Bio Mini test 3

Explain Electrochemical Gradient

- Concentration gradient + difference in electrical potential -stores more energy than a typical concentration gradient involving solutes -takes more energy to create bc the similar charges repel each other Ex: -Na+ ions increase outside cell creating a surplus of positive charge outside the cell -Inside cell, a small amount of Na+ ions is more 'negative'(in comparison) ---'positive' charge attracted to 'negative' charge = wants to balance out charges

204. Name 4 groups of producers. What do producers do? What do consumers do?

- Four groups of producers are plants, algae, cyanobacteria, and purple/green sulfur bacteria. -Producers turn inorganic carbon into organic carbon to make organic molecules. - Producers can make their own organic carbon but consumers cannot. - Consumers receive their organic carbon by eating producers or other consumers.

189. Diagram the electron transport chain in detail.

-A series of proteins embedded in the inner mitochondrial membrane -Receives electrons from NADH and FADH2 -Transfers electrons to O2, producing H2O --O2 pulls the electrons -ETC proteins pump H+ into intermembrane space -Energy of NADH/FADH2 becomes proton gradient -Protons accumulate in the inter membrane space --Electrochemical gradient = proton motive force (PMF)

219. What is cyclic photophosphorylation?

-Cyclic photophosphorylation is when the need for ATP exceeds the need for NADPH and plants begin transferring electrons from photosystem I to cytochromes in their chloroplast electron transport channel. -Allows for pumping of protons without consumption of H2O.

Glycolysis(General)

-Does not directly use O2, Produces no CO2 - 2 ATP / glucose by substrate level phosphorylation - NAD+ is the oxidizer NADH is produced = Fermentation or cell respiration regenerate NAD+ 6 Carbon atoms of glucose end up as 2 pyruvate(3carbon atoms each) Regulation step: phosphofructokinase

205. What is fixed carbon? What is unfixed carbon? Name a process that fixes carbon.

-Fixed carbon is organic carbon. It is carbon with other groups of hydrogen or carbon. Ex: Glucose carbon - Unfixed carbon: CO or sometimes HCO - -A process that fixes carbon is photosynthesis.

206. Name 3 fossil fuels. How did the carbon atoms in those fuels become fixed originally?

-Three fossil fuels are coal, natural gas (methane), and petroleum. -The carbon in these fuels became fixed originally by plants fixing inorganic carbon into organic to which animals sometimes eat. These animals then breathe out inorganic carbon, decomposed by bacteria and fungi which makes inorganic carbon, or it may be fossilized which bind their carbon to rock. Due to correct conditions and time, these fossils may become fossil fuels.

156. Name a ring lipid found in the membranes of animals, plants, fungi, and bacteria. For the bacterial ring lipid, only the class of molecules is necessary.

1. Cholesterol (animals) 2. Ergosterol (fungi) -found in the fungi Ergot 3. Stigmasterol (plants) -recall stigma of plant 4. Hopanoids (bacteria)

198. Describe the following in detail. Fermentative metabolism Fermentation of sorbitol (a simple carbohydrate) Lactic acid fermentation reaction Ethanol fermentation reactions

1. Fermentative metabolism is 2. Fermentation of sorbitol (a simple carbohydrate) is 3. Lactic acid fermentation reaction is a reaction in which the 3-carbon pyruvate is converted to the 3-carbon lactic acid and regenerates NAD+. This allows glycolysis to continue to make ATP in low oxygen situations. The NADH donates its electrons to the 3-carbon pyruvate and reduces it into the 3-carbon lactic acid. The NADH reverts back to NAD+ (this is how it regenerates NAD+) C3H3O3 (pyruvate) + NADH→ C3H6O3 (lactic acid) + NAD+ 4. Ethanol fermentation reactions are reactions that convert glucose into two molecules of ethanol

185. Name the 4 stages of cell respiration. State the net reaction for each stage, omitting water molecules. Note, for the 4th and final stage, the net reaction does not need to be balanced. State where each phase occurs in a eukaryotic cell.

1. Glycolysis: Glucose + 2 NAD+ + 2 PI + 2 ADP → 2 Pyruvate + 2 NADH + 2 ATP + 2H+ NET: 2 ATP, 2NADH -occurs in cytosol -mnemonic ---> glu nad pi pad pad = adp 2. Pyruvate Oxidation: 2 Pyruvate + 2 CoA + 2 NAD+→ 2 Acetyl-CoA + 2 NADH + 2 CO2 NET: 2 NADH -occurs in mitochondria/bacterial cytosol 3. Krebs Cycle: 2 Acetyl-CoA + 6 NAD+ + 2 FAD + 2 Pi + 2 ADP → 4 CO2 + 6 NADH + 2 FADH2 + 2 ATP NET: 2ATP, 6 NADH, 2 FADH2 -occurs in mitochondria 4. Oxidative Phosphorylation (ETC + Chemiosmosis): 10 NADH + 10 FADH2 + 34 ADP → 10 NAD+ + 10 FAD + 34 ATP -occurs in mitochondria Cell respiration intermediate molecules have 6, 3, 2, 6, 5, and 4 carbon atoms, in that order

6 Classes of Enzymes

1. Oxidoreductases - Oxidation-reduction reactions 2. Transferases - Move functional group from one molecule to another ex kinase = taking atp and transferring it 3. Hydrolases - Break bonds (adding water across a bond) ex. phosphatase uses water to break phosphate group 4. Lyases - Break bonds without adding water 5. Isomerases - Rearrange a single molecule ex. glucose becoming galactose 6. Ligases - Join two molecules using the energy of ATP ex. dehydration synthesis

171. Cardiac muscle cells must rapidly remove calcium ions from their cytosol in between each heartbeat. These cells possess a variety of transport proteins including NKA, PMCA (plasma membrane calcium ATPase, a Ca2+ pump), and NCX (Na+/Ca2+ exchanger, which is an antiporter). 1. Explain how each of these proteins contributes to the removal of calcium ions from the cytosol. 2. Calcium ions trigger muscle contraction in a concentration dependent fashion. Explain how inhibiting the NCX transporter might increase the strength of muscle contractions.

1. PMCA = Always pumps Calcium out of the cell through primary transport NKA = Pumps sodium out and potassium goes in NCX = Pumps sodium into the cell and calcium out of the cell. c. PMCA is a pump that allows Ca2+ to move from the inside of the cytosol to the outside of the cell. For every Ca2+ that goes out, ATP is hydrolyzed into ADP & a H+ comes in. Slow and works @ very low concentration of Ca2+ ions. Excrudes 150 Ca2+/sec. Form of active transport. NCX (not found in all cells, found in large influx of Ca2+ ions) is faster than PMCa & excrudes 5000 Ca2+/sec. Works @ more extreme (high) concentration of Ca2+ ions. Takes in 3 Na+ ions and pumps out 2 Ca2+ ions. Form of secondary active transport bc it uses the electrochemical gradient of the Na+ ions that is already established across the membrane. NKA (sodium potassium pump) sets up the concentration gradient of Na+ ions. It excrudes 3 Na+ ions out of the cytoplasm in exchange of bringing in 2 K+ ions. Also hydrolyzes ATP into ADP. Inhibiting the NCX transporter might increase the strength of muscle contractions because NCX is a lot faster at transporting Ca2+ ions out of the cytosol compared the the PMCA. NCX is able to transport Ca2+ ions at a rate of 5000 Ca2+ ions/sec while the PMCA is able to transport Ca2+ ions at a rate of 150 Ca2+ ions/sec. Inhibiting the NCX transporter means that muscle contractions would need to increase in strength for the PMCA to do an equivalent job of removing Ca2+ ions compared to the NCX.

Describe the Enzyme Cycle

1. Substrate(s) bind active site, forming enzyme-substrate complex -substrates held by weak interactions -active sites can lower activation energy and speed up a reaction 2. Catalysis occurs, converting substrate(s) into product(s), and making the enzyme-product complex 3. Products are released; active site is available for more substrate(s); enzyme is ready to repeat the process

184. Name 3 nucleotide-based electron carriers. What are the abbreviations for their oxidized and reduced forms? Where do these molecules 'hold' electrons when reduced?

1. nicotinamide adenine dinucleotide oxidized/ reduced form = NAD+/NADH 2. flavin adenine dinucleotide oxidized/ reduced form = FAD+/FADH2 NAD+ and FAD are used primarily to capture energy during catabolism by shuttling electrons from food molecules to oxygen molecules 3. nicotinamide adenine dinucleotide phosphate oxidized/ reduced form = NADP+/NADPH. NADPH is used primarily for anabolism

209. What is the net reaction of the light dependent reactions?

2 H2O + 2 NADP+ + 3 ADP + 3Pi → O2 + 2 NADPH + 3 ATP -occurs in the thylakoid membrane

186. What happens during glycolysis? Explain the investment, harvest, cleavage, and oxidation phases.

4 Phases of Glycolysis 1. Investment Converting ATP(3 P) into ADP(2 P) "investing" bc 2 ATP is put into the system 2.Cleavage Turning sugar(C6) and splitting it(two C3-P's) "cleavage" = to split 3. Oxidation Oxidize NAD+ to NADH[exergonic] Exergonic reaction provides energy to attach inorganic phosphate to the two C3P to make two P-C3-P (1,3 BPG), NO ATP used 4. Harvest Making 4 ATP using substrate level phosphorylation #1. P-C3-P takes 1 ADP and turns it into 1 ATP to make C3 (PEP) and uses another ADP to make 1 more ATP to make C3 (pyruvate) [makes 2 ATP] #1. P-C3-P takes 1 ADP and turns it into 1 ATP to make C3 (PEP) and uses another ADP to make 1 more ATP to make C3 (pyruvate) [makes 2 ATP] Total: Glucose + 2 ATP + 2NAD+ = 2NADH + 2 Pyruvate +4 ATP NET gain: 2ATP and 2 NADH

177. What is the net reaction of aerobic cell respiration?

6 C6H12O2 + 6 O2 → 6 CO2 + 6 H2O + ATP Sugar is oxidized (meaning it is a reducing agent). Oxygen is reduced (meaning it is an oxidizing agent) CO2 is fully oxidized carbon Water is fully reduced Reduction = gain of electrons Oxidation = losing electrons LEO GER Electrons move between reactants in redox reactions Movement of protons is neither reduction nor oxidation Losing a hydrogen atom is oxidation, but losing a hydrogen ion is not oxidation

243. What is a GPCR? Diagram its structure and explain how each domain contributes to its function.

A GPCR (Growth protein-coupled receptor) couples with a G protein. GPCRs are the largest type of receptor type in animal cells. These receptors bind diverse ligands, including ions, organic odorants, peptides, proteins, and lipids. Light-sensing receptors are also part of this family, so we could even count photons as "ligands."

218. . Diagram the Z-scheme in detail. From the point of view of plants, what are the 2 goals of the Z-scheme?

A Z-scheme works by (Goals): -Reducing NADP+ to form NADPH (need for carbon fixation) - Make ATP Both of these in just the right amount to power the calvin cycle. P680 is photosystem 2 and P700 is photosystem 1

232. What is a cell-signaling receptor? What is a cell-signaling ligand?

A cell-signaling receptor is a protein that detects signals. A cell-signaling ligand is a molecule that binds receptors.

150. What is a coupled reaction? How do reactions become coupled?

A coupled reaction is when a spontaneous reaction is used to drive a nonspontaneous reaction. This is seen during ATP hydrolysis. The energy that ATP releases when hydrolysed is used to drive reactions such as the movement of sodium and potassium. If the ATP hydrolysis releases more energy than the other reaction consumes, then coupling the two reactions will produce an overall ΔG for the coupled reactions that is negative. That is, energy released by the hydrolysis of ATP can supply the energy needed by the endergonic reaction.

152. What are the structural differences between an animal plasma membrane and a phospholipid bilayer?

A phospholipid bilayer is what can spontaneously occur in the ocean. The phospholipid bilayer is just two layers of phospholipids with their hydrophilic head pointed towards water and hydrophobic tail pointed at each other. Animal Plasma Membrane have many different structures such as the cytoskeleton, proteins, and cholesterol.

212. What is a pigment? What makes a molecule into a pigment?

A pigment is a molecule that absorbs visible light, and reflect certain wavelength of visible light. These are made up by conjugated multiple bonds. Conjugated double bonds within the pigment (chlorophyll) allows them to set up energy levels that correspond to visible light. -allow electrons to delocalize(when electrons can move from one nucleus to another)

220. When might a plant use cyclic photophosphorylation? When might a plant use the Z-scheme?

A plant may use cyclic photophosphorylation during low CO2 concentration, low light intensity, and in bacterial photosynthesis. A plant may use the Z-scheme during high CO2 concentration, high light intensity, and in green plants.

225. Diagram the anatomy of a leaf. Why would a plant close its stomata? What are the consequences for a plant if its stomata stay closed when the sun is shining?

A plant would close its stomata in order to prevent water loss. However, plants don't keep their stomata closed at all times because the CO2 levels in the leaf will be depleted ,because they are being used within the Calvin Cycle, and the O2 levels in the leaf will increase, because the light-dependent reactions will create it. This is bad because the plant will undergo photorespiration. Photorespiration steals carbons and wastes energy.

238. What is a response element? Name 5 response elements.

A response element is the region of a DNA sequence that is a regulatory gene. They regulate the transcription of genes by turning on the transcription of an adjacent coding gene when the hormone-receptor complex attaches. This produces lots of mRNA, which will form proteins. Five response elements are: Cortisol (glucocorticoid receptor) Androgens, progesterones, and estrogens Aldosterone (mineralocorticoid receptor) Thryoxine / Thryoid hormone Vitamin D

147. What is an inhibitor? What is an activator? How do they work? Explain using the concepts of enzymes breathing.

A substance that binds to an enzyme and decreases its activity is called an inhibitor. Inhibitors: 1. Noncompetitive inhibitors - bind to the enzyme in a location other than the active site, changing the shape of the enzyme and making it unable to bind to the substrate a) Allosteric inhibitor - typically bind at an "allosteric site" which can exist in either an active or inactive conformation -site serves as an on/off switch; the binding of a substrate can switch the enzymes between its active and inactive conformations (changes shape of enzyme) 2. Competitive inhibitors -compete with the substrate for the same active site, occupying the active site and thus preventing substrates from binding Activators -Bind to the allosteric site in order to give proper shape to the enzyme -Sometimes activators can just increase the productivity of an enzyme, but other times they are the "switch" that allows activators to function a) Allosteric activator -binds to allosteric sites to keep an enzyme in its active configuration, thereby increasing enzyme activity

175. Consider the following hypothetical cell. Initially, the cell has an equal number of positive and negative charges (cations and anions) on either side of its plasma membrane (extracellular, intracellular). There are equal concentrations of Na+, K+, and Cl- on either side of the plasma membrane. Consider the effects of the following events, in sequence, upon the ion concentrations and charge distributions (membrane electrical potential). A. NKA proteins are activated in the plasma membrane. How does this affect the ions and the membrane electrical properties? B. A small number of K+ channels open in the plasma membrane. How does this affect the ions and the membrane electrical properties? C. An even larger number of Na+ channels open in the plasma membrane. D. The Na+ and K+ channels close. Cl- channels open.

A. - 3 Na+ ions will diffuse out of cell and 2 K+ ions will diffuse into the cell - Higher concentration of Na+ outside of the cell B. - K+ ions will diffuse into the cell - Higher concentration of K+ inside of cell C. - More Na+ ion will diffuse out the cell - Higher concentration of Na+ outside of the cell

190. What does ATP synthase do?

ATP synthase pumps H+ ions back into the mitochondrial matrix which powers the ATP synthase complex to attach phosphate onto ADP to make ATP.

202. Which of the cell respiration enzymes is regulated, according to lecture? Why does it make sense for this enzyme to be regulated? What inhibits this enzyme? What activates this enzyme?

According to lecture, the cell respiration enzyme that is regulated is Phosphofructokinase (PFK). -It makes sense for this enzyme to be regulated because PFK catalyzes the ATP phosphorylation that converts Fructose 6-phosphate to Fructose 1,6-bisphosphate and ADP. - PFK can regulate glycolysis through allosteric inhibition. - This allows the cell to regulate the rate of glycolysis to match the cell's energy requirement. -Inhibited by ATP and citrate -Stimulated by AMP

215. Diagram an action spectrum. Explain the diagram in detail.

Action spectrum A measure of efficiency of different wavelengths of light for photosynthesis In plants, it corresponds to the absorption spectrum of chlorophylls Indicates the rate of photosynthesis for each wavelength/frequency

Secondary Active Transport

Active Transport: Secondary -Electrochemical gradient drives moment of solute #1 (usually an ion) down its gradient(high to low concentration = spontaneous/exergonic) -Solute #2 is transported up its gradient at the same time(low to high concentration = endergonic and uses energy from exergonic reaction) -ATP used indirectly to create electrochemical gradient for solute #1 -The electrochemical gradient for solute #1 is the used to move solute #2 against its gradient Cotransporter/Symporter: -moves both in OR both out Antiporter: -moves one in and the other out

161. Define: active transport. How is active transport different from passive transport?

Active transport Primary -Movement of solutes against concentration gradients(bc they are directional) -Requires energy(coupled to ATP hydrolysis) Ex: Proton pump or Na/K ATPase (Sodium/Potassium pump) -ATP is providing an irreversible step to give protein directionality In contrast to passive transport, active transport: Requires energy Moves molecules against the concentration gradient May require an ion pump

170. During periods of dehydration, mammals release antidiuretic hormone (ADH). Kidney cells in the collecting ducts respond by inserting aquaporins in their membranes. Explain how this response is adaptive. (You may need to independently research the structures involved.)

An adaptive response is a response from a cell which can lower stress. Antidiuretic hormone is a hormone created in the hypothalamus in order for your body to retain water in a state of dehydration. When your body signals that your body is in a state of dehydration it wants to retain the water in your kidney and bring it back to your body. When the Kidney cells recognize ADH it begins adding aquaporins in their membrane in order to give back water to the bloodstream.

169. Aquaporins are water channels that passively transport water molecules. Are aquaporins necessary for water to cross a membrane?

Aquaporins are not necessary for water to transport across a membrane. Although water is polar, it is still small enough for some diffusion across the membrane to occur.

230. What are relative advantages and disadvantages of the C3, C4, and CAM metabolic pathways?

C3 Plant Metabolic Pathways Pros/Con: Pros: Lowest Energy Cost Cons: High water loss in drier areas and higher photorespiration in hot areas C4 Plant Metabolic Pathways Pros/Cons: Pros: Minimize photorespiration by using a more efficient enzyme to fix CO2 and shuttling fixed carbon via malate to bundle-sheath cells. Minimize water loss because PEP brings in CO2 faster so the stomata does not have to be open as long Cons: 30% of more energy is required CAM Plant Metabolic Pathways Pros/Cons: Pros: Minimize photorespiration Loses least amount of water Cons: Energetically expensive Only in extremely dry conditions water/mild temp/wet = C3 pathway, but as soon as stroma closes it means photorespiration; cannot adapt to high temp. C4/CAM have adaptations to high temp/dry conditions but produces less sugar and require more ATP so less efficient at photosynthesis

231. Why are C3 plants called C3 plants? Why are C4 plants called C4 plants? If you performed a similar experiment on CAM plants, what would be the results?

C3 Plants and C4 Plants are named the way they are because they are named after their metabolism in the Calvin Cycle. C3 Plants use CO2 and turn it into a 3-carbon molecule C4 Plants use CO2 and ATP and turn them into a 4-carbon molecule. If you performed a similar experiment on CAM plants, the CAM plant would take CO2 and the 3-carbon molecule and turn them into a 4-carbon molecule.

227. How do C4 plants cope with photorespiration?

C4 plants cope with photorespiration by having Phosphoenolpyruvate (PEP) fix CO2 to become oxaloacetate (C4) which becomes malate. The malate moves to the bundle sheath and releases CO2 directly into the Calvin Cycle when it is degraded to pyruvate. The pyruvate then moves to the mesophyll and becomes PEP (Phosphoenolpyruvate).

140. What is a catalyst? Describe how enzymes achieve catalysis.

Catalyst: -A substance that increases the rate of a reaction by lowering the activation energy. -Enzymes achiveve catalysis -Stressing particular chemical bonds can make them more unstable and easier to break. -The process of influencing chemical bonds in a way that lowers the activation energy needed to initiate a reaction is called catalysis, and substances that accomplish this are known as catalysts Enzymes achieve catalysis by: 1. Orienting substrates 2. Straining substrate bonds 3. Creating a local environment that favors the reaction 4. Covalently bonding to the substrate 5. Stabilizes transition state intermediate ----- all 5 lower the activation energy --Enzymes do NOT change ∆G

235. How do cells recognize each other?

Cells recognize each other because the membrane proteins of the two, different cells directly interact. A common example of this is when lymphocytes recognize antigen presenting cells.

180. Diagram the structures of the following. Citric acid, pyruvate, glucose, acetic acid, CO2, hexanoic acid. What is the average oxidation number for each of the carbon atoms in each?

Citric acid has an average oxidation number of 1 for each carbon atom Pyruvate has an average oxidation number of 0.67-- for each carbon atom Glucose has an average oxidation number of 0.33- for each carbon atom Acetic acid has an average oxidation number of 0 for each carbon atom CO2 has an average oxidation number of -4 for each carbon atom Hexanoic acid has an average oxidation number of 1.33- for each carbon atom

phospholipid structure

Composition: Polar Head + phosphate group + glycerol + 2 fatty acids -pure phospholipids form a bilayer in the presence of water

228. How do CAM plants cope with photorespiration?

Crassulacean Acid Metabolism (CAM) plants cope with photorespiration by closing their stomata during the day and only opening it at night. This means that no CO2 can enter during the day. CAM plants take in CO2 at night and fix it into organic molecules. CAM plants lose the least amount of water and has the lowest amount of photorespiration compared to C3 and C4 plants.

199. Summarize deamination and amination. Which would be used to make a molecule that can fit into the cell respiration pathway? Which would be used to make a building block for protein synthesis?

Deamination is the removal of an amino group from a protein. Amino Acid → organic acid + NH3 -This is used to make a molecule that can fit into the cell respiration pathway. Amination is the addition of an amino group to an organic acid to form a protein. Organic Acid + NH3 → Amino Acid -This is used to make a building block for protein synthesis

221. What happens to the pH of the stroma during the light-dependent reactions?

During the light-dependent reactions, the pH rises because there is a lower H+ concentration. The pH of the thylakoid is becoming more acidic because the cytochrome complex is pumping H+ ions into the space.

143. Why are many enzymes sensitive to pH and temperature? Diagram and explain the reaction rate vs temperature graphs.

Enzymes = proteins = amino acids - amino acids hold a specific structure that can be disrupted by the typical factors that denature a protein( heat/pH) Rate vs Temp: - temp = motion of molecules - energy/ frequency of collisions increases, making for a better induced fit -too much energy, protein unfolds --For thermophiles = induced fit doesn't occur bc it needs for the substrate to approach site at a certain amount of collision speed

141. What is the induced fit model of enzymes?

Enzymes have active sites: -Substrates bind to the active site of an enzyme (non-covalent interactions) -Collision energy and binding energy cause a conformational (shape) change in the enzyme, resulting in tighter binding -This distorts some of the covalent bonds in the substrate, making those bonds weaker

142. Enzymes sometimes covalently bond to substrates. How can this be true if enzymes are not consumed by reactions?

Enzymes sometimes covalently bond to substrates. This can be true if enzymes are not consumed by reactions by: Whatever covalent bond the enzyme makes has to be reversed by the end.

229. Name 1 example of each of the following: C3 plant, C4 plant, CAM plant.

Examples of C3 Plants: Iris flowers Rice Grass Examples of C4 Plants: Corn Sugarcane Tropical grasses Examples of CAM Plants: Cacti Pineapple

148. Define endergonic and exergonic. Which term applies to the hydrolysis of ATP? Which term refers to processes that do not happen without further energy input?

Exergonic reactions -Spontaneous and thermodynamically allowed -Applies to the hydrolysis of ATP, which is where nucleotides are connected -reduce energy in molecules, and G<0. Endergonic reactions -not allowed and will not occur by itself -only happens when they are coupled with an exergonic reaction like in ATP hydrolysis which is strongly exergonic This is always a positive number, G>0

183. Compare and contrast oxidative cellular respiration with the burning of firewood.

Fire: -combining O2 with carbon rich compounds such as cellulose in wood -fire releases energy all at once -In fire, electrons are taken from wood (cellulose) and transferred to O2 to make CO2 and H2O Cell: -C-C, C-H rich molecules are oxidized completely (to CO2) during cell respiration -Aerobic cell respiration uses O2 -Cell respiration releases energy in small steps, allowing some of it to be captured -Each small step of cell respiration allows a small amount of energy to be captured -In cell respiration, the O2 still receives the electrons but only after it has passed through many hands, i.e. electron carriers

153. What is the 'fluid mosaic' model of a membrane? Describe 1 experiment that demonstrates the fluid mosaic model. Describe specifically one exception or extension to the fluid mosaic model.

Fluid mosaic model experiment Experiment: Label human and mouse cell membrane proteins and fuse cells Result: Proteins evenly diffuse throughout hybrid cell Conclusion: Membrane proteins are free to diffuse laterally through membrane (fluid mosaic model) -diffuses on surface/ 2D diffusion of proteins Revision: -Some proteins only diffuse laterally in portions of the plasma membrane (only the apical or only the basolateral regions of the membrane) -- want this bc cells have different functions - Fluid mosaic model refers to how the patterns (proteins) are constantly changing.

157. Describe 7 functions carried out by membrane proteins. Note, some proteins carry out more than 1 function.

Functions of Membrane Proteins: 1. Enzymes -One way to organize biochemical pathways 2. Cell-surface identity markers -cell recognition -Often involves glycoproteins 3. Intercellular junctions -Anchor cells -Create a waterproof barrier between cells -Allow rapid communication between cells 4. Transport proteins - the doors in the barrier allowing large molecules and polar molecules to enter or exit the cell 5. Signal transduction proteins (receptors) --aka cell-surface receptors -Detect signals and conditions outside cell Ex: Norepinephrine receptor 6. Anchoring to the extracellular matrix (ECM) 7. Anchoring to the cytoskeleton Memorization tool = AJ TRACE: 1. Anchor 2. Junction 3. Transport 4. Receptor 5. Anchor 6. Cell 7. Enzyme

242. What are G proteins? Name 2 large groups of G proteins. How do G proteins work?

G proteins bind nucleotide guanosine triphosphate (GTP) and nucleotide guanosine diphosphate (GDP) together. The G protein gets inserted between the receptors and the enzyme (effector). The ligand binds to the receptor which activates it and consequently activates the G protein. The activation of the G protein activates the effector protein. Two large groups of G proteins are heteromeric and monomeric The function of G Protein is to link GPCR to an effector protein. The G Protein is active when bound to GTP and inactive when bound to GDP. When a ligand attaches to a G Protein, G-Alpha disassociates and remains bound to GTP. G-Beta and Gamma remain together. G-Alpha or G-Beta and Gamma may stimulaector protein. The effector protein will then make a cellular response

167a. Describe how the structure of the cells that line the small intestines. Explain how these cells could import 100% of the glucose in the intestinal lumen into the bloodstream. Include the role of the pancreas in this process. Describe the transport processes involved.

Glucose can move from the lumen of the gut to the bloodstream by two proteins. The first protein it encounters is the Na+ driven glucose symport. With the assistance of sodium/glucose is able to cross its first membrane into the intestinal epithelium. As more glucose is pushed into the intestinal epithelium, the epithelium builds a concentration gradient. As the concentration gradient increases the glucose is more likely to enter the carrier protein mediating facilitated diffusion of glucose and cross into the extracellular fluid. It is possible for glucose to cross through the intestinal lumen and into the bloodstream because of concentration gradients.

163. Explain this statement: When glucose molecules are passively transported across a membrane they always flow from high glucose concentration to low glucose concentration, but when potassium ions are passively transported across a membrane, they do not always flow from high potassium ion concentration to low potassium ion concentration.

Glucose has many options of going through a membrane. Although glucose is too large to fit through the plasma membrane there are different proteins which can facilitate the diffusion of glucose from high concentrations to low concentrations. In order for glucose to diffuse, all it requires is a carrier protein. Potassium on the other hand requires NKA(Sodium Potassium ATPase), heat, and ATP in order to cross the plasma membrane. NKA pumps require ATP and if ATP is limited it can not quickly move through the membrane

149. Create a labeled reaction coordinate diagram for the following: Glutamic acid + NH3 → glutamine ATP + H2O → ADP + Pi ATP + Glutamic acid + NH3 + H2O → ADP + Pi + glutamine

Glutamic acid + NH3 → glutamine (Endergonic) + ATP + H2O → ADP + Pi (Exergonic) = ATP + Glutamic acid + NH3 + H2O → ADP + Pi + glutamine -exergonic reaction allows endergonic reaction to occur

234. Define the following: hormonal signaling, synaptic signaling, paracrine signaling.

Hormonal signaling is signaling molecules to travel through the circulatory system. Blood/hemolymph (animals) = endocrine Phloem (plants) Synaptic signaling is neurotransmission. Synapse = small gap between secreting and receiving cells Diffusion occurs over the small distance Secreting cells = neurons, release neurotransmitters Receiving cells = muscle fibers, glands, and neurons Receiving cells have receptor proteins immediately adjacent to where the transmitting cell releases signal molecules (increased efficiency/speed) Paracrine signaling is secreting and diffusing delivers signaling molecules to nearby cells Tissue organization

174. Kidneys need a lot of ATP to function. Using your answers above, explain why.

Kidneys use a lot of ATP in order to use the proton pumps.

214. Why do leaves usually appear green? Why do the leaves of an oak tree appear yellow or orange in the fall?

Leaves usually appear green because they contain the pigment chlorophyll a. This pigment absorbs red and blue light, thus emitting a green color. Some plants like oak trees appear yellow or orange in the fall because as temperatures dip, Chlorophyll A is broken down into smaller molecules. These molecules absorb colors that allow for the visibility of the orange color we see.

236. Compare and contrast the ligands of intracellular and extracellular receptors.

Ligands of intracellular and extracellular receptors: Intracellular Found in the cytoplasm of the cell and respond to hydrophobic ligand molecules that are able to travel across the plasma membrane Once inside the cell, many of these molecules bind to proteins that act as regulators of mRNA synthesis to mediate gene expression. Gene expression Cellular process of transforming the information in a cell's DNA into a sequence of amino acids that ultimately forms a protein When the ligand binds to the internal receptor, a conformational change exposes a DNA-binding site on the protein The ligand-receptor complex moves into the nucleus, binds to specific regulatory regions of the chromosomal DNA, and promotes the initiation of transcription Can directly influence gene expression without having to pass the signal on to other receptors or messengers Extracellular Cell surface, membrane-anchored, or integral proteins that bind to external ligand molecules Ligands that interact with cell-surface receptors do not have to enter the cell that they affect Cell-surface receptors Also called cell-specific proteins or markers because they are specific to individual cell types

208. What is the net reaction of photosynthesis, as performed in plants?

Light + 6H2O + 6CO2 -> 6O2 + glucose

144. What is a metabolic pathway? What do the arrows in a metabolic pathway indicate?

Metabolic pathway: -assembly line that takes reactant and makes a series of new reactants The pathways indicate: 1. different reactions 2. the enzymes.

182. Define the following: metabolism, anabolism, catabolism. What are 2 different types of catabolic reactions? What are 2 different types of anabolic reactions? Which of these 4 reaction types releases useful energy for a cell? Which reaction types require the cell to supply energy?

Metabolism = All of the chemical processes that a cell undergoes Anabolism = Anabolism builds molecules up Metabolic processes that require ATP/electron carriers/ NADPH since they are endergonic reactions. Simple → Complex Ex: amino acids ----> Protein Two different types of anabolic reactions are lactic acid fermentation and dehydration synthesis Catabolism - Catabolism breaks molecules down Metabolic processes that do not require ATP/electron carriers since they are exergonic reactions. Complex → Simple (Break carbon-carbon bond by oxidation) Ex: 1. hydrolysis = converts macromolecules into simpler molecules =====Starch + H2O-----> glucose 2. glycolysis = Oxidation breaks carbon-carbon bonds, releasing energy ====== Glucose + O2------>CO2 + H2O

210. What is the net reaction of the Calvin cycle?

NADPH + ATP + CO2 -----> CH2O AKA light-independent reactions, carbon fixation cycle, dark reactions -Reducing equivalents (NADPH) and ATP combine with CO2 using the enzyme RuBisCO - Does not use light directly but does require ATP and NADPH from light-dependent reactions - Will not happen in the dark -Takes place in the stroma of chloroplasts

164. Describe the functioning of the NKA. What does NKA stand for?

NKA is Sodium Potassium ATPase. The functions of NKA is to move sodium and potassium. It moves sodium from high concentration to low concentration and moves potassium from low concentration to high concentration. In order for this movement to take place it requires ATP. As a result inorganic phosphate is one of the byproducts of NKA. 1. Waits for 3 Na+ ions to bind. 2. Once bound, the protein changes shape, activates domain of protein that breaks down ATP, takes phosphate off ATP and sticks it to the protein 3. Protein becomes phosphorylated, protein opens to outside and releases 3 Na+ ions 4. Waits for 2 K+ ions to bind 5. Once K+ binds to protein binds to active site, phosphate is cut off, changes shape, reorients so that it is now open to inside of cell 6. K+ is released towards inside of cell --Cycle repeats

172. The kidney is a complex organ that consists of millions of renal tubules. Each renal tubule has a lumen. Blood is filtered in the kidneys; cells and large proteins found in the blood remain in the blood, while water and numerous small solutes enter the lumen of the renal tubules. The cells that line the renal tubules reabsorb most of these nutrients and put them back in the blood. The cells of the proximal convoluted tubule reabsorb glucose out of the renal tubule. How might this work? Consider that the concentration of sodium ions in blood is approximately 140 mM. (You may need to independently research the structures involved.)

NKA pumps sodium out and potassium in, concentration is diff?? -facilitated diffusion protein carried out by FD -symporter = secondary active transport -main = NKA - NKA(sodium potassium atpase) breaks down ATP sodium/glucose cotransport/symport in where glucose goes down its gradient.

146. Define negative feedback. Give an example of negative feedback in a metabolic pathway.

Negative feedback is when the response to the stimulus opposes the stimulus. -signified by arrow with line at head of arrow ex: When people sweat. The stimulus (high body temperature) stimulates a response (vasodilation/perspiration). This response opposes the original stimulus(high body temp) and it stops. ex Feedback inhibition ( a type of negative feedback) - Also called end-product inhibition - Enzymes often carry out a series of reactions to produce a single product (metabolic pathway) - In order to save valuable molecules and/or energy, it is sometimes advantageous to turn off the first enzyme in the pathway when enough product has accumulated - When the final product is the inhibitor, it is feedback inhibition

179. What is 1 other function that cell respiration serves? HINT: couch potato.

One other function that cell respiration serves is to create fats.

193. What is oxidative phsphorylation? Where does it occur?

Oxidative phosphorylation is basically ETC + Chemiosmosis. It's when ATP is formed as a result of the transfer of electrons from NADH or FADH2 to O2. This occurs in the inner mitochondrial membrane.

196. Why is oxygen needed for the ETCs of eukaryotes to function?

Oxygen is needed for the ETCs of eukaryotes to function because Oxygen is the final electron acceptor and is electronegative to pull electrons off of the carriers.

160. Define: passive transport. Describe 2 general types of passive transport. Describe 2 different categories of proteins that carry out passive transport. Note: the prior 2 questions are not the same question. What is the energy supply for passive transport?

Passive transport - Facilitated diffusion by passive transporters -disspiates concentration gradients or electrochemical gradients 1. "Carrier" proteins Movement of sugars, amino acids, and other small molecules -membrane that oscillates (open facing either inside the cell or outside, never both) -specific shape = binds only certain molecule (similar to enzymes) ex Glucose transporter 4 2. Channels Rapid movement of ions across a membrane Energy source is thermal due to collisions -specific = only allows certain ions through ex: water channel (aquaporin) or ion channel

226. What is photorespiration? Explain how it affects a plant.

Photorespiration is the process that occurs when there is a high amount of O2 and a low amount of CO2. This is a problem because Rubisco has trouble differentiating between CO2 and O2. Rubisco will pair RuBP and O2 instead of RuBP and CO2 which will lead to photorespiration. This wastes ATP, oxygen, and ultimately burdens the plant. In addition, it makes RuBisCO slightly toxic to the plant. It takes 40 chemical reactions, mitochondria, chloroplasts, and peroxisome organelles in order to reverse photorespiration.

176. What is pinocytosis? How does it compare to phagocytosis? What is receptor-mediated endocytosis?

Pinocytosis When a cell engulfs liquid -compartments that break off are smaller than in phagocytosis -cells that do it do it constantly -cell drinking; smaller compartments (vesicles) generally containing solutes Phagocytosis When a cell engulfs a structure - cell eating; solid particles(cells, etc) visible in phagosome Receptor-Mediated Endocytosis -When a receptor protein on the cell surface is used to capture a specific target molecule -have membrane proteins(receptors) -causes membrane to change shape -membrane becomes distorted and make a "pit" -pit becomes deeper until edges of pm fuse together until there is a vesicle inside cell ex: excretion/ bulk Pinocytosis and RM endocytosis vesicles move to endosomes are similar to phagolysosomes

233. Describe the functions of plasmodesmata and gap junctions.

Plants: The function of the plasmodesmata is to directly connect the cytosol of two cells. The plasma membrane of one cell is continuous with the plasma membrane of the other cell and forms a narrow passageway between them. The cytoplasm of both cells is thus connected and small molecules can pass from one cell to another. Animals: The function of gap junctions is to form a protein channel between two cells. One subunit of protein, called a connexon, penetrates the plasma membrane of the other and connects with that connexon and joins together. They both allow for rapid diffusion of signals produced in one cell into the neighboring cell.

145. Define positive feedback. Give an example of positive feedback in a metabolic pathway.

Positive feedback is seen during labor. The stimulus("cervical stretch") will stimulate oxytocin production which will cause a uterine contraction and push the baby further toward the cervix which causes more contractions. This response will stimulate more oxytocin, and so on until the baby is born and the stimulus stops.

143. Diagram and explain the reaction rate vs pH

Rate vs pH: -enzyme has optimal pH at peaks -different depending on the enzyme ex: pepsin enzyme in stomach favors acidic pH trypsin enzyme in intestine favors basic pH

223. What does RuBP stand for? How many carbon atoms does it have? What does G3P stand for? How many carbon atoms does it have?

RuBP stands for ribulose bisphosphate. RuBP has 5 carbons. G3P stands for glyceraldehyde 3-phosphate. G3P has 3 carbons.

224. What does Rubisco stand for? What does it do?

Rubisco stands for ribulose bisphosphate carboxylase. It catalyzes the reaction between CO2 and RuBP.

194. True or false: ADP receives electrons to become ATP.

Semi-true. ADP turning to ATP requires phosphate. A phosphate (PO43-) group contains an electron.

168. Sodium ions and potassium ions are both spherical. Na+ ions have a smaller radius than K+ ions. How is it possible for Na+ channels to reject K+ ions? How is it possible for K+ channels to reject Na+ ions?

Sodium is smaller than potassium. Sodium channels can easily reject potassium ions because potassium is too large to fit into a sodium channel. Potassium pumps can reject sodium ions because of the structure of the protein. In the structure of a potassium channel, there are oxygen atoms which build the inside of potassium. Potassium is able to cross through these channels because the position of the oxygen atoms make potassium easily lose its hydrogen sphere in exchange for the oxygen inside the protein. For sodium these oxygen molecules are too far for the sodium to exchange its hydration sphere for oxygen atoms.

159. Why do soluble molecules diffuse in water? What is the energy supply for diffusion?

Soluble molecules diffuse in water, because of a concentration gradient/entropy/disorder/heat. Entropy reasoning: - When there is a high concentration of a solute in one area, it is natural for the solutes to diffuse in order for the solution to lose its concentration gradient. - The energy supply for diffusion is heat. One of the special properties of a cell membrane is that it is capable of creating a concentration gradient by being selectively permeable.

187. What is substrate-level phosphorylation? Where does it occur?

Substrate-level phosphorylation: When ADP is directly phosphorylated to become ATP. This only occurs when a reaction is coupled with an exergonic reaction. or ATP is formed by transferring a phosphate group directly to ADP from a phosphate-bearing intermediate, or substrate This process occurs in the cytoplasm during glycolysis and in the mitochondria during the Krebs Cycle.

166. What is antiport? Name an antiporter. What is symport? Name a symporter.

Symports are co-transporters that move substances in the same direction. ex: Sucrose - H+ cotransporter Antiports are exchangers, these move substances in the opposite direction. ex: NKA

237. What are the 2 large categories of responses that cells show when exposed to signaling molecules? Describe each category and give specific examples.

The 2 large categories of responses that cells show when exposed to signaling molecules is altered gene expression and altered physiology. Altered gene expression is when there is increased transcription of a gene that results in a greater amount of a specific protein being synthesized. This generally takes hours to weeks for a response. Altered physiology is when enzymes, transporters, and/or other proteins are activated or inhibited. This generally takes milliseconds to hours for a response.

222. Explain the Calvin cycle.

The Calvin Cycle takes place in the stroma of chloroplasts. Reducing equivalents (NADPH) and ATP combine with CO2 using the enzyme RuBisCO 3C5 (RuBP) + 3CO2 ----->3C6---->6C3 6C3 +ATP + NADPH------>3C5 (RuBP) + 1 C3 (G3P) G3P can be used to build carbohydrates

154. Diagram a molecule of phosphatidylcholine in detail. Other phospholipids have slightly different structures. Which parts are different between different phospholipids? Which parts might be different between the phosphatidylcholine of salmon and the phosphatidylcholine of ostriches?

The R group of phospholipids change. Phosphatidylcholine is a phospholipid with choline at the end. The phosphatidylcholine of salmon and ostrich may differ. The phospholipid of salmon may: Have unsaturated bonds within the fatty acid which make the membrane more loose. This is necessary, because they live in cold environments. ----lipids liquid at cold temps need more unsaturated bonds The phospholipid of an ostrich may: Have more saturated bonds within the fatty acid

203. Explain the adenylate kinase reaction. What is the cellular function of AMP? Why might a cell do the adenylate kinase reaction?

The adenylate kinase reaction is ADP + ADP ⇋ ATP + AMP -When ATP concentration is low, ADP is scavenged in order to make more ATP and AMP. - AMP signals that scavenging is happening and activates PFK. - This process is reversed when ATP is high and ADP is low. - The cellular function of AMP is to stimulate Phosphofructokinase (PFK).

200. How does the catabolism of proteins relate to cell respiration? How does the anabolism of proteins relate to cell respiration?

The catabolism of proteins relates to cell respiration because it removes the amine group from proteins which allow it to fit into the cell respiration pathway. It prepares the molecule to enter Krebs cycle or Glycolysis. The anabolism of proteins relates to cell respiration because it adds the amine group to a carboxylic acid in order to form a building block for protein synthesis. Amino acids frequently have 3, 4, 5, or 6 carbon atoms ---->feed into glycolysis or TCA after deamination/desulfuration

201. How does the catabolism of triglycerides relate to cell respiration? How does the anabolism of triglycerides relate to cell respiration?

The catabolism of triglycerides relates to cell respiration because it breaks the glycerol (3 Carbons) from the fatty acid tail. The fatty acid tail now has an even number of carbons and is broken into 2-Carbon units, and fed in as acetyl-CoA

197. What is the cellular function of fermentation? How does it relate to cell respiration? What are the advantages and/or disadvantages of fermentation compared to cell respiration?

The cellular function of fermentation is to turn pyruvate to alcohols/acids. This relates to cell respiration because this is a process that regenerates NAD+ and allows glycolysis to continue without the requirement of oxygen. The advantage of fermentation is that it does not require oxygen and gives you quick bursts of energy. The disadvantage of fermentation is that it is not sustainable because of the formation of lactic acid and alcohol which causes muscle fatigue.

192. What happens to the conditions in the matrix and intermembrane space during cell respiration?

The conditions in the matrix and intermembrane space become acidic or have a lower pH because there are H+ ions accumulating in it. During cell respiration, the matrix pumps H+ ions into the intermembrane space during the ETC. The intermembrane space pumps back the ions into the mitochondrial matrix during ATP synthase.

191. What is the connection between the ETC and ATP synthase.

The connection between the ETC and ATP synthase is that the Electron Transport Chain (ETC) pumps protons into the intermembrane space. The protons in the intermembrane space accumulate and create an electrochemical gradient or a proton motor force (PMF). The PMF drives movement of protons through the ATP synthase.

195. Is the following reaction endergonic or exergonic? ADP + Pi ---> ATP + H2O

The following reaction is endergonic because it requires energy from a coupled reaction in order to become more complex (ADP -> ATP)

188. Explain this statement: When glucose undergoes aerobic cell respiration, the carbon atoms in glucose are oxidized completely, but glucose never directly interacts with oxygen molecules.

The glucose never directly interacts with the oxygen molecules because the oxygen molecules are being carried by electron transporters. The oxygen only interacts in the electron transport chain.

151. Create a labeled reaction coordinate diagram for the hydrolysis of sucrose. Show the effect of an enzyme. Also include a diagram of the transition state.

The hydrolysis of sucrose is an exergonic reaction. This diagram shows a different example, but still with an exergonic reaction using an enzyme.

178. What is the main purpose of cell respiration?

The main purpose of cell respiration is to make ATP/energy for the cell's processes by breaking down glucose.

213. What are the wavelengths of visible light? Why is visible light visible to us?

The wavelengths of visible light are 380-740 nm. Light is visible to us because our rods and cones can only interpret specific wavelengths of light in that range. We can only process those wavelengths in our brain.

158. What is a transmembrane domain? Which structures do transmembrane domains usually have? Why?

Transmembrane domain: - A region within the plasma membrane that contains a domain composed of hydrophobic amino acids arranged into alpha helices Reasoning: -Polypeptide backbone needs water to hydrogen bond = H-bonds are satisfied through alpha helices ex: N-C-C needing water to H-bonds, vs helix bonding with itself Structures: -alpha helices -beta sheets

216. Name 2 accessory pigments. What are the functions of accessory pigments.

Two accessory pigments are beta-carotene & chlorophyll b. Functions: - Enhance absorption - Protect chlorophyll from excess light - Protect cells against free radicals, highly reactive molecules with unpaired electrons that are sometimes produced by electron transfer reactions

211. How does the wavelength of light relate to the energy of a particle of that light?

Wavelength and particle energy are inversely proportional. The longer the wavelength the smaller in energy. The higher in energy, the shorter the wavelength.

155. Summarize the permeabilities of small molecules and ions through a pure phospholipid bilayer. Why will ethanol molecules cross while Na+ ions will not, even though ethanol molecules are larger than Na+ ions?

Will cross: -Gases, small uncharged polar molecules 1 .Small, nonpolar gas molecules 2. Ethanol is small and somewhat polar Sometimes crosses: -water/urea 3. Water is smaller but more polar; urea is larger and polar; both show less ability to cross than ethanol = but will sometimes pass through 4. Abundance of water means it will cross when it is a significant amount Will not cross: -large uncharged polar molecules, ions, charged polar molecules, ions 5. Ions will not cross because they must lose hydration spheres inside bilayer 6. Large charged polar molecules ex. ATP, Amino acids ex amino acids in water = zwitter ion 7. Large uncharged polar molecules ex. glucose

217. Diagram a photosystem. How does a photosystem work?

special pair held by proteins like carotenoid pigments, when light strikes pigments, they transfer energy from one pigment to the next (resonance energy transfer), electrons in special pair get super excited and they jump off special pair onto the primary electron acceptor -after they lost electrons, special pair is now oxidized