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ANAT 212 > Lecture 8 > Flashcards

Lecture 8 Flashcards

1
Q

what can proteins be modified by

A

lipids - covalently bound to lipids = like another ex of ptms

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2
Q

describe phospholipid synthesis - generally

A

synthesis on cytosolic side of er membrane
fatty acids (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

describe phospholipid synthesis - specifics

A

oh faces environment
protects hydrophobic fatty acid tail and brings to cytosolic part of er membrane and insert into membrane
CoA transferase = intermediate facilitates addition of glycerol group
hydroxyl removed and acetyl coa added
fatty acid brought by carrier into membrane and then sequential steps = to add polar head
choline attached as head into fatty acids

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4
Q

where are phospholipids and cholesterol synthesizedc

A

Phospholipids and cholesterol are synthesized on the cytosolic side of the
ER membrane
makes membranes unbalanced since has less phospholipids and more fatty acids

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5
Q

what does scramblase do

A

protein in ER membrane = flips lipids randomly
atp independent function
helps balance amount of phospholipids in outer and inner membrane
non specific = recognizes any phospholipids

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6
Q

how are lipids transported

A

secretory pathway by vesicles

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7
Q

what is flippase

A

at pm
more specific
maintains membrane asymmtry
ex = phosphatidyl serine always facing cytosol
atp depent
direcional
lipid specific

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8
Q

how are new lipids brought to pm

A

by vesicles and flipped to correct orientation

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9
Q

what maintains lateral organization and membrane asymmetry

A

mechanisms

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10
Q

how are lipids transported

A

vesicles between organelles of secretory pathway
carrier proteins through cytosol
contact sites between organelles = er and mito

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11
Q

how to control traffic of proteins

A

adding other proteins into bilayer
localization of proteins in membrane depend on other proteins that allow protein to be inserted into membrane

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12
Q

what does sequence of protein determine

A

structure
function
localization

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13
Q

what does structure of membrane proteins involve

A

added contacts with lipids

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14
Q

what does localization of membrane proteins require

A

protein based targeting mechanism

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15
Q

what are not associated with membranes

A

soluble proteins

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16
Q

which interactions important to be inserted into membrane

A

hydrophobic interactions with phospholipids

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17
Q

describe integral membrane proteins

A

tightly anchored by hydrophobic interactions with interior of bilayer

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18
Q

describe parts of integral membrane proteins

A

1 or more trans membrane alpha helices = must have
transmembrane beta barrel = depends on formation of beta strands
amphipathic alpha helix in one face of membrane - hydrophobic on one side and polar on other

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19
Q

describe alpha helix for integral membrane proteins

A

amphipathic
hydrophobic aas interaction with membrane and another part = hydrophobic or polar aas that will interact with cytosol
so alpha helix part of membrane

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20
Q

describe lipid anchored or peripheral membrane proteins

A

not integral part or transversing it

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21
Q

describe lipid anchored proteins

A

proteins covalently linked to one or more lipids or fatty acid groups
strength of anchor depends on number and type of lipid
specific aas around them to be attached

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22
Q

describe peripheral membrane proteins and name 2 types

A

attached by non covalent interactions
with integral membrane proteins
with lipid head groups

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23
Q

describe peripheral membrane proteins with integral membrane proteins

A

strong interactions

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24
Q

describe peripheral membrane proteins with lipid heads

A

weak interactions
residues that can form non covalent interactions with polar head of phospholipids = not v strong but allows proteins to localize into membrane

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25
Q

compare transmembrane proteins and lipid anchored proteins

A

tm = function in both cellular compartments, cell surface receptors, transporters
lipid anchored proteins = function in one side of membrane
intracellular signalling

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26
Q

describe trans membrane helices

A

Transmembrane α-helix is the most common form of attachment

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27
Q

describe structure of transmembrane helices

A

Like all α-helices, amino acid side chains point outwards
in transmembrane helices, side chains are hydrophobic to interact with lipids
internal hydrogen bonds maintain structure of helix
some hydrophilic aas tho

28
Q

can proteins have more than one helical domain

A

can have one or more helical tm domain
single and multipass proteins

29
Q

describe single and multiple TM helices

A

tm helices longer, more hydrophobic than interior of soluble protein
usually 18-24 aas long
hydrophobic aa = means that alpha helix inserted into membrane
can often be predicted from hydrophobicity of primary sequence
can see regions inserted into membrane

30
Q

describe hydrophobicity index

A

experimentally aas can be characterizes diff
diff indices use various methods and scales
side chains still have local proteins

31
Q

what does length of tm helices match

A

width of membrane

32
Q

describe longer tm helices

A

may partition into thicker microdomains or insert at angle in thinner membranes
sixe of alpha helix must fit thickness of membrane

33
Q

which proteins can rotate easily

A

proteins with single TM helix

34
Q

describe function of some polar aa’s in tm helix

A

could be in contact with aq environment a bit and sometimes alpha helices get together and make a pore = transmembrane transporter
need polar on interior so wont repel substrate

35
Q

describe TM helical structures

A

Multiple TM helices can fold together into functional structures embedded in the membrane
Interior between helices can be free of lipid
Many transporter proteins have multiple TM helix structure, although are not otherwise related (not homologous)

36
Q

describe transmembrane b barrels

A

in some tm domains = b strands form tm barrel = b sheets wrapped into cylinder
number of tm strands can vary
side chains point out into lipid bilayer and inside = h bonds hold strands together

37
Q

what does more beta sheets do for a b barrel

A

more = determines how big substrate they transport from one end of cell is

38
Q

when is tm protein orientation determined

A

during insertion into membrane
cannot flip - have order and direction

39
Q

are ptms the same in the cytosol

A

noo
since er is bound to sugars

40
Q

describe secretory pathway modifications

A

domains modified differently from cytosolic domains
disulfide bonds between cysteines
oligosaccharides (glycosylation)
stabilize protein structure

41
Q

describe protein modifications in the cytosol

A

phosphorylation
acetylation
methylation
ubquitination

42
Q

can membrane proteins flip

A

never
but lipids can

43
Q

how is movement of ions and polar molecules across membranes controlled

A

by proteins
mechanism depends on concentration gradient of solute

44
Q

name 2 proteins that control ions and polar molecules

A

channel
pump/transporter

45
Q

describe channel

A

allows movement along gradient
does not require energy - atp independent
regulated by opening and closing

46
Q

describe pump/transporter

A

causes movement against gradient
required energy - atp
regulated by turning atpase on and off

47
Q

describe channel proteins

A

allow regulated flow of ions or other molecules across membranes
from one compartment to other

48
Q

what can tm helices form

A

water filled channel

49
Q

describe water filled channel

A

opening controlled by cytosolic domains or subunits
some tm helices must be on polar side
selective for ions = depends on how much channel opens
how much ions get in or out

50
Q

describe voltage gated k+ channel

A

fundamental for neurons, heart, brain, cell function
Rat Brain K+ channel homotetramer = neuron signaling, homologs: heart rhythm
Pore controlled by voltage sensor, other domains

51
Q

describe ion selectivity of channel proteins

A

Channel pore contains Selectivity Filter for specific ion, eg. K+
Carbonyls from peptide backbone line the pore
Ions normally bind water
Ions with the right size can exchange water for carbonyls – partial dipoles
Wrong size cannot bind carbonyls completely and is
rejected

52
Q

give ex of ion selectivity

A

potassium and sodium = both pos but diff sizes
sodium too small to fir into channel well = only engages in a couple of interactions

53
Q

describe atp dependent transporters

A

transport of some substrates across membrane is unfavourable = against gradient
some proteins use atp hydrolysis to transport substrates
sodium potassium pump = maintains ion gradient across pm
atp binding casette - abc = transporters for small molecules = cholesterol, toxins, phospholipid flippases

54
Q

describe multidrug resistance transporter - gen

A

abc transporter with 2 symmetric atpase domains
pumps toxins out of cancer cells = resistance to chemotherapy

55
Q

describe lipid anchored proteins- modifications

A

cytosolic proteins can be covalently linked to acyl - fatty acid or prenyl chains
specific enzymes attach lipid to n terminus or cys side chain
N END RULEEE

56
Q

describe single lipid chain

A

provides transient interaction with membrane
protein bound to membrane = covalently linked to lipid = ptm

57
Q

describe 2 or more lipid chain

A

needed for strong membrane anchor

58
Q

describe acylation

A

N-Gly/N-cys = remove met and 2nd aa= cys or gly = similar to n end rule
produces amide linkage
or just with cys = thioester linkage - can be anywhere

59
Q

describe prenylation

A

depends on cysteine = has be last 4 aa away from cooh terminus = cys-a-a-x-cooh
forms thioester linkage

60
Q

which lipid modification is reversible

A

Cys S-acylation is reversible (thioester) and can be used to regulate interactions with membranes
thioester to cys = reversible - kinases, since they have many of these proteins = participates in signalling

61
Q

which lipid modification is irreversible

A

N-terminal acylations (amide) are permanent
Prenylation: special branched lipids permanently attached to Cys (thioether)

62
Q

describe cysteine

A

Sulfhydryl side chain is chemically reactive
disulfide bond formation
lipid modification = thioester, thioether –> acylation
ub e1 activating and e2 conjugating enzymes - thioester

63
Q

describe cysteine prenylation motif

A

Prenylation motif: Caax-COO- (a=alkyl side chain; x=any)
aax sequence cleaved off, Cys is prenylated

64
Q

describe gpi anchored proteins

A

Some proteins have a special TM helix removed and become covalently linked to glycosyl-phosphatidyl-inositol (GPI) anchor
Strong membrane attachment
Only on lumenal/extracellular side; attached at ER, function at exterior of PM (Extracellular matrix, neuronal receptors………)
More rotational freedom than proteins with TM helices

65
Q

what are gpi anchored proteins used for

A

folded in er lumen
provides flexibility = can more more in er lumen = more mobility
protein bound to membrane by gpi anchor = transferred for mobility

66
Q

describe multidrug resistance transporter - 3 steps

A

1 - no nucleotide = inward open, high affinity for substrate
2 - atp bound = closed, conformational change
3 - atp hydrolysis = outward open (conformational change), low affinity for substrate = release toxin
if have v high concentration of transporters

ANAT 212 (34 decks)

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