Review Final Questions from Stubbs Half
How are membranes used to store energy in cells? What is the name for energy stored in this way? Membranes store energy in the form of concentration gradients, which is a type of chemical potential. This is when the concentration of a certain molecule is built up on one side of the membrane, then when it is allowed to flow through the membrane, energy is released. Draw a phosphoglyceride. Choose specific components, and include complete molecular structures. Draw a sphingomyelin, including complete molecular structures. What is the difference between a cerebroside and a ganglioside? A cerebroside has a single simple sugar attached, where a ganglioside has an oligosaccharide, which is a string of simple sugars, attached. What types of lipids are glycolipids derived from in plants? in bacteria? in animals? In animals, glycolipids are derived from fats and oils. In plants and bacteria, they are derived from phosphoglycerides. Why do some lipids spontaneously form lipid bilayers? Lipids have a very hydrophillic head and very hydrophobic tail so they organize into bilayers to protect the hydrophobic tails. How can integral membrane proteins be removed from a membrane? Peripheral membrane proteins? Integral proteins can be removed by a detergent or organic solvent. Peripheral proteins can be removed from the membrane by an increased salt concentration, an acid, or a base. What are the two most common supersecondary structures (motifs) in integral membrane proteins? The alpha helical structure and the beta TIM barrels. What property of amino acid side chains allows us to predict the sequences of transmembrane alpha helices? Hydrophobicity Name three types of lipid that are found covalently attached to proteins, anchoring the proteins to a membrane. Lipids that are attached by a hydrocarbon chain, a fatty acid anchor, and a glycolipid anchor. What component lipids affect the fluidity of membranes, and what effect do they have? The temperature of the environment surrounding the cell affects the fluidity. When the temperature is warm, the membrane is more fluid; when it is cold, the membrane is less fluid. Cholesterol also affects the membrane by decreasing fluidity and permeability. List three ways in which membranes are asymmetric, in the sense that one surface is different from the other. 1) They have different lipid distribution. 2) Glycolipids and carbohydrates of glycoproteins are found on the outside of the plasma membrane. 3) The protein orientation of each side is different. How do the proteins in the plasma membrane of a red blood cell contribute to the shape of the cell?
Final Review Questions from Stubbs Half
Which would cross a membrane faster (give the order, from fastest to slowest): ethanol, oxygen, lysine, a protein? Oxygen, ethanol, lysine, a protein. Why does a potassium channel not allow sodium to cross the membrane? Because the ion channels are specific for each ion. A sodium ion would need a sodium channel, not a potassium channel. Briefly describe two ways in which a membrane channel can allow molecules to cross a membrane or prevent them from doing so. A membrane channel can be a voltage gated channel, which opens when there is a certain charge difference present. This usually happens when a postive or negative charged ion concentration forms. Another way a membrane channel is regulated is through a ligand-gated channel. This channel opens when a certain molecule binds to the protein, and closes when it is released. What are two sources of energy to drive active transport? Give an example of a protein that uses each type of source. Potassium is needed in high concentration inside the cell and sodium is needed in low concentration outside the cell. The cell uses a pump to maintain these necessary concentrations. There are specific binding sites where these molecules can go to cause a conformational change in the protein. Na+K+ATPase uses chemical energy to pump 3Na+ outside and 2K+ inside. Another source of energy that is used to drive active transport is a cotransport. One example is the sodium glucose cotransporter. Either a symport or an antiport is used to utilize the energy of a concentration gradient so that the molecules can be transported. What are the functions of the rough and smooth endoplasmic reticulum? At what locations in the cell are proteins modified? What types of modification are made where? Describe the structure of the Golgi network. Where in the cell are macromolecules broken down? Where are toxins modified to allow safe removal? How are plant vacuoles similar to lysosomes? How are they different? Outline the process by which a newly synthesized protein enters the ER. Outline the general process of vesicle transport. Outline the transport pathway for a protein to be secreted from the cell. Where does the transport pathway for secreted proteins diverge from the pathway for lysosomal proteins? Outline the transport pathway for a molecule entering a cell by endocytosis. What are the three known vesicle coat proteins, and for which pathways are they used? What are the functions of SNAREs? How do they carry out these functions? What is the key difference between prokaryotes and eukaryotes?
Final Review Questions from Stubbs Half
Why do most biologists not consider viruses to be living organisms? Which six elements commonly make covalent bonds in living organisms? Which four make the strongest covalent bonds? Write the general equations for the reaction of water with an acid, and with a base. What is the pK of a functional group? Could an acid have a pK of 10? If so, would you describe this acid as very strong, strong, weak, or very weak? List three types of non-covalent interaction important in biology, noting the key aspects of each. To which type do hydrogen bonds belong? What are the four classes of macromolecules? What are the precursors for each class? Which class(es) contain(s) structural molecules? Catalytic molecules? Molecules for energy storage? Draw, as a Haworth projection, a glucose molecule linked to a galactose molecule by an alpha-1,4 glycosidic linkage Write, using structural formulae, the equation for the condensation of two precursor molecules for any one of the classes of macromolecules. (This exercise is simply to see that you understand condensation structurally). Draw the structural formula for a general amino acid, with the amine and carboxylate groups in the ionized form. Use "R" for the side chain. Of the amino acids glutamate, lysine, phenylalanine, valine, and asparagine, which would most often be found on the inside of a folded protein? Which on the outside? Why? What special functions do glycine, proline, and cysteine have in folding proteins? Which five amino acid side chains are most often charged in proteins in solution? Which of these are acids? Which are bases? (For chemical precision, the un-ionized form is the acid or base.) What are the two most common types of secondary structure in proteins? What are the key dimensions associated with each? What is the most important principle in protein folding? (Which amino acid side chains go where?) What types of interaction stabilize the formation alpha-alpha of motifs? Sketch a reverse turn, showing general side chains (R1, R2 etc.), but specifying the precise location of the hydrogen bond. What is meant by the statement "sequence specifies structure"? Outline the steps in protein folding.
Final Review Questions from Stubbs Half
What is the name of the highest energy state during a chemical reaction? How does a catalyst change the energy of the participants in a chemical reaction? How do enzymes differ from other catalysts of biological reactions? Describe the most important general way in which enzymes work. Write the equation for the velocity of an enzymatic reaction as a function of substrate concentration. What is this equation called? In the equation from the previous question, what do Vmax and KM tell us about the enzyme? How do competitive and non-competitive inhibitors differ? In what way is the mitochondrial inter-membrane space effectively part of the cytosol? In what way is it effectively not part of the cytosol? Name two important functions of the mitochondrial matrix. List five similarities between mitochondria and bacteria. What are the principal chemical processes that take place in chloroplasts? In what ways are chloroplasts and mitochondria similar? What is the key difference? Compare the entry of proteins into the peroxisomes with the entry of proteins into mitochondria and chloroplasts. Most metabolic reactions are for one of three purposes. What are these purposes, and for each one, is this anabolism or catabolism? What are the three common ways in which cells store energy? Consider each of the compounds ATP, NADH and NADPH: How do they differ in energy carrying capacity? How do they differ in reducing capacity? How are NADH and NADPH used differently by the cell? Why do we need only small amounts of vitamins in our diets? (Answer only considering those vitamins that make coenzymes.) Write out the metabolic pathway from glucose to pyruvate. Include the names of all the metabolic intermediates as far as glyceraldehyde-3-phosphate. Include all involved molecules of ADP, ATP, phosphate, NAD+, and NADH. Mark the oxidation reaction. What is the committed step of glycolysis? What is the name of the enzyme that catalyzes this step? Name one activator and one inhibitor of this enzyme. Why is the reaction catalyzed by hexokinase not the committed step of glycolysis? (If you said it was in the previous question, go back and answer that question again!)
Final Review Questions from Stubbs Half
On the pathway in the first question (or better still, write out the pathway again), mark the entry points for glycerol, galactose, and fructose. Name four compounds in different pathways that can be produced from glucose-6phosphate. Name two important uses of the pentose phosphate pathway. On the pathway in the first question (or better still, write out the pathway yet again), mark the reactions that are NOT part of gluconeogenesis. Why are these reactions bypassed in gluconeogenesis? Give two ways (from different organisms) in which pyruvate can be metabolized in the absence of oxygen. Note reactions in which NADH is involved. Why are these metabolic reactions necessary? Write out the metabolic pathway in which pyruvate is completely oxidized to carbon dioxide and water. Include any metabolic intermediates mentioned in class, as well as all involved coenzymes, carbon dioxide molecules, and high energy molecules. (1) How can an oxaloacetate molecule be made from a pyruvate molecule? Note: converting the pyruvate to acetyl-CoA will not make a new oxaloacetate molecule; although the acetyl-CoA will go through the citric acid cycle to make an oxaloacetate molecule, the initial reaction will have used an oxaloacetate molecule, so there will be no net gain of oxaloacetate. (2) Why is this reaction necessary? What is the principal inhibitor of the citric acid cycle? Name four reactions from the citric acid cycle and the pathway leading in to the cycle that are affected by this inhibitor. Most regulated metabolic reactions have an important thermodynamic property in common. What is this property? For each of the complexes I, III, and IV: Outline the electron transfer process. Include any intermediate steps that you know, and note the number of electrons involved at any given point. What is the overall activity the complex? Include the overall transfer of electrons (the number involved, the starting carrier, and the final carrier), any protons pumped, and any molecules used or formed.
What are the key functional differences between Complex I and Complex II? What is the reason for these differences? In what way are FMN, FAD, and CoQ more versatile electron carriers than NAD+? Name two ways in which is NAD+ a more useful electron carrier than the others (This question does not come directly from the notes, but you should be able to answer it without consulting any other sources.) Outline the mechanism of action of ATP synthase.
Final Review Questions from Stubbs Half
In one or two lines, summarize each of the two sets of reactions that make up photosynthesis. What is the principal difference between a heme group and a chlorophyll molecule? Outline the process of electron transfer (a) in Photosystem II (b) in cytochrome b6f (c) in Photosystem I. Give the three ways in which protons can be pumped into the thylakoid lumen during photosynthesis. Outline the metabolic pathway in photosynthesis from the entry of carbon dioxide to the production of glyceraldehyde-3-phosphate. Include the involvement of any high-energy molecules. What is the enzyme that catalyzes the key step (the carbon fixation step) of this pathway? What is photorespiration? How do C4 plants avoid the problems of photorespiration? Describe the arrangement of subunits in singlet microtubules. Include GTP binding in your description. How do doublet and triplet microtubules differ from singlet microtubules? How are growing microtubules structurally related to centrosomes? List two functions of microtubule-associated proteins. Explain the action of dynein (a) on a microtubule reaching between two organelles in the cytoplasm (b) in a cilium. In what way is the effect of ATP on actin like that of GTP on tubulin? List as many functions for actin-binding proteins as you can. What is the general function of myosin? What is the energy source for this function? Describe the subunit structure of intermediate filaments. Compare the three types of cytoskeletal filaments. Include in your comparison structure (including diameter), function, and binding proteins. Describe the primary, secondary, tertiary, and quaternary structure of collagen. Compare the functions in the extra-cellular matrix of collagen, proteoglycans, and laminins and fibronectins. Compare the functions of integrins, cadherins, N-CAMs, and selectins In what ways are focal adhesions and adherens junctions similar? In what ways are they different?
Final Review Questions from Stubbs Half
In what ways are hemidesmosomes and desmosomes similar? In what ways are they different? Why do you think hemidesmosomes have that name? What are the functions of tight junctions? Gap junctions?