After midterm Flashcards
(197 cards)
1
Q
Functions of the Nucleus
A
- Storage, replication, and repair of genetic material
- Expression of genetic material (transcription and splicing)
- Ribosome biosynthesis
2
Q
Structure of the Nucleus
A
Nuclear envelope
Nuclear membrane
Nuclear pores
Nuclear lamina
3
Q
Contents of the Nucleus
A
Chromatin
Nucleoplasm
Matrix
Nucleolus
4
Q
Nuclear envelope
A
Separates transcription and translation, acting as a selective barrier that limits movement of molecules
5
Q
Nuclear lamina
A
Thin meshwork of filamentous proteins bound to the inner membrane of the nuclear envelope by integral proteins
6
Q
Nuclear envelope consists of?
A
2 parallel phospholipid bilayers
7
Q
Outer membrane of nuclear envelope
A
Binds ribosomes and is continuous with rough ER
8
Q
Inner membrane of nuclear envelope
A
Bears integral proteins, which connect to the nuclear lamina
9
Q
Attachment site for chromatin and support structure for nuclear envelope?
A
Nuclear lamina
10
Q
Nuclear pores
A
Gateways between cytoplasm and nucleoplasm
11
Q
How many pores per nucleus and how are they formed?
A
3000 to 4000 formed when inner and outer membrane fuse
12
Q
What is the nuclear pore complex?
A
Complex protein structure composed of nucleoporins that fits into the pore and projects into cytoplasm and nucleoplasm
13
Q
Has octagonal symmetry?
A
Nuclear pore complex
14
Q
What are the functions of NPC?
A
- Passive diffusion of molecules smaller than 50 kDa(fast)
2. Regulated movement of larger molecules (slow)
15
Q
Regulated movement of proteins into the nucleus requires what?
A
A nuclear localization signal, a short stretch of positively charged amino acids within the protein
16
Q
Cellular function is acutely dependent upon?
A
Nuclear import and export (nucleocytoplasmic trafficking)
17
Q
What factors are needed for nuclear import?
A
- Nuclear localization signal in cargo protein
- Karyopherins
- Energy
- Ran-Small G proteins that act as chemical messengers and triggers
18
Q
Ran-Small G proteins attached to 3 phosphate groups are?
A
Turned on
19
Q
Ran-Small G proteins attached to 2 phosphate groups are?
A
Turned off
20
Q
Nuclear exports are mostly what?
A
- Protein and RNA molecules containing NES
- Exportins bound to NES
- Ran-GTP (hydrolysis of which releases the cargo)
21
Q
Nucleolus comprises what?
A
Clusters of ribosomal DNA gathered together as one to several nucleoli that produce ribosomes
22
Q
What are the functions of the nucleolus?
A
- Ribosome biogenesis
- Synthesis of rRNA
- Processing of rRNA
- Assembly of subunits (rRNA + proteins)
- Small 40S and large 60S subunits exported to the cytoplasm
23
Q
Cytoskeleton
A
Dynamic network of protein filaments that forms the cellular scaffolding as well as transport systems for organelles and vesicles
24
Q
Primary functions of cytoskeleton?
A
- Structural support
- Intracellular support
- Contractility and motility
- Spatial organization within cell
25
3 major elements of cytoskeleton?
1. Microtubules
2. Micro-filaments
3. Intermediate filaments
26
Microtubules
Largest cytoskeletal element comprising of polymers of alpha tubular and beta tubular proteins
27
What are the two MT ends?
1. Fast growing "+" end
| 2. Slow growing "-" end
28
Structural polarity of MT
Herero-Dimers are aligned in the same direction - structural polarity - important for growth/shrinkage and direction of movement of material
29
Motor proteins that use ATP to generate force and movement?
Dynein (- end directed)
| Kinesin (+ end directed)
30
Dynamic instability of MT and what it leads to?
MTs undergo dynamic assembly and disassembly which leads to rapid turnover of most MTs within the cell
31
MT catastrophe
Rapid occurrence of shrinkage at plus end
32
Formation of Mts is regulated and controlled by what?
Microtubule-associated proteins (MAPs)
33
Central sites of MT assembly?
Microtubule-organizing centers (MTOC)
34
Intermediate filaments
Stable fibrous proteins (relative to MTs) that are exclusive o multicellular animals and they provide structural support and mechanical strength
35
Polarity of intermediate filaments?
Not polar once assembled!!
36
How are intermediate filaments formed?
1. Alpha helical domains wrap around each other forming a rope-like dimer
2. Monomers are aligned in parallel
3. Dimers are polar molecules with different N and C termini
4. Dimers associate anti-parallel
37
Microfilaments
Smallest cytoskeleton element comprising of polymers of "actin" protein
38
Functions of microfilaments?
1. Maintenance of cell shape
2. Cell movement
3. Cytokinesis
4. Muscle contraction
39
G-actin monomers
Have a polar structure as the monomers are incorporated in the same orientation
40
F-actin filaments
Are polar with a + end and a - end
41
F-actin assembly is a result of what?
G-actin polymerizing reversibly due to nucleation or elongation
42
Nucleation
SLOW
| G-actin>dimers>trimers>short filaments
43
Elongation
FAST
| Monomers add to both ends (faster at + end)
44
Polymerization and structure organization of F-actin filaments are regulated by what?
Actin-bonding proteins
45
In vesicular transport
All motor proteins are involved
46
Myosin
F-actin associated motor protein that must move towards the + end and is divided into conventional and unconventional myosins
47
Unconventional myosins
Generate force and contribute to motility in non-muscle cells
48
Extracellular Space
Extends outwards from the surface of the plasma membrane and contains a variety of secreted materials (from the cell) that influence cellular behaviour
49
What does the Extracellular space do?
1. Mediates cell-cell and cell-extracellular matrix (ECM) interactions
2. Provides mechanical protection
3. Serves as a barrier
4. Binds regulatory factors
50
Cells of bacteria, plants, and fungi are surrounded by a ____ ____, which is considered an ECM
cell wall
51
Plant cell walls are composed of what?
1. Cellulose
2. Hemicellulose
3. Pectin
4. Proteins
52
Plant cell walls do what?
1. Provide structural support to the cell and to the organism as a whole
2. Protect cell from mechanical damage and pathogens
3. Contain biochemical information for the cell
53
What does it take to make life?
1. Information
2. Chemistry
3. Compartments
54
Cell theory
1. Cell is the structural unit of life
2. All organisms are composed of one ore more cell types
3. Cells can arise ONLY by the division of pre-existing cells
55
Basic properties of cells
1. Highly complex and organized
2. Activity controlled by a genetic program
3. Can reproduce
4. Assimilate and utilize energy
5. Carry out many chemical reactions
6. Engage in mechanical activities
7. Respond to stimuli
8. Capable of self-regulation
9. Evolve
56
Two classes of cells on Earth:
1. Prokaryotic
| 2. Eukaryotic
57
Prokaryotic cells
Structurally simpler
| -Bacteria
58
Eukaryotic cells
Structurally more complex
| -Protists, fungi, plants, animals
59
Compartments
Membrane bound structures dedicated to a particular function
60
Components are not...
bound by membranes
61
Enables movement of molecules into and out of the nucleus
Nuclear pore complex
62
Contributes to cell shape and movement, provides structural support and supports the transport of material
Cytoskeletal elements
63
Viruses
Non-cellular macromolecular packages that can function and reproduce ONLY within living cells (tiny machines that take over cells)
64
Virion
Virus existing outside of cells as an inanimate particle
65
What is a vision comprised of?
- Small amount of DNA or RNA
| - Protein capsule
66
What defines the cell types that a virus can infect and the host range?
Specific proteins on a cell surface
67
What does a virus do once inside a cell?
Hijacks cellular machinery to synthesize nucleic acids and proteins (assembles new virus particles)
68
Two main types of viral infection?
1. Lytic
| 2. Non-lytic
69
Lytic
Production of virus particles ruptures and kills cell
70
Non-lytic (or integrative)
Viral DNA is inserted in host genome and viral progeny bud at cell surface. Cell can survive but often with impaired function
71
Provirus
Viral DNA inserted in host genome
72
Functions of plasma membranes
1. Cell boundary
2. Define/enclose compartments
3. Control movement of material into/out of cell
4. Allow response to external stimuli
5. Enable interactions between cells
6. Provide scaffold for biochemical activities
73
Trilaminar
3 layered structure (oreo cookie) of incredibly COMPLEX plasma membrane (6nm thick)
74
Fluid mosaic model
Model of biological membranes that says individual lipid molecules move and diverse particles penetrate the lipid layer
75
Structure of biological membranes
- Bilayer of amphipathic lipids
- Proteins
- Components are mobile and can interact
76
Amphipathic
Having both hydrophobic and hydrophilic regions
77
Due to amphipathic nature all membranes are capable of what?
Self-assembly
78
Different membranes contain what?
Different types of lipids and proteins
79
Myelin sheath
Modified plasma membrane structure that wraps around and around forming insulation
80
3 classes of membrane proteins
1. Integral
2. Lipid-anchored
3. Peripheral
81
Integral membrane proteins
Span the lipid bilayer (i.e. stick through membrane)
82
What do integral membrane proteins do?
-Act as receptors, transporters, channels and ETC
83
Lipid-anchored proteins
Attach to a lipid in the bilayer (i.e. they aren't stuck in membrane but attached to it through covalent forces)
84
Peripheral membrane proteins
Associate with the surfaces of the lipid bilayer through electrostatic charges
85
How could you easily strip off peripheral proteins?
Add salt to membrane because they are associated through electrostatic charges
86
Transduction
Communication between cells
87
What does it mean that biological membranes are asymmetrical?
They are different on the inside and outside (because they have different functions)
88
In many plasma membranes the outer leaflet contains what?
Glycolipids and glycoproteins
89
Glycolipids and glycoproteins
Lipids and proteins with carbohydrate attached
90
Membrane fluidity is determined by what?
Nature and temperature of lipids in membrane
91
Unsaturated lipids
Increase fluidity
92
Saturated lipids
Reduce fluidity
93
Warming membranes
Increases fluidity
94
Cooling membranes
Decreases fluidity
95
Liquid crystal state
Warm
96
Crystalline gel state
Cool
97
Why is membrane fluidity so important?
It is crucial to cell function
98
Balance between ordered structure and disordered structure allows for what?
1. Mechanical support and flexibility
2. Dynamic interactions between membrane components (proteins can come together reversibly)
3. Membrane assembly and modification
99
In response to changes in temperature, lipid composition of membranes can be changed how?
1. Desaturation of lipids (kink=harder to make crystals)
| 2. Exchange of lipid chains
100
Cholesterol
Totally hydrophobic --> hangs out inside membrane
101
Why is cholesterol needed?
To regulate membrane fluidity
102
What does cholesterol do?
Alters packing and flexibility of lipids
103
If cholesterol is added to a liquid crystal membrane fluidity will...
decrease
104
If cholesterol is added to crystalline gel membrane fluidity will...
increase
105
Lipid Rafts
Membrane microdomains (i.e. smlal areas that are enriched in certain types of lipids)
106
Movement of substances across cell membranes...
is HIGHLY controlled
107
What crosses membranes relatively easily?
Small, uncharged molecules (i.e. O2, CO2, NO, H2O)
108
What cannot cross membranes easily?
Large, polar, or charged compounds
109
How is transport controlled?
There are 4 main mechanisms:
1. Simple diffusion
2. Diffusion through a channel
3. Facilitated diffusion
4. Active transport
110
Simple diffusion
```
Passive transport (no energy involved) simply cross membrane
-very small, uncharged molecules
```
111
Diffusion through a channel
Protein channel allows something to simply cross membrane (passive)
-small charged molecules (ions)
112
Facilitated diffusion
Compound binds specifically to transporter (integral membrane protein) that changes conformation and releases compound on other side of membrane (passive)
-glucose
113
Active transport
Compound moves AGAINST a concentration gradient requiring the input of energy (ATP) Compound binds specifically to transporter (integral protein) that changes conformation and releases compound on other side of membrane
Na+/K+ ATPase
114
Ion channels
Formed by integral membrane proteins and are selective allowing only one type of ion to pass (channels are often gated)
115
Gated channels
Can exist in either an open or closed position
116
Voltage gated channels
Channel responds to changes in charge across membrane
117
Ligand-gated channels
Channel responds to binding of specific molecule (ligand)
118
Mechano-gated channels
Channel responds to physical force on membrane
119
Extracellular matrix
Organized network of material produced and secreted by cells
120
Glycocalyx
Assembly of carbohydrate groups attached to proteins and lipids on outside of the plasma membrane
121
What does glycocalyx do?
1. Mediates cell-cell and cell-ECM interactions
2. Provides mechanical protection
3. Serves as a barrier to some particles
4. Binds regulatory factors
122
What functions does ECM serve?
1. Sites for cell attachment
2. Physical support for cells
3. Contains regulatory factors (signals)
4. Separate/define tissues
123
Proteoglycans
Type or glycoprotein with chains of polysaccharides
124
Endosymbiont theory
The hypothesis that certain organelles of a eukaryotic cell - most notably mitochondria and chloroplasts - evolved from smaller prokaryotic cells that had taken up residence in the cytoplasm of larger host cell
125
Invagination
The infolding of plasma membrane
126
Mitochondria
Burn food you eat to extract ATP and participate in apoptosis
127
Outer mitochondrial membrane
- Contains many enzymes with diverse metabolic functions
| - Contains porins
128
Porins
Large channels that when open mitochondrial membrane is freely permeable
129
Inner mitochondrial membrane
- High protein/lipid ratio (3:1)
- Double layered folds
- Rich in cardiolipin
130
Cristae
Double layered folds that increase membrane surface area
131
Cardiolipin
Phospholipid characteristic of bacterial membranes
132
What 4 pieces of mitochondrial evidence support endosymbiont theory?
1. Prokaryotic ribosomes
2. Own genome (DNA)
3. Double membrane
4. Cardiolipin
133
What are the aqueous compartments of mitochondria?
1. Intermembrane space
| 2. Matrix
134
Oxidative phosphorylation
ATP synthesis in mitochondria
1. Electron transport and proton pumping generates electrochemical gradient
2. Proton movement down gradient powers ATP synthesis
135
Apoptosis
A normal occurrence in which a coordinated sequence of events leads to death of a cell
136
What is apoptosis characterized by?
1. Shrinkage of cell
2. Blebbing of the plasma membrane
3. Fragmentation of DNA and nucleus
4. Loss of attachment to other cells
5. Engulfment by phagocytosis
137
Blebbing
Pieces of plasma membrane start to come off like blobs unfolding
138
Pathway of apoptosis is highly coordinated why?
To get rid of cells that aren't supposed to have apoptosis happening in them
139
Proapoptotic proteins
Stimulate mitochondria to leak cytochrome c (proteins)
140
Release of cytochrome c does what?
Commits cell to apoptosis!
141
Capases
Enzymes that chew up different things
- destroy cytoskeleton
- disrupts cell adhesion
- destroys lamina
- activates DNase
142
Is the mitochondria part of cytoplasm?
YES
143
Cytoplasmic endomembrane systems
Within cytoplasm there is membrane bound organelles and vesicles and an extensive network of membranous canals and stacks of "sacs"
144
GFP
Green fluorescent protein genetically fused with a cellular protein to track cell components
145
Construction of a GFP-tagged protein
Take genes of interest, put in plasmid, inject it into nucleus to be transcribed or translated and you get a fusion protein (coding sequence for protein of interest + coding sequence for GFP)
146
Vesicular Transport (Trafficking)
- Transport of material between compartments
- Utilizes transport vesicles
- Targeted movement
147
Transport vesicles
Small, spherical, membrane-enclosed organelles that bud off donor compartment and fuse with acceptor compartment
148
How is movement is directed?
Using cytoskeleton and motor proteins and sorting signals recognized by receptors
149
What are the steps of trafficking vesicles?
1. Movement of vesicle
2. Tethering vesicle to target compartment
3. Docking of vesicle to target compartment
4. Fusion of vesicle and target membrane
150
Rabs
Proteins that tether vesicle to target compartment
151
SNAREs
Proteins that dock vesicle to target compartment
152
Organelle to plasma membrane
Exocytosis
153
Plasma membrane to organelle
Endocytosis
154
Endoplasmic reticulum
Inter-connected network of membrane-enclosed tubules and flattened sacs
155
Lumen of ER is separate from what?
Cytosol
156
Continuous with the outer membrane of the NUCLEUS
ER membrane
157
Smooth ER vs. Rough ER
Smooth ER is sort of like a specialization zone and it has less ribosomes on the outside (i.e. smooth surface)
158
What are the functions of the SER?
1. Production of steroid hormones
2. Detoxification
3. Sequestration (storage) of Ca2+
159
Why are there lots of ribosomes on RER?
It has to do with their function! Site for making lots of proteins
160
What are the functions of the RER?
1. Protein synthesis, modification and transport
2. Synthesis of membrane phospholipids
3. Glycosylation of proteins (addition of carbohydrate chains)
4. Protein folding
161
Where does all protein translation begin?
On free ribosomes
162
What proteins are synthesized in the RER?
Secreted proteins, integral membrane proteins, soluble proteins associated with inside of endomembrane system
163
How is the site of translation determined?
Ribosomes are targeted to the ER membrane by a signal sequence
164
What is the signal sequence?
Located at proteins amino-terminus (N-terminus) and contains several consecutive hydrophobic amino acids. Directs synthesis to ER moving through channel
165
What happens after translation of signal sequence?
Cotranslational protein import
166
Cotranslational protein import
1. Signal recognition particle binds to signal sequence and translation STOPS
2. Targeting of translation complex to ER (SRP binds to SRP receptor)
3. SRP is released and ribosome binds translocon (protein synthesis resumes)
4. Polypeptide enters the ER (through translocon) as it is translated
167
Translocon
Complex of proteins
168
SRP
Complex of proteins
169
Once a protein is fully synthesized and properly folded what are its 2 options?
1. Retained in the ER if that is where the protein functions
2. Transported from ER to the golgi complex for further modification and delivery to distal parts of biosynthetic/secretory pathway
170
ERGIC
Region between ER and golgi complex where transport vesicles fuse to form VTCs
171
Vesicular-Tubular Clusters
Larger fused vesicles and interconnected tubules
172
Transport from ER to golgi complex exit sites?
Membrane and ER lumen bud off to form transport vesicles
173
Material moves from ER to where?
Golgi then plasma membrane and other compartments
174
Golgi complex
Processing plant of cell (i.e. modification and packaging)
175
WAll protein synthesis starts where?
CYTOPLASM
176
Structure of golgi complex
Smooth flattened disk-like cisternae
177
CGN vs. TGN
CGN acts as a sorting station and TGN sorts protein into different types of vesicles
178
How are proteins modified as they travers the Golgi?
Step-wise (i.e. different cistern of the Golgi contain different enzymes that modify proteins)
179
Once proteins are fully processed what happens?
They are exported from the trans cistern and enter the trans-Golgi network and are sorted and delivered to final destinations
180
Transport vesicles are coated, why?
1. Helps form vesicle
| 2. Helps select cargo
181
COP proteins
Coat on transport vesicles
182
How do COPI and COPII proteins carry out their functions?
They assemble on the cytosolic surface of donor membranes at sites where budding takes place
183
Where do Cathrin-coated vesicles move?
From TGN to other vesicles
184
COPI-coated vesicles move?
In retrograde direction
185
COPII-coated vesicles move?
In anterograde direction
186
Lysosomes
Little digestive organelles
187
What is the function of lysosome?
1. Autophagy
| 2. Degradation of internalized material
188
Autophagy
Organelle turnover (i.e. destruction of organelles and their replacement)
189
How does autopahgy work?
Lysosome fuses with ER-edrived autopahgic vacuole (forming autolysosome) and contents are enzymatically digested (forming residual body)
190
Lipofuscin granules
Retained in residual body (analagous to age spots)
191
Structure of plant vacuoles
Fluid-filled and membrane-bound
192
Function of plant vacuoles?
1. Intracellular digestion
2. Storage
3. Mechanical support/turgor pressure
193
Microtubule-associated Proteins
Several different proteins that bind MTs
194
What do MAPs do?
Modulate assembly and function and mediate interactions with other cellular structures
195
2 classes of MAPs
1. Motor MAPs
| 2. Non-motor MAPs
196
Motor MAPs
Kinesin and dynein
- Use ATP to generate force
- Move material along MT track
- Generate sliding force between Mts
197
Non-motor MAPs
Tau
| -Control MT organization in cytosol
