

A

N(Ch3)3

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10
Q

Draw structure for phosphatidylserine

A
  • Nh3 (carboxylic acid no H) (and separate H)
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11
Q

Draw structure for phosphatidylglycerol

A
  • Glycerol upside down with OH instead of O
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12
Q

Draw structure for phosphatidylinositol-4,5-bisphosphate

A
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13
Q

Draw structure for Cardiolipin

A
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14
Q

Give a general description of the structure of cholesterol

A

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

It’s amphipathic

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15
Q

Is cholesterol present in eukaryotic or prokaryotic membranes?

A

Eukaryotes have cholesterol, prokaryotes do not

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16
Q

Identify the eukaryotic membrane in which cholesterol is the most prominent

A

Plasma membrane

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17
Q

Micelle

A
  • 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

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18
Q

Lipid bilayer

A
  • 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

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19
Q

Vesicle

A
  • 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.
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20
Q

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

A

The hydrophobic effect

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21
Q

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

A
  • 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
22
Q

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

A

True

23
Q

How does cholesterol impact the bilayer at low temp?

A

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

24
Q

How does cholesterol impact the bilayer at high temp?

A

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

25
Q

Integral membrane proteins

A
  • 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
26
Q

Polytopic integral membrane protein

A

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

27
Q

Monotopic integral membrane protein

A

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

28
Q

Biotopic integral membrane protein

A

Protein spans the bilayer once, extending on either surface

29
Q

Peripheral membrane proteins

A

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

30
Q

Amphitropic membrane protein

A

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

31
Q

How do detergents “solubilize” membranes and membrane protein ?

A
  • 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
32
Q

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

A
  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
33
Q

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

A

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.

34
Q

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

A

Makes the membrane more fluid

35
Q

What is the relationship between fatty acid length and fluidity?

A

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

36
Q

Liquid Ordered State

A

Below normal temperature, all types of lipid movement is restricted

37
Q

Liquid Disordered State

A

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

38
Q

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

A

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

39
Q

Flippase

A

(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

40
Q

Floppase

A

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

41
Q

Scramblase

A

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+

42
Q

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

A

Flipasses

43
Q

FRAP

A
  • 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
44
Q

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

A
  • 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
45
Q

Simple diffusion

A

Molecule diffuses across membrane, down concentration gradient

46
Q

Facilitated diffusion

A

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)

47
Q

Active Transport and what are the types

A

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

48
Q

Primary active transport

A

Use energy freed by chemical reaction (hydrolysis of ATP)

49
Q

Secondary active transport

A

Couple one molecule going down teh gradient to one molecule going up the gradient

(symport and antiport)

50
Q

Is phosphatidic acid the same as phosphatidate?

A

Yes

Biochem (15 decks)

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