FINAL Flashcards

1
Q

what are two organelles that are specific to animal cells?

A
  • extracellular matrix: specialised material outside the cell
  • lysosome: degradation of cellular components that are no longer needed
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1
Q

what are three organelles that are not found in animal cells but are found in plant cells and some other cells?

A
  • cell wall
  • vacuole (2 types)
  • chloroplast
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2
Q

cell wall two functions

A
  • cell shape
  • protection against mechanical stress
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3
Q

vacuoles two functions

A
  • degradation (like animal lysosome)
  • storage (small molecules and proteins)
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4
Q

chloroplast function

A
  • site of photosynthesis
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5
Q

distinguish between the cytoplasm, the cytosol, and the lumen

A
  1. cytoplasm: contents of the cell outside the nucleus (membrane-bound organelles)
  2. cytosol: aqueous part of the cytoplasm. does not include membrane-bound organelles, does include ribosomes and cytoskeleton
  3. lumen: inside of organelles
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6
Q

what cellular functions occur at membranes?

A
  1. compartmentalisation
  2. scaffold for biochemical activities
  3. selectively permeable barrier
  4. transport solutes
  5. respond to external signals
  6. interactions between cells
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7
Q

describe the model proposed by Singer and Nicolson in 1972

A

Fluid Mosaic Model of the Membrane
- fluid: due to mobility of lipids and some of the proteins
- mosaic: many different lipids and many different proteins
- lipid bilayer: = 1 membrane consisting of two layers of leaflets

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8
Q

define amphipathic molecules

A

have different biochemical/biophysical properties on different sides of the molecule

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9
Q

what makes phospholipid molecules amphipathic?

A

they have a hydrophilic/polar head and hydrophobic tails

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10
Q

state three types of lipids that membranes are composed of

A
  • phospholipids
  • sterols
  • glycolipids

all have hydrophilic heads as well as hydrophobic tails

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11
Q

phospholipids

A
  • there are different types of membrane phospholipids
  • most have a glycerol group (termed phosphoglycerides, of which there are different types)
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12
Q

general structure of a phospholipid

A

polar head group (hydrophilic):
- different groups
- phosphate
glycerol
hydrocarbon tails
- length: 14-24 carbon atoms
- saturated/unsaturated

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13
Q

kink

A
  • hydrocarbon tail is unsaturated
  • contains a cis-double bond
  • this causes a bend in the tail
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14
Q

what happens to phospholipids in aqueous environments?

A
  • they spontaneously self-associate into a bilayer
  • the polar head group interacts with water
  • the two hydrophobic hydrocarbon tails interact with other hydrophobic tails
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15
Q

how are sealed compartments formed by phospholipid bilayers?

A
  • a planar phospholipid bilayer is energetically unfavourable as the hydrophobic tails are exposed to water along the edges)
  • the formation of a sealed compartment shields hydrophobic tails from water
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16
Q

define liposomes and describe their uses

A

artificial lipid bilayers used to:
1. study lipid properties
2. study membrane protein properties
3. drug delivery into cells (nanotechnology)

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17
Q

how can membrane fluidity be visualised?

A

live cell imaging where laser tweezers are used to manipulate the membrane show that a membrane can be deformed without causing damage

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18
Q

describe the different types of phospholipid movement within cell membranes

A

phospholipids within each leaflet rapidly:
- diffuse laterally (side-to-side or deeper into the membrane plane)
- rotate
- flex
- RARELY move from one leaflet to other (flip-flop) on their own

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19
Q

why is cell membrane fluidity carefully regulated?

A

as it is important for function, e.g. membrane proteins for transport, enzyme activity, signaling

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20
Q

two factors affecting membrane fluidity

A
  1. temperature
  2. composition (phospholipid saturation, phospholipid tail length, lipid composition)
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21
Q

how does temperature impact membrane fluidity?

A

lower temperatures make the membrane more viscous and less fluid, which is unwanted

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22
Q

how does composition - phospholipid saturation - impact membrane fluidity?

A
  • cis double bonds increase fluidity at lower temperatures (reduce tight packing)
  • phospholipids can change from being saturated to unsaturated to alter fluidity
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23
Q

how does composition - phospholipid tail length - impact membrane fluidity?

A

shorter hydrocarbon tails increase fluidity at lower temperatures (lipid tails interact less)

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24
Q

how does composition - lipid composition - impact membrane fluidity?

A

the addition of cholesterol in animal cell membranes stiffens the membrane, making it less permeable to water

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25
Q

how are sterols typically present in animals and plants?

A

in animals, mainly cholesterol; in plants, plant sterols and some cholesterol

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26
Q

general structure of a sterol

A
  • polar head group
  • non polar rigid planar steroid ring structure
  • non polar hydrocarbon tail
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27
Q

how does the addition of cholesterol molecules impact cell membranes?

A
  • decreases the mobility of phospholipid tails (stiffens and thickens the membrane by filling space)
  • plasma membrane is less permeable to polar molecules
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28
Q

draw a diagram of a cholesterol molecule surrounded by two phospholipid molecules

A

polar head
cholesterol-stiffened region
more fluid region

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29
Q

describe how lipid movement to the other leaflet is created in the ER membrane

A
  • phospholipid synthesis adds to the cytosolic half of the bilayer
  • scramblase (a phospholipid translocator in the ER membrane) catalyses the rapid flip lop of random phospholipids from one leaflet to another
  • this ensures symmetric growth of both halves of the bilayer
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30
Q

distribution of phospholipids in the ER membrane is

A

random

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31
Q

how does distribution of phospholipids and glycolipids in the cell membrane differ from that in the ER?

A

the noncytosolic face and the cytosolic face have different lipids
- glycolipids only on noncytosolic face
- phosphatidylserine only on cytosolic face

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32
Q

how do phospholipids and glycoproteins end up on the plasma membrane?

A
  • synthesised in the membrane of the ER
  • carried in vesicles to the membrane of the Golgi apparatus
  • carried in vesicles to the plasma membrane
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33
Q

how is the orientation of the cell membrane different to that of the membranes in the cytosol?

A
  • the plasma membrane has the noncytosolic face towards the extracellular fluid and the cytosolic face towards the intracellular fluid
  • the membranes in the cytosol (vesicles, Golgi, ER) have the cytosolic face toward the cytosol and the noncytosolic facing inside the organelle
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34
Q

describe the role of the Golgi membrane in regulation lipid membrane distribution

A
  • delivery of new membrane from ER
  • Flippase enzymes in the Golgi membrane catalyse the rapid flip-flop of specific phospholipids to the cytosolic leaflet (eg phosphatidylserine)
  • some can bind cytosolic proteins at the plasma membrane (eg phosphatidylserine binds protein kinase c)
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35
Q

how are glycolipids and glycoproteins distributed on the membrane?

A
  • formed by adding sugar groups to lipids/proteins on the luminal face of Golgi
  • end up on plasma membrane, inside of organelles, on the noncytosolic face only
  • protect the membrane from harsh environments
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36
Q

can proteins flip-flop?

A

no

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37
Q

two main subsets of membrane proteins

A

integral membrane proteins
peripheral membrane proteins

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38
Q

three types of integral membrane proteins

A
  • transmembrane (cross the entire membrane, once or multiple times)
  • monolayer associated (insert halfway)
  • lipid-linked (have a lipid anchor inside the membrane)
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39
Q

peripheral membrane proteins

A

proteins do not insert into the membrane on either face of the membrane
- bound to other proteins or lipids by non-covalent interactions

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40
Q

distinguish between the extraction methods that need to be used to isolate integral membrane proteins as opposed to peripheral membrane proteins

A

integral: extraction methods use detergents (lipid bilayer destroyed)
peripheral: gentle extraction methods used (lipid bilayer remains intact)

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41
Q

describe the amphipathic properties of transmembrane proteins

A

amphipathic
- hydrophilic domains in aqueous environment (AA side chains polar)
- hydrophobic membrane-spanning domains (AA side chains non-polar)

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42
Q

what are the three main types of transmembrane proteins?

A
  1. single alpha helix (single-pass)
  2. multiple alpha helices (multipass)
  3. beta barrel (rolled beta sheet, multipass)
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43
Q

how many amino acids long would you expect a membrane-spanning alpha helix to be?

A

20-30

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44
Q

draw a single alpha helix

A

slide 32

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45
Q

draw multiple alpha helices

A

slide 32

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46
Q

draw a beta barrel

A

slide 32

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47
Q

why is it important for transmembrane proteins to not be able to flip flop?

A

each transmembrane protein has a specific orientation - essential for function

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48
Q

how are the structures of transmembrane proteins identified?

A
  1. X-ray crystallography: determines the 3D structure
  2. hydrophobicity plots: hydropathy index, where +ve ΔG means more hydrophobic, -ve ΔG means mood hydrophilic index
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49
Q

describe mono-layer associated membrane proteins

A

proteins anchored on the cytosolic face by an amphipathic alpha helix
eg proteins in membrane bending for vesicle budding (Sar1) at the ER

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50
Q

describe two types of lipid-linked membrane proteins

A
  1. protein with a GPI anchor (glycosylphosphatidylinositol). Synthesised in the ER lumen and ends up on the cell surface (noncytosolic face throughout whole process)
  2. protein with another lipid anchor (fatty acid, prenyl). Cytosolic enzymes add the anchor, which directs the protein to the cytosolic face
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51
Q

Techniques: extraction of membrane proteins with detergents

A

Triton X-100 (has both hydrophobic and hydrophilic region)

By mixing the transmembrane protein with amphipathic detergent monomers and water, you form water-soluble protein-lipid-detergent complexes and water-soluble lipid-detergent micelles, which breaks up the membrane.

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52
Q

Technique: studying the properties of membrane proteins

A

Following the purification of the protein of interest, you can add phospholipids and remove the detergent to produce a functional protein incorporated into an artificial phospholipid vesicle. This can be used to study the properties of the protein in an isolated environment.

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53
Q

Technique: lateral diffusion of membrane proteins

A
  • there is lateral diffusion of proteins within the leaflet, but no flip-flop
  • study of protein movement can be done by Fluorescence Recovery After Photobleaching (FRAP), where the protein is fused to GFP (Green Fluorescent Protein)
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54
Q

describe how FRAP works

A
  1. protein fused to GFP or labelled with fluorescent antibody
  2. photobleach an area (white)
  3. rate of fluorescence recovery: time taken for neighbouring unbleached fluorescent proteins to move into bleached area
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55
Q

look at the different possible graphs for FRAP on slide 43

A
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56
Q

can FRAP only be done with transmembrane proteins?

A

no, you can also do it with other proteins (eg cytosolic) and other molecules (eg lipids)

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57
Q

Permeability of an artificial bilayer as opposed to a cell membrane

A

Artificial bilayer (protein-free liposome): impermeable to most water-soluble molecules
Cell membrane: transports proteins to transfer specific molecules via facilitated transport

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58
Q

Movement across the lipid bilayer - small non polar molecules and small, uncharged polar molecules

A

Permeable - movement via simple diffusion through the lipid bilayer
1. high concentration to low concentration down the concentration gradient
2. more hydrophobic/nonpolar molecules have faster diffusion across the lipid bilayer

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59
Q

Small non-polar molecules

A

oxygen, carbon dioxide, nitrogen, steroid hormones

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60
Q

Small, uncharged polar molecules

A

water, ethanol - can diffuse across lipid bilayer
glycerol - cannot move across very well

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61
Q

Movement across the lipid bilayer - larger uncharged polar molecules and ions

A

Impermeable - require membrane proteins for transport

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62
Q

larger uncharged polar molecules

A

amino acids, nucleosides
glucose - a little can get across

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63
Q

Ions

A

H+, Na+, K+, Ca2+, Cl-, Mg2+, HCO3-

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64
Q

transmembrane transport proteins

A
  • create a protein-lined hydrophilic path across cell membrane
  • transport polar and charged molecules (amino acids, ions, sugars, nucleotides, various cell metabolites)
  • each transport protein is selective and transports a specific class of molecules
  • different cell membranes have a different complement of transport proteins
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65
Q

two main types of membrane transport proteins

A
  • channels
  • transporters
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66
Q

channel proteins vs transporter proteins in terms of selectivity and transport

A

channel proteins:
- selectivity: size and charge of electric solute
- transport: transient interactions as solute passes through. no conformational changes for transport through an open channel

transporter proteins:
- selectivity: solute fits into binding site
- transport: specific binding of solute. series of conformational changes for transport

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67
Q

passive transport

A

driven by the concentration gradient, no energy required

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68
Q

active transport

A

against concentration gradient, requiring energy

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69
Q

is glucose charged?

A

no

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70
Q

electrochemical gradient (electrical gradient) =

A

concentration gradient + membrane potential

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71
Q

what is the effect of the electrochemical gradient when the voltage and the concentration gradients work in the same direction?

A
  • positive ions attracted to negative ions on the opposite side of the membrane (due to resting potential)
  • this is additive to the effect of the concentration gradient
  • greater net driving force
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72
Q

what is the effect of the electrochemical gradient when the voltage and the concentration gradients work in opposite directions?

A
  • positive ions attracted to negative ions on the same side of the membrane (due to resting potential)
  • smaller net driving force
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73
Q

describe voltage across a membrane

A

differences in charges of ions

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74
Q

resting membrane potential

A

stable electrical charge difference across a cell membrane when the cell is at rest and not actively sending signals

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75
Q

describe how channel proteins work

A
  • hydrophilic pore across membrane
  • most channel proteins are selective (eg ion channels transport a specific ion, determined by ion size and electric charge
  • passive transport of solute
  • transient interactions with channel wall as solute passes through (selectivity)
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76
Q

which are faster - channels or transporters?

A

channels

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77
Q

two broad categories of ion channels

A
  • non-gated ion channels
  • gated ion channels
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78
Q

non-gated ion channels

A

always open

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79
Q

gated ion channels

A
  • some type of signal required for channel opening
  • even when open, they are not open ALL the time, they just are open for more of the time
  • specific ions are transported.
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80
Q

K+ leak channels

A
  • non gated channel
  • K+ moves out of cell
  • major role in generating resting membrane potential in plasma membrane of animal cells
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81
Q

in what organisms are ion channels found?

A

animals, plants, microorganisms

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82
Q

types of gated ion channels

A
  1. mechanically-gated
  2. ligand-gated (extracellular ligand)
  3. ligand-gated (intracellular ligand)
  4. voltage-gated
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83
Q

mechanically-gated ion channels

A

signal - mechanical stress
eg plasma membrane may get stretched and that causes it to open up

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84
Q

ligand-gated (extracellular ligand)

A

signal - ligand from outside of the cell
eg neurotransmitter

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85
Q

ligand-gated (intracellular ligand)

A

signal - ligand from inside the cell
eg ion, nucleotide

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86
Q

what is the difference between the signal to open and the transported material?

A

the signal causes the channel to open, it is not necessarily what is transported through the channel

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87
Q

voltage-gated

A

signal - change in voltage across membrane by membrane depolarisation

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88
Q

main types of transporter proteins

A
  1. passive transport by transporter proteins
    - uniport
  2. active transport by transporter proteins
    - gradient-driven pumps (symport, antiport)
    - ATP-driven pumps (P-type pump, V-type proton pump, ABC transporter)
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89
Q

how do transporter proteins work?

A

bind a specific solute
- goes through a conformational change to transport solute across the membrane

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90
Q

compare transporter proteins to channel proteins in terms of rate of transport by drawing graph

A

different kinetics - rate of transport in channels gets faster and faster as concentration difference of transported molecule increases. for transporter, because it has to undergo conformational changes, it starts off at a fast rate but eventually hits Vmax as all binding sites get saturated

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91
Q

uniport

A

one solute
- passive transport down its electrochemical gradient
- direction of transport is reversible - dependent on concentration gradient

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92
Q

glucose transporter

A

GLUT uniporter
- transports D-glucose down the concentration gradient
- can work in either direction (glucose in or out of the cell)

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93
Q

gradient-driven pump

A
  • 1st solute down its gradient, providing energy
  • 2nd solute against its gradient using this energy
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94
Q

ATP-driven pump (ATPases)

A

ATP hydrolysis provides energy to move the solute against its gradient

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95
Q

Light-driven pump (bacteria)

A

uses light energy to move solute against its gradient

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96
Q

two types of gradient-driven pumps

A

symport and antiport

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97
Q

symport

A

two solutes moved in the same direction

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98
Q

antiport

A

two solutes moved in opposite direction

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99
Q

Na+ glucose symporter

A
  • sodium going down its electrochemical gradient, providing energy
  • glucose is going against its concentration gradient
  • random oscillations between conformations which are reversible
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100
Q

occluded state

A

transporter closed - either occupied or empty

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101
Q

when do conformational changes in the Na+ glucose symporter occur?

A

both sites occupied: cooperative binding of Na+ and glucose
both sites empty: both Na+ and glucose dissociate

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102
Q

describe the process behind the Na+ glucose symporter

A
  • The symporter has two binding sites: one for Na+ and one for glucose.
  • In its outward-open state, facing the extracellular space where Na+ concentration is high, Na+ readily binds to its site on the symporter.
  • Once Na+ is bound, it increases the affinity of the transporter for glucose. When a glucose molecule binds to its site, this triggers a conformational change in the protein.
  • The transporter then transitions to an occluded state where both binding sites are inaccessible from either side of the membrane. This occluded state can only be reached when both Na+ and glucose are bound or when neither is bound (occluded-empty).
  • From this occluded state, another conformational change occurs that opens up towards the cytosol (inward-open state), where Na+ concentration is low.
  • Due to this low intracellular concentration, Na+ dissociates from its binding site and enters into cytosol.
  • The release of Na+ reduces affinity for glucose at its binding site; thus, glucose also dissociates and enters into cytosol.
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103
Q

how does Na+-H+ exchanger work

A

antiport: Na+ down its electrochemical gradient provides energy to move H+ against its electrochemical gradient
- sodium goes into the cytosol
- H+ goes out of the cell

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104
Q

what is the function of the Na+-H+ exchanger?

A
  • cytosolic pH needs to be regulated for optimal enzyme function (pH~7.2)
  • but excess H+ occurs in the cytosol from acid forming reactions, and leaks out of the lysosome
  • transporters maintain cytosolic pH: when there is a drop in cytosolic pH, the transporter activity increases and H+ is transported out of the cell
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105
Q

how is the Na+ electrochemical gradient maintained in animal cells?

A

Na+-K+ pump (plasma membrane ATP-driven pump)

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106
Q

why does the Na+ electrochemical gradient need to be maintained?

A
  • Na+ going down its electrochemical gradient provides energy for symport and antiport transporters
  • continued action of gradient-driven pumps may equalise the Na+ gradient
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107
Q

P-type pumps

A
  • use ATP
  • phosphorylated during the pumping cycle
  • many P-type pumps transport ions (H+, K+, Na+, Ca2+)
  • flippases to transport phospholipids
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108
Q

Na+ and K+ moved —– their electrochemical gradients

A

Na+ and K+ moved against their electrochemical gradients

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109
Q

sodium gradient used to:

A
  • transport nutrients into cells (eg glucose)
  • maintain pH
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110
Q

pumping cycle of the Na+-K+ pump

A
  1. 3 Na+ bind from inside the cell
  2. pump phosphorylates itself, hydrolysing ATP
  3. phosphorylation triggers conformational change and Na+ is ejected
  4. 2 K+ bind from the extracellular material
  5. pump dephosphorylates itself
  6. pump returns to original conformation and K+ is ejected
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111
Q

what do plant cells use instead of an Na+-K+ pump?

A

H+ pump
- generate H+ electrochemical gradient used for H+ driven symport/antiport
- leads to membrane potential
- H+ is moved from low (inside cell) to high (outside cell)
- solutes can then be moved into cell with H+

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112
Q

ABC transporters

A

use 2 ATP molecules to pump small molecules across the cell membrane
eg transport toxins outside of the cell but can also be source of chemotherapy resistance as cancer cells overproduce these transporters

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113
Q

V-type proton pump

A
  • found in lysosome and plant vacuole
  • uses ATP to pump H+ into organelles to acidify the lumen
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114
Q

F-type ATP synthase

A
  • structurally related to V-type proton pump, but opposite mode of action
  • uses H+ gradient (movement down) to drive the synthesis of ATP
  • in mitochondria, chloroplasts, bacteria
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115
Q

compare a V-type proton pump to a F-type ATP synthase

A

V-type: uses ATP to pump H+ against the electrochemical gradient
F-type: uses the H+ electrochemical gradient to produce ATP.

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116
Q

is the action of the F-type ATP synthase reversible?

A

yes, it depends on ATP concentration and the H+ electrochemical gradient

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117
Q

how do transporters work together to transfer glucose from the intestine to the bloodstream?

A

epithelial cells of the villus
top of epithelial cells has microvilli - very high surface area
top of epithelial cell: apical domain
side: lateral domain
bottom: basal domain to face basal lamina
basal + lateral = bas-lateral domain
at top, we have Na+-glucose symporter which uses active transport to transport glucose against its gradient into the epithelial cell
in baso-lateral region, there is an Na+-K+ pump which keeps a low concentration of Na+ in the epithelial cell to maintain electrochemical gradient
GLUT uniporter carries out passive transport down the concentration gradient into extracellular fluid, which then ends up in the bloodstream

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118
Q

tight junctions between epithelial cells

A

creates a boundary where nothing can get by. proteins can move anywhere on apical surface or basal membrane but not past these junctions
helps keep transporters in their right compartment (eg GLUT uniporter and Na+-K+ pump stay on bottom, Na+-glucose symporter stays on top)

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119
Q

generation of membrane potentials

A

K+ leak channel (passive): facilitates outward flow of K+
1. K+ leak channels closed; plasma membrane potential = 0 (positive and negative charges balanced exactly)
2. K+ leak channels open; membrane potential exactly balances the tendency of K+ to leave

Na+-K+ pump
~10% of membrane potential
maintains:
- Na+ gradient with low cytosolic [Na+]
- K+ gradient with high cytosolic [K+]
electrogenic:
- 3Na+ pumped out
- 2K+ pumped in
- net 1+ ion pumped out

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120
Q

what is the usual balance in an animal cell?

A

cells generally balance electrical charges inside and outside of cell:
- extracellular space: high [Na+], high [Cl-], low [K+]
- cytosol: low [Na+], low[Cl-], high [K+], cell’s fixed anions (nucleic acids, proteins, cell metabolites)

but:
- K+ flows out (K+ leak channels), ions diffusing from high to low
- Na+-K+ pump resulting in net 1+ ion pumped out

net result:
- bit more positive on outside (Na+, K+)
- bit more negative on inside (Cl- and fixed anions)
- forms membrane potentials

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121
Q

equilibrium =

A

resting membrane potential, which in animal cells varies from -20mV to -200mV

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122
Q

draw a diagram to show the generation of membrane potential in animal cells

A
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123
Q

generation of membrane potential in plant cells

A

plasma membrane P-type pump
- H+ pump
- generates H+ electrochemical gradient of -120 to -160mV
- used by gradient-driven pumps to carry out active transport
- electrical signaling
- regulating pH

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124
Q

the volumes taken up by organelles will…

A

differ for different cell types

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125
Q

percentage volume taken up by cytosol

A
  • half the cell volume
  • part site of protein synthesis and degradation
  • where many metabolic pathways and cytoskeleton occur
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126
Q

rough ER

A
  • over 50% of total cell membrane
  • membrane-bound ribosomes
  • synthesis of soluble proteins and transmembrane proteins for the endomembrane
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127
Q

smooth ER

A
  • doesn’t have membrane bound ribosomes
  • phospholipid synthesis, detoxification
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128
Q

percentage of total cell membrane of rough ER membrane in liver hepatocyte vs pancreatic exocrine cell

A

60% in pancreas, 35% in liver
- pancreas has to synthesise enzymes.

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129
Q

why are mitochondria so abundant in liver hepatocytes?

A

provide energy to support the many metabolic functions on the liver

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130
Q

definition of an organelle

A

discrete structure or subcompartment of a eukaryotic cell that is specialised to carry out a particular function (most are membrane-enclosed)

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131
Q

how were organelles discovered?

A

via visualisation in a light or electron microscope

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132
Q

examples of membrane-enclosed organelles

A
  • nucleus
  • endoplasmic reticulum
  • Golgi apparatus
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133
Q

examples of organelles that are not membrane-bound

A
  • nucleolus
  • centrosome

also known as bimolecular condensates

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134
Q

what is protein sorting?

A
  • proteins are nuclear encoded
  • mRNA arrives in cytoplasm and translation starts on ribosomes in cytosol
  • cytosolic protein doesn’t have a sorting signal, so its default location is the cytosol
  • some proteins have a sorting signal called a signal sequence
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135
Q

what does a signal sequence consist of?

A

a stretch of amino acid sequence in a protein which directs the protein to the correct compartment

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136
Q

each signal sequence specifies

A

a specific destination in the cell; specific signal sequences direct proteins to nucleus, mitochondria, ER, peroxisomes, etc

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137
Q

signal sequences are recognised by

A

sorting receptors that take proteins to their destination

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138
Q

post-translational protein sorting

A
  • proteins are nuclear-encoded
  • fully synthesised in cytosol before sorting
  • folded: nucleus, peroxisomes
  • unfolded: mitochondria, plastids
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139
Q

co-translational sorting

A
  • proteins are nuclear-encoded
  • they have an ER signal sequence and are associated with ER during protein synthesis in the cytosol
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140
Q

proteins that are intended for the nucleus have a

A

nuclear localisation signal (NLS) for import into the nucleus.

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141
Q

function of the nuclear import receptors

A

nuclear import receptor (sorting receptor) binds the NLS and move it into the nucleus. nuclear pores act as gates to the nucleus - proteins with the nuclear import receptor are recognised.

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142
Q

function of transcription activators

A

required in the nucleus for eukaryotic transcription - imported through the nuclear pore and binds to DNA to bind to the activated target gene

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143
Q

function of peroxisomes

A

contain enzymes for oxidative reactions
- detoxify toxins, break down fatty acid molecules

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144
Q

enzymes imported into the peroxisome through

A

a transmembrane complex - there is a peroxisomal import receptor (sorting receptor) which binds to the peroxisome import sequence (signal sequence)

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145
Q

how and why do proteins have to move into mitochondria/chloroplasts

A
  • have own genomes and ribosomes
  • but most proteins for these organelles are nuclear-encoded
  • translated in cytosol and targeted by a signal sequence for import
  • proteins are unfolded for import by association with hsp70 chaperone proteins
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146
Q

transmembrane complexes in mitochondria

A

needs proteins to be unfolded to pass through. signal sequence bound to sorting receptor, which brings it to transmembrane complexes - hsp70 proteins come off as the protein moves through. then the mitochondrial hsp70 binds to it in the mitochondrial matrix (these help the protein fold and remove the signal)

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147
Q

why do proteins sort to the ER?

A

entry point to endomembrane system (ER, Golgi, endossâmes, lysosomes, or up to plasma membrane)

148
Q

is ER signal hydrophobic or hydrophilic?

A

hydrophobic

149
Q

what is co-translational translocation?

A

insertion of protein into ER starts as translation continues (whole ribosomal complex moves together)

150
Q

ER signal sequence is usually at

A

N-terminus

151
Q

types of proteins entering the ER:

A
  1. soluble proteins
  2. transmembrane proteins (eg channel)
152
Q

are ribosomes specific to cytosol/ER?

A

no; once they are done translating protein, they move back to the cytosol and pick up any protein (no specificity)

153
Q

describe the process for co-translational translocation of a soluble protein

A
  1. translation starts, N-terminal ER signal sequence emerges
  2. recognised by SRP, elongation arrest by SRP
  3. SRP-ribosome complex binds to SRP receptor and moves it to the translocon
  4. translocon opens
  5. protein synthesis resumes with protein transfer into ER lumen
  6. signal peptidase cleaves ER signal sequence, which is hydrophobic - in lipid bilayer
  7. protein released into ER lumen
  8. translocon closes
154
Q

destination of soluble protein

A

lumen of an endomembrane organelle or secretion at PM

155
Q

co-translational translocation for transmembrane protein (N-terminal ER signal sequence)

A
  1. translation starts, N-terminal ER signal sequence emerges
  2. recognised by SRP, elongation arrest by SRP
  3. SRP-ribosome complex binds to SRP receptor which moves it to the translocon
  4. translocon opens
  5. protein synthesis resumes with protein transfer into ER lumen
  6. stop-transfer sequence, which has an internal hydrophobic segment (single-pass transmembrane protein w a membrane spanning alpha helix) enters translocon
  7. protein transfer stops and transmembrane domain released into lipid bilayer
  8. signal peptidase cleaves ER signal sequence and translocon closes
  9. N-terminus is in the ER lumen, C-terminus is in the cytosol, hydrophobic sequence is in it
156
Q

translocon

A

protein channel complex in the endoplasmic reticulum (ER) membrane that facilitates the translocation of proteins across or into the ER membrane

157
Q

destination of transmembrane protein

A

membrane of an endomembrane organelle or in the plasma membrane

158
Q

N-terminal ER signal sequence

A
  • stretch of hydrophobic amino acids at N-terminus of protein
  • removed by signal peptidase
159
Q

Internal ER signal sequence

A
  • stretch of hydrophobic amino acids (start-transfer sequence)
  • not removed - remains part of protein = membrane spanning alpha helix
  • In double-pass or multi-pass transmembrane proteins, these internal sequences work with stop-transfer sequences to embed multiple segments of polypeptides within membranes.
160
Q

similarity and differences between N-terminal and internal ER signal sequence

A

both types of sequences direct proteins to enter or integrate into the ER membrane via similar mechanisms involving SRP recognition and targeting to translocons, their positions within polypeptides and subsequent fates differ.

161
Q

differences between hydrophobic stop transfer and start transfer sequences

A

no differences other than order in the protein

162
Q

co-translational translocation for transmembrane protein (internal ER signal sequence)

A
  1. translation starts, internal start-transfer sequence emerges
  2. recognised by SRP, elongation arrest by SRP
  3. SRP-ribosome complex binds to SRP receptor which moves it to the translocon
  4. translocon opens
  5. protein synthesis resumes with protein transfer into ER lumen
  6. stop-transfer sequence enters translocon
  7. protein transfer stops
  8. start-transfer sequence and stop-transfer sequence (internal hydrophobic segments = membrane spanning alpha helices) are released into lipid bilayer
  9. translocon closes
163
Q

what components do intracellular compartments in the endomembrane system exchange?

A

lipids and proteins

164
Q

secretory pathway

A

proteins and lipids made in the ER are delivered to other compartments
- ER to outside (exocytosis)
- ER to lysosomes (via endosomes)

165
Q

endocytic pathway

A

contents moved into the cell (endocytosis)

166
Q

retrieval pathway

A

retrieval of lipids/selected proteins for reuse

167
Q

what happens to the individual leaflets of the membranes during endo/exocytosis?

A

maintain their orientation throughout

168
Q

vesicular transport

A
  • vesicle: small, membrane-enclosed organelle in cytoplasm of a eukaryotic cell
  • shuttle components back an forth in the endomembrane system (eg ER to Golgi)
  • two main components: soluble proteins inside the vesicle and transmembrane proteins embedded in membrane of vesicle
169
Q

cargo protein receptors

A

receptors can be used to select for cargo proteins and then released into the ER lumen

170
Q

constitutive exocytosis pathway

A
  • in all eukaryotic cells
  • continual delivery of proteins (transmembrane, soluble) and lipids to plasma membrane
  • includes constitutive secretion of soluble proteins (eg collagen for ECM)
171
Q

regulated exocytosis pathway

A
  • regulated secretion - in specialised cells
  • stored in specialised secretory vesicles
  • extracellular signal leas to vesicle fusion with plasma membrane and contents are released
  • eg pancreatic β cells (insulin release with increased blood glucose)
172
Q

path of a secreted protein from translation to plasma membrane

A

Translation starts on cytosolic ribosomes
* ER Signal sequence at N-terminus directs protein to ER

Co-translational translocation at ER
* Protein inserted through ER membrane by a translocon protein
* ER Signal sequence cleaved and left behind in ER membrane
* Secreted protein ends up in ER lumen

Secreted protein
* Moves in transport vesicles through secretory pathway (ER → Golgi apparatus → Plasma membrane)
* Vesicle membrane fuses with plasma membrane during exocytosis
* Secreted protein released to extracellular spac

173
Q

Path of a transmembrane protein from translation to plasma membrane

A

Translation starts on cytosolic ribosomes
* ER Signal sequence (N-terminal or Internal) directs protein to ER

Co-translational translocation at ER
* Protein inserted through ER membrane by a translocon protein
* There are different ways that a transmembrane protein can be
inserted into ER membrane

Transmembrane protein
* Moves in transport vesicles through secretory pathway (ER → Golgi apparatus → Plasma membrane)
* Vesicle membrane fuses with plasma membrane during exocytosis
* Transmembrane protein transferred to plasma membrane

174
Q

how is maintenance of membrane protein asymmetry maintained?

A
  • each membrane protein has a specific orientation
  • this is a result of membrane orientation in the ER
  • this protein symmetry is maintained through vesicular transport
175
Q

Golgi function

A

receives proteins and lipids from the ER, modifies them, and then dispatches them to other destinations in the cell

176
Q

Golgi structure

A

stack of flattened membrane-enclosed stacks (cisternae)
enters via:
- cis Golgi network
- cis cisternae
- medial cisterna
- trans cisterna
- trans Golgi network
leaves

177
Q

animal vs plant cell Golgi

A

animal cells tend to have one bind Golgi structure; plant cells have a lot of smaller Golgi spread out throughout the cell

178
Q

protein glycosylation

A
  1. starts in the ER
  2. a single type of oligosaccharide is attached to many proteins
  3. Complex oligosaccharide processing occurs in the Golgi apparatus (a multistage processing unit - different enzymes in each cisterna)
  4. glycosylation modifications for proteins and lipids (glycosylated lipids and proteins end up on the outside of cell to protect membrane + proteins from damage)
179
Q

endocytic pathway: endosomes and lysosomes

A

digest material that is no longer needed by the cell

180
Q

Endosomes

A
  • membrane-bound organelles
  • contain material ingested by endocytosis
  1. endocytic vesicles fuse to early endosomes and ingested material sorted so that it will either go to the Golgi (recycling pathway) or to lysosomes (degradation pathway)

Degradation:
2. early endosomes mature into late endosomes
3. lysosomal proteins (hydrolases, H+ pump) continue to be delivered from trans Golgi network to either late or early endosomes
4. late endosomes mature into lysosomes

181
Q

lysosomes

A
  • membrane-bound organelles
  • contain hydrolytic enzymes to digest worn-out proteins, organelles, other wast
182
Q

difference between early and late endoscope

A

late not recycling cargo anymore, committed to cargo degradation pathway

183
Q

where does digestion start?

A

at the late endosome

184
Q

how does trans Golgi know that it needs to package up lysosomal proteins into vesicles to send them to vesicles?

A

specific types of sugar groups can be added to vesicles that are signals

185
Q

types of enzymes contained in lysosomes

A

around 40 types of hydrolytic enzymes known as acid hydrolases (proteases, nucleases, lipases, etc)

186
Q

lysosomes are acidified by

A
  • H+ pump (V-type ATPase)
  • low pH needed for hydrolytic enzymes
187
Q

how does the lysosome protect the rest of the cell from digestion?

A
  • it is membrane bound
  • lysosomal membrane proteins (noncytosolic face, inside) are glycosylated for protection from proteases
188
Q

function of transport proteins in lysosomal membrane

A

transfer digested products to cytosol (amino acids, sugars, nucleotides)

189
Q

why do cytosolic proteins not have signal sequences?

A

as they stay in the cytosol`

190
Q

3 different pathways of protein movement

A

secretory pathway
endocytic pathway
retrieval pathway

191
Q

what gives vesicles directionality?

A
  • directed movement of transport vesicles
  • pulled by motor proteins associated with cytoskeleton
192
Q

define the cytoskeleton

A

a highly dynamic network of proteins with many important functions

193
Q

four main roles of the cytoskeleton

A
  1. structural support (AF, MT, IF) for cell shape
  2. internal organization of cell (MT) for organelles and vesicle transport
  3. cell division (AF, MT) for chromosome segregation and division of cell into 2
  4. large scale movements (AF) - crawling cell and muscle contraction
194
Q

three components of cytoskeleton

A

actin filaments (d:~7nm), microtubules (d:~25nm), intermediate filaments (d:~10nm)

195
Q

range of diameter of cytoskeletal filaments

196
Q

light microscopy

A
  • resolution limit of ~200nm
  • limits from wavelength of visible light
  • cannot resolve cytoskeletal filaments
197
Q

fluorescence microscope

A
  • light microscope with same resolution
  • but fluorescent labels are added to detect specific proteins (eg cytoskeletal filaments)
198
Q

transmission electron microscope

A
  • uses beams of electrons of very short wavelength
  • resolution limit of ~1nm
  • reveals detailed structures
199
Q

immunofluorescence microscopy

A
  • used to determine location of proteins within cell
  • cells are fixed (not light imagine)
  • primary antibody used to bind to specific protein of interest
  • secondary antibody binds to the primary antibody covalently tagged to a fluorescence marker
  • fluorescence microscope used to excite fluorescent marker and visualise light emitted
200
Q

draw a simplified diagram of the three types of filaments

201
Q

filaments are held together by

A

noncovalent interactions

202
Q

intermediate filaments

A
  • involved in structural support
  • different types of IF proteins
203
Q

two main types of IFs

A

cytoplasmic and nuclear

204
Q

cytoplasmic IFs

A
  • in animal cells subjected to mechanical stress
  • provide mechanical strength
205
Q

nuclear IFs

A
  • nuclear lamina - 2D meshwork formed by lamina in all animal cells
  • plants have different lamin-like proteins
206
Q

do plants need cytoplasmic IFs?

A

no; the cell wall provides most of the mechanical strength

207
Q

describe the structure of cytoplasmic intermediate filaments

A
  1. Proteins:
    - conserved α-helical central rod domain
    - N- and C- terminal domains differ
  2. Pack together into rope-like filaments
    - 2 monomers → coiled-coil dimer
    - 2 dimers → staggered antiparallel tetramer
    - 8 tetramers associate side by side and
    assemble into filament
    - most interactions are noncovalent
  • No filament polarity - because no polarity in
    tetramer (ends are the same)
  • Tough, flexible, high tensile strength
208
Q

Give an example of intermediate filaments

A

Keratin filaments in epithelial cells
- forms network throughout cytoplasm out to cell periphery
- anchored in each cell at cell-cell junction (desmosomes) and connect to neighbouring cells
- provide mechanical strength

209
Q

define an epithelium

A

sheet of cells covering an external surface or lining an internal body cavity

210
Q

function of microtubules

A
  • cell organization: vesicle transport, organelle transport and positioning, centrosome in animal cells
  • mitosis
  • structural support for cells and motile structures (flagella, cilia)
211
Q

structure of microtubules

A
  • Long hollow tubes made of individual subunits of two closely related globular proteins, α-tubulin and β-tubulin
  • form a tubulin heterodimer bound to GTP
  • This regular arrangement of α & β subunits gives the microtubule polarity (plus end (β) is different from minus end (α))
  • 13 parallel protofilaments make up a hollow tube
212
Q

all bonds between individual subunits of microtubule profilaments are

A

noncovalent

213
Q

the bonds between protofilaments are —- than the bonds within each protofilament

214
Q

can growth and disassembly of microtubules can occur at both ends?

A

yes, but is more rapid at plus end

215
Q

experiment to show that microtubule growth is faster at the plus end

A
  1. A bundle of microtubules isolated from a cilium
  2. Isolated microtubules incubated with a high concentration of tubulin (subunit) and GTP
  3. Faster growth of microtubules (more heterodimers being added) at the plus end
216
Q

dynamic instability

A

plus ends of microtubules grow and shrink, which is needed for remodelling

217
Q

dynamic instability: growing

A
  1. free αβ-tubulin dimers bound to GTP are added to growing microtubule at plus end
    (minus end stabilized at MTOC)
  2. Shortly after dimer added to microtubule, β-tubulin hydrolyzes GTP to GDP
  3. there is rapid addition of αβ-tubulin dimers which is faster than GTP hydrolysis in newly
    added αβ-tubulin dimers
  4. this leads to formation of GTP cap which stabilizes plus end
  5. Microtubule continues to grow
218
Q

dynamic instability: shrinking

A
  1. free αβ-tubulin dimers bound to GTP are added to growing microtubule at plus end
    (minus end stabilized at MTOC)
  2. Shortly after dimer added to microtubule, β-tubulin hydrolyzes GTP to GDP
  3. there is slower addition of αβ-tubulin dimers which is slower than GTP hydrolysis in newly added αβ-tubulin dimers
  4. this leads to the GTP cap being lost, so now there is GDP-tubulin at plus end which has weaker binding
  5. Microtubule disassembles
219
Q

function of an MTOC

A

have nucleating sites for microtubule growth to start assembling new microtubules
eg centrosome in animal cells

220
Q

example of a nucleation site

A

γ-Tubulin Ring Complex (γ-TuRC):
- protein complex of γ-tubulin & accessory proteins
- ring of γ-tubulin (gold) - acts as an attachment site for αβ-tubulin dimers
- minus end of microtubule at γ-TuRC
- plus end of microtubule grows out

221
Q

does the alpha tubulin or beta bind to y tubulin

222
Q

example of the dynamic nature of the MTOC (non dividing animal cells in interphase)

A
  • mos microtubules radiate from one centrosome
223
Q

example of the dynamic nature of the MTOC (dividing animal cells)

A
  • centrosome duplicates to form two spindle poles (MTOCs)
  • microtubules are reorganised to form a bipolar mitotic spindle, which requires microtubule dynamics (disassembly/assembly)
224
Q

4 functions of microtubule-associated proteins

A
  • nucleate growth of new microtubules
  • promote microtubule polymerisation
  • promote microtubule disassembly
  • stabilize microtubules (prevent disassembly) by binding to the sides and plus-end linking the protein
225
Q

Role of micro tubules in axons

A
  • how do neurotransmitters synthesized in the ER get to the axon terminals?
  • ER and Golgi apparatus are located in the nerve cell body
  • these neurons can be a meter long: from your spinal cord to your fingertip

cargo transport from the cell body to the axon is done by motor proteins on microtubule

226
Q

motor proteins for microtubules

A

kinesins and dyneins

227
Q

kinesins

A

generally move towards plus end of microtubules
eg. kinesin I: towards plus end to axon terminus, cargo of organelles, vesicles, macromolecule

228
Q

dyneins

A

generally move towards the minus end of microtubules
eg. cytoplasmic dynein: towards minus end to cell body, cargo of worn-out mitochondria and endocytosed materia

229
Q

describe the dimeric structure of kinesin-1 and cytoplasmic dynein

A
  • heads move along microtubules, use ATP hydrolysis for movement
  • tails - transport cargo
230
Q

where do microtubules position organelles?

A

microtubules go from the centrosome (MTOC) to cell periphery

the ER is pulled from the nuclear envelope to the cell periphery by kinesin-1 (towards microtubule plus end)

Golgi is held near the centrosome by cytoplasmic dynein (towards microtubule minus end)

231
Q

actin filaments are also known as

A

microfilaments

232
Q

arre actin filaments present in all eukaryote?

233
Q

what are actin filaments made of?

A
  • actin monomers
  • flexible, extensible
234
Q

what motor proteins use actin filaments?

235
Q

functions of actin filaments

A
  1. stiff, stable structures (microvilli)
  2. contractile activity
  3. cell motility (crawling)
  4. cytokinesis
236
Q

structure of actin filaments

A
  • helical filament composed of a single type of globular protein - actin monomers, which are held together by noncovalent interactions
  • an actin filament is made by two protofilaments twisted in a right-handed helix
237
Q

is an actin filament polar? explain

A
  • plus end is different from minus end
  • actin monomers all in the same orientation in each protofilament
  • growth is faster at the plus end
238
Q

what are free actin monomers bound to?

A

ATP, which is bound in the centre of the protein

239
Q

how are actin monomers added to the filament?

A
  • actin hydrolyses ATP to ADP
  • reduces strength of binding between monomers in filament
  • rapid addition of actin monomers
  • this is faster than the ATP hydrolysis in newly added actin monomers, causing actin filament to have an ATP cap, stabilising the structure
240
Q

actin polymerisation in a test tube (in vitro)

A

Actin subunits (monomers) and
ATP added to a test tube to study actin filament polymerization
Nucleation (lag phase):
* small oligomers form but are
unstable
Elongation (growth phase):
* some oligomers become more
stable, leads to rapid filament
elongation (faster at plus end)
Steady state (equilibrium phase):
* decrease in [actin subunits]
* rate of subunit addition = rate of
subunit disassociation
* length doesn’t change
* Treadmilling

241
Q

Process of actin filament growth

A

At the plus end, there is ATP-actin:
* addition of actin monomers - polymerization
* shortly after, actin hydrolyzes ATP → ADP
At the minus end, there is ADP-actin:
* loss of actin monomers - depolymerization

242
Q

what happens at Treadmilling Concentration?

A

Actin filament remains the same size and looks “stable” but there is continual exchange of monomers at ends:
* net addition at the plus end
* net loss at the minus end
Actin monomers move through the filament
until they are eventually replaced
- continuous supply of ATP needed

243
Q

cell crawling

A
  • dynamic changes in actin filaments
  • an example where actin filaments undergo treadmilling
  • actin filaments must rapidly assemble at the leading edge (red) and disassemble further back to push the leading edge (and cell forward)
244
Q

compare actin filaments to microtubules

245
Q

what are the different functions of actin filaments regulated by?

A

actin binding proteins

246
Q

6 examples of regulation by actin binding proteins

A
  • sequester actin monomers (prevent polymerization)
  • promote nucleation to form filaments
  • stabilize actin filaments (capping)
  • organize: bundle, cross-link filaments
  • sever actin filaments
247
Q

what do myosins generally do?

A

move towards plus end of actin filaments. their heads move along actin filaments, use ATP hydrolysis for movement

248
Q

two types of myosin proteins

A

myosin I
myosin II

249
Q

myosin I

A

tail domain: binds cargo
* e.g. (B) vesicles (regulated secretion)
* e.g. (C) plasma membrane (shape)

250
Q

xmyosin II

A

dimer
* tails: organized in a coiled-coil
* dimers assemble into myosin-II filaments through their coiled-coil tails
* e.g. bipolar myosin-II filament, which slide actin filaments in opposite directions
(plus end of both actin filaments) and generates a contractile force

251
Q

how do epithelial cells interact with each other and the extracellular matrix?

A

through junctions to form tissues

252
Q

what are the 5 types of junctions?

A

tight junctions
adherens junction
desmosome
gap junction
hemidesmosome

253
Q

draw a diagram labelling the positioning of the 5 different junctions

254
Q

what types of junctions are present in epithelial cells?

A

all junctions

255
Q

function of tight junction

A
  • help polarise cells
  • create a tight seal between cells, preventing mixing of the extracellular environment
  • act as fences in the membrane, preventing mixing of apical and basolateral membrane proteins
256
Q

adherens junction

A

joins an actin bundle in one cell to a similar bundle in a neighbouring cell, thus sticking 2 cells together

257
Q

desmosome

A

joins the intermediate filaments in one cell to those in a neighbour cell, thus sticking 2 cells together

258
Q

gap junction

A

allow for communication between cells:
- couple cells electrically and metabolically
- allow passage of ions and metabolites (<1000 daltons)
- not very selective as to what passes through

259
Q

how does a hemidesmosome differ from an adherens junction and a desmosome?

A

it is a cell-ECM anchoring junction

260
Q

why are mature epithelial cells polarised?

A

junctions are arranged in a specific order (ie ends are different

261
Q

give an example of the polarity of epithelial cells

A

sealing strand (tight junction belt) above the adhesion belt

262
Q

intercellular junctions in plant cells

A
  • plant cells lack cell junctions found in animal cells
  • they are surrounded by cell walls (hold cells together, provide mechanical strength)
  • plasmodesmata are intercellular junctions that allow for communication between cells
  • need to cross cell wall, so have different structure from gap junctions
263
Q

tight junctions form

A

sealing strands (a tight junction belt)

264
Q

tight junctions are composed of two transmembrane proteins:

A

Claudin and occludin
- required in both cells
- extracellular domain in one cell interacts with the extracellular domain in the neighbouring cells
- homophilic interactions (occludin attracted to occludin, claudin attracted to claudin)

265
Q

adherens junctions, desmosomes, and hemidesmosomes are also termed

A

anchoring junctions

266
Q

function of anchoring junctions

A

provide mechanical strength to the epithelium

267
Q

function of cell-cell anchoring junctions

A

link cytoskeletons of neighbouring cells

268
Q

function of cell-ECM anchoring junctions

A

link cytoskeleton to basal lamina

269
Q

two types of proteins involved in anchoring junctions

A

adhesion proteins and linker proteins

270
Q

transmembrane adhesion proteins

A
  • transmembrane proteins
  • extracellular domains interact with adhesion proteins of neighbouring cell (side) or extracellular matrix (bottom)
  • intracellular domains interact with linker proteins
271
Q

intracellular linker proteins

A
  • cytosolic proteins
  • link transmembrane adhesion proteins to cytoskeletal filaments
272
Q

each anchoring junction has specific transmembrane adhesion proteins and intracellular linker proteins. give:
- transmembrane adhesion protein
- extracellular binding
- intracellular cytoskeletal attachment

A

adherens junction:
- classical cadherins
- classical cadherin on neighbouring cell
- actin filaments

desmosome:
- nonclassical cadherins (desmoglein, desmocollin)
- desmoglein and desmocollin on neighbouring cell
- intermediate filaments

hemidesmosome:
- α6β4 integral
- extracellular matrix proteins
- intermediate filaments

273
Q

adherens junctions

A
  • form an adhesion belt that encircles the inside of the plasma membrane
  • transmembrane adhesion proteins = classical cadherins
  • cadherin proteins from neighbouring cells interact with each other via homophilic interactions (eg e-cadherin/e-cadherin)
  • intracellular linker proteins link cadherin proteins to actin filaments
  • cadherin proteins become concentrated at sites of cell-cell interactions, forming adherens junctions
274
Q

both desmosomes and hemidesmosomes link to —-; why?

A

intermediate filaments eg keratin filaments. intermediate filaments provide the most structural strength

275
Q

distinguish between desmosomes and hemidesmosomes

A
  • desmosomes are linked to keratin filaments and connect to a neighbouring cell
  • hemidesmosomes anchor keratin filaments to the basal lamina
276
Q

desmosomes

A
  • transmembrane adhesion proteins = nonclassical cadherin proteins (desmoglein, desmocollin)
  • these undergo homophilic and heterophilic binding
  • intracellular linker proteins link desmoglein and desmocollin to keratin filaments inside the cell
277
Q

hemidesmosomes

A
  • transmembrane adhesion proteins = integrins that bind to laminin in the basal lamina (ECM)
  • intracellular linker proteins link integrins to keratin filaments inside cell
278
Q

describe the structure of a gap junction

A

1 subunit = connexin
6 connexins = form connexon (hemichannel), which by itself is closed
2 connexons = form intracellular channel (open)

279
Q

passes through gap junctions:

A

cAMP, nucleotides, glucose, amino acids

280
Q

does not pass through gap junctions:

A

macromolecules, proteins, nucleic acids

281
Q

describe the gated nature of gap junctions

A

can be in an open or closed state by extracellular or intracellular signals
eg treatment with dopamine causes close gap junctions

282
Q

dramatic increase in cytosolic Ca2+ ->

A

close gap junction

283
Q

membrane damage ->

A
  • Ca2+ leaks into the damaged cell
  • gap junctions close
  • prevents loss of metabolites from adjacent cells
284
Q

describe the structure and functioning of the plasmodesmata

A
  • cytoplasmic channels which lead to a continuous plasma membrane and ER across plasmodesmata
  • intercellular free movement of soluble molecules (<1000 daltons), like sugars, ions, other essential nutrients
  • controlled trafficking of larger soluble molecules via gating, like proteins or regulatory RNAs
285
Q

callose deposition in cell wall

A
  • callose is a plant polysaccharide
  • permeability control through reversible callose deposition
286
Q

animal tissues are composed of

A

cells and extracellular matrix

287
Q

compare epithelial tissue and connective tissue

A

epithelial tissue (epithelium):
- eg intestinal lining, skin epidermis
- cells closely associated and attached to each other
- limited ECM (a thin basal lamina)
- cytoskeletal filaments provide resistance to mechanical stress

connective tissues:
- eg skin dermis, bone, tendon, cartilate
- cells are rarely connected and are attached to the matrix
- plentiful ECM
- ECM provides resistance to mechanical stress

288
Q

what gives different tissues different properties?

A

different compositions of ECM

289
Q

what is the primary component in connective tissues?

290
Q

3 major classes of macromolecules in the extracellular matrix:

A
  1. glycosaminoglycans (GAGs) and proteoglycans
  2. fibrous proteins (collagens, elastin)
  3. glycoproteins (eg laminin, fibronectin)
291
Q

connective tissue ECM: glycosaminoglycans (GAGs)

A
  • long, linear, chains of a repeating disaccharide
  • highly negatively charged (attract Na+ and water)
  • form hydrated gels, resist compression
  • space filling
  • most GAGs synthesised inside cell and released by exocytosis
292
Q

hyaluronan

A
  • simple GAG
  • long chain of repeating disaccharide subunits (up to 25,000)
  • hyaluronan is spun directly from cell surface by a plasma membrane enzyme complex
293
Q

connective tissue ECM: proteoglycans

A
  • subclass of glycoproteins
  • protein with at least one sugar side chain which must be a glycosaminoglycan (GAG)
  • typically, more extensive addition of sugars (up to 95% of total weight)
294
Q

connective tissue ECM: collagen

A
  • fibrous protein
  • provides tensile strength
  • resists stretching
295
Q

structure of typical collagen (fibril-forming collagen)

A
  • three chains wound around each other in a triple helix
  • assemble into ordered polymers to form collagen fibrils, which can then pack together into collagen fibres
296
Q

collagen is secreted as —– by —–

A

procollagen by fibroblasts (skin, tendon, other connective tissue) and osteoblasts (bone)

297
Q

once procollagen is secreted outside,

A

it is processed to collagen and assembled into large structures (collagen fibrils)

298
Q

how do cells interact with collagen in the ECM of connective tissues?

A
  • connective tissue cells that secrete collagen also organise collagen in the ECM
  • they bind to collagen in ECM through integral (cell surface adhesion receptor) and fibronectin (glycoprotein)
299
Q

fibronectin

A
  • binds collagen
  • binds integrin
300
Q

integrin

A
  • binds fibronectin (extracellular domain)
  • binds adaptor proteins - actin filaments (intracellular domain)
301
Q

connective tissue ECM: elastin

A
  • elastin is a fibrous protein
  • networks of elastin give tissues elasticity, allowing it to stretch and relax like a rubber band (resilience)
302
Q

epithelial tissue ECM: basal lamina

A

the basal lamina is a basement membrane
- specialised type of ECM
- underlies all epithelia
- thin (40-120nm thick)
- ECM is secreted by the epithelial cells
- influences cell polarity (apical - basal)

303
Q

how does the basal lamina separate the epithelia from underlying tissue?

A
  • prevents fibroblasts in underlying connective tissue from interacting with epithelial cells
  • yet allows passage of macrophages and lymphocytes
304
Q

basal lamina contains a lot of

A
  • laminin (glycoprotein)
  • type 4 collagen (fibrous protein)
  • integrin (transmembrane adhesion protein)
305
Q

basal lamina is attachment site for

306
Q

basal lamina is anchored by

A

hemidesmosomes

307
Q

basal lamina is organised by

A

laminin:
- interacts with other components of ECM
- links integrin to type IV collagen

308
Q

describe the structure and contents of the plant cell wall

A
  • more rigid than the ECM of animal tissues
  • main components: cellulose, pectin (polysaccharides)
  • cellulose microfibrils provide tensile strength
  • pectin is space filling and provides resistance to compression
309
Q

how is the plant cell wall made?

A
  • plant cells synthesise cellulose chains at the plasma membrane using a cellulose synthase complex
  • other cell wall components are synthesised in the Golgi and exported by exocytosis
310
Q

cell cycle

A
  • conserved in all eukaryotes
  • sequence of events where contents of a cell are duplicated and divided into two
311
Q

observing animal cell division in culture

A
  • cells do not divide at the same time
  • when cells do divide, all cells follow the same stages in mitosis
312
Q

3 broad cell cycle stages conserved in all eukaryotes

A
  1. cell growth and chromosome duplication
  2. chromosome segregation
  3. cell division
313
Q

M phase

A
  • nucleus and cytoplasm divide:
    1. mitosis (nuclear division)
    2. cytokinesis (cytoplasmic division)
314
Q

interphase

A

period between cell divisions (metabolic activity, cell growth, repair)
- G1 phase
- S phase (synthesis)
- G2 phase

315
Q

do all mature cells divide in multicellular organisms?

A

no; many mature cells do not divide
- eg terminally differentiated cells - nerve cells, muscle cells, red blood cells
- as they become differentiated, they lose the ability to divide

316
Q

some cells only divide when given

A

an appropriate stimulus:
- eg when damaged, liver cells start to divide to replace damage tissue

317
Q

examples of cells that normally divide on an ongoing basis

A

hematopoietic and epithelial stem cells

318
Q

G0

A

cells that do not divide are in G0
- no cell division
- metabolically active, carry out cell function

319
Q

3 checkpoints/transitions in the cell cycle

A
  • start transition (G1 -> S)
  • G2/M transition (G2 -> M)
  • metaphase to anaphase transition (aka spindle assembly checkpoint)
320
Q

what is the purpose of the cell-cycle control system?

A

to delay later events until the earlier events are complete

321
Q

problems in checkpoints can cause

A

chromosome segregation defects

322
Q

start transition

A
  • decision to enter S phase
  • is the environment favourable? eg sufficient nutrients, specific signal molecules
323
Q

G2/M transition

A
  • decision to enter mitosis
  • is all DNA replicated? is all DNA damage repaired?
324
Q

metaphase to anaphase transition?

A
  • decision to pull duplicated chromosomes apart
  • are all chromosomes properly attached to the mitotic spindle?
325
Q

cell cycle progression is controlled by

A

molecular switches

326
Q

how is entry into the next phase of the cell cycle ensured?

A
  • triggered by cyclin-dependent protein kinases (Cdks)
  • cyclin-Cdk complex is activated for entry, then inactivated (molecular switch)
327
Q

entry into the M phase

A

M-Cdk (Idk activated by M cyclin) phosphorylates other regulatory proteins

328
Q

how is entry into the next phase of the cell cycle paused?

A

by other regulators, if any answer to the questions is no:
- Cdk inhibitors block entry to the S phase
- inhibitio of activating phosphatase (Cdc25) blocks entry to mitosis
- inhibition of APC/C activation delays exit from mitos

329
Q

interphase - G1 phase

A

centrosome duplication initiated and completed by G2

330
Q

interphase - S phase

A

chromosomes replicated (decondensed)
- cohesions deposited to hold two sister chromatids together

331
Q

interphase - G2 phase

A
  • by the end of G2, the replicated chromosomes are dispersed and tangled
  • need to reorganise and condense for mitosis
332
Q

3 main steps of prophase

A
  1. replicated chromosomes condense
  2. centrosome duplication
  3. mitotic spindle assembly
333
Q

prophase - replicated chromosomes condense

A

chromosome condensation (chromatids compacted) and sister-chromatid resolution (separable units)
- cohesins removed from chromosome arms, but not from centromeres
- condensins condense DNA in each sister chromatid
- sister chromatids are resolved but remain associated at the centromere by cohesins

334
Q

prophase - centrosome duplication

A
  • centrosome duplicated once per cell cycle during interphase; initiated in G1 and completed by G2
  • each centriole in the pair of centrioles in centrosome serves as a site for assembly of a new centriole
  • duplicated centrosomes form poles of mitotic spindle
335
Q

how are microtubules arranged in a non-dividing cell?

A
  • in a radial pattern
  • plus ends radiating out
  • minus ends stabilised at the MTOC (centrosome)
336
Q

what are the two conditions required for mitotic spindle assembly to start during prophase?

A
  • disassembly and reassembly of microtubules (to go from radiating from a single centrosome to radiating from two)
  • duplicated centrosomes
337
Q

centrosome structure

A
  • centrosome matrix surrounds the pair of centrioles
  • contains y-tubulin ring complexes (y-TuRCs), which are nucleating sites to assemble new microtubules
338
Q

pair of centrioles in the centrosome

A
  • organised at right angles to each other
  • composed of nine fibrils of three microtubules each
339
Q

prophase - mitotic spindle assembly

A
  • mitotic spindle assembly starts in prophase (M phase)
  • requires microtubule dynamics (disassembly and assembly)
  • duplicated centrosomes separate
  • radial array of microtubules extend out from each to position centrosome, and will become the two spindle poles
340
Q

nuclear envelope breakdown

A

occurs at the boundary between prophase and prometaphase
- phosphorylation of lamins and nuclear pore proteins triggers disassembly of nuclear envelope into small membrane vesicles

341
Q

nuclear lamina

A
  • meshwork of interconnected nuclear lamina proteins
  • form a two dimensional lattice on the inner nuclear membrane
342
Q

pro metaphase

A
  • nuclear envelope is now disassembled
  • mitotic spindle assembly can now be completed
  • kinetochore microtubules in the mitotic spindle attach to duplicated chromosomes
  • chromosome movement begins
343
Q

mitotic spindle assembly and function requires

A
  1. microtubule dynamics (disassembly and assembly)
  2. microtubule motor protein activity (kinesics, cytoplasmic dynein)
344
Q

state the whole order of the cell cycle

A
  1. interphase (G1, S, G2 phase)
  2. prophase
  3. prometaphase
  4. metaphase
  5. anaphase
  6. telophase
  7. cytokinesis (NB: partly occurs alongside half of anaphase and telophase)
345
Q

3 microtubules involved in the mitotic spindle

A
  1. astra microtubules: anchored at the centrosome and help position the mitotic spindle. cytoplasmic dynein (motor protein) attached to PM and moves to minus ends, thus pulling centrosome towards PM
  2. non-kinetochore microtubules: cross-linked microtubules throughout the mitotic spindle. microtubule-associated proteins (kinesin-5 and others) hold the microtubules together
  3. kinetochore microtubules: attach duplicated chromosomes to the spindle poles
346
Q

kinesin-5

A

walks towards the plus end of the non-kinetochore microtubules that it associates with, which have opposite orientations. this pushes the microtubules apart, pushing the centrosomes apart.

347
Q

describe how kinetochore microtubules attach to chromosomes

A
  • kinetochores are located at the centromeres of chromosomes
  • there is one kinetochore for each sister chromatid in the duplicated chromosome
  • microtubules from both spindle poles must attach to kinetochores of sister chromatids
  • generates equal tension on both sides to line up chromosomes at equator of spindle
348
Q

connecting protein complexes

A
  • bind to sides of microtubule near plus end
  • the exposed plus end of the microtubule allows for growing or shrinking for chromosome movement so it can be placed at the centre of the cell before separation
349
Q

metaphase

A
  • all chromosomes are aligned on the metaphase plate (equator of the spindle)
  • microtubule dynamos continue to maintain the metaphase spindle (tubulin flux)
350
Q

tubulin flux through microtubules

A

to maintain the metaphase spindle, there is a continuous:
- addition of tubulin subunits at plus end
- removal of tubulin subunits at minus end
- length of kinetochore microtubules does not change

this is an example of treadmilling

351
Q

how was tubulin flux confirmed?

A
  • a small amount of fluorescent tubulin (‘speckles’) was added to observe microtubule flux
  • a time lapse video microscopy was used to follow the fluorescent tubulin movement
  • added at plus end
  • depolymerises are removing the tubulin heterodimers from the minus end
352
Q

metaphase-anaphase transition (spindle assembly checkpoint)

A

anaphase does not start until all the chromosomes are aligned on the metaphase plate

353
Q

anaphase

A

separation of sister chromatids:
- separate activated, which then cleaves the cohesin complex

354
Q

anaphase A

A
  • kinetochore microtubules are shortened (loss of tubulin at both ends) due to depolymerisation
  • sister chromatids are pulled apart towards opposite poles
355
Q

anaphase B

A
  • kinesin causes a sliding force between non-kinetochore microtubules from opposite poles, pushing the poles apart
  • cytoplasmic dynein generates a pulling force at the cell cortex, dragging the two poles apart
  • microtubule growth at the plus ends of non-kinetochore microtubules also helps push the poles apart
356
Q

telophase

A
  • chromosomes are now separated into two groups, one at each spindle pole
  • nuclear envelope reassembly takes place: there is dephospho rylation of nuclear pore proteins and lamins by phosphatase, causing the envelope lamina, and pores to reform
  • mitotic spindle disassembles
  • chromosomes decondense
  • end of mitosis!
  • contractile ring for cytokinesis is being assembled (starts in anaphase)
357
Q

cytokinesis in animal cells

A
  • contractile ring divides the cytoplasm in two
  • contractile force by contractile ring brings cell membrane in as contractile ring becomes smaller
  • contractile ring disassembles once there are two daughter cells
358
Q

structure of contractile ring

A

assembled from actin and myosin filaments at the cleavage furrow (midway between spindle poles and underneath cell membrane)

359
Q

describe how actin and myosin II motor proteins are involved in causing contractile force

A
  1. Actin filaments form a band at the division site.
  2. Myosin II uses ATP to slide actin filaments towards each other; myosin moves toward plus end, pushing actin towards respective minus ends.
  3. This sliding action constricts the ring and pulls in the membrane until cell division is complete
360
Q

role of non-kinetochore microtubules in animal cell cytokinesis

A

send a signal to the plasma membrane at the plane of cleavage to say this is where we need the contractile ring to assemble

361
Q

how does mitosis in a plant cell differ from that in an animal cell?

A
  • very similar but no centrosome (it has another mechanism to form the mitotic spindle)
  • cytokinesis in the plant cell is different due to cell wall
362
Q

telophase in plant cells

A
  • chromosomes separated into two sets
  • phragmoplast starts to form
363
Q

what is the phragmoplast?

A
  • specific structure to form cell plate
  • has microtubules, actin filaments, vesicles from Golgi
364
Q

cytokinesis in plant cells

A
  • nuclear envelope reassembled, chromosomes decondensed
  • cell plate forms
  • this is a transient membrane compartment (vesicles from Golgi fuse together) to divide into two
365
Q

G1 in plants

A

cell plate has matured into plasma membranes and cell wall between two daughter cells

366
Q

compare cell division in meiosis and mitosis

A

meiosis:
- one round of DNA replication (chromosome duplication)
- two rounds of cell division
- produces 4 haploid cells
- homologous chromosomes are paired at the metaphase plate

mitosis:
- one round of DNA replication (chromosome duplication)
- one round of cell division
- produces 2 diploid cells
- homologous chromosomes are not paired at the metaphase plate

367
Q

meiosis cell division rounds 1 and 2

A

Round 1: homologous chromosome are segregated into two daughter cells (sister chromatids remain attached)

Round 2: sister chromatids are segregated, producing 4 haploid cells

368
Q

give an example of how studying cell division in a multicellular organisms helps us understand the complexities of the cell cycle

A

biochemical studies:
- injecting cytoplasm from fertilised Xenopus eggs into Xenopus oocytes led to the discovery of cyclin-dependent protein kinases