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After midterm Flashcards

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1
Q

Functions of the Nucleus

A
  1. Storage, replication, and repair of genetic material
  2. Expression of genetic material (transcription and splicing)
  3. Ribosome biosynthesis
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2
Q

Structure of the Nucleus

A

Nuclear envelope
Nuclear membrane
Nuclear pores
Nuclear lamina

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3
Q

Contents of the Nucleus

A

Chromatin
Nucleoplasm
Matrix
Nucleolus

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4
Q

Nuclear envelope

A

Separates transcription and translation, acting as a selective barrier that limits movement of molecules

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5
Q

Nuclear lamina

A

Thin meshwork of filamentous proteins bound to the inner membrane of the nuclear envelope by integral proteins

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6
Q

Nuclear envelope consists of?

A

2 parallel phospholipid bilayers

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7
Q

Outer membrane of nuclear envelope

A

Binds ribosomes and is continuous with rough ER

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8
Q

Inner membrane of nuclear envelope

A

Bears integral proteins, which connect to the nuclear lamina

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9
Q

Attachment site for chromatin and support structure for nuclear envelope?

A

Nuclear lamina

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10
Q

Nuclear pores

A

Gateways between cytoplasm and nucleoplasm

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11
Q

How many pores per nucleus and how are they formed?

A

3000 to 4000 formed when inner and outer membrane fuse

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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

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13
Q

Has octagonal symmetry?

A

Nuclear pore complex

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14
Q

What are the functions of NPC?

A
  1. Passive diffusion of molecules smaller than 50 kDa(fast)

2. Regulated movement of larger molecules (slow)

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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

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16
Q

Cellular function is acutely dependent upon?

A

Nuclear import and export (nucleocytoplasmic trafficking)

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17
Q

What factors are needed for nuclear import?

A
  1. Nuclear localization signal in cargo protein
  2. Karyopherins
  3. Energy
  4. Ran-Small G proteins that act as chemical messengers and triggers
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18
Q

Ran-Small G proteins attached to 3 phosphate groups are?

A

Turned on

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19
Q

Ran-Small G proteins attached to 2 phosphate groups are?

A

Turned off

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20
Q

Nuclear exports are mostly what?

A
  1. Protein and RNA molecules containing NES
  2. Exportins bound to NES
  3. Ran-GTP (hydrolysis of which releases the cargo)
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21
Q

Nucleolus comprises what?

A

Clusters of ribosomal DNA gathered together as one to several nucleoli that produce ribosomes

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22
Q

What are the functions of the nucleolus?

A
  1. Ribosome biogenesis
  2. Synthesis of rRNA
  3. Processing of rRNA
  4. Assembly of subunits (rRNA + proteins)
  5. Small 40S and large 60S subunits exported to the cytoplasm
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23
Q

Cytoskeleton

A

Dynamic network of protein filaments that forms the cellular scaffolding as well as transport systems for organelles and vesicles

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24
Q

Primary functions of cytoskeleton?

A
  1. Structural support
  2. Intracellular support
  3. Contractility and motility
  4. Spatial organization within cell
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25
Q

3 major elements of cytoskeleton?

A
  1. Microtubules
  2. Micro-filaments
  3. Intermediate filaments
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26
Q

Microtubules

A

Largest cytoskeletal element comprising of polymers of alpha tubular and beta tubular proteins

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27
Q

What are the two MT ends?

A
  1. Fast growing “+” end

2. Slow growing “-“ end

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28
Q

Structural polarity of MT

A

Herero-Dimers are aligned in the same direction - structural polarity - important for growth/shrinkage and direction of movement of material

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29
Q

Motor proteins that use ATP to generate force and movement?

A

Dynein (- end directed)

Kinesin (+ end directed)

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30
Q

Dynamic instability of MT and what it leads to?

A

MTs undergo dynamic assembly and disassembly which leads to rapid turnover of most MTs within the cell

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31
Q

MT catastrophe

A

Rapid occurrence of shrinkage at plus end

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32
Q

Formation of Mts is regulated and controlled by what?

A

Microtubule-associated proteins (MAPs)

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33
Q

Central sites of MT assembly?

A

Microtubule-organizing centers (MTOC)

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34
Q

Intermediate filaments

A

Stable fibrous proteins (relative to MTs) that are exclusive o multicellular animals and they provide structural support and mechanical strength

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35
Q

Polarity of intermediate filaments?

A

Not polar once assembled!!

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36
Q

How are intermediate filaments formed?

A
  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
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37
Q

Microfilaments

A

Smallest cytoskeleton element comprising of polymers of “actin” protein

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38
Q

Functions of microfilaments?

A
  1. Maintenance of cell shape
  2. Cell movement
  3. Cytokinesis
  4. Muscle contraction
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39
Q

G-actin monomers

A

Have a polar structure as the monomers are incorporated in the same orientation

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40
Q

F-actin filaments

A

Are polar with a + end and a - end

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41
Q

F-actin assembly is a result of what?

A

G-actin polymerizing reversibly due to nucleation or elongation

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42
Q

Nucleation

A

SLOW

G-actin>dimers>trimers>short filaments

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43
Q

Elongation

A

FAST

Monomers add to both ends (faster at + end)

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44
Q

Polymerization and structure organization of F-actin filaments are regulated by what?

A

Actin-bonding proteins

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45
Q

In vesicular transport

A

All motor proteins are involved

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46
Q

Myosin

A

F-actin associated motor protein that must move towards the + end and is divided into conventional and unconventional myosins

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47
Q

Unconventional myosins

A

Generate force and contribute to motility in non-muscle cells

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48
Q

Extracellular Space

A

Extends outwards from the surface of the plasma membrane and contains a variety of secreted materials (from the cell) that influence cellular behaviour

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49
Q

What does the Extracellular space do?

A
  1. Mediates cell-cell and cell-extracellular matrix (ECM) interactions
  2. Provides mechanical protection
  3. Serves as a barrier
  4. Binds regulatory factors
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50
Q

Cells of bacteria, plants, and fungi are surrounded by a ____ ____, which is considered an ECM

A

cell wall

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51
Q

Plant cell walls are composed of what?

A
  1. Cellulose
  2. Hemicellulose
  3. Pectin
  4. Proteins
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52
Q

Plant cell walls do what?

A
  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
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53
Q

What does it take to make life?

A
  1. Information
  2. Chemistry
  3. Compartments
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54
Q

Cell theory

A
  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
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55
Q

Basic properties of cells

A
  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
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56
Q

Two classes of cells on Earth:

A
  1. Prokaryotic

2. Eukaryotic

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57
Q

Prokaryotic cells

A

Structurally simpler

-Bacteria

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58
Q

Eukaryotic cells

A

Structurally more complex

-Protists, fungi, plants, animals

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59
Q

Compartments

A

Membrane bound structures dedicated to a particular function

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60
Q

Components are not…

A

bound by membranes

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61
Q

Enables movement of molecules into and out of the nucleus

A

Nuclear pore complex

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62
Q

Contributes to cell shape and movement, provides structural support and supports the transport of material

A

Cytoskeletal elements

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63
Q

Viruses

A

Non-cellular macromolecular packages that can function and reproduce ONLY within living cells (tiny machines that take over cells)

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64
Q

Virion

A

Virus existing outside of cells as an inanimate particle

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65
Q

What is a vision comprised of?

A
  • Small amount of DNA or RNA

- Protein capsule

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66
Q

What defines the cell types that a virus can infect and the host range?

A

Specific proteins on a cell surface

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67
Q

What does a virus do once inside a cell?

A

Hijacks cellular machinery to synthesize nucleic acids and proteins (assembles new virus particles)

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68
Q

Two main types of viral infection?

A
  1. Lytic

2. Non-lytic

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69
Q

Lytic

A

Production of virus particles ruptures and kills cell

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70
Q

Non-lytic (or integrative)

A

Viral DNA is inserted in host genome and viral progeny bud at cell surface. Cell can survive but often with impaired function

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71
Q

Provirus

A

Viral DNA inserted in host genome

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72
Q

Functions of plasma membranes

A
  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
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73
Q

Trilaminar

A

3 layered structure (oreo cookie) of incredibly COMPLEX plasma membrane (6nm thick)

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74
Q

Fluid mosaic model

A

Model of biological membranes that says individual lipid molecules move and diverse particles penetrate the lipid layer

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75
Q

Structure of biological membranes

A
  • Bilayer of amphipathic lipids
  • Proteins
  • Components are mobile and can interact
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76
Q

Amphipathic

A

Having both hydrophobic and hydrophilic regions

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77
Q

Due to amphipathic nature all membranes are capable of what?

A

Self-assembly

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78
Q

Different membranes contain what?

A

Different types of lipids and proteins

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79
Q

Myelin sheath

A

Modified plasma membrane structure that wraps around and around forming insulation

80
Q

3 classes of membrane proteins

A
  1. Integral
  2. Lipid-anchored
  3. Peripheral
81
Q

Integral membrane proteins

A

Span the lipid bilayer (i.e. stick through membrane)

82
Q

What do integral membrane proteins do?

A

-Act as receptors, transporters, channels and ETC

83
Q

Lipid-anchored proteins

A

Attach to a lipid in the bilayer (i.e. they aren’t stuck in membrane but attached to it through covalent forces)

84
Q

Peripheral membrane proteins

A

Associate with the surfaces of the lipid bilayer through electrostatic charges

85
Q

How could you easily strip off peripheral proteins?

A

Add salt to membrane because they are associated through electrostatic charges

86
Q

Transduction

A

Communication between cells

87
Q

What does it mean that biological membranes are asymmetrical?

A

They are different on the inside and outside (because they have different functions)

88
Q

In many plasma membranes the outer leaflet contains what?

A

Glycolipids and glycoproteins

89
Q

Glycolipids and glycoproteins

A

Lipids and proteins with carbohydrate attached

90
Q

Membrane fluidity is determined by what?

A

Nature and temperature of lipids in membrane

91
Q

Unsaturated lipids

A

Increase fluidity

92
Q

Saturated lipids

A

Reduce fluidity

93
Q

Warming membranes

A

Increases fluidity

94
Q

Cooling membranes

A

Decreases fluidity

95
Q

Liquid crystal state

A

Warm

96
Q

Crystalline gel state

A

Cool

97
Q

Why is membrane fluidity so important?

A

It is crucial to cell function

98
Q

Balance between ordered structure and disordered structure allows for what?

A
  1. Mechanical support and flexibility
  2. Dynamic interactions between membrane components (proteins can come together reversibly)
  3. Membrane assembly and modification
99
Q

In response to changes in temperature, lipid composition of membranes can be changed how?

A
  1. Desaturation of lipids (kink=harder to make crystals)

2. Exchange of lipid chains

100
Q

Cholesterol

A

Totally hydrophobic –> hangs out inside membrane

101
Q

Why is cholesterol needed?

A

To regulate membrane fluidity

102
Q

What does cholesterol do?

A

Alters packing and flexibility of lipids

103
Q

If cholesterol is added to a liquid crystal membrane fluidity will…

A

decrease

104
Q

If cholesterol is added to crystalline gel membrane fluidity will…

A

increase

105
Q

Lipid Rafts

A

Membrane microdomains (i.e. smlal areas that are enriched in certain types of lipids)

106
Q

Movement of substances across cell membranes…

A

is HIGHLY controlled

107
Q

What crosses membranes relatively easily?

A

Small, uncharged molecules (i.e. O2, CO2, NO, H2O)

108
Q

What cannot cross membranes easily?

A

Large, polar, or charged compounds

109
Q

How is transport controlled?

A

There are 4 main mechanisms:

  1. Simple diffusion
  2. Diffusion through a channel
  3. Facilitated diffusion
  4. Active transport
110
Q

Simple diffusion

A 
Passive transport (no energy involved) simply cross membrane
-very small, uncharged molecules
111
Q

Diffusion through a channel

A

Protein channel allows something to simply cross membrane (passive)
-small charged molecules (ions)

112
Q

Facilitated diffusion

A

Compound binds specifically to transporter (integral membrane protein) that changes conformation and releases compound on other side of membrane (passive)
-glucose

113
Q

Active transport

A

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
Q

Ion channels

A

Formed by integral membrane proteins and are selective allowing only one type of ion to pass (channels are often gated)

115
Q

Gated channels

A

Can exist in either an open or closed position

116
Q

Voltage gated channels

A

Channel responds to changes in charge across membrane

117
Q

Ligand-gated channels

A

Channel responds to binding of specific molecule (ligand)

118
Q

Mechano-gated channels

A

Channel responds to physical force on membrane

119
Q

Extracellular matrix

A

Organized network of material produced and secreted by cells

120
Q

Glycocalyx

A

Assembly of carbohydrate groups attached to proteins and lipids on outside of the plasma membrane

121
Q

What does glycocalyx do?

A
  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
Q

What functions does ECM serve?

A
  1. Sites for cell attachment
  2. Physical support for cells
  3. Contains regulatory factors (signals)
  4. Separate/define tissues
123
Q

Proteoglycans

A

Type or glycoprotein with chains of polysaccharides

124
Q

Endosymbiont theory

A

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
Q

Invagination

A

The infolding of plasma membrane

126
Q

Mitochondria

A

Burn food you eat to extract ATP and participate in apoptosis

127
Q

Outer mitochondrial membrane

A
  • Contains many enzymes with diverse metabolic functions

- Contains porins

128
Q

Porins

A

Large channels that when open mitochondrial membrane is freely permeable

129
Q

Inner mitochondrial membrane

A
  • High protein/lipid ratio (3:1)
  • Double layered folds
  • Rich in cardiolipin
130
Q

Cristae

A

Double layered folds that increase membrane surface area

131
Q

Cardiolipin

A

Phospholipid characteristic of bacterial membranes

132
Q

What 4 pieces of mitochondrial evidence support endosymbiont theory?

A
  1. Prokaryotic ribosomes
  2. Own genome (DNA)
  3. Double membrane
  4. Cardiolipin
133
Q

What are the aqueous compartments of mitochondria?

A
  1. Intermembrane space

2. Matrix

134
Q

Oxidative phosphorylation

A

ATP synthesis in mitochondria

  1. Electron transport and proton pumping generates electrochemical gradient
  2. Proton movement down gradient powers ATP synthesis
135
Q

Apoptosis

A

A normal occurrence in which a coordinated sequence of events leads to death of a cell

136
Q

What is apoptosis characterized by?

A
  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
Q

Blebbing

A

Pieces of plasma membrane start to come off like blobs unfolding

138
Q

Pathway of apoptosis is highly coordinated why?

A

To get rid of cells that aren’t supposed to have apoptosis happening in them

139
Q

Proapoptotic proteins

A

Stimulate mitochondria to leak cytochrome c (proteins)

140
Q

Release of cytochrome c does what?

A

Commits cell to apoptosis!

141
Q

Capases

A

Enzymes that chew up different things

  • destroy cytoskeleton
  • disrupts cell adhesion
  • destroys lamina
  • activates DNase
142
Q

Is the mitochondria part of cytoplasm?

A

YES

143
Q

Cytoplasmic endomembrane systems

A

Within cytoplasm there is membrane bound organelles and vesicles and an extensive network of membranous canals and stacks of “sacs”

144
Q

GFP

A

Green fluorescent protein genetically fused with a cellular protein to track cell components

145
Q

Construction of a GFP-tagged protein

A

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
Q

Vesicular Transport (Trafficking)

A
  • Transport of material between compartments
  • Utilizes transport vesicles
  • Targeted movement
147
Q

Transport vesicles

A

Small, spherical, membrane-enclosed organelles that bud off donor compartment and fuse with acceptor compartment

148
Q

How is movement is directed?

A

Using cytoskeleton and motor proteins and sorting signals recognized by receptors

149
Q

What are the steps of trafficking vesicles?

A
  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
Q

Rabs

A

Proteins that tether vesicle to target compartment

151
Q

SNAREs

A

Proteins that dock vesicle to target compartment

152
Q

Organelle to plasma membrane

A

Exocytosis

153
Q

Plasma membrane to organelle

A

Endocytosis

154
Q

Endoplasmic reticulum

A

Inter-connected network of membrane-enclosed tubules and flattened sacs

155
Q

Lumen of ER is separate from what?

A

Cytosol

156
Q

Continuous with the outer membrane of the NUCLEUS

A

ER membrane

157
Q

Smooth ER vs. Rough ER

A

Smooth ER is sort of like a specialization zone and it has less ribosomes on the outside (i.e. smooth surface)

158
Q

What are the functions of the SER?

A
  1. Production of steroid hormones
  2. Detoxification
  3. Sequestration (storage) of Ca2+
159
Q

Why are there lots of ribosomes on RER?

A

It has to do with their function! Site for making lots of proteins

160
Q

What are the functions of the RER?

A
  1. Protein synthesis, modification and transport
  2. Synthesis of membrane phospholipids
  3. Glycosylation of proteins (addition of carbohydrate chains)
  4. Protein folding
161
Q

Where does all protein translation begin?

A

On free ribosomes

162
Q

What proteins are synthesized in the RER?

A

Secreted proteins, integral membrane proteins, soluble proteins associated with inside of endomembrane system

163
Q

How is the site of translation determined?

A

Ribosomes are targeted to the ER membrane by a signal sequence

164
Q

What is the signal sequence?

A

Located at proteins amino-terminus (N-terminus) and contains several consecutive hydrophobic amino acids. Directs synthesis to ER moving through channel

165
Q

What happens after translation of signal sequence?

A

Cotranslational protein import

166
Q

Cotranslational protein import

A
  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
Q

Translocon

A

Complex of proteins

168
Q

SRP

A

Complex of proteins

169
Q

Once a protein is fully synthesized and properly folded what are its 2 options?

A
  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
Q

ERGIC

A

Region between ER and golgi complex where transport vesicles fuse to form VTCs

171
Q

Vesicular-Tubular Clusters

A

Larger fused vesicles and interconnected tubules

172
Q

Transport from ER to golgi complex exit sites?

A

Membrane and ER lumen bud off to form transport vesicles

173
Q

Material moves from ER to where?

A

Golgi then plasma membrane and other compartments

174
Q

Golgi complex

A

Processing plant of cell (i.e. modification and packaging)

175
Q

WAll protein synthesis starts where?

A

CYTOPLASM

176
Q

Structure of golgi complex

A

Smooth flattened disk-like cisternae

177
Q

CGN vs. TGN

A

CGN acts as a sorting station and TGN sorts protein into different types of vesicles

178
Q

How are proteins modified as they travers the Golgi?

A

Step-wise (i.e. different cistern of the Golgi contain different enzymes that modify proteins)

179
Q

Once proteins are fully processed what happens?

A

They are exported from the trans cistern and enter the trans-Golgi network and are sorted and delivered to final destinations

180
Q

Transport vesicles are coated, why?

A
  1. Helps form vesicle

2. Helps select cargo

181
Q

COP proteins

A

Coat on transport vesicles

182
Q

How do COPI and COPII proteins carry out their functions?

A

They assemble on the cytosolic surface of donor membranes at sites where budding takes place

183
Q

Where do Cathrin-coated vesicles move?

A

From TGN to other vesicles

184
Q

COPI-coated vesicles move?

A

In retrograde direction

185
Q

COPII-coated vesicles move?

A

In anterograde direction

186
Q

Lysosomes

A

Little digestive organelles

187
Q

What is the function of lysosome?

A
  1. Autophagy

2. Degradation of internalized material

188
Q

Autophagy

A

Organelle turnover (i.e. destruction of organelles and their replacement)

189
Q

How does autopahgy work?

A

Lysosome fuses with ER-edrived autopahgic vacuole (forming autolysosome) and contents are enzymatically digested (forming residual body)

190
Q

Lipofuscin granules

A

Retained in residual body (analagous to age spots)

191
Q

Structure of plant vacuoles

A

Fluid-filled and membrane-bound

192
Q

Function of plant vacuoles?

A
  1. Intracellular digestion
  2. Storage
  3. Mechanical support/turgor pressure
193
Q

Microtubule-associated Proteins

A

Several different proteins that bind MTs

194
Q

What do MAPs do?

A

Modulate assembly and function and mediate interactions with other cellular structures

195
Q

2 classes of MAPs

A
  1. Motor MAPs

2. Non-motor MAPs

196
Q

Motor MAPs

A

Kinesin and dynein

  • Use ATP to generate force
  • Move material along MT track
  • Generate sliding force between Mts
197
Q

Non-motor MAPs

A

Tau

-Control MT organization in cytosol

Biology 1090 (2 decks)

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