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Biochemistry > Chapter 10: Membranes > Flashcards

Chapter 10: Membranes Flashcards

1
Q

what is a (cell) membrane?

A

a double layer of lipids and proteins that surrounds/encloses a cell.

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2
Q

how does Dr. Shimko describe a membrane bilayer?

A

as a 3D sheet that extends all the way around a cell or organelle and creates an exterior and interior to the cell or organelle

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3
Q

what 2 reasons does Dr Shimko give for why membranes are so important?

A
  1. they provide separation/barrier between the exterior and interior (of a cell)
  2. they prevent the movement of charged/polar species from one side of the membrane to the other
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4
Q

what is a (membrane) leaflet?

A

what you call each lipid layer in a membrane

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5
Q

why can we describe (membrane) lipid bilayers as ‘ideally’ amphipathic?

A

when/if the bilayers have equal amounts of polar and non-polar regions

the exp from the slides showed a bilayers whose polar region was the exact same length (in Angstroms) as its non-polar region

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6
Q

what is a liposome?

A

a membrane bilayer that extends out to a large size and encloses a large space

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7
Q

what is a liposome also called?

A

vesicle

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8
Q

how are vesicles/liposomes useful for (polar) drug delivery?

A

You can put your (polar) drug into a vesicle and it will fuse with the cell’s membrane, create an opening, and release the vesicle contents into the interior of the cell.

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9
Q

why do phospholipids (spontaneously) form a bilayer?

A

hydrophobic effect?

to maximize favorable interactions between hydrophobic regions (tails and other tails) and polar regions (polar head groups and aqueous environment)

to minimize unfavorable interactions (between hydrophobic tails and polar/aqueous environment and between polar heads and hydrophobic tails)

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10
Q

what comprises a biological membrane?

A

phospholipids, sterols (cholesterols), glycolipids, sphingolipids, glycosphingolipids, proteins etc

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11
Q

What are 3 types of protein structures found embedded in biological membranes?

A

integral member proteins

peripheral proteins

proteins with covalently linked tails

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12
Q

Are all membranes in your body the same?

A

No

The composition varies based on the type of cell, AND based on which leaflet you’re examining (the external/extracellular, leaflet vs the internal/intracellular leaflet)

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13
Q

Do you still need to know about sphingolipids?

A

yes

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14
Q

How can you separate a membrane leaflet?

A

cool the membrane to its solid state and pull them apart while they’re rigid

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15
Q

how does asymmetry (in composition) impact lipids’ ability to move from one leaflet to the other?

A

it makes it such that the lipids can’t move from one leaflet to another without help

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16
Q

why is it thermodynamically UNfavored for a phospholipid to move from the external membrane leaflet to the internal membrane leaflet (or vice versa)

A

this movement requires the polar/hydrophilic head to pass through a region of hydrophobic tails

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17
Q

what is transverse diffusion?

A

what you call it when a phospholipid moves from one membrane leaflet to the other

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18
Q

what is lateral diffusion?

A

what you call it when a phospholipid moves around within the leaflet it’s already in

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19
Q

which is faster: transverse diffusion or lateral diffusion?

A

lateral. Transverse rarely occurs and requires enzymes to occur with any kind of appreciable speed

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20
Q

What kind of diffusion does flippase enzyme do?

A

transverse diffusion from the external membrane leaflet to the internal membrane leaflet

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21
Q

Are flippase and flopase enzymes specific?

A

yes

they only bind to specific phospholipids

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22
Q

What kind of diffusion does floppase enzyme do?

A

transverse diffusion from the INTERNAL membrane leaflet to the EXTERNAL membrane leaflet

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23
Q

What kind of diffusion does scramblase enzyme do?

A

simultaneous diffusion of two phospholipids (where one is defusing from the outer to the inner membrane leaflet while the other is moving in the opposite direction)

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24
Q

are flippse, floppase, and scramblase enzymes considered catalysts?

A

Yes

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25
Q

what is the difference between ‘integral’ membrane proteins and ‘peripheral’ membrane proteins?

A

integral membrane proteins are so closely associated with the membrane structure that they cannot be moved/removed without disrupting the membrane itself

peripheral membrane proteins are associated with the membrane but can be removed from the membrane (with detergents or pH changes, etc) without disrupting the membrane; association with the membrane is weaker than with integral proteins

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26
Q

what is a transmembrane protein?

A

the type of integral protein that spans the (entire) membrane

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27
Q

do transmembrane proteins have to have a specific structure, size, solubility, location, directionality, etc in order to be functional?

A

yes

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28
Q

what two 2o structures are commonly found in transmembrane proteins?

A

alpha helix and beta sheets, especially beta barrels

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29
Q

what is a hydropathy plot?

A

A hydropathy plot, is a graph showing the distribution of hydrophobic amino acids over the length of a peptide sequence, which is used to predict the position of transmembrane domains within a protein

The hydropathy plot displays the hydrophobic and hydrophilic tendencies of an amino acid sequence.

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30
Q

why can some transverse proteins’ polar amino acids exist in the hydrophobic region of the membrane?

A

bc they exist in oppositely charged pairs that neutralize each other

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31
Q

which two amino acids are often found at the interface of polar head groups and hydrophobic tails in a transverse membrane protein?

A

Tyr

Trp

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32
Q

what are 3 secondary structures can be observed in transmembrane (integral) proteins?

A

alpha helix
beta sheet (especially beta barrel)
complex

33
Q

do/can transmembrane (integral) proteins start being integrated into membranes while they’re still forming?

A

yes, they need the lipids (and their hydrophobicity/hydrophilicity) in order for them to fold

34
Q

why are alpha helices so effective as transmembrane (integral) proteins?

A

They have hydrophobic regions that can embed themselves favorably into the hydrophobic part of the membrane, and hydrophilic regions that can embed themselves favorably into the hydrophilic part of the membrane

35
Q

when integrating into a membrane, is it more ideal for an alpha helix to be mostly hydrophobic or mostly hydrophilic?

A

hydrophobic

36
Q

how many residues are usually observed in a transmembrane protein that has an alpha helix structure?

A

20 residues

37
Q

what 3 things can hydropathy plots help you learn about unknown transmembrane proteins?

A

polarity, solubility, folding behavior, etc

38
Q

on a hydropathy plot, does a tall spike represent a very hydrophobic amino acid region, or a very hydrophilic one?

A

hydrophobic. The y axis shows you hydrophobicity and The higher you go, the more hydrophobic you are.

39
Q

what does the x axis on a hydropathy plot show you?

A

the section of amino acid being examined (N terminus is on the left and C terminus is on the right)

40
Q

why is hydropathy plotting useful in examining transmembrane proteins?

A

it tells/shows you which regions of the amino acid chain are hydrophobic enough to be found embedded in the membrane

41
Q

what is distinctive about the hydropathy plot produced by a beta barrel transmembrane protein?

A

because the structure has alternating hydrophobic and hydrophilic sheet sides, the graph alternates/oscilates between polar and not polar regions

You don’t see aggregated regions of polar and non polar like you would on an alpha helix graph

42
Q

why are beta barrels so effective as transmembrane (integral) proteins?

A

they have alternating polar and non-polar residues (where all the polar residues are facing the same direction/on the same face and all the NON polar regions are facing the other direction/on the other face)

This means that one face can interact favorable with the polar part of a membrane while the other face interacts favorable with the NON polar part of the membrane

43
Q

do transmembrane beta barrels have their hydrophobic face in the core or in the outside face?

A

on the outside

this is opposite of what we observe with regular, free, soluble beta barrels (which have their non-polar regions arranged as a hydrophobic core)

44
Q

what 4 amino acids are commonly found in the polar head part of the membrane?

A

Lys, Arg, Glu, Asp (because they are charged at phyisiological pH)

45
Q

what did Dr . Shimko call it when two oppositely charged amino acids can exist in the non-polar part of a cell membrane?

A

he called it a salt bridge

46
Q

what is a chemical gradient?

A

an imbalance (of a substance) inside and outside of a cell that the cell uses to manage the potential energy it needs to drive thermodynamically UNfavorable processes)

47
Q

are biological organisms generally at equilibrium with the outside environment?

A

no (not while we’re alive)

48
Q

why do chemical gradients occur in cells? In other words, why aren’t imbalances rectified automatically through osmosis?

A

The thermodynamic barrier (for moving charged/polar species across the non-polar cell membrane) is too high for this to occur without help

49
Q

are membranes selectively permeable barriers?

A

yes

50
Q

what two factors impact the likelihood of a species passing through a membrane?

A

size and polarity

51
Q

which molecules can pass through cell membrane without help?

A

hydrophobic ones

and net neutral gases (O2 and CO2)

52
Q

can water diffuse through a cell membrane?

A

not very well

53
Q

what does a permeability coefficient tell you?

A

A quantitative measure of the rate at which a molecule can cross a membrane such as a lipid bilayer; expressed in units of cm/s and equal to the diffusion coefficient divided by the width of the membrane.

54
Q

what are (membrane) transporters and what 5 types of substrates do they interact with?

A

transmembrane proteins that assist in the movement of ions, peptides, small molecules, lipids and macromolecules across a biological membrane.

55
Q

what does it mean to be a selectively permeable barrier?

A

it means that molecules/species need assistance in order to cross the barrier

56
Q

what is the main phenomena that directs movement across a membrane?

A

extracellular and intercellular concentrations of the substance being moved

57
Q

what is simple diffusion?

A

what you call it when a (small, non-polar or weakly polar) substance moves through a membrane without assistance, by traveling right through the lipids in the lipid bilayer

58
Q

why are small, non-polar or weakly polar substances able to move through a membrane without assistance (via simple diffusion)?

A

the thermodynamic barrier to this is very small

being neutral, these species do not upset the polar heads or the non-polar tails in the membraine

59
Q

what is the difference between ‘facilitated transport’ ‘facilitated diffusion’, and ‘passive diffusion’?

A

nothing. They are just listed with different names in the slides

60
Q

what is the difference between ‘active transport’ and ‘passive transport’?

A

active transport moves molecules AGAINST their gradient (towards the higher concentration)

passive transport moves molecules DOWN their gradient (towards the lower concentration)

61
Q

What kind of carriers do active transporters use: active carriers or passive carriers?

A

active carriers

62
Q

What kind of carriers do passive transporters use: active carriers or passive carriers?

A

passive carriers

63
Q

which type of molecule movement is thermodynamically favored: down the gradient or against the gradient?

A

down the gradient

64
Q

Why are membrane transporters considered catalysts?

A

they lower the activation energy barrier for polar molecules to cross the membrane

65
Q

what are 2 reasons the energy barrier is so high for moving polar species across the membrane?

A
  1. they have to shed their water shell before crossing

2. they have to overcome the unfavorable interactions with the hydrophobic tails in the membrane

66
Q

how do membrane transporters act as catalysts to reduce the energy barrier for polar species crossing the membrane?

A

they cannot reduce the energy required to remove the species’ water shell, but they can shield the species from the hydrophilic interactions on the way from the outside of the cell to the inside of the cell.

67
Q

what are the three types of membrane transporters?

A

uniport
symport
antiport

68
Q

what is the difference between simple diffusion and facilitated diffusion?

A

in simple diffusion, the molecules pass directly through the lipids in the lipid bilayer

in facilitated diffusion, the molecules travel through pores or carriers that are integrated into the lipid bilayer

69
Q

what are the two types of protein transporters used in facilitate diffusion?

A

channels (pores)

carriers

70
Q

what is the difference between a channel protein transporter and a carrier protein transporter?

A

channels/pores are open on both ends simultaneously

carriers can only be open on one end at a time

71
Q

what’s the difference between uniport, symport, and antiport transporters?

A

uniport can move once substance in one direction at a time

symport can move two substances in the same direction at a time (and both must be present in order for either to move across the membrane)

antiport can move two substances in opposite directions at a time

72
Q

if channels/pore are open on both ends all the time, how do they have selectivity/regulation?

A

they have ‘filters’ inside the shaft of the protein

exp. aquaporin

73
Q

how is aquaporin and example of a selective/regulated channel/pore?

A

it’s inner shaft is lined with a bunch of significantly non-polar amino acids and 2 Asparagines

the non-polar amino acids usher non-polar molecules down the shaft.

The Asparagine’s aren’t polar enough to attract polar or charged species such as H+

74
Q

how to molecules enter the cell through carriers when the carriers are only open on one end?

A

the molecule triggers a conformation change in the carrier via induced fit. Shape change closes the extracellular end of the carrier around the molecule, and opens the intercellular end so the molecule can flow through the carrier into the cell

75
Q

Do carriers ever have filters like how channels do?

A

Yes. Carriers can have a potassium selectivity filter where the inner shaft of the carrier is lined with carbonyls that attracts/is coordinated by K+. This triggers the carrier’s conformation change.

Doesn’t work with Na+ bc Na+ is too small to coordinate all of the carbonyls/maximize favorable interactions in order to trigger the conformation change

76
Q

what is the difference between primary active transport and secondary active transport?

A

primary consumes ATP in order to move molecules against their gradient and conserve the resulting potential energy that gets trapped in the high concentration

secondary ‘couple’ molecules traveling against their gradient with molecules moving down their gradient in order to move the first molecule without investing any energy

77
Q

what are 3 examples of how cell scan obtain the energy needed for primary active transport?

A
  1. get it from ATP hydrolysis
  2. get it from photons
  3. get it from redox rxns
78
Q

why do specific structure, size, solubility, location, directionality, etc matter to transmembrane proteins (in order to be functional)?

A

protein’s polar regions must exist near polar regions of the membrane and vice versa

79
Q

what will happen to a transmembrane protein that gets integrated into the membrane in the wrong position?

A

it will not be functional

Biochemistry (23 decks)

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