Download Cellular Structures I

FUNDAMENTALS 1: 10:00-11:00
MONDAY, AUGUST 9TH, 2010
COTLIN
I.
CELLULAR STRUCTURES
Scribe: JORDAN TAYLOR
Proof: JORDAN RIDGEWAY
Page 1 of 5
Cellular Structures and Organelles
a. We’ll start with a global picture of the cell.
II. A Lymphocyte and a Neuron
a. What’s the fundamental difference between a neuron and a lymphocyte?
b. Not function, not what they look like, but GENE EXPRESSION.
c. All cells have the same genome, but differ in which genes are expressed.
d. The compliment of genes expressed creates a profile of proteins for a given cell.
e. Proteins in the cell dictate what the cell will look like and how it functions.
f. All living cells (NOT RBCs) have a nucleus and have genes to express
g. Can be applied to cell membranes: basic structure is the same, but protein composition is different
III. Organelle Classification
a. We can classify all of our organelles into membrane bound or non-membrane bound.
b. Membrane bound organelles are bound by a bi-layer membrane
c. Non-membrane bound organelles reside in the cytoplasm; some don’t even consider them organelles
IV. Schematic of a Polarized Cell
a. What do we mean when we say a cell is polarized? A: it has two regions, with two distinct functions
b. This is a typical epithelial columnar cell, with an apical region and basal region
c. A lymphocyte is a non-polarized cell (round, free floating)
d. A neuron is a good example of a polarized cell (axonal region and dendrite region)
e. Different proteins are localized to different parts of the cell
f. Not every cell is polarized
V. Functions of Cell Membranes
a. Basically the boundary of the cell, gives cell its basic integrity, controls all importing and exporting, regulates
cell interactions (physically attached to many cells), communicating signals from one cell to another,
transduces signals (some messengers don’t cross the membrane, but signal is still transduced to the interior)
VI. Molecular Composition of Cell Membranes
a. Made up of a lipid bilayer
b. Lipid compliment: phospholipids, glycolipids, cholesterol (only animal cells)
c. Most of the lipids are amphopathic (hydrophobic and hydrophilic head group)
d. Protein compliment: can be categorized into integral proteins and peripheral proteins
VII. Fluid Mosaic Model of the Cell Membrane
a. Purple is the hydrophilic head group
b. Yellow is hydrophobic tails, tucked into the interior
c. Cholesterol molecules are also inserted
d. Proteins that are inserted into the membrane are the integral membrane proteins
e. Integral proteins that scan the entire membrane are known as transmembrane proteins
f. Peripheral membranes are loosely associated with the membrane, usually via attaches by other proteins or
lipids
g. Many membrane proteins are glycosylated (this process occurs in the ER),
h. Their glycosylations will always end up on the external side of the membrane
VIII. EM of Cell Membrane
a. Cross section of microvilli (surface projections)
b. Notice the crisp bilayer
c. Electron dense: hydrophilic protein heads
d. Election light: fatty tails
IX. Two important concepts about membranes
a. 1) Fluidity, lot’s of movement
b. The lipids and proteins can move around the membrane
c. If we fused two membranes: one with external receptors, one without…we would notice that the receptors
would be evenly dispersed after fusion
d. 2) Arrangement of proteins
e. Those proteins in the same signal transduction pathway may be tethered together for the purpose of function,
but otherwise most proteins have the ability to move around freely
X. Functions of Integral Membrane Proteins
a. Functionally, proteins can be categorized by what they do
XI. Channel Proteins/Pumps and Carriers
a. Let’s a specific ion pass through
b. They can be voltage-gated: in the case of neuron, they open with the depolarization of the membrane
FUNDAMENTALS 1: 10:00-11:00
Scribe: JORDAN TAYLOR
MONDAY, AUGUST 9TH, 2010
Proof: JORDAN RIDGEWAY
COTLIN
CELLULAR STRUCTURES
Page 2 of 5
c. They can be ligand-gated: something binds and they open
d. Channels are usually found in either the open or closed confirmation
e. Substances naturally move down their concentration gradient
f. Pumps and carriers physically bind a substrate and move it to the other side of the membrane
g. It binds, conformational change in the receptor, deposits cargo to the other side of the membrane
h. I.e.: Na/K pump used to maintain conc. gradient across membrane
i. Pump used to keep Calcium high in the lumen of the ER
j. Glucose is an example of a non-ion that we pump to maintain a gradient
XII. Surface Receptors
a. Some involved in receptor-mediated endocytosis (i.e.: bloodstream proteins) that need to be taken into the
cell
b. Some will be signaling molecules that respond to growth factors or hormones
c. Some of these signaling proteins will be associated with G-proteins
d. Many surface receptors are kinases (kinases phosphorylate proteins)
e. Some will be receptors for steroids and cytokines
f. Overall: they are receiving something from the outside and causing an outcome on the inside
g. Some are basic structural linker proteins
h. Most cells are attached to other cells or a matrix, so we need linker proteins to link internal structures with
external structures
XIII. Structure of the Nucleus
a. Identified: nucleus, double nuclear membrane, nucleolus
b. Notice inner nucleus membrane is directly continuous with the ER
c. Therefore the ER is directly linked with the nucleus
XIV.
EM of Cell Nucleus
XV. The Secretory Pathway
a. Pathway in which all the molecules move through the ER
b. Where does Protein Synthesis take place? Fundamentally, in the cytosol.
c. Some proteins are made in the cytosol and stay there. Otherwise, they are directed to the ER and proceed
with the secretory pathway. From the ER, molecules traffic to the Golgi, and then end up at the lysosome,
the plasma membrane or even back to the ER.
d. All of the tubules from the previous organelles are connected with the nuclear membrane.
e. Proteins destined for any membrane (besides mitochondria) will actually be made in the ER
f. There are channels/pumps involved in the secretory pathway to help regulate ion concentrations, also
enzymes for metabolizing, chaperonin proteins
g. The general characteristics of the plasma membrane also apply to the other organelles, but what makes them
distinct? The composition of the proteins
XVI.
The Endoplasmic Reticulum
a. 2 types of ER: 1) Smooth 2) Rough
b. Smooth ER is the site of processing for lipids
c. Rough ER is a site of ribosomal attachment
XVII. Rough Endoplasmic Reticulum
a. Notice the studded nature of the flat sacs
XVIII. Location of Protein Synthesis
a. The default pathway for a protein is production and function in the cytosol
b. If the N-terminal of the new polypeptide has a specific signal sequence, it will target it for transportation to the
ER
c. This cartoon is an example of a polyribosome. As soon as one ribosome clears some room, the next
ribosome can attach to the mRNA. This is so the cell can increase protein production.
XIX.
Ribosomes: Cytosolic and Membrane (Diagram)
a. Diagram (left): proteins made in the cytosol
b. Can then be directed to nucleus, mitochondria, chloroplasts (irrelevant), and peroxisomes
c. Diagram (right): membrane-bound ribosome
d. Can then be directed to the plasma membrane, secretory vesicle, lysosome, and also Golgi
e. What is the difference between the membrane bound and cryptozoic ribosomes? Nothing, just the proteins
being made.
XX.
Ribosomes: Protein Synthesis (Diagram)
a. An example of a protein with a signal that says “take me to the ER”
b. Ribosome will be directed to sit at the ER and synthesize protein
c. The ribosome will insert the new peptide into the ER lumen
FUNDAMENTALS 1: 10:00-11:00
Scribe: JORDAN TAYLOR
MONDAY, AUGUST 9TH, 2010
Proof: JORDAN RIDGEWAY
COTLIN
CELLULAR STRUCTURES
Page 3 of 5
d. The N terminus or amino end is hanging off (the red strand)
e. Proteins known as signal recognition proteins, recognize signal on the polypeptide
f. The ER membrane has SRP receptors
g. If signal exists, it binds SRP, SRP binds to the ER receptor, ribosome sits directly above a translocation pore
which allows the peptide to be inserted into the lumen
h. This ribosome was functioning just like any other ribosome until it was “chosen” to be called to the secretory
pathway
i. The peptide can then join a vesicle that takes it to the Golgi, and so forth
XXI.
Membrane “Bound” Protein Synthesis (Diagram)
a. How do we get a membrane protein? All membrane proteins of the secretory pathway are made in a similar
way as before.
b. When they’re made, the transmembrane regions will become “lodged” in the ER membrane, instead of being
pushed through.
XXII. The ER and Golgi Apparatus
a. All of the peptides in the lumen of the ER will leave via transport vesicles. We can see these budding off of
the ER. Eventually they will fuse with the Golgi.
b. The Golgi has 3 faces: Cis, Medial, and Trans.
c. The Cis face is next to the ER. This is where the vesicles from the ER will fuse.
d. What are the main functions of the Golgi? Modifications of proteins and Sorting of proteins.
e. Modification is primarily the glycosylation of the proteins. Some of the glycosylation occurs in the ER, but the
terminal glycosylation happens in the Golgi. (The final carbohydrates are attached or modified)
f. The vesicles will travel sequentially through the sacs: Cis, Medial, then Trans.
g. In the trans Golgi, proteins are sorted to their final destination. Some of these vesicles will be sent back to
the ER, because the ER needs proteins too!
h. Where is the default destination of the proteins? The plasma membrane
i. Other option: to the lysosome
XXIII. ER and Golgi
a. We can really see the stacks of the Golgi and the bulbs that come off the stacks.
XXIV. The Golgi Complex
a. Trans face: also known as the maturing face
XXV. Activity in the Golgi
a. Vesicles can exhibit bidirectional flow (some can go backwards to the ER)
b. After the vesicles leaves the Golgi and fuse with the plasma membrane….membrane proteins from the ER
will become part of the plasma proteins, lumen proteins will be expelled outside of the cell.
XXVI. Golgi Image
a. Nice picture of budding vesicles
XXVII. The Lysosome
a. Big, degradative organelle
b. pH is kept low, approximately 5.5
c. Many enzymes inside for dissolving proteins, nucleic acids, lipids
d. Any proteins in the Golgi destined for degradation by the lysosome will have a phosphorylated Mannose
(phosphomannose)
e. Phosphomannose is the signal that says “take me to the lysosome”
f. Proteins exist that recognize the phosphomannose and act as a transporter for the protein
g. Some vesicles will contain specific cargo destined for the lysosome
XXVIII. Lysosomes (Diagram)
a. Many transport proteins
b. Many proton pumps, pumping in H+ to keep the pH very low
c. What’s the reasoning for keeping a low pH? Helps to denature proteins, but also, it’s a safety factor for the
cell: All of these degradation enzymes are programmed to work at a low pH. If something were to happen to
the cell and contents were exposed, the dangerous enzymes would be rendered inactive, because the pH
outside is too high.
XXIX. Lysosomes (EM of Lysosome)
a. Small electron dense vesicles
XXX. Endocytosis and Endosomes
a. Endocytosis is the process of bringing in molecules, originate at the plasma membrane
b. Usually it involves receptor-mediated endocytosis
i. I.e.: our LDL particles and growth factors are brought in this way
c. Notice the invagination at the plasma membrane
FUNDAMENTALS 1: 10:00-11:00
Scribe: JORDAN TAYLOR
MONDAY, AUGUST 9TH, 2010
Proof: JORDAN RIDGEWAY
COTLIN
CELLULAR STRUCTURES
Page 4 of 5
d. Transport vesicles are usually associated with carrying cargo out and endosomes are associated with
carrying cargo in
XXXI. Phagocytosis and Phagosomes
a. Like endosomes, but phagosomes are relatively larger
b. Also involved in bringing in molecules, originate at the plasma membrane
c. Certain cells are specialized at phagocytosis
d. I.e.: bacteria, large cell debris,
XXXII. Peroxisomes
a. Part of the non-secretory pathway
i. Nucleus, mitochondria, peroxisome
b. Proteins that arrive at the peroxisome are from the cytosol with a signal that destines them to the peroxisome
c. Peroxisomes are membrane bound and degradative
d. They participate in oxidative reactions and breaking down free fatty acids
e. All of the substrates are waste products: we don’t gain any usable energy from these processes
f. Bad things can happen with peroxisomal and lysosomal biogenesis
g. Congenital defects can have drastic effects on some of the degradative processes
XXXIII. Peroxisomes (EM Image)
a. They look similar to lysosomes – small, electron dense
XXXIV. Mitochondria
a. Double membrane structure
b. Function: making ATP
c. All cells have mitochondria, some more than others (i.e.: muscle, flagella, nerve terminals)
d. Breaking down toxic stimuli
e. Facilitates programmed cell death
f. Formed by binary fission
g. They have their own DNA
h. Some protein synthesis apparatus
i. Mitochondrial genome has all the components for processing it’s own DNA as well
XXXV. Mitochondria (EM image)
a. We can see the whole membrane system
b. Outer membrane and Inner membrane
c. Outer membrane is very permeable (to small molecules), Inner membrane is very impermeable
d. Notice inner membrane space
e. Inside the mitochondria is highly folded (known as Cristae)
f. The inner membrane is where all of our electron transport chain is found
XXXVI. Organization of Mitochondria
a. Notice electron transporters and ATP synthase
XXXVII. Overview of Mitochondrial Functions
a. Notice pyruvate and other byproducts of glycolysis
b. The inner membrane is impermeable because it’s helps establish a concentration gradient (H+ and the ETC)
c. Small molecules pass easily through the outer membrane
d. Large molecules need transporter to cross even the outer membrane
XXXVIII.
Mitochondria (EM image)
XXXIX.
Inclusions
a. inclusions are random assortments of things found in the cell
b. some are functional, such as, glycogen and lipid granules, pigment granules
c. some are crystals
d. some lipofusion (age-related)
e. some are substances that the cell can’t break down or digest
f. common in nerve cells because nerve cells don’t turn very often
XL.
Non-Membrane Organelles
XLI.
Ribosomes
a. Machines that bring together mRNA, tRNA, and rRNA
b. Always consist of a small subunit and a large subunit
c. Notice the difference between the prokaryotic ribosome and eukaryotic ribosome
d. Two subunits come together in the context of protein synthesis
XLII.
Organization of Ribosomes
a. One large subunit has about 50 proteins and 3 rRNA molecules
b. The small subunit has about 30 proteins and 1 rRNA molecule
FUNDAMENTALS 1: 10:00-11:00
Scribe: JORDAN TAYLOR
MONDAY, AUGUST 9TH, 2010
Proof: JORDAN RIDGEWAY
COTLIN
CELLULAR STRUCTURES
Page 5 of 5
XLIII. Polyribosome Schematic
a. As many as 11-15 can be on the mRNA message at one time
b. All of our ribosomes are the same. Free ribosomal particles in the cell float in a common pool. Small and
Large subunits are mixed in the pool. Small and Large subunits join to form functional ribosomal machine in
the presence of mRNA. After message is completed, the subunits dissociate and rejoin the pool. There is
NO difference between any ribosomes.
XLIV. Proteasome
a. Cytosolic, macromolecule for degradation
b. Helps degrade proteins in the cell
c. Acts on: Misfolded proteins, proteins with exhausted half-lives
d. Multiple subunits of RNA make up the proteasome
e. The key molecule here is ubiquitin
i. 76 amino acid tagger
f. Proteasomes receive any protein that has been tagged with ubiquitin
g. Very important in many cell cycles and cell regulation
XLV. Cytoskeleton
a. Basically the skeleton of the cell
b. 3 major components
i. microtubules
ii. actin filaments
iii. intermediate filaments
c. All of these associate to give our cells structure and shape
XLVI. Organization of Cytoskeleton
a. Actin shown in red
i. Actin network found underside of the plasma membrane
b. Intermediate filaments shown in blue
i. Like pieces of nylon rope
ii. Stretchy and bendable
iii. Span the cell
iv. Aids in strength and support
v. Resists mechanical stress/force
c. Microtubules shown in green
i. + and – because they are polarized molecules functional in aiding traffic in the cell
ii. Where do all of our vesicles know where to go? Microtubules in addition to be structural are also “tracks”
that help navigate vesicles throughout the cell
[End 54:13 mins]