Cells and Organelles Flashcards
Describe the method of preparation of light microscopy.
- Fix the tissue in formalin to preserve structure.
- Embed the tissue in a paraffin wax
- Section the tissue and place on glass microscope slide
- Stain the tissue for light microscopy and preparation of digitized images (ie: H/E)
What is light microscopy used to identify
organelles, cells, tissues, organs
Describe Hemotoxylin
- basic dye (dye + Cl- )
- reacts with anionic groups (carry a negative charge)
- stain things blue/purple (darker) ; darkness depends on the concentration of the substances.
- BASOPHILIC
Give some examples of basophilic structures
nucleus (due to negative charge from nucleic acids in DNA/RNA) Rough ER (if a lot) due to nucleic acids Cartialge, because lots of proteoglycans/ glycosaminoglycans Glycosaminoglycans (ie: Keratin sulfate, chondroitin sulfate) due to the negative charge on the sulfate (SO4 - ) group
Describe Eosin
- acidic dye (Nat + dye - )
- react with cationic groups (carry a net positive charge)
- stain things red/pink (lighter); darkness depends on the concentration of substances
- EOSINOPHILIC or ACIDOPHILIC
Give some examples of eosinophilic structures
cytoplasmic filaments (like in muscle cells) cytoplasm, especially mitochondria extracellular structures, like type I collagen fibers
What is electron microscophy (TEM) used to identify
subcellular analysis.. the identification of organelles within the cells; electron dense = black areas, electron lucent = white area (does not necessarily correlate to basophilia/eosinophilia)
Describe the method of preparation of TEM
- tissues fixed
- embedded in plastic
- sectioned
- stained with HEAVY METAL (ie: osmium tetroxide)
TEM vs. Light microscopy
TEM allows for a more defined visualization and for examination sub-cellular
TEM uses a heavy metal to stain, LM uses H/E to stain
TEM: prep/embedded onto plastic slides, LM: embed into parrafin wax, prep onto glass slides
Describe the cell
basic structural and functional unit of the mammalian body; variations in structure (and thus function) give variability in body tissue types
What contents do all cells have
nucleus, organelles, cytoplasm
Describe the Nucleus structure, components, function, stain
- double membrane
- contains genetic information
- separates nuclear transcription of DNA to mRNA from the cytoplasmic translation of mRNA into protein
- Contain: chromatin, nucleolus, nuclear envelope, nuclear pores
What is the function of the nucleolus
site of RNA synthesis and DNA replication
initial site of ribosome assembly
What are inclusions
Cell-type specific membrane or non-membrane bound materials in cytoplasm
What are the general functions of the cell membranes?
- semi-permeable barrier that surrounds the organelles
- basic structural organization
- delimit cellular functional compartments and concentrate metabolites for biochemical pathways
- contain lipids, proteins, and carbohydrates to allow it to function
Fluid mosaic model
proteins in the plasma membrane can move laterally (PM is not a rigid structure)
What are cell membranes composed of?
-phospholipid bilayer: two fatty acid chains and a polar head group
fatty acid chains directed inward (to exclude water), heads directed towards cytoplasm/extracellular fluid
-proteins, lipids, cholesterol, carbohydrates, glycoproteins, etc. all on/in membrane
What way do the carbohydrate group of glycoproteins usually face?
Towards the extracellular side (outside of the cell)
How does the plasma membrane appear in TEM? in LM?
TEM: two outer electron dense lines (polar head groups), one inner electron lucent line (fatty acid tails); called the “trilaminar membrane)
LM: a line
Describe cholesterol; what is its function? what is its structure?
Function: Structural rigidity; prevent extremes in consistency of membrane
Structure: BOTH a hydrophilic and hydrophobic portion
-OH aligns with polar head groups (hydrophilic)
-steroid rings tuck with fatty acid (hydrophobic)
Describe Integral Membrane Proteins (general)
- partially or fully embedded in the lipid bilaryer
- CAN move laterally within the membrane
- CANNOT be removed without destroying the membrane
Describe Transmembrane Proteins (general)
type of integral membrane proteins that span the bilayer and have domains that are exposed to each surface of the membrane
glycoprotein
an integral membrane protein that has a carbohydrate attached (on the extracellular side)
Peripheral Protein
- proteins that are indirectly linked to the plasma membrane via protein-protein interactions or protein-phospholipid interactions
- DO NOT insert into the phospholipid
- usually in the cytoplasm (intracellular) and attached to cytoskeleton
Transporter Protein
- aka “pump” protein
- type of transmembrane protein that transports ions, amino acids, and sugars across membrane
- REQUIRES ATP
- basically just move things in/out of cell
Channel proteins
form pores in the membrane
Anchor Proteins
- aka “linker” proteins
- transmembrane protein that are attached to proteins in the cytoskeleton, and thus link the cytskeleton to proteins in the extracellular matrix
Receptor Proteins
transmembrane proteins that bind to extracellular proteins (ligands), which initiates cell signaling within the cytoplasm
Structural proteins
function in forming cell-cell anchoring or adhesion junctions can also form cell-ECM adhesion junctions
Describe the structure, function, and location (in the body and cell) of the glycocalyx
Structure: glycoproteins + glycolipids = carbohydrate coat on the extracellular surface of cells
Function: protect the cell surface, cell-cell interactions, hold fluids to the cell surface, receptor sites, enzymatic ractions
Found: in the small intestines and kidney (PCT)
Describe Freeze Fracture
lets you look at the organization of the PM
Freeze the cell, and hit it to break apart the cell membrane; this is how you can get integral membrane proteins out (you need to destroy the membrane). This results in a P side (Protoplasmic) and an E side (external or Extracellular side). Integral membrane proteins will go to one side.
** can do to organelle cell membranes or plasma membrane!
Which side has more proteins on it after freeze fracture? Why?
P side (faces the cell/cytoplasm), because integral proteins can be attached to the cytoplasmic face of the phosphlipid bilayer via peripheral and cytoplasmic proteins (anchored to the cytoskeleton) so when its hit the the protiens are pulled towards the cytoplasm
What does the result of freeze fracture look like in a TEM?
P side: lots of bumps (integral proteins)
E side: lots of pits (cavity left over from the integral membrane protein being pulled through
How many bilayers does the nucleus contain?
2 bilayers; 4 layers
What is chromatin? what is it made up of, and what is its function
complex of DNA, histones, and other nuclear proteins
Function: 1) to package DNA into a smaller volume to fit in the cell, 2) to strengthen the DNA to allow mitosis, 3) to prevent DNA damage, and 4) to control gene expression and DNA replicatio
What is the nucleosome? Structure/Function
smallest unit of chromatin
DNA + histones (beads on a string)
TRANSCRIPTIONALLY ACTIVE
found in euchromatin, heterchromatin and chromosomes
What are chromosomes? what are they made of/ how do they form?
- highly condensed loops of chromatin (the ones in mitosis are the most condensed form); (chromatic fibers/fibrils)
- condensing of chromatin is done via more organization around histones
Euchromatin; what is it, and what does it look like in TEM/LM?
stretched out form of chromatin
transcriptionally ACTIVE (prominent in metabolically active cells)
LM: less basophilic areas in nucleus
TEM: electron lucent areas in nucleus
Heterochromatic; what is it and what does it look like in TEM/LM
highly condensed form of chromatin
transcriptionally INACTIVE
LM: basophilic clumbs in nucleus
TEM: electon dense
Where can heterochromatin be found?
all in nucleolus:
- marginal (around the perimeter)
- karysome (clumbs distributed throughout the nucleus)
- associated with nucleolus
What is the structure of the nucleolus? how does it stain?
contains rRNA
NOT surrounded by a membrane
stain: LM: basophilic; TEM: different electron densities
Nuclear Envelope; structure/ function
Inner and outer nuclear membrane, with an intervening perinuclear space
separates the nuclear contents and function from cytoplasm
what is the inner nuclear membrane in contact with?
the nuclear lamina
what is the function of the nuclear lamina?
nuclear organization, cell cycle regulation, and differentiation
What is the perinuclear space continuous with?
the lumen of the endoplasmic reticulum;
makes sense so you can transport ribosomes; (RER is continuous with the outer membrane and inserts into the perinuclear space)
what is the outer nuclear membrane continuous with? associated with?
continuous with the endoplasmic reticulum ( SER) and associated with ribosomes
Nuclear Pores; where are they found? what is their function? what do they look like in TEM?
found when the inner and outer nuclear membranes are continous with each other;
function: bidirectional movement of molecules between the nucleaus and the cytoplasm
in TEM: look like braks/gaps in the marginal heterochromatin
Nuclear pore structure
central pore surrounded by 8 protein subunits
How are things transported through the nuclear pore?
the central pore acts like a channel where ions and small ions can freely diffuse through the; proteins need signals to actively transport through
How are proteins transported into the nucleus (from cell)? out of nucleus (to cell)
INTO nucleus: nuclear localization signal needed then active transport
OUT OF nucleus: nuclear export sequence (active transport)
Smooth ER; structure, function,location, and stain/visualization
Structure: single membrane bound network of tubules; no ribosomes
Function: lipid metabolism, carbohydrate metabolism, and detoxification
location: along the nuclear envelop (starts), in steroid secreting cells (Leydig cells, ovaries, adrenal gland), hepatocytes
Appearnace: look like tubes
Describe the SER function in hepatocytes
- Lipid metabolism: convert lipid soluble or water insoluable compounds to water soluble compounds so that they can be eliminated via urine
- glycogen metabolism
- detox
SER in cardiac and skeletal muscle
called sarcoplasmic reticulum; functions as a calcium reservoir
Rough ER visualization on TEM/ LM
TEM: has ribosomes (dots), long parallel membrane bound saces (cisternae)
LM: basophilic if lots of RER (ie: plasma cell) or else it will be eosinophilic if not a lot
What side are the ribosomes located on in RER
located on the cytoplasmic side (not the lumen side of the cisternae)
What is the function of RER
protein translation (more active the cell is in protein translation, the more RER in the cytoplasm) protein synthesis: proteins going to golgi, lysosomes, PM, and for secretion
where do the proteins synthesize in the RER go?
golgi, lysosomes, PM, and secretion
What are polysomes
non- ER membrane bound ribosomes (no structural difference)
Function of polysomes
protein synthesis
where do proteins made in polysomes travel?
nucleus, mitochondria, peroxisomes; cytosol, peripheral membrane proteins
what is the function of the golgi aparatus?
to modify, package, and sort proteins that are synthesized in the rER
what molecules go through the golgi after the rER?
secretory protein, glycoproteins, plasma membrane proteins, lysosomal proteins, and membrane lipids
what does the golgi apparatus look like?
flattened, slightly curved, membrane bounded, smooth surfaced cisternae (like a stack of flat cut open pita)
edges of the cisternae may have membrane bound vesicles
what is the function of the cis-Golgi? where is it located/what next to?
- closest to rER
- transport vesicles get proteins to cis Golgi from rER vis COP-II coated vesicles
how do proteins get to the golgi apparatus for sorting/modification?
via trasport vesicles coated in COP-II from rER to cis side of golgi
go through the travels of a protein (from synthesis to transport)
made in rER (or polysomes).
get to golgi via COP II vesicles
go through the golgi via vesicular or cisternal model
modified in the golgi
eventually get to trans golgi network where vesicles bud off and deliver their contents to appropriate location (TGN = sorting)
explain the vesicular transport model
vesicles move proteins between cisterna from the cis face to the trans face;
modified by enzymes located in specific cisternae
**basically: same vesicle moves the protein through cis –> medial –> trans through different cisternae
explain the cisternal maturation model
protein remain in one cisternae which matures from cis to medial to trans
which side is the TGN usually facing
towards the cell membrane.. because a lot of vesicles with proteins are transported to the plasma membrane
what is the function of the TGN?
where proteins are sorted
vesicles bud off from the TGN and deliver their contents to the appropriate location
what are the main ways that proteins are sorted in the TGN?
- inserted in the plasma membrane (ie: proteins and glycolipids)
- Exocytosis (leave the cell).. vesicle fuses with the plasma membrane and releases contents outside of cell
- become part of endosomes/lysosomes (IF manose 6- phosphate attached)
2 exocytosis pathways
1. constitutive secretory
- constitutive secretory: proteins are continuously modified in the golgi and delivered to the plasma membrane in transport vesicles. MOLECULES RELEASED IMMEDIATELY AFTER SYNTHESIS
ie: immunoglobulin secretion by plasma cells and procollagen by fibroblasts
**proteins delivered to PM and immediately released after synthesis
2 exocytosis pathways
2. regulated secretory
proteins temporarily stored in secretory vesicles in cytoplasm
signaled for release via hormone/neural stimulation
(ligand binds to extracellular receptor and signal cascade starts).. causes the vesicle to fuse with PM
ex: zymogen granules containing digestive enzymes by acinar cells of the pancreas
Lysosome
membrane bound organelle that have an acidic pH and contain hydrolytic enzymes
late endosome + vesicle with acid hydrolases = lysosome
what hydrolases are in lysosomes
protease, nucleases, glycosidases, lipases, phosphatases, and aryl sulfatases for the breakdown of polysaccharides, proteins, lipids, nucleic acids, phagocytosed microorganisms, cellular debris and ages organelles
what is the optimal environment for lysosomes to be active? how is this achieved
pH 5.0 (acidic)
via proton pumps in the lysosome membranes that transport H+ into the organelle to maintain a low pH
Lysosomes in TEM
active: heterogenous; rounds/irregular shape with varying electron density material inside
inactive: N/A`
Formation of lysosomes
- Acid hydrolases (glycoproteins) formed in rER and transported to Golgi for modification
- Acid hydrolases modified so that the Mannose-6-phosphate is exposed and move through the golgi to the TGN
- M-6-P receptors in TGN bind to M6P of acid hydrolase, form vesicles, and bud off of TGN (neutral pH)
- Endosomes are present in the cytoplasm of a cell (formed by endocytosis). Early endosome: pH = 6-6.8, contain H+ pumps in PM that decrease pH to 5.0 (late endosome)
- Late endosomes fuse with the vesicles with hydrolases and the acidic environment causes dissociation of the hydrolases from their receptors.. now called a lysosome
What are the ways that lysosomes breakdown things?
- Autophagy
- Phagocytosis
- some cystolic proteins carry lysosomal targeting signal that deliver the protein to lysosome for degradation
- Some things brought into cell via endocytosis become early endosome –> late endosome –> fuse with lysosome
Augtophagy
Degrade: non functional organelles
Surrounded by: ER membrane ( = autophagosome)
Autophagolysosome = autophagosome + lysosome fusion
Contents destroyed by acid hydolase, recycled or removed via exocytosis
Phagocytosis
Degrade: larger particles (bacteria)
Surrounded by: Plasma Membrane ( = phagosome)
Phagolysosome = phagosome + lysosome fusion
Contents destroyed by acid hydolase, recycled, or removed via exocytosis
Endocytosis
uptake of fluid and molecules FROM THE EXTRACELLULAR SPACE INTO THE CELL
- material is surrounded by PM, buds off inside cell, and forms a vesicle containing the ingested material
1. pinocytosis
2. receptor mediated endocytosis
pinocytosis
- uptake of extracellular fluid and its molecules
- NON SPECIFIC
- Clathrin INDEPENDENT
- Constitutive (continuous)
Receptor mediate Endocytosis (general)
- uptake of SPECIFIC molecules
- Clathrin DEPENDENT
How does recpetor mediated endocytosis work?
- molecules to be internalize by the cell (ligands) bind to specific cell surface recptors.
Receptors are concentrated in clathrin coated pits in the PM - Clathrin (cytoplasmic protein) forms a cage around the pit and helps to stabilize the pit as it starts to bud off
- clathrin-coated pits bud off from membrane and form clathrin-coated vesicles (have both receptors and ligands).. vesicles then lose the clathrin coat
- vesicle is internalized (4 different fates)
4 fates of receptor mediate endocytosis
Both receptor and ligand: 1. recycled 2. degraded 3. transported through the cell OR 4. Receptor recycled and ligand degraded
Peroxisomes
single membrane bound organelles
mostly catalase and peroxidase
formed by polysomes
involved in detox.. lots in kindeys and liver
Peroxisomes in TEM
round structures; medium electron density
MAINLY IN KIDNEY AND LIVER CELLS
what is the function of catalase and peroxidase in peroxisomes
decompose hydrogen peroxide
where are peroxisomes formed
polysomes
what is the main function of mitochondria?
ATP production (cristae increase the surface area for the biochem process/ATP production
Mitochondrial Membrane
2 membranes: outer + inner (forms cristae)
Outer mitochondrial membrane
surrounds the organelle, appears smooth, contains channels (INTEGRAL MEMBRANE PORIN) that allows for regulation of outer mem. permeability
Inner mitochondrial membrane
- folded into cristae
- increases the surface area for ATP synthesis
- contain enymes for steroidgenesis (in steroid secreting cells)
- encloses the matrix space
types of cristae
(formed by inner mitochondrial membrane)
- shelf-like
- tubulovesicular.. in steroid secreting cells ie: sex cells
- sparse/thin shelf-life (in liver cells)
granules in mitochondrial matrix
black dots
calcium reservoirs
mitchondrial genome
contain small circular DNA, RNA, and proteins
most of the proteins in mitochondria are formed in cytoplasm (polysome).. but has the potential to make its own proteins
3 protein families of cytoskeleton
- microtubules
- intermediate filaments
- microfilaments
function of cytoskeleton
- maintain cell shape
- regulate cell polarity
- involved in mitosis
- regulates movement of structures within the cell
- necessary for muscle contraction
Microfilaments
composed of Actin
-associate with actin binding proteins
Intermediate filaments
maintain structural function
- Keratin (epithelial cells)
- Vimentin
- Neurofilaments (nerve cells)
- Lamins (nuclear lamina)
Lamins of nuclear lamina during mitosis
phosphorylation = solubilzation of lamins (disassembly of nuclear lamina) dephosphorylation = reformation of nuclear lamina
occurs in mitosis! (reformation after completion of cell division
Microtubules
- dimers of tubulin
- unstable/want to disassemble, therefore organized into Microtubule organizing centers (MTOC)
Centrosome
a MTOC near the nucleus necessary in mitosis
centrioles + pericentriolar material = centrosome
Centriole
a pair of MTOC (9 sets of triplet microtubules) at right angles to each other
Inclusion
Glycogen, Lipids, Pigments, Crystals
Glycogen as an inclusion
found largely in hepatocytes and cardiac muscle cells
storage form of glucose
Lipids as an inclusion
found largely in steroid secreting cells
storage forms of triglycerides
Pigments as an inclusion
Found largely in neurons
ie: melanin and lipofuscin
crystals as an inclusion
found in leydig cells of testes
Mitosis
cell division that results in two identical daughter cells
results in cell proliferation
Prophase
- chromatin condenses (chromosomes/sister chromatids)
- nucleolus disappears
- Centrioles duplicate and move to each side
- Mitotic spindle forms
Prometaphase
- nuclear envelope disassembles
- mircotubules attach to centrosomes at kinetochores
- chromosomes arrange perpendicular to each other
Metaphase
-chromosomes aligned in mitotic spindle (metaphase plate)
Anaphase
- sister chromatids separate and migrate towards the opposite poles of mitotic spindle
- cleavage furrow begins to form
Telophase
- marks end of nuclear division
- kinectochores disassemble
- nuclear membrane reforms and chromosomes decondense to reform nucleoli
cytokinesis
division of cytoplasm via cleavage furrow
Homeostasis
growth of tissue/organ via mitosis is balanced by cell death
Necrosis
PATHOLOGICAL/ PASSIVE cell death
- due to lack of o2, nutrients, environmental conditions etc
- plasma membrane damaged, cell swells, and bursts’
- extensive tissue damage and an inflamation response
what are the histological features of necrosis
pyknosis (condensation of chromatin and shrinkage of nucleus)
karyorrhexis (fragmentation of the nucleaus)
karylysis (dissolution of the nucleus)
**KARY = nucleus
Apoptosis
programmed cell death
- DNA fragments and nucleus break into several discrete chromatin bodies
- cell is phagocytosed OR cell breaks down into several vesicles (apoptotic bodies) and then phagocytosed
what does an apoptic cell look like?
round/oval mass, with dark eosinophilic cytoplasm and dense basophilic nuclear chromatin fragments
Necrosis vs. Apoptosis
Cells: single cells/small clusters of cell (Apoptosis), contiguous cells (Necrosis)
What does the cell do? shrink (apoptosis), swell (necrosis)
Charateristic histological features: Pyknosis, karyorrhexis (both), karyolysis (necrosis)
Cytoplasm: retained (apoptosis), released (necrosis)
Inflammation? NO (apoptosis), YES (necrosis)
