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Biochemistry
bioenergetics & metabolism & membranes
| Question | Answer |
|---|---|
| Main component in composition of membranes? | lipids(phospholipids) + proteins |
| What is the diameter of a membrane? | 5-8um meaning multiple differences |
| Is the membrane visible in an electron microscope? | no |
| What are the membranes like in terms of permeability and compartments? | selectively permeable and separate compartments |
| What is the outermost layer of animal cells? | cytoplasmic membrane |
| Is the membrane ridgid or flexible? | flexible |
| What is the memb. vulnerable to&how much? | somewhat vuln. to osmotic pressure |
| FMM:waht structures are on the extracellular side? | glycolipid (sphingolipid in human) and glycoprotein made up of oligosacharrides |
| FMM:waht type of layer does it have? | lipid bilayer |
| FMM:where is cholesterol found? | cytoplasmic side in with the individual phosopholipids |
| FMM:what types of proteins are found on the cytoplasmic side? | peripheral protein or integral protein |
| FMM:what are the 2 types of peripheral proteins? | can be covalently linked to a lipid and do not span the mem. or non-covalent bond |
| FMM: how do Ca++ and peripheral proteins interact? | Ca++ embedded between negatively charged phosopholipids and negatively charged R-groups of peripheral proteins |
| FMM: What are the types of integral proteins? | single transmembrane helix or a mutiple trans-membrane helix |
| What are the three types of membrane lipids motion of single phospholipids in a bilayer? | uncatalyzed transverse "flip-flop" diffusion, trasverse diffusion catalyzed by flippase, or uncatalyzed lateral diffusion |
| How does the flippase work? | lowers activation energy for lipids to get to other side of the membrane |
| How are the lipids kept inside the bilayer? | the activation energy is high |
| Why are the inner and outer membranse not reflected as mere images in terms of lipid distribution? | the inner and outer membranes act seperately but are both hydrophobic |
| What is the key enzyme for apoptosis? | phosphatidylserine |
| What type and how many AA are needed in an alpha-helix membrane-spanning protein? | hyrdophobic AA and approx 20 of them together |
| Where do the C-terminus and N-terminus ends go in an alpha-helix membrane? | there are no rules about them needing to be on inside side or outside side of the bilayer |
| Are the majority of membrane proteins that span the membrane alpha-helix or beta-barrel? | alpha-helices |
| How are beta-barrel membrane proteins produced? | produced as monomers by bacteria |
| What are the beta-barrels released into environment as? | exotoxins |
| The beta-barrel conformation spanning a membrane needs how many AA? | 7-9 AA |
| What are barrels made up of? | 20 beta-zigzag backbones |
| What types of R-groups do Beta-barrels have? | mix of hydrophobic and hydrophilic |
| What does alpha-hemolysine do? | toxin makes holes in cytoplasmic membrane of RBCs monocytes |
| What is alpha-hemolysine produced by? | gram-positve staphylococcus aurens |
| Which beta-barrel membrane proteins are in outer membrane of gram negative bacteria? | "porins"--FepA, OmpLA, Maktoporin, TolC |
| Membrane fusion includes...? | budding of glogi vesicles, exocytosis, endocytosis, viral infection, fusion of egg+sperm, cell division |
| Only plants can do this type of membrane fusion? | fusion/formation of vacuole(s) |
| What gradients are at work if a solute is at equilibrium? | concentration gradient and charge gradient to reach no net flux of solute |
| The solute needs what type of membrane to reach what type of potential? | semipermeable membrane to reach membrane potential |
| What are the classes of transport systems? | uniport or co-transport |
| Uniport means? | one substance enters the cell |
| Co-transport is made up by...? | symport and antiport |
| What is a symport? | two substances enter the cell |
| What is antiport? | one substance comes in while one substance leaves |
| What is the point of active transport? | to use energy to transport substances against the concentration gradient |
| Primary active transport? | goes against law of thermal dynamics by going against electrochemical gradient...needs energy (ATP) to go High inside-low outside |
| Secondary active transport? | against electrochemical gradient, driven by ion moving down its gradient. as ion goes in from high to low the substance come out from high to low |
| Facilitated diffusion? | down electrochemical gradient and substrate follows gradient from high outside-low inside |
| Simple diffusion? | no transport w/ nonpolar compounds only (gases O2, CO2, CO, N) down concentration gradient |
| Ion channel? | down electrochemical gradient: may be gated by a ligand or ion |
| Ionophore-mediated ion transport? | down electrochemical gradient w/in a capsule |
| Passive transport? | no energy needed for substance to go with concentration gradient |
| What is GLUT 1 and its function? | membrane transport protein D-glucose for facilitated diffusion and passive transport |
| What does a chloride-bicarbonate exchanger consist of + function? | the exchange of CO2 in respiring tissues and in lungs. Simple diffusion b/c of gas CO2, antiport b/c one goes in and one goes out preventing formation of electrochemical gradient |
| Membrane Transport Protein in Bacteria? | symport for secondary active transport of lactose as low lactose comes in to high and high H+ comes in to low H+, facilitated diffusion gelps H+ back out to high H+, primary active transport of H+ in proton pump using ATP(feul to CO2 against gradient) |
| The transport system(s) in sodium potassium pump?=antiport, primary active transport (needs ATP), Na+ and K+ are the electrochemical gradient in nerve cells. K+ high inside and Na+ high outside. 3 Na+ out for every 2 K+ in. | antiport, primary active transport (needs ATP) |
| What are the electrochemical gradients in nerve cells? | Na+ and K+ |
| which substance is high inside and low outside with Na+/K+ pump? | K+ high inside and Na+ is high outside |
| What is the ratio of Na+/K+ in the pump? | 3 Na+ out for every 2 K+ in |
| metabolism? | sum of all BIOCHEMICAL rxn's in an organism |
| catabolism? | sum of all DEGRADATIVE rxns, yields ATP |
| anabolism? | sum of all BIOSYNTHETIC rxns, requires ATP |
| Cellular respiration gives off what? | ATP |
| Is cellular respiration aerobic or anaerobic? | aerobic |
| What happens to C and O when it goes from photosynthesis to cellular respiration? | C is reduced to an organic compound and O is oxidized to O2 |
| What does photosynthesis require? | sunlight |
| What happens to C and O when cellular respiration goes to photosynthesis? | O is reduced to H2O and C is oxidized to CO2 |
| What takes away energy in this cycle? | when C is oxidized to Co2 |
| What is the equation conversion for cellular respiration to photosynthesis? | "glucose" C6H12O + 6 O2-->6 CO2 + 6 H2O |
| High potential energy includes what side of the equation? | C6H12O + 6O2 |
| Equation for respiring tissue? | glucose-->CO2 + H2O --(carbonic anhydrase)-->HCO3- + H+ +Cl- |
| Equation for lungs? | HCO3- + H+ + Cl- --(carbonic anhydrase)-->Co2 + H2O-->glucose |
| link between oxidation and reduction? | universal electron carriers/redox partner is NADH & FADH2. they take the H from other things |
| CoA function? | means co-enzyme A which attaches to biomolecule to make the biomolecule more reactive |
| what forms when glucose id broken down? | CO2 |
| what is the universal energy carrier? | ATP |
| C-C-C:2 electrons removed it is a___? 3 electrons are removed it is a___? 4 electrons removed it is a ___? | -ketone/aldehyde -carbonyl -CO2 |
| cellular respirations goal of its first two steps? | form Co2 from breakdown of glucose with steps of glycolysis and acetyl-CoA fro pyruvate |
| Cellular respiration: Stage 1? | "Acetly-CoA production" is breaking down nutrients to C2-level (CH3-C=O-S-CoA) |
| Cellular respiration: Stage 2? | "Acetyl-CoA oxidation" is complete oxidation of carbon, NAD+ & FAD become reduced-->NADH & FADH2 |
| Cellular respiration: Stage 3? | "Electron transfer and oxidative phosphorylation" is NADH&FADH2 are oxidized, O2 is reduced, redox rxn yield energy in form of ATP |
| What occurs in the Preparatory phase of glycolysis? | in cytoplasm, phosphate is attached to glucose (C6) and its conversion to 2 glyceraldehyde 3-phosphate (C3). investment of energy is 2 glucose |
| what occurs in the payoff phase of glycoysis? | in cytoplasm, oxidative conversion of 2 glyceraldehyde 3-phosphate to 2 pyruvate (C3) with formation of 2 NADH and 4 ATP. |
| Net energy gain for glycolysis stage? | 2 ATP per glucose |
| What does a kinase enzyme do? | transfer phosphate grp from one organic molecule to another (typically involving ATP) can be a donor or recipient |
| waht class is kinases in? | Class 2 "transferases" grp transer rxn |
| what does an isomerase, mutase do? | create isomers or more functional grps within a molecules |
| What class is an isomerase, mutase in? | Class 5 "isomerases" transfer of grp with/in molecules to yields isomeric form |
| What does a dehydrogenase do? | redox rxn (w/ involvement of universal e- carriers) |
| what class is a dehydrogenase? | class 1 "oxidoreductase transfer e- |
| what does an aldolase do? | breaks covalent bonds w/in organic cmpds |
| what class is an aldolase? | class 4 "lyases add grps to double bond or formation of double bonds by removal of groups (not oxidation or condensation) |
| What doea an enolase do? | remove or add H2O to convert C-OH into -C=C- or vice versa |
| What class is enolase? | class 4 "lyases" add grp to double bond or formation of double bonds by removing grps (not condensation or oxidation) |
| enzymes do what? | catalyze cmpds or rxns |
| What does the inner membrane of a mitochondria contain? | complexes I-IV, ATP synthase |
| what does the matrix of mitochondria contain? | pyruvate dehydrogenase complex, citric acid cycle enzymes |
| rxn of Pyruvate to Acetyl-CoAt? | per glucose: 2 pyruvate (C3) --(2 NAD+) (2 CoA-SH) (give 2 NADH)-->2 CO2 (C1) + 2 Acetyl-CoA (C2) |
| PDH complex needs what? | 4 B vitamins so the person can make enough energy and not feel tired |
| The five coenzymes of PDH complex? | coenzyme A: pantothenic acid (B5) NAD+: Niacin (B3) FAD: Riboflavin (B2) TPP (thiamine pyrophosphate): B1 Lipoate (lipoyllysine) |
| The -SH end of CoA forms? | forms a thioester w/ carboxy grps |
| how many steps in the CAC or KREB cycle? | 8 |
| how many exzymes are required for the CAC or KREB cycle? | 8 |
| how many cycles does a glucose go around? | 2 times for every individual glucose |
| special alpha-ketoglutarate dehydrogenase? | similar in structure to PDH complex. 3 enzyme present in mulitple copies. 5 coenzymes, 4 derived from B vitamins |
| special enzyme Succinate DH? | protein associated with membrane by being attached to inside of mitochondria & complex II of electron transport chain |
| Respiratory chain consists of? | electron transport chain + ATP synthesis |
| Oxidative Phosphorylation goals? | produce ATP, form H2O by reducing O2, respiratory chain |
| in respiratory chain, complex I? | NADH DH, Fe2+required |
| in respiratory chain, complex II? | succinate DH, Fe2+ required, FAD prosthetic grp |
| in respiratory chain, complex III? | ubiqinone-ctochrom C, has heme and requires Fe2+ |
| in respiratory chain, complex IV? | cytochrome oxidase, contains a heme and dependent on Cu2+ and Fe2+ |
| pH in the matrix of oxidative phosphorylation? | high in matrix |
| extracellular enzymes in digestive tract? | lactose, trehalase, sucrose, glycogen |
| lactose intolerance brings about what symptoms? How? | diarrhea, abdominal cramping by increasing osmolarity in intestinal tract |
| fermentation defn? | a process that yields energy (2 ATP/glucose) by recycling NADH back to NAD+ and reducing an organic e- acceptor (pyruvate) |
| pyruvate as terminal electron acceptor | carbonyl -->hydroxy grp eith redox rxn in anaerobic skel m |
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