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BSCI 330: Cell Biology > Post Exam 3 Material > Flashcards

Post Exam 3 Material Flashcards

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1
Q

Epigenetic Inheritance

A
  • Any heritable difference that does not rely on changes in a DNA sequence
  • Basis for cell differentiation
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2
Q

Mechanisms that contribute to epigenetic changes

A
  • Positive feedback loop for regulatory proteins
  • Covalent modification to histones and chromatin structure
  • Methylation of DNA on cytosine residues
  • Prions
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3
Q

Positive feedback loop of a regulatory protein

A

Once a protein is made, it maintains its own expression which provides a stable phenotype

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4
Q

Covalent modification of histones

A

Recruits enzymes that maintain chromatin structure in daughter cells

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5
Q

Methylation of cytosine

A
  • Suppresses gene transcription
  • Methyltransferase maintains methylation patterns during DNA replication
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6
Q

Protein Aggregation (Basis of Prion Disease)

A
  • Proteins can adopt an alternate form that induces self-aggregation and catalyzes a conformational change in normally folded protein molecules to make them misfolded (prions)
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7
Q

Eukaryotic Cell Compartments

A

Subdivided into functionally distinct membrane-enclosed compartments

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8
Q

Gated Transport (Nucleus)

A
  • Bidirectional between cytosol and nucleus
  • Occurs through nuclear pore complexes
  • Selective gates that actively transport macromolecules
  • Allows free diffusion of smaller molecules
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9
Q

Transmembrane Transport (Mitochondria)

A
  • Unidirectional between cytosol and organelles that are topologically different
  • Occurs through membrane-bound protein translocators
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10
Q

Vesicular Transport

A
  • Bidirectional from ER to Golgi and to designated locations
  • Among topologically similar organelles
  • Occurs through vesicles
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11
Q

Topological Similarities

A

Compartments with similar transport mechanisms

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12
Q

Sorting signals and receptors

A
  • The movement of proteins between organelles is mediated by sorting signals and receptors
  • These signals are recognized by protein-sorting receptors
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13
Q

Nucleoporins

A

Contain unstructured regions that restrict the passage of large macromolecules between the cytosol and nucleus

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14
Q

Initiation of nuclear import

A

Nuclear localization signals (NLS) within cargo must be recognized by nuclear import receptors

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15
Q

Cargo

A

Material that is carried by vesicles

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16
Q

Nuclear Localizations Signal Sequences

A
  • Only present in nuclear proteins
  • 5 basic amino acids in a row
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17
Q

Nuclear Transport

A
  • Import of nuclear proteins through the pore complex
  • Increases order in the cell (Non-Spontaneous)
  • Consumes energy provided by GTPase: specifically Ran
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18
Q

Ran

A
  • GTP-bound protein
  • Found in the cytosol and nucleus
  • Required for nuclear import and export
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19
Q

RAN-GEF

A
  • Nuclear protein
  • Catalyzes binding of GTP to RAN
  • There is more RAN-GTP inside the nucleus than the cytosol
  • GTP bound
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20
Q

RAN-GAP

A
  • Cytosolic protein
  • Activates hydrolysis of GTP attached to RAN
  • GDP Bound
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21
Q

RAN and nuclear import/export

A
  • RAN GAP dephosphorylates RAN GTP into RAN GDP in the cytosol
  • This causes RAN GDP to pick up and bind to cargo in the cytosol
  • This is imported into the nucleus where RAN GEF replaces GDP with GTP and releases the cargo in the nucleus
  • RAN GTP is then transported out of the nucleus through nuclear pore complexes and the process repeats
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22
Q

Nuclear Import

A

RAN GTP binding to import receptor causing the cargo to be released

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23
Q

Nuclear Export

A

RAN GTP binding to export receptor causing the cargo to bind

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24
Q

NFAT and Nuclear Transport

A
  • Rise in calcium levels activates calcineurin
  • Calcineurin dephosphorylates NFAT which causes a conformational change, exposing a nuclear import sequence on the protein’s surface
  • NFAT enters the nucleus and triggers gene expression of T-cells in their role in immune response
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25
Location of proteins in mitochondria
- Outer membrane - Inner membrane - Intermembrane space - Matrix space
26
Mitochondrial transport
- Mitochondrial proteins are first fully synthesized as precursor proteins in the cytosol and are then translocated into the mitochondria - Need an import signal sequence
27
Import signal of mitochondrial transport
- Amphipathic alpha helix at N-terminus - Charged residues on one side and uncharged on the other side
28
Protein translocators of mitochondrial transport
- TOM complex (1) - TIM complex (2) - These complexes need to be unfolded
29
TOM Complex
- Functions across the OUTER membrane - All nucleus-encoded proteins must interact with TOM first - Helps insert transmembrane proteins into the outer membrane
30
TIM Complexes
- Function across the inner membrane - Spans on both the inner and outer membranes - Transport soluble proteins into the matrix - Import ATPase complex binds and pulls proteins through the TIM channel
31
Chaperones
- Place proteins in an isolated environment to assist in maintaining proper folding - Most common is Hsp70
32
Co-translational translocation (ER)
- Used by proteins entering the ER - Need an ER signal sequence
33
Types of proteins that use co-translational translocation
- Secretory proteins are destined to the lumen of any non-nuclear organelle to be secreted out of the cell - Transmembrane proteins are destined to the membrane of an organelle membrane
34
ER signal sequence
- N-terminal - Hydrophobic - Contain 8 or more AA - Recognized by SRP receptors in the ER membrane
35
SRP
- Signal recognition particle - Contain both RNA and protein components - RNA: blocks elongation factor binding site - Protein: binds signal sequence - NOT a ribozyme because it does not catalyze a reaction
36
Positively charged amino acids
ALWAYS face the CYTOSOL
37
Single-pass integral membrane protein
- Signal/start sequence is cleaved - Hydrophonic stop transfer sequence anchors the protein in the membrane
38
Multi-pass integral membrane proteins
- Multiple start and stop-transfer sequences The first start sequence is the signal sequence
39
ODD number of transmembrane proteins
N and C-terminus on OPPOSITE sides
40
EVEN number of transmembrane proteins
N and C-terminus on SAME side
41
Amount of alpha helices it takes to get past the transmembrane region once
8 alpha helices
42
Forward transport
ER to Golgi to destination
43
Retrograde transport
Used to pick up more proteins or if there was a mistake in designating proteins to the wrong destination
44
Protein coats
- Vesicular transport depends on protein coats formed at specific locations along donor compartments
45
Initial step in vesicle formation
- Transport vesicles have a cage of proteins covering their cytosolic surface - The protein coat of the vesicles is discarded to allow 2 cytosolic membrane surfaces to interact directly and fuse
46
Types of coat proteins
- COPII - COPI - Clathirin
47
COPII
Coats ER to Golgi vesicles
48
COPI
Coats vesicles moving from: - Golgi to ER - Golgi to the plasma membrane - Within the Golgi
49
Clathrin
- To/from endosomal compartments - Within endosomal compartments
50
Phosphatidyl-inositol (PI)
- Mark organelles and membrane domains - Inositols can get phosphorylated by lipid kinases - Recruit various proteins that possess lipid-binding domains
51
Lipid-binding domains
Recognize a specific type of phosphatidyl-inositol
52
Adapter proteins
- Bind to membrane proteins and recruit coat proteins - Bind to cargo receptors
53
Types of GTPases control coat assembly
- Sar-1 regulates COPII assembly - Arf proteins regulate COPI and clathrin assembly
54
What are 3 types of GTP binding proteins and what do they control?
- Arf proteins: Control coat assembly and vesicular traffic - RAN: Regulates protein transport across the nuclear membrane - Rabs: Targets the vesicle to the correct destination
55
Sar1-GDP
- Cytosol - Inactive
56
Sar1-GTP
- Integral membrane protein - ER membrane-bound - Active
57
Sar1-GEF
Sar1-GEF is activated when GDP is released from Sar1 and GTP binds to Sar1
58
Vesicle docking and tethering
- Transport vesicles must be highly selective in recognizing the correct target membrane with which to fuse - Surface markers identify vesicles according to their origin and type of cargo - Target membranes display complementary receptors that recognize the appropriate markers
59
SNARE proteins
- NOT GTP-Binding (ATP-regulated) - Provide specificity - Catalyze vesicular fusion with the target membrane
60
v-SNAREs
Vesicle
61
t-SNAREs
Target membrane
62
Rab proteins
- Small GTPases - Initial contact with the target membrane - Work with other proteins to regulate the initial docking and tethering of the vesicle to the target membrane
63
Entry of vesicles leaving the ER
- Membrane proteins have exit signals in their cytosolic tails that are recognized by COPI coat proteins - Soluble proteins bind to cargo receptors that have exit signals in their cytosolic tails (ex. KDEL receptors)
64
Vesicular Tubular Clusters
- These clusters are transport vesicles leaving the ER that fuse together to form intermediate components - Clusters travel towards the cis (close to ER) Golgi via motor proteins on microtubule tracks - Generate coated vesicles going back to ER (COPI coat): Retrograde
65
Models for how cargo travels through Golgi
- Vesicular Transport (Static) - Cisternal Maturation (Dynamic)
66
Vesicular Transport Model
- Static cisternae - Vesicles travel between them
67
Cisternar Maturation Model
- Dynamic cisternae - Cisternae move upward and change their properties slightly as they migrate
68
Exocytosis
- Vesicles carry proteins leaving the Golgi to fuse with the plasma membrane - Membrane proteins and lipids become part of the plasma membrane - Soluble proteins are secreted into the extracellular space
69
Regulation of Exocytosis
Rabs and SNAREs
70
Types of Transport from Trans Golgi (faces cytoplasm) to the Cell Exterior
- Constitutive secretory pathway - Regulated secretory pathway
71
Constitutive secretory pathway
No additional signal is needed to fuse vesicles with plasma membrane after Rabs and SNAREs
72
Regulated secretory pathway
- Concentrates cargo in small volumes - Fusion does not happen immediately when in contact with a plasma membrane until a signal is received (Usually Calcium)
73
Secretory vesicles
- Specialized for secreting products rapidly and on demand - Only release their contents in response to extracellular signals
74
Clathrin-coated vesicles
- Composed of 3 copies each of heavy chain and light chain - Arranged in a 3-arm pinwheel
75
Features of Clathrin coats
- Assemble on the plasma membrane - Recruited by adaptor proteins - Capture and package cargo molecules within the donor compartment into a budding vesicle - Coat is rapidly lost after forming
76
Dynamin
- Lipid-binding GTPase - Protein that pinches off the clathrin-coated vesicles - Oligomerizes (wraps) around the stem of the budding vesicle - Brings inner leaflet membranes of vesicles together - Fusion of these membranes releases the vesicles from the donor compartment
77
Lysosomal Enzyme Cargo
- Soluble - Carries M6P groups that are added to N-linked oligosaccharides in cis-Golgi - Recognized by M6P receptor in TGN and packaged into clathrin-coated vesicles for delivery to lysosomes
78
Intermediate organelles in vesicular transport pathways
- Vary in shape and size - Receive cargo from Golgi and Plasma membrane
79
Classes of Intermediate Organelles
- Early - Late - Recycling
80
Endosome maturation
- Early endosomes mature into late endosomes which mature into lysosomes - Becomes increasingly acidic during this process
81
Endocytosis
- Budding and internalization of vesicles - Membrane proteins and lipids are removed from the plasma membrane where some are recycled back to the surface and others will be degraded - Soluble proteins from the extracellular space will be carried into the lumen
82
Types of Endocytosis
- Based on the size of vesicles - Phagocytosis - Pinocytosis
83
Phagocytosis
- Ingestion of large particles such as microorganisms or dead cells - Vesicles are called phagosomes
84
Pinocytosis
- Ingestion of fluid and solutes - Vesicles are called pinocytic vesicles - Includes receptor-mediated endocytosis
85
Receptor-mediated endocytosis
- Triggered by extracellular signaling - Ex. Cholesterol gets into cells via this pathway
86
Transcytosis
Molecules internalized at one end of a polarized cell are transported to a different end
87
Passive Transport
- Moving a solute DOWN its concentration gradient - High to low concentration - Does NOT require energy
88
Examples of Passive Transport
- Ion channels - Facilitated diffusion
89
Active transport
- Moving a solute UP its concentration - Low to high concentration (AGAINST) - Requires energy
90
Where does the energy for active transport come from?
- ATP - Movement of something else DOWN a gradient - High energy electrons
91
Characteristics of Biological Membranes
- Semipermeable - Small, nonpolar molecules diffuse freely - Large, polar, charged molecules require channels and transporters
92
Channels
- Allows diffusion DOWN a concentration gradient - ALWAYS passive transport - Only need 1 conformational change
93
Transporters
- Use conformational changes to move substrates across the membrane - May transport down or up a concentration gradient
94
Diffusion
- Random motion of molecules: They will sometimes move toward each other or away from each other - High to low concentration - Down a concentration gradient
95
Change in free energy
Any molecule or ion moving down or up a concentration gradient requires a change in free energy
96
Diffusion of charged molecules
- Involves electrochemical gradient - Differences are additive
97
Positive Delta G
Active transport (non-spontaneous)
98
Negative Delta G
Passive transport (spontaneous)
99
Ranking of Permeability
- Hydrophobic (Best) - Small, uncharged, polar - Large, uncharged, polar - Ions (Worst)
100
Simple diffusion
- Free Diffusion is limited to small, uncharged, and non-polar molecules - Bidirectional - Unsaturable: As you increase the concentration of the molecules, you increase the rate of diffusion
101
Transporter-mediated diffusion
- Always down the concentration gradient (High to low) - Can go in or out of the cell - Saturable (similar to enzyme kinetics): Reach a maximum rate
102
Ion channels
- Allows a net flux of specific ions DOWN their electrochemical gradient - Undergo one conformational change
103
Open ion channels
- Stable state - Induced by a conformational change
104
Closed ion channels
Close when a signal arrives and closes it
105
Channel structure
- Central pore lined with hydrophilic R groups - Subunits around the pre are often formed from alpha helices - Highly selective
106
Conformational changes that OPEN an ion channel
- Ligand-gated channels - Voltage-gated channels - Mechanosensitive channels - Temperature-sensitive channels
107
Facilitated Diffusion-Passive transport
- Neutral, polar molecules that are larger than water or urea - NOT couples with an energy source - The direction of molecules follows the electrochemical gradient - Solute binds tightly to a highly specific site on protein and causes a conformational change - Transitions between states are random and reversible - Slower than ion-channel transport
108
Facilitated Diffusion Proteins
- Do not alter Delta G - Always DOWN electrochemical gradient - Act like enzymes by speeding up movement
109
Type of facilitated diffusion
Glucose transport
110
Door Analogy for channel and transport-mediated diffusion
- Ion Channel Mediated: Handicap button - Transport Mediated: Revolving door
111
Types of Active Transport
- ATPase pumps - Non-ATP pumps that use physical forces - Couples transporters that use the energy of the gradient itself
112
Coupled Transport
- Can move molecules up or down a concentration gradient - Occurs via symports and antiports
113
Symports
Move both molecules in the same direction
114
Antiports
Move molecules in opposite physical directions
115
Types of ATP-driven pump proteins
- P-type - F-type and V-type - ABC transporter
116
P-type pumps
- Move ions from one side of the membrane to another - Multipass transmembrane proteins - Ex. Calcium ATPase, Na+/K+ Pump
117
Na+/K+ Pump
- This pump has specific binding sites for sodium and potassium - Antiporter - Active transport (UP) - Have to pump both of them for both to be pumped
118
F-type pumps
- Reversible - Found in bacteria, mitochondria, and thylakoid membranes - Generate ATP through H+ gradient - Called ATP synthases as they drive the synthesis of ATP from ADP + Pi
119
V-type pumps
- Made of multiple subunits - Use ATP but NOT via a phosphorylated intermediate - Found in membranes of lysosomes, synaptic vesicles, and plant vacuoles - Regulate pH by pumping H+ into these compartments
120
ABC transporters
- Homodimers: 2 subunits - Multiple domains - Most of these transporters pump small, uncharged molecules - Some pump ions - Ex. MDR proteins
121
ABC transporters in Bacterial cells
Pump molecules INTO the cell
122
ABC transporters in Eukaryotic cells
Pump molecules OUT of the cell
123
Cytoskeleton
- System of protein filaments that provides structure and mechanical support for the cell - Made by the polymerization of the monomeric protein subunits
124
Types of fibers that make up the cytoskeleton
- Microtubules - Microfilaments - Intermediate filaments
125
Monomers of microtubules
Tubulin
126
Monomers of microfilaments
Actin
127
Monomers of intermediate filaments
- Helical proteins - Ex. keratin in epithelial cells, lamins in nucleated cells, neurofilament proteins in axons
128
Feature of cytoskeleton interactions
- Noncovalent attractions of small subunits - Disassembly and reassembly allow for changes in cell shape and internal movement of organelles/vesicles
129
Polymerization of Cytoskeleton proteins
- Requires NTP - Monomers containing NTP have a higher affinity for their binding partners - NTP-bound to (+) end of growing filament
130
NTP vs. NDP
- NTP allows for polymerization - NDP results in depolymerization
131
Actin
- Flexible filaments - Soluble and globular protein - Most abundant protein - Dispersed throughout a cell - Highly concentrated beneath the plasma membrane - Forms the basis of cell shape and structure - Aid in the contraction of muscle cells
132
Actin monomers
Globular actin (G-actin)
133
Actin polymers
Filamentous actin (F-actin)
134
ATP-G vs. ADP-G actin
ATP-G actin monomers bind more tightly to each other than ADP-G actin monomers
135
Actin +/- ends
- Actin monomers (G-actin) bound to ATP are added to the (+) end of the growing filament - Actin-ADP monomers are lost from depolymerizing the (-) end
136
Treadmilling
The addition of an ATP-G-actin monomer to the (+) end if equivalent to the removal of an ADP-G actin monomer at the (-) end
137
Proteins that regulate actin
- Arp 2 and 3: monomers nucleating - Thymosins: inhibit polymerization - Tropomodulin: capping (block) plus or minus ends - Fimbrin: stiffens cytoskeleton - Cofilin: promotes depolymerization - Profilin: promotes extension - Gelsolin: breaks down the gel of long filaments which decreases the viscosity
138
Rho family of GTPases
- These GTPases regulate the proteins that regulate actin - Act as molecular switches to control actin polymerization
139
Rho-GTP
Regulate actin bundling
140
Ran-GTP
Regulate actin polymerization
141
Cdc42-GTP
Regulate actin polymerization and bundling
142
Microtubules
- Rigid tubules that are spread throughout the cytoplasm of ALL eukaryotic cells - Form mitotic spindles and the core of cilia and flagella
143
Structure of tubulin
- Tubulin heterodimers (alpha and beta tubulin) polymerize into protofilaments which assemble into microtubules
144
Alpha tubulin
Can only bind to GTP
145
Beta tubulin
Can bind to GTP or GDP
146
Tubulin +/- ends
- Tubulin dimers bound to GTP are added to the (+) end of microtubules - GTP is eventually hydrolyzed into GDP
147
GTP cap (tublin-GTP dimer)
- The rate of polymerization at the (+) end is more rapid than GTP hydrolysis - The cap is put into place to stabilize the growth
148
Catastrophe
- GTP cap is lost - The (+) end undergoes rapid depolymerization - The rate of GTP hydrolysis exceeds the rate of polymerization
149
Compare tubulin and actin under cellular conditions
- Tubulin: growth and loss occur at the (+) end, normally has a GTP cap, and if the cap is lost then it will lead to depolymerization - Actin: growth and loss occur at both ends, Addition at the (+) end, Loss at the (-) end
150
Proteins that regulate the addition and removal of tubulin dimers
- Stathmin: binds subunits and prevents assembly - Kinesin: enhances disassembly - Katanin: breaks microtubules - MAP: binds along tubules and stabilizes them - XMAP: stabilized (+) end - TIPS: associated with (+) end and links them to other structures
151
Phases of microtubule regulation
- Nucleation - Elongation
152
Nucleation
- A small portion of tubule formed at the beginning - Associated with MTOC's
153
Elongation
Addition of tubulins and GTP-cap
154
Example of MTOC
- Centrosomes - Found in animal cells - DividedGamme prior to cell division
155
Gamma tubulin
- Found in centriole microtubules - Bound to the (-) end
156
Molecular motors
- Proteins act as molecular motors by changing shape to generate movement - The movement must be directional in order to be useful
157
Favorable movement
- ATP hydrolysis (ATP to ADP + Pi)
158
Myosin
- A motor protein that binds to actin microfilaments - Subdivided into Myosin II
159
Features of myosin II
- Heterodimer - S1 head involved with movement via ATPase activity - Neck region - Coil-to-coil region
160
Myosin II Actin Filaments
- Myosin II can associate with actin filaments which are highly stable in muscle cells - From the basic structural unit of contractility (sarcomere) - Myosin II moves these filaments through the Powerstroke
161
Microtubule motor proteins
- Kinesins - Dyneins
162
Kinesins
- Responsible for moving vesicles and organelles along nerve axons - Composed of 2 light chains and 2 heavy chains - Globular heads contain ATP binding site
163
ATP-binding site of kinesin
- Binds to microtubule which initiates ATPase activity and the movement of kinesin and cargo - Movement only occurs in the direction of (-) to (+) end
164
Cargo of kinesin
- Includes vesicles, protein complexes, and organelles - Bound to kinesin via adapter proteins
165
Dyneins
- Contain 2 ATP-binding heads - Light chain is bound to cargo through dynactin - Dynein molecules move along the microtubule from the (+) to (-) end
166
Intermediate filaments
- Composed of long helical proteins - Provide mechanical strength - Not present in every cell
167
Which cytoskeleton processes use ATP hydrolysis?
- De/polymerization of actin filament - Movement of myosin along actin - Movement of kinesin and dynein along tubulin
168
Which cytoskeleton processes use GTPase activity?
De/polymerization of tubulin filaments
169
Cellular metabolism
Occurs in small enzyme-catalyzed steps that allow energy to be stored and extracted in useful ways
170
What parts of cellular metabolism require molecular oxygen?
TCA and ETC
171
What part of cellular metabolism does NOT require molecular oxygen?
Glycolysis
172
Features of cellular metabolism
- Energy for cellular processes comes from catabolic reactions (breaking things down) - In order to harvest energy, nutrients must be oxidized (lose electrons) in small steps
173
Benefits of small enzyme-catalyzed steps
- Avoids the release of heat - Reduces the activation energy - Enzymes couple unfavorable reactions with energetically favorable reactions - Small delta G's
174
Glycolysis
- One molecule of glucose is converted to two molecules of pyruvate - Net production of 2 ATP and 2 NADH molecules - Occurs in the cytosol
175
Phases of glycolysis
- Investment - Cleavage - Energy generation
176
Investment phase
Glucose is phosphorylated twice
177
Cleavage phase
The phosphorylated molecule splits into two molecules
178
Energy generation
The two molecules are oxidized to produce NADH

BSCI 330: Cell Biology (4 decks)

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