Cell Structure Flashcards
Cholesterol effect on cell membranes
Stiffens
reduces permeability
inhibits phase changes
Membrane Function
*Establishment of specialized environments
*Boundary between inside and outside of cell
*Define intracellular compartments
*Serve as a scaffold to organize protein complexes *(molecular machines) involved in numerous biochemical reactions
*Semi-permeable barrier
*Transport
*Sensing and responding to environment – cell signaling
*Cell protection and identification
*Cell junctions and adhesion
What do cystic fibrosis, muscular distrophy and hereditary spherocytosis all have in common?
They are all diseases involving cellular membranes or membrane proteins
3 important types include:
Phospholipids
Cholesterol
Glycolipids
*All these lipids are amphipathic – possess hydrophobic and hydrophilic regions
*By mass, phospholipids and sterol make up the bulk of the membrane lipid.
*Phospholipids – 4 major types
*Quantitatively minor - but functionally very important - lipids include glycolipids and a type of phospholipid called phosphatidylinositol
It is estimated that eukaryotic membranes contain 500-1000 distinct types of lipids
Glycolipids
Some neutral, some charged
Present only on non-cytosolic leaflet (b/c that’s where enzymes that add sugar part are)
May partition preferentially into lipid rafts
Most complex are gangliosides; negatively charged sialic acid residues; enriched in neurons and apical surfaces of epithelial cells
Functions
Protection (glycocalyx)
Surface properties of membranes
Cell identification
Cell adhesion
Phosphotidylinositol
Can be phosphorylated at diff positions by kinases. Diff location –> diff steric surface –> diff fnxn. Diff proteins bind based on where PO4’s are. Phosphatases can de-phosphorylate. Lipases can clip off phosphotols from diacylglycerol parts. Both have diff signaling transduction.
How are phosphatydalinositals involved in cell signaling?
1 - binding and activating various enzymes at the membrane surface
2 - serving as a substrate for membrane-associated phospholipases
What synthesizes phosphoglycerides (phosphatidylethanolamine, phosphatidylserine, phosphatidylcholine)?
Endoplasmic reticulum
What synthesizes Sphingomyelin?
made from sphingosine, which is synthesized by the Golgi apparatus
What makes glycolipids?
also made from sphingosine, in the Golgi apparatus
What is the behavior of phospholipids in the lipid bilayer?
Can flex, rotate, and are laterally mobile within a leaflet (with regional restrictions)
-Spontaneous flipping between leaflets rare.
Flipping of membrane phospholipids is rare, but can happen how?
Flippases recognize non-homogeneity. Scrmbleases grab more randomly and mix things up.
Specialized patches of lipids and proteins are present in membranes = Lipid Rafts
3rd type of lipid asymmetry – patches of enriched areas with sphingolipids, cholesterol and certain proteins – form “rafts”. E.g. proteins w/ longer hydrophobic regions found here.
Membrane Proteins
Alpha-helical strx of transmembrane proteins – due to lack of h2o in transmembrane region, prot h-bonds w/ itself forming helical strx.
Beta-barrels are “integral membrane” proteins; very strongly bound within.
Peripheral prot’s are more easily removed; are on both sides.
How can peripheral proteins become anchored?
Add lipid group (purple squiggly tails in figure from slide). Can also have GPI anchors – oligosaccharide protein linked to anchored lipid on external surface.
_______, a heavily glycosylated membrane region, acts as a proctection barrier for cells. Also serve in cell identification due to variety of sugar moieties.
Where do membrane proteins get glycosylated?
Glycocalyx.
glycosylation occurs in ER on lumen side.
After being packaged and exported from ER, sugars face out from cell membrane.
______ can bind to both intra and extracellular material. They function in both adhesion and signaling and are common in epithelial cells.
Epithelial cancers often ignore signals that detachment has occurred. This is an example of inside-out or outside-in signaling.
Integrins
outside-in signaling occurs in epithelial cancers. integrins’ int’x w extracellular stuff due to changes in integrin reactions with intracellular components.
______ links protein in RBC’s. In most cells ______ does this.
Spectrin in RBC’s is like filamentous actin in other cells
_______ is a large integral membrane protein that self-associates in the presence of calcium ions. It is an important adhesive molecule, linking cells together that express the same type of cadherin (different types of cadherins adhere cells together in tissue-specific patterns).
Cadherin
SER
SER –lipid synthesis, Ca++ regulation, detoxification
RER
Protein Synthesis, but generally not cytosolic proteins. They’re made in ribosomes not on RER.
What determines whether a polyribosome becomes attached to an ER membrane or remains free-floating in the cytoplasm?
Signal sequence binds to signal recognition particle. Receptors are in ER for signal rec partical and becomes bound to membrane of RER.
Protein translocator
ID’s PP & forms pores, opens laterally to release prot’s into plane of membrane. Different integral membrane proteins associate differently in terms of what faces cytosol/lumen.
Integral protein introduction to membranes
piptidase clips protein which ends up in lumen. Chaperone proteins help this process by associating w/ them and help pull them into lumen as well as aiding proper folding. …lots of misfoldings can occur basis of lots of diseases; Alzheimer’s. ER has a robust system for detecting misfolded proteins. What determines single pass, multipass and what faces which direction? Signal sequence in PP itself. These sequences binds in a specific way to translocator protein. Orientation determines what faces where. # of sequences det # of passes. Upon completion, translocator has to release protein to membrane of ER…right
Glycosylation of intermembrane proteins?
Glycosylation Assembled initially on lipid molecule dolichol on ER membrane. Transferred to Asn residue via N-linked glycosylation. Can have multiple or just one Asn residue glycosylated. Process begins on cytosolic side, but is completed on lumen side. Most glycosylated proteins are N-linked, but also a limited amount of O-linked glycosylation: linked w/ Ser or Thr; heavy O-linked glycosylation in proteoglycans done in golgi.
Proteoglycans
special class of very heavily glycosylated proteins. The protein core of a proteoglycan is made in the ER, but glycosylation (via an O-linkage) occurs either in the Golgi apparatus or outside the cell by enzyme complexes embedded in the plasma membrane.
glycosaminoglycans are added one at a time, by specific glycosyl transferases. Sugars are usually sulfated and negatively charged, which attract cations and water, leading to the formation of hydrated gels.
Glycoprotein Comparisons
Proteoglycans:
O**-linked
**glycosylated** in G**o**lgi or outside cell
Up to **95% carbohydrate by weight**
Highly **charged** GAGs typically about **80 sugars long
Other glycoproteins:
N-linked
Glycosylated in ER and modified in Golgi
Usually only a few % carbohydrate by weight
Numerous short, branched oligosaccharide chains
Protein Synthesis - Quality Control
CHAPERONES help nascent proteins fold correctly (present in both cytoplasm and ER).
Misfolded proteins are ubiquinated (in cytosol) and destroyed by PROTEASOMES (in cytosol).
Misfolded ER proteins are retrotranslocated into the cytoplasm by a membrane translocase complex for ubiquitylation and disposal.
Misfolded proteins are destroyed. System is proteasomes. Also destroy normal proteins that cells need to get rid of. Where are proteasomes? Cytoplasm. Thus, target proteins need to leave ER. Chaperones (like ubiquitin) help. Glycanases trim off sugars. Proteins are tagged w/ ubiquitin (in cytosol) to be recognized and destroyed by proteasome. Cystic fibrosis; slightly misfolded, but still functional Cl- transporter. System recognizes it and destroys it….even though its functional.
_________ is believed to be the primary cause of Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, Creutzfeldt-Jakob disease, cystic fibrosis, Gaucher’s disease and many other degenerative and neurodegenerative disorders
Protein misfolding
Different ways cells address accumulation of misfolded proteins
If in cytoplasm, called Heat-Schock response. Misfolded in ER; Unfolded Protein Response. Don’t memorize differences, but know 3 mechanisms of detection and response: IRE1 – a kinase that recognizes misfolded proteins and phosphorylates itself and acts as a splicing machine splicing out mRNA and stimulates chaperone production to correct misfoldings. PERK – Increases chaperone prod & inhibits translation factors (decrease prot synth to reduce load on ER). & ATF6 – Involves protein that itself acts as a transcription factor regulating proteolysis and stimulates chaperone production to help.
OTHER FUNCTIONS OF ENDOPLASMIC RETICULUM: Lipid synthesis, Ca++ regulation and detoxification
Lipid Synthesis
Phospholipids and cholesterol are synthesized by ER enzymes that have their active sites facing the cytoplasm; scramblases equilibrate lipids between the bilayer leaflets
Ceremide is made by ER, transported to Golgi and used to make glycolipids and sphingomyelin
True false, Cells normally keep cytosolic Ca++ levels high
False, cytosolic Ca++ levels are kept very low.
ER membranes possess Ca++ transporters that actively transport Ca++ into ER lumen…(can pump back out w/ other transporters if necessary, though)
Detoxification
Most occurs in SER (less in RER)
Carried out by cytochrome p450 family of enzymes
These enzymes render foreign compounds more hydrophilic so they can be released into the bloodstream and eliminated by the kidneys
Sanfilippo syndrome
an example of compromised lysosome function
Membrane Trafficing
A central feature of ER, Golgi and lysosome functioning is the formation and transport of membrane-bound vesicles, in concert with the ability of the plasma membrane to bring into, and release material from, the cell by the processes of endocytosis and exocytosis.
Numerous prominent medical issues are known to result from specific perturbations in the functioning of these organelles.
Golgi Apparatus:
Which side is cis FACE? trans?
Just downstream of ER. “pancake” flattened sacks interconnected to tubules and vesicles. Modify proteins. Proteins get to golgi from ER via budding off vesicles. On opposite side of golgi, vesicles pinch off.
Cis – ER side; trans – exit side. Different sides have different enzymes; proteins are SEQUENTIALLY MODIFIED as they enter and leave golgi.
Golgi Function
Receives lipid and protein products from the ER
Returns ‘escaped’ proteins that should be resident in ER
Modifies glycoproteins (both trimming and addition)
Sulfation and other post-translational modifications
Glycolipid and sphingomyelin production
Adds O-linked oligosaccharides to proteoglycans
‘Post-office’ of the cell: directs material to be transported further along 3 primary routes:
- Lysosomes
- Secretory vesicles
- Plasma membrane
What’s “fuzzy coat” on membranes?
Formation of COP1 and COPII vesicles involves what process when binding?
Lots of different G proteins that act like switches depending if they are bound to GDP or GTP. Active when bound to latter. Removal of GDP and exchange for GTP turns on. Other enzymes hydrolyze GTP –> GDP.
COPII proteins have Sar-1, a small G protein. Binds to membrane and activates and rcruits other adaptor and cargo proteins which concentrates the cargo and curve the membrane. Other prot’s recruited, vesicle buds off to move to golgi (again, COPII example).
What ID’s returning proteins?
What mechanisms determine where vesicles go, and how do they fuse with their appropriate targets?
Rabs (small family of GTP-binding proteins) serve as identifiers and determine what’s appropriate to bind with.
Snares facilitate membrane fusion. V-snares are long integral membrane proteins associated w/ vesicles. T-snares are associated w/ target membranes.
Also, the lipid content of membranes (i.e. phosphatidylinositols) is a critical identifier in determining where vesicles form and fuse
Major function of the Golgi
1) oligosaccharide processing of N-linked glycoproteins made in the ER
2) Addition of mannose-6-phosphate on lysosomal enzymes
True or false, packaged “goods” leaving golgi for exocytosis are signal dependent.
False. This is the default pathway.
Goods sorted to lysosomes and those
Sorted to secretory granules require specific signals
Lysosomes.
What determines if something should be sent here?
Where do enzymes come from?
Digestive organ of the cell…are endosomes until enzymes hydrolases from golgi arrive to lower pH
Specific glycosylated oligosaccharides ID if something should be sent to lysosomes. Older parts of organelles are often sent to lysosomes (autophage). Also, external content taken in by phagocytosis (large scale) and via endocytosis (more specifically) can be fused w/ lysosomes. Hydrolytic enzymes come from golgi. When are these active? Low pH. Hence, these hydrolases are relatively inactive until they get to lysosomes.
What lowers pH in endosome?
Proton pumps.
How are lysosomal acid hydrolases packaged and delivered to endosomes?
Endocytotic vesicles can appear to be ‘coated’ or ‘uncoated.’
Coated endocytotic vesicles contain clathrin as a transient peripheral membrane protein
Many uncoated vesicles contain caveolin as a permanent integral membrane protein.
Caveolin are associated w/ signal transduction events and uptake of materials
What actually helps endocytotic vesicle pinch off of vesicle?
What removes clathrin coat?
Dynamin: protein that helps clathrin-coated transport vesicle “bud” off from membrane
Uncoating ATPases (Hsp70 family) remove clathrin coat, which is recycled
Exocytosis occurs these two ways:
Constitutive secretory pathway (unregulated)
Regulated secretory pathway (Ca++ often trigger near secretory vesicles; mast cells have lots)
Review of Vesicular Trafficking and Membrane Flow
Prominent types of coat proteins involved in vesicular trafficking:
*COPI – Golgi to ER
*COPII – ER to Golgi
*Clathrin – endocytosis, Golgi to endosomes/lysosomes
Recognition of vesicle and target membranes and membrane fusion mediated by:
*Rab proteins
*Effector proteins
*SNAREs
In addition to these pathways, another pathway exists that is able to move material across cells – transcytosis.
Mitochondrial morphology
Mitochondria tend to localize along microtubules and can establish close connections with the ER
Mitochondrial location
tend to localize to sites of high ATP utilization. Examples include numerous mitochondria aligned along the contractile myofibers in cardiac muscle, and a spiral array of mitochondria around the highly motile sperm tail (flagellum).
Mitochondrial plasticity
highly dynamic, and continually undergo fission and fusion. Regions of continuous, extensively branched arrays
How are nuclear-encoded cytosolic mitochondrial proteins recognized and imported into mitochondria?
Shape (alpha-helical strx) is what routes them into mito. TOMs transport outer –> inner membrane.
Or, TOMs transport all the way into matrix by int’x w/ TIMs.
OXA located in inner membrane and transports mito-made proteins out.
Mitochondrial biogenesis - lipid
Instead of membrane flow, ER lipids can get plucked out and placed in mito outer membrane
Peroxisomes
Single membrane bound
involved in a variety of oxidation reactions, including the production and removal of H2O2. Contain high concentrations of enzymes.
Detoxification reactions (e.g., oxidation of ethanol to acetaldehyde)
***Beta-oxidation of fatty acids into acetyl CoA***
Formation of myelin phospholipids
Peroxisomes appear to be produced through a hybrid process of budding from the ER, followed by import of peroxisomal proteins made by free ribosomes in the cytoplasm and fission. Peroxisomal proteins possess a three-amino acid import signal at their C-terminal end, and are imported into the peroxisome by translocator complexes. Defects in peroxisomal protein import and function is particularly damaging to the brain, liver, and kidneys, and is fatal shortly after birth.
Nucleus
Nucleus – 2 membranes with pores and lamina. Histones enter in thru pores, rna out. Space b/w inner and outer membranes is continuous w/ ER in places.
**The nuclear matrix is a filamentous scaffolding made up of lamins and other less well-characterized proteins and RNA**.–thought to provide sites of attachment for specific spots along chromosomes; this attachment appears to be dynamic, and can help regulate gene expression.
Chromosomes
Function of centromeres – segregation to each daughter cell so they can be identical. Euchromatin – noncondensed –active. What crx nucleolus? ***Nuclear org region–> ribosomal rna. Ribosomal protein made in cytosol brought in and join together.
Chromosomes tend ot occupy “territories”
In periodic chormosome attachment to the nuclear matrix, _____ tend to be hot spots for topoisomerase activity.
MARs
MARs intx w/ scaffolding, appear ev 50K-200K nt pairs contain mult small genes, not big enough to contain large genes. Loops function independently from neighboring loops – example of higher level of gene expression. Also thought MARs are hot spots for topo’s – to resolve torsional problems. Drugs let topo’s cut, but not repair.
______ are another correlate of higher level expression in EK chromosomes
relocation to gene “neighborhoods”, away from heterochromatic regions, and to inactive regions to quiet expression.
Nucleolus
the ribosome producing factory
The most obvious nuclear structure visible is the nucleolus. The nucleolus is a large aggregate of macromolecules, including:
rRNA genes
Precursor rRNAs
Mature rRNAs
rRNA processing enzymes
ribosomal proteins
partially assembled ribosomes
How do nuclear products such as mRNAs and ribosomal subunits exit the nucleus? How do nuclear proteins such as histones and transcription factors enter the nucleus?
Nuclear pores are permeable to small molecules (5000 daltons or less) w/o any restrictions, even if charged. >60K daltons needs to be recognized and actively transported. Nucleoporins form 8 arrays/ring-like strx. Filaments may help intx w/ transported cmpds
