Tuesday, January 6, 2008
- We have 1 midterm, 1 final exam and 6 labs. Labs are 27% with 8% from
quizzes, best 2 out of 3 (4% each). 65% is from exams: the midterm is 25%
and covers section 1 of lectures and labs 1 to 2. The final exam is worth 40%
and covers all lectures and labs 1-6.
- Midterm is different from course manual: it is actually on Friday February
27 from 2 to 4.
- There will be lab tutorials that will be held in 3 weeks, there will be 3
tutorials, one before the midterm and two before then, they appear on
alternating weeks on Mondays from 3 to 4 and will be posted next lecture.
- If you have any questions, asked the professor after lecture, come to
tutorials or ask on the course website on Blackboard. He doesn’t take
questions during the lecture.
- This is a picture of a cell and the central dogma of biology is that DNA
encodes mRNA which gets translated into proteins. You go from DNA to
proteins and proteins are functional components of living cells.
- We’re used to seeing pictures like this where the cell is static and doesn’t
move but even in a simple diagram like this, you can see there will be lot of
movement – first to transcribe DNA into mRNA there needs to be proteins on
the DNA moving along the DNA & transcribing the DNA into mRNA. Then
the mRNA needs to be transported out of the nucleus and into the cytosol. In
the cytosol is where ribosomes bind to mRNA and starts the translation into
proteins. That is movement again, movement of mRNA outside of nucleus
and into the cytosol where ribosomes will move onto the mRNA, move along
it and translate it into proteins and the proteins will move around the cell,
some will be secreted outside the cell going through the ER.
- This is all to emphasize that there is a lot of movement within a cell & from
this picture, one can appreciate that there are numerous compartments within
the cell so the cell is compartmentalized into different functional sub
compartments like the nucleus that stores DNA & is also the main site for
transcription. Then you have the cytosol & different organelles in the cytosol
such as ER that all have specialized functions. The cell is compartmentalized
in order to provide functional specialization & there is a lot of movement in
the cell that is not captured in images such as the one in the slide.
- There is a lot of movement in the cell whether it's proteins moving, whether
it's signals being transmitted from the outside of the cell to the inside of the
cell or whether it's the movement of proteins or lipids within the membranes
that surround the cell or the organelles within the cell.
- A movie is playing emphasizing movement within the cell.
- We will appreciate how active it is inside the cell eventually and we’ll
appreciate more the little subtleties we saw in the movie as we go through this
part of the course. - Here is an animal cell which has a number of compartments in it called
organelles and we’re familiar with these compartments such as lysosome
which is the site for the degradation of what the cell doesn’t need anymore,
proteins or structural components, that it doesn’t need will go to the lysosome
and be degraded.
- The mitochondria are the energy source for the cell where ATP is produced.
- The nucleus is where the genetic material DNA is stored and site of
transcription from DNA to RNA.
- The Golgi is the site of protein modifications and sorting.
- The endoplasmic reticulum – you have two types: you have the rough ER
that is transcribing transmembrane proteins and proteins that will be secreted
outside the cell surrounding these little specks called ribosomes that are
actively translating proteins from mRNA & delivering them into the ER. You
also have smooth ER which is a major site of lipids in the cell.
- You can see all these compartments that are separated from each other have
specialized roles in the cell.
- He has highlighted 2 compartments or properties of the cell: the
extracellular matrix and the lysosomes that are specific to animal cells – the
extracellular matrix plays an important role in the adhesion of the cell to a
specific location & also plays an important role in maintaining cell shape &
another role in cell development.
- In contrast, plant cells have some specific organelles that aren’t mainly
found in animal cells – a major one are chloroplasts that are the site of
photosynthesis and are found only in plants and not animal cells.
- A vacuole plays a prominent role in a plant cell – they are mainly composed
of this large vacuole and there are 2 types of vacuoles: one acts like a
lysosome that is found in animal cells and the other ones are for storage of
proteins and certain small molecules and they can actually be storage spaces
for antimicrobial compounds so when the cell gets punctured, the compounds
ooze out of the cell and will kill whatever is trying to invade it.
- Okay so you have a vacuole, chloroplast and importantly a cell wall
surrounds plant cells and not animal cells – the cell wall is a rigid structure
and makes the cell often look square so it is involved in maintaining cell
shape as well as help protect from external stresses such as temperature,
mechanical stress, insect invasion or bacterial invasion so the cell wall
surrounds the plant cell.
- Importantly, of course plant cells also have structures such as a nucleus,
endoplasmic reticulum, Golgi apparatus, peroxisomes (the site of degradation
of many fatty acids), mitochondria and plasma membranes and are also found
in animal cells – the ones listed in the slide are in both animal and plant cells.
- There are lots of different compartments with functional specialization.
- Cytoplasm is the space outside the nucleus, everything outside the nucleus
in the cell shown in the slide. The cytoplasm would include the organelles
- The cytosol is the aqueous component of the cytoplasm so it doesn’t include
- The lumen is the aqueous part inside organelles – so inside the mitochondria
there for example, inside the organelles is the lumen. - In section 3 we will cover the membrane components, so the membranes
that define the different organelles within the cell & actually make the
boundary of the cell by the plasma membrane. So what are the components of
these membranes that delimit the organelles & the cell itself? – that is the 1 st
- Then there is a conundrum b/c if you separate your cell from the
environment, you need ways of transporting small molecules or getting
signals across from one side of the membrane to the other so we are going to
look at how cells can transport small molecules across these membranes in
both organelles & the plasma membrane (Lectures 2-4).
- Lectures 5-6 we’re going to look at protein sorting so how do proteins get to
different places in the cell – they all start out on ribosomes in the cytoplasm
& then get shuttled to different compartments of the cell. Some proteins will
end up in the membrane, some will be secreted outside the cell & others may
be retained within the cell. Just to emphasize, it all starts in the nucleus DNA
mRNA cytoplasm where it is translated into proteins and that is where
- Vesicle trafficking will be lectures 7-8 so how do things get around the cell
in vesicles – so basically one important thing is things that are destined for
membranes or outside the cell must be translocated through vesicles – they
will start out in the ER, so these are transmembrane proteins or things
destined for the outside of the cell, & will be translocated into the ER,
through the Golgi apparatus & then shuttled to their appropriate compartment
- Exocytosis & endocytosis is the final part of vesicle trafficking. One of the
destinations of vesicle trafficking is exocytosis, translocation of things
outside the cell & we’ll also cover how things get into the cells through
endocytosis, so how do cells take up molecules from the outside?
- Finally we’ll go into a different type of movement which is the transduction
of signals from the outside of the cell to the inside of the cell – this should
read lectures 10, 11, 12 & not 13 in the slide, so lectures 10 – 12 will be
signal transduction or transmission of signals from outside of the cell to the
inside of the cell.
- You see there is movement that will occur at all these different parts of the
section 1 lectures.
- We start with membrane structure – they delimit the cells & organelles.
- Cell membranes enclose the cell and the organelles – it is an important thing
to keep in mind because this is what allows the different compartments to
maintain their functional distinction from the rest of the cell so you have
division of the cell into compartments and this defines the boundaries of these
compartments and maintains differences b/w the cytosol, the organelles & the
extracellular environment. These differences are what’s required to maintain
different functions in each of these different compartments.
- It is important to realize that it is the cell membranes that allow the cell and
the organelles to maintain these differences. - To emphasize again, this is not always obvious, so where are these cell
membranes localized? It is important to realize that it isn’t just the plasma
membrane that is a cell membrane.
- The first top-left arrow points at the plasma membrane and then there is the
nucleus that is also surrounded by a membrane (going counterclockwise in
- The ER is also surrounded by a membrane.
- Here is the Golgi, Golgi stacks would be surrounded by membrane, different
- Then there is a lysosome for example that would be surrounded by a
- The vesicles here that would be budding off the Golgi are also surrounded
- The mitochondria and the chloroplasts in plants would all be surrounded by
membrane so you can see that cell membranes are found throughout the cell
and it's not only limited to the plasma membrane.
- So again the cell membranes divide the cell into compartments & control
the movement of molecules b/w these different compartments.
- There are 2 major components to all these cell membranes: one is a lipid
bilayer, and the lipid bilayer is the basic unit of each of these cell membranes.
This is shown in the cross-section and what that means is that there are 2
leaflets to each bilayer, an outer leaflet and an inner leaflet – each one of
them is a bilayer of lipids and this structure is very fluid, meaning it's not a
static structure, things can move around within this layer. The PM of a
mammalian cell has the viscosity roughly equal to olive oil so you can
imagine that it is quite fluid & things could move around within this lipid
- This is the structural component of cell membranes & the functional
components are mainly carried out by membrane proteins & they’re shown in
the slide in green in the cross-section of the lipid bilayer. These proteins can
be transport proteins that allow the movement of small molecules across the
membranes b/c again, a lot of these cell membranes will divide the
compartments & keep specific molecules out of these compartments & then
these membranes can have proteins that selectively allow specific molecules
to enter into these compartments – this is carried out by transport proteins.
- Then there is the transmission of signals from outside the cell to the inside
of the cell and is carried out by transmembrane receptors, these would be
proteins found in the lipid bilayer that would allow for transmission of a
signal from the outside of the cell to the inside of the cell.
- Membrane proteins can also be receptors that recognize specific molecules
outside the cell & allow the cell to respond inside.
- The structural component again is the lipid bilayer and the lipids that
compose the bilayer are called amphiphilic which means they have both
hydrophilic or a polar head group (which is the ball structure) and also have a
hydrophobic or non-polar tail.
- What happens is that these amphiphilic molecules will associate
spontaneously into a lipid bilayer facing their hydrophobic tails towards one
another and the hydrophilic or polar head groups towards the aqueous
environment which is found either outside or inside the cell (the cytosol) –
basically the environment of a cell is aqueous. What happens to these
amphiphilic lipid molecules is they point their fatty acid tails away from the
aqueous environment and point their head groups towards the aqueous
environment forming the lipid bilayer.
- That basic structure of lipid bilayers in the cell. - We will look at for example, since it's a lipid bilayer, there are 2 faces to it
and if we look at the plasma membrane, there is one side of the plasma
membrane that will be facing the cytosol which is called the cytosolic face
and the other side of the lipid bilayer is called exoplasmic face so these are
the lipids with their head groups facing the outside of the cell. You have the
cytosolic face facing the cytosol – these would be the head groups facing the
cytosol and the exoplasmic face facing the outside of the cell.
- Every lipid bilayer has this property, even if we look at the Golgi, you’ll
have a lipid bilayer and in red there, it would be the cytosolic face because
this lipid bilayer is facing the cytosol and the brown layer which is facing the
lumen of the Golgi would be the luminal face of this lipid bilayer.
- These lipid bilayers in cells are mainly composed of phospholipids so they
have a polar head group and two hydrophobic tails shown.
- There are many different categories of phospholipids & in an aqueous
environment, these phospholipids will spontaneously form/self associate into
a bilayer. If you drop these phospholipids into water for example, they would
spontaneously form a lipid bilayer with tails facing each other & the
hydrophilic heads facing the aqueous environment or water. This would be
called an artificial bilayer. In water if you drop these phospholipids, they will
form a bilayer.
- We mentioned that lipid membranes are fluid – that means that lipids can
move. This movement is limited, lipids can move in lateral diffusion so they
can move from side to side – this is very rapid so lipids can move very
rapidly within one leaflet, they can also flex so they can move their tails back
and forth & they can also rotate but notice that all of these movements are
within one leaflet – lateral diffusion is within one leaflet, flexion is within one
leaflet and rotation is within one leaflet.
- Flip-flop from one leaflet to another is very rare and it doesn’t happen
spontaneously very often, the movement of one lipid from one leaflet to
another is a very rare event and this is what is called a flip flop.
- The rate of movement within a lipid bilayer or within one of the leaflets of
the lipid bilayer depends on the structure of the lipid.
- Animation: it shows different structures will move at different rates.
Description: you have 2 different lipids, you can see the fatty acid chains,
there are fatty acids that are straight saturated fatty acid and unsaturated fatty
acid chains have little kinks in it. You can see from the movie that different
types of lipids would move at different rates within this lipid layer – the
saturated ones move slower but the unsaturated move faster. The structure of
these lipids determines how rapidly they move within the leaflet of the lipid
- Although it doesn’t happen spontaneously, there will be flip-flop of lipids
from one leaflet to another. There are enzymes in cell membranes that carry
out this function of flipping one lipid from one leaflet to the other leaflet.
- An example of this is phospholipids that are synthesized on the cytosolic
leaflet of the ER need a phospholipid translocator that will rapidly flip-flop
the lipid that is newly synthesized on the cytosolic side to the noncytosolic
- You can see there would be a problem if there wasn’t this flip flop where
this lipid bilayer would be growing only on one leaflet and then you wouldn’t
be able to grow the lipid bilayer so what happens is that since all of the lipids
are synthesized on the cytosolic side of the ER, once it’s synthesized on the
cytosolic side, there is an enzyme catalyzing the flip flop of one of these lipids to the noncytosolic leaflet. This evens things out so that there will be
equal distribution of lipids on the cytosolic side and on the luminal side of the
ER. This is why these flip flops are needed and one of the reasons is that
phospholipids are only synthesized on one side of the ER.
- Just to go into the lipid components in more detail, we mentioned that a
major component of cell membranes is phospholipids – these are the most
abundant in cell membranes and an example of these is phosphatidylcholine
shown in the slide.
- We aren’t going to go into the structure of these phospholipids but you can
see there is the polar hydrophilic head group and two non-polar hydrophobic
tails or fatty acid tails that may be saturated or partially unsaturated fatty acid
tails so this is phosphatidylcholine, there is also sphinomyelin,
phosphatidylserine, these are all examples of phospholipids.
- The phospholipid composition is important for the function of cell
membranes because some membrane proteins require specific phospholipids
for their function, either they will be activated by specific phospholipids or
they will bind to specific phospholipids so they need specific phospholipids
in that membrane in order to function so we’ll see the different membranes in
the cell will have different composition of phospholipids and that can be very
important for protein function.
- Another lipid component of cell membranes are steroids. In animals, the
major steroid would be cholesterol shown in the slide. It has a rigid steroid
ring structure & a little polar head group & a non-polar hydrocarbon tail
which allows cholesterol to insert itself into a lipid leaflet as shown in the
slide so the hydrophobic polar head group can interact with the polar head
groups of the phospholipids & then the steroid ring & the non-polar
hydrocarbon tail can insert itself into the hydrophobic component of the lipid
- In animals, cholesterol is the major type of steroid but in plants, cholesterol
is very rare – instead there are many plant specific steroids found in
membranes of plants.
- In animal cells, cholesterol and phospholipids can be up to 1:1 ratio and we
all know cholesterol b/c if it builds up too much in your system, it can cause
- One of the major roles or the major properties of cholesterol in lipid
membranes is that it decreases the mobility of phospholipids. We saw that
phospholipids can move in a leaflet but if there is a lot of cholesterol in that
leaflet, then it decreases the mobility of these phospholipids & makes the
plasma membrane less permeable to molecules that can normally can traverse
the plasma membrane.
- Overall, cholesterol makes lipid bilayers more rigid & decreases mobility of
phospholipidsnd it also decreases the permeability of the plasma membrane.
That is the 2 major lipid component of cell membranes.
- Glycolipids are the 3 major component of cell membranes and as implied
are sugar groups attached to lipid molecules.
- You can see the lipid molecule and this particular one has a galactose sugar
attached onto it.
- Lipids are glycosylated in the lumen of the Golgi apparatus, that is where
the sugar will be added onto lipids & then glycolipids are found in the plasma
membrane & very rarely but on some intracellular membranes. They are
synthesized in the Golgi & most of them end up in the plasma membrane &
about 5% of the total lipids in the outer leaflet of the plasma membrane are
actually glycolipids in animal cells.
- We say the outer leaflet and this will become more apparent also since the sugars are added on the luminal side of the Golgi apparatus, the sugars or
these glycolipids will end up on the extracellular face of the plasma
membrane. Basically, anything that will be on the luminal side of the Golgi
will end up on the outer leaflet of the plasma membrane.
- Glycolipids are on the outer leaflet of the plasma membrane, their synthesis
is on the luminal face of the Golgi & they are involved with the interaction of
the cell with the environment & they protect also from harsh conditions. So
they have very general roles and they are important roles but they’re mainly
found on the extracellular face of the plasma membrane.
- This brings up an important point where the leaflet, the bilayer of a cell
membrane is nonuniform, there is asymmetrical distribution of different lipids
within the membrane. We just mentioned that glycolipids are on the
exoplasmic or the outer leaflet of the plasma membrane but you also have
phospholipids such as phosphatidylserine shown on the slide that has negative
charges & that is found on the cytosolic face of the plasma membrane. This is
important because it plays an important role in signaling.
- One protein called protein kinase C actually binds to phosphatidylserine and
is activated by the phosphatidylserine and therefore requires this specific
phospholipid to be present on the cytoplasmic side of the plasma membrane
in order to be activated.
- The plasma membrane & the lipid bilayers in general are not uniform in
terms of which phospholipids or just lipids in general are found on the outer
or inner leaflet – there is an asymmetrical distribution of lipids within the
- That is the structural component of cell membranes, the 2 component &
the functional component of cell membranes are membrane proteins.
- The membrane proteins provide the specific functions of certain membranes
surrounding organelles or the cell & they can associate with the lipid bilayers
in a number of different fashions highlighted in the slide.
- The first way is transmembrane proteins.
- Transmembrane proteins transverse the entire lipid bilayer as shown in the
slide and are also called amphiphilic so that means again, they have a
hydrophilic domain which is aqueous so that hydrophilic domain will be
exposed to the outside or inside of the cell, the cytosol, that is the aqueous
environment & they also have a hydrophobic component & this is the
membrane spanning domain that will make contacts with the hydrophobic
chains of the lipids that make up the bilayer. Amphiphilic means they have
both hydrophilic & hydrophobic components to them.
- You have different types of transmembrane proteins – you can have a single
pass transmembrane proteins and this is basically made up of one alpha helix
that will traverse the lipid bilayer. You have multi-pass that have multiple
alpha helices that traverse the lipid bilayer & you can also have some beta
barrels that will be more rigid & also traverse the lipid bilayer.
- Most of these are glycosylated – if these are glycosylated then they’re glycosylated also on the luminal side of the Golgi, mainly in the Golgi and if
they’re glycosylated on the luminal side of the Golgi, the glycosylated
residues of the transmembrane proteins will be exoplasmic or facing the
outside of the cell – this is the same as for the glycolipids added on the
luminal side of the Golgi, they also face the outside of the cell.
- Many transmembrane proteins are glycosylated & the sugar residues are
added in the lumen of the Golgi & therefore the sugars will face the outside
of the cell.
- A different way of associating with membranes is anchoring with one
amphiphilic alpha helix on one side of the lipid bilayer so one leaflet of the
lipid bilayer. So this alpha helix here is actually amphiphilic itself so one side
of the alpha helix is hydrophobic associating with the inside of the lipid
bilayer & the other side is hydrophilic & interacting with the aqueous
environment of the cytosol. Here within one alpha helix, this alpha helix is
amphiphilic and has both a hydrophobic and hydrophilic component & this
protein can then associate with the lipid bilayer with one leaflet.
- This is in contrast to transmembrane proteins that would completely traverse
the lipid bilayer.
- You can also get lipid anchored membrane proteins. This instead of the
protein traversing the plasma membrane, they are actually modified in the
cytosol by the addition of a fatty acid chain or a prenyl anchor. These are both
hydrophobic anchors that can then anchor the protein in the lipid bilayer, as
shown in the slide. This is the protein in the slide and this would be either a
fatty acid or prenyl anchor.
- Now for different types, a myristoyl is a type of fatty acid anchor that is
added to the N terminal glycine of proteins. A palmitate is a fatty acid anchor
that is added to internal cysteine & a prenyl anchor (different types are
farnesyl or geranylgeranyl anchors) that are added to a C terminal cysteine.
- You can see the different anchors are added to different locations on a
protein. Both types are synthesized in the cytosol, this is important b/c
transmembrane proteins are synthesized in the ER – those will associate with
the PM or the cell membrane by traversing it completely whereas these lipid
anchored membrane proteins are synthesized in the cytosol & their anchors
are added in the cytosol & then they will associate with their appropriate
- Both types will be directed to the cytosolic face. The protein will be
synthesized in the cytosol, the anchor is added & this protein dissociates with
the cytosolic face of the lipid bilayer.
- These are shown just to give you an idea of what the structures look like –
you don’t need to memorize what the specific structures of these are but
mainly to know where they are associated in the protein.
- The myristyl anchor or the myristate anchor is added to the N terminal
glycine and will anchor the protein (peace sign protein).
- Then there is the palmitoyl anchor that will anchor from an internal cysteine
& you can see that this would be the sulfur group from that cysteine that
would be associated with the palmitoyl anchor & that will anchor it into the
- Then a farnesyl anchor that has a slightly different structure but the
important thing is again you have that sulfur group from the cysteine but this
time it is a C terminal cysteine on the protein now that the farnesyl anchor
will be associated with.
- N terminal glycine, internal cysteine and C terminal cysteine is where the
anchors are added in these specific cases & then all of them will end up on
the cytosolic face of the lipid bilayer. - Another example is the GPI anchor. This is another anchor that can be
added to proteins & this will allow it to associate with the one leaflet of the
lipid bilayer shown in the slide. This would be the GPI anchor that is
associated with the protein.
- Importantly, this one is added to proteins in the ER. You’ll get the GPI
synthesized in the ER & then it will be added onto the protein. Then it will
end up on the cell surface so again, synthesized inside the compartment of the
ER & ends up on the surface of the cell.
- This was the same for glycolipids & glycoproteins – if you get a modified
on the luminal side of an organelle, it ends up on the surface of the cell.
- Finally, you have proteins that are not directly associating with the
membranes but they’re bound to either face to proteins that are associated
with the membrane, with the modifications or through the mechanisms just
covered. These are all called peripheral membrane proteins, so you would
have a transmembrane protein and then you would have a peripheral
membrane protein that is associated with the membrane protein on either
face, it could be either the exoplasmic or the cytoplasmic face of the cell
where these peripheral membrane proteins could associate with other
- One of the differences is that these are mainly non-covalent interactions that
are occurring with these other proteins that are integral membrane proteins &
for a biochemist that means that these proteins are much easier to extract
from a cell & that is one of the key features of the different types of proteins
and is that these peripheral proteins are easier to extract from cells than for
example, fatty acid modified proteins or especially transmembrane proteins.
- Peripheral membrane proteins only need a gentle extraction procedure that
doesn’t destroy the lipid bilayer to extract it from the cell.
- This is in contrast to integral membrane proteins which in order to be
extracted from the cell, you need to be able to destroy the membrane with