Organelles Flashcards
What are cell membranes primarily composed of? How is it arranged?
(Only lipid components are listed)
Phospholipids (most abundant)
Glycolipids (only on outside)
Cholesterol
The phospholipids are arranged so the extracellular and intracellular leaflets are hydrophilic, and the space in between the leaflets is hydrophobic.
What is a glycolipid? Does it have a specific orientation?
A glycolipid is a protein with a carbohydrate chain located ONLY on the extracellular leaflet.
What is special about glycolipids?
The carbohydrate chains coming off the glycolipid determine what the cell is able to interact with.
The carbohydrate chains are collectively called the glycocalyx.
What is the difference between an integral protein and a peripheral protein?
Integral: transmembrane protein (it spans the entire membrane)
Peripheral: interacts/involved with membrane but doesn’t really enter/cross it. (?typically associated with integral proteins?)
What purpose does cholesterol serve in the membrane?
It increases rigidity of the membrane, preventing components from moving around (especially in membranes with high unsaturations or in high heat conditions)
(For block 3, cholesterol does not affect fluidity. For everything else, it does.)
How would you sum up the differences between prokaryotic cells and eukaryotic cells?
Prokaryotic cells are much smaller than eukaryotic cells, and carry no organelles/cytoskeleton.
Prokaryotic DNA is circular and singular, as opposed to the multiple linear DNA molecules of eukaryotes.
Differentiate between gram negative and gram positive cells.
Gram negative: stain pink, contains TWO membranes and a THIN cellular wall in between them
Gram positive: stain purple, contains ONE membrane and a THICK cellular wall on top of it.
What are the functions of the membrane?
- Transporter proteins regulate movement of molecules across membrane
- Protect cell and provide structure
- compartmentalize biological activity
- contribute to cellular signalling (via membrane proteins)
- provide structure for biochemical activity (like ATP production)
What are the protein components of the cell membrane?
- Channel/Pump proteins
- Transporters
- Receptors
- Adhesion molecules
- Gap junctions
(try and understand what each does)
What special quality do membrane lipids have that contribute to how they comprise the membrane?
They’re amphipathic, meaning they have hydrophobic and -philic components.
Describe the general structure of a phospholipid.
One hydrophilic (polar) head
Two hydrophobic (nonpolar) hydrocarbon, fatty acyl tails
What determines membrane properties and how?
Phospholipid tail length and degree of saturation.
An unsaturated tail will form a ‘kink’ due to cis-double bonding. More kinks = more fluid membrane.
What happens to the membrane during apoptosis? What facilitates this?
Phosphatidylserine will ‘flip,’ inducing phagocytosis by macrophages.
Facilitated by ‘flippase’ enzymes.
What determines how lipids will assemble into aggregates?
Their hydrophobic interactions with water.
What lipid types become what aggregates?
Fatty acids - Micelles
Phospholipids - Bilayer, Liposomes
Note: shape of individual lipids determines what aggregates they will form.
What holds the membrane leaflets (extra- and intracellular) together? What property do membranes have because of this?
Van der Waals interactions = weak bonds between hydrophobic tails.
This means that membranes are fluid and self-healing!
Why is membrane fluidity important?
It is essential for exocytosis, endocytosis, and membrane trafficking/biogenesis
How can the function of membrane lipids/proteins be disrupted?
Interference with anchoring(?)
What can increase the fluidity of a membrane?
- unsaturated fatty acid tail (cis-double bond kinks)
- short chain
- increase in temperature
What is an acanthocyte? What is another name for it?
A red blood cell with too much cholesterol, which causes its shape to deform. It will have 5-10 irregular, blunt, finger-like projections, and is less susceptible for deformation.
aka spur cell
What is dangerous for a patient with a high reticulocyte count? What has caused their condition?
(See slide 28 for details)
If the patient eats anything sharp, they’re in danger. Clotting time has been increased (PT) and distorted cholesterol balance in plasma and RBC membrane will cause the bleeding to clot very slowly.
What conditions are acanthoctyes associated with?
Spur cell anemia, chronic liver disease
What are lipid rafts?
islands of cholesterol and glycosphingolipids (long saturated tails) that are less fluid and more thick than the surrounding leaflet. They stick out a little due to the longer tails of the glycosphingolipids
What are contained by lipid rafts?
integral and peripheral membrane proteins: clustering allows them to function together
GPI anchors: glycolipid that anchors the proteins to the plasma membrane
Name the enzymes responsible for lipid movement within the bilayer (flip-flop) and their functions.
Flippases - phospholipid specific
Scrambalases - non-specific scrambling: mix up newly-synthesized PLs. Activate during apoptosis.
What is the typical ratio of lipids to proteins in PMs?
1:1
Note: Proteins are larger and heavier than lipids, so this ratio still means that there are about 50 phospholipids per protein.
What are the functions of membrane proteins?
- Transport
- Anchor membrane to macromolecules on either side
- Signal Transduction (receptors)
- Enzymatic activity
- Cell Identity markers
List the 3 classes of membrane proteins. What do they do?
Integral
- signalling and adhesion, channels, transporters/pumps
Peripheral
- part of cytoskeleton, cytochrome C
Lipid-anchored (peripheral)
- signalling and adhesion
What are the lipid anchors, and where do they operate?
GPI anchors
- link proteins to outer leaflet
Fatty acylation or Prenylation
- link proteins to inner leaflet.
In RBCs, what are the four membrane proteins plus one cellular component that gives the RBC its deformable structure?
Transmembrane Proteins:
- Band 3
- Glycophorin
Peripheral:
- Ankyrin
- Protein 4.1?
Spectrin network is the meshwork that reinforces the bilayer.
Describe how the RBC membrane proteins interact with each other and the spectrin network to allow for a deformable structure.
Band 3 is interspersed throughout membrane. Ankyrin binds to Band 3 proteins and Glycophorins, attaching the spectrin cytoskeleton to the membrane. Ankyrin also is then linked to Protein 4.1, which is bound to Actin filaments.
(See slide 40 for a picture OR DRAW ONE YOURSELF YOU LAZY TWIT)
What causes Hereditary Spherocytosis and what can result from it?
A defect in RBC spectrin, ankyrin, or protein 4.1. A defect with spectrin may involve spectrin deficiency.
This condition may cause hemolytic anemia, due to the RBCs becoming spherocytes.
What are spherocytes? How do you distinguish these from normal RBCs?
They are RBCs that have all but lost deformability, and have taken a smaller, spherical shape that is vulnerable to splenic sequestration and destruction.
Spherocytes appear the same as normal RBCs, but noticeably lack the area of central pallor (where the indentation of a normal RBC would be).
How do the locations of membrane proteins in relation to the ACTUAL CELL affect their function?
Apical: regulation of secretion/intake
Lateral: cell-to-cell communication/attachment
Basal: anchoring/adhesion of cell
What are tight junctions, and where are they located?
The interaction of a transmembrane protein with another transmembrane protein of another cell. This interaction is impassable by other proteins, and is always located at the apicolateral border of cells.
What functions does the glycocalyx serve?
- Protection (from acid and enzymes)
- Recognition and Cell adhesion
- Repulsion (negative charge of sialic acid sugars)
- Embryonic Development (guide embryonic cells to destination)
- Different in cancer cells, which allows for immune recognition/anti-cancer therapy
The primary markers for cell recognition are:
carbohydrates
- attachment for bacteria, viruses, toxins, other cells
- WBCs attach to selectins expressed by activated endothelial cells.
Why does the nucleus require compartmentalization?
- protect DNA from harsh cytosolic environment
- separate ribosomes from pre-mRNA to prevent translation
Describe the nuclear envelope and its characteristics/components.
It has a double lipid bilayer with a perinuclear space (intramembraneous)
- Outer membrane and perinuclear space continuous with rER membrane and lumen
- Inner membrane supported by nuclear lamina
What is the Nuclear Pore Complex (NPC)? What is composed of?
Protein complex that allows transport of cargo in and out of nucleus.
Composed of Nucleoporins (glycoproteins)
- Cytoplasmic ring = 8 subunits
- Luminal ring = 8 subunits
- Nuclear ring = 8 subunits
How selective is the NPC? What are examples of cargo it would transport?
Small molecules (~9 nanometers) are passively diffused
Macromolecules are selectively, actively transported.
- import: proteins, snRNPs, snoRNPs
- export: mRNA, tRNA, ribosomes
How does the NPC import/export cargo?
Cargo Proteins have either a Nuclear Localisation Signal (NLS) or Nuclear Export Signal (NES).
Appropriate protein binds the NLS/NES and nucleoporins, importing/exporting the cargo proteins
- Importin and Exportin
The NPC requires energy. How does it acquire it?
RAN GTPase (G-protein) will switch on or off depending on location, facilitating transport. They bind to GDP or GTP.
What do GEFs and GAPs do? Where are they located?
GAPs hydrolyze (attack) GTPs GEFs exchange GDPs for GTP
GAPs are always in the CYTOPLASM, GEFs are always in the NUCLEUS.
Describe the mechanism of importing/exporting a cargo protein.
Import:
- Importin will bind cargo and import it.
- RAN GEF will bind a GTP and bind to importin, causing it to release cargo in nucleus.
- RAN-GTP bound Importin will travel to cytoplasm
- RAN GAP will break GTP into GDP, and break RAN GDP off Importin,
Export:
- RAN GEF makes RAN-GTP complex, which binds to exportin, causing it to pick up cargo and export it.
- RAN GAP will break RAN-GTP to RAN-GDP and remove it, causing exportin to drop cargo in cytoplasm.
- Exportin will return to nucleus to repeat cycle.
What mRNA is allowed through the NPC?
RNA-protein complexes. Export proteins will only allow mature mRNA through (5’ cap, poly A tail, spliced).
What is the Nuclear Lamina and what is its function?
Network of proteins including Lamins (intermediate filaments) A, B, and C, which are high-tensile proteins.
It lines the inner surface of nuclear envelope to maintain structure and protect the membranes. It also provides an anchoring site for chromosomes and a method of regulation for transcriptioni factors.
Where do chromatin fibers bind to the nuclear lamina (and inner membrane)?
On their telomeres and centromeres. Each chromosome will only occupy its defined territory, and will not overlap with another.
What happens to the nuclear lamina and envelope during mitosis? How?
It disintegrates.
Cdk1 will phorphorylate the lamins of lamina, prepping for lamina disassembly.
Inactivation of Cdk1 will dephosphorylate the lamins, marking reassembly of the envelope and lamina.
What are laminopathies? What are examples?
They are (rare) conditions in which the components of the nuclear lamina/envelope have defects, typically regarding lamin assembly and attachment to the nuclear envelope.
Examples:
- Skeletal/Cardiac Muscular Dystrophy
- Lipodystrophy
- Progeria
When do the symptoms of laminopathies typically present?
During childhood.
What are general results of having defects with lamin assembly/attachment to the nuclear envelope?
Fragile nuclear envelope (can affect physically stressed tissues like muscle, bone, skin, etc.)
Disrupts nuclear function: aberrant distribution of chromosomes or interaction with specific TFs is altered.
What are examples of Skeletal and Cardiac Myopathies?
Emery-Dreifuss Muscular Dystrophy
Dilated Cardiomyopathy
What is the pathology of Emery-Dreifuss Muscular Dystrophy?
Defect: Mutation in Emerin or Lamin A/C
Symptoms: Muscle weakness and atrophy. Sudden heart failure is common due to conduction defects and heart failure.
Cytology: Nuclear envelope is disrupted; chromatin extruded into the plasma.
What is the pathology of Dilated Cardiomyopathy?
Defect: Lamin A/C (rare cause)
Symptom: Nuclear lamina is very fragile; results in cell death due to nuclear structures/contents being damaged. Leads to congestive heart failure.
Note: on an X-ray the heart will appear to be much larger than normal.
What is the pathology of Lipodystrophy?
Defect: Lamin A/C
- preLamin A interacts with adipocyte TF, which impairs differentiation.
Symptoms: Accumulation of adipose tissue in face and neck, but significant peripheral lipoatrophy with muscle prominence.
What is the pathology of Hutchinson-Gilford Progeria Syndrome?
Colloquially known as ‘premature aging’
Defect: Altered Lamin A
- Unstable nuclear envelope. Bleb (herniation) formation and NPC clustering interference with importin/exportin function. Results in progressive nuclear damage and premature cell death, especially in cells that undergo more mechanical stress than other cells.
Symptoms: prominent eyes, alopecia, loss of subcutaneous fat, aged-looking skin, joint stiffness.
Note: Autosomal Dominant, but can USUALLY ONLY result from germ-line mutation due to condition preventing viable reproduction.
What the hell does Lamin A do that makes it so important to all the laminopathies??
It binds to:
- Architectural partners
- Chromatin partners
- Gene-regulation partners
- Signalling partners
What are the prominent subnuclear structures? Which ones have membranes?
Nucleoli
Speckles
Cajal Bodies (CB)/Gems
NONE OF THEM HAVE MEMBRANES.
Briefly describe the function of each of the subnuclear structures.
Nucleoli: rRNA transcription and modification using snoRNPs.
“ribosome factories”
- PARTIAL assembly of ribosomes
Speckles: involved in mRNA modification using snRNPs
CBs/Gems: produce and modify snoRNA and snRNA before sending out into the cytoplasm. Usually paired. Gems also contain SMN (Survival of Motor neurons Protein)
What are the RNA molecules involved in subnuclear function? What is their pathway of maturation and end destination?
snRNA/snoRNA
snRNP/snoRNP
sn = small nuclear sno = small nucleolar
- CBs/Gems produce and modify snRNA and snoRNA.
- snRNA/snoRNA is sent out into the cytoplasm, where they complex with proteins.
- Complexes are now called snRNP/snoRNP
- snRNP will head toward the Speckles for mRNA modification/splicing, snoRNP will head toward the Nucleolus(or multiple) for rRNA modification.
What is the pathology of Spinal Muscular Atrophy?
Defect: SMN Mutation - leads to defective snRNP assembly -> defective pre-mRNA splicing -> loss of motor neurons in spinal cord and brainstem.
Symptoms: Sudden onset/rapid progression of:
- muscle weakness/atrophy
- hypotonia
- Dysphagia and feeding difficulties.
What does the number of nucleoli in a nucleus and their sizes say about a cell?
Larger nucleoli/multiple nucleoli indicate ribosomal activity (aka protein production) of the cell.
What produces snRNA and snoRNA?
RNA pol II
What will snoRNP do specifically that contributes to ribosome assembly?
snoRNA region of RNP will have short sequences that are complementary to the rRNA. Base-pairing will catalyze base-modification of pre-rRNA (methylation).
What happens to the nucleolus during and after mitosis?
It will disassemble during mitosis, and then reassemble around NORs following termination of mitosis.
What are NORs?
Nucleolar Organization Regions. they contain rRNA and serve as a hub for nucleolus to reform around once cell has bypassed mitosis and resumed rRNA synthesis.
What are the substructures of the Nucleolus? What are some major structures/identifiers of these substructures?
Fibrillar Centers: NORs (pre-rRNA genes located here) and TX inactive DNA
Pars Fibrosa (dense fibrillar components): rRNA undergoing TX and cleavage/modification by snoRNPs
Pars Granulosa (granular component): diffuse grey area of nucleolus. This is where initial assembly of ribosome proteins from rRNA begins.
What kind of cells need prominent/multiple nucleoli? List some examples.
Cells that replicate many times. These cells require many proteins. Examples are:
- pancreatic cells
- plasma cells
- stem cells (developing hematopoietic precursors)
- cancer cells
Describe the relationships of the nuclear membrane, rER, and sER.
The outer leaflet of the nuclear membrane is continuous with the rER, and the rER is continuous with the sER.
What is the function of the rER?
The rER is responsible for protein production and modification (temporarily studded with ribosomes).
The ER is responsible for targeting and sending vesicles with its protein/lipid products.
What is the function of the Golgi Apparatus?
Postage center! Packages and transports molecules from the ER out of the cell (or to other organelles?).
Where do the protein products of the rER go?
- ER
- Golgi Apparatus
- Endosomes
- Lysosomes
- the Plasma Membrane
- Secretion (out of the cell)
Describe the pathway through which a transmembrane (TM) protein would reach the plasma membrane.
- TM proteins ‘threaded’ into rER membrane
- membrane will pinch off to form a vesicle.
- Vesicle moves to and becomes a part of the Golgi Apparatus
- the Golgi Apparatus will pinch off the membrane containing the TM protein again and send it to the Plasma Membrane.
NOTE: notice how the TM protein never actually moves, the membrane that carries it is the component that does the actual moving.
How do lysosomal enzymes become a part of lysosomes?
Same way as TM proteins to PM, except vesicle budding off of rER is a lysosome instead.
What is the function of the sER? How does its function differ across cells?
General function:
- Membrane lipid synthesis/modification
In Hepatocytes:
- Detoxification
- Lipoprotein production
In skeletal muscle cells:
- Store/release calcium for muscle contraction.
- forms a network called the Sarcoplasmic Reticulum
In what cells is the sER most prominent? What happens when it is stimulated?
Cells that synthesize steroids, triglycerides, and cholesterol.
Increases in size to secrete steroids/detoxify drugs.
What proteins are captured by the ER?
- TM proteins
- Soluble Proteins (enter ER lumen for secretion/delivery to organelle)
What types of translocation are proteins involved in?
Cotranslational
Post-translational
What kinds of proteins undergo Cotranslational translocation?
Same proteins that are captured by the ER.
TM proteins, Soluble Proteins
What kinds of proteins undergo Post-translational translocation?
Pretty much every other protein. These are discharged in the cytosol.
(Ex. proteins targeted to nucleus, mitochondria, peroxisomes)
Describe the mechanism of Cotranslational Translocation.
- Protein has an ER Signal Sequence (usually at N Terminus)
- Signal Recognition Particle (SRP) binds to ER signal sequence
- SRP binds to SRP receptor in ER membrane
- SRP complex brings ribosome to a Translocon and transfers the ribosome to a translocation channel
- SRP complex displaces; Ribosome transfers growing polypeptide chain through lumen of translocon.
Where does the ER signal sequence go during translocation? Why?
It remains in the lumen of the membrane (in the translocon) because it is hydrophobic.
What is BiP and why i s it important?
BiP (Binding Protein) is a lumenal ER chaperon, and it helps fold proteins properly as it is translated. It will bind the peptide that is in the lumen and pull it further into the ER.
What happens to an improperly folded protein?
It will never get further than the lumen of the translocon.
What is the fate of the ER signal sequence? What enzyme performs this function?
It is cleaved as the protein enters the ER lumen.
Signal peptidase
What happens to a protein chain that has an additional hydrophobic region?
It becomes a Single-Pass TM Protein. The additional hydrophobic region will remain in the lumen of the translocon as the protein is synthesized. When synthesis is completed, the ER signal sequence is cleaved, and the finished protein is left embedded in the membrane as an integral protein..
What is the additional hydrophobic region of a Single-Pass TM protein called?
Stop-transfer signal.