CLASS: FUNDAMENTALS I
8-9-2011
10:00-11:00
Cotlin
I.
II.
III.
IV.
V.
VI.
Cell Structures and Organelles
Scribe: Joseph Vaught
Proof: Joseph Vaught
Page 1 of 6
Intro Slide [S1]
A Lymphocyte and a Neuron [S2]
a. A lymphocyte and a neuron, what is the basic difference between these two types of cells.
b. What kind of cell is a lymphocyte? Very basically speaking. A white blood cell involved in the immune
response.
c. What kind of cell is a neuron? Involved in signal transduction.
d. What’s the basic difference between these two types of cells, very basically? What genes are transcribed
and expressed, right? The only cells without a nucleus or DNA are red blood cells, they get rid of their
nucleus as they’re pushed. Other than that, basically every cell is the same. It has the same basic material
and structures and characteristics. The only thing that is different is the genes transcribed and the proteins
expressed.
e. This cell, the lymphocyte, it’s not attached to anything it’s going to roam around, and it’s got all these
special characteristics for moving around and pumping out antibodies. This cell here, the neuron, it’s
stationary. It’s going to have lots of receptor transporters for signal transduction and action potentials, it’ll
have adapters to keep it stabilized with other cells.
f. The only big difference between any two cells is its proteins that are expressed. The proteins that it express
will give it its shape and structure and that will indicate what its function is in the body. So I think this helps
us remember that pretty much in fundamentals one you’re going to be getting the material all based on the
basic biochemical, physiological properties of the cell. Pretty much any cell can do all the same things it’s
just depending on whats expressed.
g. Each cell has a population of what we usually call housekeeping genes or proteins and those are things that
all cells will express regardless, and what might some of those be? What might be a housekeeping protein
that almost every cell will have?
h. Ribosomes, some of your replication machinery, some of the kinda of proteins involved in glycolysis, things
that just keep the cell going. The other genes are all differential to expression and those you’ll get to much
later when you get to fundamentals II. We’ll start saying what makes an epithelial cell different from a
muscle tissue, so you probably wanna keep that in mind that in this course you’re probably gonna learn the
things that all cells can do.
i. So for the next two hours we’re just gonna just kinda go over what makes a cell a cell, and some of this
should be a review.
Organelle Classification [S3]
a. So we can categorize this into basically two broad ranging categories, these are membrane bound you’ve
talked a lot about the membrane; those organelles who’s contents and functions are membrane bound
versus those without a membrane which are just large macromolecules with molecular structure just
floating around the cell not enclosed in a membrane.
Schematic of a Polarized Cell [S5]
Fluid Mosaic Model [S5]
a. So let’s start with the plasmar membrane, that’ll pretty much define all of this. We call it a fluid mosaic
model; we call it that because it is fluid. It has proteins and lots of lipids in this double membrane fashion
and it is fluid because all of these proteins here and these cholesterols and these proteins here, none of
them are attached to each other. Proteins are going to be fluid within them, some of the proteins are going
to be anchored within them, but for the most party the proteins are going to be fluid within them.
Functions of Cell Membranes [S6]
a. So what are the functions? It gives shape and integrity of the cell, it controls movement so anything going in
or out of the cell has to diffuse or go through a transporter, it is involved in cell-to-cell interaction- many
cells need to be anchored to another cell.
b. Acts as recognition board- cell receptors found on the membrane.
CLASS: FUNDAMENTALS I
8-9-2011
10:00-11:00
Cotlin
VII.
VIII.
IX.
X.
XI.
XII.
Cell Structures and Organelles
Scribe: Joseph Vaught
Proof: Joseph Vaught
Page 2 of 6
c. Transport system and signal transduction- external membrane receptors take the signal and bring it to the
internal environment.
Molecular Composition of Cell Membranes [S7]
a. Two major components- a lipid and a protein. Phospholipids with modified head groups, which you’ll hear
about later. Glycolipids are those which have sugars attached to them they are lipids which have been
glycosylated.
b. There are cholesterol molecules that give rigidity to the cell membrane.
c. Arrangement of lipids gives unique structure.
d. All of the lipids are considered amphipathic, which means they have a hydrophobic region and a hydrophilic
region. The hydrophobic regions are at the core of that bilayer, and the hydrophilic regions are on the
external surface facing extracellular cytosol.
e. Proteins are integral, embedded either partially or completely in the membrane, or peripheral which means
they’re not attached to the membrane but they’re anchored by specific attachments on either side.
EM of Cell Membrane [S8]
a. Electron micrograph of microvilli at the surface with a black lined double membrane. The black lines are the
electron dense hydrophilic region with a lighter hydrophobic core.
Two Important Concepts About Membranes [S9]
a. This picture describes the flow of proteins. It’s a fluid structure with them moving together. One has an
assortment of proteins unlabeled and one has labeled proteins and eventually they coalesce to form one
large structure with labeled and unlabeled regions distributed.
b. Among these there is a defined anchoring. There are integral membrane proteins like transmembrane
proteins because it completely spans the membrane, such as a multi-pass, which is a transmembrane
protein.
c. This is a glycoprotein, with a protein core with a chain of sugars attached.
d. This is a phospholipid, and similarly we have a glycolipid; which is just a lipid with a sugar attached.
e. A peripheral membrane protein is just attached on either intra- or extra-cellular side.
f. Sugar modifications will always be found extracellularly. Are put on in secretory pathway so will always be
extracellular.
Functions of Integral Membrane Proteins [S10]
a. Assortment of varieties of integral membrane proteins. Pumps, channels, receptors, linkers, enzymes;
classified by what they do. Most will have regions spanning both sides of membrane. So will be more active
or fluid than others.
Channel Proteins [S11]
a. Channel protein will allow the passage of ions, can be gated in multiple ways such as voltage-gated so they
open if a voltage changes. Normally when channels are open things can flow through and when they are
closed things don’t. When a channel is open ions flow down a concentration gradient.
b. Sodium is high outside of a cell; when a channel is open sodium is going to flow in. It’s considered all or
nothing. There are leaky channels involved in neurons, but normally they are all or nothing either open or
closed.
c. There is ligand-gated where something binds to open the channel.
d. Mechanically gated ones are opened just by movement.
e. Pumps and carriers are those which will physically bind and transport a molecule. Na+ and K+ pumps bind
ions and move them across their concentration gradients.
f. Calcium is often sequestered in the endoplasmic reticulum to create a concentration gradient. Glucose is a
small molecule treated the same way.
Surface Receptors [S12]
CLASS: FUNDAMENTALS I
8-9-2011
10:00-11:00
Cotlin
XIII.
XIV.
XV.
XVI.
XVII.
XVIII.
XIX.
XX.
XXI.
Cell Structures and Organelles
Scribe: Joseph Vaught
Proof: Joseph Vaught
Page 3 of 6
a. Surface receptors can be involved in taking up molecules through endocytosis. LDL receptors bind LDL and
take it into cell- basic endocytosis.
b. Some are basic enzymes like kinases, which is a protein which adds a phosphate to something. A
phosphatase is something that dephosphorylates a molecule. An extracellular signal triggers their
intracellular action.
c. There is a class of proteins called G-proteins. They utilize GTP as a signaling molecule. Some of these are Gprotein receptors.
d. Some are steroid receptors which recognize steroids or cortisol in the bloodstream. We have surface
receptors and nuclear receptors which can bind them. These usually just transport things in or out of a cell.
e. There are linkers /structural proteins which maintain shape of the cell; there is cell-to-cell attachment, cellto-matrix attachment to things in environment, and scaffold to the cytoskeleton which is inside the cell. All
are involved in giving the cells shape and structure.
f. All of the characteristics of a cell’s plasma membrane are the same for internal plasma membranes. ER
membrane is still fluid mosaic with proteins through it and differs only in proteins found.
The Cell Nucleus [S13]
a. Nucleus is a double-membrane bound organelle continuous with the endoplasmic reticulum.
b. Has a gated nuclear pore complex which regulates movement in and out of small molecules other than ions.
Structure of the Nucleus [S14]
a. Cytoskeletal proteins outside of it keep its structure, while inside there is a dense network of intermediate
filaments known as the nuclear lamina which is a layer of proteins which helps keep its structure in tact.
b. Genetic material inside with a nucleolus present for ribosome assembly. Nuclear envelope is the double
membrane system.
c. The endoplasmic reticulum is the site of protein synthesis for membrane proteins, so we find ribosomes
here. There is smooth ER and rough ER. Smooth ER has no ribosomes attached while rough ER has
ribosomes attached.
Diagram Slide—Unnamed [S15]
a. EC stands for euchromatin and HC stands for heterochromatin. Heterochromatin is condensed and not
transcriptionally active. The euchromatin is actively transcribing so it is open and loose and not as easily
discerned.
b. The nucleolus is the site of ribosome assembly which can be categorized as the fibrous region and the
granulosa region which identifies the rRNA and the actual granular proteins.
EM of the Cell Nucleus [S16]
a. EM slide arrow points at nuclear pores which we know from distinct breaks. Dark stuff is heterochromatin.
Nucleus and Nuclear Envelope [S17]
Structure of the Nuclear Envelope [S18]
a. The nuclear envelope separates the contents of the nucleus from everything else. One of the main goals is
to protect our DNA and only transcribe what we need to make proteins of.
Diagram of the NPC [S19]
The Nuclear Pore Complex (NPC) [S20]
a. Nuclear pore complex has more than 100 proteins making up the structure. Lots of transport proteins which
regulate what goes in and what goes out, and there’s a structural protein called an importins which import
molecules.
b. Small molecules can diffuse and large ones cannot. Large ones have a nuclear localization signal.
c. RNAs are transported as a ribonuclear protein which is an RNA coated in proteins.
d. All of this movement is very high energy expenditure.
Diagram of the NPC [S21]
CLASS: FUNDAMENTALS I
8-9-2011
10:00-11:00
Cotlin
XXII.
XXIII.
XXIV.
XXV.
XXVI.
XXVII.
XXVIII.
XXIX.
XXX.
XXXI.
XXXII.
XXXIII.
XXXIV.
XXXV.
Cell Structures and Organelles
Scribe: Joseph Vaught
Proof: Joseph Vaught
Page 4 of 6
a. Protein synthesis occurs in cytosol but replication and transcription occurs in the nucleus and the mRNA
molecules leave nucleus. Translation occurs in the cytosol and then proteins are made and sorted. Some
proteins which need to be transported back in are transcription factors, DNA polymerases and other
replication/transcription proteins.
b. Things like mRNA, tRNA, RNA subunits need to be transported out.
c. Ribosomal proteins need to be brought into nucleus, packaged with the RNA, and then packaged and sent
back out.
EM of the Nuclear Pore Complex [S22]
a. NPC looks like a basket with a plug sort of keeping the pore closed.
The Chromatin Material [S23]
a. We only open and unwind the sections of DNA we need to to transcribe.
b. During interphase the cell is just going about its business and it’ll have both euchromatin and
heterochromating. Once it enters mitosis everything condenses.
c. Histones, fibrous proteins, matrix proteins are all associated with this. You never want to have free floating
DNA so even unwound DNA is bound by some proteins.
d. There’s a large ribosomal subunit and a small, and both are complexes of multiple proteins and RNA. We
make our rRNA in nucleus and proteins in cytosol, they’re taken into nucleus and assembled and then
transported back out.
e. Primary transcript is processed in the nucleus.
Diagram Slide—Unnamed [S24]
Nucleolus [S25]
The Nucleolus [S26]
The Functional Unit of Euchromatin [S27]
a. Functional unit of euchromatin is the nucleosome, which is the smallest unit of packaging we see, it consists
of 8 histone proteins, which are scaffolds, which allow 166 base pairs to wrap around them.
b. When we need to transcribe a particular region we have transcription factors, which activate and then
proteins, which come and unwind DNA.
The Nucleosome [S28]
Schematic of Chromosome Packaging [S29]
a. Multiple levels of packaging or condensation. Double helix coils around histones to form a nucleosome and
there is further twisting until we form a chromosome.
Cartoon Depicting DNA Packaging [S30]
Diagram Slide—Unnamed [S31]
Ribosomes [S32]
a. Ribosome is a non-membrane macromolecule with a large and small ribosomal subunit. A giant enzyme
factory which brings together mRNA and tRNA to synthesize a polypeptide. A polypeptide is just a chain of
amino acids, which after formed and folded it is usually a protein.
Organization of Ribosomes [S33]
a. Each subunit consists of one or more rRNA molecules and many proteins.
Diagram Slide—Unnamed [S34]
a. Ribosomes can be used many times; once they make a protein they can disassemble and be used again.
b. Ribosomes can associate with the ER if the product needs to be a part of a secretory pathway.
Diagram Slide—Unnamed [S35]
a. As many as 15 ribosomes can be on one mRNA if we need to make a protein quickly, and this is usually
called a polyribosome.
CLASS: FUNDAMENTALS I
8-9-2011
10:00-11:00
Cotlin
Cell Structures and Organelles
Scribe: Joseph Vaught
Proof: Joseph Vaught
Page 5 of 6
b. There a subtle differences between prokaryotic and eukaryotic ribosomes but they are very conserved
molecules. Both types consist of a large and small subunit consisting of multiple proteins.
c. A common pool of subunits made in the nucleolus and transported into cytosol where they assemble around
mRNA in a 5’ to 3’ fashion and translates a polypeptide. Once it reaches the 3’ end it disassembles and goes
back into the pool unit it assembles on a new mRNA.
d. These are making proteins in the cytosol which may be packaged and used elsewhere.
e. Some mRNA have a signal which says ‘take me to the ER’. The ribosomes move to the ER attached to the
membrane where they begin making proteins inside of the ER.
XXXVI. Location of Protein Synthesis [S36]
a. After either a cytosolic or ER-bound ribosome is used their subunits go into the common pool, so there is no
difference between the functions of these ribosomes. The difference is where they’re located.
b. Cytosolic ribosomes hop onto an mRNA in the cytosol and make cytosolic proteins if there is no other signal
present. Some mRNA have a signal which tells the ribosome to go to the nucleus, mitochondria, chloroplast,
or peroxisome.
c. Glycolysis occurs in the cytosol and that is where they are made.
d. Oxidative phosphorylation proteins are made in the cytosol and have a signal, which tells the ribosome to
take them to the inner leaflet of the mitochondria.
XXXVII. The Secretory Pathway [S37]
a. Plasma membrane, RER, lysosomes and Golgi proteins are going to have a signal telling them to be
translated into the ER so they can get into the membrane system of their targets. These get into the
secretory pathway, which includes the ER, golgi apparatus, traffic to the plasma membrane, secretory
vesicles from packaged material, endosomes (vesicles which bud at plasma membrane). The lysosome is
part of the secretory pathway and may have stuff brought directly to it.
b. Endocytosis is materials budding into the cells and exocytosis is materials budding out of the cells.
c. Once in the ER the protein will have a signal to stay in the ER or be sent to the golgi.
XXXVIII. The Endoplasmic Reticulum [S38]
a. All proteins in the secretory pathway normally travel anterograde out towards the plasma membrane.
Backwards flow is called retrograde.
b. The ER is a continuous system of membrane stacks which is the site of some protein synthesis. Smooth ER is
more involved in lipid metabolism and synthesis and is continuous with the nuclear envelope. The rough ER
is the sight of membrane and secretory protein synthesis.
c. It is important in signaling such that we maintain in the lumen (inside of organelles) high in calcium. We
want to flood the cytosol with calcium in the muscle but sometimes we want to sequester it, which we do in
the ER. Contains enzymes for drug and small molecule metabolism.
d. Many items have a bidirectional flow between the golgi and the ER.
XXXIX. Rough Endoplasmic Reticulum [S39]
XXXX. Diagram Slide—Unnamed [S40]
a. Signal recognition particle is the protein, which recognizes the protein signal, which takes it to a special sight
called a translocon on the ER membrane to have the protein made on the ER membrane. The protein is
situated on a pore and the proteins made are inserted into the lumen of the ER. If no signal was present it
would be packaged into a vesicle and put into the secretory pathway.
XXXXI. Diagram Slide—Unnamed [S41]
a. Proteins that need to be integrated into the membrane have an internal sequence, which is usually
hydrophobic to get stuck into the membrane of the lipid bilayer.
XXXXII. The ER and Golgi Apparatus [S42]
XXXXIII. The Golgi Complex [S43]
CLASS: FUNDAMENTALS I
8-9-2011
10:00-11:00
Cotlin
Cell Structures and Organelles
Scribe: Joseph Vaught
Proof: Joseph Vaught
Page 6 of 6
XXXXIV. Activity in the Golgi [S44]
a. The golgi has 3 faces, the cis face (forming face), the medial face, and the trans face. The cis face is always
receiving vesicles from the ER where it processes them and sends it to the trans face to go to the membrane
or the lysosome.
b. The three compartments are the site of all protein modifications such as glycosylations. This is where they
are directed to different departments to direct it away from its default path to the plasma membrane.
c. The Golgi stacks are not connected.
d. SNARE proteins help direct flow of proteins through Golgi.
e. Coat proteins are involved in telling proteins where to go.
XXXXV. Diagram Slide—Unnamed [S45]
XXXXVI. ER and Golgi [S46]