Cell Bio Exam 4

Describe the types of molecules transported by nuclear export receptors.

RNA, mRNA, and the ribosomal subunit sections made of RNA

Name several uses for the metabolite pyruvate

- pyruvate dehydrogenase complex uses pyruvate to produce acetyl CoA - During fermentation, lactate dehydrogenase converts pyruvate to lactate Pyruvate is converted to the amino acid alanine - Pyruvate is converted into oxyloacetate In short pyruvate is converted into: alanine, acetyl-CoA, ethanol, lactate, and oxyloacetate

Identify the three reactions in glycolysis that are so energetically favorable that they are effectively irreversible, and review how gluconeogenesis circumvents these steps to convert pyruvate into glucose.

1,3,10 (everything w/ ATP). To circumvent this, Gluconeogenesis uses different enzymes to circumvent this and more energy to do it. The enzyme phosphofructokinase catalyzes the phosphorylation of fructose-6-phosphate to form fructose 1,6-bisphosphate in step 3 of glycolysis. This reaction is so energetically favorable that the enzyme will not work in reverse. To produce fructose 6-phosphate during during gluconeogenesis, the enzyme fructose 1,6-bisphophatase removes the phosphate from fructose 1,6-bisphosphate in a simple hydrolysis reaction. Coordinated feedback regulation of these two enzymes helps a cell control the flow of metabolites toward glucose synthesis or glucose breakdown. Another path of regulation is through allosteric regulation by metabolites (products). Products bind to sites that are not active sites

List the end products of glycolysis

2 ATP, 2 pyruvate, 2 NADH

List the activated carriers produced for each molecule of acetyl CoA that enters the citric acid cycle

3 NADH, 1 FADH2, 1 GTP (eventually becomes ATP) per turn

Identify the molecule that serves as the main source of chemical energy in a cell

ATP

Identify the molecules that provide the energy to convert carbon dioxide into sugars.

ATP and NADPH

Present the reactions by which ATP is generated by the substrate-level phosphorylation in steps 7 and 10 of glycolysis

ATP is produced in step seven when one of the phosphates on 1,3-bisphosphoglycerate is removed and added to a molecule of ADP to produce ATP and 3-phosphoglycerate. The enzyme that catalyzes this reaction is phosphoglycerate kinase. In other words: Step 7 is the transfer to ADP of the high-energy phosphate group that was generated in step 6 forms ATP. In a long explaination: the newly formed high-energy phosphate bond in 1,3-bisphosphoglycerate is transferred to ADP, forming a molecule of ATP and leaving a free carboxylic acid group on the oxidized sugar. Step 10 is the transfer to ADP of the high-energy phosphate group that was generated in step 9 forms ATP, completing glycolysis.

Differentiate between the mechanisms of ATP production by glycolysis and by oxidative phosphorylation

ATP production from glycolysis can occur in aerobic and anaerobic organisms within the cytosol. While oxidative phosphorylation occurs in the mitochondria and only occurs in organisms that can use a terminal electron acceptor and an electron transport chain and it requires a membrane-bound compartment. In eukaryotic cells, oxidative phosphorylation takes place in the mitochondria, and it depends on an electron-transmport process that drives the transport of protons (H+) across the inner mitochondrial membrane. ATP production in oxidative phosphorylation produces around 30 molecules of ATP while glycolysis alone only produces 2 net ATP.

Describe the consequence of phosphorylating glucose in the first step of glycolysis

By phosphorylating glucose in the first step by hexokinase, it cannot leave the membrane. It is trapped in the cell. As a result, this keeps the concentration gradient for glucose entering the cell favorable.

State where the citric acid cycle takes place in animal cells, in plant cells, and in prokaryotes

Animal cells - mitochondria Plant cells - mitochondria Prokaryotes - cytosol (TCA only takes place in aerobic bacteria or bacteria that can use other terminal electron acceptors)

Summarize how electron carriers are able to transfer a proton from one side of the membrane to the other

As an electron passes along an electron-transport chain, it can bind and release a proton at each step. Let's say an electron carrier, protein B, picks up a proton (H+) from one side of the membrane when it accepts an electron (e-) from protein A; protein B releases the proton to the proton to the other side of the membrane when it donates its electron to the electron carrier, protein C. In this example, the transfer of a single electron thereby pumps the equivalent of one protein across a membrane.

Outline how conformational change in cytochrome c oxidase pumps protons across the inner mitochondrial membrane.

As the electron hits whatever is holding it (sulfur ion cluster) which (add to this) The confirmation changes creates a proton wire (Residues brought close to one another that can transfer protons. In other words: Pumping occurs because the transfer of electrons drives allosteric changes in the conformation of cytochrome c oxidase that cause protons to be ejected from the mitochondrial matrix. Cytochrome c oxidase is the final electron carrier in the respiratory chain which has the highest redox potential of all. This protein complex removes electrons from cytochrome c, thereby oxidizing it-hence the name "cytochrome c oxidase". The exceptionally high electron affinity stems in part from a special oxygen-binding site within cytochrome c oxidase that contains a heme group plus a copper atom. It is here that nearly all the oxygen we breathe is consume. When the electrons that had been donated by NADH at the start of the electron transport chain are handed off to O2 to produce H2O.

Summarize why cells need enzymes to maximize the energy that can be harvested from the oxidation of a fuel molecule such as glucose

Because they need to be broken down into smaller pieces to extract as much energy from them as possible. Enzymes are needed because they allow for a large amount of energy to be harvested over a series of small reactions and this allows that energy to be useful for the cell. Without the enzymes, most of the energy from a reaction like oxidation of glucose being done in one step would be released as heat.

Summarize how clathrin-coated vesicles select their cargo molecules and then bud from their parent membranes.

Bud from parents by starting off as a clathrin-coated pit; then shapes itself into a vesicle; a GTP-binding protein called dynamin constricts the vesicle and pinches it off from the parent membrane Select their molecules by a second class of coat proteins called adaptins; adaptins help capture specific cargo molecules by trapping the cargo receptors that bind them Basically, adaptins see a receptor and bind the molecules they want the clathrin-coated vesicles to carry

Express the ratio at which cells maintain the concentrations of ATP and ADP, and state how cyanide works to upset this balance.

Cells maintain a ratio with a very high ATP concentration and a small ADP concentration, keeps the hydrolysis of ATP favorable 10 ATP: 1 ADP Cyanide disrupts the electron transport chain and halts the generation of the proton gradient and ATP synthesis

Present two strategies cells use to isolate and organize their various chemical reactions, and identify which approach is more highly developed in eukaryotes than in prokaryotes.

Cells use specific organelles that have membranes to keep chemical reactions contained inside that organelle. This method is more developed in eukaryotes because prokaryotes do not have membrane-bound organelles Attachment to the cytoskeleton is the second strategy. It is used by both prokaryotes and eukaryotes

Describe the structure of a chloroplast and indicate the functions of its membranes and compartments, including where chlorophyll and the photosynthetic machinery are contained.

Chloroplast are larger than mitochondria. They have a highly permeable outer membrane and a much less permeable inner membrane in which various membrane transport proteins are embedded. Together these two membranes form the chloroplast envelope, separated by a narrow intermembrane space. The inner membrane surrounds a large space called the stroma, which contains many metabolic enzymes and is analogous to the mitochondrial matrix. One difference between the chloroplast and mitochondria is that the inner membrane of the chloroplast does not contain the molecular machinery needed to produce energy. Instead, the light-capturing systems, electron-transport chain and ATP synthase that convert light energy into ATP during photosynthesis are all contain in the thylakoid membrane. This third membrane is folded to form a set of flattened, disclike sacs, called the thylakoids, which are arranged in stacks called grana. The interior of each thylakoid is thought be be connected with that of other thylakoids creating the thylakoid space-a compartment that is separate from the chloroplast stroma.

Contrast the constitutive and regulated exocytosis pathways, and describe the behavior of the proteins secreted by each pathway.

Constitutive exocytosis pathway - is used by the cell to deliver new components of the plasma membrane to it as well as to deliver soluble proteins that may be released into the extracellular matrix to nourish other cells or to become a part of the extracellular matrix Regulated exocytosis pathway - is used to release molecules into the extracellular space in response to an extracellular signal. This pathway allows for aggregation of vesicles containing the molecule to gather along the plasma membrane before they are signaled to be released. The molecules in these secretory vesicles fuse with the plasma membrane to release their contents.

Review how the use of malonate, which inhibits the enzyme succinate dehydrogenase, revealed the cyclical nature of the citric acid cycle

Cycle: A -> B -> C - > A -> B -> C. You have a block at B, so you know it is a cycle if A is made when a block is added between A and B and A still builds up after the addition of C.

Distinguish between free ribosomes and membrane-bound ribosomes.

Differ in the proteins they are making at any given time Free ribosomes - unattached to any membrane; make what proteins the membrane-bound ribosomes aren't making Membrane-bound ribosomes - attached t the cytosolic side of the ER; make proteins that are being translocated into the ER

Summarize the amount of ATP energy invested and the amount recouped during the breakdown of a glucose molecules during glycolysis

During the investment stage of glycolysis, 2 ATP are invested. The first ATP is invested to phosphorylate glucose and the second is invested when it is used to add a second phosphate to frutocose-6-phosphate. Then during the payoff stage 4 ATP are produced. Two are produced from each glyceraldehyde-3-phosphate that is produced from the end of stage 1 of glycolysis. As a result, the net ATP formed from glycolysis is 2.

List the membrane-bound organelles that can receive proteins directly from the cytosol.

ER, Nucleus, mitochondria

Name the organelle that serves as an entry point for proteins destined for all organelles or for the cell surface.

ER, allows the necessary protein to be put into a vesicle so that it can enter the Golgi apparatus

List the organelles that form the endomembrane system and review how the interiors of these organelles communicate with one another and with the cell exterior.

ER, golgi apparatus, peroxisomes, endosomes, nucleus, and lysosomes They communicate via vesicles, also through direct contact, and the presence of signal sequences on their proteins

List the components of a photosystem

Each photosystem consists of a set of antenna complexes, which capture light energy, and reaction center, which converts that light energy into chemical energy.

Summarize how the regulation of phosphofructokinase and fructose 1,6-bisphophatase control whether glucose will be synthesized or oxidized.

Either phosphofructokinase in on and fructose 1,6-bisphosphate is off or vice versa. 1,6 bisphosphatase is inhibited by low levels of ATP and phosphofructokinase is activated by low levels ATP. Phosphofructokinase is inhibited by high levels of ATP and turn the enzyme off. Fructose 1,6 bisphosphate is inhibited by low levels to leads to production of more glucose. In other words: Phosphofructosekinase is activated by by-products of ATP hydrolysis-including ADP, AMP, and inorganic phosphate-and it is inhibited by ATP. thus, when ATP is depleted and its metabolic by-products accumulate, phosphofructokinase is turned on and glycolysis proceeds, generating ATP; when ATP is abundant, the enzyme is turned off and glycolysis shuts down. The enzyme that catalyzes the rever reaction during gluconeogenesis, fructose 1,6-bisphosphatase is regulated by the same molecules but in the opposite direction. This enzyme is thus activated when phosphofructokinase is turned off, allowing gluconeogenesis to proceed. Another path of regulation is through allosteric regulation by metabolites (products). Products bind to sites that are not active sites

List the major membrane-enclosed organelles of the eukaryotic cell and briefly describe the function of each.

Endosomes - sorting of enclosed material ER - synthesis of lipids; synthesis of proteins for membrane and to some organelles Golgi apparatus - modification and packaging of proteins and lipids Peroxisomes - oxidative breakdown of toxic molecules; Lysosomes - intracellular degradation; digest materials within the cell

Contrast the endocytic and exocytic pathways in terms of directionality, purpose, and participation of certain organelles and membranes.

Exocytosis - removing molecules from the cell, uses endosomes, used to remove foreign or unwanted particles or moving molecules to the extracellular matrix (adding polysaccharides to membrane proteins) Endocytosis - bringing foreign molecules into the cell, uses endosomes, the Golgi apparatus if staying in the cell, or the lysosome if being broken down. Used to bring molecules into the cell for degradation or incorporations

Recall the function and fate of the protein coat that surrounds transport vesicles.

Function: helps shape the membrane into a bud and captures molecules for onward transport Fate: it is shed once the vesicle leaves the cell

List three categories of food molecules that can serve as energy sources for cells, and identify the sugar whose breakdown generates most of the energy produced by the majority of animal cells

Proteins (amino acids), Polysaccharides (simple sugars), and Fats -lipids (fatty acids and glycerol). Glucose is the sugar that generates the most energy

Review how pyruvate and fatty acids move from the cytosol to the mitochondrial matrix, and identify the metabolic intermediate into which both are converted before entering the citric acid cycle.

Glucose is converted to pyruvate before it enters the mitochondria Fats are broken down to fatty acids, delivered to the mitochondria, and converted to Acetyl-CoA once inside the mitochondria. In other words: In animal cells and other eukaryotes, pyruvate produced during glycolysis and fatty acids derived from the breakdown of fats enter the mitochondrian from the cytosol. Once inside the mitochondrial matrix, both of these food-derived molecules are converted to acetyl CoA and then oxidized to CO2.

Compare the number of ATP molecules generated by glycolysis with the number produced by the complete oxidation of glucose to water and carbon dioxide.

Glycolysis alone generates a net of 2 ATP. Complete oxidation of glucose generates about 30 ATP.

List the types of covalent modifications that take place in the ER and describe the functions these modifications serve.

Glycosylation: when proteins enter the ER lumen or ER membrane are converted to glycoproteins in the ER by the covalent attachment of short, branched oligosaccharide side chain composed of multiple sugars. This process is carried out by glycosylating enzymes present in the ER but not in the cytosol. In other words: Glycosylation - adds oligosaccharides to proteins that will be transported to the glycolax to play a role in cell-cell recognition, to protect the protein from degradation, to keep the protein in the ER until it is properly folded, or by ensuring it is transported to the correct organelle or location by acting as a signal sequence. Formation of disulfide bonds - help stabilize protein structure

Compare the redox potentials of components in the electron transport chain and state which way electrons will flow.

Goes from low electron affinity to high. The lower the redox potential, the lower the molecules' affinity for electrons-and the more likely they are to act as electron donors. Redox potential are expressed in units of volts. Electrons will move spontaneously from a redox pari with a lox redox potential (or low affinity for electrons), such as NADH/NAD+, to a redox pair with a high rex potential (or high affinity for electrons), such as O2/H2O

Describe the conditions under which ATP synthase will act as a proton pump and hydrolyze ATP.

If the gradient is switched everything will be reversed. If reverse ATP synthase can turn into an ATP hydrolase, which means it will generate ADP and inorganic phosphate from ATP

Explain why NADH does not donate its electrons directly to molecular oxygen in living systems.

In Short: It would be a waste of energy The energy release would be damaging for the cell He may ask us Arrange the order of the electron path Figure 14-14

Compare where mitochondria are located in a heart muscle cell, sperm, and fibroblast.

In cardiac muscle cells, mitochondria are located close to the contractile apparatus, ATP hydrolysis provides the energy for contraction. In a sperm, mitochondria are located in the tail, wrapped around a portion of the motile flagellar that requires ATP for its movement. Fibroblast it's by the RER due to excreted protein production. Overall, mitochondria are present in the area that the cell requires the most energy and is most metabolically active.

Summarize the ramifications of metabolites being substrates for a number of different enzymes

In short, you get substrate competition.

Summarize how the energy supplied by GTP is used to drive nuclear transport.

In short: Ran-GTP binds to the import receptor once it enters the nucleus, causing the receptor to release the protein into the nucleus. With Ran-GTP still bound, it travels out of the cell with the import receptor where Ran-GAP binds to Ran-GTP, causing it to hydrolyze its GTP to GDP, transforming it to Ran-GDP. Ran-GDP releases the import receptor, which is ready to pick up the next protein. Ran- GTP gets transported back into the nucleus where Ran-GEF binds to it, causing it release its GDP and bind a GTP, converting it back into RNA-GTP

Recall how proteins destined to function in the ER are kept in the ER—or returned to the ER if they accidentally enter the Golgi apparatus.

Proteins destined to function in the ER are retained in the ER because of the ER signal sequence that they contain. If these proteins manage to escape to the Golgi, the Golgi recognizes that sequence and sends the protein back to the ER.

Summarize the stages involved in generating ATP by oxidative phosphorylation.

In short: The stages are generation of electron carriers, electrons are donated to an electron transport chain to generate a proton gradient, and then the proton gradient is used by an ATP synthase to generate ATP. In more words: This membrane-based process for making ATP consists of two linked stages: one sets up an electrochemical proton gradient, and the other uses that gradient to generate ATP. Both stages are carried out by special protein complexes embedded in a membrane. 1. In stage 1, high-energy electrons-derived from the oxidation of food molecules or from sunlight or other chemcial sources are transferred along a series of electron carriers, called an electron transport chain, embedded in a membrane. These electron transfers release energy that is used to pump protons, derived from the water that is ubiquitous in cells, across the membrane and thus generate an electrochemical proton gradient. An ion gradient across a membrane is a form of stored energy that can be harnessed to do useful work when the ions are allowed to flow back across the membrane, down their electrochemical gradient. In stage 2, protons flow back down their electrochemical gradient through a membrane-embedded protein complex called ATP synthase, which catalyzes the energy-requiring synthesis of ATP from ADP and inorganic phosphate (Pi). This ubiquitous enzyme functions like a turbine that couples the movement of protons across the membrane to the production of ATP.

Contrast the fermentation pathway in an oxygen-starved muscle cell with the pathway in a yeast cell that is growing anaerobically.

In short: ethanol fermentation produces CO2. Whereas, we do not produce CO2. The oxygen starved cell will use fermentation to make lactate acid to produce NAD+. Unlike the yeast cell who will produce NAD+, alcohol (ethanol) and CO2. We do not produce CO2.

Review how glycogen synthesis and breakdown is coordinated by feedback regulation.

In short: high level ATP will stimulate glycogen synthesis and high levels of ADP will stimulate glycogen breakdown (replaces energy you don't have)

Compare how proteins are sorted in the cis and trans Golgi networks.

In the cis network, the proteins enter the Golgi apparatus from the ER and can either continue through the Golgi stacks, or if they have an ER retention signal, will be returned to the ER The trans network of the Golgi is where proteins bound for the plasma membrane or lysosomes exit the Golgi in transport vesicles.

Review how intermediates of glycolysis and the citric acid cycle can be used to synthesize other molecules needed by the cell.

Intermediates in glycolysis and TCA can be pulled out in their respective cycles and can be used in other pathways. These are controlled by product inhibition, feedback inhibition. Enzymes are shutting everything. According to the book, glycolysis and the citric acid cycle provide the precursors needed for cells to synthesize many important organic molecules. The amino acids, nucleotides, lipids, sugars, and other molecules. In turn this serves as the precursors for many of the cell's macromolecules.

Recall why-and in which step-glycolysis would halt in the absence of oxygen in cells that cannot carry out fermentation.

It would halt in step 3, but the cell would have an influx of NADH, and if the cell cannot convert the NADH to NAD+ then glycolysis will halt, because it does not have enough NAD+ to continue the process

List four enzyme types involved in glycolysis and indicate their functions

Kinase: catalyzes the addition of a phosphate group to molecules. In glycolysis a kinase transfers a phosphate group from ATP to a substrate in steps 1 and 3; other kinases transfer a phosphate to ADP to from ATP in steps 7 and 10. Isomerase: catalyzes the rearrangment of bonds within a single molecule. In glycolysis isomerases in steps 2 and 5 prepare molecules for the chemical alterations to come. Dehydrogenase: catalyzes the oxidation of a molecule by removing a hydrogen atom plus an electron (a hydride ion, H-). In glycolysis, the enzyme glyceraldehyde 3-phosphate dehydrogenase generates NADH in step 6. Mutase: catalyzes the shifting of a chemical group from one position to another within a molecule. In glycolysis the movement of a phosphate by phosphoglycerate mutase in step 8 helps prepare the substrate to transfer this group to ADP to make ATP in step 10.

Summarize how misfolded or not fully assembled proteins are retained in the ER.

Proteins that are misfolded or unable to assemble properly are retained in the ER because chaperones hold the proteins in the ER until they are properly folded or assembled and also prevent the aggregation of misfolded proteins. If the proteins continue to accumulate, they are transported to the cytosol where they are degraded by proteasomes.

List the evidence suggesting that both mitochondria and chloroplasts evolved from bacteria that were engulfed by ancestral cells.

Mitochondria and chloroplasts share many of the features of their bacterial ancestors. Both organelles contain their own DNA-based genome and the machinery to replicate this DNA and to make RNA and protein. The inner compartments of these organelles-the mitochondrial matrix and the chloroplast stroma-contain DNA and a special set of ribosomes. Membranes in both organelles - the mitochondria inner membrane and the chloroplast thylakoid membrane- contain the protein complexes involved in ATP production Binary fission is how they replicate (same way that bacteria replicates) Not activate in the endomembrane system which includes organelles that talk to one another

Identify the eukaryotic organelles that are surrounded by double membranes.

Mitochondria, chloroplasts, nucleus

List the components of the electron transport chain in their order of operation, including mobile electron carriers, and describe the functions of each.

NADH → NADH dehydrogenase (complex 2) → ubiquinone → cytochrome C reductase complex (complex 2) → cytochrome C → cytochrome C oxidase complex (complex 3) → oxygen = H2O The first respiratory complex in the chain, NADH dehydrogenase, accepts electrons from NADH. These electrons are extracted from NADH in the form of a hydride ion (H-), which is then converted into a proton and two high-energy electrons. That reaction H- -> H+ + 2e-, is catalyzed by the NADH dehydrogenase complex itself. After passing through this complex, the electrons move along the chain to each of the other enzyme complexes in turn, using mobile electron carriers to ferry them between the complexes. This transfer of electrons is energetically favorable: the electrons are passed from electron carriers with a weaker electron affinity to those with a stronger electron affinity, until they combine with a molecule of O2 to form water. This final electron transfer is the only oxygen-requiring step in cell respiration, and it consumes nearly all the oxygen that we breathe.

Contrast the evolution of the nucleus with that of mitochondria and chloroplasts.

Nucleus - "invagination" (ew what) of the plasma membrane. Mitochondria and chloroplasts - endosymbiotic theory; engulfing of other bacteria by primitive eukaryotic cells where they initially lived in symbiosis but then evolved to where we are now

Summarize how light energy, captured by a chlorophyll molecule in an antenna complex, gets transferred to the chlorophyll special pair in the reaction center.

Once light energy has been captured by a chlorophyll molecule in an antenna complex, it will pass randomly from one chlorophyll molecule to another until it gets trapped by a chlorophyll dimer called the special pair, located in the reaction center. The chlorophyll special pair holds its electrons at a somewhat lower energy than the antenna chlorophylls, so the energy transferred to it from the antenna gets trapped there. Note that in the antenna complex, it is energy that moves from one chlorophyll molecule to another, not electrons.

Compare the amount of energy provided by stored fats and stored glycogen

Oxidation of a gram of fat releases about twice as much energy as the oxidation of a gram of glycogen. Glycogen binds a great deal of water, producing a Six fold difference in actual mass of glycogen required to store the same amount of energy as fat

Name the atoms or molecules that are oxidized or reduced by cytochrome c oxidase.

Oxidized: cytochrome C oxidase. Reduced: oxygen (O2). Cytochrome c oxidase oxidizes cytochrome c reductase. Cytochrome c oxidase reduces cytochrome c oxidase

Review how nuclear import receptors escort proteins bearing a nuclear localization signal from the cytosol into the nucleus.

Prospective nuclear proteins are imported from the cytosol through nuclear pores. The proteins contain a nuclear localization signal that is recognized by nuclear import receptors, which interact with the cytosolic fibrils that extend from the rim of the pore. After being captured, the receptors with their cargo jostle their way through the gel-like meshwork forming the unstructured regions of the nuclear pore protein until nuclear entry triggers cargo release. After cargo delivery, the receptors return to the cytosol via nuclear pores for reuse. Similar types of transport receptors, operating in the reverse direction, export mRNAs from the nuclear. 1. The nuclear import receptors bind to the protein with the nuclear localization sequence 2. The receptor then interacts with the cytosolic fibrils of the nuclear pore, leading to the protein entering the actual pore 3. The nuclear import receptor then grabs onto repeating amino acid sequences within the tangled meshwork within the center of the pore. 4. A pathway opens up through the meshwork that allows the nuclear import receptors to bump along the repeating AA sequences until it enters the nucleus and releases the protein

Review the membrane potential and pH gradients across the inner mitochondrial membrane, and state in which direction it is energetically favorable for protons to flow.

Protons will flow in the direction towards the higher pH (less protons) and more negative membrane potential

Describe the structure of the nuclear envelope.

Perforated by nuclear pores that form gates where molecules enter or leave the nucleus A nuclear pore is composed of a complex of about 30 different proteins, each present in multiple copies; many of these protiens contain extensive, unstructure regions in which the polypeptide chains are largely disordered. These unstructured regions created a meshwork that prevents the passage of large molecules but allow small, water-soluble molecules to pass freely and nonselectively between the nucleus and the cytosol

Differentiate between photosystems I and II, indicate the electron carriers to which they transfer their high-energy electrons, and state the source of the electrons that replace those donated by their chlorophyll special pairs.

Photosystem I captures the energy from the sunlight. The reaction center of this photosystem passes its high-energy electrons to a different mobile electron carrier, called ferredoxin, which brings them to an enzyme that uses the electrons to reduce NADP+ to NADPH. It is the combined action of these two photosystems that produces both the ATP (photosystem II) and the NADPH (photosystem I) required for carbon fixation in stage 2 of photosynthesis. In more detail: photosystem I transfers high-energy electrons to an enzyme that produces NADPH. When light energy is captured by photosystem I, a high-energy electron is passed to a mobile electron carreir called ferredoxin (Fd), a small protein that contains an iron-sulfur center. Ferredoxin carriers its electrons to ferredoxin-NADP+ reductase (FNR), the final protein in the electron-transport chain that catalyzes the production of NADPH. Electrons are supplied to a photosystem II by a water-splitting enzyme that extracts four electrons from two molecules of water, producing O2 as a by-product. Their energy is raised by the absorption of light to pwoer the pumping of protons by the cytochrome b6-f complex. Electrons that pass through this complex are then donated to a copper-containing protein, the mobile electron carrier plastocyanin (pC), which ferries them to the reaction center of photosystem I. After a second energy boost from light, these electrons are used to generate NADPH.

Name components of the photosynthetic electron transport chains and describe their functions

Photosystem II: plastoquinone, cytochrome b-f complex, ATP sythase plastocyanin. Photosystem I: ferredoxin, ferredoxin-NADP+ reductase

Summarize how the pyruvate produced by glycolysis is converted into acetyl CoA, and state where the process takes place

Short Version: In mitochondria, the decarboxylation of pyruvate gives the energy required to attach the acetyl group on CoA. Long Version: Pyruvate is converted into acetyl CoA and Co2 by the pyruvate dehydrogenase complex in the mitochondrial matrix. The pyruvate dehydrogenase complex contains multiple copies of three enzymes - pyruvate dehydrogenase (1), dihydrolipoyl transacetylase (2), and dihydrolipoly dehydrogenase (3). This enzyme complex removes a CO2 from pyruvate to generate NADH and acetyl CoA. Pyruvate and its products-including the waste product, CO2. In the large multienzyme complex,reaction intermediates are passed directly from one enzyme to another. To get a sense of scale, a single pyruvate dehydrogenase complex is larger than a ribosome.

Review how and where the fatty acids derived from fat are converted into acetyl CoA

Short Version: The fatty acids are converted into acetyl-CoA in the mitochondria of the cells and then the acetyl-CoA is used for the TCA cycle Long Version: Fatty acids derived from fats are also converted to acetyl CoA in the mitochondrial matrix. Fats are stored in the form of triacylglycerol. Three fatty acid chains are linked to this glycerol through ester bonds. Enzymes called lipases can hydrolyze these ester bonds when fatty acids are needed for energy. The rleased fattty acidsare then couple to coenzyme A in a reaction requiring ATP. Thesis activated fatty acids (fatty acyl CoA ) are subsequently oxidized in a cycle containing four enzymes. Each turn of the cyle shrotens the fatty acyl CoA molecule by two carbos and generates one molecule each of FADH2, NADH, and acetyl CoA. Fats are insoluble in water and spontaneously from large lipid droplets in specialized fat cells called adipocytes.

Compare the locations and fates of the ER signal and stop-transfer sequences of single-pass transmembrane proteins to the start-transfer and stop-transfer sequences of multipass transmembrane proteins.

Single-pass ER membrane proteins are synthesized through the membrane and until they reach a stop-transfer sequence; at this point the protein is released and the N-terminal sequence is cleaved off, with the stop-transfer sequence left inside the lipid bilayer. These proteins have a defined orientation that does not change even if they are transported to another organelle. Multi-pass proteins have start-transfer sequences and stop-transfer sequences that work in pairs with the start-transfer sequence initiating translocation and then the stop-transfer sequence stopping or pausing it. The hydrophobic sequences form membrane-spanning alpha helices.

Outline the three stages of catabolism, indicating where each takes place and identifying the stage's major prodructs

Stage 1 mostly occurs outside cells, with the breakdown of large food molecules in the mouth and the gut-although intracellular lysosomes can also disgest such large molecules. In a short overview: stage 1 of catabolism: digestion: occurs in lumen of GI tract is when large food molecules are broken down into their buidling blocks by enzymes in either the intestine or in lysosomes. Then they enter the cytosol of the cell. Stage 2 starts intracellularly with glycolysis in the cytosol, and ends with the conversion of pyruvate to acetyl groups on acetyl CoA in the mitochondrial matrix. In a short overview stage 2 is Glycolysis: when glucose is broken down into pyruvate, ATP, and NADH (activated carriers) in cytosol. Pyruvate is taken to the mitochondrial matrix. where it is converted into CO2 and acetyl CoA (activated carrier) and NADH. At the same time, fatty acids are broken down into acetyl CoA through oxidation in the mitochondrial matrix as well. Stage 3 begins with the citric acid cycle in the mitochondrial inner membrane and concludes with oxidative phosphorylation on the mitochondrial inner membrane. The NADH generated in stage 2 adds to the NADH produced by the citric acid cycle to drive the production of large amounts of ATP by oxidative phosphorylation. In a short overview: the third stage of catabolism is TCA: acetyl CoA is transformed into citrate to be used in the citrate acid cycle. This process produces CO2 and NADH. The electrons from NADH are brought to the inner membrane of the mitochondria where they will be used by the electron transport chain to drive oxidative phosphorylation and create ATP (by using oxygen)

Summarize the possible fates of glyceraldehyde 3-phosphate generated by the carbon fixation cycle.

Sugar synthesis, starch synthesis (carbohydrate storage), fat synthesis (for energy storage in fat droplets), and amino acid synthesis

Compare the processes of vesicle tethering, docking, and fusion, and list the proteins involved in each.

Tethering molecules are filamentous transmembrane protein involved in the docking of transport vesicles to target membranes. Tethering molecules help it get close to the cells (mainly involved in the docking process) and SNAREs help it fuse by holding the vesicle extremely close to the cell. This proximity allows their membrane lipids to interact, enabling fusion.

Explain how ATP synthase acts as a motor to convert the energy of protons flowing down an electrochemical gradient into the chemical bond energy in ATP.

You couple reactions We are using mechanical energy. The stalks rotates to generate. If reverse ATP synthase can turn into an ATP hydrolase, which means it will generate ADP and inorganic phosphate from ATP.

Relate what would happen if an ER signal sequence were removed from an ER protein and attached to a cytosolic protein.

The ER protein would be moved to the cytosol, and the cytosolic protein would move into the ER.

Describe the structure and location of the Golgi apparatus.

The Golgi apparatus sits between the ER and the plasma membrane with the cis face on the side of the ER and the trans face on the side closer to the plasma membrane. The Golgi apparatus is structured like a stack of sacks laying on top of each other. Some cells have more stacks of Golgi than others.

Review how the signal-recognition particle (SRP) and SRP receptor guide proteins containing an ER signal sequence to the ER membrane.

The SRP binds to both the exposed ER signal sequence and the ribosome, thereby slowing protein synthesis by the ribosome. The SRP-ribosome complex then binds to an SRP receptor in the ER membrane. The SRP is released, and the ribosome passes from the SRP receptor to a protein translocator in the ER membrane. Protein synthesis resumes and the translocator starts to transfer the growing polypeptides across the lipid bilayer.

Explain how nuclear pores restrict the passage of larger molecules while allowing small, water-soluble molecules to pass freely between the nucleus and cytosol.

The fibers inside the nuclear pore form a gel-like material that only allows small molecules to pass through it.

Identify the source of energy for the transport of proteins into the ER.

The force of the ribosome pushing it through the membrane. The energy from synthesizing the proteins also provides energy for this process.

Outline how investigators used an artificial system including bacteriorhodopsin and ATP synthase to demonstrate the role that a proton gradient plays in producing ATP.

The investigators used bacteriorhodopsin as a proton pump and ATP synthase in a synthetic membrane and determined that the proton gradient is what generates the energy for ATP synthesis Also allowed scientists to determine the orientation that ATP synthase needed to be within the membrane to generate ATP from the gradient

Describe the structure of a mitochondrion and distinguish the functions and compositions of its different membranes and compartments.

The mitochondria contains an outer membrane, an inner membrane, an inner-membrane space, and a mitochondrial matrix. The invaginations of the inner membrane (cisternae) contain the machinery for the electron transport chain. The proton gradient for ATP synthase is generated in the intermembrane space and the ATP is produced into the mitochondrial matrix.

Review where the proteins found in mitochondria and chloroplasts are synthesized.

The mitochondrial and chloroplast proteins are synthesized in the cytosol

Recall how and where additional oligosaccharides are added to glycoproteins within the Golgi stack.

The modification of oligosaccharides on proteins takes place in the Golgi stacks depending on how early that modification would occur. Early modifications occur closer to the cis face while those happening later take place closer to the trans face. These modifications often occur in the order through which the protein travels through the Golgi stacks.

Identify the origin of the oxygen atoms used during the citric acid cycle to produce carbon dioxide.

The oxygen atoms are derived from water. NOT molecular oxygen

Articulate how mitochondrial proteins are recognized and transported into the mitochondrial matrix, and describe the role played by chaperones inside the organelle.

The protein is brought to the mitochondria and the import receptor binds. Chaperones pull the protein into the mitochondrial matrix

Contrast the conformation adopted by proteins during nuclear transport and that of proteins transported into mitochondria and chloroplasts.

The proteins are unfolded as they are brought into the mitochondria and then they return to their folded form once inside the mitochondria.

Relate redox potential to electron affinity and describe how the redox potentials of reduced/oxidized nicotinamide adenine dinucleotide and oxygen/water align with their functions in the respiratory chain.

The redox potential goes from low to high with the lowest electron affinity in NADH passing its electrons to NADH dehydrogenase which has a slightly higher electron affinity, and so on and so forth with O2 having the highest electron affinity within the electron transport chain.

Compare a polyribosome and the rough ER.

The rough ER has ribosomes coating the outside of it and synthesizing the proteins that will be incorporated into the ER membrane of the ER lumen Polyribosomes are when many ribosomes bind to an mRNA molecule as it is translated. Regarding mRNA molecule directing synthesis of a protein with an ER signal sequence, the polyribosome becomes riveted to the ER membrane by the growing polypeptide chains, which have become inserted into the ER membrane.

Recall the direction in which protons are pumped across the inner mitochondrial membrane and describe the resulting pH difference in the mitochondrial matrix and intermembrane space.

You have voltage difference pulling it across and a pH gradient (proton gradient) pulling it across. More protons = lower pH

Review the consequences of disrupting electron transport in mitochondria.

You won't have ATP production, so eventually the cell will die from a lack of ATP. This is most detrimental to neurons and muscle cells because they need a lot of energy

Explain how the generation of 1,3-bisphosphoglycerate in step 6 of glycolysis drives the production of ATP in step 7

The short version: It is part of the uncoupled reactions, so the favorable reaction (6), enables step 7 to take place. In step 6, the favorable oxidation of C-H bond rxn is couple with the unfavorable NADH formation and phosphorylation of the sugar. Step 7 - favorable breakage of high energy phosphate bond coupled w/ ATP formation. The long version: It is the committed step. In this process, a short-lived covalent bond is formed between glyceraldehyde 3-phosphate and the -SH group of a cysteine side chain of the enzyme glyceraldehyde 3-phosphate deydrogenase. The enzyme also binds noncovalently to NAD+. Glyceraldehyde 3-phosphate is oxidized as the enzyme removes a hydrogen atom and transfers it, along with an electron, to NAD+ forming NADH. Part of the energy released by the oxidation of the aldhyde is thus stored in NADH, and part is stored in the high-energy thioester bond that links glyceraldehyde 3-phosphate to the enzyme. A molecule of inorganic phosphate displaces the high-energy thioester bond to create 1,3-bisphosphoglycerate, which contains a high-energy phosphate bond. This begins a sustrate-level phosphorylation process. Then in step 7, the high-energy phosphate group is tranferred to ADP to form ATP, completing the substrate-level phosphorylation.

Explain the unfolded protein response and outline the consequences of triggering this program.

The unfolded protein response is triggered when the number of misfolded or misassembled proteins builds up in the ER to the point that chaperones cannot control it. Triggering the unfolded protein response leads to the activation of transcription factors that help to halt protein synthesis and also results in the expansion of the ER itself. If the expansion of the ER is still not enough to control the aggregation of misfolded protein, the UPR sends a signal to the cell to undergo apoptosis and die.

Contrast the destinations of the transmembrane and water-soluble proteins that are transferred from the cytosol to the ER.

The water-soluble proteins are destined either for secretion (by release at the cell surface) or for the lumen of an organelle of the endomembrane system. The transmembrae proteins are destined to reside in the membrane of one of these organelles or in the plasma membrane. If it gets stuck in the membrane it get it stays in the membrane. 1. water-soluble, completely translocate across the ER membrane to be released in the ER lumen, destined for secretion or to become part of the lumen of an endomembrane system organelle 2. transmembrane proteins - become embedded in the ER membrane, destined to reside in the membrane of an endomembrane system organelle or in the plasma membrane

Review how proteins are selected for glycosylation in the ER and how these sugars are attached to the protein.

These proteins have a 3 amino acid sequence, including an asparagine, that serve as the signal sequence to the cell that this protein needs to be glycosylated. These proteins are synthesized into the ER where there is dolichol attached to the wall of the ER lumen, and once the asparagine to be glycosylated is translated into the ER lumen, an oligosaccharyltransferase moves the standard oligosaccharide attached to the dolichol to the amino group at the end of the asparagine side chain and attaches it to that nitrogen. The protein's oligosaccharide group undergoes more modification in the Golgi apparatus to become the specific oligosaccharide it is meant to be.

Outline the process that allows much of the energy contained in the high-energy electrons of activated carriers to be stored in the high-energy phosphate bonds of ATP.

They are used to power the proton pump and it goes into electrical energy into the gradients of the protons pumps. (the proton proteins create a gradient, so the energy is now in the gradient). Think of a water wheel. Oxygen, from inhalation, is consumed at the end of ETC. In other words: Pyruvate and fatty acids enter the mitochondrial matrix where they are convered to acetyl CoA. The acetyl CoA is then metabolized by the citric acid cycle, which produces NADH (and FADH2). During oxidative phosphorylation, high-energy electrons donated by NADH (and FADH2) are then passed along the electron-transport chain in the inner membrane and ultimately handed off to oxygen (O2); this electron transport generates a proton gradient across the inner membrane which is used to drive the production of ATP by ATP synthase.

Outline the fate of the acetyl group carbons that enter the citric acid cycle.

They complete one turn around TCA, then after that turn they can be released on subsequent turns as CO2.

Describe the fate of proteins that lack a sorting signal.

They stay in the cytosol

Define Cellular Respiration

a process by which cells harvest the energy stored in food molecules; usually accompanied by the uptake of O2 and the release of CO2 in other words, the organisms's cells harvest useful energy from the chemical-bond energy locked in sugars as the sugar molecule is broken down and oxidized to carbon dioxide and water. The energy released during these reactions is captured in the form of "high-energy" chemical bonds-covalent bonds that release large amounts of energy when hydrolyzed-in activated carriers such as ATP and NADH

Outline how when food is scare, cells can break down glycogen to produce energy via glycolysis

This process is dependent on hormonal control aka glucagon which will act on liver cells to stimulate the breakdown of glycogen. In other words: when food is scare, fasting cells, mobilize glucose that has been stored in the form of glycogen, a branched polymer of glucose. It is sotred as small grandules in the cytoplasm of many animal cells, but mainly in liver and muscle cells. The synthesis and degradation of glycogen occur by separate metabolic pathways, which can be rapidly and coordinately regulated to suit an organism's needs. When more ATP is needed than can be generated from food-derived molecules available in the bloodstream, cells break down glycogen in a reaction that is catalyzed by the enzyme glycogen phosphorylase. This enzyme produces glucose 1-phosphate, which is then converted to the glucose 6-phosphate that feeds into the glycolytic pathway. The glycogen degradative and synthetic pathways are coordinated by feedback regulation. Enzymes in each pathway are allosterically regulated by glucose 6-phosphate, but in opposite directions: in the synthetic pathway, glycogen synthetase is activated by glucose 6-phosphate, whereas glycogen phosphorylase, which breaks down glycogen is inhibited by glucose 6-phosphate as well by ATP. This regulation helps to prevent glycogen breakdown when ATP is plentiful and to favor glycogen synthesis when the glucose 6-phosphate concentration is high. The balance between glycogen synthesis and breakdown is further regulated by intracellular signaling pathways that are controlled by the hormones insulin, epinephrine, and glucagon.

Review the events that take place in stage 2 of photosynthesis and indicate where these reactions occur

This stage occurs in the chloroplast stroma and continues into the cytosol. During this stage, the ATP and the NADPH produced by the photosynthetic electron-transfer reaction of stage 1 are used to drive the manufacture of sugars from CO2. These carbon-fixation reactions, which do not directly require sunlight begin in the chloroplast stroma. There they generate a three-carbon sugar called glyceraldehyde 3-phosphate. This simple sugar is exported to the cytosol, where it is used to produce a large number of organic molecules in the leaves of the plant, including the disaccharide sucrose, which is exported from the leaves to nourish the rest of the plant.

Outline the events that take place during stage 1 of photosynthesis and compare this process to the oxidative phosphorylation that occurs in mitochondria.

This stage occurs in the thylakoid membrane. Stage 1 of photosynthesis resembles that oxidative phosphorylation that takes place on the mitochondrial inner membrane. In this stage, an electron-transport chain in the thylakoid membrane harnesses the energy of electron transport to pump protons into the thylakoid space; the resulting proton gradient then drives the synthesis of ATP by ATP synthase. What makes photosynthesis very different is that the high-energy electrons donated to the photosynthetic electron transport chain come from a molecule of chlorophyll that has absorbed energy from sunlight. Thus, the energy-producing reactions of stage 1 are sometimes called the light reactions. Another major difference between photosynthesis and oxidative phosphorylation is where the high-energy electrons ultimately wind up: those that make their way down the photosynthetic electron-transport chain in chloroplasts are donated not to O2, but to NADP+, to product NADPH

Recall the location, functions, and ultimate fate of the ER signal sequence on soluble proteins.

Unfinished protein/polypeptide being moved from ribosome to ER lumen in this process

Outline the mechanisms by which proteins can enter membrane-enclosed organelles, and identify the organelles that use them.

Vesicles, pores

Explain why oxygen is required for the citric acid cycle to continue

Without oxygen, You get a build up of NADH, because the electrons cannot be cycled and handed off in the ETC for the use in generating ATP.

Define gluconeogenesis and identify the type of cell in mammals in which the reaction is likely to occur

gluconeogenesis is a set of enzyme-catalyzed reactions by which glucose is synthesized from small organic molecules such as pyruvate, lactate, or amino acids; in effect, the reverse of glycolysis. In short, gluconeogenesis is when you create glucose from pyruvate. It takes place in the liver.

Recall the role that ribulose 1,5-bisphosphate plays in the carbon fixation cycle.

ribulose 1,5-bisphosphate is the molecule that the carbons from CO2 are added to in the calvin (carbon fixation) cycle