Module 8

vesicle

a small structure within a cell consisting of fluid enclosed by a lipid bilayer formed during exocytosis or endocytosis

Smooth ER (function)

* totally smooth ER is rare -- found in specialty cells * found as transitional ER in most cells --- looks partly smooth --- found at ER exit sites ----- ribosome detach after protein synthesis ----- finished proteins/lipids packed in vesicles ----- vesicles depart ER for golgi * generally related to lipid/phospholipid synthesis -- steroid synthesis -- detoxification -----metabolites, drugs, alcohol (e.g by cytochrome P450 in liver) -- attachment of receptors to membranes -- gluconeogenesis (esp. liver) -----glucose-6-phosphate enzyme in SER

organelle

A tiny cell structure that carries out a specific function within the cell

How do cytoskeleton components assist in vesicle transport? A) what is the function of microtubules in directing vesicle transport? B) what motor proteins are associated with microtubules and why is the direction of travel important? C) what is the function of actin microfilaments in vesicle transport? D) what motor proteins are associated with actin?

A) Microtubules act as tracks in the intracellular transport of membrane bound vesicles and organelles. This is for long range movement. The microtubule has a plus and a minus end for directionality purposes. B) dynein and kinesin are the motor proteins associated with vesicle transport on microtubules. Dynein walks in the minus direction and kinesin walks in the plus direction C) Most of the organelles in a cell are associated with actin microfilaments and are used in short distance vesicle transport within the cell. Similar to microtubules, actin filaments are used as tracks for vesicles to be transported along through the use of motor proteins. Actin filaments have a pointed and barbed end meant for directionality purposes. D) actin filaments have two motor proteins directly associated with vesicle transport, Myosin VI and myosin V. Myosin VI has been shown to be associated with golgi-derived vesicles and cytoplasmic vesicles. Since the actin filament has directionality it is known that myosin VI and V also have pointed or barbed end directionality respectively.

transport vesicle

a small structure within a cell consisting of fluid enclosed by a lipid bilayer formed during exocytosis or endocytosis and transports materials within the cytoplasm

glycosylation

Addition of a carbohydrate group to a molecule.

Are actin filaments and microtubules important for phagocytosis or exocytosis? Yes or no and why?

Both actin filaments and microtubules do play an important role in phagocytosis, but only actin filaments are important for exocytosis. This is because the cytoskeleton creates the structural lattice of the cell and allows for egestion to occur through the use of the actin filaments.

What are some common membrane-bound compartments in eukaryotic cells?

Cytosol nucleus ER Golgi apparatus Lysosomes Endosomes Mitochondria Peroxisomes

Signal sequence

ER signal sequences targets ribosome to RER some have ER signal sequence as their first few amino acids and are bound to SRP mRNA encoding a protein with no ER signal sequence remains free in cytosol

Describe the basics structure and key function of a peroxisome

Function: * organelles for special metabolic processes * get name for production of hydrogen peroxide by oxidation of toxic materials -- dealt with by catalase and peroxidase enzymes * oxidation of toxic molecules * oxidation of fatty acids -- long chain fatty acids in animals (rest go to mitochondria) -- all fatty acids in plants and yeast * lipid biosynthesis -- cholesterol and plasmalogens (special membrane lipids found in heart and brain) Structure: * small vesicles found around the cell. Have a single membrane that contains digestive enzymes for breaking down toxic materials in the cell. Differ from lysosome by type of enzyme they contain.

rough ER (function)

Function: * produce lysosomal enzymes (cellular digestion) --- glycosideases (break apart complex sugars into individual subunits) --- proteases (break down protein) * manufacture proteins for export from the cell * manufacture integral membrane proteins --- EX. Rab, V-snare & T-snare proteins * initial glycosylation of proteins (attaches covalently bonded carbohydrates) --- N- linked glycosylation (attaches to nitrogen)

free ribosomes

In the RER protein synthesis takes place this process explains dynamic nature of RER and why most ER is rough or partly rough begin protein synthesis in free ribosomes -- some proteins remain in cytosol -- some have ER signal sequence as first few amino acids

Describe the basics structure and key function of a lysosome

Key Function: * intracellular degradation *organelles for digesting materials -- dismantle and recycle worn-out cell parts; release amino acids, sugars etc. for metabolism * digest materials from outside cell (phagocytosis) -- fuse with endocytotic vesicle * can "eat" old organelles (autophagy) or digest whole cell as part of apoptosis (autolysis) Structure: * single membrane sacs filled with enzymes. Shape and size will vary based on the organism. * contain hydrolytic enzymes -- function in acidic conditions * maintain a very low internal pH (<5.0) -- V-type ATPases use ATP to pump protons into lysosome

What are the main functions of the SER? Name a key function of smooth ER in specialized cells -- A) adrenal glands -- B) liver tissue

Main Function: - Found in specialized cells, associated with transport. Is generally related to lipid/phospholipid synthesis. -the smooth ER functions in lipid synthesis (i.e the production of oils, phospholipids and steroids), detoxification of drugs and poisons, as well as calcium pumping (in myocytes related to nerve impulses and contraction). A) adrenal glands -- the smooth ER functions in the synthesis of steroid hormones in the adrenal glands B) Liver muscle Tissues -- the smooth ER functions in the production of cytochrome P450 enzymes in the liver (hepatocytes) and functions in the detoxification of non-water accumulate in membranes. As well as gluconeogenesis by the glucose-6-phosphate enzyme

What are the major functions of the golgi complex?

Major Functions: * protein processing and delivery -- proteins in vesicles from ER are further modified * post-translational protein modifications -- occur in cisternae -- O-linked glycosylation -- Nitrogen and sulfur modification (amination; sulfation) * preparation of extracellular matrix proteins -- proteoglycans (found in cartilage) -- collagen * lipid transport (e.g. membrane lipids) * lysosome formation *macromolecule synthesis -- in plants golgi synthesizes pectin (polyglucose) * vesicles sent from golgi -- to cell membrane for export -- to organelles for incorporation

What are some different types of vesicle-mediated cellular transport? Consider movement of materials between cellular compartments, and in and out of the cells.

Membrane bound vesicles are used for transport in cells. They move proteins, lipids and other materials. Vesicle transport exists in three forms. 1) intracellular transport, which would be the movement between ER, golgi and other structures. 2) exocytosis, the unregulated and regulated export of materials out of the cell. 3) endocytosis, in the form of phagocytosis (cellular eating) and pinocytosis (cellular drinking).

What is the source of energy for moving vesicles?

Motor proteins moving along microtubules or microfilaments are powered by ATP. Motor proteins actively convert chemical energy into kinetic energy for their travels. Since vesicles are actively bound to these motor proteins, they act as the energy exchange mechanism for directed movement of vesicles within the cell.

Describe the basics structure and key function of a vacuole

Structure: Membrane-bound sacs within cells Functions: * import/export (endocytosis, exocytosis) -- from cell membrane: ----- phagocytosis (eating) and pinocytosis (drinking) * storage of nutrients and waste * plant cells use large vacuoles of water for turgor pressure * maintenance of homeostasis -- vacuoles containing H+ can control pH of cytosol

How and where does the Golgi receive proteins for processing?

The golgi is composed of a cis-face and a trans-face. The Golgi receives proteins for processing from the ER in the form of vesicles. Vesicles fuse with the cisternae membranes of the Golgi, releasing their components.

What are the major functions of rough ER

The major function of the rough ER is that it is a site of protein synthesis and export of proteins . All transmembrane proteins are synthesized by the ER. Proteins that enter the lumen of ER are for modification and packaging in transport vesicles. The rough ER is a site of ER membrane phospholipid assembly. Functions: * produce lysosomal enzymes (cellular digestion) -- glycosideases -- proteases * manufacture proteins for export form cell * manufacture integral membrane proteins -- Rab, V-snare and T-snare proteins * initial glycosylation of proteins -- N-linked glycosylation

Describe the appearance and the structure of smooth and rough ER

The structure of the ER is contagious with the nuclear envelope and is located primarily around the nucleus. It consists of a folded membrane structure, composed of flattened sacs and interconnected tubules, and is stabilized by the cytoskeleton. Up to 50% of membranes in cell are ER. The ER exists in 2 types; rough and smooth endoplasmic reticulum Smooth ER: Rarely is ER actually smooth in most cells, usually only partly rough and partly smooth. The ER only appears as smooth when it is not extensively complexed with membrane bound ribosomes. Rough ER: Has a rough appearance in micrographs due to the presence of many ER-associated ribosomes.

ER Lumen

a site for protein synthesis in the rough ER proteins that enter the lumen of the ER are for modification of packaging in transport vesicles -- 3 dimensional folding -- glycosylation (addition of carbohydrates) -- packaging for transport to golgi or cell membrane

Describe the mechanics of vesicle transport: How are vesicles formed (describe the behaviour of membrane bilayers) How is the movement of vesicles organized and controlled (give general description)

Vesicles are formed when the membrane bulges out/invaginates and pinches off, taking with it proteins and etc. This is called budding. The membrane bilayer is reformed upon the removal of the vesicle. Movement of vesicles is controlled and organized by the cytoskeleton. The cytoskeleton provides "tracks" for movement. Vesicles provide "transport vehicles" for cargo. Motor proteins connect the cargo transporters to tracks by binding and power movement by acting as motors. These motor proteins are dependent on ATP binding and hydrolysis for energy. These motor proteins convert chemical energy to kinetic energy. The direction and location of motor proteins is specific as well. As myosin walks on microfilaments and dynein and kinesin walks on microtubules. Myosin is found in two forms myosin VI and myosin V which walk in the pointed and barbed directions of the microfilament respectively. Similarly with dynein and kinesin walk in the minus and plus directions of the microtubule respectively.

vacuole

a cavity within the cytoplasm of a cell, surrounded by a single membrane and contains fluid, food or metabolic waste.

peroxisome

a membrane bound organelle of the endomembrane structures that occupies 1% of total cell volume and is present in approx. 400/cell main function: - oxidation of toxic molecules - organelles for special metabolic processes * get name from production of hydrogen peroxide -- H2O2 produced by oxidation of toxic compounds (e.g. EtOH) -- dealt with by catalase and peroxidase enzymes - Contain >50 different enzymes * function in oxidation of fatty acids -- long chain fatty acids in animals (rest go to mitochondria) -- all fatty acids in plants and yeast * functions in lipid biosynthesis -- cholesterol and plasmalogens (special membrane lipids found in heart and brain)

How can we quantify vesicle transport in and out of cells (phagocytosis and exocytosis)? * describe a simple experiment that can measure rates of phagocytosis and exocytosis. * describe how rates of vesicle transport can be used to determine the involvement of cytoskeleton components in transport.

a model organism that uses phagocytosis as their ingestion technique could be allowed to ingest a material that they would not be able to digest thus the material would be visible upon exocytosis from he organism. Phagocytosis and exocytosis can be quantified in this manner by counting the number of vesicles entering or exiting the cell as a function of time. The function of the cytoskeleton in vesicle transport can be determined through the use of actin and microtubule inhibitors. Through this we would be able to determine which filaments were attributed to each aspect of phagocytosis and exocytosis. To elaborate if actin or microtubules are inhibited this will disrupt the normal trend for the ingestion and egestion of materials. Through the process of selective inhibition the rates of the specific components of the cytoskeleton can be examined based on their resulting deviations from the normal ingestion/egestion rate of the organism.

What are the three main protein components of the cytoskeleton?

actin filaments intermediate filaments microtubules

Where might proteins go after processing, and how are they delivered?

after processing proteins are sent to endomembrane structures ( e.g. lysosomes, vesicles, ER) or to the cell membrane (in the form of cell membrane integral proteins, membrane phospholipids, and exported proteins). Proteins are delivered in budded vesicles secreted from the golgi into the cytoplasm where they wait for signals before fusion with cell membrane.

endocytosis

also known as phagocytosis (cellular eating) of solutes or as pinocytosis (cellular drinking) of liquids specifically defines as the taking in of matter by a living cell by invagination of its membrane to form a vacuole

pinocytosis

an aspect of endocytosis defined as "cellular drinking" of liquid into the cell by the budding of small vesicles from the cell membrane

phagocytosis

an aspect of endocytosis defined as the "cellular eating" of solutes by phagocytes which when engulfing a solid particle forms an internal compartment known as a phagosome.

glycoprotein

any of a class of proteins that have carbohydrate groups attached to the polypeptide chain

membrane fusion

based in the movement of vesicles through golgi during regulated secretion of vesicles, after budding from golgi, vesicles park in cytoplasm and wait for signal before fusion with cell membrane also defined as the process by which two initially distinct lipid bilayers merge their hydrophobic cores, resulting in one interconnected structure

endomembrane system

composed of the different membranes that are suspended in the cytoplasm within a eukaryotic cell. These membranes divide the cell into functional and structural compartments or organelles the endomembrane structures are the ER and golgi complex and is composed of membrane bound organelles - peroxisomes - lysosomes - vacuoles - vesicles * think organization and compartmentalization

cytoskeleton

defined as a network of filament and tubules which form interlinked framework in cytoplasm. - provide support for all cellular parts -provide strength and structure to cells -provide "tracks" for intercellular transport the cytoskeleton is dynamic and constantly growing and breaking down to remodel the cell architecture composed of 3 principle components 1. intermediate filaments 2. microtubules 3. actin filaments

Actin Filaments

filaments in the cytoplasm of eukaryotic cells that form part of the cytoskeleton. They are primarily composed of linear polymers of protein subunits (actin), but in cells are modified by and interact with numerous other proteins myosin walks on these

Briefly describe the pathway a vesicle follow from ingestion to egestion.

firstly, the cell needs to engulf the material and fuse together at the top so that way is still has an outer and inner membrane but the vesicle that has been created can be completely within the cell. This is known as a food vacuole. Lysosomes which contain digestive enzymes then fuse with the food vacuole so as to digest the materials within. The indigestible materials found within the food vacuole are now needed to be removed from the cell. This begins the process of exocytosis. The vesicle will now be moved to the membrane via actin filaments. Myosin motor proteins move the vesicle along the actin filament to the membrane by the conversion of ATP into kinetic energy. The vesicle is fused with the membrane of the cell and is allowed to spill its contents to the outside of the cell. The vesicle is recycled into the cell for reuse in other transportation.

Endosome

function in sorting of endocytosed material a membrane bound compartment inside eukaryotic cells. It is a compartment of the endocytic membrane transport pathway originating from the trans Golgi membrane endosomes represent a major sorting compartment of the endomembrane system in cells

cytochrome P450

functions with the smooth ER in the detoxification of drugs and poisons and is found in large quantities in liver (hepatocytes) and detoxify non-water accumulate in membranes

SER in Specialty Cells

has different functions in each cell type EX: adrenal gland cells -- manufacture glucocorticoid hormones like cortisol research example: Cholesterol and steroid synthesizing smooth endoplasmic reticulum of adrenocortical cells contain high levels of proteins associated with the translocation channel

golgi complex

it is an endomembrane structure main function: - modification, sorting and packaging of proteins and lipids for either secretion or delivery to another organelle - protein processing and delivery -- proteins in vesicles from ER are further modified -macromolecule synthesis -- in plants golgi synthesizes pectin (polyglucose) and other polysaccharides - vesicles sent from golgi -- to cell membrane for export -- to organelles for incorporation Structure: - Stacks of flattened sacs (like pancakes) --- separate from each other (unlike ER) --- sacs are called cisternae - receives vesicles from ER -- to the cis-face of golgi -- vesicles fuse with cisternae membranes - send vesicles toward cell plasma membrane -- trans-face of golgi -- new vesicles form as "buds" on cisternae

intermediate filaments

linear polymers of protein subunits part of the cytoskeletal structure made of proteins serve to provide structural stability and strength to the cytoskeleton and are intermediate in diameter between microfilaments and microtubules

lysosome

organelles for digesting materials - dismantle and recycle worn-out cell parts -- release amino acids, sugars, etc. for metabolism -digest materials from outside cell (phagocytosis) -- fuse with endocytotic vesicle -contain hydrolytic enzymes -- function in acidic conditions -maintain very low internal pH (<5.0) -- V-type ATPases use ATP to pump protons into lysosome - can "eat" old organelles (autophagy) or digest whole cell as part of apoptosis (autolysis)

microtubules

part of the cytoskeletal structure linear polymers of protein subunits a microscopic tubular structure present in numbers in the cytoplasm of cells, sometimes aggravating to form more complex structures

endoplasmic reticulum (ER)

part of the internal cell structures of the endomembrane structures main functions: - synthesis of most lipids -- especially membrane lipids -synthesis of proteins for distribution to many organelles and to the plasma membrane -- all transmembrane proteins synthesized by ER - protein packaging and transport -- proteins for export from the cell -- proteins to be sent to the Golgi and other organelles composes 12% of the total cell volume and there is only 1 per cell Structure: - contiguous with nuclear envelope - located primarily around nucleus - has a folded membrane structure --- flattened sacs and interconnected tubules --- extensive: up to 50% of membranes in cell are ER - stabilized by cytoskeleton two types of ER (based on appearance) - rough ER - smooth ER

Provide and example of how proteins may be processed in the golgi.

proteins in vesicles from the ER are further modified in the Golgi. For example glycosylated proteins may have sugars synthesized or modified. Or O-linked glycosylation can be a form of processing in the golgi. Nitrogen and sulfur modifications may occur as well through amination and sulfation.

Trans-face of golgi

sends vesicles toward cell plasma membrane new vesicles form as "buds" on cisternae

autophagy

the "eating" of old organelles by lysosomes in the endomembrane the cell maintains homeostasis by protein degradation and turnover of the destroyed cell organelles for new cell formation.

What is a cytoskeleton and what are its main jobs in the cell?

the cytoskeleton is a network of filaments and tubules the form an interlinked framework within the cell. It functions in providing support for all cellular parts, as well as strength and structure to cells. The cytoskeleton provides "tracks" for intracellular transport. Since the cytoskeleton of the cell is dynamic it is constantly growing and breaking down to remodel the cell architecture. The cytoskeleton is composed of 3 principle parts; intermediate filaments, microtubules and actin filaments.

autolysis

the destruction of cells or tissues by their own enzymes, especially those related by lysosomes. lysosomes in the endomembranes can digest whole cells as part of apoptosis (autolysis)

How are endomembranes organized within eukaryotic cells, from the nuclear envelope, to the endoplasmic reticulum (ER), to the golgi complex?

the endomembrane structures consist of the endoplasmic reticulum and golgi complex as well as membrane-bound organelles (peroxisomes, lysosomes, vacuoles, vesicles). think organization and compartmentalization ER is folded to allow for higher surface area golgi composed of separate flattened sacs called cisternae Nuclear envelope is composed of an inner and outer nuclear membrane with the ER Lumen in between and is contiguous with ER If we were to start at the nucleus, we could diagram or describe the nuclear envelope as a double membrane structure, but the two membranes are actually attached to each other at the nuclear pores. It is better described as though the membrane has folded in on itself to form the double layer. Likewise the ER is farther out, but is continuous with the nuclear envelope. Again, it is as if the same membrane folds outward and forms all the layers of the ER. So, the lumen of the ER is connected to the intermembrane space of the nuclear envelope. The golgi, on the other hand, is physically separate from the ER. It also is layered and folded, and has a lumen of its own. The "connection" between the ER and golgi is via vesicles; the interior of these vesicles is analogous to the lumen of the membrane structures.

Describe the structure and organization of the golgi complex.

the golgi complex is structured into flattened separated sacs called cisternae. Composed of a cis-face and a trans-face. The cis-face being that which is closest to the ER and the trans-face being that which is closest to the plasma membrane. Cisternae of the middle of the golgi is called the medial cisternae with the cis/trans cisternae to the respective sides.

Cis-face of Golgi

the side of the golgi apparatus that receives vesicles from the ER the vesicles fuse with cisternae membranes

perinuclear space

the space between membranes usually about 20-40nm wide the outer nuclear membrane is continuous with the endoplasmic reticulum membrane.

Exocytosis

the unregulated and regulated export of materials form the cell

Rough ER (Protein Synthesis)

this process explains dynamic nature of RER and why most ER is rough or partly rough All ribosomal subunits are cytosolic to start --- assemble when bound to mRNA exported through nuclear pores protein synthesis is done as free ribosomes --- some proteins remain in cytosol --- some have ER signal sequence as first few amino acids ER signal sequence targets ribosome to RER * SRP binds signal sequence-> SRP receptor in ER membrane binds SRP-> protein translocator allows growing polypeptide chain to pass through ER lumen

vesicle budding

vesicles gather their large cargo in a process called budding. These vesicular intermediates bud from a donor compartment and fuse with an acceptor compartment. budded off from the ER

Membrane-bound ribosomes

when a ribosome begins to synthesize proteins that are needed in some organelles the ribiosome making this protein can become "membrane-bound". In eukaryotic cells this happen in a region of the ER called the rough ER