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