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BIOL 200 > unit two > Flashcards

unit two Flashcards

1
Q

what are the 4 main features of the biological membrane?

A
  1. the membrane is a bilayer
  2. the membrane is organized but fluid
  3. the membrane has different permeability for different types of molecules
  4. the membrane is asymmetric
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2
Q

what are the three main molecules that make up the bilayer?

A

lipids, proteins, and carbohydrates (only on the outside of the membrane)

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3
Q

what are the characteristics of lipids?

A

lipids are a broad category of molecules that can have different structures

they are instead characterized by their chemical properties: mainly having high hydrophobic content

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4
Q

what are the 4 types of lipids?

A
  1. phospholipids
  2. sterols
  3. fatty acids
  4. triglycerides
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5
Q

how do phospholipids behave in water?

A

form bilayers or liposomes (spheres)

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6
Q

how do sterols behave in water?

A

form a monolayer on the water surface

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7
Q

how do fatty acids behave in water?

A

form micelles

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8
Q

how do triglycerides behave in water?

A

form droplets

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9
Q

why do lipids behave differently in water?

A

because of the way water likes to form hydrogen bonds

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10
Q

what does water like to form hydrogen bonds with?

A

with other water molecules (energetically favourable)

these h-bonds are continually breaking and reforming

water molecules are constantly rotating

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11
Q

what is the hydrophobic effect?

A

a hydrophobic molecule forces water to reorganize into a cage around the hydrophobic molecule, and affects water’s ability to form H-bonds

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12
Q

what happens to entropy when hydrophobic molecules cluster?

A

entropy of hydrophobic molecules decrease, but the entropy of the water increases

overall system increases in entropy

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13
Q

what are the properties of lipids required to form membranes?

A
  • amphipathicity
  • shape
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14
Q

what are triglycerides?

A

fat

form droplets in water

3 fatty acids (tails) esterified to a glycerol (backbone) (through condensation reaction)

storage form of fatty acids

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15
Q

what does it mean by bilayer formation requires amphipathicity?

A

they must be able to associate with water

they must form relatively stable sheets in water

must be amphipathic: have both hydrophobic and hydrophilic components

typically hydrophilic head and hydrophobic tail

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16
Q

describe the general shape of a phospholipid

A

hydrophilic head
- polar group tip
- phosphate group
- glycerol

hydrophobic fatty acid tails

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17
Q

what is the shape of a fatty acid ( in water)?

A

form micelles because they are cone shaped

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18
Q

what are the shape of phospholipids (in water)?

A

cylindrical shaped - therefore creating the bilayer

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19
Q

what happens to free energy in the hydrophobic effect?

A

free energy to maintain the system is minimized if the hydrophobic regions (lipid tails) cluster together to limit contact with water, increasing the motional freedom of water

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20
Q

what is the experimental evidence that phospholipids form bilayers?

A
  1. will spontaneously form bilayered sphere in water (liposomes)
  2. spontaneously form planar bilayers across a small hole (1mm) between 2 compartments
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21
Q

what do the chemical properties of bilayers suggest about their recovery?

A

they are self-sealing and self-healing

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22
Q

what is the fluid mosaic model?

A

biological membranes were described as a 2D liquid where chunks of proteins are in a sea of lipids

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23
Q

what is lateral diffusion in membrane fluidity?

A

diffusing side to side

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24
Q

what is transverse diffusion?

A

flipping to other leaflet

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25
Q

what kind of movement happens in membrane fluidity?

A

lateral diffusion

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26
Q

why does transverse diffusion not occur (without enzymatic help)?

A

the phosphate group of the phospholipid would have to pass through the hydrophobic region of the membrane, which is not energetically favourable

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27
Q

can transverse diffusion occur?

A

yes, but with enzymatic help

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28
Q

what is FRAP?

A

fluorescence recovery after photobleaching

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29
Q

what are the steps of FRAP?

A
  1. label a molecule (lipid or protein) with a fluorescent marker
  2. photo-bleach an area in the cell (the fluorochromes in the area will be destroyed so they won’t emit light anymore)
  3. measure how long it takes for fluorescence to return to that area (because of lateral diffusion)
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30
Q

what is the effect of temp on lipids?

A

cold temp - membranes freeze and assume a more ordered, crystalline-like state with very low fluidity and is very fragile

as temp decreases, molecular motion slows down, and molecules are trapped by LDFs

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31
Q

how can a cell change its lipids to maintain appropriate fluidity?

A

degree of unsaturation in lipids
fatty acid tail length
amount of sterol in the membrane

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32
Q

do plants & fungi or animals use tactics to change their lipids more often?

A

plants and fungi because they can’t regulate their body temperature

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33
Q

how does fatty acid saturation change lipids to affect fluidity?

A

a higher number of saturated lipids
- more tightly packed; more interactions; less fluid

a higher number of unsaturated lipids
- more kinks in the fatty acid tails due to double bonded structure
- more fluid

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34
Q

how does fatty acid tail length affect fluidity?

A

shorter tail length = less SA = fewer VDF = more fluid

35
Q

how does amount of sterol affect fluidity?

A

sterols are short and rigid lipids; they stick in between phospholipids

at low temp, sterols increase fluidity (prevents tight packing of fatty acids)

at high temps, sterols decrease fluidity (the ring structure stiffens the membranes)

36
Q

what are sterols in animals called?

A

cholesterol

37
Q

what are sterols in plants called?

A

phytosterol

38
Q

what are microdomains?

A

aka lipid rafts

thicker and stiffer region in the plasma membrane rich in specific types of lipids (sphingomyelin & cholesterol)

more ordered than surrounding membrane

they are less fluid than the rest of the membrane

39
Q

how are membranes organized?

A

microdomains & protein adhesion to other molecules

40
Q

where can the proteins adhere to (organization)?

A

to proteins inside the cell

to ECM

to neighbouring cells

41
Q

what are tight junctions?

A

tight junctions are adhesions between neighbouring epithelial cells that form “kissing points” between two cells so nothing leaks in between the cells (nothing can diffuse past)

segregates tops and sides/ bottoms of cells in to distinct membrane domains

42
Q

what cells are tight junctions important for?

A

cells like the intestine epithelium

43
Q

what molecules affect permeability?

A

lipids and proteins

44
Q

what can diffuse through the bilayer?

A

gases and hydrophobic molecules diffuse freely across lipid bilayers

small uncharged polar molecules diffuse fairly well across lipid bilayers

45
Q

what cannot diffuse through the bilayer?

A

diffusion of large uncharged polar molecules across lipid bilayers is negligible

charged substances (ions) cannot diffuse across the lipid bilayer

46
Q

what are the levels of protein structure?

A

primary, secondary, tertiary, and quaternary

47
Q

what are the type of non-covalent bonds involved in protein structure?

A

electrostatic attractions (ionic)

hydrogen bond

van der waals attractions

48
Q

what is primary structure?

A

the amino acid sequence

49
Q

what is residue?

A

amino acid within the peptide

what is left after the dehydration reaction

50
Q

what is secondary structure?

A

H-bonds form between chemical groups of the polypeptide backbone (NOT THE R-GROUPS)

the H-bonds stabilize the shapes formed

forms alpha helix or beta sheets

51
Q

how are the r-groups in the alpha helix facing?

A

they face outwards from the helix

the h-bonds are repetitive all the way along the backbone of the alpha helix

parallel to the long axis of the helix

52
Q

how are the r-groups in the beta sheets facing?

A

they face both directions, alternating

up and down, away from the peptide backbone

53
Q

what are protein domains?

A

secondary structure elements fold into domains (other substructures) within a tertiary structure

in between 2nd and 3rd structure

different domains are associated with different functions

can have more than 1 domain

54
Q

what is the quaternary structure?

A

stabilized by a combination of hydrophilic or hydrophobic interactions, or both, between the biopolymers

stabilized by all factors stabilizing the tertiary structure of the constituent biopolymers

the 3D configuration of different biopolymers making up a molecular complex consisting of several subunits

stabilized primarily by interactions involving the r-groups and groups from the backbone

include disulfide bonds

55
Q

how would you expect a polypeptide to fold in the aqueous environment of the cell?

A
  • hydrophobic part clusters inside
  • hydrophilic part lines the exterior
56
Q

what kind of amino acid side chains are on the surface of the final folded protein complex?

A

hydrophobic, non-polar AA

57
Q

how are bilayer assembly and protein structure formation similar?

A

both are driven by thermodynamics

non-covalent and covalent interactions ensure the most stable final conformational state

increase the stability of the system

58
Q

what are bilayer assembly and protein structure formation examples of?

A

molecular self-assembly

59
Q

what determines how the proteins fold?

A

the chemical properties of the polypeptide chains (each amino acid)

60
Q

what is each folding level dependent on?

A

on the primary sequence for proper folding and proper function

also the environment the protein is folding in

61
Q

what are the types of membrane proteins?

A

integral proteins

peripheral proteins

62
Q

what are integral proteins?

A

proteins directly attached (embedded) into the membrane

amphipathic (inside bilayer = hydrophobic; outside bilayer = hydrophilic)

can be monomeric or multimeric

have asymmetry

63
Q

what are peripheral proteins?

A

bound to the membrane surfaces through non-covalent association with other membrane proteins

stick to surface of transmembrane proteins

have asymmetry

64
Q

what is the transmembrane domain?

A

part of the membrane protein that passes through the lipid bilayer

most transmembrane domains are alpha helices, though some are beta barrels

65
Q

how do you make a pore?

A

either with multiple helices or with one beta sheet in the beta barrel

66
Q

what does a beta barrel look like?

A

one beta sheet inside the barrel

the inside contains water

the outside is exposed to the hydrophobic portion of the bilayer

67
Q

what characteristics would a membrane spanning domain have?

A

non-polar AA

67
Q

how can we determine if a protein is embedded in the cell membrane?

A

hydropathy

68
Q

what is hydropathy?

A

a bioinformatics tool that helps predict alpha helix transmembrane domains

computer generated

based on the properties of the AA in the peptide sequence, and how these properties are also influenced by their neighbours

69
Q

describe the hydropathy graph

A

the peak represent strongly hydrophobic regions (domains)

of peaks = # of domains

dashed line represents threshold hydrophobicity to be considered a domain

above 0 = hydrophobic

below 0 = hydrophilic

the span of amino acids also has to be long enough to pass through a membrane (20 AA)

Y - axis : average hydropathy index

X - axis : amino acid number

70
Q

what are the general steps of protein purification?

A
  1. isolation: the solubility properties of integral and peripheral proteins are different
  2. unfold/ linearize proteins by adding SDS & break disulfide bonds
  3. separate proteins by size with a polyacrylamide gel matrix (SDS-PAGE)
71
Q

describe step one in protein purification

A

isolate your protein (peripheral and integral are different)

isolate all proteins from cells grown in culture (in vitro)

open cells to collect proteins into solution

isolating depends on the proteins solubility - some are soluble in aq environments, some aren’t

72
Q

how do you isolate peripheral proteins?

A

peripheral proteins are attached indirectly to membrane by non-covalent interactions

we use a salt solution to weak protein-protein interactions by disrupting electrostatic bonds

73
Q

why can we not use salt to disrupt transmembrane proteins?

A

because they embedded in the bilayer

74
Q

what holds integral proteins in the membrane?

A

van der waals associations

75
Q

how can we isolate transmembrane proteins?

A

using detergent - harsh treatments: replace the membrane with detergents, to solubilize these proteins

the detergent monomers attack the protein and turn into micelles

76
Q

what are the requirements for being a detergent?

A

must be amphipathic

can be ionic

must be soluble in water (phospholipids and sterols are amphipathic but remain insoluble)

77
Q

describe step 2 in protein purification

A

protein with two subunits A and B and joined with a disulfide bridge

use SDS to denature - coats the entire peptide with negative charge so they are all uniform equal charge to mass ratio - so the size is the only thing that matters - the overall negative charge draws it to the anode

and mercaptoethanol to help break the disulfide bonds

78
Q

describe step 3 in protein purification

A

separate proteins by size with a polyacrylamide gel matrix (SDS-PAGE)

current goes from top to bottom

the largest one will face most resistance so it will stay at the top

the smallest one will face least resistance so it will move the most to the bottom

79
Q

what does it mean that the membrane is asymmetric?

A

the two halves (leaflets) are the membrane are different from each other

lipids: composition of outer leaflet is different than that of inner leaflet of the bilayer

proteins: associated with the membrane (both peripheral and embedded) also have a specific orientation within the membrane

carbohydrates: are only found on the non-cytosolic side

80
Q

how does the cell make asymmetry in the plasma membrane for lipids happen?

A

new phospholipids synthesized by enzymes in the cytoplasmic face of the ER

81
Q

what are flippases? and what do they do?

A

enzymes in the membrane that move phospholipids from one leaflet to the other

flippases/ floppases: uni-directional

scramblases: bi-directional

maintains asymmetry

82
Q

how do proteins affect membrane symmetry?

A

transmembrane proteins are inserted into the ER membrane in a specific orientation. asymmetry is maintained throughout the endomembrane system

peripheral proteins: different proteins attach to different sides of the cell membrane (through specific interactions with other membrane proteins)

83
Q

how do carbohydrates affect membrane asymmetry?

A

carbohydrates are only attached to the non-cytosolic side in the golgi

protects the cell from damage

provides unique indentifiers

BIOL 200 (3 decks)

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