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BIOC 212 > Membrane proteins > Flashcards

Membrane proteins Flashcards

1
Q

What are the roles and components of the Secretory pathway?

A

Protein/Secretory pathway components synthesis in ER → transformed in the Golgi → secreted in plasma membrane, extracellular or other organelle of secretory pathway through vesicles

  • INTERNALIZATION (enter the cell) through endosomes → fused to lysosomes
  • Degradation in Lysosomes
    *Never in direct contact with cytosol, spearated by membrane
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2
Q

Are all organelles connected/in contact with the secretory pathway?

A

No!
- Not mitochondrias

*The nucleus and cytosol are not in contact with the secretory pathway,
Secretory pathway includes: ER, Golgi, Exterior of the membrane

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3
Q

What is the Lumen?

A

Lumen = interior of the secretory pathway organelles → ER, Golgi,
- Continuity in components of all secretory pathway organelles

*Components of the lumen are never in contact with the ones of the nucleus/cytosol

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4
Q

Where are the membrane proteins synthesized?

A

All protein synthesis is done in the cytosol

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5
Q

How What is the lumen environment similar to? and not similar to?

A

Similar to extracellular space → blood plasma → salts, pH, proteins, cofactors

Different from cytosol

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6
Q

How is transport done from one component to another of the secretory pathway?

A

Through vesicle transport:
- plasma membrane of organelle forms a closed vesicle → Budding
- Travels in cytosol staying closed
- Releases its content to target organelle of the secretory pathway → fusion

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7
Q

What are the main differences between contents or the cytosol and of the lumen/extracellular space?
Which one can make disulfide bonds?

A

Cytosol = reducing environment, No disulfide bonds
Lumen = oxidizing environment (losing electrons), Disulfide bonds can be made

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8
Q

What are important functions of the biological membranes?

A
  • Provide enclosure to the cell + to organelles within the cell
  • Allow regulated transport between compartements
  • Provide sites for biochemical reactions within the cell
  • Suport contacts with enviroment outside the cells
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9
Q

What reactions are allowed in the cell by the fact that biological membranes provide possibility to have different environments?

A

Photosynthesis, oxidative phosphorylation (cytosol)
VS
Metabolism of biological molecules: lipids glycans, etc. (lumen)

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10
Q

What form of contacts with the outside environment of the cell are supported by the presence of biological membranes?

A
  • Cell motion
  • Recognition of other cells
  • Cell fusion
  • Transmission of signals from exterior to interior of the cell
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11
Q

What are the properties of biological membranes? (4)

A
  • Form HYDROPHOBIC barriers between aqueous compartments within the cell (cytosol and organellar lumens)
  • Flexible and can be formed into different shapes
  • Selectively permeable
  • Can store energy as concentration gradients: voltage (nerve cells), pH, K+, Na+, Ca++
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12
Q

What does it mean for the plasma membrane to be selectively permeable?

A
  • Small hydrophobic molecules can transpass the barrier
  • Hydrophilic and big hydrophobic molecules need transport proteins to cross
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13
Q

What are the structural components of membranes?
What is its model?

A

FLUID MOSAIC MODEL
2 components: Lipids and Proteins

  • Lipids are organized into a bilayer → polar exterior and hydrophobic interior
  • Hydrophobicity = barrier to water-soluble molecules
  • Membrane proteins can rotate and diffuse laterally, but can NEVER flip
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14
Q

What are the 3 major lipids in the plasma membrane?
And Characteristics?

A
  • Phospholipids → in all membranes
  • Glycolipids → only in plasma membranes (no in ER or Golgi)
  • Cholesterol → all membranes, preferentially in plasma membrane

All have a polar head and hydrophobic tails
Lipid composition determines physical proterties of membrane
→ mobility (diffusion, rotation, can flip from 1 layer to the other)
→ curvature, thickness

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15
Q

What is the general structure of phospholipids?

A

Polar head groups:
- Choline or other charged group
- Phosphate (1 negative charge)
- Glycerol

– Ester Linkage –

Hydrophobic/fatty acid tails:
- different lengths
- Saturated or unsaturated (1 or more double bonds)
- Found in many different combinations with head groups

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16
Q

Which is the most abundant lipid in membranes?

A

phospholipids

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17
Q

What are the different phospholipids charged head groups?

A
  • Phosphatidyl-choline (PC) → (1 positive charge to neutralize phosphate)
  • Phosphatidyl-ethanolamine (PE) → ( 1positive charge to neutralize phosphate)
  • Phosphatidyl-serine (PS) → (1 positive charge + 1 negative charge so net negative charge)
  • Sphingomyelin (SM) → same group as choline but has amide linkage tails like a glycerolipid, Ceramide basis
  • Phosphatidyl-inositol (PI)

Head group size and charge affect lipid mobility

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18
Q

What is phosphatidyl-inositol?

A

A phospholipid head group
Not abundant but can be phosphorylated and act as signaling molecule

  • Sugar attached to the phosphate, this sugar has -OH groups that can be phosphorylated
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19
Q

What are the characteristics of fatty acid tails?

A
  • Hydrocarbon chain of 14 - 24 C
  • Saturated or not (varying # of double bonds)
  • Saturated → straighter, more flexible
  • Double bonds (cis) → bends in the tail, less flexibility, shorter length
  • Types of tails in membrane determine its thickness and fluidity (more double bonds = more fluidity)

*Synthesized in cytoplasm

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20
Q

What are glycolipids?

A

They are lipids found on the outside surface of the plasma membrane only

Structure:
Basis = ceramide (includes 1 fatty chain, 1 fatty acid tail + amide linkage)
Head group = glucose, GalNac, Gal, NANA sugars or combinations
head groups → important for contacts with environment and other cells

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21
Q

What is the role of cholesterol in membranes?

A

*Structually different from other lipids

Steroid ring structure → very rigid:
- lateral mobility, rotation → much lower
- Less mobility of surrounding phospholipids
- Makes fatty acid tails more rigid

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22
Q

What is the structure of cholesterol in membranes?

A
  1. Polar head group (-OH)
  2. Rigid steroid ring structure (stiffened region)
  3. 1 nonpolar hydrophobic tail (more fluid region)
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23
Q

How is the membrane asymmetric?

A
  • Lipid composition at each side is different
  • Important for PLASMA MEMBRANE function
  • Exterior has glycolipids
  • Interior → stronger negative charge (high PS levels)
  • Not absolute asymmetry, but actively maintained by phosphorylation of phosphatidyls (usually in interior)
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24
Q

What are the main components of the outer leaflet and inner leaflet of the plasma membrane?

A

Outer leaflet (facing extracellular space):
- Phosphatidyl-choline (PC)
- Sphingomyelin (SM)
- Glycoplipids

Inner leaflet (facing cytosol):
- Phosphatidyl-ethanolamine (PE)
- Phosphatidyl-choline (PC)
- low amout of PI for signaling

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25
Q

Which lipids is the plasma membrane mostly rich in?

A
  • Cholesterol
  • SM
  • PC
  • PE
    -GL → *Very little but only found in PM
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26
Q

Which lipids is the ER membrane mostly abundant with?

A
  • PC
  • PE
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27
Q

Which lipids is the mitochondria membrane mostly abundant with?

A
  • PC
  • PE
    *Dosen’t have SM nor GL
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28
Q

What are microdomains?

A

Regions of a membrane that are organized laterally (sideways), in patches

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29
Q

What are lipid rafts?

A

Special micro domains in Plasma membrane and trans-Golgi:
- Enriched in Cholesterol → Thicker than surrounding membrane
- Lipids with longer tails cluster in rafts
- Different proteins content and biological functions

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30
Q

Why does cholesterol binding thickens the membrane?

A

It straightens the lipid tails

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31
Q

What is the polarity/hydrophobicity of cholesterol like?

A

Very hydrophobic because of the rings
*Has weak hydroxyl polar head

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32
Q

Name the lipids in increasing order of size.
And compare to protein and AA sizes

A

Cholesterol < Phosphorylation lipids < Glycolipids

AA < phospholipids < proteins

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33
Q

What are the types of membrane proteins?

A

Integral membrane proteins:
- Transmembrane Helices → Type 1 and 2
- Transmembrane barrels

Amphipatic alpha helix
Lipid anchorage proteins :
- Acylation and Prenylation
- Glycosyl-phosphatidyl-inositol anchor

Lipid anchorage via GIP
Peripheral membrane proteins

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34
Q

Explain phospholipid synthesis.

A

Synthesized on the cytosolic side of the ER membrane (not ER lumen side)

  1. Fatty acids (acyls) binding protein brings fatty acid-OH to the membrane
  2. Fatty acids are attched to CoA in chemically reactive states
  3. Glycerol-phosphate, head group added in sequence by enzymes
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35
Q

Where are phospholipids and cholesterol synthesized?

A

In the cytosolic side of the ER membrane

36
Q

How does synthesis and insertion of lipids in the ER membrane occur?

A
  1. phospholipids + cholesterol synthesized in cytosolic side of ER membrane (Not ER lumen side)
  2. phospholipids add to cytosolic half of the bilayer → makes membrane unbalanced
  3. Scramblase catalyzes flipping of phospholipids → symmetric growth of both halves of bilayer

*lipids are transported by secretory pathway by vesicles

37
Q

What is Scramblase?

A

Enzyme responsible for flipping of the phospholipids from cytosolic side of ER membrane to the ER lumen side
ATP-independent → functions bc of “concentration gradient” between both layers

38
Q

How is asymmetry maintained in the PLASMA membrane?

A

*After delivery of new membrane by exocytosis/vesicles, lipids might not be in the right layer

Flippase proteins maintain membrane asymmetry:
- ATP-dependent
- directional
- specific phospholipids to cytoplasmic monolayer

PM NOT as random as ER

39
Q

How does the transport of lipids occur?

A

Maintain lateral organization + membrane asymmetry

Lipids are transported by:
- Vesicles between organelles of the secretory pathway
- Carrier proteins through the cytosol
- through direct physical contact sites between organelles → ER and mitochondria

40
Q

Which 3 main aspects of proteins are determined by their AA sequence?

A
  1. 3D structure → function
  2. Post-translational modifications
  3. Where the protein is located in the cell (in the membrane?, in which compartment? in the cytosol?) → proteins in the cytosol ≠ lumen ≠ membrane
41
Q

What PTM do membrane proteins undergo?

A

Addition of lipid groups
- Acylation / prenylation

Soluble protein are NOT associated with membrane proteins

42
Q

Are soluble proteins associated with membranes?

A

No, because they are polar and membranes are hydrophobic inside

43
Q

What are 3 different integral membrane proteins?
What is common to all of them?

A
  • 1 or more transmembrane alpha-helix
  • Transmembrane beta-barrel → make a cylinder
  • Amphipatic alpha-helix in one face of the membrane (doesn’t touch both side of the membrane) → hydrophobic on one side (membrane side) and polar on other (cytosol side), less abundant
    *All tightly anchored by hydrophobic interactions with interior of the lipid bilayer
44
Q

What are lipid-anchored membrane proteins?

A

Proteins that are covalently bound to one of more lipids or fatty acid groups on the membrane
- The strength of the anchor depends on number and type of the lipids its attached to

45
Q

What are lipid-anchored and peripheral membrane proteins?

A

Lipid-Anchored:
- Covalently interacts with membrane

Peripheripheral membrane proteins:
- Attached by non-covalent interactions
- Have strong protein:protein interactions with integral membrane proteins → localizes them in the cell
- Or can have weak interactions with lipid head groups → localization role too

46
Q

What are the main differences in functions between transmembrane proteins and lipid-anchored proteins?

A

Transmembrane proteins:
- Function in both cellular compartements (both ends)
- Cell surface receptors, transporters

Lipid-Anchored proteins:
- Function in one side of the membrane (either side though)
- Intracellular signalling

47
Q

What are the characteristics of a transmembrane helix?

A
  • Most common form of attachement
  • Side chains point outwards and are hydrophobic to interact with lipids → G, A, C, L, F (important)
  • Can have few polar groups on the ends to interact with polar head of lipids
  • 18-24 AA long → longer than normal intradomain helix, longer for thicker membranes, angled for thinned membranes
  • Protein with single TM can rotate easily
48
Q

What amino acids form the side chains of transmembrane helices?

A

Glycine, Alanine, Cysteine, Leucine, Phenylalanine

49
Q

What does the structure of a group of multiple TM helices looks like?

A
  • Can for a channel/port for ions for example
  • Can have hydrophilic side chains that make the port a hydrophilic environment
50
Q

What is the structure and characteristics of transmembrane beta-barrels?

A
  • beta-strands wrapped into a cylinder → TM barrel
  • # TM strands can vary
  • Side chains point out into lipids bilayer and inside
  • H-bonding holds strands together
51
Q

Why are membrane proteins never flipped?

A

Because the asymmetry in protein membrane configuration → cytosolic side doesn’t do same PTM as lumenal side (reducing vs oxidizing envrionments)

Modification in the lumenal/extracellular side:
- Disulfide bonds between cysteines
- addition of oligosaccharides (glycosylation)
→ Stabilize protein structure

Cytosolic modifications:
- Phosphorylation, Ubiquitination, Acetylation, Methylation

52
Q

What are the differences between channels and pumps/transporters?

A

Chanels and pumps = Usually beta barrel or multi-pass (alpha helices) proteins

Channels:
- Mvt along gradeint
- No energy requirements
- Regulation = opening and closing

Pumps:
- Mvt against gradient
- ATP-dependent
- regulated by turning ATPase on/off

53
Q

What are the characteristics of channel proteins?

A

Allow flow of ions (or other molecules) across membranes

TM helices can form water-filled channel → opening controlled by cytosolic domains/subunits

Selective Filter for specific ions :
- Carbonyls (=O) from peptide backbone line the pore (replace O from H2O they bind in the cytosol)
- Ions normally bind water → if right size for the channel → can exchange H2O for =O → partial dipoles
- If wrong size, can’t completely bind carbonyls → rejected

ex: voltage-gated K+ channel → neuron signaling, heart rhythm → controled by voltage sensors

54
Q

What are ATP-Binding Cassette (ABC) transporters?
Give an example.

A

Large family of membrane transporter proteins

transport small molecules → cholesterol, toxins, phospholipid flippases
(against concentration gradient)

Multidrug resistance transporter:
- ABC transporter with 2 symmetrical ATPase domains
- pumps toxins out of cancer cells → resistance to chemotherapy
- NBD1/2 (nuclear binding domains) in cytosolic side (intracellular) + TMD1/2 inside the membrane
3 states:
1. No nucleotide → inward open, high affinity for substrate to come and bind
2. ATP bound → closed (with substrate)
3. ATP hydrolysis → outward open, low affinity for substrate (release outside of cell)

55
Q

What PTM can undergo cytosolic proteins in order to become lipid-anchored?
What is required for strong membraen anchor?

A

Can be convalently linked to acyl (fatty acid) → acylation or phenyl chains → prenylation

  • Single lipids chains provide transient interaction with membrane
  • 2+ lipids chains need for strong membrane anchor
  • Specific enzymes attach to N-terminus or Cys side(C-term) chain
56
Q

What is required for Acylation of cytosolic proteins → lipid anchored)? What is the name of the bond?

A

N-terminus methionine has to be cleaved → Need Glycine or Cysteine as 2nd AA
Glycine or Cys → amide linkage
Cysteine anywhere → thioester linkage
G and C not involved in N-end rule, so works out

Need multiple acylations for strong membrane anchor

57
Q

What is required for Prenylation of cytosolic proteins (→ lipid anchored)? What is the name of the bond?

A

Need a prenyl group at the end of protein:
motif = Cys-a-a-x-COO-
a = alkyl side chain, x = any
aax sequence cleaved off, Cys is prenylated
Thioether linkage with cystein (has S) and prenyl group

58
Q

Which lipid modifications in the cytosol (acylation and prenylation) are permanent vs reversible?

A

Cys S-acetylation → reversible (thioester) → signaling (often done by kinases)

All prenylations are permanents
Acylations → Amide to N-Gly and Amide to N-Cys → Permanent

59
Q

What PTM can Cysteine AA undergo? (Chemically reactive Sulhydryl side chain)

A
  • Disulfide bond formation
  • Ubiquitin E1 activating, E2 conjugating enzyme (thioester)
  • Lipids modification (Thioester, Thioether) → Acylation
  • Prenylation motif: Caax-COO-
60
Q

What are GPI-anchored proteins?

A

Starts as transmembrane protein → Has special TM helix removed → covalently linked to GPI anchor → More rotational freedom than proteins with TM helices to move farther in ER lumen, staying attached to membrane

*GPI = glycosyl-phosphatidyl-inositol (anchored in the PM)

  • Strong membrane attachement
  • Only on lumenal/extracellular side
  • Function at exterior of the PM (in the lumen)
61
Q

What happens to the structure of an integral membrane protein in the absence of a membrane?
What happens to lipid-anchored and peripherial proteins?

A

Integral membrane proteins: different 3D structure because of its hydrophobic AA
Lipid-anchored and peripherial proteins: no change

62
Q

Where is sorting information for each protein carried? Why is it important?

A

Sorting information is important because all proteins are encoded by nuclear genes, translated in cytosol
- Sorted during/after translation to their correct compartment

Sorting information is carried inside the proteins themselves

63
Q

Where do sercretory pathway proteins go after/during translation?

A
  1. ER for ALL of them
  2. Transport to further compartements → Golgi, PM, endosomes, lysosomes
64
Q

What are some characterstics/sections of ER?

A

Outer and inner nuclear membrane are continuous with ER
Rough ER = many attached ribosomes, secretory protein synthesis
Smooth ER = no ribosomes, sites of lipid synthesis

65
Q

What are the properties of targeting signals on proteins?

A
  • Sequence within a protein that specify its organelle localization → signal peptide
  • Can also be a PTM
  • Are often idependent from the structure or biochemical function of protein
  • May be removed by proteolysis after targeting is complete, or form part of the native structure
  • ## Recognized by their pattern, not usually exact sequence
66
Q

What are the targeting steps for targeting proteins to their specific organelle localization?

A
  1. Recognize a signal on a protein:
    - Ribosome begins translating polypeptide with a signal
    - Signal Recognition Particle (SRP) = soluble protein that binds signal and ribosome during translation (at the exit tunnel) → Slows down translation by binding to ribosome
    *SRP-GTP binds (not SRP-GDP)
  2. Connect protein to the membrane:
    - SRP Receptor (SRP-R) = membrane protein → binds ribosome-SRP complex (rlly only binds the SRP)
    - SRP-R links ribosome to translocon pore in ER
  3. Translocate protein into or across the membrane (in translocon):
    - Energy of translation on ribosome drives polypeptide through the translocon

*For secretory signal peptides → CO-TRANSLATIONALLY

67
Q

How were targeting signals discovered?

A

Observation: newly translated secretory protein larger than its final form
Hypothesis: extra sequence is a targeting signal peptide whose main function is to direct insertion into ER
- Signal peptide must start mechanism to connect ribosome to transcation pore
- Signal peptide is cleaved off after trageting is finished

68
Q

What is the Ribosome Exit Tunnel?

A

Path, in large (60S) subunit by which nascent polypeptide exit the ribosome
- Neutral, polar, too small for tertiary folding
- Surface around exit site provides binding sites for ER targeting mechanisms
- 30-40 AA of nascent polypeptide between peptide-transferase site and the exit

69
Q

What is the signal peptide pattern for proteins of the secretory pathway?

A

8-16 Hydrophobic AA + short polar regions on each side

  • In most cases, at the N-terminus (beginning)
  • Often cleaved off after translocation
70
Q

What are signal anchors?

A

Signal peptides that also become TM helices:
- Not cleaved off
- Can be in different places in the protein
- longer hydrophobic region → 18-24 residues

Also bound by SRP-GTP for type 2 proteins to bring to translocon

71
Q

Where do secretory pathway proteins start their translation?

A

IN THE CYTOSOL
Almost all proteins are coded for by nuclear genes and their mRNA is translated (start) in the cytosol with ribosomes

72
Q

What is the structure/functions of SRP?

A

Signal Recognition Protein
- Ribonucleoprotein → 6 protein subunits + 1 RNA
- Signal sequence recognition subunit with GTPase activity
- Translation regulatory domain (slow translation down when binds to the ribosome)
- RNA strand = flexible linker

73
Q

How does SRP interact with ribosomes?

A
  1. SRP samples ALL nascent polypeptides that emerge from ribosomes
  2. If signal peptide is recognized, SRP attached tightly to both the signal and the ribosome → pauses translation at ribosome and binds GTP
74
Q

How is the ribosome transfered from the SRP-R the the translocon?

A
  1. Ribosome-SRP complex binds to SRP-R on ER membrane (cytosolic side)
  2. Ribosome moves to the translocon and becomes tighlty bound
  3. SRP and SRP-R dissociate from ribosome → translation resumes, polypeptide translocated into lumen, lumenal polypeptide never in contact with cytosol
75
Q

How is GTPase activity involved in SRP and SRP-R’s roles in the targeting signal of secretory pathway proteins?

A
  1. SRP attached to ribosomes = GTP-bound state
  2. SRP-R (also GTPase) recognizes SRP-ribosomes = GTP-bound state
  3. GTP hydrolysis by both SRP and SRP-R dissociate them and recycle them

GTP = “switch”

76
Q

What the properties of the ER translocon? Sec61 complex

A
  • Sec61 protein has 2 parts → both sides of aqueous pore
  • Inactive pore = plugged by part of protein
  • When closed: plug + lateral gate closed
  • Open: Signal peptide is in the lateral gate opening and translocating polypeptide is in the center (where the plug was)
  • Lateral opening allows signal peptidase to have direct access to signal peptide to cleave it
  • Active pore is open, but tightly sealed onto ribosome
  • Inside of pore = neutral, polar
  • 2 parts of pore open laterally to integrate TM helices into membrane
77
Q

What are the steps of translocation of lumenal proteins from the cytosol to the ER lumen?

A
  1. Singal peptide triggers opening of the translocon
  2. Polypeptides are translocated in an extended, unfolded state right out of the ribosome → translocon → Mvt of polypeptide is driven by energy or translation pushing it out of the ribosome
  3. Signal peptidase (transmembrane protein) often removes signal peptide during translocation → not sequence-specific, but has preferred site
78
Q

What are the steps for integration of TM helices in the membrane?

A
  1. Signal peptide starts translocation of lumenal part
  2. TM helix is recognized by translocon and integrated laterally into membrane during translation
  3. Cytosolic part is translated in the cytosol
79
Q

What are Type 1 TM protein and Type 2 TM proteins?

A

Type 1 TM protein: N-terminus in lumen, C-terminus in cytosol

Type 2 TM protein: N-terminus in cytosol, C-terminus in lumen

80
Q

What are the steps for integration of signal anchor in the membrane?

A
  1. Signal anchor open translocon like a signal peptide
  2. Translocon recognizes charged next to the signal anchor to determine orientation in membrane → positive changes in cytosol, negative charges in the lumen (will be neutralized that way)
  3. Signal anchor is recognized as a TM domain and integrated laterally
81
Q

What post-translational modification do ALL proteins of the secretory pathway undergo?

A

N-linked Glycosylation → covalent bonding of glycans Asn side chain in Asn-X-Ser/Thr motif
- Help stabilize that native state
- Protect against proteases
- Function in cell surface signaling

*Multiple Asn side chains that have that motif can be motified this way
*Irreversible

82
Q

What is a glycan?

A

Covalent attached to asparagine side chain → Asn-X-Ser/Thr motif

Structure starting from N-terminus of asparagine → 2x N-acetylglucosamine + multiple mannose + 3 glucose at the end

83
Q

What is Oligosaccharyl transferase (OST)?

A

Enzyme responsible for N-Glycosylation, this PTM depends on OST accessibility
*It is a membrane protein

*Acts during translocation at the ER membrane

Can N-glycosylate multiple AsnxSer/Thre sites depending on accessibility

84
Q

Do all TM protein have a signal peptide?

A

No, Type 2 only have anchor signal later in their sequence

85
Q

What are the main differences in linkage for acylation and prenylation?

A

Acylation = bound to fatty acid (N-term or S from Cys bound to C=O from fatty acid)
N-Gly or N-Cys → amide linkage
Cys → thioesther linkage (REVERSIBLE)

Prenylation = bound to a fatty acid via prenyl group (Cys-CH2-fatty acid tail)
Cys → thioether linkage

86
Q

How is the signal peptide released after being cleaved?

A

It’s released laterally by the translocon lateral gate
*same for signal anchor

BIOC 212 (15 decks)

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