Eukaryotes, cell structure Flashcards
1
Q
How do bacteria replicate?
A
Binary fission
2
Q
What is a membraneless cellular compartment called?
A
A biomolecular condensate
3
Q
Give an example of a biomolecular condensate
A
Rubisco enzyme
4
Q
What 2 structures do biomolecular condensates require?
A
Scaffold macromolecules and client proteins
5
Q
Give the overall structure of the nuclear envelope
A
Outer nuclear membrane
Perinuclear space (20-40nm)
Inner nuclear membrane
6
Q
How do proteins enter the nucleus? What do they require?
A
They require a Nuclear Localization Signal (NLS) and are transported by importin through nuclear pores
7
Q
What can passively diffuse through the nuclear pore?
A
Small molecules like metal ions and ATP (cutoff: ~30,000 Da or ~9 nm diameter)
8
Q
What is the role of importin in nuclear import?
A
It binds to NLS-containing proteins and facilitates their entry into the nucleus
9
Q
What regulates nuclear import and export? Briefly state how
A
Ran-GTPase, a protein that switches between GTP- and GDP-bound states
10
Q
What gradient does nuclear export require?
A
Gradient of Ran-GTP and Ran-GDP across nuclear membrane
11
Q
What is the NES?
A
Nuclear Export Signal; required for protein export via exportin and Ran-GTP
12
Q
What is the nuclear lamina?
A
A fibrous mesh of intermediate filaments beneath the inner membrane, maintaining nuclear shape
13
Q
How is chromatin organised in the nucleus?
A
Each chromosome occupies a distinct “territory,” and associates with the nuclear lamina
14
Q
What are the 3 types of endoplasmic reticulum?
A
Rough ER, Smooth ER, and Transitional ER
15
Q
What is the function of the rough ER?
A
Protein production and folding
16
Q
What is the function of the smooth ER?
A
Lipid biosynthesis, detoxification (e.g., cytochrome P450), and calcium storage in muscle (sarcoplasmic reticulum)
17
Q
What is the transitional ER?
A
Specialized regions that form vesicles to transport proteins/lipids to the Golgi
18
Q
What is the basic structure of the golgi?
A
Stacked cisternae: cis (entry), medial, and trans (exit)
19
Q
What happens to the Golgi during cell division?
A
It breaks up and later reforms
20
Q
What is the function of the Golgi apparatus?
A
Modifying, sorting, and packaging proteins and lipids for transport
21
Q
What is the vesicular transport model?
A
Cargo moves between stable cisternae via vesicles; enzymes stay in place
22
Q
What is the cisternal maturation model?
A
Cisternae themselves mature and move; enzymes move backward via vesicles
23
Q
What determines where a vesicle goes?
A
Specific protein coats and signals on cargo/vesicle
24
Q
Name the 4 types of coated vesicles and their roles
A
Clathrin-coated: Golgi/endosome to membrane.
COPI-coated: Retrograde transport from Golgi.
COPII-coated: Anterograde from ER.
Retromer-coated: Endosome retrieval to Golgi.
25
What structure constitutes more than half the total membrane of the average animal cell?
The endoplasmic reticulum
26
What is the role of the transitional ER?
To produce vesicles with proteins or lipids for transport to Golgi apparatus
27
What is the cis-complex of the Golgi apparatus?
Adjacent to ER - receives proteins from the ER
28
Where does the trans complex of the Golgi apparatus sit?
Toward the plasma membrane
29
In 1 word, what is the structure of a clathrin coated vesicle?
Triskelion
30
What is an SRP?
A signal recognition particle
31
What are the 3 main modes of protein transport across a membrane?
Gated transport (e.g., nuclear pores)
Protein translocation (e.g., into the ER lumen during synthesis)
Vesicular transport (using membrane-bound vesicles)
32
What guides a protein with an ER signal into the ER?
SRP (Signal Recognition Particle), which brings the ribosome to the ER translocator via the SRP receptor
33
What are the key steps of co-translational translocation?
ER signal sequence on the new peptide is recognized by SRP.
SRP binds to SRP receptor on the ER membrane.
Ribosome is guided to the translocator channel.
Protein is synthesized directly into the ER lumen.
Protein unfolds during entry and refolds inside the ER.
34
What are the 4 steps in vesicle formation?
Cargo selection
Membrane bending
Protein coating
Coat disassembly
35
What prevents complete entry of a transmembrane protein into the ER lumen?
The Stop-transfer sequence
36
What happens to the protein during translocation into the ER?
It unfolds to pass through the translocator and refolds afterward
37
What mediates vesicle fusion?
v-SNAREs (on vesicle) and t-SNAREs (on target membrane) zip together, forcing membrane fusion
38
How is SNARE pairing highly specific?
Only complementary v-SNAREs and t-SNAREs can interact and zip together
39
What proteins are involved in vesicle tethering and docking?
Rab GTPases interact with tethering proteins on the target membrane
40
What 3 things determine a vesicle's location?
Coat proteins = address label
Phospholipid profile = postcode
Rab GTPases = postman
41
What are the 2 types of exocytosis?
Constitutive: continuous delivery of membrane components.
Regulated: vesicles released in response to a stimulus (e.g. insulin, histamine)
42
How is insulin secretion regulated in terms of exocytosis?
High glucose → ATP ↑ → K⁺ channel closes → Ca²⁺ influx → vesicles with insulin fuse with membrane
43
What triggers histamine release from mast cells?
A stimulus detected by surface receptors triggers regulated exocytosis of histamine granules
44
What are the 2 main types of endocytosis?
Phagocytosis: uptake of large particles ("eating")
Pinocytosis: uptake of fluid and small molecules ("drinking")
45
How does a cell balance volume while pinocytosing its own membrane?
Through membrane recycling and regulated surface area dynamics
46
What is ACE2?
A receptor for SARS-CoV-2 and a regulator of blood pressure and fluid homeostasis, highly expressed in lung, heart, and kidney cells
47
What are endosomes?
Intracellular sorting organelles in eukaryotic cells that play a crucial role in the endocytic pathway, transporting molecules and lipids between the plasma membrane, Golgi apparatus, and lysosomes
48
What are early and late endosomes?
Early: near the plasma membrane; Late: deeper in cytoplasm. Endosomes acidify over time (pH 5–6) via H⁺ pumps
49
What are lysosomes?
Acidic compartments with hydrolytic enzymes (≈40 types) to degrade proteins, lipids, nucleic acids, and sugars
50
How is the acidic environment in lysosomes maintained?
Using an ATP-driven proton (H⁺) pump
51
What is the plant vacuole and what are its functions?
Large, fluid-filled organelles (30–90% of cell volume) used for storage, degradation, turgor pressure regulation, and pH homeostasis
52
What do peroxisomes contain?
Oxidative enzymes like catalase and urate oxidase
53
What is a key product and function of peroxisomes?
Hydrogen peroxide (H₂O₂), used to oxidize lipids and detoxify compounds (e.g., alcohol)
54
How are peroxisomes formed?
Via vesicular transport of peroxisomal membrane proteins from the ER
55
What kind of cell has no mitochondria?
Red blood cell
56
What kind of cells have over 1000 mitochondria per cell?
Liver
57
What is the inner mitochondrial membrane folded into?
Cristae
58
How many protein complexes and proton pumps are there in the ETC?
4 complexes and 3 pumps
59
What enzyme converts ADP to ATP in the ETC?
F1 ATPase
60
What 3 components do chloroplasts have in common with mitochondria?
Double membrane, highly permeable outer membrane, tight intermembrane space
61
What compartment contains the molecular machinery for photosynthesis?
Thylakoid
62
What is a thylakoid stack called?
Granum
63
What is the thylakoid membrane impermeable to?
ATP and NADH
64
What simple 3 carbon sugar is produced in the stroma as a precursor for other molecules?
Glyceraldehyde-3-phosphate
65
What is the most abundant enzyme in the world?
RUBISCO
66
What is a ribosome made up of?
RNA and proteins
67
What is the size of the eukaryotic ribosome? What is each subunit?
80S ribosomes
40S (small) subunit
60S (large) subunit
68
What is the Svedberg unit?
Sedimentation rate in ultracentrifugation
69
What is the size of the prokaryotic ribosome? What is each subunit?
70S
Small subunit 30S
Large subunit 50S
70
How many tRNA binding sites are there on a ribosome?
3
71
What are the names of the tRNA binding sites on a ribosome?
EPA
72
What is the advantage of having the A and P sites of a ribosome very close together?
No stray base in between (maintain
correct reading frame)
73
What enzyme has a large amount of activity in the ribosomal translation mechanism?
Peptidyl transferase
74
What bonds connect amino acids?
Peptide
75
How many protofilaments are there per microtubule?
13
76
What is the basic building block of a microtubule?
⍺ & β tubulin heterodimer
77
Which end of the microtubule is beta-tubulin?
Plus end
78
How similar % are yeast and human tubulin to each other?
75%
79
Which tubulin-bound GTP gets hydrolysed to GDP in microtubule growth? Alpha or beta?
Beta-tubulin bound GTP is hydrolsed to GDP
80
What are the 2 terms used commonly to describe microtubule dynamics?
Nucleation
Polymerisation
81
What 3 things does microtubule nucleation require?
Gamma-tubulin
Accessory proteins
High concentrations of alpha beta tubulin heterodimers
82
What complex promotes microtubule nucleation?
Gamma-tubulin ring complex
83
What is the primary MT organising centre in most cells?
Centrosome
84
What does the Dynamic Instability behaviour of MT require?
Constant energy input - GTP
85
How does microtubule catastrophe occur?
When GTP in β-tubulin is hydrolysed, GDP-bound β-tubulin makes MT unstable
86
What does a growing microtubule contain?
A GTP cap
87
How can the plus end of a growing MT be stabilised?
Attaching to another molecular or cellular structure
88
What does taxol do?
Stabilises microtubules, so there is no shrinkage
Works as a very potent anti-cancer drug
89
What does colchicine do?
Binds free tubulin dimers
prevent MT polymerisation
Used for gout
90
What are the motor proteins that bind MTs? What directions do they take?
Kinesin (plus-end directed)
Dynein (minus-end directed)
91
What process do motor proteins use to move?
ATP hydrolysis
92
What part of chromosomes do MTs attach to?
Kinetochore
93
What structure forms the base of cilia and flagella?
A centriole
94
Describe the organisation of microtubules in cilia and flagella
“9 + 2” arrangement
9 outer MT doublets + 2 central MT pairs
95
What proteins connect the outer doublets of microtubules in cilia and flagella?
Nexins
96
How do cilia and flagella move?
MT doublets are linked (by linking proteins)
Dynein movement results in MT bending of
doublets, rather than sliding
Creating waves or beating motions
97
What 5 places can you find actin filaments?
Microvilli (e.g. intestinal epithelial cells)
Contractile Bundles in cytoplasm
Filopodia of migrating cells
Contractile ring during cell division
Contractile bundles stained with fluorescently-labelled Phalloidin
98
Describe the structure of actin filaments
Made up of actin monomers
Actin monomer within the filaments have the same orientations
Two-stranded helical protofilament with a
twist repeating every 37nm
Extensive lateral interactions between two
strands prevent strand separation
99
What does the head to tail structure of actin monomers create?
Polarity
100
What is bound in the deep cleft of an actin monomer?
Either ADP or ATP
101
Which end do microfilaments grow faster?
Plus end (barbed)
102
Describe the process of polymerisation of an actin filament (treadmilling)
Actin monomer in cytosol carry ATP,
ATP is hydrolysed to ADP when actin monomer assembles into growing actin filament
ADP remains trapped within filament until the actin monomer dissociates from filament
103
Why does actin treadmilling occur?
Actin-ATP & Actin-ADP have different conformation and binding affinities
Actin-ADP is less stable, so has a lower affinity to neighbour, easier to dissociate from filament
104
When does actin treadmilling occur?
When actin monomer concentration is intermediate
Rate of addition at plus end = Rate of
loss at minus end
105
What are the 4 steps of the general cell migration model?
Protrusion
Adhesion
Contraction
Release
106
What is the role of bundling proteins in actin structures?
Bundling proteins stabilize actin filaments in structures such as filopodia and microvilli
107
Which bundling protein is specifically associated with filopodia?
Fascin
108
What are filopodia?
Slender, finger-like cytoplasmic extensions that protrude from the cell membrane, primarily composed of actin filaments
109
Which bundling protein is found in the microvilli of gut epithelium?
Vilin
110
What are myofibrils composed of?
Multiple sarcomeres
111
What are muscle fibres composed of?
Multiple myofibrils
112
What structure does Myosin-II form in skeletal muscle?
Dimers that assemble into the thick filament
113
How does myosin-II generate force?
By coupling ATP hydrolysis to conformational changes that allow it to "walk" along actin filaments
114
What is the most durable kind of cytoskeleton?
Intermediate filaments
115
Describe the structure of an intermediate filament
1. Alpha-helical monomer (no nucleotide binding)
2. Coiled-coil dimers (Two parallel coils wound together)
3. Two dimers side-by-side
- antiparallel tetramer
- Tetramer held by lateral interactions
4. Association with another tetramer
5. 8 tetramers twisted into filament
116
What are the 4 families of intermediate filaments?
Keratin
Vimentin
Neurofilaments
Nuclear lamins
117
How do keratin filaments link directly through cells?
Through desmosomes
118
What acts as the glue between different cytoskeletons?
Plectin
119
Why is binary fission important for prokaryotes?
It allows rapid asexual reproduction roughly every 20 minutes.
120
What limits the size of prokaryotic cells?
Surface area to volume ratio diffusion rates and the need to maintain high concentrations of enzymes and substrates.
121
How does SA:vol ratio affect prokaryotic cells?
Smaller cells have a higher surface area relative to their volume allowing efficient exchange of nutrients and gases.
122
Why does diffusion limit prokaryotic cell size?
As cell size increases diffusion rates decrease making molecular transport inefficient.
123
Why are high concentrations of compounds needed in cells?
To allow biochemical reactions to occur efficiently.
124
What is compartmentalisation in eukaryotic cells?
Division of the cell into membrane-bound organelles allowing localisation and concentration of cellular processes.
125
Why is compartmentalisation important?
It enables differentiation and specialisation of cell functions and supports complex multicellular organisms.
126
What are organelles?
Subcellular compartments often membrane-bound with specific structures and functions.
127
What do transport systems in eukaryotic cells require?
ATP and organisation for cell signalling and intracellular movement.
128
What are biomolecular condensates?
Non-membrane compartments formed by aggregation of macromolecules like proteins or nucleic acids.
129
How do biomolecular condensates form?
Scaffold molecules like RNA or proteins form weak reversible interactions creating dynamic liquid-like droplets.
130
What is phase separation?
The coexistence of different biomolecular condensates within a larger structure.
131
Give an example of a biomolecular condensate
Rubisco enzyme compartments in photosynthetic bacteria or the pericentriolar material of centrosomes.
132
What microscopes have advanced our study of cells?
From Hooke's microscope to light confocal and electron microscopes.
133
What does digitisation allow in microscopy?
Still images and live-cell imaging.
134
What is GFP and why is it useful?
Green fluorescent protein from jellyfish used to label proteins in living cells.
135
What is the origin theory for mitochondria and chloroplasts?
Endosymbiosis where an archaeon engulfed bacteria leading to a symbiotic relationship.
136
Why do mitochondria and chloroplasts support endosymbiosis theory?
They have double membranes and their own DNA.
137
What makes archaea like Asgard lineage important?
Their genomes resemble eukaryotes and they divide slowly and form protrusions.
138
What is the nuclear envelope?
A double membrane that encloses the nucleus.
139
What is the structure of the nuclear envelope?
Outer membrane perinuclear space inner membrane.
140
What are nuclear pores?
Fusion points of inner and outer membrane gated by nuclear pore complexes.
141
What is the nuclear pore complex (NPC)?
A large protein structure that controls transport into and out of the nucleus.
142
How do small molecules move through NPCs?
They diffuse freely.
143
How are large proteins transported into the nucleus?
They must have a nuclear localisation signal (NLS) recognised by importins.
144
What is importin?
A receptor protein that binds NLS-containing proteins and transports them into the nucleus.
145
What regulates nuclear import?
Ran-GTPase system with Ran-GTP in nucleus and Ran-GDP in cytosol.
146
How does Ran-GTPase work?
Ran-GTP binds importin in nucleus to release cargo Ran-GDP releases importin in cytosol.
147
What is nuclear export?
Transport of RNA and proteins out of the nucleus using exportin and Ran-GTPase.
148
What is the nuclear lamina?
A fibrous mesh supporting the inner nuclear membrane and nuclear shape.
149
What happens to the nuclear lamina during division?
It disassembles and reforms.
150
What associates with the nuclear lamina?
Chromatin associates in discrete non-random locations.
151
What is the nucleolus?
A membraneless biomolecular condensate that synthesises rRNA and assembles ribosomes.
152
What is the endoplasmic reticulum (ER)?
An organelle continuous with the outer nuclear membrane with rough and smooth regions.
153
What is the function of rough ER?
Protein synthesis and folding with ribosomes on the surface.
154
How are proteins processed in rough ER?
They are translocated into the ER lumen modified and quality-checked.
155
What is the function of smooth ER?
Lipid synthesis metabolism and detoxification.
156
What is the sarcoplasmic reticulum?
Specialised smooth ER in muscle storing calcium ions.
157
What is the transitional ER (t-ER)?
ER region forming vesicles to send proteins and lipids to the Golgi apparatus.
158
What is the structure of the Golgi apparatus?
Stacks of flattened membrane sacs called cisternae.
159
What is the cis face of the Golgi?
The side facing and receiving vesicles from the ER.
160
What is the trans face of the Golgi?
The side directing vesicles toward the plasma membrane or other locations.
161
What are the functions of the Golgi?
Protein modification sorting and directing cellular traffic.
162
What are the two models of Golgi trafficking?
Vesicular transport model and cisternal maturation model.
163
What is the vesicular transport model?
Cargo moves through Golgi cisternae while resident enzymes stay in place.
164
What is the cisternal maturation model?
Cisternae move forward carrying cargo while enzymes are recycled.
165
What are coated vesicles?
Vesicles with protein coats for directed transport between organelles.
166
What are clathrin-coated vesicles?
Vesicles from Golgi or plasma membrane with triskelion structures.
167
What are COPI vesicles?
Vesicles for retrograde transport from Golgi to ER.
168
What are COPII vesicles?
Vesicles for anterograde transport from ER to Golgi.
169
What is the retromer complex?
A coat system that returns cargo from endosomes to the Golgi or plasma membrane.
170
What is the VSVG-GFP experiment?
A temperature-sensitive protein model to study protein trafficking.
171
How does temperature affect VSVG-GFP?
Misfolded at 40C trapped in ER refolds at 32C and moves to Golgi.
172
What does the VSVG-GFP experiment show?
The dynamic process of protein movement through ER Golgi and out to membrane.
