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Cell Biology Performance Goals for Exam I


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Identify by name and chemical properties the major functional groups found on the carbon backbones of biological molecules.
hydrocarbon- hydrophobic, non-polar, neutral, hydrophobic interactions
hydroxyl- hydrophilic, polar, neutral, hydrogen bonding
carboxyl- hydrophilic, polar, negative charge at pH greater than 4, hydrogen bonding, ionic interactions
amino- hydrophilic, non-polar, positive charge below pH 8-10, hydrogen bonding, ionic interactions
phosphate- hydrophilic, polar, negative charge at pH 7, ionic interactions
carbonyl- hydrophilic, polar, neutral, hydrogen bonding
sulfhydryl- relatively hydrophobic, polar, neutral, disulfide bonds
Explain how non–covalent interactions hold molecules together.
ionic bonds- formed by charged side groups
hydrogen bonds- formed between two polar side groups or a polar side group and water, oxygen and nitrogen become negativish while hydrogen becomes positivish
hydrophobic interactions- hydrogen bonding excludes non-polar molecules so non-polar molecules aggregate in order to minimize the surface contact to water
Van der Waals forces- electric dipoles between molecules at close range, nonspecific force between two complementary shaped surfaces
1. includes fatty acids, triglycerides, phospholipids, glycolipids, and sterols
2. used for signaling, membranes, and energy storage
fatty acid
a lipid with long hydrocarbon chain with a -COOH end (barely soluble)
a lipid polymer with three fatty acids condensed with glycerol used mainly to store energy and in membranes
phospholipids and glycolipids
two lipids tails attached to a backbone, a third polar, hydrophilic head group
a lipid cyclic hydrocarbon used to modify chemical properties of membranes and as the basis of signaling molecules and metabolic precursors
3-9 carbon backbone, position of side groups sets physical and chemical properties, -OH and -C=O groups react internally to form rings, very hydrophilic
built of 5 carbon sugar (ribose or deoxyribose), 1-3 phosphates, 1 of 5 nitrogenous bases; sugar and phosphate form linear polymer backbone with bases pointing outward; nucleotides are linked into a chain through phosphodiester bonds; backbone is negatively charged, polar, and very hydrophilic; hydrogen bonds connect complimentary base pairs; DNA stores genetic code in cell; RNA carries information, forms structural elements, catalyzes reactions, and controls cell processes
amino acid
composed of an amino group, an R group, and a carboxyl group; R groups differ in size, hydrophobicity, charge, and hydrogen bonding ability; R groups affect a protein's 3D structure, function, and ability to interact with other molecules; proteins function as the main catalysts in cells and in cell structures, movements, signaling, and regulation
Draw both a condensation and hydrolysis reaction for a given set of monomers.
Hydrolysis: AB + water= A + B
Condensation: A + B= AB + water
List as well as visually identify the major classes of amino acids, and describe the key physico–chemical properties for each class.
simple non-polar- hydrocarbon side chains, hydrophobic
unusual non-polar
polar non-charged- hydroxyl or carbonyl side chain, hydrophilic, hydrogen bonding
polar negative charged- carboxylic acid side chain, hydrophilic, hydrogen bonding
polar positive charged- amino side chain, hydrophilic, hydrogen bonding
Explain how primary amino acid sequence, disulfide bonds, hydrogen bonding and other intermolecular interactions generate alpha–helices and other secondary structures.
Proteins have a linear sequence of amino acids specified by DNA instructions. Disulfide covalent bonds can form between cysteines and cause the protein to fold. Amino acids react to form 3D structures (polar vs. nonpolar). Regularly spaced hydrogen bonds on every fourth amino acid coils chain into stiff rod. Chain folds back on itself to form hydrogen bonds between groups large distances apart.
Explain how forces lead to domain formation, and higher orders of protein structure.
Domains form independently according to intermolecular interactions. They perform distinct functions and may reshuffled due to mutations. Domains are brought together to form 3D protein structure, which ranges from globular to fibrous.
Know the general purposes for coenzymes and cofactors, and describe at least two relevant examples of each.
Coenzymes and cofactors are specific small ions or molecules that help proteins and other molecules work correctly. Cofactors are usually metal ions. Magnesium is part of the reactive core of the enzyme DNA polymerase. Zinc-fingers found in transcription factors help the protein form a particular structure. Coenzymes are more complex and extend functional properties of proteins. Many are carriers for specific atoms or functional groups. Thiamine is required for enzymes that transfer aldehyde groups. Coenzyme A carries acyl (2-carbon) groups.
Explain (and give examples in support) the general principles of Gibbs free energy, free energy change for a reaction, and activation energy for a reaction.
The energy in the covalent bond of molecules that is available for work is Gibbs free energy. Free energy change is the difference in the Gibbs free energy of the products and the substrates. Cellulose and oxygen are at a higher energy than carbon dioxide and water. Activation energy is required to strain chemical bonds, raise overall kinetic motion, overcome molecular forces stabilizing the substrate, and form transient chemical bonds between the substrates.
Describe three ways cells drive reactions.
Keep concentrations of substrate much higher than concentration of product. Use one product as the substrate for another reaction. Couple a reaction with positive delta G to one with negative delta G.
Describe at least three major mechanisms by which enzymes catalyze reactions.
Enzymes direct substrates into a transition state with the lowest activation energy. Mechanisms include increasing local concentration of substrates and orienting substrates to favor a particular interaction. Transient changes to the substrate include inducing changes in charge and bending or straining to destabilize the substrate. Another method is temporarily destabilizing the enzyme itself by altering the R groups.
Summarize the major structural similarities and differences between phospholipids and glycolipids.
Phospholipids and glycolipids both have two tails, a backbone, and a head group. Phospholipids have two fatty acid tails, a glycerol backbone, phosphate, and a variable head group which can be polar or non-polar, charged or non-charged. Glycolipids have a fatty tail, a fatty acid tail, a serine backbone, and choline or sugars as the head group.
Draw a schematic diagram showing all major components of a cell membrane.
Lipid bilayers is composed of phospholipids and glycolipids. The hydrophilic/polar heads are located on the periphery with the hydrophobic tails in the middle. Sterol increases hydrophobicity.
Use the physicochemical properties of membrane lipids to explain why lipid translocation between the two halves of a bilayer is rare.
The hydrophilic head cannot go through the hydrophobic middle very easily.
Explain how and why non–saturated hydrocarbon tails affect the fluidity of the lipid bilayer.
Non-saturated hydrocarbon tails have double bonds in them. These double bonds introduce kinks into the chain, causing the lipids to not pack as tightly. Because they do not pack as tightly, a lower temperature is required to line them up to form a solid. This is especially important for plants because their cells are at the temperature of whatever it is outside.
Predict which membrane is more or less fluid.
Whichever membrane has more double bonds is more fluid.
Identify environmental conditions under which saturated or unsaturated lipids would be more common.
Saturated would be more common at higher temperatures while unsaturated would be more common at lower temperatures.
Describe the locations and give general functions for membrane–associated carbohydrates.
Glycolipids are almost always located on the outside membrane because they interact with the outside world.
Describe the location, physical properties, and major features of integral proteins.
The portion in the bilayer is usually an alpha helix 20-30 amino acids long and featuring mainly hydrophobic R groups. The few hydrophilic groups pull in helices and and hold them together. Membrane proteins often have attached oligosaccharide, making it a glycoprotein, which are used for protein processing, cell-cell recognition, and ligand binding sites.
Describe the location, physical properties, and major features of peripheral proteins.
Peripheral proteins are associated with lipids and other proteins via non-covalent intermolecular interactions. They can be forced off by high salt concentration, pH change, or change in the anchoring molecule.
Describe the location, physical properties, and major features of lipid-anchored proteins.
Lipid-anchored proteins, which can be on intra- or extracellular faces, are covalently linked to membrane phospholipids and glycolipids. The covalent bond is cleaved by treatment with phospholipases.
When given the position and function of a protein or domain, predict what general classes of amino acids would be expected in that domain or protein.
Amino acids in bilayer will be hydrophobic. Amino acids associated with peripheral proteins will be charged and polar.
Provide specific examples of biologically relevant integral, peripheral, and lipid–anchored proteins.
Cells recognize glycoproteins (integral proteins with attached oligosaccharide). Specific human and pig glycoproteins form the basis for transplant rejection. Peripheral proteins like spectrin and ankyrin are the major component of the membrane scaffold. Two lipid-anchored proteins, Src and Ras, have been implicated in the transformation of a normal cell to a malignant state.
Describe pores/channels.
Channels are selective and allow only one type of ion to pass through. The flow is driven by simple diffusion. Gating is regulated by environmental stimuli including voltage changes, chemical signals, physical stimuli, and membrane changes.
Describe passive carrier proteins.
A molecule binds, causes protein shape change, and bound item is carried across the membrane. This does not require energy. An example of this is the glucose symporter, which can be regulated by bringing the transport proteins inside the cell.
Describe active transporters/pumps.
Pumps can actively transport molecules against their concentration gradients using ATP. The sodium-potassium pump sets up an electrical and chemical gradient.
Explain the general differences between catabolic and anabolic cellular processes. Define examples of each.
Catabolic processes break things down and capture energy. Anabolic processes build things and use energy. Both of these can consume ATP. An example of a catabolic process is breaking glucose down into carbon dioxide and water. An example of a anabolic process is synthesizing nucleic acids from nitrogenous bases.
Explain why glucose catabolism (glycolysis) is considered the central process of cellular metabolism.
Many reactions branch off the central path of glycolysis. Anabolic reactions use intermediates as substrates. Catabolic reactions come back by the same path.
Give examples of macromolecular monomers and intermediates that are produced or degraded via the central processes.
The carbon that is used to manufacture serine comes from 3-phosphoglycerate. If a cell wants to destroy serine, it can strip off the amino group and convert it back to 3-phosphoglycerate. Often the anabolic pathway of succinyl CoA to heme, but heme-like chlorophyll is catabolized in intestinal epithelial cells. Actin and myosin are also broken down by cleaving off an amino group.
Define a redox reaction. Explain why reduced molecules contain more Gibbs free energy than oxidized ones.
A redox reaction occurs when the number of electrons or the amount of energy in a molecule changes. In oxidation a molecule loses electrons; in reduction a molecule gains electrons. Reducing adds more energy. Reduced molecules contain more Gibbs free energy because electrons move downhill to less negative redox potential (delta E) and release energy in the process.
Explain the evolutionary origin of plastid organelles.
Redox reactions have a problem with the stage with the unpaired electron. Radicals are extremely destructive, so cells have to be able to control redox reactions. About 2.5 billion years ago, a group of organisms split off from the prokaryotes. Around 2 billion years ago, a very early eukaryote engulfed a bacterium for its nutrients. This bacterium had the ability to undergo redox reactions. After plants and animals split 1.5 billion years ago, plants engulfed a second plastid that had the ability to form high-energy, reduced bonds.
List at least two pieces of evidence for why plastids are believed to be endosymbionts.
Every mitochondria has its own DNA which codes for proteins. These proteins resemble bacterial proteins. Mitochondria were endocytosed. Their outer membrane resembles cell membrane while the inner membrane looks like bacterial membrane.
Explain the major redox reactions in the two photosystems used for photosynthesis.
Photons of light excite electrons in the ring structure of the chlorophyll. The antennal pigments all transfer the energy they gain to the reaction center. Once enough energy builds up at the P680 chlorophyll, an electron jumps off completely and goes through similar reactions until it reaches plastoquinone. The free radical plastoquinone is going to want another electron. Once it gets that -2 charge, it picks up two hydrogens to form plastoquinol. When P680 loses its electron, it becomes positively charged. Manganese can donate electrons to P680. Manganese then becomes positively charged, but it has the ability to split water and go back to neutral. The hydrophobic molecular oxygen diffuses through the membrane and the proton gradient is built up. Plastoquinol diffuses inward toward the lumen. When it passes near cytochrome b6f, it oxidizes again. It transfers two electrons to cyt b6f and drops two protons into the lumen. When the electrons are transferred to cyt b6f, energy is released. Cyt b6f uses this energy to pump two protons into the lumen. Cyt b6f then releases the electrons to plastocyanin. At the same time, photosystem I is absorbing sunlight. P700 drops an electron when it gets excited. The electron is transferred through intermediates to ferredoxin, which has an extremely large redox potential. It reduces NADP+, at the same time removing hydrogen from the stroma. P700+ is regenerated from plastocyanin.
Explain the differences between NAD+, NADP+, NADH, and NADPH.
NAD+ and NADP+ are oxidized molecules that can accept two electrons to form reduced NADH and NADPH. NADP+ has a phosphate group on the ribose of the adenine. NADP+ is used in anabolic reactions because the phosphate is used to put molecules together while NAD+ is used in catabolic reactions.
List the four major contributors to the proton gradient across the thylakoid bilayer, and how that gradient is used to manufacture ATP.
The four major contributors are the removal of four protons from the stroma by plastoquinone, the cleaving of two waters to leave four protons in the lumen, the pumping of four protons across the membrane by cyt b6f, and the removal of two protons from the stroma by two NADP+. As hydrogen flows down its concentration through ATP synthase, ATP is made.
Balance a general equation for inputs, outputs of carbon in a light–independent (Calvin) cycle of a C3 plant.
Enzyme complex called Rubisco combines three carbon dioxides and three 5-carbon ribulose bisphosphates. Three unstable, 6-carbon intermediates form. These split, forming six 3-carbon molecules, five of which are used to regenerate the three molecules of ribulose bisphosphate. Rearrangement using 9 ATP and 6 NADPH forms 3-carbon glyceraldehyde 3-phosphate and three 5-carbon ribulose bisphosphate.
List and balance the carbon inputs and outputs of general glycolysis.
Two phosphate groups are added to glucose using two ATPs, resulting in fructose 1,6-bisphosphate. This is cleaved to produce two 3-carbon glyceraldehyde 3-phosphate. From those two G3Ps, two NADHs and four ATPs are produced and two pyruvates are formed.
Explain why cells must regenerate NAD+.
In glycolysis, NAD+ must be able to oxidize glyceraldehyde 3-phosphate. If no NAD+ is present, no redox reaction will happen. NADH also has a lot of energy stored in it with its two nitrogenous bases and two sugars. Throwing it away would be too costly.
Major mechanisms by which different cells regenerate NAD+.
Some cells add two electrons back to pyruvate to generate lactic acid. Other cells removed carbon dioxide from pyruvate and add two electrons to form ethanol. In the aerobic path, electrons are transferred to the super electron hungry oxygen and hydrogens are added to make water.
Describe the general inputs and outputs of the citrate cycle.
3-carbon pyruvate loses carbon dioxide and two electrons (to form NADH) to become 2-carbon acetate. Acetate is attached to the carrier molecule coenzyme A. Acetyl CoA is transported into the matrix of mitochondria. It binds to 4-carbon oxaloacetate producing the very energetically favored 6-carbon citrate. Rearrangements occur, and carbon dioxide and high-energy electrons are released which are picked up by NAD+. This happens again. Phosphate is also used to made GTP from GDP. 4-carbon succinate is oxidized to fumarate, reducing FAD to FADH2 in the process. Fumarate is rearranged into the oxidized malate, which reduces NAD+, regenerating oxaloacetate.
Explain in general terms the role of citrate cycle in amino acid and fatty acid catabolism and anabolism.
To burn fatty acids, we convert them back to 2-carbon acetate and send them through the citrate cycle. Fatty acids are made using exact opposite of condensation reaction. In amino acid catabolism, the amino (toxic waste group) and R groups are cut off, leaving a 2-carbon acetate to feed into citrate cycle. All twenty amino acids can be fed into some point of the citrate cycle. Amino acids can be manufactured by pulling precursors out of the citrate cycle.
Explain the function of each complex in the electron transport system.
NADH dehydrogenase in iron-containing Complex I aligns NADH to release its electron to Complex I. Complex I transfers the electrons to ubiquinone. The energy released is used by Complex I to pump four protons into the intermembrane space. Ubiquinone picks up two hydrogens to form ubiquinol and migrates up and over to transfer the electrons to Complex III. It releases its two hydrogens into the intermembrane space. Complex III donates electrons to cytochrome c. The energy released is used to pump two protons into the intermembrane space. The peripheral molecule cyt c migrates to release the electrons to Complex IV. Complex IV dumps electrons onto oxygen and uses energy released to pump two more protons. Two protons are picked up by 1/2 O2 with two electrons to form water. Complex II picks up electrons from FADH2 and transfers them to ubiquinone.
Describe the structure and operation of both the F1 and Fo components of the mitochondrial F1/Fo ATPase complex.
Fo complex in membrane is a water wheel pore which hydrogen diffuse back indirectly. Diffusion of hydrogen rotates attached gamma subunit of F1 complex. Subunit a consists of two offset hydrogen half-channels. Subunit c has twelve copies which surround gamma subunit. Each c subunit has a hydrogen binding pocket lined with - amino acids. Protons from intermembrane space pass into top half of subunit a, bind to c, and rotate away from a. Transfer of twelve protons rotates subunit c/gamma complex 360 degrees. Protons is released into matrix at twelfth position. The F1 complex in matrix is bound to the inner membrane and makes ATP. Rotation of the central gamma subunit controls molecular shape of three ATP synthase complexes. Complexes are made up of alpha/beta subunits. As they go around in one open (cannot bind ADP), loose (binds ADP and phosphate), and tight (aligns ADP and phosphate so they react) cycle, one ATP is formed.
Explain how cells regulate their overall rate of ATP production.
Intracellular [ADP] determines general rate of respiration. High ADP triggers rise in respiration rate; O2 consumption also rises. As ATP accumulates, O2 use drops. If there is ample ATP, cells shift molecules away from energy production. Cells emphasize branch products, anabolic reactions and store energy as glycogen, fat droplets. Cells can also uncouple electron transport to produce heat.
When given the properties of an inhibitor of the electron transport chain, predict which carriers will accumulate in their oxidized state and which will accumulate in their reduced state.
If you drop an inhibitor in, the molecules downstream are going to donate their electrons to oxygen and become oxidized. The molecules upstream are going to stay reduced.
Explain how different cell types cooperate to maximize ATP production.
Two or more different cells can divide tasks so that one does not have to maintain all functions. For example, liver and muscle cells are tied by the lactate pathway. Muscle often must work anaerobically; if it had to maintain a system for dealing with lactate buildup as well, fewer cellular resources could be distributed to the mechanics of muscle movement. Instead, muscles simply generate lactate as they work and dump it into blood. The liver hepatocytes extract lactate from blood, and convert it back to glucose via the process called gluconeogenesis. Alternatively, they take lactate and cycle it through to make amino acids, fats, or other useful macromolecular monomers that can be shipped back to the muscle cells.
overall PSII reaction
2 H2O (4 photons) 4 H+(lumen) + O2 + 4 e-
overall PSI reaction
4 e- + 2 H+(stroma) + 2 NADP+ (4 photons) 2 NADPH
overall light reaction
2 H2O + 2 NADP+ (8 photons) 1 O2 + 2 NADPH
CO2 + H2O  O2 + sugars
sugars + O2  CO2 + H2O

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