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Cell Phy 2013 Exam1
Cell Physiology 2013
| Question | Answer |
|---|---|
| Why does the electron microscope have a physical limitation in solution | Due to the wavelength of light. Slices must be thin enough to allow for electrons to pass |
| Key component that defines cell | Membrane bi-layer |
| What is the fundamental purpose of the nucleus? | To separate transcription from translation. Allows for larger amount of regulation |
| Why does the nucleolus stain dark? | Despite high activity, it stains nucleolus stains dark due to ribosome assembly |
| Relation between chromatin density and activity. (heterochromatin vs. euchromatin) | More dense (heterohromatin)is less active. Less dense (euchromatin) is more active. More activity= more protein synthesis |
| Function of nuclear lamina | Regulate assembly and disassembly of nuclear envelope. Organize chromatin |
| What components do all functional chromosomes have? | Centromere, Replication Origin(s) and Telomere |
| Transcription vs. Translation | Transcription: DNA is used to synthesis RNA Translation: RNA is used to synthesis proteins |
| Job and formation of the ribosome. | Synthesizes protein, putting amino acids together. Formed from 2 main RNA chains (rRNA) and about 50 other proteins |
| Role of nuclear pores | These holes in the nuclear envelope transport molecules between the nucleus and cytosol |
| Chromatin | The complex of DNA and protein |
| Relationship between chromosome number and species complexity | None |
| What occurs during interphase? | Chromosomes are replicated |
| What happens during mitosis? | Chromosomes become highly condensed and then are separated and distributed to the two daughter nuclei |
| Chromosome banding | Occurs when chromosomes are digested, then stained |
| Nucleosome | Protein-DNA complex. The "beads"/attached DNA of the "beads and string", that is chromatin |
| What specific parts compose the nucleosome | 2 molecules each of H2A, H2B, H3, and H4 (makes an octomer), as well as double stranded DNA that is 147 BP long |
| 3 functions of non-histone proteins | 1. Structural components of chromatin concerned with higher order compaction of nucleosomes. 2. Enzymes involved in DNA replication, RNA transcription, histone modification,RNA processing 3. Control of gene expression |
| Role of histone tail | They are subject to several different types of covalent modifications that in turn control critical aspects of chromatin structure and function |
| Histone H1 | This linker histone is larger than the individual core histones. It binds to each nucleosome, contacting both DNA and protein, and changes the path of DNA as it exits the nucleosome. Crucial for compacting nucleosomal DNA |
| Relation between structure of chromatin and the expression of genes | Histone modifications attract specific proteins to a stretch of protein that has been appropriately modified. These new proteins determine how and when genes will be expressed, as well as other biological functions |
| The DNA helix makes ____ tight turns around the histone octamer and has the ______ groove compressed on the inside of the turn. | 1.7; minor |
| Form in which 30nm fiber is stacked. | zig-zag |
| Remodeling Complex A vs. B | A: Opens histones in way which allows for addition of DNA-binding proteins B:After gene expression, DNA replication, etc., B leads to disassociation of DNA binding proteins. |
| Miller Spread | Spreading technique for electron microscopic visualization of gently dispersed interphase chromatin. Good for analysis of genetic activities in vivo. It provides a unique view of transcription and RNA processing at the level of individual active genes. |
| What happens when a gene that is normally expressed in euchromatin is experimentally relocated into a region of heterochromatin? | It ceases to be expressed; it is silent. |
| Why does digestion of chromatin usually lead to 147 nucleotide appearance on gel electrophoresis? When does it lead to more? | Wrapped around each histone bead is a 147 nucleotide pair double helix, which provides protection. Depending on strength of digestor, you may get more than 147 due to presence of linker DNA components. |
| DNA S phase and M phase | S phase= 6-8 hour period for DNA replication M phase= Cell mitosis |
| Role of DNA ligase | Join Okazaki fragments (seals nicks) |
| Role of DNA helicase | Pry double stranded DNA apart |
| SSB proteins | Single-Strand DNA-binding proteins. Work to stabilize the unwound, single-stranded conformation of DNA, and prevent DNA from annealing to itself |
| Role of sliding clamp | Keeps DNA polymerase firmly on the DNA when it is moving, and releases it as soon as it runs into a double-stranded region of DNA |
| RNA Pol-alpha | Begins polymerization for leading and lagging strand |
| RNA Pol-delta | Takes over polymerization for lagging strand from Pol-alpha |
| RNA Pol-epsilon | Takes over polymerization for leading strand from Pol-alpha |
| What is the role of topoisomerase? How does topoisomerase I differ form topoisomerase II? | As replication moves along, over-winding occurs. Topoisomerase works to relieve that tension that would otherwise stop replication. I= cuts 1 strand, no energy needed II= cuts both strands, ATP required |
| What nucleotide pairs normally serve as location for replication origin | Regions of DNA high in A-T pairs |
| What begins the process of DNA replication? | Binding of special initiator proteins to the DNA double strand separates strands, allowing for helicase and polymerase to add. |
| When are histones synthesized | Mainly in the S phase, when the level of histone mRNA increases about fiftyfold as a result of increased transcription and decreased mRNA degradation |
| End-replication problem/ solution | Lack of ability to put RNA primer at end of lagging strand= DNA should lose part of its sequence during each replication. Solved by presence of telomeres which serve as buffers to the coding DNA, and telomerase which replenishes telomeres |
| T-loop | Protruding single stranded telomere end of DNA loops back and tucks its terminus into the duplex DNA of the telomeric repeat sequence |
| DNA Proofreading mechanisms | -Correct pairing is already energetically favored -Exonucleolytic proofreading clips out mismatched pairs after the base has been added (3'-5' proofreading) |
| How are errors that escape from the replication machine removed? | Via the strand-directed mismatch repair system which detects the potential for distortion in the DNA helix from the misfit between noncomplementary base pairs |
| Transcription | RNA synthesis. Segment of DNA is copied into mRNA |
| Translation | Protein synthesis. mRNA is translated into specific amino acid sequences (protein) |
| Role of DNA Primase | Synthesizes short (about 10 nucleotides) RNA primers on lagging strand |
| ARS sequences | Autonomously replicating sequence. Contains the orgin of replication in the yeast genome. Very A-T rich which makes for easy separation for replication due to less hydrogen bonding. |
| DNA re-replication | When DNA replicates more than once in single cycle. Very undesirable. Normally blocked by prohibiting origin licensing (event which leads to formation of new replication origins) |
| rRNA | - 70-80% of total RNA - Present in ribosomes - Synthesized in nucleolus |
| tRNA | - single-stranded - large number of unusual bases - clover leaf pattern - at least one species per amino acid |
| mRNA | - about 3-5% of total - translated on ribosomes into proteins - capped at 5' end, and poly-A tail |
| Relation between RNA Polymerases and Amanitin | Poly I= rRNA, not inhibited by Amanitin Poly II= mRNA, strongly inhibited by Amanitin Poly III= tRNA, moderately affected by Amanitin |
| In order for cells to regulate transcription, they must regulate __________ structure | chromatin |
| ___________ __________ dictates direction polymerase operates. | Promoter sequence; always the same for each gene |
| RNA polymerase makes RNA in _______ direction | 5'-3' |
| Reason for "Christmas tree" formation during transcription | Many RNA polymerases are working simultaneously, as mRNA is synthesized between the start and termination signal on DNA (adding to the 3' end),you get increasing lengths |
| As soon as transcription occurs, there are _________ | rearrangements |
| Newly synthesized RNA very quickly associates itself with _________ | Proteins |
| Signal in _______ signals polymerase to cleave and add ___________ __________ | DNA; Poly-A tail |
| Eukaryotes and splicing | Eukaryotes have ability to apply differential splicing of RNA, thereby eliminating 1 gene-1 protein. Multiple proteins can be formed through 2-step splicing mechanism. Sequences= significant |
| How many steps is the splicing mechanism? | 2 |
| From single RNA transcript, how many mRNAs can be generated? | Multiple |
| T/F. All RNA transcripts make it from nucleus to the cytoplasm. | False |
| RNA must __________ to make it from the nucleus to the cytoplasm | Squeeze through a nuclear pore |
| How do RNA Polymerases work? | They catalyze the formation of phosphodiester bonds that link the nucleotides together to form a linear chain. |
| Major difference between DNA and RNA polymerase. | RNA Polymerase can start an RNA chain without a primer |
| How does termination signal stop the elongating polymerase during transcription? | Formation of hairpin actually works to "pull" the RNA transcript from the active site |
| Major difference in RNAs between bacteria and eukaryotes | Eukaryotic nuclei have three RNA Polymerases types, Polymerase I, II, and III |
| Which Polymerase form transcribes the most genes for Eukaryotes? | Poly II |
| 2 main differences in the way in which the bacterial and eukaryotic enzymes function. | 1. Bacterial RNA polymerase requires only a single additional protein (sigma factor for transcription in vitro. Eukaryotes require several (called general transcription factors) 2. Euk. transcription deals with higher order chromatin structure |
| Role of general transcription factors | 1. Help position eucaryotic RNA polymerase correctly at promoter 2.Aid in pulling apart two strands of DNA 3. Release RNA polymerase from promoter into elongation mode once transcription begins |
| Role of elongation factors | Proteins that decrease the likelihood that RNA polymerase will dissociate before it reaches the end of a gene |
| Steps needed for formation of a complete mRNA | Transcription, 5' guanine cap, poly-A tail, and splicing out of introns |
| Possible role for introns | The presence of numerous introns in DNA allows genetic recombination to readily combine the exons of different genes (By spreading them out more, allowing for opportunity to crossover). Also allows for multiple proteins from one gene |
| Spliceosome | The large assembly of RNA (RNA=snRNA=small nuclear RNAs) and protein molecules that performs pre-mRNA splicing in the cell |
| Effective way in which wayward splicing is prevented. | The active site is created only after the assembly and rearrangement of splicing components on a pre-mRNA substrate. |
| Spliceosome catalytic site is formed by ______ moleecules | RNA |
| Enzyme responsible for addition of Poly-A tail. | Poly-A polymerase adds 200 A nucleotides to the 3'end produced by cleavage |
| When is mRNA exported into the cytosol. | Only when the proteins present on an mRNA molecule collectively signify processing was successfully completed. Translation occurs in cytosol |
| Exosome | Large protein complex responsible for degrading improperly processed mRNAs and other mRNA debris |
| hnRNPs | Heteroregenous nuclear ribonuclear proteins. Play an important role in distinguishing mature mRNA from the debris leftover from RNA processing |
| Nuclear pore complexes | Aqueous channels in the nuclear membrane that directly connect the nucleoplasm and cytosol, allowing for successfully processed mRNAs to be transported to the cytosol |
| Most abundant RNA in cell | rRNA |
| Which polymerase produces rRNA? | Poly-I |
| Why can the cell produce adequate quantities of rRNA? | It contains multiple copies of the rRNA genes |
| Role of the nucleolus | It is a ribosome producing factory. rRNAs are chemically modified, cleaved, and assembled into the two ribosomal units |
| The size of the nucleolus reflects what? | The number of ribosomes that the cell is producing |
| RNA Poly- III requires which transcription factor? | 5S |
| 4 Main steps of RNA synthesis | 1. Interaction of RNA polymerase w/ DNA to form binary complex 2.Initiation of RNA chains 3. Elongation (which has 5 of its own substeps) 4.Selective termination |
| How many tRNA's per eukaryote cell? | 100 |
| Nucleolin | An abundant RNA-binding protein apparently only associated with rRNAs |
| Role of nuclear envelope inner and outer membranes | Inner- organizes chromosomes, binds lamina proteins and chromatin Outer- similar and contiguous to ER, ribosomes often present |
| Scheme of nuclear pore | -8 column components -8 annular components -luminal subunits -2 rings on each side -nuclear cage extending into the nucleoplasm |
| Nuclear Localization Signals | Responsible for the selectivity of the active nuclear import process. Protein complex requires these signals in order to be imported into the cell |
| Nuclear Import Receptors | To initiate nuclear import, most nuclear localization signals must be recognized by these receptors |
| Nuclear Export | Works like nuclear import but in reverse. Relies on nuclear export signals on the molecules to be exported, and on complementary nuclear export receptors |
| Ran | Monomeric GTPase which provides the energy needed (via GTP hydrolysis)to import nuclear proteins through the NPC |
| How many conformational states does Ran exist in? | Two states (GAP and GEF), depending on whether GDP or GTP is bound |
| Ran and nuclear gradient | Ran-GAP is located in the cytosol and Ran-GEF is located in the nucleus. This gradient of the two conformational states of Ran drives nuclear transport in the appropriate direction |
| Main way in which cells control transport | Often times cells control transport by regulating nuclear localization and export signals; these can be turned on or off, often by phosphorylation of amino acids close to the signal sequences. |
| Nuclear lamina | Gives shape and stability to the nuclear envelope, to which it is anchored by attachment to both the NPCs and integral membrane proteins of the inner nuclear membrane. Also directly interacts with chromatin. Composed of lamins |
| True or False. Nuclear localization signals are cleaved off after transport into the nucleus. | False. They are not cleaved off. Presumably because nuclear proteins need to be imported repeatedly. |
| Where are the proteins that function in the nucleus synthesized? | In the cytosol; they are then imported |
| Lamins | Make up nuclear lamina. Contain nuclear transport signal and regulate dissolution of nuclear envelope. |
| What is the Translational Machinery | 1.mRNA 2.Aminoacyl-tRNA 3.Ribosomes 4.Soluble Protein Factors |
| tRNA | serves as adaptor molecule that can recognize and bind both to the codon, at another site, the amino acid |
| Where is the amino acid which matches the anti-codon, attached on the tRNA? | 3' end |
| Aminoacyl-tRNA synthetases | Enzyme which controls recognition and attachment of the correct amino acids by coupling each amino acid to its appropriate tRNA |
| Steps for Amino Acid activation | 1. Amino acid is first activated through the linkage of its carboxyl group to AMP (hydrolyzed by ATP) 2.AMP-linked carboxyl group is then transferred to a hydroxyl group on the sugar at the 3' end of the tRNA molecule |
| Hydrolytic editing | tRNA synthetases fix incorrectly attached amino acids by removing their own coupling errors. Selects for amino acids which are wrong but similar to the correct one |
| How is AA binding regulated? | 1. Correct amino acid has the highest affinity for the active-site pocket of its synthetase and is therefore favored 2.Hydrolytic editing |
| On which end of the growing polypeptide chain are amino acids added? | C-terminus |
| Where is protein synthesis carried out? | Ribosome (Complex catalytic machine) |
| Compare and contrast eukaryotic and prokaryotic ribosomes | -Both composed of one large and one small subunit -differences in size exist |
| What's the job of the ribosome small subunit? Large subunit? | Small- provides framework on which the tRNAs can be accurately matched to the codons of the mRNA Large-Catalyzes formation of the peptide bonds that link the amino acids together |
| Describe the ribosomes RNA-binding sites | Each ribosome has one binding site for mRNA an three binding sites for tRNA(A, P, and E sites) (no more than two of these three are occupied at a given time.) |
| What enzyme is responsible for the formation of the peptide bond? | Peptidyl transferase |
| Role of polyribosomes (Polysomes) | Allows for multiple initiations on a given mRNA. Once one is thread and goes for a bit, another ribosome adds on. Allows for creation of more protein in a given time |
| Major steps in initiation of translation | 1.Small ribosomal subunit (followed by initiation factors [eIF]) is bound to mRNA 2.Initiator tRNA moves along mRNA until AUG found 3. Initiation factors dissociation 4. Large ribosomal subunit binds and new tRNA binds to A site 5. Peptide bond formed |
| Major steps in elongation during translation | 1. New RNA binds vacant A-site; old tRNA leaves E-site 2.New peptide bond formed 3.Large subunit translocates relative to small subunit, leaving two tRNAs in hybrid sites 4.Small subunit translocates, bringing its mRNA 3 nucleotides through ribosomes |
| Major steps in termination of translation | 1. Release factor bearing a stop codon binds to A-site 2.Completed polypeptide released |
| How is translational accuracy promoted? | It takes a hefty amount of free energy expenditure. Incorrectly base-paired tRNAs preferentially dissociate, as triggered by GTP hydrolysis |
| Major difference between inhibitors which effect procaryotes only and those which effect eucaryotes only? | Those which effect procaryotes only normally lack the ability to pierce the internal membranes of the eucaryote cell |
| Ubiquitin | Small regulatory protein that has been found in almost all tissues (ubiquitously) of eukaryotic organisms. It directs proteins to compartments in the cell, including the proteasome which destroys and recycles proteins. |
| Methods of regulation of protein synthesis in Eukaryotes | -Control in Reticulocytes by Heme eIF-2-phosphorylation -Phosphorylation of 40s subunit -Polyamines -Selection of specific mRNAs |
| Proteasome | Abundant ATP-dependent protease that deliberately destroys aberrant cell proteins |
| What is the most common result from the tagging of protein by ubiquitin? | Usually results in their destruction by the proteasome |
| What determines how the cell interprets the ubiquitin message? | The number of ubiquitin molecules added and the way in which they are linked together |
| Steps for marking Proteins with Ubiquitin. | 1. ATP catalyzed attachment of ubiquitin to E1 molecule 2.E1 molecule facilitates attachment of ubiq. to E2-E3 complex 3.Target protein binds to complex and ubiquitin added |
| What happens to ubiquitin after the protein is associated with is destroyed or helped. | Ubiquitin is then recycled for further use |
| Co-transitional Protein Folding | Growing polypeptide chain does not achieve its final conformation at the time of release. Instead N-terminal domain is formed first, and while this folds C-terminal is formed (slower process overall) |
| Hsp60 vs Hsp70 | Similarity: Both have affinity for the exposed hydrophobic patches on incompletely folded proteins and hydrolyze ATP Difference: Hsp60=barrel like, acts after protein is synthesized. Hsp70=binds before protein leaves ribosome |
| Lipid Rafts | Specialized domains which are stabilized by proteins. Rafts are thicker than the other layers of the bilayer and better accommodate certain proteins. They are therefore a method to concentrate membrane proteins for transport or assembly |
| Role of membrane proteins | They perform most of the membrane's specific tasks and therefore give each type of cell membrane its characteristic functional properties |
| Cortical Skeleton and Membranes | The cortical cytoskeleton gives membranes mechanical strength and restricts membrane protein diffusion |
| Key differences between lipid rafts and the rest of the plasma membrane | -Lipid rafts contain 3-5 fold the amount of cholesterol found in the surrounding bilayer -Lipid rafts are enriched in sphingolipids -Hydrophobic mismatch at the boundary between the two (due to height mismatch) |
| Role of inositol phospholipids in the cytosolic leaflet of the plasma membrane | Aids in conversion of extracellular signals into intracellular signals. Can do so by either (1) creating docking sites for intracellular signal proteins or (2) cleaving and generating fragments which help to relay the signal into the cell |
| Secretory Pathway | (1) Membrane-bound polyribosomes in ER (2)Transport vesicle (3) Golgi appartus (4)Transport vesicle (5) Extracellular space |
| Methods for proteins to move from one compartment to the next. | Gated transport, transmembrane transport, or vesicular transport. |
| Where are the sorting signals that direct a protein's movement through the compartment system located? | In the protein's amino acid sequence |
| Rough ER | Rough ER: Membrane bound ribosomes, high protein assembly, Proteins are folded in the lumen, protein quality control in lumen,transfers proteins to Golgi for further processing |
| Smooth ER | Smooth ER: More tubular than rough ER, forms separate sealed interconnecting network, works to manufacture and metabolize lipids, production of steroid hormones, detoxification, Ca 2+ homeostasis, degradation of glycogen |
| Differences in density between smooth and rough ER microsomes | Smooth=low density and float on top of centrifuge. Rough=High density and float at middle of centrifuge |
| Major phospholipid made by ER | phosphatidylcholine |
| Where does phospholipid synthesis occur? | Exclusively in the cytosolic leaflets of the ER membranes |
| Steps to synthesize phosphatidylcholine | (1) Fatty acyl CoA catalyzed by acyl transferase, forming phosphatidic acid (2)Phosphatidic acid catalyzed by phosphatase forming diacylglycerol (3)Diacylglycerol catalyzed by choline phosphotransferase forming phosphatidylcholine |
| The role of phospholipid translocators | Because new lipid molecules are added only to the cytosolic half of the bilayer and lipid molecules do not flip spontaneously, a membrane bound phospolipid translocator is required to do the flipping |
| Phospholipid Translocator for ER? For Plasma Membrane? | Scramblase and Flippase respectively |
| Signal hypothesis | The information determining the association of specific ribosomes with ER membranes is contained in the amino terminal segment of the protein: the "Signal Peptide" |
| Steps of the Signal Hypothesis | (1) ER signal seq. emerges from ribosome and leads it to attach to translocator (2)Signal peptidase associated with translocator clips off the signal sequence during translation and the mature protein is released into lumen (3) translocator closes again |
| The two types of translocation | Co-tranlational translocation (importation of protein before complete synthesis) Post-translational translocation (Importation of protein after synthesis) |
| Membrane bound rinosomes | When attached to the ER, polyribosomes have permanently bound mRNA molecules. Ribosomes are bound to membrane as well but move and get recycled |
| Components involved in ER signal sequence guidance to the ER membrane? | Via at least two components: a signal-recognition particle (SRP), which cycles between the ER membrane and the cytosol and binds to the signal sequence, and an SRP receptor in the ER membrane |
| Steps for ER signal sequences and SRP to direct ribosomes to ER membrane | (1) Binding of SRP to signal peptide causes a pause in translation (2) SRP-bound ribosome attaches to SRP receptor in ER membrane (3) Translation continues and translocation begins (4)SRP and SRP receptor displaced and recycled |
| Translocation | Importation of protein into ER lumen |
| How is a soluble secretory protein translocated across the ER membrane? | Dual recognition. Translocator opens pore allowing the transfer of the polypeptide chain across the lipid bilayer loop. After translocation, pore closes then translocator opens laterally. Hydrophobic signal sequence diffuses into bilayer and degrades |
| Types of transmembrane proteins that can be integrated into the ER membrane | (1) Single-pass transmembrane protein cleaved w/ cleaved signal sequence (2) Double-pass transmembrane protein (3) Single-pass transmembrane protein w/ internal signal sequence |
| Co- and Post-translational Modifications of Proteins in RER | (1) Bulk transfer of mannose and glucose-rich oligosaccharides from lipid-linked intermediates to asparagine residues (2) Cleavage of signal sequences (3) Catalysis of disulfide bond formation (4) Hydroxylation of pro and lys residues (collagens) |
| How are most proteins synthesized inthe RER glycosylated? | Via the addition of a common N-linked oligosaccharide to the Asn of a growing polypeptide chain during translocation |
| Calnexin | ER-membrane-bound chaperone protein which binds incompletely folded proteins containing one terminal glucose on N-linked oligosaccharide. Removign terminal glucose, removes calnexin attachment |
| Degradation of misfolded ER proteins | Once misfolded, protein exits ER lumen via an accessory exit protein which opens the ER protein translocator. The protein is then bound by ubiquitin and degraded by a proteasome |
| How are incorrect disulfide bonds repaired on the protein within the ER lumen? | Via protein disulfide isomerase |
| Steps to signal chaperone of misfolded ER protein | (1) Misfolded proteins in ER signal need for chaperones (2)Activated kinase turns into an endoribonuclease (3)Endoribonuclease cuts specific RNA molecule which becomes mRNA (4)mRNA leads to gene reg protein which enters nucleus and activates ER Chap ge |
| How are proteins bound to ER membrane? | Via a GPI anchor which attaches after the protein C-terminal peptide is cleaved |
| Relationship between SER and carcinogens | SER actually activates carcinogens via oxidation reactions |
| All cell membrane lipids orginate in the _______ | Smooth ER |
| Free and bound ribosomes are biochemically and structurally __________ | indistinguishable |
| SSR cycle occurs during _______ ________ | every cycle |
| Ran-GTPase acts as a _______ _______ for chromatin during cell division | positional marker |
| Role of inhibitory cytosilic proteins | Anchor gene reg. proteins to the cytosol or mask localization signals |
| How is it ensured that only completed antibodies leave the ER? | The chaperone BiP is thought to bind to all incompletely assembled antibody molecules and to cover upa n exit signal. |
| Role of the Golgi Apparatus | (1) Synthesis of glycoproteins and glycolipids (2)Proteolutic processing of preproteins (3)Packaging of lipoproteins and secretion granules (4)Membrane biogenesis (5)Recycling surface membrane components |
| Vesicular-tubular clusters | ER-Golgi Salvage/ Intermediate compartment Located between the ER and the Golgi, this compartment mediates trafficking between the ER and Golgi complex, facilitating the sorting of cargo. Retrieves intrinsic ER proteins and cycles receptors |
| How are Vesicular-tubular clusters formed? | When ER-derived vesicles fuse with one another. |
| The retreival pathway for returning escaped proteins back to the ER depends on __________________ | ER retrieval signals |
| Method in which proteins are selectively retained in the compartments in which they function. | ER resident proteins bind to one another, thus forming complexes that are too big to enter transport vesicles efficiently |
| Main Golgi compartments | Trans Golgi Network, Golgi Stack (trans cisterna, medial cisterna, cis cisterna) and the cis Golgi network |
| Role of the "Trans Golgi Network" | Has secretory vesicles and sends modified molecules to lysosome, plasma membrane, or to secretory vesicle. Deals with sulfation of tyrosines and carbohydrates |
| What side of Golgi faces faces ER? | The cis face of the Golgi stack is that closest to the ER |
| Role of cis Golgi network | Receives vesicular-tubular clusters from ER and sorts them. Deals with Phosphorylation of oligosaccharides on lysosomal proteins |
| What takes place in cis cisterna? | Removal of Man |
| What takes place in medial cisterna? | Removal of Man and addition of GlcNAc |
| What takes place in trans cisterna? | Addition of Gal and NANA |
| The main classes of asparagine-linked (N-linked) oligosaccharides found in mature mammalian glycoproteins | Complex oligosaccharides and high-mannose oligosaccharides (they possess the same core region) |
| What determines if the oligosaccharide is converted to the complex form? | IF it is accessible to the processing enzymes in the Golgi, it will likely convert. If it's inaccessible, it'll probably remain in a high-mannose form |
| What happens after the yielding of the final core of three mannoses that is present in a complex oligosaccharide | The bond between the two N-acetylglucosamines in the core becomes resistant to attack by a highly specific endoglycosidase (Endo H) |
| How does the Golgi differ fundamentally from the ER as a biosynthetic organelle? | For the Golgi, all sugars are assembled inside the lumen from sugar nucleotides. For the ER, N-linked precursor oligosaccharide begins assembly in the cytosol and finishes in the lumen |
| When does concentration of secretory products occur? | Occurs both during movement through Golgi complex and during secretory granule maturation |
| T/F Concentration of secretory products occurs in all cells. | False, not in collagen or immunoglobulins |
| T/F Concentration of secretory products is not dependent on expenditure of energy | True |
| What defines the maturity of a Golgi secretory vesicle? | Increasing cargo concentration. At its most mature point, there is maximum concentration of secretory proteins |
| What ion plays most critical roles in exocytosis? | Ca 2+ |
| 5 main steps of exocytosis of secretory products | (1)Stimulation by secretagogues (2) Movement of secretory granule to plasma membrane (microtubules likely involved) (3)Fusion of secretory granules with plasma membrane (4) Fission of fused membrane (5) Discharge of content of granules |
| Docking vs Fusion of vesicle | Docking is when vesicle membrane first encounters the main membrane. Fusion is when it actually meshes with the main membrane and releases its contents |
| Main functions of lysosomes | Intracellular digestion, turnover of cell components, removal of material during developmental processes, release of enzymes for medium extracellular action, involvement in thyroid hormone release, fertilization, role in storage disease |
| Lipofuscin pigment granules | The product of the oxidation of unsaturated fatty acids, these pigment granules are composed of lipid-containing residues of lysosomal digestion |
| Lysosome pH as opposed to cytoplasm pH | 5 vs 7.2 |
| How does Trans Golgi Network know where to send proteins for autodigestion | Lysosome Hydrolases are marked with mannose 6-phosphate (MSP receptors) |
| Process of delivery of lysosome enzymes to lysosome | Hydrolase precursor made formed in Golgi and marked with covered M6P. An enzyme binds GlcNAc and then cleaves it, exposing M6P. M6P receptor dependent transport commences and vesicle with inactive enzymes binds to high acidity lysosome |
| What type of membrane does autophagy have? | Double membrane |
| Key function and components of peroxisomes | Consumes lots of oxygen, and performs oxidation rxns to break down some molecules (ex. fatty acids), role in myelination Components-(1) Particles rich in peroxidase, catalase, D amino-acid oxidase, urate oxidase (2) In many tissues contain Nucleosids |
| Peroxisome proliferation | Peroxisomes have proteins on their exterior which catalyze protein import. Specific peroxisome related proteins are brought into peroxisome which provides for ample supply for fission. Fission occurs and two daughter cells formed. |
| Where does peroxisome precursor vesicle originate from? | ER |
| Endocytosis | General term applied to uptake fluid, specific chemicals, and particles by cells |
| Caveolae | Deep invaginations which form pinocytic vesicles |
| Potocytosis | Type of receptor-mediated endocytosis in which small molecules are transported across the plasma membrane of a cell. The molecules are transported by caveolae (rather than clathrin-coated vesicles) and are deposited directly into the cytosol. |
| Receptor-mediated endocytosis | Macromolecules bind to complementary transmembrane receptor proteins, accumulate in coated pits, and then enter the cell as receptor-macromolecule complexes in clathrin-coated vesicles |
| Clathrin-coated pits | Begin endocytic part of endocytic-exocytic cycle. Pit that quickly invaginates. |
| Exocytosis Process | Cargo molecules bind cargo receptors, drawing in adaptin and clathrin. Bud is formed in the plasma membrane and eventually vesicle is formed. Dynamin cuts off passage back to the cell body and vesicles floats off. Clathrin disassociates |
| What triggers phagocytosis? | Binding of molecule to extracellular receptors |
| Where/ how can proteins move after the TGN | (1) Signal mediated diversion to lysosomes (2) Signal mediated diversion to secretory vesicles [regulated secretion] (3)Constitutive secretory pathway |
| Receptor-mediated endocytosis of LDL | (1) LDL binds to LDL receptor, vesicle formed and floats into cytosol (2) Vesicle fuses with early endosome, and disassociates from LDL receptor (3) Movement from early endosome to lysosome. Receptors are recycled |
| Coat for vesicles leaving ER | COPII |
| Where do clathrin, COPI and COPII operate? | clathrin- TGN and plasma membrane COPI- Golgi (including TGN), early endosome COPII- ER |
| Role of Rab and SNARE | Ensure specificity in targeting because they are surface markers which are displayed and identify each transport vesicle according to their origin and type of cargo membrane. Target membranes have complementary receptors. |
| Rab vs. SNARE | Rab direct the vesicle to specific spots on the correct target membrane, and then SNARE proteins mediate the fusion of the lipid bilayers. |
| In contrast to the structure of the Rab proteins, Rab effector structure... | Is not highly conserved; it varies greatly |
| How do SNAREs provide an additional layer of specificity to the transport process? | They help to ensure that only correctly targeted vesicles fuse |
| In the cell, other proteins recruited to the fusion site, presumably Rab effectors, cooperate with SNAREs to... | Accelerate fusion |
| V-SNAREs vs T-SNAREs | V=vesicle T=target |
| Role of NSF | After a v-SNARE and t-SNARE have mediated the fusion of a transport vesicle on a target membrane, the NSF binds to the SNARE complex and, with the help of 2 accessory proteins, hydrolyzes ATP to pry the SNAREs apart |
| Where does GTP hydrolysis occur in docking, fusion etc. of a transport vesicle? | After membrane fusion, in process of forming the GDP dissociation inhibitor (GDI) |
| Sorting of membrane enzymes in TGN occurs how? What about in endosomes? | (1)Direct sorting of membrane proteins (Indirect sorting of membrane proteins |
| Name one location with a huge concentration of mitochondria. | Retinal cells |
| T/F There are ribosomes in the mitochondria | True |
| Length of Mitochondrial DNA/ Max coding capacity | 15-17 kb pairs/ 5000 amino acids |
| How much of their own proteins do mitochondria code for? | A handful. The rest are coded for by nuclear DNA |
| Differences between chloroplasts and mitochondria in regards to lipids | Mitochondria import most of their lipids. Chloroplasts synthesize most of their own |
| Role of phospholipid exchange proteins | Move phospholipids of the bi-layer from the ER membrane to the mitochondrial membrane |
| Mitochondria only contribute ____, ____, and ____ to its genetic system. All other genetic proteins are a result of ... | mRNA, tRNA, and rRNA. coding from the nucleus and importation from the cytosol |
| Process of protein importation into mitochondrial matrix | (1)binding signal sequence on protein to receptor TOM complex (2)Insertion into membrane through TOM complex and into matrix through TIM23 complex (3)Cleavage of signal peptide |
| Methods in in which protein is imported into mitochondrial inner membrane or intermembrane space | (1)TOM translocator, (2)full importation into matrix followed by binding to OXA complex on inner membrane (3)importation just into space directly, followed by protease cleavage (4)intermembrane space chaperones +TIM22 complex |
| 2 main stages of ATP formation | (1) ETC drives pump which forms H+ gradient (2) H+ flow back into matrix drives ADP phosphorylation via ATP synthase |
| What forces drive pyruvate import, phosphate import and ADP-ATP exchange? | pH gradients for the imports. Voltage gradient for the exchange |
| The redox potential ______ as electrons flow down the respiratory chain to oxygen | Increases |
| How do myofibers become multinucleated? | Fusion of myoblasts |
| Hierarchy of muscle components | Muscle , Myofiber bundles, myofiber, myofibril |
| Dark and light part of muscle | Dark= A-band (which includes M-line and H-band), Light= I-band (which includes Z-band) |
| For each electron that moves through the ETC, how many protons are pumped? | 1 |
| How does electron move from one complex to the next in ETC | Ubiquinone and cytochrome 1 |
| How many protons must move through ATP synthase in order for an ATP to be made? | 3 |
| Membrane proteins for ETC | NADH complex, cytochrome b-c1 complex, cytochrome oxidase complex |
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