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ANAT 212 pre midterm > Professor Ugalde lecture 8 > Flashcards

Professor Ugalde lecture 8 Flashcards

1
Q

On what side of the membrane are phoshpholipids synthesized?

A

cytosolic side of the ER membrane

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2
Q

Where are fatty acids attached and how are head groups added in phoshpholipid synthesis?

A

fatty acid (acyls) are attached to coenzyme A in chemically reactive states
-Glycerol phosphate, head group added in sequence by enzymes

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3
Q

Where are phospholipds and cholesterol synthesized?

A

cytosolic side of the ER membrane

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4
Q

What protein in the ER membrane flips lipids rapidly in lipid synthesis?

A

Scramblase flips lipids randomly and it is an ATP independent function

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5
Q

How are lipids transported after they have been synthesized?

A

transported through secretory pathway by vesicles, and then later they are flipped to correct orientation

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6
Q

What protein maintains membrane assymetry at the plasma membrane?
What is the role of this protein, is it energy dependent, is it specific/what for?

A

Flippase protein maintains membrane assymetry by flipping from outer membrane to cytosol, it is ATP dependent, directional, and lipid specific

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7
Q

What are the 3 ways lipids are transported

A

VCO
V-by vesicles between organelles and secretory pathway
C-by carrier proteins through cytosol
O-through contact sites between organelles

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8
Q

In between what organellese can components of the membrane be exchanged by contact?

A

in the ER and mitchondria

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9
Q

what type of information does the sequence of the protein determine and what does the amino acid sequence determine?

A

structure, function, and localization
-amino acid sequence determines where the protein should be anchored

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10
Q

what does localization of membrane proteins require, and what does the structure involve contact with?

A

-localization of membrane proteins requires protein based targeting mechanims
structure of membrane proteins involves contacts with lipids

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11
Q

Where/how are integral membrane proteins tightly anchored?

A

they are tightly anchored by hydrophobic interactions with the interior of the lipid bilayer

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12
Q

What are the different types of integral membrane proteins?

A
  1. 1 or more transmembrane alpha helices
  2. transmembrane beta-barrel
    3.amphpathic alpha helix in one face of the membrane (one polar and hydrophobic side
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13
Q

What are lipid anchored proteins, and what does their strength depend on?

A

-they are proteins which are covalently linked or one or more lipids/fatty acid groups
-the strength of the anchor depends on number and type of lipid

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14
Q

What peripheral membrane proteins attached by?

A

non covalent interactions

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15
Q

what are the 2 types of peripheral membrane protein/what are they interacting with?

A

-they are interacting strongly with integral membrane proteins
-they also have weak interactions with lipid head groups

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16
Q

where do transmembrane proteins function, what do they act as?

A

they function in both cellular compartments (lumen/exterior and cytosol)
-they act as cell surface receptors and transporters

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17
Q

what are the characteristics of lipid-anchored proteins?

A

-they function in one side of the membrane
-they take part in intracellular signaling

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18
Q

what is the most common form of attachment?

A

transmembrane alpha helices

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19
Q

where do amino acid side chains point in alpa helices

A

they point outwards

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20
Q

in transmembrane helices why are the side chains hydrophobic, and what maintains the structure of the helix?

A

-side chains are hydrophobic to interact with lipids
-internal hydrogen bonds maintain structure of helix

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21
Q

How do transmembrane helices differ than soluble (cytosolic proteins)?

A

TM helices are longer and more hydrophobic, consisting of 18-24 amino acids long since they have to be long enough to be inserted in the PM.

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22
Q

how do you predict if transmembrane helices are present in a protein?

A

can be predicted from the hydrophobicity of primary sequence

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23
Q

how does the length of TM helices relate to the membrane?

A

length of TM helices matches the width of membrane

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24
Q

what do longer TM helices partition into?

A

they partition into thicker microdomains, or insert at an angle in thinner membranes

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25
Q

What is the advantage of just have one TM helix

A

the protein can rotate easily

26
Q

What can multiple TM helices fold together into?

A

they can fold together into functional structures embedded in the membrane

27
Q

What does the interior of the TM helices not contain

A

the interior is free of lipids

28
Q

where does the polar group of TM helices face?

A

they face the cytosol making hydrophillic interactions

29
Q

Why is the interior of the TM membrane polar?

A

to allow polar groups to get transported through (creating a hydrophillic environment, common for ions)

30
Q

how are transmembrane barrels formed, and what determined what can be transported through them?

A

beta sheets wrap into a cylinder, how wide the beta sheet is determines what can be transported

31
Q

where do the side chains point out in TM beta barrels, and what holds the strands together on the inside?

A

side chains point out into the lipid bilayer
-and on the inside hydrogen bonds hold strands together

32
Q

how is transmembrane protein orientation determined?

A

during its insertion into the membrane, there is some directionality

33
Q

in the secretory pathway how are lumenal/extracellular domains modified differently from cytosolic domains, and what do they stabilize?

A

-there are disulfide bonds between cysteins
-oligosaccharides (glycosylation)
-they also stabilize protein structure

34
Q

what mods are only found in the cytosolic domains

A

phosphorlyation, ubiquitination, acetylation, methylation

35
Q

do membrane proteins flip?

A

no they do not, unlike lipids

36
Q

what controls the movement of ions and polar molecules across membranes, and what does this mechanism depend on?

A

-controlled by proteins, also allows for regulated flow of ions
-mechanism depends on the concentration gradient of the solute

37
Q

differences between a channel and pump/ transporter

A

answer in pic

38
Q

How are the TM helices formed water filled channel controlled?
What characterisitcs do the channel proteins have?

A

opening and closing is controlled by cytosolic domains or subunits, and some TM helices must be polar on one side
-they are also selective for ions

39
Q

How are voltage gated sodium channels controlled

A

-pore is controlled by voltage sensor, and other domains

40
Q

what does the channel pore contain?

A

it contains a selectivity filter for specific ions (ex. K+)

41
Q

What lines the pore of channel proteins?

A

carbonyls from peptide backbone line the pore

42
Q

what can ions do in the channel protein with water?

A

ions normally bind with water, and ions with the right size can exchange water for carbonyls (partial dipoles)

43
Q

What happens when the wrong size ion tries to bind to channel protein?

A

wrong size ion cannot bind carbonyls and is rejected

44
Q

what are examples of some proteins that use ATP hydrolysis to transport substrates

A

Na+-K+ pump maintains ion gradient across PM

45
Q

Whhat are ATP-binding Cassette (ABC) transporters used to transport?

A

small molecules like cholesterol, toxins, and phospholipid, flippasses

46
Q

What domains does a multidrug resistance transporter have?
What do they do?

A

ABC transporter with 2 symmetrical ATPase domains
-they pump toxins out of cancer cells- resistance to chemotherapy

47
Q

What are the 3 steps of a multidrug resistance transporter?

A
  1. when there is no nucleotide-inward open, high affinity for substrate
  2. ATP bound-closed
  3. ATP hydrolysis: outwards open, low affinity for substrate (releases toxin out)
48
Q

How can cytsolic proteins be linked in lipid anchored proteins?

A

cytosolic proteins can be covalently linked to acyl (fatty acid) or prenyl chains)

49
Q

what does the single lipid chain provide in lipid anchored proteins?

A

it provides transient interactions with the membrane

50
Q

how many lipids are needed for a strong membrane anchor?
where do specific enzymes attach?

A

two or more lipid chains needed for strong membrane anchor
-specifci enzymes attach lipid to N-terminus or Cys side chain

51
Q

What can Cys-S-acylation regulate?

A

-they can be used to regulate interactions with membranes and they are reversible (thioester)

52
Q

What is the difference betweem acylations and prenylation

A

N-termminal acylations are permanent
-prenylation has special branched lipids which are permanentl attached to Cys (thioether)

53
Q

what is the sulfhydryl bond in terms of reactivity?

A

-it is chemically reactive

54
Q

What does disulfide bond formation do in terms of structure/bond?

A

-disulfide bond formation (in the lumen of the ER they are covalent and stabilize structure)

55
Q

WHat is a lipid modifcation

A

thoester,thioether—>acylation

56
Q

What are ubioquition E1 and E2 doing?

A

-ubiqiotin E1 activating and E2 conjugating enzymes (thioester)

56
Q

What are ubioquition E1 and E2 doing?

A

-ubiqiotin E1 activating and E2 conjugating enzymes (thioester)

57
Q

what does the prenylation motif do, and what is its sequence?

A

-it anchors proteins to the membrane
-it has Caax-COO- (a=alkyl side chain, x=any)
-aax sequence is cleaved off, Cys is prenylated

58
Q

How do proteins become GPI anchored?

A

Some proteins have special TM helix removed and become covalently linked to glysosyl-phosphatidyl-inositol (GPI) anchor
-it has a strong membrane attachment

59
Q

What does GPI protein provide, and what faces the lumen/exterior

A

-provides mobility to protein in the lumen, more than TM helices
-sugar usually faces lumen or exterior (not cytosol)

60
Q

Where are GPI proteins attached?

A

only on lumenal/extracellular side;attached at ER, function at exterior of PM (extracellular matrix (neuronal receptors..)

61
Q

What happens to the structure of an integral membrane protein in the absence of a membrane? what about lipid anchored and peripheral proteins?

A

the integral membrane protein will have a diff 3D structure bc its hydrophobic AA will not interact with fatty acids and instead will collapse in the interior of the protein.
-Lipid anchored and peripheral proteins will have the same structure since they are just anchored

ANAT 212 pre midterm (9 decks)

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