BIOL 1090 Flashcards
1
Q
Who is credited with introducing the word cell into biology?
A
Robert Hooke
2
Q
The cell theory states…
A
- The cell is the structural unit of life
- All organisms are composed of 1 or more cell types
- Cells can arise only by the division of a pre-existing cell
3
Q
When was the cell theory developed?
A
- First two points in 1839 by Schleiden & Schwann
- Last point in 1855
4
Q
What are the basic properties of cells?
A
- highly complex and organized
- Activity controlled by a genetic program
- Can reproduce - make copies of themselves
- Assimilate and utilize energy
- Carry out many chemical reactions - enzymes
- Engage in mechanical activities
- Respond to stimuli
- Capable of self-regulation
- They evolve
5
Q
What are the two classes of cells on Earth?
A
Prokaryotic & Eukaryotic
6
Q
Prokaryotic vs. Eukaryotic cells…
A
Prokaryotic - bacteria and structurally simpler
Eukaryotic - Protists, fungi, plants and animals. Structurally more complex
7
Q
What distinguishes a prokaryotic from a eukaryotic cell?
A
The way the DNA is packaged
8
Q
Cellular organization is very..
a) normal and conserved throughout evolution
b) complex and conserved throughout evolution
c) consistent and conserved throughout evolution
d) conserved and conserved throughout evolution
A
c) consistent and conserved throughout evolution
9
Q
What is the usual size of range for a cell?
a) 10^-2 m
b) 10^-3 m
c) 10^-6 m
d) 10^-9 m
A
c) 10^-6 m
10
Q
small wavelength indicates…
A
high energy
11
Q
The living cell is very..
a) dynamic and exists in 4D
b) large and exists in 4D
c) dense and exists in 4D
d) exciting and exists in 4D
A
a)
12
Q
What is an organelle?
A
- A membrane bound compartment with a characteristic content and a specific function
13
Q
What is a compartment?
A
- A separate section or part of something
- An area in which something can be considered in isolation from other things
14
Q
What does a compartment achieve?
A
- Compartmentalizes
- Sequesters
15
Q
Compartmentalizes stands for..
A
divides a whole into separate parts or sections
16
Q
Sequesters stands for..
A
keeps contents from mixing with others
17
Q
How is a compartment formed?
A
- the boundary
- the contents
18
Q
Biological membranes contain…
A
a hydrated lipid bilayer
19
Q
Amphipathic means..
A
o Having both hydrophobic (non-polar) and hydrophilic (polar) regions
20
Q
Membrane fluidity is determined by..
A
- The nature of lipids in membrane
- Temperature
21
Q
How does unsaturated and saturated lipids affect fluidity?
A
unsaturated lipids increase fluidity while saturated lipids decrease fluidity
22
Q
How does temperature affect fluidity?
A
warming increases fludity (liquid crystal) while cooling decreases fludity (crystalline gel)
23
Q
Balance between ordered structure and disordered structure allows:
A
- Mechanical support and flexibility
- Dynamic interactions between membrane components
- Membrane assembly and modification
24
Q
cholesterol regulates..
A
membrane fluidity
25
if cholesterol is added to a liquid crystal membrane, fluidity will..
decrease
26
If cholesterol is aded to a crystalline gel membrane, fluidity will..
increase
27
What do 'Fluid' and 'Mosaic' stand for?
Fluid - individual lipid molecules move
| Mosaic - diverse 'particles' penetrate the lipid layer
28
what are the 3 classes of membrane proteins?
Integral - membrane proteins span the lipid bilayer
Lipid-anchored - proteins attach to a lipid in the bilayer
Peripheral - membrane proteins associate with a surfaces of the lipid bilayer
29
Biological membranes are..
Asymmertrical
30
two leaflets have distinct..
lipid composition
31
in many plasma membranes, the outer leaflet contains..
glycolipids and glycoproteins
32
Structure of biological membranes
- 6 nm thick
- stable
- flexible
- capable of self assembly
33
Membranes have different ________, in different _____, and within an individual ____
Functions, cells, cell
34
Different areas of the plasma membrane...
perform different functions
35
How are biological membranes dynamic?
- lipids move easily, laterally, within leaflet
- lipid movement to other leaflet is slow
- membrane proteins diffuse within the bilayer
36
How do membrane proteins diffuse within the bilayer?
- movement of proteins is restricted
- some proteins do not move
- rapid movement is spatially limited
- long range diffusion is slow
- biochemical modification can dramatically alter protein mobility in the membrane
37
Lipid rafts are..
- membrane micro-domains
- small areas of the plasma membrane that are enriched in certain types of lipids
- relatively rigid
- some membrane proteins accumulate in rafts
- may form 'functional compartment'
38
The movement of substances across cell membranes
- lipid bilayers do not allow many compounds to pass through them freely
- small, uncharged molecules cross membranes relatively easily
- large, polar, charged compounds cannot easily cross lipid bilayers
- specific mechanisms exist for the controlled transport of many substances across membranes
39
What are the 4 basic mechanisms for moving molecules across membranes?
- simple diffusion
- diffusion through a channel
- facilitated diffusion
- active transport
40
What is simple diffusion?
- very small molecules
- uncharged
- down a concentration gradient
- O2, CO2, H2O (osmosis)
41
What is diffusion through a channel?
- small, charged molecules
- down a concentration gradient
- Na+, K+, Ca2+, Cl-
42
How are ion channels formed?
by integral membrane proteins that line an aq pore
43
ion channels are..
- selective, allowing only one type of ion to pass
| - often gated (can be opened/closed)
44
What are the 3 types of gated channels and explain each
- Voltage-gated channels - (K+) channel responds to changes in charge across membrane
- Ligand-gated channels (acetylcholine) - channel responds to binding of specific molecule
- mechano-gated channels (cations channels in inner ear) - channel responds to physical force on membrane
45
What is facilitated diffusion?
- compound binds specifically to integral membrane protein called a facilitative transporter
- change in transporter conformation allows compound to be released in other side of membrane
- compound moves down a concentration gradient
46
What is active transport?
- compound binds specifically to integral protein called an active transporter
- change in transporter conformation allows compound to be released on other side of membrane
- compound moves against concentration gradient
- requires input of energy
47
What are the functions of biological membranes?
- cell boundary
- define/enclose compartments
- control movement of material into/out of cell
- allow response to external stimuli
- enable interactions between cells
- provide scaffold for biochemical activities
48
Early Endo-membrane work revealed...
- membranous vesicles
| - extensive network of membranous canals and stack of sacs
49
Cisternae stands for
Sacs
50
End-membrane organelles are part of a _______ system in which materials are shuttled ____ and _____ from one part of the cell to another
- Dynamic
- Back
- Forth
51
How are organelles of the endo-membrane system functionally distinct from one another?
- contain a particular set of proteins
- perform a unique set of activities
- provides compartmentation and functional diversity
- conserved in eukaryotes
- dynamic structures
52
How do cells utilize several membrane trafficking pathways?
- Transport of macromolecules
- two main secretory (biosynthetic) pathways
- Endocytic pathway
53
What are the two main secretory pathways?
- constitutive - materials transported in secretory vesicles & continuously discharged into extracellular space
- Regulated - materials are stored as membrane-bound packages that are discharged only in response to a specific stimulus
54
What's a cell free system?
- Do not contain whole cells
55
Describe the RER
- Presence of ribosomes bound to its cytosolic surface; network of flattened sacs continuous with the outer membrane of nuclear envelope
56
Describe the SER
- Lacks associated ribosomes; curved, higher tubular elements; smooth vesicles
57
What are the functions of the RER?
- Protein synthesis, modification and transport
- synthesis of membranes
- Protein folding (quality control)
58
What are the functions of the SER?
- synthesis of steroid hormones
- Detoxification of diverse organic compounds in liver cells
- Carbohydrate metabolism
- Sequestration of Ca2+ in muscle cells
59
In the _________, _________ synthesize polypeptides from ____
- Cytoplasm
- Ribosomes
- mRNA
60
Translation in the cytoplasm begins on free ribosomes, and is then completed in 1 of 2 ways, what are the two ways?
- Translation is completed on free ribosomes
| - translation is completed by ribosomes attached to ER membrane (RER)
61
protein translation
- selected sites on DNA are transcribed into pre-mRNAs, which are processed into mRNAs
- mRNAs are trasnported out of nucleus
- go into the cytoplasm where they are translated into polypeptides by ribosomes that move along the mRNA
- polypeptides fold into their final conformation
62
How is the site of translation determined?
- ribosomes are targeted to the ER membrane by a 'signal sequence' in the protein being translated
- - Protein contains 'signal sequence'
o Located at its amino (5')-terminus
o Contains several consecutive hydrophobic amino acids
- Signal sequence directs synthesis to ER
- Protein moves through channel into ER
o This is co-translational import
- Protein moves through channel into ER
63
Translocon
- Groups of 2-4; hour glass-shaped protein-lined channel in RER membrane
- Ring of 6 hydrophobic amino acids at centre of pore/channel
- Pore can be plugged by a short helical plug
64
Co-translational import: synthesis of secretory proteins
- After translation and synthesis of signal sequence
o A signal recognition particle (SRP) binds to signal sequence - translation stops
o Targeting of translation complex to ER
♣ Translation complex = (SRP/ribosome/nascent polypeptide)
♣ SRP binds to SRP receptor
o SRP and SRP receptor are g proteins; hydrolyze GTP
o SRP is released and ribosome binds translocon; nascent polypeptide passes into ER lumen; signal peptide cleaved by signal peptodase; protein gets folded using ER chaperones (eg. BiP-binding protein); translocon closes; ribosomes released
65
Co-translation import of integral membrane proteins
- Transmembrane domain = stop-transfer sequence
o Positively charged amino acids next to the transmembrane segment are oriented toward the cytosol
- Initially, translation the same as for secretory proteins
- Protein does not pass completely through translocon
- Nascent polypeptide contains "stop-transfer sequences" = hydrophobic transmembrane segment (TMD)
- Translocon opens laterally and inserts TMD of nascent polypeptide into lipid bilayer of ER membrane
o Translocon orients polypeptide with the positively charged residues (next to transmembrane domain) exposed to the cytosolic surface of ER membrane
66
Once the protein is fully synthesized and properly folded, 1 of 2 options is taken
- 1. It is retained in the ER (if that is where the protein functions)
-Once in the ER, a protein is part of the biosynthetic/secretory endomembrane system and may ultimately become part of a compartment therein, or be secreted
o ER, Golgi, lysosome, plasma membrane
- 2. It is transported from the ER to the Golgi complex for further modification and delivery to distal parts of the biosynthetic/secretory pathway
- Transport from ER to Golgi complex
o Exit sites
♣ Membrane and ER lumen bud off to form transport vesicles
♣ ER-Glogi Intermediate Compartment (ERGIC)
• Region between ER and Golgi complex
• Transport vesicles fuse to form larger vesicles & interconnected tubules
o Vesicular-tubular clusters (VTCs)
• These then form the 'cis-Golgi network'
67
Examples of vesicular transport
- ER Golgi
- Organelle PM
o Exocytosis
o Secretion of neurotransmitter
- PM Organelle
- Organelle organelle
o Endocytosis
- Material moves from ER to Golgi and then to the plasma membrane and other compartments
- [proximal distal]
68
Golgi Complex named after
Camillo Golgi - 1906 Nobel prize
69
Proteins are modified 'step-wise' as they traverse the Golgi
- N-linked oligosaccharides
o Synthesis begins in ER
- Protein with N-linked oligosaccharides arrives from ER
- O-linked oligosaccharides
o Synthesis/modification entirely in Golgi
- Modification of proteins in Golgi can also contribute to protein targeting
70
Modification of glycoproteins takes place in cisternae Golgi complex
- Steps in the glycosylation of a typical N-linked oligosaccharide in the Golgi complex
- As the oligosaccharide moves through the cis to trans stacks it gets modified though the action of integral membrane proteins whose active sites face the lumen of the Golgi cisternae
71
Structure of the Golgi complex
o Smooth, flattened, disk-like cisternae
♣ (~0.5 - 1 micron in diameter)
o ~ 8 (or fewer) cisternae/stack
♣ range from a few to several 1000 stacks per cell
o curve like a shallow bowl
o shows polarity
♣ cis - medial - trans cisternae
♣ cisternae are biochemically unique
o membrane supported by protein "skeleton" (actin, spectrin)
o scaffold linked to motor proteins that direct movement of vesicles into and out of the Golgi
72
Functions of the Golgi complex
- processing plant of the cell
- synthesis of complex polysaccharides
- modification of proteins and lipids
o glycosylation (glycoproteins and glycolipids)
- transport and sorting of proteins
73
What is the advantage of having the different regions of the Golgi
- CGN acts as a sorting station
o Sorts whether proteins should continue on to the next Golgi station or be shipped back to the ER
- TGN sorts protein into different types of vesicles
o Vesicles go to Plasma membrane or other intracellular destinations (e.g. lysosomes)
74
Fully processed proteins are exported from the trans cisterna, enter the trans-Golgi network (TGN) and are then sorted and delivered to their final destinations
- Endosomes
- Secretory granules
- Lysosomes
- Plasma membrane
75
Vesicular transport = trafficking
```
- Utilizes transport vesicles (coated vesicles)
o ~50-100 nm in diameter
o Have protein-based coat on surface
o Coast has 2 functions
♣ Helps form the vesicle
♣ Helps select cargo
• Material inside/on vesicle
- Bud off donor compartment
- Fuse with acceptor (or recipient) compartment
```
76
How do COPI and COPII proteins carry out functions (I) and (II)?
- COPI and COPII proteins assemble on the cytosolic surface of donor membranes at sites where budding takes place
77
Clathrin
- Coated vesicles move from TGN to other vesicles (lysosomes, endosomes, plant vacuoles)
- COPI - coated vesicles move in retrograde
- COPII- coated vesicles move in anterograde direction
78
Vesicular transport: overview
- Trafficking vesicles to a compartment
- COP proteins help from the Transport Vesicles
- 1. Movement of vesicle
o uses cytoskeleton and motor proteins
o COP proteins specify direction of Vesicle movement
- 2. Tethering vesicle to target compartment
o via proteins called Rabs
- Docking of vesicle to target compartment
o Uses proteins called SNAREs
- Fusion of vesicle and target membrane
79
Retrieval of resident ER proteins
- Amino acid sequence that directs protein back to ER is the ER retrieval signal
- Located at carboxy terminus of protein
- Soluble/luminal ER proteins contain KDEL (Lysine-Aspartic acid-glutamic acid-Leucine) retrieval signal
- KDEL receptors in membranes of CGN and cis Golgi bind to retrieval signal of 'escaped' proteins
- KDEL Receptors bind to COPI complex proteins and are incorporated into COPI vesicles
Escaped proteins reach the ER in (COPI-coated) retrograde transport vesicles
80
Vesicular Transport
- Trafficking vesicles to a particular compartment
o Movement of vesicle
♣ Uses cytoskeleton and motor proteins
o Tethering vesicle to target compartment
♣ Uses proteins called Rabs
o Docking of vesicle to target compartment
♣ Uses proteins called SNAREs
o Fusion of vesicle and target membrane
81
Clathrin Coated Vesicles: CCVs
- Clathrin forms a 'triskelion'
- Composed - 3 heavy and 3 light chains
- Triskelions interact - polyhedral lattice, a basket like structure that surrounds a vesicle
- CCV
o Adaptor proteins between chlathrin lattice and the cytosolic face of the vesicle
o Selectively sort cargo at - TGN, cell membrane & endosomal compartments
82
COPI-coated vesicles..
move in retrograde direction
83
COPII-coated vesicles..
move in anterograde direction
84
Electron Micrographs
- A sequence of events in the formation of a CCV at the surface of the plasma membrane
- Initially a clathrin coated pit forms. The cargo receptors extend through the membrane and interact with cargo molecules in the cytoplasm. As the process continues, the vesicles round up and pinch off
85
Lysosomes
```
- Digestive organelles
o 25 nm- 1000 nm
o Internal pH of 4.6
♣ H+-ATPase
o Hydrolytic enzymes
♣ Acid hydrolase
o Lysosomal membrane
♣ Glycosylated proteins
o Protective lining next to lumen
```
86
Lysosome Function
- Autophagy
o Organelle turnover
♣ Destruction of organelles and their replacement
o Lysosomes fuses with ER-derived autophagic vacuole
♣ Forms autolysosome
o Contents enzymatically digested
♣ Forms residual body
• Released (exocytosis)
• Retained (lipofuscin granules)
- Degradation of internalized material
o E.g. plasma membrane components, bacteria (in phagocytic cells)
87
Plant Vacuoles
- Fluid-filled membrane-bound
- Take up ~ 90% of cell colume
- Tonoplast
o Vacuolar membrane
o Contains active transport systems that generate high interior [ion]
88
Functions of Plant Vacuoles
```
- Intracellular digestion (~ lysosomes)
o Low pH, acid hydrolases
- Storage
o Solutes and macromolecules
o Toxic compounds
♣ Defense mechanism
♣ Harmful by products of cellular metabolism (no excretory system)
- Mechanical support; tugot pressure
o Support to soft tissue cells
Stretches cell wall during growth
```
89
Autophagosomes
- Double membranes
90
- Exocytosis
o Involves the fusion of secretory vesicles with the PM followed by discharge of vesicle contents
o The luminal surface of the vesicle membrane becomes part of the outer surface of the PM while the cytosolic surface becomes the inner surface of the PM
91
- Endocytosis
o Involves the invagination of PM to form cytoplasmic vesicles that are transported into the cell interior
92
Peroxisomes
- Micro bodies - membrane bound ca. 1 um vesicles
- Crystalline core; catalase
- Major role in H2O2 based redox
- Do not have own DNA/ protein machinery
- Majority of peroxisomal proteins are imported directly from the cytosol
- A few proteins brought in via the ER
- Movement along cytoskeletal filaments
- Involved in ROS scavenging and signalling
- Peroxisome extensions
o Formed transiently following oxidative stress
- Peroxisome extensions called peroxules
- Undergo fission
93
The living cell
- To propagate/proliferate - replace itself
- Goes through cell cycle to ensure its survival
o To harvest energy
o To ensure that all products are utilized most efficiently
- Plastid - that can be molded - flexible
- Based on colour
- Leucoplasts
- Chloroplasts
- Chromoplasts
- Both shape & function can differ
- A variety of plastids
- Different types are interconvertible
94
What is common between all plastids
- Plastid stroma - filled extensions are called stromules
- Plastids are motile
- Produce dynamic extensions
- Contain own DNA
- Prokaryotic ribosomes
- Outer membrane contains porins
- Inner membrane - impermeable
95
Thylakoids
- Photosynthetic machinery on a system of flattened membrane sacs
96
Grana
- Stacks of thylakoids
97
Lumen
- Space inside thylakoid
98
Stroma
- Outside the thylakoid but insides inner envelope
| Contains proteins responsible for carbohydrate synthesis
99
Harvesting Light
- Several hundred Chl molecules act together as one photosynthetic unit
- The antenna system harvests light of various wavelengths & transfers excitation energy to the reaction center
100
Photosynthesis consists of
light dependent & light independent (dark) reactions
101
Light dependent
- Solar energy absorbed & stored in ATP (cell's primary source of chemical energy) and NADPH (main source of reducing power)
102
Dark reactions
- Carbohydrates synthesized from CO2 using energy from ATP/NADPH
103
Chlorophylls absorb strongly in
violet-blue & red
104
Carotenoids absorb strongly in
green region
105
Chlorophyll-a is most efficient
in promoting photosynthesis
106
Plastids are surrounded by
a loose ER cage
107
Proteins and lipids exchanged between
plastids and the ER
108
Plastids have their own DNA & ribosomes but
are also controlled by nuclear encoded proteins
109
Many plastid proteins involve
post-translational import
110
Chloroplasts have 6 sub-compartments to which proteins can be delivered
- Outer chloroplast membrane
- Inner chloroplast membrane
- Inter-membrane space
- Stroma
- Thylakoid membrane
Thylakoid lumen
111
Proteins targeted to chloroplasts have N-terminal transit peptide
- Stroma targeting domain (STD)
| - Thylakoid transfer domain (TTD)
112
TOC
Translocon of outer chloroplast membrane
113
TIC
translocon of inner chloroplast membrane
114
Protein import into chloroplasts
- Nuclear encoded genes synthesized in cytosol imported through pores in envelope
- STD - containing proteins (1a)
- TTD containing proteins (1b)
- STD- containing proteins remain in stroma after removal of STD
- TTD-containing proteins move into thylakoid membrane or into the thylakoid lumen
115
Aerobic mitochondria dependent respiration is the reverse of Photosynthesis
- Aerobic respiration in the mitochondrion results in energy generation
- Requires material for breaking down
- Plants generate the energy rich compounds that can be broken down for releasing energy
116
Mitochondrion: Karp Chapter 5 structure
- Usually depicted as oval, double membrane organelles, mitochondria undergo rounds of fusion & fission & their shape can change to be considered tubular
117
Mitochondria have two membranes
- Outer Mitochondrial Membrane (OMM)
o High lipid, low protein
o Contains many enzymes with diverse metabolic functions
o Porins
♣ Large channel proteins
♣ When open, membrane is freely permeable (e.g. to ATP)
- Inner Mitochondrial Membrane (IMM)
o High protein:lipid ratio (3:1)
o Double-layered folds = Cristae
o Cristae
♣ Increase membrane surface area
♣ Contain machinery for aerobic respiration and ATP formation
o Rich in phospholipid called cardiolipin
♣ Characteristic of bacterial membranes
118
Aqueous compartments of mitochondria
```
- Inter-membrane space
o The space between the OMM and IMM
- 2. Matrix
o High protein - gel-like consistency
o Mitochondrial ribosomes
o Mitochondrial DNA (mtDNA)
♣ Encodes polypeptides that are integrated into the IMM, ribosomes, tRNA
```
119
Major function of mitochondrion provide cells with energy (ATP) obtained from glucose
- Glycolysis
o Occurs in the cytoplasm outside mitochondria
- Pyruvic acid oxidation
o Occurs entirely in mitochondrial matrix
- Tricarboxylic acid (TCA) cycle (a.k.a. Krb Cycle)
o Occurs mainly in matrix - ends in the IMM
- Oxidation and breakdown of 1 molecule of glucose = 36 ATP
120
Oxidative Phosphorylation: ATP synthesis in the Mitochondria
- Step 1
o Electron transport and proton pumping
♣ Generates an electrochemical gradient
- Step 2
o Proton movement down electrochemical gradient powers ATP synthesis
- When ATP formation is driven by energy released from electrons removed during substrate oxidation, the process is called oxidative phosphorylation
121
Oxidative phosphorylation: step 1
- High energy electrons pass from co-enzymes (NADH and FADH2) in the matrix to electron carriers in IMM
- Series of e- carriers
o Respiratory enzyme complexes I. II. III. IV
♣ = electron transport chain
- Energy transfer at each complex used to pump H+ from matrix into inter-membrane space
- Eventually, lower energy electron (e) transferred to terminal e- acceptor (O2)
H2O produced
122
Electron-transport chain in the inner mitochondrial membrane
- Electrons enter the ETC - from NADH and FADH2
- Pass to ubiquinone (UQ) in the lipid bilayer - reduce ubiquinone - onto complex III
- Peripheral protein cytochrome c (Cytc)
- Electrons next move to the complex IV - finally to O2 to H2O
123
Oxidative Phosphorylation: step 2
- Controlled movement of protons back across IMM
o Via ATP synthase
o Potential energy in electrochemical gradient across IMM converted to ATP in the matrix
124
Protein import into Mitochondria
- Many mitochondrial proteins translated in cytosol - imported post-translationally
- Contains removable N'-targeting sequence "pre-sequence"
o - 20-35 amino acid residues, net +ve charged
- Chaperones direct protein to import complex on the outer membrane
- TOM complex (translocase of outer membrane)
- Tom - transport proteins from cytosol into inter-membrane space
- Protein then bound by TIM (translocase of inner membrane)
- Protein escorted into matrix by chaperones
- Pre-sequence - removed and protein refolds
125
Mitochondrial play an important role in programmed cell death (apoptosis)
```
- Apoptosis is characterized by
o Shrinkage of cell
o Blebbing of the plasma membrane
o Fragmentation of DNA and nucleus
o Loss of attachment to other cells
o Engulfment by phagocytosis
```
126
Normal and Apoptotic cells
- Why is it needed?
o Elimination of damaged cells
o Promoting/advancing development
o Involves caspases - cysteine proteases cleave a select group of essential proteins
127
The intrinsic Pathway of apoptosis
- Initiated by intracellular stimuli
o E.g. Genetic damage, hypoxia, virus
- Pro-apoptotic proteins stimulate mitochondria to leak proteins
o E.g. cytochrome c
- Release of apoptotic mitochondrial proteins commits the cell to apoptosis
- Cell disintegrates into condensed apoptotic body - recognized by specialized macrophages. PCD does not spill cellular content into the extracellular environment
128
The Nucleus Characteristics
o 5-10% of cell volume
o ca. 10 um diameter
o Typically one/cell
129
Functions of the Nucleus
o Storage, replication and repair of genetic material
o Expression of genetic material
Ribosome biosynthesis
130
Structure of the Nucleus
```
o Nuclear envelope
♣ Nuclear membrane
♣ Nuclear lamina
♣ Nuclear pores
o Nuclear content
♣ Chromatin
♣ Nucleoplasm
♣ Nuclear matrix
Nucleolus
```
131
Nuclear Envelope (NE): Strucutre
- 2 parallel phospholipid bilayers
o Outer membrane
♣ Binds ribosomes and is continuous with rough ER (RER)
o Inner membrane
♣ Contains integral membrane proteins that connect to nuclear lamina
o Membranes separated by 10-50 nm
♣ Intermembrane space continuous with ER lumen
132
Functions of Nuclear Envelope
- Separates nuclear content from cytoplasm
o Separates transcription & translation
- Selective barrier
o Allows limited movement of molecules between nucleus and cytoplasm
Binds nuclear lamina
133
Structure of the nuclear lamina
```
o Thin meshwork of filaments
♣ Lamins (type of intermediate filament)
♣ Approx. 10 nm diameter
♣ Integrity regulated by phosphorylation
o Bound to inner surface of Nuclear Envelope (NE)
♣ Support structure for NE
♣ Attachment sites for chromatin
o Mutations in a lamin gene (LMNA) implicated in Hutchinson-Gilford Progeria Syndrome, a rare disease that causes premature aging in children
```
134
Nuclear function is dependent upon protein import
```
- Structural proteins
o Nuclear lamins & matrix
o DNA packaging
- DNA replication
- DNA repair
- Transcription
- RNA processing & export
- Ribosome synthesis & export
- Inner and outer membranes of NE fuse at pores
o Approx. 120 nm diameter
- Gateways between cytoplasm & nucleoplasm
o 3000 to 4000 pores/nucleus
o Facilitate nucleo-cytoplasmic transport
```
135
Nuclear Pore Complex (NPC)
```
- Protein structure fills nuclear pore
o Supramolecular complex
♣ 1.25X105 kDa
♣ 100s of polypeptides
• nucleoporins (NUPs)
• Approx. 30 different NUPs
o Fits into the port, reduces functional diameter to approx. 9 nm
o Extends into cytoplasm and nucleoplasm
o Octagonal symmetry
```
136
Structure of the NPC
- FG-domains phenylalanine-glycine (FG) repeats in NPC proteins help create a mesh
- NUP136 in plants contains FG repeats
- FG-domains bind transport receptors and mediate active transport through NPC
- Prevent diffusion of proteins > 40 kD to/from nucleus
137
Functions of the NPC
- Passive diffusion of small molecules (
138
Factors needed for nuclear import
- Cargo protein contains a nuclear localization signal (NLS)
o Stretch of positively charged amino acids near c-terminus of protein
- Karyopherins
o Family or proteins; transport receptors
♣ Importins (alpha and beta)
- Energy
- Ran
o Small G protein
o (Guanine nucleotide-binding proteins) that act as chemical messengers & triggers of molecular processes
139
What are G-proteins or GTPases?
- Molecular switches
o When attached to a complex with 3 phosphate groups (guanosine TriPhosphate [GTP]) they are turned/switched on (activated). When attached to a complex with only 2 phosphate groups (Guanosine DiPhosphate [GDP]), they get turned off (inactive)
o Ran = RAs realted Nuclear protein ca. 25 kDa (RAt Sarcoma - protein subfamily of small GTPases)
140
Nuclear import model
- NLS containing protein & importin heterodimer - interact with cytoplasmic filaments - carried through NPC - FG repeats - interacts with Ran0GTP - disassociates the complex --- b-importin + RanGTP out --- a-importin + exportin out
141
Nuclear Export
- Mostly proteins and RNA molecules
o RNA molecules complexed as ribonucleoproteins (RNPs)
- Cargo proteins contain a nuclear export signal (NES)
- Exportins (type of karyopherin) bind NES
o Leads to export
- Ran-GTP required to assemble export complex
- Exportin-RNP-Ran-GTP or exportin-protein-ran-GTP complex transported to cytoplasm
- Ran-GTP hydrolysis to Ran-GDP releases cargo
142
Nucleolus
- In an interphase cell clusters of ribosomal DNA (rDNA) are gathered together as one to several nucleolus (nucleoli) that produce ribosomes
143
Function of the nucleolus
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- Ribosome biogenesis
o Synthesis of rRNA
o rRNA processing
o assembly of subunits (rRNA + proteins)
o 40S and 60S subunits are exported to cytoplasm
- tRNA synthesis
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144
The cytoskeleton
- A dynamic network of protein filaments that forms the cellular scaffolding as well as transport system for organelles and vesicles
- Three major elements
o Microtubules
♣ Hollow, unbranched tubules of tubulin
♣ Outer diameter 10-12 nm
o Intermediate filaments
♣ Fibrous, various proteins
♣ Diameter 10-12 nm
o Microfilaments
♣ Solid, thin, branched, actin polymers
♣ Diameter 8 nm
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- Functions of the cytoskeleton
- strucutre and support
- intracellular transport
- contractility and motility
- spatial organization
146
Microtubules (MT)
- Largest cytoskeletal element (25 nm diameter)
- Polymer of proteins alpha-tubulin and beta-tubulin
o Alpha/beta heterodimers form long protofilaments
o 13 protofilaments form longitudinal array hollow cylinder
o Heterodimers aligned in same direction
- (Head to tail) structural polarity
- MTs have fast-growing "plus +" end and slow growing "minus" end
- Structural polarity is important for MT growth/shrinkage and direction of movement of material along MT
147
Microtubules undergo dynamic assembly and disassembly
- In vivo, this leads to rapid turnover of most MTs within cell (half-life is minutes)
o Dynamic instability
- Shrinkage can occur very rapidly at the 'plus' end (termed 'catastrophe')
- Microtubule-Orangizing Center (MTOC) = central sire of MT assembly
- Centrosome is a major MTOC in animal cells
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Formation of MTs is regulated/controlled by Microtubule-Associated Proteins (MAPs)
- Several different proteins that bind MTs
o Modulate assembly, function
o Mediate interactions with other cellular structures (e.g. Vesicles/organelles)
149
2 classes of MAPs
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- Motor MAPs
o 2 main types: kinesin and dynein
o Use ATP to generate force
o Can move material along MT track
o Can generate sliding force between MTs
- Non-motor MAPs
o Control MT organization in cytocol
♣ E.g. Tau protein in neurons)
- Defective Tau protein = neurofibrillary tangles = Alzheimer's
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150
Motor MAPs
- Microtubule-associated (Dynein and Kinesin) can power intracellular transport
- Dynein
o Minus end-directed
- Kinesin
o Plus-end-directed
151
Microfilaments
- Smallest cytoskeletal element (~8 nm)
- Polymer of the protein 'actin'
- Polypeptide = 42 kDa, binds ATP
o Individual molecules = G-actin (globular)
o Polymerized filament = F-actin
- Several well-characterized functions
o Maintenance of cell shape
o Cell movement
o Cytokinesis
o Muscle contraction
152
Filamentous (F)-actin
- G-actin monomers have polar structure
- Monomers are incorporated into the filament in the same orientation
- Actin filament (F-actin) is polar
o Plus and minus end
153
F-actin assembly
- Globular (G)-actin polymerizes reversibly
- Nucleation (slow)
o G-actin dimers and trimers short filaments
- Elongation (fast
o Monomers add to both ends
Faster at plus end
154
Myosin is a motor protein associated with F-actin
- Large number of myosins; ATP dependent
- Most move toward plus end of microfilament
- Divided into 2 broad groups
o Conventional & unconventional myosins
- Unconventional myosins generate force and contribute to motility in non-muscle cells
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Intermediate Filaments (IF)
- Intermediate size (10-12 nm diameter)
- Exclusive to multicellular animals
- Provide structural support, mechanical strength
- Stable (relative to MTs or microfilaments)
- Fibrous proteins, contain central alpha-helical domain
- 5 classes (I-V); examples
o Keratins: epithelial cells
o Neurofilaments: neurons
Lamins: nucleus of all cells
156
Structure of intermediate filaments
- Alpha-helical domains wrap around each other forming rope-like dimer
o (Coiled-coil = 2)
- Monomers are aligned in parallel; IF dimers are polar molecules
- 2 dimers associate anti-parallel to make tetramer. Therefore assembled filaments are not polar
157
The extracellular space
Extends outwards from the surface of the plasma membrane and contains a variety of secreted materials that influence cellular behaviour
158
Extracellular space ..
mediates cell-cell & cell-extracellular matrix (ECM) interactions
provides mechanical protection
serves as a barrier
binds regulatory factors
159
Many cells of multicellular organisms ______ an ECM
contact
160
ECM
organized network of material produced and secreted by cells
161
ECM serves many important functions
sites for cell attachment
physical support for cells
contains regulatory factors
separate/define tissues
162
Most ECM have a
glycocalyx
163
Glycocalyx
cell coat
assembly of carbohydrate groups attached to proteins and lipids on the outside of the plasma membrane
mediates cell-cell and cell-ECM interactions
provides mechanical protection
serves as a barrier to some particles
binds regulatory factors
164
components of the ECM are produced by cells and assemble into a _____
network
165
proteins and glycoproteins
collagen, fibronectin, laminin
166
proteoglycans
proteins with chains of polysaccharides
167
plant cell walls
composed of cellulose, hemicellulose, pectin and assorted proteins
provide structural support to cell and to organism as a whole
protect cell from the mechanical damage and pathogen attack
contain/convey biochemical signals for cell
168
plant cell walls composed of
cellulose microfibrils embedded in a polysaccharide matrix
169
listeria monocytogenes
a major food-borne bacterial pathogen - causes listeriosis
unpasteurized dairy or raw food
uses actin assembly-inducing protein (ActA) that allows bacterium to use the actin polymerization machinery
very motile: rocketing motility
170
Virus
non-cellular macromolecular packages that can function and reproduce only within living cells
171
outside of cells, a virus exists as
an inanimate particle (virion)
172
virion comprises of
```
small amount of DNA or RNA (encoding a few to hundreds of genes)
protein capsule (capsid)
```
173
viruses bind to a cell surface via specific proteins and enter into cell
this define the cell types that virus can infect and the host range
174
wide host range
rabies can infect cells in dogs, bats and humans
175
narrow host range
human cold and influenza viruses infecct epithelial cells of human respiratory system
176
once inside a cell, the virus then hijacks cellular machinery to synthesize nucleic acids and proteins
assembles new virus particles
177
two main type of viral infection
lytic - production of virus particles ruptures (and kills) cell
(influenza)
non-lytic or integrative
- viral DNA is inserted in host genome (provirus)
viral progeny bud at cell surface; cell can survive, often with impaired function (HIV)
178
The transfer of information from DNA to protein is a two step process in all organisms
DNA --> mRNA --> protein
179
- A gene is a ______ region of DNA
transcribed
180
RNA uses the pyrimidine uracil instead of ______
thymine
181
The RNA pentose sugar is ______, not a deoxyribose
ribose
182
The DNA double helix is ______ _______ during transcription
locally unwound
183
DNA sequences position the ____ ______ to begin transcription at the beginning of a _____ and cause it to _______ at the end of the gene
RNA polymerase, gene, dissociate
184
In ________, genes are closely spaced and several can be __________ on a single RNA molecule from a _______ ________
prokaryotes, transcribed, common promoter
185
In prokaryotes, transcription and translation can occur _____________
simultaneously
186
Eukaryotes have additional levels of complexity - the primary transcript is processed and exported to the cytoplasm for _______
translation
187
The promoter of a eukaryotic protein coding gene
- Unlike prokaryotic RNA polymerase, eukaryotic RNA polymerase cannot initiate transcription on their own
o Require transcription factors binding to the promoter to help assemble or stabilize the polymerase and associated transcription machinery
188
Sequences in eukaryotic promoters also position the RNA polymerase for accurate initiation of transcription
- The TATA box is a highly conserved feature of many protein-coding genes
189
- A gene consists of its _______ and the transcribed sequence
promoter
190
The primary transcript is processed in eukaryotes
- The poly A tail is NOT encoded in DNA; it is added enzymatically by a template-independent RNA polymerase
191
Introns
o Inverting sequences
o Noncoding sequences located between coding sequences
o Introns are removed from the pre-mRNA and are not present in the mature mRNA
o Introns are variable in size and may be very large
192
Exons
o Coding and noncoding sequences
| o Composed of the sequences that remain in the mature mRNA after splicing
193
The mature mRNA contains both coding and non-coding sequences
- The non-coding sequences are untranslated and are therefore referred to as the 5' or 3' untranslated region
194
Prokaryotes
o -10 and -35bp regions upstream of start site
o polymerase binds DNA
o several genes can be transcribed on one mRNA transcript
o mRNA does not undergo further processing
o transcription and translation can occur simultaneously
o termination requires a hairpin sequence followed by 6 A's, polymerase falls off
195
Eukaryotes
o TATA box and CAAT box ~ - 20 and - 80bp upstream of mRNA start site
o Transcription factors bind DNA, which then recruits the polymerase
o Typically, one gene per mRNA transcript
o mRNA is further processed (5' cap, 3' poly A tail added, introns removed)
o Transcription occurs in the nucleus, translation occurs in the cytoplasm
o Polymerase recognizes termination sequences AAUAAA, and the mRNA is cleaved at downstream GU site
196
In prokaryotes, an RNA sequence helps position the ribosome near the 5' end to begin _______ at the beginning of a coding ________ or open ___________
translation, sequence, reading frame
197
In eukaryotes, a ______________ helps position the ribosome at the 5' end of the mRNA and the ribosome scans progressively to locate an AUG. the RNA sequence around the AUG influences where translation begins
cap-binding protein
198
The ribosome scans from the 5' end of the mRNA until a suitable start _____ is found
codon
199
Proteins are assembled on the _______ according to the mRNA sequence
ribosome
200
Amino acids joined by peptide bonds form
a polypeptide chain
201
Each amino acid unit in a polypeptide is called a
residue
202
A polypeptide chain has polarity, with an alpha-amino group at one end and an
alpha-carboxyl group at the other
203
Many genes consist of the ____ sequence, a promoter, and one or more enhancers
transcribed
204
Proteins that regulate transcription
- Basal transcription factors are proteins that bind to specific sequences within the promoter to facilitate RNA polymerase binding
- Basal factors are expressed I most, if not all cells
- Regulatory transcription factors are proteins that bind to sequence elements in promoters or enhancers, thereby facilitating (or repressing) the function and RNA polymerase
- Expressed themselves in more restricted, tissue-specific patterns
205
Chromosomes are not uniformly condensing
- Heterochromatin and euchromatin
| - Actively transcribed genes lie within euchromatin
206
DNA compaction is regulated and is additional level of control over gene expression
- Many regulatory proteins modify histone tails, thereby making the chromatin more or less accessible to basal transcription factors
