BIOLOGY 1. (2) alberts

Cytoplasm

Contents of a cell that are contained within its plasma membrane but, in the case of eukaryotic cells, outside the nucleus

Cytosol

Contents of the main compartment of the cell, excluding the nucleus and membrane bounded compartments such as ER and mitochondria. the main site of protein degradation

Gated transport

Movement of proteins through nuclear pore complexes between the
cytosol and the nucleus.

Organelle

Membrane-enclosed compartment in a eukaryotic cell that has a distinct
structure, macromolecular composition, and function.

Signal sequence

Protein sorting signal that consists of a short continuous sequence of
amino acids.

TRUE OR FALSE
The biological membranes that partition the cell into functionally distinct
compartments are impermeable.

FALSE
lipid bilayers themselves are impermeable to hydrophilic molecules but biological membranes, which contain proteins in addition to the bilayer are not. they are selectively permeable

TRUE OR FALSE
Like the lumen of the endoplasmic reticulum (ER), the interior of the
nucleus is topologically equivalent to the outside of the cell.

FALSE
the nucleus is topologically equivalent to the cytoplasm because the outer and inner membrane are continuous with one another

TRUE OR FALSE
ER-bound and free ribosomes, which are structurally and functionally
identical, differ only in the proteins they happen to be making at a particular
time.

TRUE
Ribosomes all begin translating mRNAs in the cytosol. the mRNAs for certain proteins encode a signal sequence for the ER membrane. after synthesis, the nascent protein along with the ribosome and the mRNA is directed by the signal sequence to the ER membrane. Ribosomes translating mRNA without such a sequence remain free in the cytosol

TRUE or FALSE
Each signal sequence specifies a particular destination in the cell.

TRUE
Signal sequences that specify particular cellular destinations have characteristic features that allow their interaction with appropriate sorting receptors, which guide them to their target compartment

Is it really true that all human cells contain the same basic set of membrane-
enclosed organelles? Do you know of any examples of human cells
that do not have a complete set of organelles?

The vast majority of cells in the human body do have a complete set of membrane enclosed organelles. Certain specialised cells do not. e.g. Red Blood Cell. only a plasma membrane enclosed cytosol
Cells that make up the lens of the eye lack a mitochondria

Why do eukaryotic cells require a nucleus as a separate compartment
when prokaryotic cells manage perfectly well without?

Eukaryotic gene expression is more complicated. Prokaryotic cells do not have introns that interrupt the coding sequences on their genes, so that an mRNA can be translated immediately after transcription. In eukaryotic cells most RNA transcripts must be spliced before translation. The nuclear envelope separates the transcription and translation processes in space and time.

What is the fate of a protein with no sorting signal?

The protein will remain in the cytosol

Which
type of protein synthesis—in the cytosol or on the ER—do you think is
responsible for the majority of protein synthesis in a liver cell?

In cells that do not secrete large amounts of protein, the majority of protein synthesis is likely to occur in the cytosol.

List the organelles in an animal cell that obtain their proteins via gated
transport, via transmembrane transport, or via vesicular transport.

The nucleus is the only organelle that receives its proteins by gated transport.
The ER mitochondria and peroxisomes all receive their proteins by transmembrane transport, mediated by specific protein translocators that reside in the membrane
The golgi apparatus, secretory vesicles, early and late endosome and lysosomes all obtain their proteins via vesicular transport

Nuclear export signal

Sorting signal contained in the structure of macromolecules and complexes
that are transported from the nucleus to the cytosol through
nuclear pore complexes.

Nuclear Pore Complex (NPC)

Large multiprotein structure forming a channel through the nuclear
envelope that allows selected molecules to move between nucleus and
cytoplasm. It has a nuclear basket and each NPC contains aqueous passages, through which small water soluble molecules can diffuse passively

How does selective import into the nucleus occur?

The nuclear localization signal (NLS) are responsible for the selectivity of the active nuclear import process.
To initiate nuclear import, most. NLS must be recognized by nuclear import receptors that are sometimes called importins , export requires exportins. Importins and exportins belong to the karypherin family.
The importin finds the nuclear pore complex via FG repeats of the nucleoporins, of which there are 30 form the npc.
FG for phenylalanine and glycine

Ran

Monomeric GTPase present in both cytosol and nucleus that is required
for the active transport of macromolecules into and out of the nucleus
through nuclear pore complexes.

nuclear lamina

Fibrous meshwork of proteins on the inner surface of the inner nuclear
membrane.

Nuclear import receptor

Protein that binds nuclear localization signals and facilitates the transport
of proteins with these signals from the cytosol into the nucleus
through nuclear pore complexes
also known as Importin

Nuclear Localisation Signal (NLS)

Sorting signal found in proteins destined for the nucleus and which enable
their selective transport into the nucleus from the cytosol through the
nuclear pore complexes.

outer nuclear membrane

The portion of the nuclear envelope that is continuous with the endoplasmic
reticulum and is studded with ribosomes on its cytosolic surface.

TRUE OR FALSE
The nuclear membrane is freely permeable to ions and other small molecules
under 5000 daltons.

TRUE
due to the perforated membrane

TRUE OR FALSE
To avoid the inevitable collisions that would occur if two-way traffic
through a single pore were allowed, nuclear pore complexes are specialized
so that some mediate import while others mediate export.

FALSE
individual nuclear pores mediate transport in both directions. its unclear how traffic is avoided

TRUE OR FALSE
Some proteins are kept out of the nucleus, until needed, by inactivating
their nuclear localization signals by phosphorylation.

TRUE
gene regulatory proteins are usually regulated in this way. preventing gene activation or repression until the proper time

TRUE OR FALSE
All cytosolic proteins have nuclear export signals that allow them to be
removed from the nucleus when it reassembles after mitosis.

FALSE
resident cytosolic proteins are efficiently excluded from reassembling nuclei by the mechanism or reassembly. the nuclear envelope is initially closely applied to the surface of the chromosomes, excluding all proteins except those bound to mitotic chromosomes. once the envelope is complete, other residents of the nucleus are imported via their nuclear localisation signals.

The inner and outer nuclear membranes form
a continuous sheet, connecting through the nuclear pores. Continuity
implies that membrane proteins can move freely between the two
nuclear membranes by diffusing through the bilayer at the nuclear pores.
Yet the inner and outer nuclear membranes have different protein compositions,
as befits their different functions. How do you suppose this
apparent paradox is reconciled?

- proteins on the inner membrane are anchored by interactions with components of the nucleus such as the nuclear lamina and chromosomes.
- the nuclear pore proteins may restrict the free diffusion of other proteins as they are a boundary between the inner and outer layer.

How is it that a single nuclear pore complex can efficiently transport proteins
that possess different kinds of nuclear localization signal?

Transport is mediated by a variety of nuclear import receptors that are encoded by a family of related genes.

How do you suppose that proteins with a nuclear export signal get into
the nucleus?

proteins with a nuclear export signal also have a nuclear localisation signal, therefor allowing them to shuttle between the nucleus and cytoplasm.

Nuclear localization signals are not cleaved off after transport into the
nucleus, whereas the signal sequences for import into other organelles
are often removed after import. Why do you suppose it is critical that
nuclear localization signals remain attached to their proteins?

at each mitosis, the contents of the nucleus and the cytosol mix when the nuclear envelope disassembles. when the nucleus reassembles, the nuclear proteins must be selectively reimported. by contrast, the contents of other organelles never mix wit the cytosol. at mitosis, the ER and Golgi break up into vesicles which retain the luminal contents.

How does the Ran-GTP-GDP cycle in nuclear export/import work?

Ran can exist in a gdp and gap bound form. In the cytosol, the ran gdp Form dominantes, due to ran gap, gtpase activating protein.
Rangdp is imported into the nucleus via its own import receptors.In the nucleus, ran gtp dominates due to rangef (gdp/gtp nucleotide Exchange factor)
The gradient of these two forms drives the nuclear transport in the appropriate direction

Mitochndria

Membrane-enclosed organelles, about the size of bacteria, that carry out
oxidative phosphorylation and produce most of the ATP in eukaryotic
cells.
has a double membrane.
contain DNA and ribosomes but still require protein import from cytosol.

Mitochondrial hsp70

Part of a multisubunit protein assembly that is bound to the matrix side
of the TIM23 complex and acts as a motor to pull the precursor protein
into the matrix space.--\> ratchet

Multisubunit protein assembly that transports proteins across the mitochondrial
outer membrane.

TOM complex

Mitochondrial precursor protein

Protein encoded by a nuclear gene, synthesized in the cytosol, and subsequently
transported into mitochondria.

TRUE OR FALSE
The TOM complex is required for the import of all nucleus-encoded
mitochondrial proteins.

TRUE
regardless of their final destination in the mitochondrion, all proteins that are synthesised in the cytosol must first enter the TOM complex. after this complex, the pathways of import diverge.

TRUE OR FALSE
The two signal sequences required for transport of nucleus-encoded proteins
into the mitochondrial inner membrane via the TIM23 complex are
cleaved off the protein in different mitochondrial compartments.

FALSE
only one of the signal sequences is cleaved. the N-terminal signal is cleaved off the imported protein. the second signal is very hydrophobic and at the new N-terminus. it directs the protein to the inner membrane either the TIM23 or OXA complex. the second signal is not cleaved, it anchors the protein in the membrane

TRUE OR FALSE
Import of proteins into mitochondria and chloroplasts is very similar;
even the individual components of their transport machinery are homologous,
as befits their common evolutionary origin.

FALSE.
import of proteins is similar but the components of import machinery are not related. the functional similarities have come through convergent evolution, reflecting the common requirements for transport across a double membrane system

Nucleus

contains the genome, aside from mitochondrial and chloroplast DNA, and is the principle site of DNA and RNA synthesis

Endoplasmic Reticulum and its relevance in immune cells

Makes up approximately half of the total area of membrane in a eukaryotic cell. Rough with ribosomes bound and smooth without.
its three main functions are
- protein synthesis
- lipid synthesis
- ca 2+ storage

huge ca 2+ storage and is therefore very important for intracellular signalling in immune cells. also important for plasma cells

Ribosomes

organelles that are not membrane enclosed. They synthesise soluble and integral membrane proteins

Golgi Apparatus

organised structures of disc like compartments called golgi cisternae
receives proteins and lipids from the ER and dispatches them to various destinations while covalently modifying them
is the central organelles of post translational modifications

Lysosomes

Contain digestive Enzymes that degrade defunct intracellular organelles as well as macromolecules and particles taken in by endocytosis
pH is ~5 (cellular is 7.2)
contains many acid hydrolyses ( nucleases, proteases, glycosides, lipases, sulfatases, phosphatase, phospholipase)
have ATP dependent H pumps to maintain pH

Endosomes

endocytosed material must first pass through a series of endosomes to get to the lysosome.

Peroxisome

Small vesicular compartments containing enzymes that are used in various oxidative reactions
Breakdown of long chain fatty acids by oxidation (beta oxidation)
H2O2 is used by catalase to oxidise other substrates (alcohol, formaldehyde)
conversion of fatty acids into acetyl-coA which is exported and used for biosynthesis
Critical for generation of plasmalogen which is a major phospholipid component of myelin sheaths

what is a physical property of granulocytes that can be used to identify them under the microscope?

they do not have round nuclei. Polymorphonuclear

what does the nucleus of a eosinophil, a neutrophil and a basophil look like?

e: u shaped
n: multiple joined by thin strands
b: like a sausage balloon twisted in the middle

what are megakaryocytes

produce platelets in the bone marrow

what are the forms of nuclear DNA

Heterochromatin: Highly condensed form
Euchromatin: less condensed form--\> composed of 30nm fibres and looped chromosome domains

Signal Patch

sorting signal composed of multiple internal amino acid sequences that form a specific 3D arrangement of atoms on the proteins surface.

Nuclear disassembly and reassembly during the cell cycles

when a nucleus disassembles during mitosis, the nuclear lamina depolymerises
-phosphorylation of the nuclear lamina by the cyclin dependent kinases (cdk) activated at the onset of mitosis
- proteins of the inner nuclear membrane are phosphorylated, and the nuclear pore complexes disassemble and disperse in the cytosol.
- nuclear envelope membrane proteins diffuse throughout the ER membrane

JAK-STAT pathway

Essential pro inflammatory signalling pathway initiating the acute response to an infection --\> fever

Regulation of nuclear import via phosphorylation

JAK is activated upon ligand mediated receptor dimerisation which causes transphosphorylation.

Activated JAK phosphorylates STATs at the conserved tyrosine in the c terminus. phosphorylation allows STAT dimerisation and entry into the nucleus using importin alpha 5 and the ran nuclear import pathway.
once in the nucleus, STAT1 binding with DNA competes with the importin a5 binding.
the Nuclear export signal of STAT is masked when the dimers are bound to DNA, the DEphosphorylation of STAT by a nuclear phosphatase causes DNA release and NES becomes accessible for CRM1 mediated nuclear export

NF-AT signalling pathway

Nuclear Factor of Activated T-cells
Pathway triggered if antigen is recognised on a DC
In a resting Tcell, NFAT is phosphorylated (on nuclear import signal)
Activation of the pathway leads to Ca influx which leads to calmodulin activation. act Calmodulin binds the protein phosphatase calcineurin which dephosphorylates the nuclear import signal of NFAT and binds the nuclear export signal.
the NFAT calcineurin complex enters the nucleus and activated transcription
REGULATION VIA DEPHOSPHORYLATION

Regulation of nuclear RNA export. mi, sn, t, r and mRNA

sn, r, t and miRNAs are exported via the ran GTP/ exporting system
sn and rRNA with CRM1
t and miRNA with Xpot 1 and 5 respectively
mRNA is unknown, exported as large mRNP complexes

Structure of ER

the rough ER form oriented stacks of flattened cisternae each having a luminal space of 20-30nm
the smooth er membrane is connected to these cisternae and forms a fine network of tubulus 30-60nm in diameter.
this together forms a net like labyrinth

the smooth ER

portion of the endoplasmic reticulum that is free of ribosomes. usually scant in normal cells. in specialised cells however, like cells that specialise in lipid metabolism, it is abundant and has additional functions

what are the two pathways of protein transport into the ER. characteristics

cotranslational with the SRP through a water filled aqueous channel in the translocator, sec 61, and post translational. post translational requires atp. also uses sec 61 but also a host of accessory proteins that associate to sec61 complex. (Sec62, Sec 63, sec 71 and sec 72) Bip chaperone important
Sec A in eukaryotes

difference between eukaryotic and prokaryotic post translational translocation?

in eukaryotes ATP hydrolysis occurs in the er and pulls the protein in, in bacteria hydrolysis outside pushes the protein in

what is the SRP

signal recognition particle. is a ribonucleoprotein consisting of one RNA and 6 protein subunits. Binds to the ER signal sequence and halts translation until the ribosome mRNA complex is attached to the ER

ER signal sequences vary greatly. how is it possible that the SRP can bind all of them?

each er signal sequence has 8 or more non polar amino acids at its core.
The crystal striation of SRP allows us to understand how it can bind different sequences. the signal sequence binding site is a large hydrophobic pocket lined by methionines. due to the unbranched flexible side chains of the methionines, the pocket is sufficiently plastic to accomodate different hydrophobic signal sequences.

structure and binding of SRP.

SRP has a rod like structure that wraps itself around the large subunit of the ribosome. one one end it binds the signal sequence of the emerging peptide and at the other end it binds the elongation factor binding site

how does SRP independent post translational translocation occur?

in eukaryotes, the chaperone BiP and ATP are needed. sec61 complex is used alongside associated proteins, sec 62, 63, 71 and 72. these proteins span the membrane and use a small domain on the luminal side to deposit the chaperone BiP onto the polypeptide chain as it emerges into the ER lumen. the removal of BiP is ATP dependent

What types of transmembrane proteins do you know?

Type I: the NH2 terminus is on the luminal side of the ER
Type II: the carboxy terminus is at the luminal side of the ER

How are proteins inserted into the ER membrane?

the proteins contain stop transfer sequences alongside the initial start transfer sequence.

how is the orientation of protein in the membrane determined?

the charge of the amino acids on either side of the stop transfer sequence determine the orientation. positive outside and negative inside

Important multipass proteins in the immune system

Tetraspannins
have four transmembrane segments. CD9, CD81, CD82 and CD63
expressed in professional APC. crucial regulators of antigen presentation. involved in both loading and trafficking of MHCII

What is GPI?

GLycosylphosphatidylinositol. It anchors proteins to the membrane. attached to the C terminus of the protein and may be used to redirect proteins to lipid rafts

BCR and lipid rafts

in the resting state, the BCR is not in a lipid raft. upon antigen engagement, the BCR relocated within rafts

what is FcyIIIb?

a GPI linked neutrophil specific IgG FC-receptor
affinity receptor for polyvalent immune complex IgG and decoy receptor that binds IgG complexes without triggering activation. Basically you can have signal transduction without activation of neutrophils

what is the most common post translational modification in the ER

N linked glycosylation on Asparagine. 90% of glycoproteins. All membrane proteins are glycosylated

most common method of glycosylation

a 14 sugar precursor containing glucose, n-acetylglucosamine and mannose is added en bloc to the protein. this precursor is on the transmembrane protein dolichol and is transferred by the membrane bound enzyme oligosaccharyl transferase.

O-Glycosylation

less common. the oh group of serine or threonine. IgA antibodies are o-glycosylated

how is correct folding ensured?

with the help of the ER chaperones calnexin and calreticulin. they bind to incompletely folded proteins, retain them in the ER and prevent them from irreversible aggregating
they recognise N-linked oligosaccharides that only have one of the original three precursor glucoses on the core. When the third glucose is removed, the chaperones release the protein and it can leave the ER. The chaperones can distinguish properly folded proteins from incompletely folded proteins with the help of glycosyl transferase which continuously adds a glucose to oligosaccharides that have lost their last glucose. it only however adds glucose to unfolded proteins.

an unfolded protein undergoes continuos cycles of glucose trimming (glucosidase) and glucose addition ( glucose transferase), maintaining affinity for calnexin and calreticulin until it is fully folded.

How are misfolded proteins distinguished from incompletely folded proteins?

with the help of N-linked oligosaccharides. they serve as timers to measure how long a protein has been in the ER
the slow trimming of a particular mannose on the core oligosaccharide tree by mannosidase creates a new oligosaccharide structure that ER luminal lectins of the retrotranslocation apparatus recognise. Proteins that fold and exit the er faster than the mannosidase can remove its target mannose escape degradation

What is the common feature of the multiple translocator complexes that move different proteins from the ER into the cytosol?

They all contain a E3 ubiquitin ligase that attaches ubiquitin the the unfolded protein as they are exiting the er, marking them for destruction

What happens when misfolded proteins accumulate in the ER and the cytosol?

ER-- unfolded protein response
Cytosol-- heat shock response

what is the unfolded protein response?

there are three parallel signal pathways that execute the unfolded protein response:
- IRE1
-PERK
-ATF6
they all contain sensors for misfolded proteins that induce signal cascades that cause the activation of genes to increase the protein folding capability of the ER

Explain the IRE1 pathway

regulatory RNA splicing is the key regulatory switch here
1. misfolded proteins in the ER signal the need for more ER chaperones. bind and activate the transmembrane kinase.
2. the activated kinase unmasks its endoribonuclease activity
3. the endoribonuclease cuts specific RNA molecules at two positions, removing introns.
4. the two exons are ligated forming an active mRNA
5. mRNA is translated to make a transcription regulator that enters the nucleus and activated genes encoding ER chaperones.

How are new mitochondria generated?

via growth of existing organelles

What are the outer membrane and inner membrane translocators of the mitochondria?

Outer: TOM complex and SAM complex
Tom for all proteins regardless of their final destination. SAM for inter membrane proteins that are to be inserted into the outer membrane
Inner: - Tim22 complex--\> proteins from the outside that need to be integrated into the inner membrane, from inter membranous space
- Tim23 complex (has import ATPase)
inner membrane for proteins that are to be transported into the mitochondria. ratchet system with mitochondrial Hsp association and disassociation
- OXA complex
for mitochondrial proteins that are to be inserted into the inner membrane

how are mitochondrial proteins typically imported?

as unfolded precursors. this precursor has a signal sequence which is recognised and bound by the receptor protein in the tom complex. the precursor is inserted though the membrane by the tom complex. translocation into the matrix by the TIM23 complex. cleavage of the signal peptide

Zellweger syndrome

patients have defective protein import into peroxisomes resulting in abnormal brain, liver and kidney development and early death

what are the different types of vesicle coats? and where do they transport from/to?

Clathrin--\> from and to plasma membrane and from the golgi
COPI--\> from the golgi
COPII--\> from the ER

How are vesicles leaving the ER formed?

COP II Membrane proteins are packed into budding transport vesicles through interactions between adaptor proteins of the inner COPII coat and exit signals on the cytosolic tails of the membrane proteins. some of the membrane proteins function as cargo receptors, binding soluble proteins in the ER lumen.

What are the proteins of the COPII coat?

Sar1GTP. Sar GEF regulated Sar1. it can only be membrane bound when it is GTP bound
Sec23/24 tether cargo receptors
Sec13/31 form the outer coat of COPII vesicles
SAR1 is in the cytosol in an inactive, soluble factor available,
bound to GDP in an amphiphilic helix
2. in the ER membrane Sar1-GEF -\> exchange of GDP -\> GTP,
conformational change
3. SAR1 is now membrane-bound and active (donor membrane)
- for vesicle formation: COPII needs adaptor proteins
o SEC24 and SEC23 (only binds if 24 has bound) are inner coat
protein
o SEC24 binds to the cargo receptor that has bound a cargo in
the ER lumen
o SEC23 binds to SEC24 and Sar1-GTP --\>complex formation
o SEC13/31 are producing the outer coat
- ER vesicles can accommodate large cargo like collagen
- after vesicle budding the coat disassembles -\> GTP hydrolysis acts as a
timer --\> is the anchoring factor, without the coat falls apart

what happens after ER vesicle formation?

the COPII coat disassembles after GTP in Sar1 is hydrolysed to GDP. NFS is recruited to the vesicle initiating the unwinding of the vesicles t and v SNAREs which then allows homotypic membranes fusion. The er vesicles become vesicular tubular clusters

What is the resting position of v and t SNAREs on a vesicle?

They are coiled together to prevent the vesicle from reacting. Once NSF binds to the vesicle, it disentangles the SNAREs, allowing binding on neighbouring vesicles. NSF requires ATP

What are the steps of SNARE mediated vesicle fusion?

1. Tethering of rab protein on vesicle to rab effector protein on target membrane.
2. Docking
3. Fusion--\> trans SNARE complex
4. SNARE dissociation

What are the steps of bilayer fusion?

- tight paring between v and t SNAREs forces the lipid bilayer into close proximity which expels the water molecules from the interface
- the lipid molecules in the two interacting cytosolic leaflets flow between the membranes to form a stalk
- hemifusion
- fusion

What are rab proteins used for?

They guide transport vesicles to their target membrane.
Rab1 ER and Golgi
Rab2 Cis Golgi
Rab8 Cilia
Rab5 Early endosomes, plasma membrane, clathrin coated vesicles

How does targeting with rab proteins work?

1. Tethering: Rab effector proteins on the target membrane bind to Rab-GTPs
2. Docking: Pairing of SNARE proteins
3. Fusion: Rab-GAP hydrolyses Rab-GTP into Rab-GDP initiating rab dissociation and membrane fusion
4. cytosolic Rab GDP is bound and stabilised by a GDP dissociation inhibitor (GDI)

How are ER resident proteins retained in the ER ?

They contain a KDEL (lysine, aspartic acid, glutamic acid, leucine). KDEL receptors in the Golgi initiate COPI formation for transport back into the ER

Structure of the Golgi network. Order from ER?

Cis face- cis golgi network- cis cisterna- medial cisterna- trans cisterna- trans golgi network- trans face

What are the models of transport through the Golgi?

there are two models of transport
Model I: Cisternal maturation model
the golgi is seen as a dynamic structure that matures from early to late by acquiring then losing specific golgi resident proteins. new cis cisternae continually form as vesicular tubular clusters from the ER and progressively mature to become a medial cisternae and then a trans cisternae
Model II vesicle transport model
golgi cisternae are long lived structures that retain their characteristic set of Golgi resident proteins firmly in place. Cargo proteins are transported from one cisternae to the next by transport vesicles

in what cellular processes is autophagy relevant?

presentation of cytosolic proteins in MHC II

How are the different golgi transport models supported?

The cisternal maturation model is supported by studies using golgi enzymes from different cisternae that were fluorescently labelled with different colours. such studies performed in yeast where the golgi are not stacked show a that individual cisternae change colour

The vesicle transport model is supported by studies that show that cargo molecules are present in small COPI coated vesicles and that these vesicles can deliver them to Golgi cisternae over large distances.

Golgin proteins

up to 400nm long. are filamentous proteins attached to golgi stacks that catch and interact with Rab proteins on transport vesicles. they help to retain golgi transport vesicles close to the organelle.

what are the two broad classes of Sugar structures that can be added to proteins in the golgi?

Complex oligosaccharides --\> bear a negative charge
High mannose oligosaccharides --\> humans don't usually have these on their cell surface proteins. used as a detection mechanism by e.g. the complement system

What is the function of the glycocalyx and what are the major classed of glycans in eukaryotes?

the glycocalyx is a highly charged layer of membrane bound biological macromolecules attached to a cell membrane. It functions as a barrier between a cell and its surroundings

the major classes of glycans are:
- N-glycans
- O-glycans
- Glycolipids
- Anchors
- Glycosaminoglycans

Cathrin-coated vesicle formation.

Dominate protein transport from the Golgi to the Plasma membrane. also mediate the transport from the plasma membrane to the eadosomal-lysosomal system.
FORMATION
1. Coat assembly and cargo selection AP2 binds PIP2 which changes the conformation of AP2 to be able to bind to the cargo receptor. and the the cargo can bind to the cargo receptor.
2. Bud formation
3. vesicle formation --\> membrane bending and fusion proteins such as dynamic are involved in this process
4. uncoating