Eukaryote cell structure Flashcards
1
Q
Give a simple overview of the prokaryotic cell structure.
A
Simple composition, genetic material folded into nucleoid, no nuclear membrane, few internal membranes, cell size limited.
2
Q
Why are bacteria so successful?
A
Reproduce by binary fission by asexual reproduction, separation of one into two in 20-30mins.
3
Q
What are limitations of prokaryotic cell size?
A
Surface area : volume ratio, diffusion rate of molecules, need for high conc of compounds and enzymes.
4
Q
What happens to SA : V as volume increases?
A
Decreases.
5
Q
What is compartmentalisation?
A
Allows all enzymes and compound necessary for a process to be localised and concentrated.
6
Q
What do eukaryotes sub-divide specific tasks into?
A
Membrane bound organelles.
7
Q
How is an active and organised transport system achieved throughout the cell?
A
Energy (ATP) and cell signalling.
8
Q
What is an organelle?
A
Subcellular compartment or large molecular complex, often but not always membrane enclosed, that has distinct structure composition and function.
9
Q
What are biomolecular condensates?
A
Compartment without membrane barrier, based on selective aggregation of macromolecules (condensates).
10
Q
What are notable examples of biomolecular condensates?
A
P-granules in worms, pericentriolar material of centrosome, PhyB condensates in plant nucleus, RUBISCO enzyme in photosynthetic bacteria.
11
Q
How are condensates formed?
A
Require scaffolds e.g. nucleic acids or proteins, forms multiple weak fluctuating binding interactions within themselves.
12
Q
What are client proteins?
A
Specific proteins and nucleic acids that are recruited into condensates - concentrated zones of enzymes.
13
Q
What are condensates like structurally?
A
Liquid like behaviour, highly dynamic and reversible properties, can coexist as larger structure even with different properties, liquid-liquid phase separation.
14
Q
How does compartmentalisation allow for highly specific functions?
A
To differentiate and specialise into specific functions, specialised cells collectively form specialised tissues/organs.
15
Q
What are key characteristics of eukaryotic cells?
A
Larger than bacteria and archae, all have nucleus, multiple membrane bound organelles common to all, unicellular or multicellular.
16
Q
What are the different types of microscopes used to view cells?
A
Hooke, light, confocal, electron.
17
Q
What does moving images instead of only still microscopic images allow for?
A
View live cells instead of only fixed/dead cells.
18
Q
What is fluorescent proteins?
A
Identified in jelly fish, Nobel prize in chemistry 2008, GFP-fusion protein: track protein of interest.
19
Q
What do multi-coloured fluorescent images do?
A
Track multiple proteins in vivo.
20
Q
What is the role of dynamic fluorescent movies?
A
Perfect for understanding protein localisation, and function by studying dynamic nature of protien.
21
Q
What other disciplines allow for further observations and understanding?
A
Genetics, biochemistry, genomics.
22
Q
What are similarities between plant and animal cells?
A
Membrane bound organelles, nucleus, mitochondria, ER, golgi.
23
Q
What are differences between plant and animal cells?
A
Cell wall, chloroplast, size.
24
Q
What are examples of double membrane organelles?
A
Nucleus, mitochondria, chloroplasts.
25
What do mitochondria and chloroplasts have their own of?
DNA.
26
What was symbiosis?
Engulfment of bacteria by ancient archaeon 1.5bil years ago.
27
What is the archaea genome similar to?
Eukaryotic genome.
28
What is Asgard lineage?
Archaea with most eukaryotic like gene.
29
What is the role and internal structure of the nucleus?
Contain genetic information of cell, DNA organised into chromosomes, nuclear envelope, double membrane,nucleolus.
30
What is chromatin?
DNA + protein.
31
What is a dynamic nucleus?
DNA-packaging protein tagged with GFP, chromosomes condensation, nuclear envelope breakdown during mitosis.
32
What is the structure of the nucleus?
Nuclear envelope, two membranes, outer nuclear membrane, peri nuclear space (20-40nm), inner nuclear membrane.
33
What is RNA made in nucleus bound to?
Many proteins.
34
Where are proteins made?
In the cytosol.
35
What do freeze fracture and electron microscopy techniques show?
Inner/outer membrane of nucleus, shows nuclear pores.
36
How many nuclear pores does the average mammalian cells contain?
Thousands.
37
What are nuclear pores structurally and functionally?
Diameter of about 120nm, point of fusion between inner and outer membrane, not just a hole, gated by nuclear pore complex (NPC), made up of 30 different proteins.
38
What is the role of the nuclear pore revolving door?
Small molecules diffuse through nuclear pore (passive diffusion), molecular cut off around 30,000 Da about 9nm diameter, proteins above this size cannot passively enter the nucleus.
39
What is the revolving door of nuclear pores?
A revolving door with bouncer (NPC).
40
Proteins created in cytosol can be transported through NPC if they have what?
A nuclear localisation signal (NLS) - specific amino acid sequence.
41
By what receptor protein is NLS recognised by?
Importin.
42
What does importin do?
Binds NLS-containing protein - transport into nucleus via NP.
43
What does nuclear import require?
Ran-GTPase (a very small protein that hydrolyse GTP).
44
What do Ran-GTPase switch between?
GTP and GDP binding states.
45
What kind of process is nuclear import?
Highly regulated and active.
46
What does the cytosol use and do in nuclear import?
Ran-GDP to release importin.
47
How does nuclear export happen?
Nuclear-export sequence (NES) on protein to be exported binds to exportin.
47
What does the nucleus use and do in nuclear import?
Ran-GTP to bind importin.
48
What does nuclear export require other than NES?
Ran-GTPases and gradient of Ran-GTP and Ran-GDP across nuclear membrane.
49
What is nuclear export important for?
Export of RNA transcribed from nucleus to cytosol.
50
What is the nuclear lamina?
Tough fibrous mesh underneath the inner nuclear membrane, made up of intermediate filament.
51
What does nuclear lamina act as?
A scaffold that maintains the shape of nucleus.
52
What do the nuclear envelope and lamina do during each cell division?
Disassemble and re-form.
53
In length, how much DNA is in the nucleus of human cells?
Over 2m.
54
What associates with nuclear lamina mesh work?
Chromatins (DNA wrapped in proteins).
55
How are chromatins located in the nucleus?
Not randomly distributed, each has its own discrete location.
56
What is the nucleolus?
Centre of ribosomal RNA production, responsible for synthesis and assembly of RNA and protein to form ribosome, membrane-less compartment, bio molecular condensate.
57
What are ribosomes for?
Protein translation.
58
What is the ER function and structure?
Continuous with outer nuclear membrane, organised into interconnected tubes and flatten sacs, share single internal space, constitute more than half total membrane of ~animal cell, 10% total cell volume.
59
What is the single internal space shared in ER?
ER lumen.
60
What are the two main types of ER?
Rough ER and smooth ER.
61
What is the rough ER like?
Ribosomes on surface for protein synthesis.
62
What is the smooth ER like?
Biosynthesis and metabolism of lipid.
63
What is the third, secondary type of ER and its function?
Transitional - produced vesicles with proteins or lipids from transport to golgi.
64
What is the role of the rough ER?
Proteins translocated into ER lumen while being translated from mRNA, simple modification on newly-synthesised protein and folding quality check.
65
What is the role of smooth ER?
Diverse function, highly specialised, enriched in cel types for lipid metabolism, synthesis of lipid from production of lipoprotein, enzymes for drug detoxification.
66
What is the specialised smooth ER in muscles?
Sarcoplasmic reticulum.
67
What does storing calcium ions in sarcoplasmic reticulum do?
Regulates muscle contractions.
68
What is transitional ER like?
Half rough half smooth, exit sites of protein leaving ER.
69
What is the structure of Golgi apparatus?
Collection of flattened membrane enclosed sac known as cisternae.
70
What is the cis-complex?
Adjacent to ER - receive proteins from ER.
71
What is the trans-complex?
Toward plasma membrane.
72
What are the functions of the golgi apparatus?
Protein modifications and sorting for traffic within cell.
73
What are the two major models that explain vesicle trafficking through golgi?
Vesicular transport model, cisternal maturation model.
74
What is the vesicular transport model?
Cargo proteins moved between cisternae, resident enzymes stay in same cisternae.
75
What are resident enzymes?
Proteins that modify incoming cargo proteins.
76
What is the cisternal maturation model?
Cargo proteins stay in cisternae, resident enzymes move between cisternae.
77
Which transport model is correct?
Both supported by solid evidence, dependent on which model system, likely employs both models.
78
How do vesicles know where to go?
Coated transport vesicles.
79
What are the four types of coated transport vesicles?
Clathrin, COPI, COPII, retromer.
80
What are clathrin coated vesicles?
Golgi - endosome - plasma membrane, triskelion structure.
81
What are COPi coated vesicles?
From golgi (retrograde movement).
82
What are COPII coated vesicles?
From ER (anterograde movement).
83
What are retromer coated vesicles?
Endosome retrieval at golgi apparatus.
84
How does dynamic trafficking of proteins happen?
Vesicular stomatitis virus G protein (VSVG), temperature sensitive variant of VSVG - GFP protein, movement of VSVG-GFP from ER to golgi back out to plasma membrane.
85
What happens at 40C vs 32C during dynamic trafficking of proteins?
Misfolded trapped in ER, protein refold trafficking resume.
86
What three ways can proteins move across membrane barriers?
Gated transport (nuclear pore), protein translocation (synthesised into compartment), vesicular transport (membrane bound vesicles).
87
What are the first two steps of co-translational translocation?
Newly made peptide with ER signal sequence binds to SRP, SRP guides ribosome and RNA to translocator through binding to SRP receptor on plasma membrane.
88
What are the last two steps of co-translational translocation?
Protein translation occurs through translocator into ER lumen.
89
What does SRP stand for?
Signal recognition particle.
90
What is co-translational translocation overall?
Protein translation + translocation.
91
What prevents complete entry into ER lumen during co-translational translocation?
Stop-transfer sequence.
92
What does the protein become at the end of co-translational translocation?
Transmembrane protein - one side ER lumen, one side cytosol.
93
How are vesicles coated?
Cargo selection, membrane bending, protein coating, coat disassembly.
94
What three things do vesicles know where to go due to?
Vesicle coat, phospholipid profile, Rab GTPases.
95
How does Rab GTPase guide vesicles to destination?
GTP-binding = active, GDP-binding = inactive.
96
What are the first two steps of vesicle membrane fusion?
Rab GTPase interacts with tethering proteins on target membrane, vSNARE and tSNARE interacts for fusion.
97
What are v and tSNARE like and what’s their roles?
Have highly specific complementarity to determine if vesicle can fuse to destination, zip to force membranes together.
98
What is exocytosis?
Movement out of a compartment to deliver newly made proteins, lipids and carbs to cell surface.
99
What is endocytosis?
Movement into a compartment.
100
What is the passage proteins, lipids and carbs take during exocytosis?
ER — golgi - plasma membrane.
101
What is constitutive exocytosis?
Continuous supply of plasma membrane with new lipid and proteins.
102
What is regulated exocytosis?
Secretory vesicles stored, released upon stimulus.
103
How is regulated exocytosis used in insulin secretion?
Glucose uptake results in increase ATP, ATP inhibits potassium channel causing membrane depolarisation, open up calcium channels that trigger exocytosis of vesicles storing insulin.
104
Where does regulated exocytosis of insulin secretion take place?
Pancreatic beta-cells.
105
Where do allergic reactions arise from?
Mast cells.
106
How does an allergic reaction work?
Stimulus received by receptors on mast cell surface results in exocytosis of histamine granules.
107
What is endocytosis?
Internalisation of large/small molecules and/or liquid.
108
What are the two different types of endocytosis?
Large - phagocytosis (eating), small - pinocytosis (drinking).
109
What happens to endocytic vesicles?
Bud inward and are delivered to either lysosomes (digestion) or endosomes (recycled to plasma membrane).
110
What is phagocytosis?
Internalisation of large particles such as bacteria via lysosomes (degradation), also important for scavenging dead/ damaged cells.
111
What are phagocytes?
Immune cells that perform phagocytosis e.g. macrophages and neutrophil.
112
What needs to be activated before phagocytosis?
Cell surface receptors on phagocytic cells.
113
What is pinocytosis?
Uptake of small volume of extracellular fluid and bits of their own plasma membrane.
114
What remains unchanged when macrophages remove up to 3% of their own plasma membrane per min?
Cell volume and total surface area.
115
What is receptor-mediated endocytosis?
Selective uptake of certain macromolecules (effective enrichment) without needing to take up large amount of fluid.
116
Explain the receptor-mediated endocytosis model for cholesterol via low-density lipoproteins (LDLs).
LDL circulate in blood, bind to LDL receptors on cell surface, LDL + receptors are internalised, LDL - lysosome (released cholesterol), receptors recycled.
117
How can viruses enter via receptor-mediated endocytosis?
Hijack receptor mediated endocytosis trafficking to enter host cell, use receptor binding domain of spike protein on surface, binds receptor on plasma membrane and activate endocytosis.
118
What is ACE2 and its role?
Angiotensin converting enzyme 2 receptor, homeostasis of blood pressure and fluid regulation, highly expressed in heart, kidney, lung cells.
119
How is Sars-Cov2 related to ACE2?
Hijacks receptor for entry for replication and dissemination.
120
What is a synaptic cleft?
Space between two neurons.
121
How are synaptic clefts important in exocytosis and endocytosis?
Exocytosis of neurotransmitter in responses to AP, neurotransmitter binds to receptor on another neuron, signal transmitted, neurotransmitter re-uptake via dedicated transmembrane channel, endocytosis of synaptic vesicle to endosome of form vesicle directly.
122
What are endosomes and their functions?
Intracellular sorting organelles for maturation and trafficking, connected to membrane tubes and large vesicles, important for recycling of membrane receptors and lysosomal degradation.
123
What’s the difference between early and late endosomes?
Early are under plasma membrane, late are closer to nucleus.
124
How is the acidic interior (pH 5-6) of endosomes achieved?
ATP-driven H+ pump in endosomal membrane.
125
What are lysosomes structurally and functionally?
Degrade protein, nucleic acid, lipid, oligosaccharides, contain about 40 types of hydrolytic enzymes.
126
How is the acidic environment of lysosomes achieved and why is this important?
Have H+ pump to enrich H+ ions in lysosome lumen, enzymes optimally active in acidic environment (pH5.0).
127
What do lysosomes have special transporters for?
To export useful metabolites out to cytosol.
128
What is a plant vacuole?
One or several very large fluid filled vesicles, can occupy between 30-90% of total cell volume, like lysosomes but have other diverse functions.
129
What are the key functions of the plant vacuole?
Storage (nutrient or waste), degradation compartment, for cell size increase, controller of turgor pressure, maintain pH homeostasis.
130
What are peroxisomes?
Single membrane-enclosed organelles.
131
What are the oxidative enzymes that peroxisomes contain?
Catalase and urate oxidase.
132
What is the role of peroxisomes?
Produces hydrogen peroxide (H2O2), catalase uses H2O2 to oxidise lipids and detoxify harmful metabolites.
133
What is peroxisome biogenesis?
Vesicular transport of peroxisome membrane protein ER.
134
What can peroxins and translocator transport?
Can translocate fully-folded protiens.
135
What are peroxisomes dependent on?
Highly dependent on phospholipid metabolism e.g. myelin sheath.
136
What's some examples of neurological disorders that peroxisome mutations can cause?
Zellweger syndrome, ALD.
137
What are mitochondria like characteristically?
Highly variable, dynamic and plastic, often associated with cytoskeleton.
138
In what way do mitochondria vary among cell types?
RBCs have none, liver cells have more than 1000 per cell.
139
Why are mitochondria described as having a double membrane structure?
Have outer and inner membranes.
140
What is the outer membrane of mitochondria like?
Contains large channel forming proteins (porin), permeable to molecules <5000 Da.
141
What is the inner membrane of mitochondria like?
Folded into cristae, contains proteins for ETC and ATP synthase, also contains transport protein in and out matrix.
142
Why is the inner membrane of mitochondria folded?
Greatly increases surface area.
143
What is the matrix of mitochondria and what are its components?
Highly conc mixture of enzymes and DNA - mitochondrial DNA genome and ribosomes/tRNA, enzymes for oxidation of pyruvate and fatty acids for citric acid cycle.
144
What is the inter membrane space, structurally and functionally?
Conc of small molecules same as cytosol, higher conc proteins, release of cytochrome c for apoptosis.
145
Where and by what process is ATP produced in mitochondria?
In mitochondrial inner membrane via oxidative phosphorylation.
146
What are the steps of oxidative phosphorylation to produce ATP.
Acetyl CoA production, activated e- carrier NADH/FADH2, movement along ETC, electrochemical gradient, proton flow to matrix, turns ATP synthase.
147
How is ATP produced in mitochondria?
Via ETC.
148
How many protein complexes and proton pumps are there in the ETC?
Four large protein complexes and only three proton pumps.
149
What happens during electron transfer from NADH?
A hydride ion (hydrogen with 2e-) is removed from NADH and converted to a proton and two electrons.
150
What does build up of H+ ions in intermembrane space cause?
Membrane potential -> electrical gradient, pH gradient -> chemical gradient.
151
What happens when the H+ carrier spins rapidly within the stationary head of F1 ATPase?
F1 ATPase converts ADP to ATP, ATP synthesised in matrix is pumped back out to intermembrane space, ADP back into matrix, by ADP/ATP carrier protein on inner membrane.
152
Where are ATP synthase found in mitochondria?
Dotted along the cristae membrane.
153
What can mitochondrial dysfunction lead to?
Myoclonic epilepsy, ragged red fibre disease, leber hereditary optic neuropathy, mitochondrial encephalopathy, lactic acidosis, stroke like episode syndrome.
154
What are chloroplasts?
Organelles for photosynthesis, plants, algae, photosynthetic bacteria, light +CO2 - organic molecules, creator organelles for oxygenated world, bigger than mitochondria.
155
How do chloroplasts have a similar structure to mitochondria?
Double membrane, highly permeable outer membrane, tight intermembrane space.
156
What is the extra compartment that chloroplasts contain and what’s its function?
The thylakoid, contains molecular machinery for photosynthesis.
157
What are stacks of thylakoid called and what do these contain?
Grana, contains molecular machinery chlorophyll.
158
What light do chlorophyll absorb or reflect?
Absorb blue and red light, green light reflected (poorly absorbed).
159
What does the reflection of green light cause?
Plants look green.
160
How many photosystems do chloroplasts contain?
Two.
161
What does photosystem 2 do?
Water-spilling enzyme produces O2, excited electrons passed down via carrier to P1, electrochemical gradient, ATP synthesis.
162
What is the thylakoid membrane impermeable to?
ATP and NADPH, so no diffusing back into lumen.
163
What are ATP, NADPH and CO2 used for in the stroma?
To produce simple 3-carbon sugar, can be exported and used as precursors for synthesis of other metabolites.
164
What is the key enzyme is carbon fixation during the light independent reaction and what’s its characteristics?
RUBISCO, slow enzyme, most abundant.
165
What can happen to sugars made in the chloroplast?
Can be stored as starch or exported.
166
What can happen to exported sugars from the chloroplast?
Can be broken down and imported into mitochondria for efficient ATP synthesis.
167
What is the O2 released by chloroplasts and the CO2 released by mitochondria used for?
O2 used in oxidative phosphorylation, CO2 used in carbon fixation.
168
How are prokaryotic and eukaryotic ribosomes very similar in structure?
Two subunits, large and small, several million dalton in size.
169
What is the composition of ribosomes by mass?
2/3 rRNA, 1/3 ribosomal proteins.
170
What’s the structure of eukaryotic 80S ribosomes?
40S small subunit, 60S large subunit.
171
What is a Svedberg unit (S)?
Sedimentation rate in ultracentrifugation.
172
Where are ribosomes assembled?
In nucleolus.
173
What are the components of a ribozyme?
Ribonucleic acid + enzyme.
174
What determines the overall ribosomal structure?
rRNA is folded into highly compact and precise 3D structures.
175
Where are ribosomal proteins located?
On surface and fill gaps and crevices of folded RNA core.
176
What are the comparisons of prokaryotic vs eukaryotic ribosomes (respectively)?
2.3MDa vs 3.3, 54 proteins vs 79, 3rRNA vs 4, large subunit 50S vs 60S, 33 proteins vs 46 in large subunit, 23S rRNA vs 25, small subunit 30S vs 40S, 21 proteins vs 33 in small unit, 16S rRNA vs 18S.
177
What are the four binding sites that ribosomes contain?
One for mRNA, three for tRNA (A, P, E).
178
How many tRNA sites are occupied at once?
Two.
179
What is the first step in the ribosome translation mechanism?
tRNA charged with AA form base pair with comp codon on mRNA.
180
What is the importance of the A and P sites for tRNA being very close?
No stray base in between to maintain correct reading frame.
181
What is the second step of the ribosome translation mechanism?
Peptidyl transferase activity to form new peptide bonds between AAs.
182
What’s the third step in the ribosome translation mechanism?
Large subunit translocate relative to small, position tRNA in exit site.
183
What’s the fourth step in the ribosome translation mechanism?
Small subunit translocate exactly three bases back to original position.
184
How is the ribosome translation mechanism reset?
Ejection of used tRNA, empty A-site ready for next charged tRNA to bind.
185
When does translation repeat until?
Until reaching a STOP codon.
186
What are polyribosomes especially important for?
Highly translated proteins.
187
What happens in bacteria that makes ribosome action faster?
Simultaneous transcription and translation.
188
What is the overall microtubule (MT) structure?
Hollow tube, 13 protofilaments per MT, plus (B tubulin) and minus ends.
189
What are the basic building blocks of MTs?
Alpha (a) and beta (B) tubulin heterodimers.
190
What does each dimer of a MT make?
Two lateral contacts + two longitudinal contacts.
191
What are the characteristics and functions of a and B tubulin?
Highly conserved, each bind to one GTP molecule, heat to tail arrangement.
192
How similar are yeast and human tubulin to alpha and beta?
75% similar.
193
What’s the difference between a-bound GTP and B-bound GTP?
a-bound not hydrolysed, B-bound hydrolysed to GDP.
194
What are the two terms often used to describe MT dynamic?
Nucleation and polymerisation.
195
What is MT nucleation?
The initiation of MT (start from scratch).
196
What is MT polymerisation?
The growth of MT (elongation of existing MT).
197
What does spontaneous MT formation require?
Very high concentrations of a and B tubulin heterodimers.
198
What is MT nucleation in vivo catalysed by?
Third type of tubulin, y-tubulin.
199
What does y-tubulin + accessory proteins create?
y-tubulin ring complexes that promote MT nucleation.
200
What are y-tubulin ring complexes enriched in?
MT-organising centre in specific intracellular location.
201
What does MTOC stand for?
MT-organising centre.
202
What is the primary MTOC in most cells?
Centrosome.
203
What are centrosomes enriched in to promote MT nucleation?
y-tubulin ring complexes.
204
How do MTs grow form centrosomes?
Plus-end MT grows outward relative to centrosome.
205
Why are MTs described as being dynamically instable?
Some grow, some shrink, non-eqm behaviour.
206
What does dynamic instability behaviour of MT require?
Constant input of energy - GTP.
207
What’s difference between MT growth vs shrinkage?
Growth = GDP-bound B-tubulin > GTP-bound B-tubulin vs shrinkage = GTP-bound B-tubulin > GDP-bound B-tubulin.
208
Why is MT shrinkage termed a catastrophe?
Growing MT has a GTP-cap, when GTP in B-tubulin is hydrolysed, GDP-bound B-tubulin makes MT unstable = self-peeling.
209
How can plus end of growing MT be stabilised?
By attaching to another molecule or cellular structure.
210
What does dynamic instability of MTs allow?
Growing MT to explore the cellular space.
211
How does Taxol affect MT stability and dynamics and what is it used for?
Stabilises tubulin in MT lattice, no shrinkage, very potent anti-cancer drug.
212
How does Colchicine affect MT stability and dynamics and what is it used for?
Binds free tubulin dimers, prevent incorporation into MT (no MT polymerisation), used medicinally.
213
What do both taxol and colchicine result in?
Mitotic arrest (cell death).
214
How are MTs important for organelle positioning?
MT help position organelles in euk cell, e.g. golgi pulled inward along MT closer to nuclear periphery.
215
How are MTs important for vesicle movement?
Act as the highway for vesicle movement.
216
What does vesicle movement depend on?
Motor proteins.
217
What motor proteins bind to MT and how?
Kinesin (plus-end directed), dynein (minus-end directed).
218
How does the motor-binding domain provide energy for movement?
In pairs, bind and hydrolyse ATP.
219
How is an in vitro MT gliding assay performed?
Purified kinesin proteins immobilised on glass surface, fluorescent polymerised MT stabilised with Taxol, put together + ATP.
220
What are MT gliding assays important for?
Useful tool to characterise properties of motor proteins.
