Bild 1 Cooper Final
Describe the properties of water that make it biologically valuable to life and why.
The four properties of water that make it biologically valuable to life are: ice is less dense than liquid water, cohesion and adhesion, high heat capacity, and a "universal" solvent. Ice being less dense than liquid water is a result of liquid water having more transient hydrogen bonds and ice having more stable hydrogen bonds, meaning that the hydrogen bonds in liquid water are forming and breaking more because the atoms are moving faster than in ice (a solid). Thus, solid water forms a solid crystalline structure, and the hydrogen bonds are more stable. This is an essential property to life because it allows for life to exist in areas such as ponds in extreme cold environments, as only the top of the pond will freeze, keeping the bottom warmer and from being frozen, meaning life below will still be able to prosper. Cohesion is the attraction of water molecules to themselves, as they want to stick together to form hydrogen bonds. Cohesion is also responsible for surface tension. Adhesion is when water sticks to things other than itself (if the surface is somewhat charged or polar). Together, these two properties are essential to life. For example, in trees, water moves from the roots to the trees through both cohesion and adhesion; cohesion is when the water molecules stick to each other, and adhesion is when the water molecules stick to the tree itself. The next property is water's high heat capacity, meaning that water has a relatively high specific heat, meaning it takes a large amount of heat for one gram of a substance to change its temperature by one degree celsius. This is essential for life as it is the main reason our global temperature does not rise in heat too much, and why the Earth has a much cooler temperature than other planets. Water can thus absorb a significant amount of heat without a significant rise in temperature. The final property is water acting as a "universal" solvent. Water is not a universal solvent, but it can dissolve a lot of things; water can dissolve anything that is polar or charged. This is essential for life because everything in our cells is dissolved in water, and our cells are essential for life (and wouldn't function without the water in them).
What is a phosphorylation cascade? How does it allow for signal amplification and what is the advantage of this?
Two types of enzymes: kinases add phosphate groups and phosphatases remove them. Generally, when a phosphate group is present on a protein, the protein is active, when it gets removed it is inactive. A phosphorylation cascade works by a signaling molecule involved in some sort of reception (g protein, ion, etc). The activity that the reception does causes the first kinase to become activated. The kinase's job is to add phosphate groups to its target (generally another kinase) that is inactive. The kinase is going to cut up an ATP to put a phosphate group on the next kinase, which now has a phosphate group and is active. Its next target may be a protein or another kinase. This can go on for a long time. Acting in opposition is the phosphatases, which cuts the phosphate group back off and inactivates it. The kinase gets activated, activates a few of its targets, and then it gets turned back off, and the kinases that it activates do the same thing. The series of things phosphorylating each other continues on until you get to the protein that is actually going to do the thing you want to do. The series of kinases activate each other in sequence until you get to the thing that is going to do the job. Each time a phosphate group (negative) is added to a protein, the protein's structure is changed to a form where it can do its job. This is advantageous because of signal amplification, which is the idea that kinase 1, before it gets inactivated, doesn't just activate one of its targets. It will have time to activate many, and each of those can go on to activate more, and each of those can activate many of its targets, and so on. Each step is amplified, and a chain reaction is created.
Compare and contrast the structures of starch and cellulose. Relate the differences in structures to their different roles in the cell.
Both starch and sugar are polysaccharides, both made of glucose. Starch has a highly branched structure and serves the purpose of converting glucose into energy as well as energy storage, whereas cellulose is unbranched, linear, and low in energy and serves the purpose of structure in plants. Cellulose is also almost impossible to break down by humans and is also around ten times smaller than starch. Each unbranched cellulose molecule is also held together by hydrogen bonds created microfibril, in contrast to starch not having any. Because cellulose is unbranched and linear, it can easily serve its purpose as a form of structure in plants in their cell walls by being able to mold into the shape that is necessary for the cell walls. For starch, it can easily serve its purpose as a form of energy storage and conversion of glucose because its highly branched structure allows for it to cover a lot of ground and have a high amount of surface area in which energy can be stored.
Some cancer treatment drugs act by stopping spindle fiber depolymerization. Why is this an effective mechanism? What limitations or risks does this come with?
Cancer cells are cells that don't respond properly to the cell control signal. The checkpoints that tell a cell to stop dividing don't work, so the cells just continue dividing. Stopping spindle fiber depolymerization causes the cell to get stuck in anaphase. First, the connections between the sister chromatids break, then the microtubules depolymerize and pull the chromatids apart. With this, the cell can't proceed any further, effectively stopping the cell from continuing and being able to divide. A limitation of this would be the fact that there are thousands of different ways to evade the cell cycle control system, so the cancer cells would possibly be able to avoid this depending on the combination of traits they have. A risk of this would be the fact that this could possibly affect non-cancer cells and cause one to not be able to reproduce those cells. For example, if the drug happened to affect skin cells, perhaps one wouldn't be able to regrow skin because of that.
Compare and contrast competitive and noncompetitive inhibitors. Outline an experiment to determine if a newly discovered inhibitor is a competitive or non-competitive inhibitor. Include which outcomes you expect for each.
Competitive and noncompetitive inhibitors both stop enzyme function by binding to the enzyme and changing it in some way. For competitive inhibitors, enzyme function is stopped by the competitive inhibitor binding in the active site and physically blocking the substrate so the enzyme can't convert it. For noncompetitive inhibitors, the noncompetitive inhibitor binds somewhere else on the enzyme, causing a change of shape in the enzyme. This change of shape prevents the substrate from binding to the enzyme, as the shape of a substrate must exactly match the enzyme it is attempting to bind to. The difference between the two is based on where the inhibitor binds, being the active site (competitive inhibitors) versus elsewhere (noncompetitive inhibitors. In order to discover if a specific inhibitor is competitive or noncompetitive, one could test the inhibitor at different concentrations of substrates while immersed in a solution and see how much, if any, activity is taking place. If the concentration of substrate is significantly increased and there is still some activity taking place, then that means that sometimes the inhibitor is binding and other times the substrate is binding. This would allow one to determine that the inhibitor is competitive, meaning that the enzyme will still be undergoing some activity. If the concentration of the substrate is significantly increased and the substrate is not binding at all, that means that only the inhibitor is binding to the enzyme and that it is not a race at all between the inhibitor and the substrate, meaning that it is a noncompetitive inhibitor. The enzyme is essentially turned off, and no activity is taking place.
Describe factors that affect a molecules ability to enter the cell by diffusion. Provide examples of two molecules that can't diffuse into the cell and how the cell transports them.
Factors that affect a molecules ability to enter the cell by diffusion include size, polarity, and concentration. In order to pass through the phospholipid bilayer without using energy or through proteins, the molecule must be small, non-polar, and moving with the concentration gradient. If a molecule such as K+ needs to enter the cell, it does so through a protein in a process known as a sodium potassium pump, where three Na+ are channeled through a pump out of the cell in exchange for two K+, a process which requires. Another molecule that cannot diffuse through the cell through simple diffusion is water, as it is polar. Water enters through osmosis, where aquaporins, a type of transmembrane protein, transport it across, going with the concentration gradient.
What are the ways that meiosis results in increased genetic variability? Explain how and when each happens.
In prophase of meiosis 1, crossing over occurs. Crossing over is the process in which the double chromatid homologous pairs exchange chromosome segments by crossing over with each other. This process occurs with non sister chromatids. This creates diversity because genes from each parent are allowed to intermix. The new combination of genes can lead to new traits because of the fact that genes frequently interact with one another. Another way meiosis results in increased genetic variability would be mutations, in which a nucleotide in the DNA getting switched up. This most likely happens in S phase. When replicating the DNA, the sister chromatids are most likely not perfectly identical. The polymerase that does DNA replication isn't perfect, of which results in mutations that introduce genetic variation. A third way genetic diversity is increased would be by independent assortment, which occurs in metaphase of meiosis 1. Independent assortment is the process in which sister chromatids separate and are randomly distributed to the daughter cells (gametes). Because of the crossing over from meiosis 1, non-identical chromatids in meiosis 2 chromosomes are formed. In anaphase of meiosis 2, the centromere that joins the chromatid pairs dissolves and two chromosomes of each type are formed. The chromosome that goes to the gamete is random, meaning that each gamete has a unique combination of genetic material, increasing genetic variability.
Explain the role of oxygen in aerobic cellular respiration and why anaerobic respiration produces less ATP than aerobic respiration.
Oxygen serves as the terminal electron acceptor in the step of oxidative phosphorylation. Oxygen is responsible for synthesizing ATP by accepting electrons from broken down macromolecules. In addition, oxygen is responsible for the formation of water, as the electrons it accepts from the electron transport chain are combined with hydrogens in order to form water (2H+ + ½ O2 -> H2O). Anaerobic respiration produces less ATP than aerobic respiration because of the lack of oxygen as the terminal electron acceptor. Oxygen is very electronegative, meaning it has a very strong pull of electrons. Anything not oxygen (at least, concerning respiration) will be less electronegative, meaning it will have a weaker pull on electrons, and thus produce less ATP in the step of phosphorylation because it will take more of the same compound in order to produce the same amount of ATP as oxygen.
Describe photorespiration and explain how C4 and CAM photosynthesis minimizes this issue.
Photorespiration is the process in which rubisco (at low frequencies) starts using oxygen when carbon dioxide runs out. Rubisco is trying to make a sugar, however, it is attaching oxygens rather than carbons, creating a bad sugar (trash). In addition to the useless sugar, ATP is used up in the process, wasting energy. In hot/arid climates, plants have evolved variations of photosynthesis in order to minimize photorespiration. C4 plants, in contrast to normal photosynthesis (AKA C3), have a spatial separation of CO2 uptake and rubisco function. Plants that undergo C4 are generally found in dry/hot environments, however not environments that are very hot/dry. C4 plants have two layers of cells, being the mesophyll and bundle sheath cells. In order to combat photorespiration, C4 plants have their stomata in the mesophyll, where CO2 enters, while rubisco is in the bundle sheath cells. This combats photorespiration because CO2 is converted into a storage form (as an organic acid) when it is not peak heat time outside and then pumped into the bundle sheath cells during those periods, where it is converted back into CO2. This allows the pumping of CO2 into the cells gradually. When the stomata is open, the cell intakes a lot of CO2, and then when it is hot, it closes to avoid water loss ( minimizing photorespiration). This allows the plant to artificially keep CO2 levels near rubisco high for some period of time (although not forever). C4 plants perform a similar process in more extreme environments. Because these plants are in more extreme environments, there is no good time of day for the cell to open its stomata (as it is always hot); C4 plants thus have temporal separation. At night, the plant opens its stomata and brings in CO2 (again, converting it into an organic acid for storage). During the day, when photosynthesis is possible, the stomata is closed and the plants slowly convert the organic acid into CO2, so rubisco always has enough CO2 to do the calvin cycle, meaning it won't have to use oxygen, minimizing photorespiration.
Explain the construction of a protein from primary to quaternary structure.
Primary structure of a protein is a linear sequence of amino acids which must be in the correct order. One side of the linear sequence is an amino end, whereas the other is a carboxyl end. The sequence is constructed from a set of 20 amino acids, each having the same general structure (central carbon, carboxyl group, hydrogen, and amino group), but differing in the R-group (which determines which amino acid it is). The primary structure is held together by peptide bonds. Secondary structure is when the polypeptide chain coils or folds, giving the protein its 3-D shape. One type of secondary structure is an alpha helix, which is similar to a spring, held together by hydrogen bonds in the middle. The other type is beta pleated sheet, which is more folded or pleated, and is held together by hydrogen bonds between adjacent polypeptide units of the chain. Tertiary structure is the comprehensive 3-D structure and the most complex. It is held together by various means. One of those is hydrophobic interactions, which contribute to the folding and shape. Depending on if the R-group is hydrophobic or hydrophilic, it will either attempt to avoid water or attempt to be surrounded by water, respectively. Hydrogen bonding is also present between the R-group and the polypeptide chain, responsible for holding the protein in its shape (established by the hydrophilic interactions). Ionic bonding can also occur as a result of the folding between the positively and negatively charged R-groups (acid and base). The R-groups of cysteine can also result in the formation of a disulfide bridge, a very strong type of covalent bond. Hydrophobic interactions and van der Waals interactions also occur between hydrophobic amino acids. The final structure of a protein is quaternary structure (although not always present). Quaternary structure is the result of multiple tertiary structure chains interacting with one another to form, which may or may not be the same.
Explain the importance of protein shape to its function.
Protein shape determines protein function as a result of the order of the amino acids. If the order is changed even by one amino acid in the primary structure, then the entirety of the polypeptide chain is messed up (as each subsequent layer is dependent on the previous). The function of a protein is dependent on its ability to recognize and bind with another type of molecule, depending on if it is an enzymatic, defensive, storage, transport, hormonal, receptor, contractile/motor, or structural protein.
Explain the evidence in support of the Endosymbiont Theory for the origin of mitochondria and chloroplast
The Endosymbiont theory is supported by the fact that mitochondria have double membranes and chloroplast have triple membranes, suggesting that they were once prokaryotic cells (as prokaryotes also have their own membrane). In addition to that, mitochondria have their own set of circular DNA, which is very similar to the DNA of bacteria (structurally and in size). They also have their own set of ribosomes, which are very similar to bacteria (more so than eukaryotic ribosomes). One last evidence would be the fact that they reproduce inde pendently through binary fission (as bacteria and archaea do), meaning that when a cell divides, mitochondria and chloroplast don't necessarily divide, rather they do so on their own and rely on having one in the previous cell in order to reproduce (i.e. if a cell doesn't have mitochondria, when it divides the new cells won't have mitochondria because it isn't capable of creating them).
Describe the chemical bonds involved in the formation of water (how the oxygen and hydrogen atoms connect) AND how water sticks to other water molecules.
Water is formed when two hydrogen atoms covalently bond to an oxygen atom (an intramolecular bond), meaning they share their electrons with one another (rather than donating electrons) in order to complete both of their valence shells. Because oxygen is such an electronegative element, however, the sharing is unequal, resulting in the electrons spending more time around the oxygen, leading to a slightly negative charge around the oxygen and a slightly positive charge around each of the hydrogens; thus, the molecule is polar. The polar covalent bonds between the molecules result in water molecules sticking to one another relatively easily (a property known as cohesion), as the slightly negative oxygen attracts to two slightly positive hydrogens (of two different molecules), and each hydrogen is attracted to another oxygen. These bonds between each molecule are known as hydrogen bonds (an intermolecular bond), and are relatively weak bonds, however, they generally appear in large numbers due to each molecule being able to form four bonds, so they are strong in numbers. While hydrogen bonds are most prevalent between water molecules, they are also possible between a water molecule and any other molecule that has a slightly positive and/or slightly negative side (such as NH3).