Cell & Molecular Biology III
Which of the following is not part of the process known as oxidative phosphorylation?
ATP is produced in the cytosol as glucose is converted into pyruvate
Oxidative phosphorylation, as it occurs in modern eukaryotes, is a complex process that probably arose in simple stages in primitive bacteria. Which mechanism is proposed to have arisen first as this complex system evolved?
ATP-driven proton pumps
Types of active transport:
ATP-driven pumps - proteins that undergo a series of conformational changes that pump ions or molecules across the cell membrane. The hydrolysis of ATP generates the energy necessary to drive the cycle of conformational changes in the pump. Gradient-driven or coupled pumps - transport of ions or molecules against their electrochemical gradient by coupling their transport with other ions or molecules that are moving down their electrochemical gradient. These can be symporters where the coupled ions or molecules move in the same direction or antiporters where they move in opposite directions.
Overall energy production of cellular respiration
Accounting of ATP generated from a single glucose molecule ● Glycolysis ○ 2 ATP directly produced ○ 2 NADH yield 3 ATP via OxPhos ■ Transport from cytosol to mitochondria is costly which reduces yield some ● Pyruvate → acetyl CoA ○ 2 NADH yield 5 ATP via OxPhos
Mitochondria
Mitochondria have inner and outer membranes that create compartments essential for the chemiosmotic coupling that generates ATP. Key structures: ● Outer membrane ○ Porins in this membrane allow passage of all molecules < 5000 da ● Inner membrane ○ Limited permeability - requires transporters to move materials across ○ Location of electron transport chain ● Intermembrane space ○ Between inner and outer○ Composition similar to cytosol of cell ● Matrix ○ Within inner membrane ○ Specialized composition ○ Site of citric acid cycle
Neuron signaling function:
Action potentials - rapidly propagate electrical signals within a neuron ● In response to a depolarization of the membrane, voltage-gated Na + channel open and further depolarize the membrane. This leads to the opening of more voltage-gated Na + channels and a wave of depolarization propagates along the axon of neuron ● voltage-gated Na + channels has a refractory period where they cannot be opened again this limits the rate of neuron firing and facilitates directional propagation of the action potential ● Components of the response ○ Resting membrane potential ○ Depolarizing stimulus ○ Threshold potential - membrane potential at which the voltage-gated Na + channels open ○ Action potential - large peak of depolarization - membrane shifts from negative to positive - ○ voltage-gated K + channels to open - K + leaves cell and membrane potential returns to resting state . ● Video summary: https://www.youtube.com/watch?v=oa6rvUJlg7o
Which of the statements below is false.
Activated carrier molecules store heat energy for the cell to use later.
The Na+ Ca2+ exchanger (diagrammed below) moves Ca2+ against its electrochemical gradient and out of cardiac cells by coupling Ca2+ export with the import of Na+. This an example of what type of transport:
Antiport
Eukaryotic cells evolved from _____________ and endosymbiotic ____________.
Archaea; Bacteria
Creating a membrane out of which of the phosphatidylcholine molecules below would produce the most fluid membrane:
B -
FRAP
B bleach, straight line
Mitochondria are dynamic and their size and number can vary with the energetic demands on a cell over time
Mitochondria originated as a prokaryotic endosymbiont within the proto-eukaryotic cell. They carry their own (reduced) genome and transcription, translation, DNA replication all happen within the mitochondria - separate from the rest of the cell. Many parts of the original mitochondrial genome have been transferred to the host cell's genome. Mitochondria are maternally inherited and each mitochondrion is made of proteins from the host genome and its own genome. Conflicts between these two genomes can cause dysfunction and disease.
Patch Clamp
Molecule A
Identify the activated carrier (w) produced at step 4 of the citric acid cycle.
NADH
The citric acid cycle is outlined below. Some of these reactions produce activated carrier molecules that are used in the electron-transport chain or as energy for other reactions. Identify the activated carrier (X) produced at step 3 of the cycle.
NADH
The citric acid cycle is outlined below. Some of these reactions produce activated carrier molecules that are used in the electron-transport chain or as energy for other reactions. Identify the activated carrier (z) produced at step 8 of the cycle.
NADH
NADH and FADH2 carry high-energy electrons that are used to power the production of ATP in the mitochondria. These cofactors are generated during glycolysis, the citric acid cycle, and the fatty acid oxidation cycle. Which molecule will lead to the production of the most ATP?
NADH from the citric acid cycle
In the light reactions of photosynthesis, ferredoxin can donate electrons to _____________ or ______________ .
NADP+, plastoquinone
Stage 2 of photosynthesis, sometimes referred to as the dark reactions, involves the reduction of CO2 to produce organic compounds such as sucrose. What activated carrier is the electron donor for carbon fixation?
NADPH
Cells use membranes to help maintain set ranges of ion concentrations inside and outside the cell. Which of the following ions is the most abundant outside a typical mammalian cell?
Na+
The membrane phospholipids of Eukaryotes are most similar to:
Bacteria
The three domains of life have distinct cell structure and biochemistry
Bacteria • Prokaryotic - no nucleus • Peptidoglycan cell wall • Membranes with unbranched fatty acids • Distinct rRNA Archaea • Prokaryotic - no nucleus • No peptioglycans in cell wall • Membranes with branched fatty acids • Distinct rRNA Eukaryota • Eukaryotic - membrane bound nucleus • No peptioglycans in cell wall (if present) • Membranes with unbranched fatty acids • Distinct rRNA
The Na+-glucose transporter, moves glucose into the cell, against its concentration gradient. What property of this transporter ensures that glucose moves in one direction and is not transported out of the cell?
Binding of glucose requires the transporter first bind Na+
Fatty acids can be used to generate energy for the cell. Which of the following fatty acids will yield more energy?
CH3-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-COOH
The enzyme ribulose bisphosphate carboxylase (Rubisco) normally adds carbon dioxide to ribulose 1,5-bisphosphate. However, it will also catalyze a competing reaction in which O2 is added to ribulose 1,5-bisphosphate to form 3-phosphoglycerate and phosphoglycolate. Assume that phosphoglycolate is a compound that cannot be used in any further reactions. If O2 and CO2 have the same affinity for Rubisco, at which ratio of CO2 to O2 will the greatest net synthesis of sugar occur?
CO2 : O2 - 3:1
Place the following molecules in order of their diffusion rate across the lipid bilayer from high to low
CO2, H2O, Na+
The fusion of synaptic vesicles depicted below occurs when voltage-gated channels open allowing _________ ions into the synaptic terminal.
Ca2+
Which of the following does not affect the diffusion of water into and out of the cell
Charge on the membrane
If the vesicle below, that has been exported from the Golgi apparatus, fuses with the plasma membrane, the portion of the transmembrane protein indicated by the arrow will be projecting into which space?
Cytosol
The chemical reactions of glycolysis occur in the __________________________.
Cytosol
Eurkaryotic cell
Nucleus: - Contains DNA genome - Site of transcription and DNA replication - Double membrane - Nuclear pores Mitochondria - Site of Citric Acid Cycle and Cellular Respiration Endosomes - Carry endocytosed material - Deliver to Golgi - Or mature into lysosomes Peroxisome - Degrade toxins - Oxidization reactors Lysosomes: -Degrade macromolecules - Acidified lumen - Develop from endosomes Endoplasmic reticulum: - Membrane synthesis - Protein folding - Protein modifications Cytosol - Site of translation (at ribosomes) - Site of glycolysis Golgi apparatus -Protein modifications - Protein sorting and distribution - Receives and distributes vesicles
In oxidative phosphorylation, ATP production is coupled to the events in the electron-transport chain. What is accomplished in the final electron-transfer event in the electron-transport chain?
O2 is reduced to H2O
Glycolysis key points
Occurs in the cytosol Oxygen is not required One glucose molecule → 2 pyruvate molecules Uses 2 ATP at steps 1 and 3 (per glucose) Steps 6-10 occur 2x per glucose molecule Uses 2 NAD+ at step 6 (per glucose) Produces 2 NADH at step 6 (per glucose) Produces 2 ATP each at steps 7 and 10 (per glucose)
A molecule moves down its concentration gradient by __________________ transport, but requires __________________ transport to move up its concentration gradient.
Passive; Active
Human infants have a much larger portion of brown adipose tissue than adult humans. It was found that the mitochondria in brown adipocytes (brown fat cells) have a protein called uncoupling protein (UCP) that transports protons from the intermembrane space into the matrix. The function of uncoupling protein is to:
Produce Heat
The inner mitochondrial membrane is largely impermeable and the transport of materials into and out of the mitochondrial matrix requires specific transporters. The import of pyruvate into the matrix of the mitochondria is powered by coupling it with the energetically favorable import of ________________.
Protons (H+)
The membrane is selectively permeable barrier
Rapid: Small non-polar molecules diffuse through (O2, CO2, N2, and steroid hormones) Moderate: Small uncharged polar molecules (H2O, ethanol, glycerol) ● Large molecules and ions cannot cross membrane - require transport proteins (amino acids, glucose, nucleotides) Ions: cannot go in
In the -barrel hydrophilic pore depicted in green below, which amino acid side chain would you expect to be facing the inside of the barrel/pore?
Serine
What do you expect to happen to the rate of fatty acid beta-oxidation in a cell that has its O2 supply diminished?
Decrease
fixed input of glucose into glycolysis
Decrease
The catabolism of carbohydrates involves several different classes of enzymes. Which class of enzyme catalyzes the oxidation of a molecule by removing an electron (hydride ion).
Dehydrogenase
The structure indicated below has abundant neurotransmitter receptors and receives input from other neurons. On what part of the neuron would you expect to find this structure?
Dendrites
New membrane phospholipids are synthesized in the ____________________ and added to the _____________ side of the membrane.
Endoplasmic Reticulum; Cytosolic
Membrane Eq. were equal
Equilibrium potential will be zero
Membrane Eq. switch ion
Equilibrium potential will decrease
Membrane Eq. raise temp
Equilibrium potential will increase
Eukaryote
Eukaryotic cells are 10-100x larger than prokaryotic cells Eukaryotic cells: ○ membrane bound organelles with specialized functions ○ complex and dynamic cytoskeleton (e.g. actin filaments, microtubules) ○ Organelles that carry their own genomes - mitochondria and chloroplasts Prokaryotes are life's greatest biochemists with much greater metabolic diversity than eukaryotes
The mitochondrial ATP synthase consists of several different protein subunits. Which subunit binds to ADP + Pi and catalyzes the synthesis of ATP as a result of a conformational change?
F1 ATPase head
The ATP synthase is found only in the mitochondria of eukaryotic cells
False
The structure of a membrane channel determines whether material moves into or out of the cell.
False
True or False: ATP generated in the light reactions of photosynthesis is exported from the chloroplast as a source of energy for processes throughout the plant cell.
False
True or False: Only compounds with negative redox potentials can donate electrons to other compounds under standard conditions.
False
If you wanted to move all of the phospholipids indicated in pink (below) from the cytosolic to the luminal face of the membrane, which enzyme would be best suited for this job? In what organelle would you find this enzyme?
Flippase; Golgi Apparatus
Which of the molecules below is a saturated fatty acid? (ignore the numbering)
Flipping between leaflets
Identify the activated carrier (v) produced at step 5 of the citric acid cycle.
GTP
All 6 carbons in glucose are eventually transferred to a CO2 and diffuse away from the cell as waste. Which of the following processes in obtaining energy from food do not directly generate CO2
Glycolysis
Which sub-cellular structure would you not expect to find in a prokaryotic cell:
Golgi Apparatus
During Stage 2 of oxidative phosphorylation, ATP synthesis is powered by movement of __________ ions through the __________.
H+; ATP synthase
The oxygen we breathe ultimately ends up as part of which product of aerobic respiration:
H2O
Which of the following molecules are consumed by light reactions of photosynthesis:
H2O
The archaea are distinct from all other domains of life in that they:
Have membrane phospholipids with branched fatty acids
The flux of water into or out of cell - osmosis is driven by concentration gradients only
Hypotonic - water goes in because of higher solutes inside cell (Cell bursts) Isotonic - goes in and out Hypertonic -water goes out because of higher solutes outside of cell (Cell shrivels)
Yesast cells Anaerobic
In an environment containing O2
Fermentation is an anaerobic process (does not require oxygen)
In muscle cells - pyruvate is converted to lactate (lactic acid) and generates regenerates NAD + in the process. This occurs during exercise when the oxygen supply to muscle tissue is insufficient to support the citric acid cycle. In yeast - pyruvate is metabolized to ethanol and CO2 and regenerates NAD + for in the process
CO2 dark reactions
Increase
Conversion
Increase
All of the following changes to membrane permeability will inhibit the triggering of an action potential except:
Increased Na+ permeability
The concentrations of ions (atoms carrying an electrical charge, positive or negative) differ inside and outside of cells.
Inside cell ○ High K+ ○ Low Na+ ○ Low Ca 2+ ○ Low Cl- Outside cell ○ Low K+ ○ High Na+ ○ High Ca 2+ ○ High Cl
In the transmembrane -helic protein depicted in red below, what amino acid would you expect to find in the region of the protein indicated with the arrow?
Isoleucine
The catabolism of carbohydrates involves several different classes of enzymes. Which class of enzyme catalyzes the rearrangement of bonds within a single molecule.
Isomerase
Which of the following best describes the behavior of a gated channel?
It opens more frequently in response to a given stimulus.
Action Potential
K+ leak channels
What is the redox potential of the electron carrier at step B In the diagram of the electron transport chain below.
+230 mV
What is the redox potential of the electron carrier at step X In the diagram of the electron transport chain below.
+30 mV
Ionotropic neurotransmitter receptors are an example of what type of gated ion channel:
Ligand-gated
Which class of enzyme catalyzes the breaking of bonds within a molecule.
Lyase
Endosomes can mature and transform into this other organelle?
Lysosome
Types of gated ion channels:
Mechanically gated channels - Opened by tension on the cell membrane ● Present in hair cells of the inner ear. These cells transduce sound into a nerve impulse ● The cells are arranged in a tonotopic map in the cochlea. Cell in certain positions in the cochlea respond to specific frequencies of sound. Voltage-gated ion channels - Open in response to changes in the membrane potential of the cell. ● Voltage-gated sodium channels mediate the action potentials of neurons Ligand-gated ion channels - Open when a molecules binds to the channel protein ● Neurotransmitter-gated ion channels mediate the transmission of signals between neurons.
Movement of ions across the membrane is determined by solute concentration and membrane potential and requires a channel or transporter
Membrane potential - distribution of charged solutes across the membrane Electrochemical gradient - Combined forces of concentration gradient and membrane potential combined
The chemical reactions of citric acid cycle occur in the
Mitochondria
The conversion of pyruvate into acetyl-CoA by the pyruvate dehydrogenase complex occurs where in the eukaryotic cell?
Mitochondria
Notothenia nudifrons is a species of fish that inhabits Antarctic waters and lives at temperatures below 0°C yet maintains membrane fluidity and permeability comparable to mammals with much higher body temperatures. What feature of membrane composition would you not expect to find in this species:
. High concentrations of phospholipids with saturated fatty acid tails
■ Ubiquinone (RedOx +30 mV)
1. Embedded in inner mitochondrial membrane (hydrophobic tail) 2. Freely diffuse in membrane 3. Transfers e-to cytochrome c reductase complex
Enzymes
1. Kinase - addition/transfer of a phosphate group to or from ATP, and sometimes GTP 2. Isomerase - rearrange of bonds in the molecule 3. Dehydrogenase - oxidize molecule by removing H - (electrons) and reduce activated carriers (NADH, and FADH2 ) 4. Mutase - shift chemical group from one position to another 5. Lyase - Cleaves C-C, C-O, C-N, and other bonds. These enzymes have names ending in "..lase" 6. Synthase - catalyzes synthesis - linking of molecules. Typically without ATP involved
Two hypotheses for the origin of the endomembrane system:
1. Vesicles secreted by the proto-mitochondria form endomembrane Evidence for: • Eukaryotic membrane lipids more similar to bacteria than archaea • No known Archaeon with endomembrane or ability to endocytose Evidence against • Vesicle/pore-forming proteins are archaeal in origin 2. Endomembrane was formed from invaginations of the plasma membrane Evidence for: Vesicle/pore-forming proteins are archeal in origin Evidence against: Eukaryotic membrane lipids more similar to bacteria than archaea No known Archaea with endomembrane or ability to endocytose
Glycolysis generates more energy than it expends. What is the net number of activated carrier molecules produced in this process (number and type of molecules produced minus the number of those molecules used as input)?
2 ATP, 2 NADH
In the light reactions, each O2 produced yields 4 electrons which ultimately reduce 2 NADP+ to 2 NADPH. Assuming ATP, H2O, and CO2 are not limiting, how many O2 molecules would need to be produced in the light reactions to drive one cycle of the Calvin cycle in the dark reactions?
3
● Cytochrome c oxidase complex
:○ Pumps four H+ to the intermembrane space ○ Complex of 13 protein subunits ○ Heme and Cu - O2 binding site ○ Transfers e- to O2 to form H2O (RedOx +820 mV) ■ Requires four e-to form H2O - avoids the formation of harmful O2
Monochromatic light of which wavelength shown below would you expect to generate the most energy through photosynthesis in a typical green plant?
A
Creating a membrane out of which of the phosphatidylcholine molecules below would produce the most fluid membrane
A \
Citric Acid Cycle in Detail:
Step 1 - acetyl-CoA + oxaloacetate → citrate a. Enzyme citrate synthase 2. Step 2 - citrate → isocitrate a. Enzyme - aconitase (aka Citrate Hydro-Lyase) 3. Step 3 - isocitrate → 𝛼-ketoglutarate a. Enzyme - isocitrate dehydrogenase b. Produces - 1 NADH, CO2 4. Step 4 - 𝛼-ketoglutarate → succinyl-CoA a. Enzyme - 𝛼-ketoglutarate dehydrogenase complex b. Produces - 1 NADH, CO2 5. Step 5 - succinyl CoA → succinate a. Enzyme - succinyl CoA synthetase (aka - succinate thiokinase) b. Produces - 1 GTP 6. Step 6 - succinate → fumarate a. Enzyme - succinate dehydrogenase b. Produces - 1 FADH2 7. Step 7 - fumarate → malate a. Enzyme - fumarase (aka malate hydro-lyase) 8. Step 8 - malate → oxaloacetate a. Enzyme - malate dehydrogenase b. Produces - 1 NADH c. The oxaloacetate product now cycles to step 1 and starts the cycle again
Glycolysis
Step 1 - glucose → glucose 6-phosphate (net ΔG⁰' = -4.0) a. Enzyme - hexokinase b. Consumes - 1 ATP 2. Step 2 - glucose 6-phosphate → fructose 6-phosphate (net ΔG⁰' = +0.4) a. Enzyme - phosphoglucose isomerase 3. Step 3 - fructose 6-phosphate → fructose 1,6-bisphosphate (net ΔG⁰' = -3.4) a. phosphofructokinase b. Consumes - 1 ATP 4. Step 4 - fructose 1,6-bisphosphate → dihydroxyacteone phosphate + glyceraldehyde 3-phosphate (net ΔG⁰' = +5.7) a. Enzyme - aldolase b. Splits substrate into two products 5. Step 5 - dihydroxyacteone phosphate → glyceraldehyde 3-phosphate (net ΔG⁰' = +1.8) a. Enzyme - triosephosphate isomerase b. Subsequent steps use this product and one from step 4 6. Step 6 - glyceraldehyde 3-phosphate → 1,3 bisphosphoglycerate (net ΔG⁰' = +1.5) a. Enzyme - glyceraldehyde 3-phosphate dehydrogenase b. Produces - 1 NADH c. Creates high energy phosphate bond 7. Step 7 - 1,3 bisphosphoglycerate → 3-phosphoglycerate (net ΔG⁰' = -4.5) a. Enzyme - phosphoglycerate kinase b. Produces - 1 ATP 8. Step 8 - 3-phosphoglycerate → 2-phosphoglycerate (net ΔG⁰' = +1.1) a. Enzyme - phosphoglycerate mutase 9. Step 9 - 2-phosphoglycerate → phosphoenolpyruvate (net ΔG⁰' = +0.4) a. Enzyme - enolase b. Conformational changes here and in step 8 increase the free-energy of the phosphate bond 10. Step 10 - phosphoenolpyruvate → pyruvate (net ΔG⁰' = -7.5) a. Enzyme - pyruvate kinase b. Produces - 1 ATP
Glycoproteins and glycolipids have _____________ groups attached to the portein or lipid molecules and are typically found on the _______________ face or leaflet of a membrane.
Sugar; Extracellular
Other energy sources:
Sugars are not the only source of energy the cell can utilize. Acetyl-CoA and activated carriers can be generated from fatty acids through the Beta-oxidation cycle in the mitochondria. ● Each turn of cycle trims two carbons from acyl chain and produces: ○ 1 - Acetyl-CoA, 1- NADH, 1- FADH ● The yield of energy depends upon the length of the acyl chain ○ Longer hydrocarbon chains yield more energy ○ Double bonds will result in less FADH produced (skips the first step of the cycle) and ultimately less energy Amino acids can also be converted to Acetyl-CoA or other citric acid cycle intermediates. These processes are specific to the amino acid type and we will not discuss them in detail.
The ATP synthase
The ATP synthase is a multisubunit transmembrane protein embedded in the inner mitochondrial membrane that uses the energy of the H+ gradient to make ATP. ● The H+ carrier subunit allows H+ to pass down its concentration gradient from the inner membrane space to the matrix. ● The flow of H+ causes the ATP synthase to rotate clockwise and provides energy for F1
2. Citric acid cycle and oxidative phosphorylation
The Citric Acid Cycle generates high electrons from acetyl-CoA through a cycle of chemical reactions in the matrix of the mitochondria. Pyruvate from glycolysis is imported into the mitochondria and converted to Acetyl-CoA and CO2 through a series of reactions catalyzed by a complex of three enzymes 1) Pyruvate dehydrogenase, 2) Dihydrolipoyl transacetylase, and 3) Dihydrolipoyl dehydrogenase. The acetyl molecule is linked to coenzyme A with a high-energy thioester bond.
Gluconeogenesis
The Glycolysis pathway can be run backward (for the most part) to form sugars from pyruvate. The balance between Glycolysis and Gluconeogenesis is determined by the immediate abundance of substrates and products and ultimately the energetic state of the cell. Glycolysis requires 2 NAD+ per glucose to proceed. There are two ways to do this:
Uncoupling protein
The H+ electrochemical gradient can also be used to generate heat. Uncoupling proteins are H+ channels that circumvent the ATP synthase and allow H+ to flow down its gradient.
Transport in the mitochondria
The H+ electrochemical gradient is used to drive the coupled transport of materials into and out
Energetics of oxidative phosphorylation
The electron transport chain harvests energy by transferring electrons along a series of molecules from low to high Redox potential states. ● Redox potential is the measure of a molecule's affinity for an electron. ● A molecule with a low redox potential will readily transfer its electron to a molecule with a higher redox potential. ● An electron loses energy when transferred from a low to high redox state and this energy can be captured to power the production of ATP.
In the electron transport chain, FADH2 generates relatively less ATP than NADH. Why?
The electrons from FADH2 enter the chain at a later step
Which of the following statements about resting membrane potential is true?
The resting membrane potential for most animal cells is negative because the inside of the cell is more negatively charged than the outside of the cell.
The redox potential of water is +820 mV which means this molecule has a very high affinity for electrons. To oxidize water requires altering this potential or pairing this molecule with another molecule that has an even greater redox potential. Photosystem II and the water-splitting enzyme oxidize water by which mechanism?
The special pair of chlorophyll in photosystem II have a very high redox potential in their unexcited state (+1200 mV)
Complex membrane bound organelles are a distinct feature of eukaryotes - where did they come from?
There are organelles that have their own DNA apart from the nucleus and are suggested to have originated from endosymbiotic bacteria according to the endosymbiotic theory. These organelles are mitochondria and plastids. Key evidence: The ribosomal RNA of mitochondria and chloroplasts is most similar to the rRNA of bacteria
K+ leak channels are found in the plasma membrane. These channels open and close in an unregulated, random fashion. What do they accomplish in a resting cell?
They allow a flux of K+ ions out of the cell creating a negative membrane potential.
The Na+-K+ pump transports _____ Na+ ions out of the cell, and ______ K+ ions into the cell for every _____ ATP consumed.
Three, two, one
Data for the mobility of three different membrane proteins (X, Y, and Z) using fluorescence recovery after photobleaching (FRAP) are shown below. In (A), (B), and (C) the tracks of the position of individual membrane-proteins over time are plotted. Which individual protein track is consistent with the FRAP profile of Protein X?
Track B
Two major classes of membrane transport proteins
Transporter: Solute binding site Channel: ions flow through Transporters can be saturated • Channels cannot be saturated Transporters bind molecules, undergo a conformational change, and then release them on the other side of the membrane. Therefore, movement across the membrane is limited by the number of transporters because they can become saturated when there are more molecules to transport than transporters available. Channels are selective openings in the membrane that allow molecules to flow down their electrochemcial gradients. Channels cannot be saturated. Transport can occur passively (without the cell spending energy) if the ion or molecule is moving down its electrochemical gradient (from high to low concentration and/or towards opposite charge) ● Example - Selective ion channels ○ Passive - allows flux of ions down their electrochemical gradient ○ 1000x faster than transporters >10^6 ions per sec. ○ Selectivity mechanism i. Water molecules are stripped from the ion ii. Ion forms transient ionic bonds with amino acid side chains in the channel as it passes - correct bonds must be formed for raid passage
True or False: Under certain conditions, ATP synthase can hydrolyze ATP to ADP and use that energy to pump H+
True
Step six of the citric acid cycle generates FADH2 that transfers its electrons to __________________ in the electron transport chain through the action of the __________________________ complex.
Ubiquinone; Succinate Dehydrogenase Complex
Identify the structure indicated on the plant cell below:
Vacuole
Plant cells
Vacuole -Fluid-filled organelle - Structural support Cell-wall - Made of cellulose - Structural support Chloroplast: - Site of photosynthesis - Carries own genome
In the light reactions, the proton gradient used to produce ATP is generated by which of the following mechanisms:
Water splitting
Below is a list of breakthroughs in energy metabolism in living systems. Which is the correct order in which they are thought to have evolved? W - H2O-splitting enzyme activity X - light-dependent transfer of electrons from H2S to NADPH Y - the fermentation of organic molecules Z - oxygen-dependent ATP synthesis
Y, X, W, Z
Citric acid cycle summary:
Yields: A. 2 CO2 B. 3 NADH C. 1 FADH2 D. 1 GTP *also 1 NADH and 1 CO2 from pyruvate to acetyl-CoA by pyruvate dehydrogenase complex ● B-D are energy carriers that will be delivered to the inner membrane of the mitochondria and produce a huge amount of ATP via oxidative phosphorylation ● Changing abundance of any intermediate will impact the rate of all reactions in the cycle. ● Glycolysis and citric acid cycle intermediates are an important source for anabolism of: nucleotides, lipids, amino acids, and other molecules in the cell.
Eukaryotic cells are distinct from all other domains of life in that they:
a genome enclosed in a membrane-bound nucleus
The plasma membrane of animals cells is anchored to and supported by the cell cortex a structure composed of:
a network of actin filaments
Peptidoglycan
a polymer of sugars and amino acids that makes up the cell wall of bacteria Penicillin kills bacteria by disrupting the polymerization of the peptidoglycan cell wall.
The illustration below shows the changes in the membrane potential of a neuron during an action potential. Which of the features noted below indicate the membrane potential that triggers the opening of the voltage-gated Na+ channels.
b
Both excitatory and inhibitory neurons form junctions with muscles. By what mechanism can inhibitory neurotransmitters prevent the postsynaptic cell from firing an action potential?
by opening Cl− channels
The illustration below shows the changes in the membrane potential of a neuron during an action potential. At which of the points indicated would you expect voltage-gated ion channels to be inactivated?
c
Which of the following components of the electron-transport chain does not act as a proton pump?
cytochrome c
Animal cell
does not have a cell wall or chloroplast and a small vacuole
Which reaction does the enzyme phosphofructokinase catalyze?
fructose 6-phosphate → fructose 1,6-bisphosphate
Which reaction does the enzyme hexokinase catalyze?
glucose → glucose 6-phosphate
What is the molecule that leaves the Calvin cycle to be converted into glucose?
glyceraldehyde 3-phosphate
If you shine light on chloroplasts and measure the rate of photosynthesis as a function of light intensity, you get a curve that reaches a plateau at a fixed rate of photosynthesis, x, as shown below.
increasing the number of reaction centers that contain special pair chlorophylls
In anaerobic conditions, skeletal muscle produces _____________.
lactate only.
At the beginning of the light reactions in photosynthesis, ________-energy electrons are taken from __________.
low; H2O
Neurotransmitters and neurotransmitter receptors
mediate communication between neurons at sites called synapses - the small gaps between neurons where chemical signals are exchanged. When stimulated, the presynaptic neuron releases neurotransmitter molecules into the synaptic cleft: Depolarization opens Ca 2+ channels ● Ca 2+ promotes fusion of synaptic vesicles ○ Synaptic vesicles contain neurotransmitter ○ Fuse with the plasma membrane of the presynaptic terminal ○ Release neurotransmitter into synaptic cleft Neurotransmitter diffuses across the synaptic cleft and binds to the neurotransmitter receptor in the postsynaptic neuron. Neurotransmitter receptor functions: ○ Neurotransmitter-gated ion channels (ionotropic receptors) can excite or inhibit neurons depending upon the ions they allow through ○ Metabotropic receptors can excite, inhibit, and alter other aspects of neuron physiology through intracellular signaling cascades P sychoactive drugs alter synaptic transmission ● Block reuptake of neurotransmitter and/or ● Bind to neurotransmitter receptors ○ Agonist - mimics the neurotransmitter ○ Antagonist - binds to the receptor but does not activate - block the action of neurotransmitte
Which of the following stages in the breakdown of the piece of toast you had for breakfast generates the most ATP?
oxidative phosphorylation
You measure the pH of the matrix a mitochondrion at 7.9. What would you expect the pH its intermembrane space to be?
pH 7.2
The energy in food is stored in chemical bonds How do we get it out in a usable form?
phosphoanhydride bonds: ATP - Adenosine triphosphate GTP - Guanosine triphosphate Electron carriers: FADH2 Flavin adenine dinucleotide NAD Nicotinamide adenine dinucleotide Cells obtain energy catabolizing (usually by oxidizing) macromolecules in food, especially sugars. To capture the energy released when sugars are oxidized to CO2 and H2O, the cell breaks this process down into a series of small steps each catalyzed by a different enzyme. This releases the energy in the chemical bonds of the sugar molecule in small increments that can be used to create high-energy chemical bonds in activated carriers like ATP or high-energy electrons in NADH. Digestion: ○ Food is first mechanically broken down by the teeth and gut ○ Within the gut, enzymes are secreted that break down polymeric molecules to simple monomers (e.g. Proteins → amino acids, Fats → glycerol + fatty acids, Polysaccharides (starch) → sugars) ○ These monomers can then taken up by cells through specific membrane transporters ● Glycolysis: ○ Occurs within the cytosol of the cell ○ Breaks down glucose → pyruvate ○ Require input of 2 - ATP ○ Yields 4 - ATP, 2 - NADH - ATP are produced by substrate-level phosphorylation ○ Does not require oxygen ● Citric acid cycle: ○ Occurs within the mitochondria ○ Acetyl-CoA (derived from pyruvate) → 2 CO2 ○ Produces 3 - NADH, 1 - FADH2, and 1 - GTP ○ GTP produced by substrate-level phosphorylation ○ Oxygen is required to regenerate electron acceptors ● Oxidative phosphorylation (detailed in Lecture 14) ○ Occurs across the inner membrane of mitochondria ○ Takes energy from activated carriers NADH and FADH2 produced in the citric acid cycle and uses it to pump H+ ○ The H+ gradient used to convert ADP → ATP ○ Captures a huge amount of energy in ATP
Which type of lipids are the most abundant in the plasma membrane?
phospholipids
Oxidative Phosphorylation (OxPhos)
produces the majority of the ATP in the cell when oxygen is available. In eukaryotic cells OxPhos occurs in the mitochondria. ATP is produced through chemiosmotic coupling, a process with two major steps; 1) High-energy electrons from, activated carriers (NADH and FADH2) generated in the citric acid cycle) move along the electron transport chain and give up energy that is used to pump protons (H+) across the inner mitochondrial membrane to create a large gradient. Oxygen is the final electron acceptor in the transport chain.2) The H+ gradient is then used to drive the ATP-synthase that phosphorylates ADP →ATP.
The lateral movement of transmembrane proteins can be restricted by several different mechanisms. Which mechanism best describes the process by which nutrients are taken up at the apical surface of the epithelial cells that line the gut and released from their basal and lateral surfaces?
protein movement is limited by the presence of a diffusion barrier (e.g. tight-junctions)
The final product of glycolysis is ___________.
pyruvate
In anaerobic conditions, fermentation is necessary to
regenerate NAD+ for glycolysis
Transporters, in contrast to channels, work by
specific binding to solutes
Flippase; Golgi Apparatus
the membrane reseals
In light reactions of photosynthesis, a proton gradient is generated and ATP is synthesized. Where do protons become concentrated in the chloroplast?
thylakoid space (lumen)
● Succinate dehydrogenase complex
○ Includes succinate dehydrogenase enzyme that is part of Citric acid cycle ○ Transfers two electrons (e -) to the ubiquinone from FADH2 ○ e- entering the chain here skip the first H+ pump and so generate slightly less energy ○ There are comparable complexes associated with beta-oxidation of lipids that handle the FADH2 generated there.
● Cytochrome c reductase complex
○ Pumps four H+ to the intermembrane space
Electron transport chain in detail
● NADH dehydrogenase complex ○ Oxidizes NADH ■ NADH from the citric acid cycle, Beta-oxidation, Glycolysis ○ Pumps four H+ to the intermembrane space ○ transfers two electrons (e-) to the ubiquinone
ATPase subunit to catalyze the phosphorylation of ADP → ATP
● Produces 3 ATP per rotation and up to 100 ATP per sec. ● The ATP synthase can also hydrolyze ATP → ADP and use that energy to run counter-clockwise and pump H+
OxPhos uses energy from transfer of electrons from NADH → O2
● Transfer occurs through steps in the electron transport chain ● NADH - low redox potential - -320 mV ● O2 - high redox potential - +820 mV ● Change in redox potential of -1,140 mV = -219.6 KJ/mol of energy