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CMBC
Cell Bio
379
Biology
Graduate
08/18/2014
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Term

Vitamin K and Ubiquinone

 Definition
Vitamin K and ubiquinone also utilize the 5-carbon isoprenoid unit (highlighted in red).  Vitamin K is important in blood coagulation and in the developing embryo.  Ubiquinone is part of the mitochondrial electron transport chain.
Term
How can membrane proteins move? What are the limitations?
 Definition
Membrane proteins can move laterally but sometimes are attached
tomcytoskeleton or located on lipid rafts and have restricted
Term
In phospholipids in membrane what is special about tail? What does it do?
 Definition
One chain is saturated and one is unsat. having a kink.
Makes lipid more fluid, in memebrane, like cholesterol.
Term
What do phospholipids form in water?
 Definition
Liposomes. which consist of two layers of phospholipids in contact at the ends of their fatty acid side chains. The abilityto form liposomes is determined by the interaction between the fatty acyl chains of the phospholipids in each layer."
Term
What does cholesterol do in a membrane?
 Definition
Cholesterol fillls in gap decreases permability, but increses fluidity.
Term
What is the sterol in mammalian cells?
 Definition
he sterol present in mammalian cell membranes is cholesterol. This hydrophobic molecule is rendered amphipathic by the presence of the hydroxyl group at position 3"
Term
Where is cholesterol localized in the membrane?
 Definition
Cholesterol also appears to be localized inmembrane regions that are rich in glycolipids and glycosylphosphatidyl inositol-anchored proteins (GPI-anchored proteins), in structures called lipid rafts.
Term
Where are glycolipids found in the membrane?
 Definition
Glycolipids are the most asymmetrically distributed lipids in the membrane. y distributed lipids in the membrane.They are found exclusively on the noncytosolic face of the bilayer (extracellular or inside organelles). They tend to self-associate and may cluster in lipid rafts (more about lipid rafts soon).
Term
What is a gagioside?
 Definition
Gagioside: most abundant nerve cell. Have net neg. charge b/c of one or more silac acid and olligosaccharides.(relativly short carbohydrate.
**in epethelial cells glycolipids are used as a protective role. Charged glycolipids such as gangliosides alter e-potential signaling calcium ions.(clotting)
**also used for cell recognition and adhesion.
**some bacterial cells use glycolipids to target specific cells.
Term
Why can prokaryotes not have sugar in membrane?
 Definition
Need endoplasmic reticulum, which send vesicles of sugar to membrane in eukaryotes.
Term
What is the average % of proteins in membranes? Where is protein highest? Where is it lowest?
 Definition
Thus, although the average membrane contains about 60% lipid and 40% protein, the mitochondrial inner membrane contains almost 80% protein, whereas the myelin membrane or sheath that surrounds axons contain only about 20% protein.
Term
What do bacteria not have in membranes?
 Definition
- bacteria have no cholesterol, sphingomyelin, or glycolipids; their membranes are largely phosphatidyl- ethanolamine.
Term
What do mitochondria have very little of in membranes?
 Definition
-Mitochondria have very little cholesterol in their membranes.
Term
What has a lot more glycolipids in it then other membranes?
 Definition
Myelin
Term
What are 3 main classes of lipids in mammalian membranes?
 Definition
phospholipids, sterols, glycolipids.
Term
Where are most negatively charged phospholipids?
 Definition
Most of the negatively charged phospholipids are on the cytosolic face. (inside cell)
Term
Red blood cells contain what that is in the outer layer?
 Definition
In the red blood cell membrane, most of the lipids which contain choline (phosphatidylcholine & sphingomyelin) are in the outer layer; "
Term
Where is the terminal primary amine? What does this contribute to?
 Definition
terminal primary amine (phosphatidylethanolamine & phosphatidylserine) are in the inner layer. Phosphatidylserine has a net negative charge, so this contributes to the membrane potential (difference in electrical charge across the membrane)"
Term
Where is Choline? Where are amines? How can P-serine appear?
 Definition
Choline: most lipids with choline outer layer. P-ethanolamine and p-serine: inner layer
-P-serine can appear by deactiving its translocator that brings it in the cell or scramblase which transfers non specifically in bith directions. Bith signal apoptosis
Term
What are peripheral proteins?
 Definition
Peripheral proteins: attached covalently to membrane lipids
Integral proteins: have specific rotation relative to the two faces of membrane
Term
What are integral proteins?
 Definition
have a portion of the molecule buried in the lipid bilayer and always have a specific orientation relative to to the two faces of the membrane.
Term
Why do alpha helix exist in the membrane?
 Definition
Amino acid are in alpha helix to hide hydrophilic portion in membrane and then only side chains matter.
Term
What is a beta barrel?
 Definition
The other way to allow hydrogen-bonded peptide bonds to be buried in the lipid is to form βετα-barrels." "They are most commonly found in the outer membrane of mitochondria and in many bacteria"
Term
What are the four lipid anchors?
 Definition
"Fatty acids: amide-linked myristic acid or thiol-linked palmitic acid; cytosolic orientation.
Prenyl anchor: (on C-terminus); cytosolic orientation. -Cholesterol: cytosolic orientation. Glycosylphosphatidylinositol: this is the GPI anchor, on the apical extracellular face.
Term
Where does glycosylation?
 Definition
Glycosylation occurs on the non-cytosolic side of the bilayer because of the way in which carbohydrates are added in the ER and Golgi."
Term
What has a carbohydrate layer on it?
 Definition
The outer surface of some sub cellular organellles have a layer of carbohydrates.
- often mediates cell to cell and cell to extracelluar matrix interactions.
Term
What are the four ways of restricting the lateral mobility of specific plasma proteins?
 Definition
1) can be tethered to macro molecules inside
2)outside of cell can interact with other proteins
3)diffusion restricted by cell dif. barriers
4)span bi layer and are anchored
Term
how is cytoskeleton linked to membrane?
 Definition
The cytoskeleton is linked to the membrane by the indirect binding of spectrin tetramers to some band 3 proteins via ankyrinmolecules, as well as by the binding of band 4.1 proteins to both band 3 and glycophorin (not shown). "
Term
How is spectrin dimers linked?
 Definition
Spectrin dimers are linked together into a netlike meshwork by junctional complexes composed of short actin filaments, band 4.1, adducin, and a tropomyosin molecule that probably determines the lengthof the actin filaments. "
Term
What is spectrin?
 Definition
Spectrim: intacellular cyto skeleton protein. Linked together by junctional complexes composes of short actin filaments band 4.1,adducin and tropomyosin.(prob determines lenghth of actin filament)
Term
Where can proteins be localized?(raft)
 Definition
Proteins can also be localized into lipid rafts which appear on the apical face of the cell. The apical plasma membrane (in cells exposed to an external environment) is often enriched in glycosphingolipids, which can be protective.
Term
What are lipid rafts? What accumulates there?
 Definition
These lipid rafts are somewhat thicker than normal lipid bilayer, and are enriched in cholesterol and glycosphingolipids. Membrane proteins
with unusually long transmembrane domains also accumulate in these rafts, along with some carbohydrate-binding proteins (lectins). These lipid rafts are formed in the Golgi network and then transported to the apical membrane.
Term
What are SNARE?
 Definition
pewriter (Black):
Comment: SNAREs are membrane proteins involved in targeting transport vesicles to specific organelles within the cell. They also play an important role in the fusion of the vesicle
membrane with the organelle's membrane.
Term
How does HIV bind to membrane?
 Definition
Viral gp120 attaches CD4 on membranes. Allowing HIV fusion protein to attach then change releasing HIV into cell
Term
What is membrane fission?
 Definition
Membrane fission is the process of breaking membranes apart and can be considered the reverse of fusion. It is a very common process in cells, since it is utilized in the formation of endocytic vesicles.
Term
What are the integral membrane proteins?
 Definition
cadherins, immunoglobulins, selectins, integrins
Term
What do cadherins do?
 Definition
he members of the cadherin family direct many calcium-dependent cell-cell interactions, e.g., E-cadherin is involved in the formation of epithelial sheets.
Cadherin functions as dimers, with repeating domains. Ca++ makes the repeatsrigid and permits binding in a homophilic manner with an identical cadherin
on the adjacent cell. Cadherins mediate the formation of adherens junctions between cells. The adherens junction encircles the cell, just below the tight junction. Cadherin linked to actin.
Term
What is an immunoglobulin?
 Definition
Immunoglobulin: adhesive molecules that function in abscense of calcium. Ex)N-CAM modulates nerve cells.(some can be heavily glycosated and it can prevent adhesion)
Term
What is a selectin?
 Definition
he homing of neutrophils to a region of inflammation is initiated by the expression of a selectin on the surface of endothelial cells in response to a cytokine, and the subsequent interaction with specific glycoprotein
carbohydrates on the surface of neutrophils in the circulation. The interactioncauses the neutrophil to attach loosely to the vascular lining and "roll" along its surface until its movement is slow enough for tighter interactions to occur (via integrins) and for the process of extravasation to take place.
Term
What is lectin?
 Definition
Lectin=sugar binding proteins
Term
Why are selectins and cadherins similar? How do they attach to cytoskeleton?
 Definition
The selectins, like the cadherins, are calcium-dependent. Named for having carbo binding motif. Most involved in immune system.
Attach to cyto skeleton via anchor proteins.
Term
Where does L selection appear? Where does P selection appear? Where does E selection appear?
 Definition
*L-selectin appears in leukocytes(WBC)
P-selectin appears on platlets and on endothelial cells activated by inflam.
*homing of neutrophils to a region of inflamation initiated by selectin.
E-selectin appears on activated endothelial cells.
Term
What are integrins composed of?
 Definition
Integrins are composed of an alpha-subunit (with 4 cation binding sites) and a beta-subunit (with a single cation binding site). The intracellular part binds to cytoskeletal components. The alpha and beta subunits have a variety of
isoforms that are encoded in separate genes and can form a variety of heterotypic dimers.
Term
What are the molecules that compete for binding to integrins?
 Definition
Molecules that compete for binding to integrins are
called disintegrins. Such compounds are found in some snake venoms, and others are being developed for therapeutic use, e.g., to block inflammation
Term
What are integrins?
 Definition
ntegrins are a family of heterodimeric transmembrane receptors that bind to a 3-4 amino acid sequence in proteins in the extracellular space in the presence of calcium. These receptors are the sites at which many cells bind to extracellular matrix. VIa fibronectin
Term
WHat is integrin B3?
 Definition
For example, integrin-β3 in the cell membrane ofblood platelets is responsible for binding the clotting factors fibrinogen and
von Willebrand factor
Term
How does colligin effect if body knows cell is damaged?
 Definition
Thrombocin bind colligin, which typically stays inside o healthy cells. If found in intracellular environment then body knows damage occurred.
Term
Why does compartmentalization allow for? Who does not have it?
 Definition
No sub compartments in prokaryotic cell.
-Sub compartmentalization allows for separate bio chemistry allowing for more complex life,
Term
what produces the extracellular matrix?
 Definition
Fibroblast cells produce extra cellular matrix.
Term
What is microscopy?
 Definition
Microscopy: light microscopy, including fluorescence microscopy; transmission and scanning electron microscopy; atomic force microscopy.
Term
How are antibodies used to study cells?
 Definition
Antibodies: provide specificity in conjunction with biochemical and molecular studies as well as with immunolocalization using microscopy. For cellular localization, green fluorescent protein (GFP) and related fluorophores provide related tools (discussed shortly)
Term
How are radio isotopes used to study cells?
 Definition
Radioisotopes: labeling in pulse chase experiments (see the animation referenced under additional resources)
Term
How is Centrifugation used to study cell?
 Definition
Centrifugation: used in cell fractionation
Term
What are Bioinformatics?
 Definition
computational biology used for the analysis of large data sets generated in a variety of genome projects.
Term
What is the limit with light microscopes?
 Definition
"The limit of resolution of the light microscope is imposed by the wavelength of visible light, which is on the order of a few hundred nanometers."
Term
Explain TEM how is it similar to light microscope?
 Definition
Transmission Electron Microscopy (TEM) is similar to light microscopy. Instead of visible light passing through optical lenses, a beam of electrons passes through a series of magnetic "lenses" that focus the beam on the sample and then on the detector. "
Term
Explain SEM.
 Definition
In Scanning Electron Microscopy (SEM), the surface of the specimen is imaged by observing the beam of electrons that is reflected by the surface."
Term
WHat is the method of choice for most specimens?
 Definition
"Confocal microscopy in conjunction with fluorescent labels or dyes is currently the method of choice for most specimen. A laser light is focused in such a way that it excites fluorescence only at a specific depth in the sample"
Term
What is our view of cells based on?
 Definition
Our view of cells is based on light microscope and electron microscopy.
Term
What is delta G?
What is Delta H?
What is delta S?
 Definition
ΔG is the overall free energy of a process; ΔH is the enthalpy; T is the absolute temperature; ΔS is the entropy, or "randomness" of the system."
Term
What are three factors that determine rate of diffusion?
 Definition
1. Size
2. Polarity of the molecule.
3. Concentration gradient"
Term
What effects charged solutes across a membrane?
What effects uncharged solutes across the membrane?
 Definition
For uncharged solutes, itdepends only on the concentration gradient. For ionic solutes, it depends on the concentration gradient plus a term for the electrical gradient"
Term
Which is better for drug absorption: more water-soluble or more lipid- soluble?"
 Definition
If the molecule is too hydrophilic (water-soluble), the first equilibrium lies far to the left; very little drug gets into the lipid bilayer. If the molecule is too hydrophobic (lipid-soluble), the first equilibrium lies far to the right, but the second one lies far to the left. The drug gets trapped in the lipid. In fact, such drugs can be highly concentrated in fat stores, and remain in the body for a very long time."
Term
Transport proteins have affinity for specific solutes, and a conformational change in the protein translocates the solute from one side of the membrane to the other. Energy for this movement may be provided by ?
 Definition
"Energy for this movement may be provided by (1) concentration gradients; (2) electric potential gradients; (3) coupling to an energy source (ATP hydrolysis)."
Term
What are ion channels?
 Definition
"Ion channels. Channel proteins form pores extending from one side of the membrane to the other. Carefully regulated channel proteins have developed to enable ions to cross membranes (to control pH, regulate membrane potential, signal changes, etc.)."
Term
What does facilitated diffusion and active transport involve?
 Definition
Facilitated diffusion is the movement of a solute by means of a carrier (transporter protein) down a concentration gradient.
Active transport is the movement of a solute against a concentration gradient. This transport may be driven by (a) direct coupling to ATP hydrolysis, or (b) by cotransport of another solute down its concentration gradient."
Term
What are the three types of port transports?
 Definition
The transport may involve (a) a single solute traveling in one direction [uniport], or (b) two solutes co-transported in the same direction [symport], or (c) two solutes exchanged in opposite directions across the membrane [antiport]."
Term
What is glucose transport into red blood cells?
What is the transporter? How does it work?
 Definition
Facilitated diffusion uniport(glucose)

Almost all mammalian cells use glucose from the blood as the major source of cellular energy, and most of these cells transport glucose across the cell membrane with a facilitated diffusion uniport called GLUT1 (GLUcose Transporter 1). The transporter is conveniently studied in red blood cells. The energy comes from the glucose concentration gradient, and only glucose is transported, in the direction of its concentration gradient."
Term
What is Cl-/HCO3- exchange in red blood cells?
What is the major protein in red blood cells that facilities exchange?
 Definition
Facilitated diffusion anti port for both.
The major membrane protein of red blood cells is called AE1 (Anion Exchange protein 1; "band 3"). AE1 is a facilitated diffusion antiport protein which exchanges
Term
glucose/Na+ transport into intestinal and kidney cells;?
 Definition
Active symport: glucose/Na+ transport into intestinal and kidney cells;
Term
What type of transport is Na+/K+ ATPase?
 Definition
Active antiport: Na+/K+ ATPase •"
Term
What can the rate of diffusion be limited by?
 Definition
The rate of diffusion may be limited by both the concentration gradient and the amount and efficiency of the transporter protein."
Term
What is the effect of AE 1 on the net charge? Why?
 Definition
" AE1 is a facilitated diffusion antiport protein which exchanges a chloride ion (Cl-) for a bicarbonate ion (HCO3-). Since there is no net change in charge across the membrane, this transporter is not affected by the membrane electrical potential gradient."
Term
What is the process for the body as far as expelling and intaking C02? (cellular perspective)(part 1)
 Definition
"In the systemic capillaries, where CO2 pressure is high, red blood cells pick up CO2 (which is not very water-soluble), and an enzyme called carbonic anhydrase converts much of it to bicarbonate, HCO3-, which is very water-soluble. water-soluble. AE1 rapidly transports most of the HCO3- out of the cell into the plasma, in exchange for Cl-."
Term
What is the process for the body as far as expelling and intaking C02? (cellular perspective)(part 2)
 Definition
n the pulmonary capillaries, the reverse takes place: since CO2 pressure is low, CO2 diffuses out of the red blood cells; carbonic anhydrase converts HCO3- into CO2 which is immediately removed, driving the equilibrium in the reverse direction; AE1 rapidly transports HCO3- into the erythrocyte, exchanging Cl- back into the plasma, and feeding more HCO3- into the carbonic anhydrase reaction."
Term
Explain how muscle cells use Ca++?
 Definition
Muscle cells keep their intracellular Ca++ concentration low by storing Ca++ in an organelle called the sarcoplasmic reticulum. When the muscle cell is stimulated by an action potential, Ca++ is released from the sarcoplasmic reticulum into the cytosol, stimulating muscle contraction. The sarcoplasmic reticulum has a Ca++ ATPase which moves Ca++ against a high concentration gradient from cytosol back into the sarcoplasmic reticulum, using energy released by ATP hydrolysis.
Term
what type of transport is glucose in epithelial cells? What type of transporter?
 Definition
Some texts refer to this as secondary active transport (where primary active transport is transport that is directly coupled to ATP hydrolysis). Intestinal epithelial cells need to transport glucose into the cell from an external environment which may contain higher or lower concentrations of glucose than exist inside the cell. In the case of the SGLT1 transporter, movement of glucose is driven by co-transport with Na+; recall that the concentration of Na+ inside the cell is low relative to that outside the cell, so transport is driven by the Na+ concentration gradient. The electrical gradientalso favors movement of Na+ into the cell
Term
How many Na and K are pumped in and out? why? how much body energy does this system use?
 Definition
Na+/K+ exchanger which is coupled to ATP hydrolysis; 3 Na+ ions are pumped out of the cell for every 2 K+ ions pumped in. The ion gradients are necessary to maintain"

typically consumes about a third of the total energy requirement of a cell
Term
How do Ion channels differ from transport proteins?
 Definition
• A single channel may conduct >107 ions/second (compare with turnover rates of 102-103/sec for carrier proteins)
• Movement is always in the direction of the electrochemical gradient. There is no primary active transport (directly coupled to ATP hydrolysis) through ion channels."
Term
How do channels selectively choose K over Na when the molecules move through the channel?
 Definition
we see that a K+ ion can interact with 4 amide oxygen atoms in the channel; this state is about equal in energy to that shown above left. Below right, we see that the smaller Na+ ion can only interact well with 2 of the 4 oxygen atoms in the channel; this is a less favorable situation than above right, so Na+ ions tend to stay in the water outside the channel rather than entering it.
Term
The gating (opening & closing) of ion channels can be controlled and modified in several ways. What are they?(part1)
 Definition
Some ion channels are voltage-gated (opened/closed by changes in membrane potential)
Some ion channels are ligand-gated (opened/closed by binding of ligands to receptor sites on the channel protein). These ligands include many neurotransmitters, hormones, and second messengers.
Term
The gating (opening & closing) of ion channels can be controlled and modified in several ways. What are they?(part2)
 Definition
• Some ion channels are gated in response to sensory stimuli such as mechanical stress.
• Some ion channels are self-regulating (they close themselves after being open for some period of time) • Some drugs and toxins act by closing or opening ion channels"
Term
Volted gated channels have how many transmemebrane helical segments?
How many proteins in a sodium channel?
 Definition
Voltage-gated ion channels typically have 24 transmembrane helical segments. Sodium channels are one long continuous protein.
Term
What are the proteins make up in potassium channels?
 Definition
potassium channels are homotetramers (4 copies of a protein having 6 transmembrane segments). There is a loop segment between helix 5 & helix 6 which makes up the selectivity pore. In the voltage-gated channels, helix 4 is the voltage sensor."
Term
How are voluted gated channels in acted?
 Definition
The voltage-gated channels are believed to inactivate by a "ball and chain" mechanism. There is a globular N-terminal domain which is thought to be the "ball" or "plug"."
Term
what is Gramicidin D?
 Definition
Gramicidin D is a channel-forming ionophore. It is a peptide which makes a doughnut-shaped structure that floats in the lipid bilayer. It is polar on the inside, and non-polar on the outside. If two gramicidin molecules align, the dimer forms a cation channel which allows H+, K+, and Na+ to pass(in roughly that order)
Term
Transmission of a nerve impulse to a muscle cell and its subsequent contraction involves sequential function of several different ion channels. What are they?(part 1)
 Definition
When the nerve impulse reaches the end of the nerve cell, it opens voltage- gated Ca++ channels; Ca++ causes release of acetylcholine into the synapse.
• Acetylcholine binds to receptors on the muscle cell membrane; these receptors are ligand-gated Na+ channels, which allow Na+ to enter the cell.
• The flow of Na+ into the cell opens voltage-gated Na+ channels; more Na+ enters, more channels open, amplifying the depolarization (action potential).
Term
Transmission of a nerve impulse to a muscle cell and its subsequent contraction involves sequential function of several different ion channels. What are they?(part 2)
 Definition
• Depolarization of the muscle cell activates voltage-sensitive proteins in the transverse (T) tubules; these, in turn, open Ca++ release channels in the sarcoplasmic reticulum, increasing intracellular Ca++ concentration and causing contraction of the muscle cell. After muscle contraction, several transport systems are required to restore the resting state and the resting membrane potential:
• In the plasma membrane, Na+/K+ ATPase restores the Na+ gradient and the membrane potential by pumping Na+ out of the cell and K+ in.
Term
Transmission of a nerve impulse to a muscle cell and its subsequent contraction involves sequential function of several different ion channels. What are they?(part 3)
 Definition
• In the plasma membrane, a Na+/Ca++ exchanger, driven by the Na+ gradient, helps to re-establish the Ca++ gradient.
• In the sarcoplasmic reticulum, a Ca++ ATPase actively pumps Ca++ ions back into the sarcoplasmic reticulum, helping to re-establish the Ca++ gradient."
Term
How does glucose absorbed in small intestine?
 Definition
In the small intestine, epithelial cells are able to absorb glucose from the lumen and then transport it through the cell into the extracellular fluid at the basal end of the cell.
Term
What is the specific process of glucose absorption?(part 1)
 Definition
In the microvilli at the apical end of the cell, a glucose/Na+ co-transporter (active symport) moves glucose into the epithelial cell, driven by the electrochemical Na+ gradient. g electrochemical Na+ gradient.
• The resulting high intracellular concentration of glucose drives transport of glucose out of the cell into the extracellular fluid at the basal membrane, through the GLUT2 glucose transporter (uniport).
Term
What is the specific process of glucose absorption?(part 1)
 Definition
• The Na+ gradient is maintained by a Na+/K+ ATPase in the basal and lateral membrane of the epithelial cell. The process depends on the fact that apical and basal ends of the cell are separated by tight junctions. These keep the transporters localized in one end of the cell or the other."
Term
The parietal cells lining the stomach are able to secrete hydrochloric acid (H+/Cl-), a substance which does not normally occur anywhere else in the body. How is this accomplished?(part 1)
 Definition
by a series of carriers and ion channels. Carbon dioxide enters the cell by diffusion. The enzyme carbonic anhydrase converts carbon dioxide + water to bicarbonate ion and H+ ion. A H+/K+ ATPase (active antiport) pumps the H+ ion into the lumen of the stomach, moving K+ ion into the cell. A K+ ion channel recycles potassium ions back out of the cell.
Term
The parietal cells lining the stomach are able to secrete hydrochloric acid (H+/Cl-), a substance which does not normally occur anywhere else in the body. How is this accomplished?(part 2)
 Definition
The bicarbonate ion produced by the carbonic anhydrase is exchanged out of the cell for a chloride ion (facilitated diffusion antiport). The chloride ion moves from inside the cell to the lumen of the stomach, via a chloride ion channel. H+ and Cl- enter the lumen of the stomach Intracellular pH is maintained--both the acid (H+) and the alkaline HCO3- leave the cell. K+ ion cycles in & out. ATP is consumed."

--
Term
(protein lecture) What are Chaperones?
 Definition
"Chaperones (top figure, above) are proteins with hydrophobic interiors that provide an environment in which misfolded proteins can more easily reach their favored conformations. ATP hydrolysis provides energy to "massage" the protein."
Term
How is damage prevented from misfiled proteins?
 Definition
"If they still have extensive hydrophobic side chain exposure, they could aggregate and cause damage to the cell. To prevent this, proteasomes (above) bind to these misfolded proteins and digest them."
Term
What is a proteasome?
 Definition
Proteasomes are abundant in the cytosol and nucleus, making up almost 1% of cell proteins. They are composed of a central hollow cylinder (yellow segment in the figure above) containing proteolytic sites, and a pair of "cap" structures (blue, above)that regulate entry into the proteasome.
Term
How are proteins broken down?(part 1)
 Definition
Most of the proteins destined for degradation in the proteasome are tagged with multiple copies of a small protein, ubiquitin. The polyubiquitin tag is recognized bythe cap structure, and the protein is threaded into the proteolytic core, where it is broken down to small peptides. core, where it is Ubiquitination and proteasome degradation is also a pathway used for regulation and controlled destruction of proteins when they need to be down-regulated."
Term
How are proteins broken down?(part 2)
 Definition
degradation and aggregate to form Sometimes misfolded proteins avoid or resist degradation and aggregate to form aberrant quaternary structures that damage tissue. This may be the result of a mutation, as in the case of sickle cell anemia, in which a single amino acid change makes hemoglobin prone to aggregate into fibers that disrupt the red blood cell.
Term
How are proteins broken down?(part 3)
 Definition
It can also occur as cells age, and become less efficient in quality control of protein folding. These peptides, called beta-amyloid, can associate to form dense fibrillar aggregates. One component of Alzheimer's disease is the processing of a membrane protein into extracellular peptides of 39-43 amino acids. These peptides, called beta-amyloid, can associate to form dense fibrillar aggregates."
Term
what are prion diseases?
 Definition
If the normal 4-helix structure converts to the beta-sheet structure, it becomes resistant to proteases and can induce the same kind of conformational change in other copiesof the protein. The misfolded protein actually resists digestion, so that eating such tissue from another animal can cause misfolding of proteins in the consuming organism. This is the basis of Creutzfeld-Jakob disease and bovine spongiform encephalopathy (BSE, mad cow disease). "
Term
What happens to useful protein folds?
 Definition
Protein folds which prove to be useful get duplicated and reused (by gene duplication)."
Term
What is immunoglobulin fold?
 Definition
immunoglobulin fold (so named because it was first observed experimentally in immunoglobulins) is formed by seven antiparallel strands of beta-sheet, stabilized by a disulfide bond. An immunoglobulin is formed of two heavy chains (each composed of four immunoglobulin domains) and two light chains (each composed of two immunoglobulin domains)."
Term
What is a protein domain?
 Definition
: Typical protein structure is made up of more then one domain. Often linked through relativley unstructured polypeptide chains. Domains can be shuffled and recombinedin may ways to make complex proteins
Term
How can mass spectrometry be used to study proteins?
 Definition
"Nowadays, mass spectrometry can be used. It measures mass-to-charge ratios for molecules, and, under some conditions, can fragment the molecule in useful ways."
Term
Where does the most abundant sources if proteins sequence information come from?
 Definition
Since the advent of automated gene sequencing, the most abundant source of protein sequence information comes from translation of gene sequences
Term
What are homologs?
 Definition
"Proteins of similar structure within the same or different organisms are called homologs."
Term
Implicatoin of sequence conservation?
 Definition
invariant primary structure suggests invariant (conserved) tertiary structure. However, it is notable that tertiary structure is often much more conserved than primary structu
Term
What are orthologs?
 Definition
Homologs that were separated by a speciation event and perform the same function in called orthologs. Homologs that were separated by a gene duplication event generally mutate and perform different functions in the same organism; these are called paralogs."
Term
WHen are disulfide bridges common in proteins?
 Definition
Disulfide bridges are common in proteins that operate in extracellular spaces. Typical examples are snake venoms and other toxins, peptide hormones, digestive enzymes, immunoglobulins, milk proteins, etc. Formation of a disulfide bond can help to stabilize protein conformation. "
Term
What two side chains can be linked to form a disulfide bridge?
 Definition
Tow cysteine side chains.
Term
How are the viscolelesatic properties determined?
 Definition
The viscoelastic properties of various natural products are at least partly determined by disulfide bridges (e.g., keratin of wool and hair, glutelin of corn). Under oxidizing conditions, disulfide formation is favored; under reducing conditions, the disulfide is converted to free thiols."
Term
What does proteolyctic cleavage do?
 Definition
Proteolytic cleavage is a common post-translational modification. In some cases it is necessary in order for a protein to adopt its active conformation. The figure above, left, illustrates schematically that insulin is produced initially as a single chain substance called proinsulin. Proteolytic processing removes part of the chain and allows the remaining (now two) chains to adopt the biologically active conformation.
Term
How is insulins activity terminated?
 Definition
Insulin’s activity is terminated by another proteolytic processing step. Proteolysis of prohormones and proproteins allows the remaining (now two) chains to adopt the biologically active conformation. Insulin’s activity is terminated by another proteolytic processing step. Proteolysis of prohormones and proproteins to produces active forms is a common way to regulate protein activity."
Term
What is pre protein?
 Definition
Many secretory proteins are synthesized as preprotein" that is a precursor with a short-lived peptide extension of the N-terminus (figure above right). The extensions, called signal peptides (with predominantly hydrophobic residues), can cause the protein to be trafficked to specific parts of the cell; subsequently the signal sequence can be removed by proteolysis."
Term
How do blood factors circulate?
 Definition
Many blood clotting factors circulate as inactive precursors (most of the time, you don’t want your blood to coagulate). When vascular injury occurs, these clotting factors are activated by proteolytic processing at the site of injury. When vascular injury"
Term
How does the light detecting component in our eye get activated?(get super powers)
 Definition
"On the left we see the backbone ribbon representation of rhodopsin, the light- detecting component of the visual system. Cradled in the center of the rhodopsin protein is retinal (green spheres), derived from vitamin A"

** proteins bind prosthetic groups/
Term
How are fibrin clots stabilized?
 Definition
Lys-Gln side chain cross-linking is seen, for example, in stabilizing fibrin clots."
Term
What is hydroxylated in collagen?
 Definition
-In collagen, some proline and lysine residues are hydroxylated. -
Term
in what does methylation occur?
 Definition
Methylation occurs in some histones, myosin, actin, ribosomal proteins
Term
How is histone activity regulated?W
 Definition
Acetylation is involved in regulating the activity of histones
Term
WHere have N terminal modifications been observed?
 Definition
N-terminal modifications have been observed, including acetylation (c-type cytochromes, actin, myosin, tropomyosin); formylation (some bee venoms, lamprey hemoglobin); conversion of Glu to pyro-glutamate (immunoglobulins, some snake venoms)."
Term
Electrophoresis can be used for: (part 1 )
 Definition
(1) Separation of proteins on the basis of net charge differences. e.g., gel or paper electrophoresis. This method can be used either preparatively or analytically, but is commonly used for the latter purpose.
Term
Electrophoresis can be used for: (part 2)
 Definition
Analysis of Purity. The homogeneity of a protein can be assessed rapidly by electrophoresis and subsequentstaining of the protein embedded gel, using silver or Coomassie blue dye. use of immunochemistry is called Western blotting. boiling. Disulfides may be reduced by addition of 2-mercaptoethanol . Samples are applied in the lanes of an upright gelapparatus (above left) containing a cast slab of polyacrylamide. This method is known commonly as SDS-PAGE (polyacrylamide gel electrophoresis).
Term
Electrophoresis can be used for: (part 3 )
 Definition
In this manner, the separation of proteins is based on size, since the cross-linked polyacrylamide gel matrix serves as a molecular sieve Samples are often denatured (unfolded) completely through the addition of sodium dodecyl sulfate (SDS) accompanied by boiling. Disulfides may be reduced by addition of 2-mercaptoethanol
Term
What is ion exchange chromatography?
 Definition
"Ion exchange chromatography utilizes charge and the acid-base behavior of proteinsfor separation. "
Term
What is affinity chromatography?
 Definition
"Affinity chromatography depends on the column material having a specific affinity for the desired protein. of gel filtration chromatography. Separations on the basis of size can be achieved by the technique of gel If the protein of interest has an affinity for metal ions, the packing material could be one which binds the correct metal ion."
Term
What is a way to obtain 3D structure information?
 Definition
"Another method to obtain 3-D structure information is by use of NMR spectroscopy. In NMR spectroscopy, the nuclei of some atoms (1H, 13C, 15N) resonate in the radio frequency range, and signals can be detected when two atoms are close to each other (<5 Å) in space
Term
What is amyloidosis? What is proteopathy?
 Definition
Amyloidosis refers to any condition in which proteins aggregate in insoluble beta-sheets. The term proteopathy has also been coined to describe protein misfolding that leads to adverse symptoms or disease."
Term
What are Glycoproteins?
 Definition
Glycoproteins are defined as proteins that contain covalently attached carbohydrate.
Term
What are there functions?
 Definition
Function. Glycoproteins are usually found in extracellular spaces or on the noncytosolic side of membrane systems, but a small number have been found in the cytosol, the nuclear envelope, and the nucleoplasm. Within these spaces, the function of the carbohydrate portion of glycoproteins serves a variety of functions.
Term
Functions of carbohydrates?
 Definition
-recognition(selectins)
-Trafficking(lysosome signal)
-physical properties( mucin)
Stabilize proteins(EPO)
Term
Functions of carbohydrates?(part 2)
 Definition
Modulate activity(transcription factors)
protein quality control(ER chaperon)
Store energy(glycogen)
Term
Function of glycoproteins in carbohydrates?
 Definition
Recognition: Trafficking signal for transport to lysosomes, for removal from serum, for receptor-mediated endocytosis; cell-cell recognition, e.g., during tissue formation or during lymphocyte invasion at site of inflammation.
Term
Function of glycoproteins in carbohydrates?
 Definition
Physical properties: mucins line and protect stomach; anti-freeze GPs in cold-water fish depress freezing point of water; hyaluronic acid (glycosaminoglycan, not technically a glycoprotein) increases viscosity of water, makes viscous lubricating fluids for joints
Term
Function of glycoproteins in carbohydrates?
 Definition
Stabilize proteins: erythropoietin (40% carbohydrate) more susceptible to removal and degradation if carbohydrates are removed
Term
Function of glycoproteins in carbohydrates?
 Definition
Modulate activity of proteins: e.g., some transcription factors
Term
Function of glycoproteins in carbohydrates?
 Definition
Protein quality control: Flag incompletely folded proteins for chaperones in
ER.
Term
Function of glycoproteins in carbohydrates?
 Definition
Store energy (glycogen)--more detail in Medical Biochemistry
Term
In oliogosaccharide the carbohydrate is attached to?
 Definition
Most often, the carbohydrate is attached to Asn (N-linked) or to Ser or Thr (O-linked).

*An individual glycoprotein may contain >1 carbohydrate chain. Different types of carbohydrate chains may be present on the same protein.
Term
When are sugars attached to glyoproteins?
 Definition
glycosyltransferase enzymes, and on the presence of the proper substrate, and on the presence of the necessary activated sugars (usually a sugar with a nucleoside diphosphate or a nucleoside phosphate).
Term
Is glycoproteins synthesis sequential or templated?
 Definition
Glycoprotein synthesis is sequential. For example, in the synthesis of the blood group A and B antigens (above), the GalNAc or Gal cannot be added until the fucose is in place.
Term
Is glycoproteins synthesis sequential or templated? How does this effect it being linear or branched?
 Definition
Glycoprotein synthesis simply requires that the appropriate precursors and enzymes are present. As a result, the carbohydrate portions of glycoproteins are not constrained to being linear. In fact, many are branched.
Term
what is Microheterogeneity? How does it apply to glycoprotiens and how they are synthesized?
 Definition
Microheterogeneity (small variations) may be observed as a result of the non- templated synthesis of these chains.
Term
What is a N linked glycoprotein?
 Definition
These carbohydrates have from about 8 to 25 residues and are linked via an N- glycosidic bond to Asn residues. The Asn is usually in the sequence Asn-X- Ser/Thr, but not all such sequences are glycosylated.
Term
What is the core structure on N linked glycoproteins?
 Definition
conserved core structure
Term
What is a Nlinked gycoprotein with mannose called? and why?
 Definition
N-linked glycoproteins is called high mannose (shown above left) because it has mannosyl-mannose substituents on the core structure.
Term
What is the other class of glycoproteins?
 Definition
called complex (shown above right) because substituents on the core consist of a short chain composed of multiple sugar types, e.g., Sia → gal→ glcnac → core.
Term
What is a hybrid glycoprotein?
 Definition
There are also hybrid glycoproteins, which contain both high-mannose and complex N- linked carbohydrates.
Term
Where is a N linked carbohydrate, with out the protein, formed?
 Definition
The carbohydrate chain, without the protein, is first formed on a lipid carrier (dolichol) located in the membrane of the ER. The first stage takes place in cytoplasm on a phosphate of a membrane-embedded dolichol.
Term
What is the bridge called when the first sugar links to the dolichol?
 Definition
The first sugar is linked to dolichol by a pyrophosphate bridge. This high-energy bond activates the oligosaccharide for its eventual transfer from the lipid to the protein.
Term
Where does synthesis of the oligosaccharide start?
 Definition
The synthesis of the oligosaccharide starts on the cytosolic side of the ER membrane and continues on the lumenal face after the (Man)5(GlcNAc)2 lipid intermediate is flipped across the bilayer by a transporter protein.
Term
What happens after it is flipped across the bi layer?
 Definition
All the subsequent glycosyl transfer reactions on the lumenal side of the ER involve transfers from dolichol-P- glucose and dolichol-P-mannose; these activated, lipid-linked monosaccharides are synthesized from dolichol phosphate and UDP-glucose or GDP-mannose (as appropriate) on the cytosolic side of the ER and are then thought to be flipped across the ER membrane.
Term
What happens after the oligosaccharide is assembled?
 Definition
After this oligosaccharide is assembled, it can be transferred en bloc to an asparagine side chain of a nascent polypeptide as it enters the lumenal side of the rough ER.
Term
What does tunicamycin do?
 Definition
The antibiotic tunicamycin, an analog of UDP-GlcNAc, inhibits the first reaction in the pathway. Tunicamycin is not a clinically useful antibiotic; it is a lab tool to help us understand glycoproteins.
Term
What happens after the N linked carbohydrates transfer to the protein?
 Definition
After transfer to the protein, the carbohydrate chain is processed by enzymes that remove some sugar residues and add others. These reactions are fairly specific for specific organelles. Removal of sugars generally occurs in the ER and/or early Golgi, while subsequent modifications of the basic structure occur in specific "parts" of the Golgi
Term
WHat happens to N linked carbohydrates in ER ?
 Definition
Processing begins in the ER with the removal of two glucoses from the oligosaccharide initially transferred to the protein. The chaperone folding step then takes place
Term
What happens next?
 Definition
Then a mannosidase in the ER membrane removes a specific mannose. The remaining steps occur in the Golgi stack. This yields the final core of three mannoses that is present in a complex oligosaccharide.
Term
What happens next?
 Definition
At this stage, the bond between the two N-acetylglucosamines in the core becomes resistant to attack by a highly specific endoglycosidase (Endo H). Since all later structures in the pathway are also Endo H-resistant, treatment with this enzyme is widely used to distinguish complex from high-mannose oligosaccharides (Endo-H does not occur naturally in the body--it is a laboratory tool to help us understand glycoproteins).
Term
What happens at the end?
 Definition
Finally, additional N-acetylglucosamines, galactoses, and sialic acids may be added. These final steps in the synthesis of a complex oligosaccharide occur in the cisternal compartments of the Golgi apparatus.
Term
What is role of N linked glycosylation in ER protein folding?
 Definition
The ER-membrane- bound chaperone protein calnexin binds to incompletely folded proteins containing one terminal glucose on N-linked oligosaccharides, trapping the protein in the ER. Removal of the terminal glucose by a glucosidase releases the protein from calnexin.
Term
What does glucosyl transferase do?
 Definition
A glucosyl transferase is the crucial enzyme that determines whether the protein is folded properly or not: if the protein is still incompletely folded, the enzyme transfers a new glucose from UDP-glucose to the N-linked oligosaccharide, renewing the protein's affinity for calnexin and retaining it in the ER.
Term
How long does folding occur for?
 Definition
The cycle repeats until the protein has folded completely. Calreticulin functions similarly, except that it is a soluble ER resident protein. Another ER chaperone, ERp57 (not shown), collaborates with calnexin and calreticulin in retaining an incompletely folded protein in the ER.
Term
How are specific glycoproteins targeted to the lysosome?
 Definition
A particularly interesting processing pathway is that used to add a 6-0- phosphate to some terminal mannosyl residues. This structure is a signal used to target specific glycoproteins to the lysosome.
Term
What happens during phosphorylation of mannose residues on lysosomal enzymes?
 Definition
In the first reaction, GlcNAc phosphotransferase in the cis-Golgi transfers GlcNAc-P to carbon atom 6 of one or more mannose residues. This enzyme has a recognition site that binds to signal segments present only in cathepsin D and other lysosomal enzymes.
Term
What happens during phosphorylation of mannose residues on lysosomal enzymes?(part 2)
 Definition
In the second reaction, a phosphodiesterase removes the GlcNAc group, leaving a phosphorylated mannose residue on the lysosomal enzyme. Thus, a signal sequence encoded in the protein leads to formation of a mannose-6-phosphate that ultimately causes the lysosomal enzyme to be transported to the lysosome
Term
What is olinked glycoproteins?
 Definition
In O-linked glycoproteins, carbohydrates are attached to side chain –OH of Ser, Thr, or hydroxy-Lys. Glycosylation takes place in the Golgi. The carbohydrates may be quite diverse.
Term
What is enzyme involved in for secreted and extracellular glycproteins?
 Definition
O-linked sugar chains (usually < 15 sugars) are synthesized by a one-by-one addition of sugars to the protein substrate. The first enzyme involved for secreted and extracellular glycoproteins is usually an N-acetyl- galactosaminyl transferase, e.g., UDP-GalNac + HO-protein ------> GalNac-O-protein + UDP
Term
For intracellular glycoproteins the sugar attached is?
 Definition
For intracellular glycoproteins, the sugar attached to Ser or Thr is usually N- acetyl-glucosamine (GlcNAc).
Term
What is a major group of glycol proteins that carry o linked carbohydrate chains?
 Definition
A major group of glycoproteins that carry O-linked carbohydrate chains are the mucins, components of the mucus secretions associated with many epithelia of the body. These glycoproteins are generally at least 50% carbohydrate and have been described as bottle-brush glycoproteins because of the large number of attached carbohydrate chains.
Term
What are proteoglycans? (o linked proteoglycans?)
 Definition
The members of this special group of glycoproteins are generally called proteoglycans (or in old literature, mucopolysaccharides). These molecules contain linear polysaccharides of the form (X-Y)n, where n > 20. Generally, Y is a uronic acid (e.g., glucuronic acid or iduronic acid) and X is a hexosamine (e.g., N-acetylglucosamine or N-acetylgalactosamine).
Term
What are GAGs?
 Definition
These polysaccharide chains, called glycosaminoglycans (GAGs), are usually attached to Ser residues in the sequence of Ser-Gly of core proteins via a unique sugar sequence. The presence of the uronic acids, and usually sulfates, imparts a strong negative charge to members of this group.
Term
What forms disaccharide repeating structure?
 Definition
There appears to be an enzyme complex that contains 2 transferases, which act together to form the disaccharide repeating structure. Sulfation and the conversion of D-glucuronic acid to L-iduronic acid occur after chain polymerization.
Term
C terminally linked carbohydrates?
 Definition
A number of membrane proteins have been found to contain phosphatidyl inositol linked through a carbohydrate chain to the carboxyl group on the C- terminal end of the protein.
Term
Why is glycogen unique?
 Definition
Glycogen is a rather unique glycoprotein. The core protein, glycogenin, catalyzes addition of glucose molecules to itself, from UDP-glucose to the – OH group of a Tyr side chain. It can add up to 8 glucoses to itself, after which another enzyme, glycogen synthase, adds many more glucoses.
Term
What are Glycosidases?
 Definition
Glycosidases: These are enzymes that usually have specificity for the sugar residue which supplies the reducing group involved in a glycosidic bond.
Term
What are Exoglycosidases?
 Definition
Exoglycosidases, by far the most common, act on non-reducing ends of carbohydrate chains, e.g., sialidase is specific for terminal sialic acid residues.
Term
What are Endoglycosidases?
 Definition
Endoglycosidases can cleave interior linkages, e.g., α-galactosidase is specific for the cleavage of α-linked galactosyl residues.
Term
What are lectins?
 Definition
Lectins are carbohydrate-binding proteins, distinct from antibodies or enzymes, which have specificity for specific carbohydrate structures.
Term
WHat is ELAM-1?
 Definition
For example, ELAM-1 (endothelial-leukocyte adhesion molecule) is present on vascular endothelium after stimulation by specific polypeptide growth factors (e.g., IL-1). The presence of this lectin on the cell surface allows circulating neutrophils to bind to the vascular lining and subsequently extravasate into surrounding tissue to aid in the defense against infection.
Term
What can aldehyde function of sugars at neutral PH do?
 Definition
The aldehyde function of sugars is reactive at neutral pH and will combine with free amino groups, e.g., ε-amino groups of Lys and free N-terminals of proteins. The resultant product can rearrange to form a stable ketoamine and more complicated structures called advanced glycation endproducts (AGEs).
Term
How does non enzymatic glycation relate to hemoglobin?
 Definition
Various blood proteins, most notably hemoglobin, even under normal conditions, contain some of these added carbohydrate units. This glycated hemoglobin is called HbA1c. The level of HbA1c is increased several fold in diabetics with poorly controlled blood sugar levels, an observation that is used clinically to monitor the ability of patients to maintain "normal" blood sugar levels over extended periods. Whereas blood glucose measurement tells you the current blood glucose concentration, the HbA1c value reflects the average blood glucose concentration over the preceding 1-3 months.
Term
What is bombay disease?
 Definition
Patients have antibodies in blood which react against all of the major blood types.
Term
Why can people with A or B antigen use type O?
 Definition
Normally, everyone produces the O antigen. People who have the A antigen have a gene which makes an N-acetyl-galactosaminyl transferase; this transferase adds N-acetyl-galactosamine to the O antigen. People who have the B antigen have a gene which makes a galactosyl transferase, which adds galactose to the O antigen.
Term
What is different about people with bombay disease?
 Definition
People with the Bombay phenotype lack the gene for the fucosyl transferase which is responsible for completing the O antigen; if the fucose is not attached, the N-acetyl-galactosaminyl transferase and galactosyl transferase are not able to add their respective sugars.
Term
Explain mutation?
 Definition
In this case, the mutation is not in the antigenic glycoproteins, but in an enzyme which processes those glycoproteins. Thus, the fucosyl transferase is referred to as the primary gene product and the antigenic glycoprotein is referred to as the secondary gene product.
Term
What are chaperone proteins? How are they powered?
 Definition
Chaperones (top figure, above) are proteins with hydrophobic interiors that provide an environment in which misfolded proteins can more easily reach their favored conformations. ATP hydrolysis provides energy to "massage" the protein."
Term
What could happen to proteins that do not fold properly even with help of chaperones? How is it prevented?
 Definition
If they still have extensive hydrophobic side chain exposure, they could aggregate and cause damage to the cell. To prevent this, proteasomes (above) bind to these misfolded proteins and digest them."
Term
What are proteasomes composed of? How common?
 Definition
Proteasomes are abundant in the cytosol and nucleus, making up almost 1% of cell proteins. They are composed of a central hollow cylinder (yellow segment in the figure above) containing proteolytic sites, and a pair of "cap" structures (blue, above)that regulate entry into the proteasome.
Term
What are proteins destined for degradation by proteasomes composed of?
 Definition
Most of the proteins destined for degradation in the proteasome are tagged with multiple copies of a small protein, ubiquitin. The polyubiquitin tag is recognized bythe cap structure, and the protein is threaded into the proteolytic core, where it is broken down to small peptides.
Term
What is a pathway used to control proteins when they need to be down regulated?
 Definition
Ubiquitination and proteasome degradation is also a pathway used for regulation and controlled destruction of proteins when they need to be down-regulated."
Term
What do misfolded proteins sometimes do that avoid degradation? What is an example? What does this example do?
 Definition
Sometimes misfolded proteins avoid or resist degradation and aggregate to form aberrant quaternary structures that damage tissue. This may be the result of a mutation, as in the case of sickle cell anemia, in which a single amino acid change makes hemoglobin prone to aggregate into fibers that disrupt the red blood cell.
Term
How can misfolded proteins effect Alzheimer's?
 Definition
It can also occur as cells age, and become less efficient in quality control of protein folding. These peptides, called beta-amyloid, can associate to form dense fibrillar aggregates. One component of Alzheimer's disease is the processing of a membrane protein into extracellular peptides of 39-43 amino acids. These peptides, called beta-amyloid, can associate to form dense fibrillar aggregates."
Term
What is the basis for Creutz Jakob disease and mad cow disease?
 Definition
If the normal 4-helix structure converts to the beta-sheet structure, it becomes resistant to proteases and can induce the same kind of conformational change in other copiesof the protein. The misfolded protein actually resists digestion, so that eating such tissue from another animal can cause misfolding of proteins in the consuming organism.
Term
What happens to protein folds that are useful?
 Definition
"Protein folds which prove to be useful get duplicated and reused (by gene duplication)."
Term
What is the immunoglobulin fold?
 Definition
"immunoglobulin fold (so named because it was first observed experimentally in immunoglobulins) is formed by seven antiparallel strands of beta-sheet, stabilized by a disulfide bond. An immunoglobulin is formed of two heavy chains (each composed of four immunoglobulin domains) and two light chains (each composed of two immunoglobulin domains)."
Term
What is a domain?
 Definition
Typical protein structure is made up of more then one domain. Often linked through relativley unstructured polypeptide chains.
Term
What is a fibronectin molecule composed of?
 Definition
a fibronectin molecule composed of four consecutive fibronectin type 1 modules. The figure above, center, shows that these domains can be shuffled and recombinedin may ways to make complex proteins
Term
How is sequencing of proteins done today? Explain process.
 Definition
Nowadays, mass spectrometry can be used. It measures mass-to-charge ratios for molecules, and, under some conditions, can fragment the molecule in useful ways."
Term
What is the most abundant source of protein sequence information?
 Definition
"Since the advent of automated gene sequencing, the most abundant source of protein sequence information comes from translation of gene sequences
Term
What are homologs?
 Definition
Proteins of similar structure within the same or different organisms are called homologs."
Term
What are orthologs?
 Definition
Proteins of similar structure within the same or different organisms are called homologs."
Term
What are paralogs?
 Definition
Homologs that were separated by a gene duplication event generally mutate and perform different functions in the same organism; these are called paralogs."
Term
When/where are disulfide bridges common in proteins?
 Definition
Disulfide bridges are common in proteins that operate in extracellular spaces. Typical examples are snake venoms and other toxins, peptide hormones, digestive enzymes, immunoglobulins, milk proteins, etc. Formation of a disulfide bond can help to stabilize protein conformation.
Term
How are viscoelastic properties partly determined?
 Definition
The viscoelastic properties of various natural products are at least partly determined by disulfide bridges (e.g., keratin of wool and hair, glutelin of corn). Under oxidizing conditions, disulfide formation is favored; under reducing conditions, the disulfide is converted to free thiols."
Term
What is a Proteolytic cleavage?
 Definition
Proteolytic cleavage is a common post-translational modification. In some cases it is necessary in order for a protein to adopt its active conformation.
Term
explain how insulin relates to this?
 Definition
he figure above, left, illustrates schematically that insulin is produced initially as a single chain substance called proinsulin. Proteolytic processing removes part of the chain and allows the remaining (now two) chains to adopt the biologically active conformation. Insulin’s activity is terminated by another proteolytic processing step. Proteolysis of prohormones and proproteins allows the remaining (now two) chains to adopt the biologically active conformation. Insulin’s activity is terminated by another proteolytic processing step.
Term
What is a pre protein?
 Definition
preprotein" that is a precursor with a short-lived peptide extension of the N-terminus (figure above right). The extensions, called signal peptides (with predominantly hydrophobic residues), can cause the protein to be trafficked to specific parts of the cell; subsequently the signal sequence can be removed by proteolysis."
Term
Do blood clotting factors circulate active or inactive? Why?
 Definition
as inactive precursors (most of the time, you don’t want your blood to coagulate). When vascular injury occurs, these clotting factors are activated by proteolytic processing at the site of injury. When vascular injury"
Term
What is light detecting component of visual system? What is at center?
 Definition
On the left we see the backbone ribbon representation of rhodopsin, the light- detecting component of the visual system. Cradled in the center of the rhodopsin protein is retinal (green spheres), derived from vitamin A.
Term
What is seen for stabilizing fibrin clots?
 Definition
Lys-Gln side chain cross-linking is seen, for example, in stabilizing fibrin clots."
Term
What is hydroxylated in collagen?
 Definition
-In collagen, some proline and lysine residues are hydroxylated.
Term
Where does methylation occur?
 Definition
-Methylation occurs in some histones, myosin, actin, ribosomal proteins.
Term
What is acetylation involved in regulating?
 Definition
Acetylation is involved in regulating the activity of histones."
Term
What is electrophoresis used for?(part1 )
 Definition
"Electrophoresis can be used for: (1) Separation of proteins on the basis of net charge differences. e.g., gel or paper electrophoresis. This method can be used either preparatively or analytically, but is commonly used for the latter purpose
Term
What is electrophoresis used for?(part 2)
 Definition
Analysis of Purity. The homogeneity of a protein can be assessed rapidly by electrophoresis and subsequentstaining of the protein embedded gel, using silver or Coomassie blue dye.
Term
What is use of immunochemisty called?
 Definition
A radion nuclide label and image plate o IgG enzyme staining will work as well. Use of immunochemistry is called Western blotting
Term
Explain SDS-PAGE.
 Definition
Disulfides may be reduced by addition of 2-mercaptoethanol . Samples are applied in the lanes of an upright gelapparatus (above left) containing a cast slab of polyacrylamide. This method is known commonly as SDS-PAGE (polyacrylamide gel electrophoresis). In this manner, the separation of proteins is based on size, since the cross-linked polyacrylamide gel matrix serves as a molecular sieve
Term
What is ion exchange chromatography?
 Definition
Ion exchange chromatography utilizes charge and the acid-base behavior of proteinsfor separation.
Term
How is separation based on size achieved?
 Definition
Separations on the basis of size can be achieved by the technique of gel filtration chromatography.
Term
What is affinity chromatagraphy?
 Definition
When it depends on the column material having a specific affinity for the desired protein.
Term
What is method to obtain 3D structure?
 Definition
Another method to obtain 3-D structure information is by use of NMR spectroscopy. In NMR spectroscopy, the nuclei of some atoms (1H, 13C, 15N) resonate in the radio frequency range, and signals can be detected when two atoms are close to each other (<5 Å) in space."
Term
What is amyloidosis?
 Definition
Amyloidosis refers to any condition in which proteins aggregate in insoluble beta-sheets. The term proteopathy has also been coined to describe protein misfolding that leads to adverse symptoms or disease."
Term
How are eukaryotic cells organized?
 Definition
that include the nucleus, which is bounded by the nuclear envelope, and the cytoplasm.
Term
What does the cytoplasm contain?
 Definition
The cytoplasm contains membrane- enclosed organelles with a variety of functions, a cytoskeletal network, and other soluble and insoluble macromolecular complexes (e.g., metabolites, enzymes, ribosomes, proteasomes, accumulated cell products like fat or glycogen).
Term
What three classes of proteins make up the cytoskeleton?
 Definition
The cytoskeleton provides a structural scaffold and modulates cellular organization dynamically through a dense network of three classes of protein filaments--microfilaments, intermediate filaments and microtubules.
Term
How are prokaryotic cells different from Eukaryotic?
 Definition
Eucaryotic cells (10-20 times larger than procaryotes) use membrane- enclosed organelles to organize dynamic processes and chemical reactions efficiently in functionally specialized spaces (this level of organization is not needed for simple 1-2 μm prokaryotic cells).
Term
What is the cytosol usually made up of?
 Definition
. The cytosol is usually about 20% protein [many enzymes of intermediary metabolism for glycolysis, gluconeogenesis, and biosynthesis of sugars, nucleotides, and amino acids function here (presented in Biochemistry)]. Most protein synthesis takes place in the cytosol, which is organized by the cytoskeleton.
Term
major differences of liver hepatotcyte and pancreatic exocrine cell as far as percentage of cell membrane?

(reference for next question)
 Definition
Liver Hepatocyte Pancreatic Exc
Plasma membrane: 2 5
Rough ER 35 60
Smooth ER 16 1
Mitochondria:(outer) 7 4
inner: 32 17
Term
aware of trends in cells about cytosol, mitochondria and nucleus!!
 Definition
-the cytosol is usually about half of the cell volume; -- mitochondria usually occupy a greater volume than other organelles;
-the nucleus usually occupies more volume than some of the less abundant organelles.
Term
Where are proteins synthesized? What does it require?
 Definition
Proteins are synthesized in the cytosol from mRNA templates and then delivered to specific destinations within the various organelles. This process requires specific sequence signals in the molecule that is being transported
Term
How are newly synthesized proteins transported?
 Definition
Newly synthesized proteins are generally transported as unfolded proteins to their correct location using different signal sequences within the primary sequence recognized by transmembrane translocators.
Term
What is exception?
 Definition
Nuclear-targeted and peroxisome-targeted proteins are exceptions, because they can be delivered as folded proteins.
Term
Where are signal sequences encoded? How are they recognized?
 Definition
The information is encoded in the primary sequence of a protein, and, depending upon the example, may be located at the N-terminus, the C-terminus or within a protein. The signals are recognized by translocators that deliver proteins to specific destinations.
Term
What are three ways proteins can be transported?( part 1)
 Definition
Proteins can move from one compartment to another by gated transport (cytosol <--> nucleus; indicated by the arrow inside the nucleus pointing to the cytosol in the TEM on the left),
Term
What are three ways proteins can be transported?( part 2)
 Definition
transmembrane transport (cytosol <--> other membrane compartments; indicated by the arrow in the cytosol in the TEM),
Term
What are three ways proteins can be transported?( part 3)
 Definition
vesicular transport (all other paths)
Term
Where are signals that direct movement contained?
 Definition
Signals that direct a given protein's movement through the system and determine where in the cell it is sent are contained in each protein's amino acid sequence
Term
What encloses the nucleus?
 Definition
It is enclosed by the nuclear envelope and houses the genetic material (DNA organized into chromosomes) together with the machinery for DNA replication and RNA transcription and processing in the nucleoplasm.
Term
What characterized the nucleoplasm?
 Definition
The nucleoplasm is characterized by regions of darkly- staining, highly condensed heterochromatin and lightly-staining, less condensed euchromatin. The nucleolus, rich in RNA and protein, is the site for rRNA synthesis and ribosome assembly.
Term
Explain nuclear envelope (part 1)
 Definition
The nuclear envelope is a double membrane structure punctuated by nuclear pores--3000-4000 per single nucleus--which are distributed throughout interfaces of the inner and outer nuclear membranes.
Term
Explain nuclear envelope (part 2)
 Definition
Just inside the inner nuclear membrane, the nuclear envelope is supported by a nuclear lamina, which consists of an organized thin network of intermediate filaments. The outer nuclear membrane is continuous with the endoplasmic reticulum (ER)
Term
How is protein movement regulated in nucleus?
 Definition
Normal cell function depends on the regulated movement of proteins such as transcription factors in and out of the nucleus and the sequestration of immature RNAs within the nucleus. Nuclear pores provide a gate mechanism that controls the exchange between the nucleus and cytosol, which are two separate but topologically continuous aqueous compartments. Import of the glucocorticoid receptor shown in lecture 1 exemplifies this gated transport mechanism.
Term
What is Hutchinson-Gilford Progeria?
 Definition
Hutchinson-Gilford Progeria is a rare childhood disorder caused by mutations in lamin A, the major protein of the nuclear lamina. Affected individuals appear normal at birth, but then age rapidly and die early in their teens from diseases characteristic of old age, such as atherosclerosis and heart failure.
Term
What causes similar diseases?
 Definition
Mutations in several other nuclear envelope proteins cause similar diseases, perhaps by de-stabilizing interactions with chromatin. Dr. Oblinger will present the cytoskeleton in later CMCB lectures.
Term
Explain Nucleolus?
 Definition
The nucleolus is the most conspicuous, best characterized nuclear substructure. It is not enclosed by a membrane, but is instead a specialized region surrounding transcriptionally active ribosomal RNA (rRNA) gene clusters where the major stages of ribosome biogenesis are orchestrated.
Term
Explain ribosome biogenesis?(part1 )
 Definition
Within the nucleolus, rRNA is transcribed and processed and the large and small ribosomal subunits are assembled. Ribosomal proteins synthesized in the cytoplasm enter the nucleus through nuclear pores and migrate to the nucleolus where they participate in ribosome assembly.
Term
Explain ribosome biogenesis?(part 2)
 Definition
The mature ribosome subunits are then transported into the cytoplasm where they are assembled into complete ribosomes when protein synthesis/translation is initiated (discussed in later lectures; for now, be aware that the ribosome functions in translation whereby messenger RNA (mRNA) sequences are read and translated into amino acid sequences that form corresponding proteins).
Term
What does composition and size of nucleolus say about cell?
 Definition
The composition and size of the nucleolus reflect cellular metabolic activities. In cells making large quantities of protein, it can occupy >25% of the nucleus.
Term
How is transport regulated between nucleus and cytoplasm?
 Definition
Nuclear pores allow for regulated transport between the nucleus and cytoplasm. Salts and small metabolites (<5K) readily diffuse through the pores. Smaller proteins can diffuse across, but increasingly larger ones do so more slowly, and those larger than 60K barely can. The size of the pore determines the cutoff to free diffusion.
Term
How are larger proteins transported?
 Definition
A gated transport mechanism regulates the entry and exit of larger proteins in their native conformation, ribosomal subunits and ribonucleoprotein complexes
Term
WHat is example of signal sequence in NLS?
 Definition
Proteins destined for the nucleus have a signal sequence, which in this case is a nuclear localization signal (NLS). The NLS is recognized by a nuclear transport receptor such as import in.
Term
Explain basic sequence in NLS.(Part 1)
 Definition
-The basic scheme of NLS-protein importation begins when importin-α first binds to the NLS sequence, and acts as a bridge for importin-β to attach. The importin-β— importin-α—cargo complex then associates with the nuclear pore fibrils and diffuses through the nuclear pore.
Term
Explain basic sequence in NLS.(Part 2)
 Definition
nside the nucleus, the GTP- binding protein Ran binds to the importin complex and causes release of the cargo. The Ran-importin complex moves through the pore to the cytosolic side, GTP is hydrolyzed to GDP, and the importin is released for another cycle.
Term
How are nuclear export receptors similar?
 Definition
nuclear export receptors utilize a similar mechanism for the export of proteins, ribosomal subunits and RNA from the nucleoplasm through the nuclear pores into the cytosol.
Term
What are mitochondria? What do they do?
 Definition
Mitochondria are membrane-enclosed organelles present in virtually all eucaryotic cells.
-Mitochondria are envisioned as the cellular power plant to produce ATP, which is the energy currency for most energy-requiring processes in cells. They are enclosed by two membranes. The inner membrane is involved in electron transport, and it contains the ATP synthase machinery
Term
How are mitochondria involved in calcium signaling?
 Definition
Mitochondria are involved in calcium signaling and homeostasis, perhaps through activities coordinated with regions the endoplasmic reticulum and plasma membrane, and are important players in driving some mechanisms of apoptotic cell death
Term
Explain outer membrane.
 Definition
The outer mitochondrial membrane contains the protein porin, which forms channels in the membrane. Porin channels allow water, salts, metabolites, and small proteins (up to about 5K) to pass through freely.
Term
What is inter membrane space?
 Definition
The intermembrane space is between the inner and outer membranes. Because the outer mitochondrial membrane is highly permeable, the intermembrane space is essentially continuous with the cytosol.
Term
Explain inner mitochondrial membrane
 Definition
The inner mitochondrial membrane may be extensively folded, forming numerous cristae that effectively increase the surface area available for important membrane proteins that function in the oxidation reactions of the electron transport chain and the ATP synthase that makes ATP (next slide).
Term
Explain inner mitochondrial membrane
 Definition
It is composed of about 70% protein and 30% lipid and contains a specialized lipid called cardiolipin that makes the inner membrane highly impermeable. Cardiolipin (right) has four fatty acid chains and is made up of two phospholipids linked to a third glycerol molecule.
Term
Explain mitochondrial matrix.
 Definition
The mitochondrial matrix is the most interior compartment. It contains high concentrations of enzymes, including those required for the oxidation of pyruvate and fatty acids and for the citric acid cycle.
Term
What drives ATP production?
 Definition
Briefly, electron transport through a series of protein complexes provides the driving force for the pumping of protons (H+) from the mitochondrial matrix to the intermembrane space. This creates both a concentration gradient and an electrical gradient across the inner membrane. In turn, these gradients drive the ATP synthase complex so that ADP + phosphate is converted to ATP.
Term
What is endosymbiotic theory?
 Definition
The top figure illustrates the endosymbiotic theory that mitochondria evolved from bacteria endocytosed by primitive eucaryotic cells over one billion years ago.
Term
What supports this theory?
 Definition
In support of this theory, mitochondria have their own DNA, RNA, and protein synthetic machinery in the mitochondrial matrix. The mitochondrial DNA encodes only a small number of the proteins needed to build a functional mitochondrion and contributes less than 1% of the DNA in the cell (bottom figures)
Term
What is mitochondrial DNA in humans like?
 Definition
In humans, mitochondrial DNA is a simple circular DNA similar to that of procaryotes and lacking histones (with about 2-10 mitochondrial DNA copies per mitochondrion). The observations that the mitochondrial protein synthetic machinery more closely resembles that of bacteria and that mitochondrial ribosomes are sensitive to many antibacterial antibiotics are also consistent with this theory.
Term
How do mutations in mitochondria cause genetic diseases?
 Definition
Mutations in mitochondrial or nuclear genes for mitochondrial proteins cause a variety of diseases by compromising the function of particular mitochondrial complexes.
Term
These diseases include?
 Definition
The list of diseases includes
FBSN-familial bilateral striatal necrosis;
LHON-Leber hereditary optic neuropathy;
MILS-maternally inherited Leigh syndrome;
NARP-neurogenic muscle weakness,
ataxia, retinitis pigmentosa.
Term
are mitochondrial proteins exported?
 Definition
It is thought that none are.
Term
How are proteins imported into mitochondria?
 Definition
Mitochondrial membranes contain a series of protein translocators that import cytosolically synthesized proteins into various compartments of the mitochondrion.
Term
Names of translocators?( don't need to know)
 Definition
he outer membrane has the TOM complex (TOM = translocator of outer membrane) and the SAM complex. The inner membrane has TIM23 (TIM = translocator of inner membrane), TIM22, and OXA complexes.
Term
How are mitochondria inherited? What is inheritance? How does it effect future generations if mutant variations exist?
 Definition
Mitochondrial disease inheritance is non-Mendelian. It is passed from mothers to both sons and daughters, but in the next generation, only the daughter's offspring would be affected. b/c son does not pass on mitochondria to children.
Term
WHat are peroxisomes?
 Definition
Peroxisomes function in the oxidation of long chain fatty acids and other substrates in reactions that produce highly reactive hydrogen peroxide, H2O2.
Term
What is peroxisome enzyme?
 Definition
The peroxisomal enzyme catalase uses this H2O2 to oxidize substances such as phenols and formaldehydes. These oxidation reactions are unique to peroxisomes and differ from the reactions in mitochondria.
Term
How are peroxisomes related to myelin of nerve?
 Definition
Peroxisomes carry out the first step in the synthesis of plasmalogens, the ether lipids abundant in myelin of nerve.
Term
What is membrane around peroxisomes?
 Definition
peroxisomes are surrounded by a single bilayer membrane.
Term
Where are peroxisomes synthesized? What proteins are required?
 Definition
Most peroxisomal enzymes are synthesized on free ribosomes in the cytosol and imported. Unlike mitochondria, which require proteins to be unfolded for import, peroxisomes are able to import folded (even oligomeric) proteins.
Term
What is current model of peroxisome biogenesis?
 Definition
A current model for peroxisome biogenesis suggests that a precursor vesicle containing some peroxisomal proteins buds off from the ER membrane.
Term
What is zwellweger syndrome?
 Definition
Zellweger syndrome is an autosomal recessive genetic disorder caused by mutations in any of several genes involved in the import of peroxisomal proteins/peroxisome biogenesis. It is usually fatal within 6 months of age. Affected individuals have enlarged livers, jaundice, high levels of copper and iron, a lack of muscle tone, glaucoma and vision disturbances and severe retardation, resulting from peroxisome abnormalities.
Term
What are components of ER?
 Definition
The ER membrane creates an internal space, the ER lumen (also called the cisternal space), which may be 10-15% of the total cell volume. The ER membrane physically separates the ER lumen from the cytosol and then selectively regulates the entry and exit of molecules between the ER lumen and the cytosol.
Term
What cells have rough ER? Which have greater amount of smooth?
 Definition
The rough ER is actively involved in protein synthesis, and predominates in most cells. Cells heavily involved in lipid biosynthesis contain a greater amount of smooth ER, such as cells in the adrenal cortex that synthesize steroid hormones from cholesterol and hepatocytes in the liver that function in detoxification.
Term
What are functions of the Endoplasmic Reticulum
 Definition
-Lipid synthesis, exchange and movement(smooth ER)
-Detoxification of lipid soluble compounds(smooth ER)
-Calcium Sequestration(mostly smooth)
-Protein synthesis and processing
Term
Where are lipids synthesized? Why does it have to be done here?
 Definition
The ER membrane synthesizes virtually all major classes of lipids necessary for generating new cell membranes--phospholipids, sphingolipids, cholesterol and steroids.

-Due to the insolubility of lipids, lipid synthesis requires a special environment that is provided by the ER membrane.
Term
Where is the site of lipid synthesis?
 Definition
The cystosolic face of the ER membrane is the site of lipid synthesis.
Term
What aids ER in moving lipids?
 Definition
A scramblase/flippase, or phospholipid translocator, equilibrates phospholipids between the two leaflets of the ER membrane lipid bilayer by flipping phospholipids from the cytosolic to the lumenal half.
Term
What is the smooth ER function?
 Definition
The smooth ER functions to modify a variety of lipid-soluble toxins, including drugs, insecticides, petroleum products, carcinogens and other compounds, converting them to water-soluble derivatives that can be secreted from the cell.
Term
What cytochrome is involved in this? What are the cells in liver called that have significant amount of smooth ER?
 Definition
The cytochrome P450 family of enzymes is involved in these detoxification reactions. Hepatocytes in the liver are actively engaged in detoxification, and also produce lipoprotein particles that carry lipid in the blood. As you might expect, hepatocytes (shown here) have significant amounts of smooth ER.
Term
What does the ER do with Calcium?
 Definition
The ER membrane actively transports calcium from the cytosol, generating a high concentration of calcium ions in the ER lumen, and maintaining a low calcium ion concentration in the cytosol.
Term
Why does the ER store Calcium?
 Definition
It enables cells to regulate physiological processes such as muscle contraction by regulating cytosolic calcium levels (in muscle cells, the ER is “expanded” into the sarcoplasmic reticulum, which specializes in storing and transporting calcium for the purpose of regulating muscle contraction).

-ATPase retakes up calcium against concentration gradient back in to ER where it is available for later contractions.
Term
What produces lipid droplets?
 Definition
ER
Term
What is Rough ER involved in synthesizing?
 Definition
The rough ER is involved in the synthesis of secreted proteins and membrane proteins of the plasma membrane, ER, Golgi complex, intermediate compartments and lysosomes.
Term
Where does all synthesis of proteins occur? and what is the exception?
 Definition
Initially, synthesis of all proteins (translation) begins on ribosomes in the cytosol (one exception, mitochondrial protein synthesis in mitochondria).
Term
What happens as translation proceeds?
 Definition
As translation proceeds, if a signal peptide is translated from a region of the corresponding mRNA, the entire complex of mRNA, ribosomes and newly forming (nascent) polypeptide is brought to a site on the ER membrane. There, translation continues and the nascent polypeptide is transferred (delivered/translocated) across the membrane into the ER lumen. Often, the signal sequence is at the N- terminus, encoding about 20 hydrophobic amino acids (long enough to span a membrane).
Term
Explain how polypepetide gets across the lipid bilayer? Signal?(part 1)
 Definition
Once the signal peptide is translated, it is recognized on the ribosome by the signal recognition particle (SRP), which binds to the growing nascent polypeptide-mRNA-ribosome complex. Translation is interrupted until SRP interacts with its SRP receptor in the ER membrane and the complex is correctly positioned on the ER membrane.
Term
Explain how polypepetide gets across the lipid bilayer? Signal?(part 2)
 Definition
The SRPs (structural model, upper right) are composed of 6 protein subunits and a small RNA. SRPs cycle between the cytosol and the ER membrane, binding to signal sequences on nascent polypeptides and the SRP receptor (an integral membrane protein) in the ER membrane.
Term
Explain how polypepetide gets across the lipid bilayer? Signal?(part 3)
 Definition
When the SRP-ribosome complex binds to the SRP receptor, the interaction then leads to association with a protein translocator complex (translocon) within the ER membrane. The SRP is released, and translation continues, with the growing chain feeding through the translocon in a process of cotranslational transport.
Term
Explain how polypepetide gets across the lipid bilayer? Signal?(part 4)
 Definition
The signal sequence probably triggers the opening of the translocon pore, and the aqueous channel that is created is essentially sealed off from the cytosol by the tight interaction between the ribosome and translocon.
Term
Explain how proteins enter ER?(part 1)
 Definition
Nascent protein elongates through channel in large ribo sub unit.
- once emerges in cytosol Signal recognition protein(SRP) recognizes signal on Nascent protein.

SRP: composed of ribosomes and RNA
Term
Explain how proteins enter ER?(part 2)
 Definition
On ctyostolec surface of membrane there is an interaction with SRP receptor, which ER membrane protein.

-protein translocator becomes positioned in way the protein can be threaded though into Lumen.
Term
What is a translocon?
 Definition
-Provides a channel for deliver across the lipid bilayer into the ER lumen.

-The translocon (protein translocator, sec61 complex) includes several protein complexes that together form an aqueous pore in the membrane through which the newly synthesized polypeptide chain crosses the membrane lipid bilayer.
Term
What happens to ribosome after translocon is complete?
 Definition
When translation is complete and translocation through the translocon comes to an end, the ribosome is released into the cytosol, where it returns to the pool of ribosomes that can be used for the translation of proteins on free or membrane-bound polysomes. The translocon pore closes again at the end of this process.
Term
What ever starts on inside of rough ER lumen ends where?
 Definition
Goes though--> to inside of vesicle--> inside of golgi--> inside vesicle---> outside of cell.(exterior)
Term
Rough endoplasmic continuum is __________ with smooth ER.
 Definition
Continuous
Term
Where does protein synthesis?
 Definition
In cytosol.
Term
Proteins that are being sent to outside of cell or secreted, what happens?
 Definition
Protein translation stops momentarily and brought to cell surface of endoplasmic reticulum. by signal recognition particle.
Term
What happens to signal that brought proteins into ER lumen?
 Definition
The signal is clipped off by signal peptidase.
Term
How are membrane proteins and orientation related to topography?

Where are sugar groups found?
 Definition
Membrane proteins are oriented within the membrane, and display a topology that is established during biosynthesis. The sugar groups on glycoproteins and glycolipids face the exterior (outside) and not the cytosol.
Term
How does orientation effect proteins in membrane of ER?
**integrating single pass transmembrane
 Definition
N termanl start tranfer sequence of protein into membrane and internal stop transfer sequence prevents rest of protein from entering cell. Leaving part in cytosol and part in ER lumen.

**signal can be located in internal protein.(flexible idea)
Term
What happens for multi pass transmembrane proteins?

What is example? What does it do?
 Definition
A series of start and stop transfer signals are used.

Rhodopsin, a plasma membrane protein that functions to process light in the retina, is one such multipass membrane protein.
Term
WHat happens with GPI and some membrane proteins?
 Definition
Some membrane proteins are converted to glycosylphosphatidyl- inositol (GPI) anchored membrane proteins in the ER. A short sequence of amino acids in the lumenal region right next to the transmembrane domain is recognized by an endopeptidase that both cleaves the protein and transfers the remaining exoplasmic region to a preformed GPI anchor contained in the ER membrane.
Term
what does this allow for?
 Definition
This alteration results in the elimination of the cytosolic domain and provides the protein with a GPI anchor that allows it to diffuse in the plane of the lipid bilayer.

**Remember that the inside of the ER lumen corresponds topologically to the outside of the cell; as a result, a mature GPI-anchored protein will face the outside, extracellar environment.
Term
How is asymmetry and orientation of membrane proteins critical for protein function?
 Definition
The asymmetry and orientation of membrane proteins (cytosolic [“inside”]) versus lumenal or extracellular [“outside”]) are critical for protein/cell function. These properties are established by this unique cotranslation- translocation process that utilizes topogenic sequences during the synthesis of transmembrane proteins on the rough ER.
Term
Where does glycosylation begin? What happens?
 Definition
Glycosylation begins in the rER by the addition of N-Asn- linked sugars. N-glycoprotein processing continues in the ER by the removal of 3 terminal glucose residues and one mannose residue.
Term
Where are disulfide bonds found?
 Definition
Disulfide bonds that commonly stabilize tertiary and quaternary structures of noncytosolic proteins are formed in the ER.
Term
Addition of N linked oligosacchardies? What happens?
 Definition
or a protein becoming a glycoprotein with N-linked carbohydrates, the branched (high mannose) carbohydrate structure, which is preformed on a dolichol phosphate intermediate (lower left), is added to sequence-specified Asn residues.
Term
Addition of N linked oligosacchardies? What happens?( what to notice about oligosaccharide)
 Definition
otice that the branched oligosaccharide is positioned toward the lumenal face of the ER membrane so that it can be effectively transferred to the growing polypeptide chain when the Asn appears in the ER lumen.
Term
Why is the oligosaccharide pre branched?
 Definition
The preassembled, branched oligosaccharide is the cell’s solution to the challenge of coordinating the rapid process of translation with the slower process of oligosaccharide chain formation, which uses glyosyltransferases to add one carbohydrate at a time. That initial oligosaccharide structure is modified by the removal and addition of sugars as the glycoprotein progresses through the secretory pathway.


Correct folding of newly synthesized proteins is facilitated by a number of ER proteins, called chaperones.
Term
Explain how cell checks for quality control in protein folding?
 Definition
Protein folding and the assembly of multimeric proteins are critical activities within the ER. Quality control of protein structures is effectively maintained, so that unfolded, misfolded and partly folded and assembled proteins are retained selectively in the ER or returned to the ER by retrieval if they happen to move forward into the cis Golgi. Often, misfolded proteins and unassembled subunits are targeted for degradation (later slide)
Term
What is BIP?
 Definition
BiP [Binding Protein]) assists in folding by binding transiently to new proteins in order to keep them unfolded and prevent misfolding or aggregation.
Term
WHat is Calnexin and Calreticulin?
 Definition
Calnexin and calreticulin are two other homologous ER proteins that promote and monitor folding by cyclical binding to a terminal glucose in N-linked oligosaccharides.
Term
What is PDI?
 Definition
For example, the enzyme protein disulfide isomerase (PDI) catalyzes the formation of disulfide bonds so that the most stable conformation is achieved.
Term
WHat happens sbecuase many chaperones are ER resident proteins?
 Definition
Many chaperones are ER resident proteins, present in the ER at high concentrations and retained by a mechanism that retrieves them if they escape into the cis Golgi. These ER-retained proteins have a C-terminal Lys-Asp-Glu- Leu (KDEL) sequence that is recognized by KDEL receptors
Term
What is cystic fibrosis? What causes it?
 Definition
Cystic fibrosis is a lethal autosomal recessive disease affecting almost 3,000 births each year. Pathogenesis is the result of abnormal ion and water transport that leads to retained secretions and mucus and impaired cellular defense, as outlined above. Epithelia, notably airway epithelia, are affected. The disease is caused by mutations in CFTR , the cystic fibrosis transmembrane conductance regulator. The most common mutation is a phenylalanine deletion, Δ508F, which is found in 70% of CF individuals.
Term
What does mutation cause?
 Definition
The Δ508F mutation interferes with proper folding of CFTR and causes it to be retained in the ER. As a result, CFTR fails to reach the plasma membrane where it is needed to function as a regulated chloride channel. It has been shown that this particular mutated CFTR can function as a channel and therapies based on promoting folding to allow
trafficking to the cell surface are being investigated.
Term
What happens if misfiled protein is released?
 Definition
If proper folding and assembly fail to occur, misfolded proteins may be removed by cellular quality control mechanisms. The ER-associated degradation (ERAD) diagrammed here involves translocation to the cytosol (retrotranslocation, through a modified translocation complex, associated with exit proteins), followed by ubiquitination and proteasomal degradation in the cytosol.
Term
How can ER stress be caused?
 Definition
When proteins accumulate in the ER (particularly when they are misfolded), conditions of ER stress can be created.
Term
What is one response to ER stress?(least severe)
 Definition
One compensatory mechanism is the unfolded protein response (UPR), by which production of chaperones is upregulated through the activation of a unique signaling ER sensor and signal transduction mechanism (to “handle” the excess unfolded protein).
Term
What is sever response to ER stress?
 Definition
Under severe ER stress, an ER overload response (EOR), also involving ER signaling, may trigger upregulation of cytokines, apoptosis or cell death.
Term
Gogi:

Are vesicles regulated?
 Definition
Membrane vesicles and tubules provide the carriers, and are engaged in both delivery and return. The processes of membrane budding and membrane fusion are regulated so that contents are delivered to the correct target.

-vesicles return to membrane
Term
What are three types of coated vesicles?
 Definition
Three types of coated vesicles have been characterized and these differ in their coat proteins and in the transport steps for which they are used.
Term
What are three types of coated vesicles?
 Definition
Clathrin-coated vesicles function in transport between the Golgi apparatus and the plasma membrane, while COPI and COPII-coated vesicles usually cycle between the ER and Golgi cisternae.
Term
How do three different coated vesicles different?
 Definition
Three types of coated vesicles have been characterized and these differ in their coat proteins and in the transport steps for which they are used.
Term
WHat do coats of do to membranes?
 Definition
Clathrin, COPI and COPII coats form vesicles with characteristic properties. Physical properties of the coats deform the membrane to form vesicles
Term
What happens to clatherin coat before becoming a vesicle?
 Definition
The coat forms a curved, basketlike lattice on the cytosolic face that physically deforms the membrane patch into a vesicle and completely encloses the vesicle when it buds off.
Term
What is clatherin coat made of?
 Definition
The polygonal network is assembled from clathrin triskelions.
Term
What is COPI and COPII?
 Definition
TCOPI and COPII coats are on vesicles that transport cargo early in the secretory pathway and clathrin coats carry cargo from the late Golgi through endosome/lysosome/plasma membrane transport steps.
Term
How is the assembly of coats regulated?
What are names?
 Definition
The assembly of coats is regulated by monomeric GTP-binding proteins.

- ARF: Clathrin and COPI 1

-Sar1: COPII
Term
How does vesicle form and bind?
 Definition
When the coat proteins assemble, the membrane curves, forming a vesicle, which next pinches off from the donor membrane. GTP hydrolysis causes the disassembly of the coat--which then exposes the v-SNARE for membrane fusion with the target membrane.
Term
Where is COPII found? Coat proteins? and Associated GTPase?
 Definition
ER to cis golgi:
Sec 23/SEC 24 and Sec 13/ Sec 31
Complexes Sec 16

Associated GTPase; Sar 1
Term
Where is COPI found? Coat proteins? and Associated GTPase?
 Definition
-cis golgi to ER
Coatomers containing seven different COP subunits

Associated GTP ase: ARF
Term
Where is clathrin found? Coat proteins? and Associated GTPase?

Explain trans-golgi ones?
 Definition
Clathrin + AP1 complexes: trans-golgi to endosome:Associated GTP ase: ARF

Clathrin + GGA: trans-golgi to endosome: Associated GTP ase: ARF
Term
Where is clathrin found? Coat proteins? and Associated GTPase?

Explain plasma membrane to endosome?
 Definition
Clathrin + AP2 complexes

Associated GTP ase: ARF
Term
Where is clathrin found? Coat proteins? and Associated GTPase?

Golgi to lysosome, melanosome or platlet vesicles
 Definition
AP3 complex: ARF
Term
Proteins that exit golgi have what vesicles?
 Definition
Proteins that are properly folded and assembled are able to exit the ER and progress to the Golgi apparatus. They are collected and packaged into COPII-coated vesicles at ER exit sites, which are seen in the electron microscope as smooth membrane regions of transitional (part rough, part smooth) ER that form into vesicular-tubular clusters (next slide).
Term
What vesicles form at the ER exit site? What happens to ER resident proteins?
 Definition
The COPII coated vesicles formed at ER exit sites next organize into vesicular tubular clusters that progress to the cis Golgi network (the forming face of the Golgi complex). Meanwhile, ER resident proteins that escape from the ER are retrieved by a return transport mechanism that utilizes COPI-coated vesicles.
Term
What do retreiveal pathways do?
 Definition
Retrieval pathways help to conserve the cell’s proteins and lipids.
Term
HOw id delivery to correct target membranes regulated?
 Definition
-specificity of membrane fusion is controlled by more than 20 different SNARE's.
Associations with specific monomeric Rab GTPases (>30) regulate specificity through the vesicle docking step.
Term
What is structure of golgi?
 Definition
The Golgi apparatus is organized as a series of sequential stacks of disc-shaped cisternae, with distinct cis, medial, and trans compartments.
Term
What is entry and exit?
 Definition
Cis (forming) ---> trans(exit)
Term
What is processing of proteins and lipids by golgi?
 Definition
The Golgi apparatus functions in the sequential processing of (glyco)proteins and lipids by 1) carbohydrate addition, removal and modification and 2) phosphorylation and sulfation.
Term
What happens in trans golgi network?
 Definition
Within the trans Golgi network, molecules are packaged and sorted for delivery to other cellular destinations
Term
How is targeting of lysosomes mediated?
 Definition
Targeting to lysosomes is mediated by a mannose 6-phosphate signal (1).
Term
What is constitutive secretion?
 Definition
In constitutive secretion, also known as the default pathway, molecules are delivered from the Golgi complex in secretory vesicles to the plasma membrane in an ongoing manner, without any regulation of membrane fusion that leads to product release.
Term
What is regulated secretion?
 Definition
In regulated secretion, products are stored in secretory granules and released only upon stimulation by a specific agent.
Term
What is concentration of products in secretary vesicles?
 Definition
Secretory products are segregated and highly concentrated in secretory vesicles. Proteins destined for regulated secretion are sorted and become further concentrated in the trans Golgi network. As secretory vesicles mature, vesicle contents condense further.
Term
How are inactivated zymogens and proteins formed?
 Definition
Some proteins, including polypeptide hormones such as insulin (shown here and in the previous slide), neuropeptides and secreted hydrolytic enzymes, are synthesized as inactive precursors that are later proteolytically cleaved to release active molecules
Term
How are inactivated zymogens and proteins activated?
 Definition
These cleavage events may begin in the trans Golgi network, and can continue in secretory vesicles, or are activated at the time of release.
Term
How is Insulin synthesized?
 Definition
Insulin is synthesized as a proprotein that is cleaved by two endopeptidases (PC2 and PC3) and then by a carboxypeptidase to generate the active insulin hormone
Term
What is function of polarized cells?
 Definition
In such polarized cells, some secretory (and plasma membrane) products are delivered specifically to the apical or basolateral domains of the plasma membrane.
Term
How is structure of golgi maintained?
 Definition
Overall, the structural composition and function of the cis, medial, and trans Golgi cisternae are maintained, despite the active movement of proteins and lipids in both directions. An associated, dynamic matrix scaffold stabilizes the structure of the Golgi apparatus.
Term
What is Phagocytosis?
 Definition
) Phagocytosis: In professional phagocytes, very large particles, degenerating cells, and microorganisms are internalized (last slide) and sent to lysosomes via phagolysosomes.
Term
What is Endocytosis?
 Definition
Endocytosis: This most common and best studied route (to be presented in more detail shortly) takes macromolecules from the extracellular fluid into endocytic vesicles, and then progressively through the endocytic pathway, from early to late endosomes, and then to lysosomes. This process of internalization is also called pinocytosis, translated as “cell drinking.”
Term
What is Autophagy?
 Definition
Autophagy: By this process, old and worn out parts of a cell are sequestered and sent to lysosomes for degradative “recycling.” A mitochondrion and peroxisome are engulfed in a double membrane-bounded structure, the autophagososome, in the lower right transmission electron micrograph.
Term
What is process of lysosome development?
 Definition
Early endosome--> Late Endosome--> Endolysososme--> lysososome
Term
WHat is lysosome? WHat is PH? How is it maintained?
 Definition
Lysosomes are cytoplasmic organelles bounded by a single membrane that contain a wide variety of hydrolytic enzymes. The interior of the lysosome has an acidic pH of about 5, which is maintained by an ATP-dependent proton pump.
Term
How is targeting of lysosome mediated?
 Definition
Targeting to lysosomes (1) is mediated by a mannose 6-phosphate signal, which is added to lysosomal enzymes in the cis Golgi, during their biosynthesis
Term
Are receptors or enzymes recycled in lysosome enzyme delivery?
 Definition
Delivery of lysosomal enzymes uses mannose 6 phosphate signal and clathrin coats and can involved recycling of enzymes and receptors through endosomes the plasma membrane and TGN.
Term
What is I-cell disease?
 Definition
lysosomal storage disease:
In these patients, lysosomal enzymes failed to get the M6P signal because of a defect in the GlcNAc-phosphotransferase. When the mutated enzymes were synthesized, they were secreted instead of being sorted to lysosomes, and they accumulated in the medium.
Term
Explain endocytic pathway?
 Definition
Multidirectional trafficking through the TGN, lysosomes, endosomes & the plasma membrane promotes active exchange among compartments. Trafficking through the endocytic pathway and traffic control is mediated by the molecular machinery of the cell.
Term
Clathrin coated vesicles utilize 4 types of molecules?(part 1)
 Definition
The clathrin-coated vesicle utilizes 4 types of molecules: (1) specific receptors--transmembrane proteins with hydrophilic domains on each side of the membrane; (2) adaptins (AP complex), which recognize both the receptor and clathrin;
Term
Clathrin coated vesicles utilize 4 types of molecules?(part 2)
 Definition
(3) clathrin and (4) dynamin, which is involved in the release of the vesicle from the membrane.
Term
Explain how cells gets cholesterol?
 Definition
When cell needs Cholesterol.
1) cell produces LDL receptors
2)LDL receptors bind adaptins and in trun bind clathrin.
3)LDL taken in by cell mediated endocytosis
4)The LDL is concentrated in clathrin coated pits and bind endosomes.
5) then ends up in lyossomes and degraded into free cholesterol
Term
Clinical consequence of LDL endocytosis?
 Definition
Atherosclerosis: plaque building up
Term
What is familial hypercholesterolemia?
 Definition
f familial hypercholesterolemia, LDL receptors are defective because they lack the cytoplasmic portion that binds to adaptins in the clathrin-coated pits (B). Although LDL binds to the receptor on the extracellular/outside surface of the plasma membrane, without the adaptin binding domain it cannot be concentrated in clathrin-coated pits and cannot be effectively internalized by receptor-mediated endocytosis.
Term
What are Caveolae?
 Definition
Caveolae (meaning “little caves”) were the first endocytic vesicles recognized by electron microscopy.
Term
What is Caveoli?
 Definition
Caveoli are cholesterol- and glycolipid-rich regions--a specialized subset of plasma membrane-associated lipid rafts. GPI-anchored plasma membrane proteins, which include many membrane receptors and signaling molecules, can be concentrated in caveolae, suggesting functions in signal transduction.
Term
What is transcytosis?
 Definition
Transcytosis is a highly specialized process that results in the movement of molecules from the extracellular fluid on one side of a cell to that on the other. This is a common process in highly polarized epithelial cells that line body cavities.
Term
Do virus and toxins use endocytosis?
 Definition
Uptake of viruses and toxins. At least some viruses and AB-toxins, which are composed of an active (A) subunit and multiple binding (B) subunits, use endocytosis to gain entry into a cell.
Term
Where is sulfating accomplished?
 Definition
Sulfation is accomplished in the trans Golgi, trans Golgi network.
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