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BIOL 130 Study Notes Unit VIII Cell Communication

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University of Waterloo
BIOL 130
Richard Ennis

BIOL 130 Unit VII Study Notes Membrane Enclosed Organelles Revisited: • The list of compartmentalized organelles within the cell (i.e. the animal cell) include: o Peroxisomes o Lysosomes o Golgi apparatus o Mitochondrion o Endoplasmic reticulum o Nucleus o Plasma membrane • Ultimately, proteins need to be able to go in and out of cell, which requires them to be sorted somehow as they pass in and out of these various compartments of the cell! • Relative volumes occupied by major membrane-enclosed organelles in the average liver cell: o Cytosol – 54%  only 1 o Mitochondria – 24%  around 1700 of them o Endoplasmic Reticulum – 12%  only 1 o Nucleus – 6%  only 1 o Golgi Apparatus – 3%  only 1 o Peroxisomes – 1%  around 400 of them o Lysosomes – 1%  around 300 of them o Endosomes – 1%  around 200 of them • Fun fact: the area of the rough ER exceeds that of the plasma membrane! How did Eukaryotes get Internal Membranes? • Ancient eukaryotic cells were believed to be like prokaryotes with initially no internal membranes o Its plasma membrane carried out all membrane-related functions • The plasma membrane became invaginated o Creates the endomembrane system • And after, recalling unit 1, mitochondria and chloroplasts are thought to have evolved by the engulfing of prokaryotes by early eukaryotic predators o This is known as the Endosymbiont Theory Recall Unit 1: The Role of the Cytoskeleton • The cytoskeleton serves many functions: o Cell shape o Cell motility o Moves/positions organelles o Moves materials within the cell o Moves chromosomes during mitosis The Signal Sequence: • A signal sequence is a chain of amino acids that can be 16-60 amino acids long • Signal sequences, as their name suggests, direct proteins to specifically to their destined organelles • Once the proteins arrive, they are sorted, and these signal sequences are usually cleaved/removed • Errors related to signal sequences may involve the deleting or transferring of a sequence to a wrong protein o Causes the protein to go to the incorrect organelle Three Methods of Importing Proteins into Organelles: • In general, protein sorting is the transfer of proteins into the cellular compartments where those proteins are actually needed o The transport of proteins does require energy! • Synthesis of virtually all proteins begins in the cytosol on FREE RIBOSOMES • Three methods of importing proteins include: o 1) Transport through nuclear ports o 2) Transport across membranes o 3) Transport by vesicles Method 1: The Nucleus • The nucleus has a double membrane, often referred to as the “nuclear membrane” o Things can go in and out of the nucleus through the nuclear pore, which is actually a complex! • Note how the nuclear membrane is related to the endoplasmic reticulum: o The inner and outer bilayers of the nuclear membrane are separated by a space that is continuous with the space inside the ER, providing direct contact between them! • The structure of the nuclear pore complex can be seen below: • Many molecules pass through the nuclear pore o 500 molecules through each of the 3000-4000 pores PER SECOND o But the traffic of molecules is regulated and is very selective • Proteins that are imported into the nucleus requite a localization signal sequence o A nuclear signal sequences needs to be attached to a protein if its destination is the nucleus o An escort molecule, whose job is to recognize the attached signal sequence, then needs to come and pick up the protein and brings it into the nucleus • Nuclear pores therefore act as gateways into the nucleus o If a molecule (including proteins) is small enough, it can pass freely though the pore o However, the passage of larger molecules is an active (i.e. energy-requiring) process that also requires the protein to have a nuclear localization signal!  Examples of such processes:  Nuclear localization (import) signals: o Amino acid sequence that tags a protein that is meant to be imported into the nucleus by nuclear transport (with the signal and the escort molecule)  Nuclear export signals: o Amino acid sequence that tags a protein to be exported out of the nucleus o Things that go INTO the nucleus:  Histones (probably b/c DNA molecules are associated with histones to create higher order DNA structures)  Ribosomal proteins  Proteins required for RNA TRANSCRIPTION and DNA REPLICATION  dNTPs and rNTPs o Things that go OUT of the nucleus:  Mature, properly processed mRNA (to be used in translation outside)  Ribosomal RNA (rRNA) that is made in the nucleolus Method 2(A): Transport across Membranes – A Look at Mitochondria & Chloroplasts • Recall that from unit 1, mitochondria and chloroplasts have their own double membranes o In fact, chloroplasts in particular also have a third membrane (the thylakoid membrane) • Despite having their own genome and ribosomes, most mitochondrial and chloroplast proteins are encoded by the cell’s nuclear genome o Means that mitochondria and chloroplasts must import proteins • Proteins that are destined to go to the mitochondria and/or chloroplast are made by free ribosomes in the cytosol (most proteins are) o Signal sequences are placed on the nitrogen of the protein (at the N-terminus) o They must be moved across both outer and inner membranes at special sites where both layers are in contact o Proteins must unfold to be imported, then refolded, and its signal sequence is removed o Subsequent transport within the organelle then requires another signal sequence • As seen in the diagram above, the precursor protein displaying a mitochondrial signal sequence can bind onto a receptor protein on the outside o Its signal will match the signal receptor’s site, allowing the protein translocator to move to the protein and align the outer and inner membranes o This allows the protein to pass through, unfolded, and go into the mitochondria and refold o Its signal sequence is then removed when it arrives fully inside Brief Side-note: Synthesis of all Proteins Starts on Free Ribosomes • mRNA can remain freely in the cytosol or if it encodes for a protein meant to go to the ER, then it remains membrane-bound onto the ER. • In either regards, there exists a common pool of ribosomal subunits in the cytosol capable of synthesizing proteins by translating the mRNA wherever it is: o So if the mRNA is freely in the cytosol and needs to be translated, then ribosomal subunits will form into polyribosome complexes and translate the mRNA in the cytosol o Alternatively, polyribosome complexes can also be bound to the ER membrane to synthesize proteins by translating mRNA that is bounded to the ER as well! Method 2(B): Transport across Membranes – A Look at the Endoplasmic Reticulum • The ER is the most extensive endomembrane system • It acts as an entry point not only for its own proteins, but also as an entry point for… o The rest of the endomembrane system (i.e. the Golgi, lysosomes, endosomes) o The cell surface o Secretory proteins • Once a protein enters the ER’s membrane or lumen, it will does not re-enter the cytosol UNLESS it is secreted out ER Signal Sequence & SRP Direct Ribosomes to the ER: • If an mRNA is supposed to encode a protein targeted to the ER, then it will remain membrane-bound onto the ER • When the ribosomal translation unit is synthesizing the growing polypeptide chain using the mRNA, the peptide chain has a specific ER sequence signal that can be picked up by a signal recognition particle (SRP) o SRPs are actually riboproteins made up of RNA and proteins and its job is to recognize the ER signal and escort the growing polypeptide meant for the ER, towards the ER membrane • The SRP binds onto the sequence signal and then connects to an SRP receptor in the ER membrane • This allows the ribosomal translation unit to bind to the translocation channel and the polypeptide will begin to enter the ER as it’s being synthesized! • The SRP is displaced and goes out looking for another ER signal sequence Two Types of Proteins Transferred to the ER: • Water soluble proteins (hydrophilic) – translocated completely across o Destined for secretion or the lumen of an organelle • Prospective transmembrane proteins – translocated only partially across o Destined for plasma membrane, ER membrane, or membrane of another organelle • Water soluble proteins: o These proteins cross all the way into the lumen o Proteins of water soluble, when displaying their signal sequence, can be fed into the translocation channel as it emerges from the ribosome that synthesized it o Signal peptidase comes and cleaves off its signal sequence; protein completely goes in ER • Transmembrane Proteins (i.e. “Single-Pass” Transmembrane Proteins) o These proteins are translocated only partially across the ER membrane o They have a hydrophobic start-transfer signal sequence, recognized by the ER translocation channel, but they also have a hydrophobic stop-transfer sequence
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