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BIO 202 > Exam 2 > Flashcards

Exam 2 Flashcards

1
Q

What is the membrane made of?

A

Phospholipid bilayer, which is embedded with protein and lipid molecules

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2
Q

What is Sphingosine

A

an amphipathic phospholipid, embedded in membrane

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3
Q

What is spingomyelin?

A

A phospholipid with an NH group

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4
Q

3 components of a cholesterol molecule?

A

Polar head group, rigid steroid ring structure, nonpolar HC tail

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5
Q

What does cholesterol do in the membrane?

A

embeds itself, creates stiffness in middle

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6
Q

What is the special properties/structure that amphipathic molecules have?

A

Cone structure which forms into micelle (cone/circle shape) or into the lipid bilayer

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7
Q

What occurs to planar phospholipid bilayer when exposed to water?

A

Will seal into energetically favorable compartment

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8
Q

What are the 3 movements of the membrane/phospholipids?

A

Flexion, flip-flop, lateral diffusion
1. Flexion- wiggling/full rotation of lipids
2. Flip-flop, rarely occurs, phospholipids moving to other side of membrane
3. lateral diffusion- often, moving and wiggling

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9
Q

What are unsaturated HC chains like?

A

tails are kinked due to x2 bonds, more compact

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10
Q

What are saturated HC chains like?

A

Wider, harder for the relative movement of phospholipids

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11
Q

Membrane composition is regulated based on

A

needs of cell

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12
Q

The lipid bilayer’s symmetry?

A

Lipid bilayer is asymmetrical, extracellular space has more glycolipids and phosphatidylcholine, and sphingomyelin
cytosolic side: has phosphatidylethanolamine and phosphatidylserine

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13
Q

What happens if a membrane’s lipid bilayer is not kept asymmetrical

A

Immune system will attack

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14
Q

What are glycolipids?

A

Similar to sphingomyelin, have sugar groups added, ex. sialic acid which is attached
- role in cell recognition and signaling

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15
Q

Permanent membrane proteins

A

Transmembrane proteins that use hydrophobic alpha helices to span the whole membrane, embedded in membrane until death ex. channel proteins, carrier proteins, receptor proteins

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16
Q

Non-permanent

A

Peripheral proteins that are attached to integral proteins/lipid heads, (signaling proteins), a hydrophobic chain can be added to associate w protein (palmitoylation), Binding pocket regulated proteins

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17
Q

What is palmitoylation

A

Addition of a fatty acid to a protein, can anchor peripheral proteins to lipid bilayer. Stability and helps w signaling pathways

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18
Q

What are examples of lipid anchoring?

A

Myristylation, palmitoylation, and Farnesylation
1. Myristylation- adds fatty acid to terminal amino grp of a protein, amide bond, helps protein associate with inner surface of cell membrane
2. Palmitoylation- adds fatty acid to cysteine side chains, increases hydrophobic interactions w lipid bilayer
3. Farnesylation- attaches farnesyl to protein with thioether linkage, anchors protein to membrane

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19
Q

What does membrane fluidity help with? Why is it important that many membrane proteins are glycosilated?

A

This allows for lateral movement of proteins, this helps with function and folding, Glycosylation is important for stability, protein function and cell-cell recognitions

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20
Q

What is Bacteriorhodopsin?

A

a multi-pass protein, high in concentration, in cell membrane, creates proton pump that generates ATP, allows H+ ions to pass through membrane in response to light

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21
Q

What are lipid rafts?

A

Specialized regions within lipid bilayer of cell membrane, enriched in lipids, proteins and cholesterol, attracts cholesterol because of the extra fatty acids, makes more rigid,

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22
Q

Explain how membrane proteins can be restricted to certain parts of the cell

A

Certain proteins can be restricted to parts of the cell because of tight junctions, the apical side proteins (exterior/lumen), lateral plasma membrane (between adjacent cells), Basal Plasma Membrane (connects basal lamina) structural suppotr

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23
Q

How is sperm an example of restriction of proteins in certain parts of cells

A

Sperm exhibits apical-basal polarity, specific proteins are restricted to apical or basal regions

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24
Q

What does Cortical cytoskeleton adds strength and structure?

A

The cortical cytoskeleton cytoplasmic side made up of proteins that peripherally interact

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25
What is spectrin
Lines intracellular side of plasma membrane, Actin associated protein, it is a spacer protein, has short regions of actin, has coiled coil dimers,
26
What is Ankyrin and how is it related to spectrin
Ankyrin is a family of proteins that mediate attachment of integral membrane proteins to the sceptrin-actin cytoskeleton. N terminal domain that binds to sceptrin
27
What are membrane bending proteins?
inner mitochondrial membrane has curves, insert fat cells into one leaflet,
28
The luminal environment of each organelle is tightly regulated
pH values can change this, the nucleus, ER and cytosol are similar, pH can affect enzyme function, stability of proteins, signaling and transport
29
Why is the pH of lysosomes what it is?
pH is acidic, break down waste materials, acidic pH is optimal for activity of these enzymes
30
How are small molecules moved against membranes?
Transporters and channel proteins
31
Examples of transporter proteins
Glucose, amino acids, Na+,K+ pump, Ca2+ pump,
32
What is moved with channel proteins
Ions, water
33
Channel proteins need
conformational change
34
Uniport
Transport 1 molecule or ion at a time, never are totally open, facilitated diffusion bc w gradient
35
symport?
Moving 2 molecules same direction (often 2ndary active transport)
36
What type of transport is the Na+, glucose transporter?
Symport --> Na+ move down their conc gradient, provide E for glucose to go against their gradient (Na goes into cell first, then glucose) into cytosol
37
Antiport?
1 molecule moves 1 way, 1 moves other (2ndary active transport)
38
Type of transport of Na, Ca and explain
Antiporter, Na+ ions into the cell down their concentration gradient, provide E, Ca out of the cell, maintains intracellular Ca level
39
2 Types of passive transport
channel mediated, and with transport-mediated
40
Active Transport requires
Energy
41
Example of concentration gradient w no membrane potential
42
43
3 ways energy can come from for transport
Coupled transporter, ATP-driven pump, Light-Driven pump
44
What is coupled transportation?
Uses ATP, pump consumes ATP, then primary active transport (symport and antiport), uses pre-existing gradient to move other molecule
45
What does a P-type pump move?
H+, K+, Na+, Ca 2+
46
What does an ABC transporter move?
uses 2 ATP to move small molecules
47
What type of pump is the Ca 2+ pump and explain
P-type, in smooth ER, ER has high Ca 2+ inside, ATP binds, opens on cytosolic side, Ca2+ binds, triggers conformational change, ATP--> ADP, then, ADP is released, H binds on other side, P is released and H leaves
48
What is the sodium pump?
P-type pump, helps maintain charge gradient, moves 3 Na+ out of the cell against its ion gradient, then moves 2 K+ into cell with the ion gradient,
49
Channels create
openings in membrane, allow for movement against concentration gradient,
50
What do aquaporins do?
facilitate movement of water across membranes
51
What is an example of aquaporins?
the cells lining the kidney, H2O osmose into cell, aquaporins cluster together to form clumps of proteins,
52
How are channels selective?
Channels are selective because they only allow 1 H2O in at a time, H bonds with the chain w asparagine residues, form H bond w H2O, then, ensure water molecules fit through channel in single file
53
What is the structure of the ion channels?
1. outer helix- in contact with hydrophobic core of the lipid bilayer- stabilizes ion channel 2. inner helix- interacts with ions, selectivity 3. pore helix- assists in opening of ion channel, forms structure of channels pore (gating mechanism) 4. vestibule- entryway for ions, 5. selectivity filter- narrowest part, ion selectivity, amino acids that create specific environment for ions 6. selectivity loop- ions interact w amino acids,
54
Example of ion channel selectivity
K+, the selectivity loop is lined with corbonyl O atoms, mimic the hydration shell of K+ ions, allow to pass through but exclude, Na+ (size, charge and hydration energy) Na+ not large enough to interact with filter
55
4 different types of gated channels
Voltage-gated, ligand-gated (extracellular), ligand-gated (intracellular), mechanically gated
56
Mechanically gated channels
response to physical activity, stimulation of ciliary membranes or a membrane that gets pushed on
57
What do voltage sensors do?
detects changes in the membrane potential and respond by moving within the membrane, contributes to opening or closing of the channel, when voltage changes sensors trigger conformational changes
58
What is the inactivation gate?
closes the channel to stop ion flow, ensures that ions do not continue to flow indefinitely
59
What is the voltage gated channel made of
alpha helices make up central channel, outer helix (w hydrophobic core), inner helix (ions), pore helix (gating mechanism), selectivity filter/loop (specific amino acids in alpha helical structure),
60
Membrane depolarization
When a neuron or muscle cell receives a stimulus, causes opening of Na+ channels, Na+ ions flow into cell, action potential triggered, action potential propagates along axon/nueron, then K+ open and leave the cell, repolarization
61
On electron micrograph what does membrane, mitochondria and ER look like
Membrane- continuous lines mitochondria ER twisting everywhere
62
Where do ribosomes begin?
cytoplasm initially,
63
Where does translation occur?
Free ribosomes or rough ER
64
What happens to proteins after translation?
Once synthesized, protein goes to nucleus or stays in cytoplasm, (to get into nucleus need gated transport) (nucleus- DNA polymerase, Histones, regulatory)
65
What are signal sequences? structure?
primary structure- signal sequence triggers movement to specific location, they are rich in lysine and Argene (nucleus), alpha helices
66
Nucleus structure
Nuclear envelope, has inner and outer membrane, continuous with each other, ER lumen in between inner and outer membrane, outer is continuous with rough ER
67
How is the nuclear envelope attached to cytoplasmic cytoskeleton?
Nuclei is help in correct place, example: neurons move up and down the cell, regulated by cytoskeleton
68
nucleolis
synthesis
69
KASH domain proteins
transmembrane proteins, (outer nuclear membrane) interact with SUN domains, connect to nuclear lamina, KASH domain interacts with motor proteins (connecting nucleoskeleton to cytoplasmic cytoskeleton)
70
Nuclear lamina is made of
Lamin, gives nuclei round shape
71
What is Lamin-A
Has farnesyl grp, needs to be farnesylation to interact with nucleus, needs to be defarnesylation to interact with membrane,
72
Nuclear shape and aging
unstable Lamin, unstable nuclear lamina, premature aging
73
Nuclear pores
Embedded in nuclear envelope, Lamin is embedded in, there are connected with ring proteins
74
Structure of nuclear pore
Membrane ring outer, scaffolding nucleoporins (proteins), channel nucleoporins -- Scaffolding nucleoporins have cytosolic fibrils that bind to proteins and anchor themselves, nucleoporins attached to nuclear basket, channel nucleoporins have filter selective (monitor proteins that can pass in, ions can pass)
75
Nuclear import signal
(on cargo) needed to pass through nuclear pore complex, can be primary structure or folded proteins, need 3 lysine, Argene and lysine
76
Nuclear import receptors
Protein needs to bind to this in order to go into nucleus, has nuclear import signal, can also have add on protein that piggy backs
77
Is RAN GTP in or out of nucleus?
Inside
78
Explain the process of import into a nucleus
import receptors bind to cytosolic fibrils (coming from scaffolding protein), stabilize, then move through channel nucleoporins, then interact with the basket, RAN-GTP shuffles in, binds and changes shape, cargo is released because binding pocket broken, binding pocket for basket which brings nuclear localization signal back out of nucleus
79
Nuclear export
- Nuclear export receptors, bind to RAN GTP, creates binding pocket for proteins that have nuclear export signal which is bound to RAN GTP, then brought out, RAN GTP hydrolyzed, shuttled back in
80
What is RAN GEF
in nucleus, put new GTP on RAN, bring things out of cell
81
What is RAN GAP and where?
Outside in cytoplasm, hydrolyzes to GDP so that nuclear import signal can bind to cargo, release RAN from receptors.
82
What is NFAT and explain process
1. can be phosphorylated (not bound to proteins), nuclear export signal is exposed 2. with high levels of Ca (in cell), calcineurin is activated and removes the phosphate, binds to export signal, go into nucleus
83
How is import into nucleus regulated by proteolytic cleavage?
SCAP has cholesterol binding pockets, if high levels of cholesterol binds to SREBP, stay in ER membrane, if cholesterol drops, alters conformation, proteins trafficked to Golgi, in golgi lumen, SREBP cut off, then 2nd cut in SREBP-- this portion goes to nucleus (soluble)
84
What is SREBP
regulates cholesterol and lipid biosynthesis, low levels of cholesterol in cell, need piece of protein to go into nucleus
85
Mitochondrial Structure
outer, inner, mitochondrial matrix, intermembrane space
86
What is the mitochondrial import signal sequence
every 3-4 has arginine/lys, stripe bonds to chaperone proteins, chaperone recognizes what needs to go to nucleus, guide to mitochondrial translocators
87
What do chaperone proteins do?
bring protein to mitochondria
88
TOM complex
translocator outer membrane, smaller, proteins want unfolded, have receptor proteins that interact with chaperone proteins
89
SAM complex
embedded in membrane, outter membrane translocator
90
TIM 23
associated with TOM complex
91
TIM 22 and OXA
brings into inner mitochondrial membrane, TIM22 from intermembrane space
92
Proteins that need to go all the way into mitochondrial matrix
1. proteins held unfolded, brought to TOM complex, interact with receptor domain 2. brought to intermembrane space, interact with TIM 23, pulled into mitochondrial matrix
93
Cytosolic hsp70
chaperone proteins, holds unfolded, requires ATP to take off when entering channel,
94
Mitochondrial hsp 70
interacts with translocator, grabs protein after TIM 23, consumes 1 ATP, pulls incoming protein in
95
Stop transfer sequence?
region of protein that creates hydrophobic alpha helix, creates transmembrane protein, (inner mitochondrial membrane)
96
How do we get inter membrane space proteins? (mitochondria)
Can get this with stop transfer sequence, if proteins have cysteines that bind with Mia 40, grabs before interacting with TIM 23, (in membrane) or interacting with OXA (in membrane)
97
How are proteins brought into chloroplast? What is different about chloroplasts?
Has thylakoid space, TOC and TIC complex
98
What guides thylakoid proteins into space? translocators?
SEC pathway, TAT pathway
99
How do you get things into thylakoid?
SRP-like pathway, Spontaneous insertion
100
Proteins synthesized on Free ribosomes?
proteins going into nucleus, mitochondria and cytosol
101
Proteins synthesized from rough ER
secreted proteins, membrane proteins, lysosomal proteins, ER and Golgi resident proteins
102
What is the path of the endomembrane system?
Nucleus, rough ER, vesicles, golgi apparatus, secretory vesicles, plasma membrane/other
103
2 pools of ribosomes in cytosol
1. common pool 2. membrane bound
104
Rough ER ribosomes translation
first thing to come out is the rough ER sequence, recruit signal recognition particle, pause translation until gets to ER translocator, then continues, then free or ER ribosomes
105
How are ribosomes brought to the ER
1. recognition of signal sequence, by signal recognition particle, 2. binds, pauses translation 3. SRP-ribosome complex is brought to ER membrane binds to SRP receptor on ER 4. then, SRP is released, protein translocator takes ribosome, translation continues, and it is pushed into ER lumen
106
What is the SRP?
An RNA protein complex, protein makes up most of binding pocket, blocks continuation of translation when bound
107
Protein translocator?
Multi-pass membrane, cylinder with seam to open and close, in the lipid bilayer of the ER membrane, attaches to polypeptide chain and forms channel into ER membrane
108
What happens when there is a stop transfer sequence
ER translocator pops off, after stop (in cytosol)

BIO 202 (3 decks)

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