Cell bio: Chapter 15

Approximately how many mitochondria in the cell?

1700 - variable of cell type.

Many proteins are glyscosylated (for protection) on what in the ER?

Asparagines

The location of the ER translator sequence on either the N terminus or the C terminus helps determine orientation. Explain.

If its on the N terminus, its going to go through the translocon first but if its in the C terminus, then it will go down first.

What makes up the double membrane of the nuclear envelope?

Inner nuclear membrane and outer nuclear membrane.

What is the role of peroxisomes?

Oxidative breakdown of toxic molecules.

What determines the orientation of the protein within the ER membrane?

The amount of transmembrane proteins within the ER membrane.

What is the protein translocater of translocon?

Will recognize the signal sequence (ER) and the special enzyme signal peptidase will cut the enzyme/peptide because its not needed anymore. The translator is going to keep feeding the polypeptide into the lumen and when it gets into the lumen it can fully fold into its three-dimensional structure.

Degrades lipids

lipases

In which process do Rab proteins function?

vesicle tethering (Rab proteins are a family of small GTPases that are specific for each type of organelle and vesicle. Rab proteins on vesicles are recognized by tethering proteins on the target membrane and help capture and tether the vesicle for later docking and fusion.)

Proteins are transported into organelles by which three mechanisms?

- Proteins enter the nucleus through the nuclear pores. - Proteins get transported across membranes. - Proteins are transported by vesicles.

How do proteins get transported across the membrane?

- Proteins unfold to enter mitochondria and chloroplasts. - Protein enter peroxisomes from both the cytosol and the ER. - Proteins enter the ER while being synthesized.

Describe the lifecycle of a clathrin-coated vesicle.

1) Coat assembly and cargo selection- The cargo receptor is typically chemically modified in some way which allows them attract adaptor proteins (adaptin). 2) Bud formation- The receptor is coated with clathrin coated pits which begins to form a cage like strucutre that forces deformation of the membrane which eventually forms a vesicle. 3) Vesicle Formation- Dynamin forces breaking of the vesicle from the PM using GTP. 4) Uncoating- Clathrin then breaks off of the vesicle and the naked transport vesicle is free to go to the endosomes and then lysosomes.

Describe the endocytosis of cholesterol.

1) Endocytosis- On the cells surface there are LDL receptors. LDL is a large particle that has a bilayer around it with cholesterol and triglycerides inside. They are endocytosed through a series of adaptor proteins, clathrin causes a conformational change in the membrane. 2) The clathrin coated vesicle gets rid of clathrin and uses tethers and SNARES to fuse with endosomes. 3) From the endosome, the LDL cargo is delivered to the lysosome where hydrolytic enzymes break down LDL and releases free cholesterol. 4) The receptors bud off of the lysosome and return to the PM.

Describe briefly the process of nuclear import receptors.

1) GTP is hydrolyzed, Ran-GDP dissociates from receptor. 2) The protein binds to the receptor 3) Ran-GTP binds to the receptor 4) Protein delivered to nucleus

Endocytic pathway in epithelial cells such as in the lumen of the intestine.

1) Recycling of transport vesicles from the early endosomes. 2) Degradation in the lysosomes 3) Transcytosis- transported across the cells interior to a different chemical environment.

Approximately how many endosomes in the cell?

200

Approximately how many lysosomes in the cell?

300

Approximately how many peroxisomes in the cell?

400

Approximately what percentage of the volume of a typical eukaryotic cell is comprised of cytosol?

50% (The volume of a typical eukaryotic cell is about 50% cytosol and the remaining 50% is occupied by membrane-bound organelles.)

Vesicle budding is driven by a cage-like structure called what?

A clathrin coat (these cage like structures is what deforms the membrane to form the cicular structure.

What is an aerobic eukaryotic cell?

A type of cell that uses oxygen.

What is nuclear lamina?

A type of intermediate filament. They are just underneath the inner nuclear membrane. Made out of intermediate filaments which is part of the cytoskeleton and gives structure to the nucleus. During mitosis they break up the network so nucleus disappears. Chemical modifications allow the envelope to fall apart and nucleus to disappear. When mitosis is completed in the 2 daughter cells there is reassembly of the nuclear lamina to bring the envelope back together.

What is an anaerobic archaeon?

A type of prokaryote that does not need oxygen.

What is phagocytosis?

A way to engulf larger molecules. Example: White blood cell during bacterial infection.

What is autophagosomes?

An autophagosome is a spherical structure with double layer membranes. It eventually fuses with lysosomes and hydrolytic enzymes will spill on the inside and degrade whatever is in it.

If a protein needs to go in and out of the cell then it needs what?

An import and export sequence.

What are SNARES?

Are molecular motors that drive the biological fusion of two membranes. Part of the motor assembly is in the vesicle membrane and part is in the target membrane. Once the vesicle is docked, SNARE proteins can be activated to fuse the vesicle and target membranes together.

What are adaptor proteins?

Are proteins that mediate the formation of vesicles for intracellular trafficking and secretion.

As the growing polypeptide chain is coming through the translocon these trasnferases recognize asparagine and immediately transfer these glycosylation motif onto what?

Asparagine

Which of the following accurately describes a step in GTP-driven nuclear transport?

Binding of Ran-GTP to the receptor releases the cargo protein. (GTP hydrolysis ensures that nuclear import occurs in the proper direction. This is accomplished by a small GTPase protein called Ran. In the nucleus it is in its GTP-bound form and binds to nuclear import receptors, causing them to release their cargo. It is then shuttled back to the cytosol with the nuclear import receptor, and upon entry, hydrolysis of GTP is stimulated, and leads to release of the receptor to bind more cargo.)

What is the nuclear import receptor?

Binds to a nuclear protein's NLS to take it into the nuclear pore.

What are endocytic pathways?

Bringing things into the cell and breaking them down.

How do clathrin-coated vesicles select their cargo molecules?

Cargo receptors bind specifically to cargo proteins and to clathrin. (Vesicles destined for different compartments have different types of protein coats. The cargo for these vesicles is selected by specifically binding to cargo receptors that interact with a specific type of protein coat.)

What is a phagosome?

Cell that picks up a foreign particle by phagocytosis

What is lysosomal degradation?

Cellular membranes enter the lysosomal compartment by endocytosis, phagocytosis, or autophagy. Within the lysosomal compartment, membrane components of complex structure are degraded into their building blocks. In the lysosome, proteins are degraded by proteolytic enzymes, the cathepsins.

How are misfolded proteins and incompletely assembled proteins retained in the ER?

Chaperone proteins bind them and prevent their entry into vesicles. (Misfolded proteins or incompletely assembled protein complexes are bound by chaperone proteins that help guide their proper folding. This prevents them from leaving the ER or from aggregating and causing issues while folding is attempted.)

Co-translational meaning.

Describes import of a protein into the ER before the polypeptide chain is completely synthesized

Activation of chaperone genes plus other genes that increase the protein-folding capacity of what?

ER

What is endocytosis?

Endocytosis is the process of capturing a substance or particle from outside the cell by engulfing it with the cell membrane, and bringing it into the cel; Import to the intracellular space (aka retrograde transport)

What are acid hyrolases?

Enzymes thtat work well low temperatures and acidic pH.

Which of the following is a difference between exocytic and endocytic pathways?

Exocytic pathways often start with synthesis of proteins, whereas endocytic pathways involve breaking down macromolecules like proteins. (Endocytic pathways and exocytic pathways both use transport vesicles to move lipids, membrane components, proteins, and soluble molecules from the outside of the cell to inside of the cell or vice versa. Endocytic pathways bring molecules in from the outside of the cell into an endosome, which can then mature into a lysosome. Endocytosed molecules do not travel to the Golgi in vesicles.)

What is exocytosis?

Exocytosis describes the process of vesicles fusing with the plasma membrane and releasing their contents to the outside of the cell; Export to the extracellular space

What is the hydrophobic stop-transfer sequence?

Generally serve to halt the translocation of polypeptide chains across the endoplasmic reticulum membrane and become integrated as transmembrane α-helices.

Which of the following organelles is surrounded by a single membrane?

Golgi apparatus (The nucleus, mitochondria, and chloroplasts are each surrounded by a double membrane, and organelles like the Golgi apparatus, lysosomes, and the endoplasmic reticulum have a single membrane.)

Chaperone proteins

Help new proteins fold into their normal shape

What is the driving force that brings the receptor back to pick up new cargo?

Hydrolysis of GDP

Endocytosis vs. Exocytosis

In exocytosis, the Golgi moves things through vesicles to the extracellular space. In endocytosis, an early endosome likes the the vesicles to secretory pathways and degradation pathways. The vesicle would then either go to a late endosome and then to a lysosome where it will undergo lysosomal degradation or it could also go to the plasma membrane.

What is the role of lysosomes?

Intracellular degradation. Full of degradation enzymes that could break down all types of macromolecules such as proteins, nucleic acids, fatty acids, lipids.

What is vesicular transport?

Is a membrane protein that regulates or facilitates the movement of specific molecules across a vesicle's membrane. An active transport process that uses cellular energy molecules such as ATP to fuel transport of molecules from one location to another in living organisms.

What is the nuclear localization signal (NLS)?

Is an amino acid sequence that 'tags' a protein for import into the cell nucleus by nuclear transport. Typically, this signal consists of one or more short sequences of positively charged lysines or arginines exposed on the protein surface.

Why is LDL called a lipoprotein?

It is made of both lipids and specialized proteins.

What is LDL?

Low density lipoprotein which delivers cholesterol through the bloodstream to a variety of places in the body.

What is topology?

Means orientation in the membrane. N and C terminus and the number of transmembrane domains.

What are tight junctions?

Membranes of neighboring cells are pressed together, preventing leakage of extracellular fluid

unfolded protein response (UPR)

Molecular program triggered by the accumulation of misfolded proteins in the endoplasmic reticulum. Allows cells to expand the endoplasmic reticulum and produce more of the molecular machinery needed to restore proper protein folding and processing. There is a limit to how many unfolded proteins a cell can withstand. If there are too many proteins made and not enough chaperone proteins then you can clog the ER. If this isn't resolved then cells will go through apoptosis.

Are tethering proteins always used?

No, it requires just SNAREs on the vessel itself and target membrane. They begin to form coiled structures that forces the membrane to come together.

What are some examples of membraned enclosed organelles?

Nucleus, ER, Golgi, Lysosomes, Peroxisomes, endosomes

What is autophagy?

Occurs typically when starvation occurs. Can also occur (self eating) when the cell has too many organelles and is not in the process of cell division. (degrades organelles)

Dephosphorylates proteins

Phospatases

Hydrolyzes phospholipids.

Phospholipases

Describe localization in pre pro insulin.

Pre pro insulin has an ER specialization sequence. It is put into the ER lumen and then that localization sequence is cut off by a special enzyme in the ER. The whole thing then traffics through the rest of the secretory pathway and gets cut up into two chains. Eventually you end up with your insulin molecule that has a beta and an alpha chain with disulfide bonds between them.

What is protein oligmomerization?

Protein oligomerization may often be an advantageous feature from the perspective of protein evolution and has probably evolved by a variety of mechanisms. The study of protein oligomerization may provide insights into the early protein environment and the evolution of modern proteins.

When moving proteins into mitochondria and chloroplasts what must happen?

Proteins must fold.

What are lamins?

Proteins that make up filaments.

What is an ER signal sequence?

Recognized by a bunch of proteins that tell this ribosome to go to the ER membrane.

What is the secretory pathway?

Rough ER to Golgi to secretory vesicles to Plasma Membrane

What is signal peptidase?

Signal peptidase is a membrane-bound proteolytic enzyme that cleaves signal peptides from secretory proteins targeted to the lumen of the endoplasmic reticulum. Enzymes that convert secretory and some membrane proteins to their mature or pro forms by cleaving their signal peptides from their N-termini.

What are multi-pass membrane proteins?

Single-pass membrane proteins cross the membrane only once, while multi-pass membrane proteins weave in and out, crossing several times.

Transport vesicles carry what?

Soluble proteins and membrane between compartments

What is the role of endosomes?

Sorting of endocytosed material.

Removes sulfinations off of proteins.

Sulfatases

What is the role of the ER?

Synthesis of most lipids; synthesis of proteins for distribution to many organelles and to the plasma membrane; responsible for proteins secreted through the secretory pathway and membrane proteins.

What is a t-SNARE?

Target SNARE. Is recognized by the v-SNARE and will become coiled.

Vesicle docking depends on what?

Tether and SNARE's

What are tethers?

Tethers determine whether a potential fusion interaction should occur, through recognition of specific proteins found on a vesicle surface.

Vesicle budding is driven by what?

The assembly of a protein coat

Sugars always face which environment?

The external environment

Lysosomes use ATP to constantly bring in protons in the organelle. This results in what?

The lysosome to be very acidic

What is the significance of a signal sequence?

The signal sequence is going to tell proteins in the Golgi where proteins are suppose to be going and they get packaged into vessels and for example if a vesicle needs to go to endosomes then there will be some specific SNAREs and tether proteins that will be present there.

How are the tails of the proteins that make up the nuclear pore oriented?

Their tails face into the inside of the pore creating a mesh like environment.

What happens when there is are 2 hydrophobic stop-transfer sequence?

Then it spans the bilayer twice.

Signal sequences are involved in protein sorting. Explain.

There are signal sequences for specific localization in the cell. For example for import to the ER the signal sequence will contain hydrophobic stretches that signals to the ER membrane that a this specific polypeptide needs to go into the ER.

What was the shift of energy source between prokaryotes and eukaryotes?

There was a shift from production of ATP through fermentation to using oxidative phosphorylation and the ETC or cellular respiration.

What are nuclear pores?

They allow for very selective import and export of molecules and in and out of the nucleus.

Proteins enter ER while what is occuring?

They are being synthesized by ribosomes.

If there is an odd number of transmembrane domains what happens to N and C termini?

They are going to be on opposite sides of the membrane.

What type of nuclear import receptor sequences are needed?

They contain a bunch of positively charged amino acids like proline, lysine, arginine.

What type of nuclear export receptor sequences are needed?

They contain hydrophobic amino acids like leucine, phenylalanine and methionine.

How did early prokaryotes obtain energy?

They were using fermentation as their energy source so glycolsysis was the major pathway before they evolved to having mitochondria.

What is the trans Golgi network?

This is a sorting station of the Golgi complex where proteins are parceled into different types of vesicles heading either to the plasma membrane or to various intracellular destinations. Furthest from ER.

What is the cis Golgi network?

This is the portion of the Golgi complex which serves as an entry point closest to the endoplasmic reticulum that functions primarily as a sorting station that distinguishes between proteins to be shipped back to the endoplasmic reticulum and those that are allowed to proceed through the Golgi.

Most proteins are covalently modified in the ER. T/F

True

Proteins are further modified and sorted in the Goldi. T/F

True

Secretory proteins are released from the cell by exocytosis. T/F

True

Tethers work together with SNAREs to direct vesicles to the right membrane. T/F

True

The ER is continuous with the nuclear envelope. T/F

True

The size of the ER is controlled by the demand for protein folding. T/F

True

Exit from the ER is controlled to ensure protein quality. T/F

True (example of chaperone proteins)

What is Rab?

Type of G protein, that mediates vesicle tethering by binding to its tethering protein. Present on the vesicle and if active (GTP bound) it interacts with tethering proteins present on target membrane.

What is an example of an endocytic pathway?

Uptake of cholesterol by cells (important part of membrane composition)

What is transcytosis?

Vesicles undergo endocytosis on one side of a cell, move across the cell, and then undergo exocytosis on the opposite side. As the vesicles fuse with the plasma membrane, the vesicular contents are released into the extracellular fluid.

What is a v-SNARE?

Vesicular SNARE. Recognizes by the t-SNARE becomes coiled.

A single-pass transmembrane protein destined for one of the organelles in the endomembrane system/secretory pathway would be marked by what type of signal sequence?

a cleaved N-terminal ER signal sequence and an internal stop-transfer sequence (roteins that are destined for the ER lumen have an N-terminal signal sequence—a hydrophobic region that, once cleaved, releases the protein to the interior of the ER. If the protein also contains an internal stop-transfer sequence, the transfer of the protein is halted once it reaches this hydrophobic region, and it remains embedded in the ER membrane. The N-terminal signal sequence is still cleaved to release the N-terminal end from the membrane.)

pH of lysosome

about 5

The process of tranlocating things into the ER is what?

co-translational

The environment of the lumen is similar to what?

extracellular environment

) Which of the following is a covalent modification that occurs mainly in the ER?

formation of disulfide bonds (Two major covalent modifications occur in the ER. Certain proteins need disulfide bonds to form between cysteines to stabilize their structure, and some proteins have a branched oligosaccharide added to them, which is then matured in the Golgi into the final structure glycoprotein structure.)

Degrades sugars

glycosidases

Lysosomes contain ____________ enzymes that can break down diverse macromolecules, cell parts, and microorganisms.

hydrolytic (Lysosomes are a compartment in the cell where ingested cell particles, organelles, or macromolecules can be digested for recycling. The macromolecules from ingestion or from these cell parts are broken down into their building blocks by hydrolytic enzymes and are then exported out of the lysosome for reuse.)

Proteins encoded by nuclear genes and destined for the mitochondrial matrix are

in possession of a signal sequence for targeting to the mitochondria. (Mitochondrial proteins that are encoded by genes in the nucleus are synthesized on free ribosomes in the cytosol. A signal sequence in the proteins is recognized by import machinery that transports the unfolded protein across both membranes at once.)

Nuclear pores restrict larger molecules from traversing the membrane due to their

interwoven meshwork of protein fibrils. (A nuclear pore is a large passage in the nuclear membrane whose opening is filled with protein fibrils that allow passage of small, water-soluble molecules. Larger molecules are impeded from entering by this meshwork of protein fibrils (unless they have a nuclear localization or export sequence).)

Degrades nucleic acids

nucleases

Fully folded proteins can be transported into which of the following organelles?

nucleus (Transporters in the membranes of mitochondria and chloroplasts unfold the protein during transfer. Proteins destined for the endoplasmic reticulum are transported as they are being synthesized, thus the proteins are unfolded. Nuclear transport occurs on folded proteins.)

Which of the following compartments receives proteins directly from cytosol?

peroxisomes (Proteins destined for the nucleus, mitochondrion, peroxisomes, and chloroplasts are transported from the cytosol. Proteins destined for the Golgi, lysosomes, and endosomes are transported into the endoplasmic reticulum as they are being synthesized and are then transported via vesicles to their final destination.)

Which of the endocytic pathways involves the ingestion of large particles or microorganisms and is performed mainly by specialized cells?

phagocytosis (The endocytic pathways are phagocytosis and pinocytosis. Pinocytosis involves the intake of molecules and fluid and is active in all cells. Phagocytosis is a process by which microorganisms or large particles are ingested by a specialized phagocytic cell, such as those in the immune system.)

Degrades proteins

proteases

Which of the following pathways helps selectively concentrate substances to be ingested by their binding to proteins on the cell surface?

receptor-mediated endocytosis (Receptor-mediated endocytosis is a form of pinocytosis where specific molecules are concentrated on the cell surface by their binding to receptors. The receptors are then taken up in a clathrin-coated vesicle for delivery to the endosome.)

Which of the following organelles is the site of steroid hormone synthesis in endocrine cells?

smooth endoplasmic reticulum (The endoplasmic reticulum (ER) is the location of synthesis for proteins (rough ER) and many lipids including steroid hormones (smooth ER).)