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Biol 331 > Midterm > Flashcards

Midterm Flashcards

1
Q

What are the 4 principles of cell theory?

A
  1. All organisms are composed of 1+ cells (Schwann)
  2. Cell = structural unit of life (Schwann)
  3. cells only arise by division from pre-existing cell (Virchow)
  4. Cells contains genetic info in form of DNA and info is passed from parent –> daughter cell
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2
Q

What are the fundamental Properties of All cells (9)

A
  1. Cells = complex + organized (highly ordered and consistent)
  2. Cells store, use, transport genetic info
  3. cells acquire + use energy (almost all energy comes from sun)
  4. Cells carry out array of diff chem rxn (chem. changes require enzymes to ↑ rate
  5. cells are involved in mechanical activities (transporting materials, cell movement)
  6. cells respond to stimuli (have receptors)
  7. cells can self regulate (activity requires highly complex + organized molecular tools)
  8. cells evolve (evolved from common ancestral cell)
  9. cells reproduce by division
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3
Q

Features in EUKARYOTES and not in prokaryotes

A
  • membrane bound organelle
  • division of cells into nucleus and cytoplasm
  • complex chromosome composed of DNA and proteins capable of compaction
  • complex membrane organelles (ER, golgi, lysosome, endosome, etc)
  • can do aerobic respiration or photosynthesis
  • complex cytoskeletal systems and motor proteins
  • complex flagella and cilia
  • phagocytosis
  • sexual reproduction (meiosis and fertilization)
  • has 3 RNA synthesizing enzymes (RNA polymerase)
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4
Q

what is covalent bond?

A

e- shared between 2 atoms (bond sharing)

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5
Q

what is noncovalent bonds?

A

weak attractive bond of oppositely charged regions

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6
Q

Name and describe the 3 noncovalent bonds

A
  1. Ionic Bond: electrostatic interaction between oppositely charged molecules
  2. hydrogen bond: electrostatic interaction between H (electropositive) and a second electroneg. atom
  3. van der waals: Attractive force held by electrical force (charge)
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7
Q

What are polar molecules?

A
  • hydrophilic
  • uneven distribution of charge bc of different electronegativities

ie. H2O

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8
Q

What are nonpolar molecule?

A
  • hydrophobic
  • nearly symmetrical distribution of charge bc atoms have approx. same electronegativity

ie. CH3

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9
Q

what is the hydrophobic effect?

A

tendency of nonpolar molecules to aggregate together to minimize interactions w/polar H2O (basis for formation of lipid bylayer membrane)

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10
Q

How do you identify polar UNcharged Amino acids?

A

hydrophilic side chain has partial + or - due to electronegative atoms such as O and N

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11
Q

How do you identify polar charged Amino acids?

A

hydrophilic side chain has + or - charge (act as acid or bae)

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12
Q

How do you identify non polar Amino acids?

A

hydrophobic side chain consists of C and H

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13
Q

what are membranes?

A
  • composed of lipids
  • are bilayers consisting of phospholipids
  • also contains proteins (that determines membrane penetrability)
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14
Q

What side does the polar and nonpolar regions of the phospholipid bilayer face?

A
  • polar phosphate face surface
  • nonpolar fatty acid tail faces inside
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15
Q

Is the phospholipid bilayer hydrophilic, hydrophobic or amphipathic? And what use is that?

A
  • amphipathic
  • bilayer prevents random movement of substances in/out of cell
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16
Q

what are fatty acids?

A

long, unbranched hydrocarbons (nonpolar and hydrophobic) chains

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17
Q

What are saturated fatty acids? And how does it affect fluidity?

A
  • lacks double bonds
  • makes it less fluid
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18
Q

what are unsaturated fatty acids and how does it affect fluidity?

A
  • has one or more double bonds that introduces bend. (naturally occurring fatty acid has cis double bond)
  • bend = cannot pack together tightly ∴ ↑ fluidity
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19
Q

Name the 3 major lipid membrane lipids

A
  1. Phosphoglycerides
  2. Sphingolipids
  3. Cholesterol
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20
Q

Describe what a phosphoglyceride is and where it is built on. What is one example

A
  • one of the 3 major membrane lipids (most membrane phospholipid falls into this category)
  • built on glycerol backbone
  • consists of glycerol, one saturated and one unsaturated fatty acid tail, phosphate and an additional group

ex. phosphatidylcholine

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21
Q

What are the overal charges of H (PA), Choline (PC), Serine (PS), Ethanolamine (PE), and Inositol (PI) on the Phosphatidylcholine (a type of phosphoglyceride)?

A

memorize it stupid

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22
Q

Describe what are sphingolipids, where it is buit on and purpose of them? What is one example?

A
  • one of the 3 major membrane lipids. less abundant (only some are considered phospholipids)
  • build on sphingosine
  • amphipathic. additional groups gets added at head group
  • tends to have highly saturated fatty acid chains
  • roles: signal transduction, membrane structure, sensing

Example: ceramide, (usually ends with -sides or -ide or start with sphingo-)

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23
Q

what happens when you add a carbohydrate onto a sphingolipid? And how does that affect humans?

A

it becomes a type of glycolipid (glycosphingolipid)

  • alterations in glycolipid abundance can lead to neurological disease (tay-sachs)
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24
Q

describe cholesterol and what does it do

A
  • one of the 3 major membrane lipid (only 20-30% of plasma membrane lipids)
  • amphipathic
  • hydrophilic faces surface while the rest is embedded in fatty acid tails
  • impairs movement of fatty acid tails of phospholipids
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25
Q

How does membrane lipid asymmetry affect the membrane and what are some examples?

A
  • affects membrane permeability, surface charge, membrane shape, and stability

EXAMPLE

  • PE: promotes curvature
  • PS: (-)ve interacts w/transmembrame proteins
  • PI: roles in signal transduction
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26
Q

what are membrane carbohydrates and how does it link to lipids and proteins?

A
  • acts as receptors in sorting membrane proteins and cell recognition (eg. recognizing blood type antigen)
  • 10% covalently linked to lipids (glycolipids)
  • 10% covalently linked to proteins (glycoproteins)
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27
Q

what does lipid composition determine/do?

A
  • physical state of membrane
  • facilitates protein interactions
  • roles in signal transduction
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28
Q

What are the 7 membrane functions?

A
  1. compartmentalization
  2. scaffold for biochemical pathways (scaffolded close enough allowing interaction)
  3. selectively permeable barrier (so stuff can go in/out)
  4. solute transport
  5. response to external stimuli (plasma membrane = 1st point of contact for other cells)
  6. cell-cell communication
  7. energy transduction (energy conversion)
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29
Q

What does fluidity (viscosity) determine?

A

determines physical state (thats influenced by temp)

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30
Q

what is transition temperature? What is crystalline gel and liquid crystalline gel?

A

:)))))

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31
Q

what are 3 factors that affect lipid membrane transition (aka transition temp or fluidity) and explain them

A
  1. Saturated fatty acids: less fluid
    Cis-unsaturated fatty acids: bend @ double bonds which INCREASES membrane fluidity
  2. Cholesterol Content: flat rigid, hydrophobic rings (brings atoms closer together) = impair movement of fatty acid and causes INTERMEDIATE FLUIDITY
    (Graph: no cholesterol = sharp transition state (its linear.)
  3. Fatty acid chain length: shorter chain = ↓ interactions = less energy to break apart = more fluid
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32
Q

why is balance for fluidity/rigidity is important

A
  • maintains structural organization + mechanical support
  • allows interactions (clusters of proteins)
  • membrane assembly/cell growth/cell division
  • cell movement, secretion, endocytosis
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33
Q

How does membrane fluidity respond to cold environments? (hint: 3 ways)

A

(You need to find ways to ↑ fluidity)

  1. Desaturates single bonds to double bonds (DB) (via enzyme called desaturase which ↑ DB)
  2. Reshuffles chains between phospholipids to creates 2 unsaturated fatty acids (Kinda like resonance) (↓ temp = ↑ fluidity)
  3. △s types of phospholipids that it synthesizes so that it synthesizes more unsaturated bonds and shorter chain lengths
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34
Q

What is Integral membrane protein and describe the 3 classes

A
  • Permanently anchored or part of membrane
  1. Monotopic Protein: only spans 1 layer
  2. Bitopic: spans both layers ONCE
  3. Polytopic: Spans both layer MULTIPLE times

2 and 3 considered transmembrane proteins

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35
Q

What is a transmembrane protein? what is its role?

A
  • a protein that completely passes through bilayer and contains 1+ transmembrane domains
  • act as receptors, channels or have roles in e- transportation
  • amphipathic (Transmembrane domains (inside) = hydrophobic; proteins at surface = hydrophilic)
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36
Q

whats glycophorin A

A

single transmembrane domain. (red blood cell plasma domain )

glycoprotein determines blood group

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37
Q

what is a peripheral protein? And its roles?

A
  • sits on membrane
  • associated with weak non-covalent bonds
  • composed of multiple polypeptides (some integral, some peripheral)
    -Dynamic (can be recruited to/released from membrane)

roles: signal transduction, mechanical support for membranes, anchor for integral protein, enzymes

  • MOSTLY HYDROPHILIC (POLAR)
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38
Q

are amino acids usually polar or nonpolar

A

non polar

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39
Q

What is spectrin and what does spectrin do?

A

It is a peripheral membrane protein that gives Red blood cell its concave shape

  • flexible and supportive
  • on internal surface
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40
Q

What are lipid anchored proteins and describe the 2 types (where they are located and their roles)

A
  • it sits on outside of bilayer either on extracellular or cytoplasm side
  • covalently linked to lipid molecule
  1. GPI-Anchored Protein: protein (green) attaches to oligosaccharide (GPI) that attaches to phospholipid (PI) membrane
    - faces extracellular space only
    - roles: cell adhesion, receptors
  2. Protein is attached to hydrocarbon chains that are embedded into bilayer
    - located in cytoplasm
    - roles: signal transduction
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41
Q

what does a phospholipid look like?

A

-.-

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42
Q

what is phospholipid dynamics? Explain why one of them is thermodynamically unfavourable

A

Phospholipid dynamics: how phospholipid can move

  1. Lateral shift (horizontal): moves easily
  2. Transversion Diffusion: flip-flop. restricted.

Thermodynamically Unfavourable: transversion bc polar hydrophilic head group needs to pass through nonpolar region

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43
Q

what is passive diffusion

A
  • does not require energy (ATP)
  • uses diffusion ( [↑] to [↓] until equilibrium) OR osmosis L–>H
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44
Q

What are the 2 types of simple diffusion in membrane transport?

A
  1. diffusion via lipid bilayer
  2. diffusion through channel
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45
Q

What is diffusion through a lipid bilayer? and what can and cannot penetrate it?

A
  • form of passive membrane transport (simple)
  • uses osmosis [↓ solute] to [↑ solute]
    hypertonic, hypotonic, isotonic
  • stuff that can pass through: small inorganic (O2, CO2, H2O), solutes w/↑ lipid solubility (caffeine)
  • stuff that cannot: ions (anything charged), polar organic solutes (sugar, amino acids), anything large
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46
Q

what is diffusion through a channel and what are the 2 types

A
  • form of passive membrane transport that goes with [gradient]
  1. Aquaporin: channel protein transporting H2O. cells become more permeable ∴ faster, better diffusion through bilayer
  2. Ion channels: transmembrane structure permeable to ions (Na+, K+, Ca2+, Cl-).
    - most highly selective
    - gated so conformation can change
    Three types of Ion Channels:

A. Voltage Gated Channel: open/close based on difference in ionic charge on either side of membrane

B. Ligand gated channel: open/closes depending on ligand (it binds to channel to △ conformation)

C. Mechano-gated Channel: open/closes depending on mechanical forces (eg. stretching, hearing, head movements)

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47
Q

what is hypertonic

A
  • higher [solute] outside cell
  • dehydration
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48
Q

what is hypotonic

A
  • lower [solute] outside cell
  • swelling
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49
Q

what is isotonic

A
  • equal [solute]
  • just right
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50
Q

what is active transport? what direction does it go in?

A
  • requires energy (ATP) wow paywalled
  • can move against gradient (L→H)
  • protein undergoes conformational △
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51
Q

what is facilitative transport? what direction does it go in? How fast is it? What does it transport? Example?

A
  • [h] –> [L]
  • transmembrane protein going under conformational △ when solute enters and spits it out to other side
  • bidirectional (with concentration gradient)
  • has saturation-type kinetics (if [↑], it can reach max speed)
  • slower than ion channels
  • Transports: polar and charged molecules (glucose, amino acids)
  • EX. glucose transporter GLUT4
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52
Q

what is primary active transport

A

energy gained from hydrolysis of ATP

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53
Q

what is secondary active transport?

A

energy gained from flow of substance in a [gradient]

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54
Q

name and describe the 3 types of primary active pumps

A
  1. P-Type pump: (A sodium potassium pump) pump gets phosphorylated
    - ATPase = phosphorylated
    - contributes to membrane potential (voltage)
    - 1ATP: 3Na+ OUT and 2 K+ IN
    Defects: endocrine system, hypertension, neuromuscular disorders
  2. V-type ion pumps: use ATP w/o phosphorylation. Transports H+ protons across organelles + vacuoles
    - maintains ↓ pH of lysosomes
  3. ABC transporters: ATP binding casette transporters. share similiar ATP binding structures
    -transports: ions, lipids, peptides and nucleosides
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55
Q

explain the steps of the P-Type pump in primary active transport (8)

A
  1. E1 (facing cytosol) = ↑ affinity for Na+ ions. ATP is bound
  2. Protein closes when ion is in protein
  3. hydrolysis of pump (phosphorylation) ATP–>ADP + P
  4. ADP release cause conformational △ (E1 to E2)

5-6. K+ ions go in and protein closes + gets dephosphorylated

7-8. K+ released into cytosol. ATP binds (E2 to E1) ∴ ↓ K+ affinity

rate of transport is slower than ion channels

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56
Q

describe secondary active transport and the 2 types

A
  • uses potential energy created by [gradients]
  1. Symporter: transports 2 substances in same direction AKA cotransporter
  2. AntiporterL transports 2 substances in opposite directions AKA exchanger
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57
Q

what is In vivo

A

still in cell (within the living)

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58
Q

what is FRAP? (fluorescence recovery after photobleaching) and describe the steps

A
  • used to study movement of membrane components
  1. Label membrane component w/fluorescent dye (with a fluorescent antibody that recognizes proteins
  2. photobleach portion of cell
  3. monitor rate of fluorescence recovery (rate of diffusion)
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59
Q

Explain this graph

A

Higher fluorescence (one on very top) = most able to freely diffuse

lowest fluorescence (bottom one) = least able to diffuse freely

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60
Q

What is In Vitro

A

in a test tube or petri dish (within a glass)

need to isolate cell

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61
Q

What is the first step in isolating membrane proteins? What does the pellet and supernatent contain?

A

lyse the cell + collect plasma membrane

Pellet 1: Insoluble (membrane+ proteins)
Supernatent: soluble (no membrane here)

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62
Q

What is the second step in isolating membrane proteins? What does the pellet and supernatent contain?

A

isolate the peripheral protein using high salts.

pellet 2: insoluble (contains transmembrane)
Supernatent: soluble (contains peripheral membrane proteins)

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63
Q

why do we use high salts to isolate peripheral protein?

A

salt ions will compete w/charged amino acids of peripheral proteins + disrupt noncovalent interactions therefore releasing peripheral

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64
Q

What is the third step in isolating membrane proteins? What does the pellet and supernatent contain?

A

isolate the transmembrane by using strong detergent

pellet 3: insoluble (contains GPI-Anchored lipid proteins)
Supernatent: soluble. contains transmembrane

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65
Q

why do we use detergent to isolate transmembrane?

A

Detergents is used to substitute phospholipid to stabilize transmembrane and make them soluble in water

detergents have similar structure to phospholipids and so they “cover” the transmembrane making it hydrophilic

66
Q

What is the fourth step in isolating membrane proteins? What does the pellet and supernatent contain?

A

isolate GPI-anchored proteins by treating it with PI-PLC

Pellet 4: insoluble (nothing left)
supernatent 4: GPI-anchored protein

67
Q

why do we use PI-PLC when isolating GPI-Anchored proteins?

A

PI-PLC hydrolyses the bonds between the phosphate and hydrophilic head thus allowing protein to break away with GPI still attached

68
Q

explain Gel electrophoresis and why we use SDS

A

Seperation of charged molecule to determine size or protein expression

SDS is used to denature protein
- (-)ve amphipathic detergent giving proteins (-)ve and denatres (unfold) proteins

69
Q

What is A and B telling us?

A

A: Largest protein
B: thik band = increase expression

70
Q

what is a neuron?

A

a nerve cell specializing in communication with other cells by using electrical impulses

71
Q

What does dendrites, Axon, myelin sheath and terminal knob do?

A

dendrites: receive info

axons: conducts outgoing info to knob

terminal knob: transmits impulses to target cell

myelin sheath: lipid rich membrane that wraps axon

72
Q

what is membrane potential? What is Negative voltage? What is resting potential and what is the voltage of it?

A

Membrane Potential: Difference in charge

Negative voltage: when inside of cell is more (-) than outside

Resting potential: nerve cell in unexicited state (-70mV)

73
Q

what contributes to differences in charge across membrane? (2)

A
  1. Na+/K+ ATPase pumping 3 Na+ OUT and 2K+ IN
  2. K+ ions flowing out via potassium leak channels (not gated)
74
Q

Describe action potential including resting potential, depolarization, and repolarization

A

Action potential: changes in membrane potential after stimulus. basis for neural communication

  1. Resting potential: nothing really happens except K+ leak channel making inside more (-)
  2. Depolarization: stimulus causes voltage to be -50mV which causes Na+ channels to open. It opens until 40mV. inside of membrane more positive
  3. Repolarization: 40mV causes K+ channels to open until -80mV then channel closes
75
Q

what is hyperpolarization?

A

when channel dont close fast enough making it more negative than resting potential

76
Q

define nerve impulse and the 2 types of conduction

A

its a action potential spreading to other portion of membrane

  1. continuous conduction: occurs in unmyelinated axons
  2. saltatory conduction: occurs in myelinated axons
77
Q

What is the steps of continuous conduction? What is the refractory period?

A
  1. action potential signal causes internal to be positive while external is negative
  2. action potential wants to travel this internal (+)ve flows to (-)ve. Depolarization + –> -

Refractory period: Na+ channel cannot open in this phase

78
Q

What is saltatory conduction

A

impulses faster

Na+ and K+ Channels in nodes of Ranvier (unmyelinated part).

action potential goes from node to node (still + to -)

79
Q

what do the labeled parts do?

A
  • Presynaptic cell: transmits impulse to postsynapse
  • Synaptic vesicles: neurotransmitter storage on terminal knob
  • Neurotransmitters: Chemical that binds to ion channel in post synapse
  • Synaptic cleft: space seperating 2 cells

Postsynaptic cell: receives impulse from presynapse

80
Q

describe the steps of Synaptic transmission

A

1+2. Nerve impulse causes depolarization thus opening Na+ gates. Na+ diffuses into presynaptic cell

3+4. Influx of Ca+ causes synaptic vesicles to move out of presynapse. It releases neurotransmitters that bind to ion channel receptors (ligand gated)

Depending on what neurotransmitters it can cause an excitatory step (5A) or inhibitory (5B)

5A. Excitatory: influx of Na+ excites cell causing depolarization on postsynapse (MORE LIKELY TO CAUSE ACTION POTENTIAL)

5B. Inhibitory: influx of Cl- causing hyperpolarization on postsynapse (LESS LIKELY TO CAUSE ACTION POTENTIAL

81
Q

Describe the endomembrane system and what it includes

A

interconnected cytoplasmic system

includes: ER, golgi, endosomes, lysosomes, vacuoles

82
Q

What is the first direction of transport in the endomembrane system?

A

transport material from organelle (donor) to organelle (recipient)

  • vesicle become part of recipient
83
Q

How fo proteins know where to go?

A

sorting signals (amino acid sequence, attached oligosaccharides are recognized by receptors)

84
Q

What is the second direction of transport in the endomembrane system? What are the 2 types?

A

Secretory Pathway: transports materials out of cell

  1. Constitutive Secretion: Continuous, automatic secretion of most cells (from synthesis site to outside of cell)
    - contributes to formation of plasma membrane
  2. Regulated Secretion: materials in membrane-bound compartments releases in response to stimuli
85
Q

what does the ER synthesize?

A

lipid/cholesterol, steroid hormone (a lipid), secreted proteins, integral membrane proteins

86
Q

what is the golgi responsible for?

A

Modifications

87
Q

What is the third direction of transport in the endomembrane system? What are steps? (2)

A

Endocytic Pathway: transports materials into cell

  1. Endosome: first destination. responsible for sorting. (later endosome = more acidic)
  2. Lysosome: endosome fuses with lysosome for cargo degradation
    - has hydrolytic enzymes and acidic pH
    - Role: breakdown material + organelle turnover
88
Q

What os autoradiography?

A

process of following radioactively-labeled materials in cell

89
Q

what is the pulse chase experimeny?

A

Following digestive enzymes from synthesis to secretion

  1. Pulse: radio labeled amino acid incorporated in digestive enzymes
  2. Chase: moniter the radio labeled enzymes
90
Q

what are mutant phenotypes good for?

A

help determine function of mutant or deleted gene when comparing it to WT

91
Q

Describe the endoplasmic reticulum

A

dynamic system of membrane and vesicles in ER lumen

92
Q

what is the SER and its functions and what does it synthesize

A
  • lacks ribosome; interconnected curved tubes attached to ER

Synthesizes lipids

Functions:
- synthesis of steroid hormones
- synthesis of membrane lipids (phospholipids)
- control lvls of Ca2+ in muscles

93
Q

what is the RER and its functions and what does it synthesize?

A
  • has ribosome bound on membrane sys. facing cytoson
  • network of cisternae (attached to nucleus)

Function:
- protein secretion
- protein synthesis
- addition of sugars initiated

94
Q

What does the RER ribosomes do?

A

creates 1/3 of proteins
- creates secreted proteins (destined to leave cell) and integral and soluble proteins (remain in endomembrane system)

95
Q

what is co-translational translocation?

A

peptides synthesized by free ribosome moving into lumen

96
Q

describe the steps of secreted and soluble protein synthesis (0-4)

A
  1. Free ribosome synthesize proteins with a signal sequence (with a hydrophobic tail)
  2. signal recognition particle (SRP) binds to signal sequence on peptide and ribosome which halts protein synthesis
  3. SRP guides complex to ER by attaching to SRP receptor
  4. polypeptide transferred to translocon. Hydropohobic tail removes plug (SRP detach and floats away)
  5. polypeptide enters ER lumen while peptide synthesis resumes until termination

signal sequence removed by enzyme

chaperon aids protein folding

97
Q

describe the steps of integral membrane protein synthesis (2)

A
  1. SRP recognizes hydrophobic transmembrane domain as signal sequence (and enters lipid bilayer)

Proteins orient themselves

    • charge amino acid = cytosolic end bc sytosol leaflet as more PS and PI which are -
98
Q

what are the positively charged amino acids? (3)

A

.

99
Q

what side is the cytosol and lumen on?

A

.

100
Q

what are the role of free ribosomes?

A

2/3 of proteins
- proteins gets released into cytosol
- synthesis of peripheral proteins on cytosolic surface
- proteins transported to nucleus, mitochondria and chloroplast

101
Q

what is glycosylation? what are the 2 types of glycosylation?

A
  • process of proteins –> glycoproteins
  • aids in protein folding + stabilization, sorting
  1. N-Linked Glycosylation (common)
    - initiated in RER
    - linked to asparagine (Asn)
  2. O-linked glycosylation
    - linked to Serine (ser) or threonine (Thr)
    - occurs in golgi
102
Q

Describe the N-linked Glycosylation (ER) steps (5)

A
  1. (In Cytosol) Sugars gets embedded in membrane + dolichol phosphates added
  2. Sugar chain is added by glycosyltransferase
  3. structure flipped thus facing lumen
  4. remaining sugars added
  5. complete oligosaccharide transfered (by enzyme oligosaccharyltransferase) to polypeptide with asparagine
103
Q

Explain the quality control of misfolded protein steps (4 + 2 diff ending)

A
  1. Glucosidase I and II removes 2 glucose from protein
  2. glycoprotein (w/one glucose) recognized by calnexin (folds final folding)
  3. calnexin takes last glucose (as ticket) and folds protein
  4. if protein is not folded properly (exposed hydrophobic residue), UGGT recognizes it and adds 1 glucose so Calnexin can refold

5A. Folded properly = exit to golgi

5B. Multiple folding failures = degraded in proteosome (in cytosol)

104
Q

Explain the steps when exiting the ER (5)

A
  1. Membrane vesicles with cargo bud from ER
  2. vesicles fuse with e/o to form vesicular tubular carrier (VTC)
  3. Fuses with cis golgi network (CGN)
  4. Travels to golgi cistermas
  5. Fuses with trans golgi network (TGN)
105
Q

What does the cis golgi network do? (CGN)

A

sorts proteins (either they go to golgi or go back to ER)

106
Q

What does the trans golgi network do? (TGN)

A

SORTS PROTEINS INTO DIFFERENT VESICLES

107
Q

where is cisface

A

closer to ER

108
Q

where is transface

A

closer to exit

109
Q

what does glycosylation in golgi do? Order for sugar incorporation depends on what?

A
  • modifies new proteins leaving ER
  • order of sugar incorporation depends on glycosyltransferases in golgi
  • all o-linked carbohydrates assembled here
110
Q

What is the first model of movement through golgi and what is its evidence?

A

Vesicular transport Model:

  • golgi cisternae = stable
  • vesicles bud from one compartment and fuses with next

Evidence
- golgi cisternae have different enzymes
- lots of vesicle bud from golgi cisternae

111
Q

What is the second model of movement through golgi and what is its evidence?

A

Cisternal Maturation Model

  • cisternae formed @ cisface moves to transface + matures as they move
  • more supported

Evidence
- drug blocking vesicle formation @ ER disappears leading to golgi disappearing

  • large materials move from cis to trans w/o appearing in vesicle
112
Q

what is anterograde

A

transports “forward”
cis to trans

113
Q

what is retrograde

A

transports (backwards)
Trans to cis

114
Q

what is a clatherin-coated vesicle?

A

it moves materials from TGN to endosome, lysosome and plant vacuoles

115
Q

what is the COPII-Coated vesicle?

A

moves cargo forward (ER to golgi)

116
Q

what is the COPI-coated vesicle

A

moves cargo backwards (Trans to cis)

117
Q

Explain the structure of COPII (Sar 1, Sar 1 GTP, Sec23, Sec24, Sec 13 and Sec 31) and how they form

A
  1. Sar1: (CopII protein coat, G protein) Initial protein that turns GDP to GTP
  2. Sar1 GTP: conformational change to insert in cytoplasmic leaflet (introduce bend)
  3. Sec23/Sec24: dimer bends it more
  4. Sec 13/sec 31: forms the structural scaffold/cage (GTP–> GDP)
118
Q

In short, what does the COP II protein coat do? (2)

A
  1. bends membrane
  2. select + concentrate proteins to be transported
119
Q

what is Sar1 considered as

A

initial protein

120
Q

what is Sec24 do?

A

primary adaptor protein interacting w/everything

121
Q

what is a coatamer

A
  • copI coated vesicle structure
  • thick protein coat on membrane
122
Q

what is ARF1

A
  • cop1 coated vesicle structure
  • membrane bending protein (using GTP) and similar to Sar1
123
Q

How do COP1 retrieve ER proteins

A
  1. soluble ER proteins contain KDEL signal. KDEL receptor shuttle it from cis golgi to ER
  2. ER membrane proteins have KKXX retrieval signal
124
Q

how to vesicles fuse? (4)

A
  1. vesicles moves towards membrane
  2. tethering complexes attaches to e/o
  3. SNARE proteins attaches together (integral proteins) to form 4 bundles
  4. interaction of v-SNARE and t-SNARE fuses vesicle and membrane
125
Q

what are the 2 types of tethering complexes?

A
  1. rod-shaped/fibrous (longer) (looks like rope)
  2. multiprotein complex (closer) (looks like grapes)
126
Q

what determines specificity during vesicle fusion?

A

Rabs

they recruit specific tethering proteins + interact with motor proteins

127
Q

where is v-SNARE and t-SNARE located?

A

v-SNARE = put in vesicles when budding happens

t-SNARE = in target membrane

128
Q

ability of vesicles to fuse with specific membrane is determined by a combo of ___, ___, and ___.

A

Rabs, tethering proteins, SNARE

129
Q

what are some lysosome types?

A

phosphates, nucleases, protease, GAG-hydrolyzing enzyme, polysaccharidase & oligosaccharidase, sphingo-hydrolyzing enzyme

130
Q

what is the optimal lysosome pH and how is it achieved?

A
  • acidic pH (~4.6)
  • achieved through acid hydrolysis or proton pump
131
Q

Explain the 2 roles of lysosome

A
  1. break down material (endocytosis)
  2. organelle turnover (autophagy): destruction + replacement of cell organelle
    - organelle surrounded by double membrane structure (Autophagosome)
    - fuses with lysosome
132
Q

what are lysosome storage disorders?

A
  • deficient lysosomal enzymes = high undegradation of materials
133
Q

what is the lysosomal sorting signal and where is it added?

A

phosphorylated mannose (mannose 6-phosphate)

where: phosphate added to mannose of N-linked carbohydrate

134
Q

describe how clatherin cloated vesicles target lysosomal enzymes to lysosomes

A
  1. Mannose residue are phosphorylated in golgi (turned to mannose 6 phosphate)
  2. lysosomal enzymes incorporated into clatherin coated vesicles (cis to trans)
  3. vesicle formation is complete
  4. clatherin coat is disassembled
  5. vesicle fuses with endosome for sorting

6a. MPR (receptors) returned to golgi

6b. lysosomal enzymes delivered to lysosomes

  1. (seperate process) MPR also found in plasma membrane
135
Q

what does the GGA adaptor do?

A

connects clathrin to MPRs

136
Q

what are MPR

A

Mannose 6-phosphate receptor (MPR): transmembrane protein that recognizes and captured proteins w/mannose 6 phosphate signal

137
Q

default destination for proteins moving through endomembrane system

A

Towards TGN

or constututive secretion

138
Q

What are the 2 types of endocytosis

A
  1. Bulk-Phase endocytosis
    - pinocytosis (drinking)
    - non specific uptake of extracellular fluids
  2. Receptor-mediated endocytosis
    - clatherin mediated
    - specific molecules binding to receptors on plasma membrane surface
    - eg. hormone, growth factors, certain nutrients
139
Q

what is endocytosis

A

putting things in a vacuole

140
Q

what does the AP2 (adaptor) do

A

links cytoplasmic tails of plasma membrane receptors with clathrin

141
Q

what is dynamin? what does its structure look like? how does it move?

A
  • g protein required for clathrin coated vesicle to bud from membrane
  • they polymerize to form ring
  • GTP hydrolysis ( conformational change) induces movement in dynamin ring
  • vesicle is cleaved and dynamin disassembles
142
Q

what is the first outcome of endocytosis? (Recycling pathway)

A
  1. housekeeping receptors take in materials used by cell (ie. cholesterol, ions, etc)
  2. receptors first transported to early endosome for sorting
  3. ligands dissociate due to acidic pH
  4. receptors concentrated into recycling conpartment of early endosome
  5. vesicles return treceptors to cell surface to be used again
143
Q

what is the second outcome of endocytosis (degradation pathway)

A
  1. signalling receptors bind ligands that affect cellular activity (hormone, growth factor)
  2. transported to early endosome for sorting and to late endosome
  3. late endosome fuse with lysosome for receptor degradation
144
Q

what does receptor degradation do

A

prevents cell from being further stimulated by hormone/growth factor

145
Q

what do intermediate filaments do

A

structure and function

146
Q

what do microtubules do

A

structure, assembly, kinesin and dynein

147
Q

what do microfilaments (actin filaments) do

A

contraction and cell motility

148
Q

explain the cytoskeleton’s general features

A
  1. structural support: shapes it, resists deformation’
  2. transport of materials within cell
  3. contraction and motility (flagella movement)
  4. spatial organization
  5. cell division
149
Q

Microtubule structure and function

A
  • cytoskeleton filament held together by weak non-covalent bond
  • hollow, unbranched, tubular structures made of tubulin
  • role: cell support, motors
  • composed of 13 protofilaments
150
Q

what are protofilaments assembled from?

A
  • dimers of one alpha and one beta tubulin
  • asymmetric
151
Q

where is the alpha tubulin

A

negative end

152
Q

where is the beta tubulin

A

positive end

153
Q

what is a centrosome and its structure

A
  • type of microtubule organizing center initiating microtubule formation
  • composed of 2 centriole surrounded by PCM (loosly organized fibrous lattice) and centriole (cylinder composed of microtubules)
154
Q

when centrosomes replicate, what does centrioles do?

A

it recruits PCM (loosely organized lattice) to form new centrosome

155
Q

why is the gamma tubulin important in initiation of microtubule formation?

A

(gamma on - end)

Gamma-TURC in PCM (acts as cap)

Alpha and beta tubulin assemble on gamma tubulin

g protein (hydrolyzes GTP to GDP)

156
Q

on a microtubule, on which end does growth happen?

A

+ end

157
Q

what are factors affecting stability of microtubules

A
  • microtubule interacting proteins (MAPS)
    • TIPS (PROTEINS) binds at growing end
  • temperature (cold = disassemble)
158
Q

Describe the steps of microtubule dynamics (4)

A
  1. in growing microtubule, tip consists of tubulin GTP dimers in open sheet
  2. tube closure associated with hydrolysis of GTP
  3. GDP tubulin = diff conformatoon introducing mechanical strain (MAPS stabilize microtubule)
  4. in absence of stabilization, protofilaments curl outwards (catastroph shrinkage)
159
Q

Explain the globular head and tail in a kinesin structure

A

globular head: binds microtubules
- ATP hydrolysis
- conserved sequences

Tail: binds to cargo
- diverse sequence

160
Q

Describe kinesin movement

A
  • moves along microtubule towards positive end
  • leading head binds one ATP, hydrolize it (ADP+P) to create power stroke and swings trailing head forward
161
Q
A

Biol 331 (2 decks)

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