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This document provides a summary of basic chemistry concepts including:
- The structure of atoms, elements, and compounds. Elements are distinguished by their number of protons.
- Definitions of atomic number, mass number, and valence. Valence is the combining power of atoms during bonding.
- Electronegativity influences the formation of chemical bonds, with more electronegative elements attracting electrons more strongly. This determines whether bonds are ionic, covalent, or hydrogen bonds.
- Ionic bonds form between elements with large electronegativity differences, covalent bonds form between elements with similar electronegativity, and hydrogen bonds are weak attractions between polar water molecules.
This document provides a summary of basic chemistry concepts including:
- The structure of atoms, elements, and compounds. Elements are distinguished by their number of protons.
- Definitions of atomic number, mass number, and valence. Valence is the combining power of atoms during bonding.
- Electronegativity influences the formation of chemical bonds, with more electronegative elements attracting electrons more strongly. This determines whether bonds are ionic, covalent, or hydrogen bonds.
- Ionic bonds form between elements with large electronegativity differences, covalent bonds form between elements with similar electronegativity, and hydrogen bonds are weak attractions between polar water molecules.
This document provides a summary of basic chemistry concepts including:
- The structure of atoms, elements, and compounds. Elements are distinguished by their number of protons.
- Definitions of atomic number, mass number, and valence. Valence is the combining power of atoms during bonding.
- Electronegativity influences the formation of chemical bonds, with more electronegative elements attracting electrons more strongly. This determines whether bonds are ionic, covalent, or hydrogen bonds.
- Ionic bonds form between elements with large electronegativity differences, covalent bonds form between elements with similar electronegativity, and hydrogen bonds are weak attractions between polar water molecules.
1. Review structure of an atom, element and compound.
Atoms have an inner dense nucleus of positive charge composed of protons and neutrons. Surrounded by electrons which form a negatively charged shell around the nucleus. 2 in the first shell, 8 in the second and thats probably all you really need to know. The majority of an atom is empty space with little electrons flying around. Elements are distinguished by the number of protons they have. Compounds are just elements bonded together. Ionicly (ionically?) bonded compounds form salt and that dumb crystal lattice structure thing.
2. Define and distinguish among atomic number, mass number, and valence. Atomic number is the number of protons the element has. Mass number is an integer which is basically # of protons and number of neutrons in an atom added up. According to Wikipedia valence is just the combining power of two atoms, hence valence electrons are electrons shared/given up/whatever when two atoms combine. Isotopes are related to mass number, basically different number of neutrons than the normal element.
3. What is the main reason that elements might react with other elements? No idea. My guess is electron negativity. Valence. Stuff involving the ability to combine.
4. Define electronegativity, and explain how it influences the formation of chemical bonds. Electronegativity is basically how bad an atom wants electrons. Fluorine is the most electronegative element. Basically every atom wants equilibrium and wants to be stable. Which means they just want to no valence electrons; they want a complete shell. So elements on the left have a couple electrons on the next shell that they want to get rid of. So they have very low electron negativity. The halogens or whatever group 17 really want electrons badly so they can be best buds with the stable noble gases. Thats why you get a lot of group 1 with group 17 bonding. Easiest example to illustrate ionic bonds. But then there are those goody 2 shoe elements that like to share with each other and be all nice. Thats because their electronegativity is very similar so they want it equally badly. So there are your basic diatomic molecules, which can bond with each other: H, N, O, F, Cl, I, and Br. Also anything involving C probably (I think) have covalent bonds.
5. Distinguish the following from each other: ionic bond, covalent bond, and hydrogen bond. Ionic bond = 1 guy really wants it more than the other. In terms of structure the electron is much closer to the atom with higher electron negativity. This is random but also useful to know, because of this interaction we can say that the shorter the bond length, the more energy it takes to break it. Covalent bond = sharing equally. Mostly equal distance between stuff Hydrogen bond = really weak bond that results from weird ass structure of water. There are partial poles because the molecule is bent, creating a quasi positive charge down near hydrogen and quasi negative charge up around oxygen. So basically water can bond with itself very weakly because water molecules are crazy.
6. Describe the properties of water that result from its polarity and hydrogen bonding. Cohesion and Adhesion. Stick to itself and other things, respectively. It explains why plants dont randomly fall down and why plant stuff bends and wilts.
7. Explain the basis for the pH scale. pH = -log(concentration of H + ions in a solution) pH + pOH = 14, K water = 1 x 10 -14 , so [H + ][OH - ] = 1 x 10 -14
8. What do a low pH and a high pH reading mean? Low pH = acidic, high pH = basic.
9. How are the hydronium and hydroxide ions formed from water? One water gives a hydrogen to another. The water that gave becomes hydroxide and the water that was given to becomes hydronium.
10. Using the bicarbonate buffer system as an example, explain how buffers work. Basically bicarbonate is a weak base/amphoteric solution. But its in our bloodstream as a buffer to prevent our plasma or whatever from becoming too basic. When we breathe in oxygen and it goes to our blood cells, the waste product is carbon dioxide. Now we dont want too much carbon dioxide because its an acid and it will lower our pH. However, carbon dioxide can bond with water to form carbonic acid (H2CO3). Carbonic acid can give up a hydrogen to form bicarbonate if there is a rise in pH. This is because giving up a hydrogen increases the hydronium or H + concentration which will lower the pH again. But if the pH is low then bicarbonate will form carbonic acid. So yea thats how were all alive.
Atoms to Molecules 11. What are the 6 elements essential to life Sulfur, Phosphorus, Oxygen, Nitrogen, Carbon, Hydrogen
12. How does each of these elements function in living systems? Basically carbon is found in every organic molecule so its pretty important. Phosphorus is found in ATP and monomers for important things. Sulfur gives conformation to proteins which define function. Nitrogen is in our DNA, and makes up a nitrogenous base. Hydrogen is like Oxygen we breathe. CHO are found in a lot of monomers of importante things
13. What are some additional elements with functions that are found in the body? Calcium, Potassium, Iron, Iodine (hormones for thyroid)
14. Describe which SPONCH atoms are found in carbohydrates, lipids, proteins, and nucleic acids and how monomers of carbohydrates and proteins can generally form into various polymers. Carbs: CHO, monomers combine through dehydration synthesis., monomer = monosaccharide Lipids: CHO, phospholipids also have P Proteins: CHONS, amino acids combine through dehydration synthesis. Nucleic Acids: CHONP
15. Use models or other representations to explain how processes such as dehydration synthesis and hydrolysis, result in molecular exchange. How about no. One side drops an H and another drops an OH and form water while the monomers combine. Note that the drops occur at the OH portions and when combined the carbons on either end share the oxygen.
Biogeochemical Cycling Uptake, Use, Storage, Circulation, and Excretion 16. In the nitrogen cycle, atmospheric nitrogen must be transformed into a usable form for organisms. Nitrogen fixation is the process by which N 2 (atmospheric nitrogen) is reduced to NH 3 (ammonia) by the bacteria rhizobium on the nodules of legume roots. Nitrification is essential then to turn NH 4 +, which was changed by rhizobium using H+ in the soil from NH3, into nitrite (NO2-) by oxidation and then nitrite to nitrate (NO3-) by oxidation again. Nitrifying bacteria conduct each step so that plant roots can now absorb the NO3- to use. Assimilation is then how an organism might use up the obtained nitrogen and use it to make molecules such as proteins, DNA, RNA, et. AS the plants die, decomposition, the process of breaking down proteins, wastes , and other parts of the organism, takes place by bacteria and fungi. The organic nitrogen that is returned from the animal is converted back to ammonium by ammonifying bacteria in the process called ammonification. The process may start from here again to cycle nitrogen through different organisms to the atmosphere, etc. in its different forms. 17. In the carbon cycle, photosynthetic organisms, such as plants, use carbon dioxide (CO2) during photosynthesis thus converting the carbon into organic forms that consumers, such as animals, can use. The amount of atmospheric CO2 that plants and phytoplankton remove from the atmosphere is replenished by the amount of CO2 added to the atmosphere through cellular respiration by different organisms. The burning of fossil fuels and wood (carbon reservoirs) also releases significant amounts of Co2 back into the air. Volcanoes, too, have released significant amounts of CO2 back into the atmosphere. 18. A plant organism may take up the NO 3 - that was fixed by the nitrifying bacteria in the soil. It is able to be assimilated or used by the organism because NO 3 - is an inorganic available form for any plant. The nitrates can be absorbed by dissolving into water and being taken up by the epidermal cells of the roots (root hairs modified cells) which are permeable to water. The soil solution (including those nitrates) is drawn into the hydrophilic walls of epidermal cells and passes along cell walls and extracellular spaces into the root cortex providing more membrane surface area for absorption. Plants will export the minerals from the soil with water from the roots to the shoots by entering the xylem of the vascular cylinder. From there the xylem sap, water and dissolved minerals in the xylem, get transported long distances by bulk flow to the veins that branch throughout each leaf. The transport of xylem sap involves loss of water through transpiration as that is what initiates the transpirational pull of water using waters adhesion and cohesion properties. (As water evaporates, dissolved minerals in water move through the plant as the water in lower regions of the plant is pulled up as well because its cohesive with water in higher regions of the plant) Plants will then use an enzyme to reduce nitrates to NH 4 + which other enzymes can incorporate into amino acids and nucleic acids thus making it an organic available source of nitrogen. The amino acids will be used to make proteins such as enzymes, structural support, and to use in simple processes such as in active transport. The nucleic acids will be DNA which provides the genetic information for the plant, and RNA which helps plant cells in the process of developing the proteins mentioned. Nitrogen is returned to the soil when organisms die and become decomposed by the different bacteria and fungi in the soil. Plants also release some nitrogen back through the root system as waste products when it is not used in the plant. This nitrogen may be denitrified when it is returned to the soil and returned back to N 2 which will diffuse back into the atmosphere. 19. Carbon, nitrogen, and phosphorous are essential elements to living organisms because of their roles in different biomolecules. Carbon is what make compounds organic and is found in all of the organic molecules (Carbohydrates, lipids, proteins, and nucleic acids), phosphorous is found in phospholipids, ATP molecules, and nucleic acids, and nitrogen is found in amino acids of proteins and nucleic acids. Carbohydrates provide the energy for simple processes such as maintaining homeostasis, growth, and reproduction since it can be converted into ATP during cellular respiration. ATP provides energy for daily activities when one phosphate group breaks away from the rest of the molecule and the breaking of the bond releases energy. Proteins are used for structural support and protection in the body (which can control internal body conditions), fight off infections in the body (antibodies), speed up chemical reactions (enzymes, regulate metabolism and growth (hormones), and even help sperm cells move along in reproduction in the form of flagella. Finally, nucleic acids such as DNA and RNA contain the genetic information of the different organisms and will instruct the body on how to make proteins and influence the organisms various characteristics. This is also the information that the organisms will pass on during reproduction. 20. Due to waters polarity/partial negative and positive charges that allow it to create hydrogen bonds, water has many unique properties. Water molecules are very cohesive due to this fact because at each given moment, many of the molecules in liquid water are linked by hydrogen bonds. The linkages make the water more structured than most liquids, holding the structure together which is ultimately cohesion. Water also has a high specific heat, amount of heat that must be absorbed or lost for 1 gram of a substance to change by 1 degree Celsius. Heat must be absorbed to break hydrogen bonds and so most of the heat must be used to break these bonds before molecules can start moving faster and the temperature can rise. Water is also less dense in solid form because as water freezes the molecules become locked into a crystal lattice where each water molecule makes hydrogen bonds with four partners. These hydrogen bonds keep the molecules at arms-length from each oteher which is far enough to make ice less dense than water. Finally, water is also the universal solvent due to its polarity. Its slightly charged regions will attract ions or make hydrogen bonds with nonionic polar molecules. Water molecules eventually surround the different molecules, separating them from each other and eventually dissolving the involved compound. 21. Different properties of water affect living systems. Waters cohesive property contributes to the transport of water and dissolved nutrients against gravity in plants. The cohesiveness also relates to waters high surface tension which allows organisms such as spiders to walk across ponds. Waters high specific heat helps to stabilize ocean temperature and create a favorable environment for ocean life. Its capability to absorb and store large amounts of heat while only raising a few degrees in temperature in the winter also prevents temperature fluctuations on land to make life possible. Then, if ice sank eventually all bodies of water would freeze solid. Now, floating ice insulates a body of water when it cools which prevents it from freezing and thus allowing life to exist. Water is also the solvent of life: different polar compounds (or ions) are dissolved in water of biological fluids such as blood, plant sap, and cell liquid. 22. Cohesion and adhesion allows transport of water and dissolved nutrients against gravity in plants. Water from roots reaches the leaves through a network of water-conducting cells in a process called bulk flow. The cohesion of the water within the xylem gives it a tensile strength almost of a steel wire. When water evaporates from leaves, hydrogen bonds causes the leaving water molecules to tug molecule by molecule all the way down the water column in the xylem. The adhesion, clinging of one surface to another, is also essential. The adhesion of water to the hydrophilic cell walls of xylem cells by hydrogen bonding helps to counter gravitys downward force. The upward pull on the xylem sap creates tension within the vessel elements and tracheids, kind of like elastic pipes. The tension pulls the pipe walls inward and the tension of the transpirational pull also lowers water potential in the root xylem so that water flows passively from the soil, across the root cortex, and into the vascular cylinder. 23. Plants have an extra-large vacuole to store more things since they dont have as many opportunities to get rid of waste. Cacti cells have extreme water retention and efficiency. 24. Justify and explain how cell activities can be affected by interactions with biotic and abiotic factors. Cell activities are ultimately dependent on a lot of factors outside of the organisms influence. For example, when drought occurs, plants can reduce the rate of transpiration, resulting in a decrease in water loss. Cells can perform transpiration less frequently to conserve water due to the water deficit. An abiotic factor such as drought can influence a change in cellular activities. However, plants can also increase the rate of transpiration in their cells in response to hot and humid days. This helps to cool the leaves via evaporative cooling. Heat stress is also an abiotic factor that ultimately dictates how the plant regulates its cells. Even if its a hot and dry day its no problem for a plant. Dryness can usually dehydrate many plants which can spell disaster as the plant closes its stomata to conserve water but loses evaporative cooling. Some plant cells can synthesize heat- shock proteins, which help other proteins from denaturing. The dryness and hotness of the weather forced the plant to use some of its cells to produce a specialized and situational protein in order to survive. A biotic factor that dictates cell behavior could be infection. The hypersensitive response is a response that attempts to quarantine the infection site by sealing off the area and essentially ordering all cells to destroy themselves. 633-635.
25. Explain how organism activities can be affected by interactions with biotic and abiotic factors. Big abiotic factors for plants are gravity and sunlight. The light causes the plant to grow towards it, and statoliths, dense cytoplasmic components in a cell, can detect gravity. The aggregation of statoliths at the low points of these cells triggers a redistribution of calcium, causing a lateral transport of auxin within the root. Auxin in high concentration inhibits cell elongation, resulting in a slow growth on the roots lower side and prevent the plant from falling due to structural instability. Gravity causes a plant to slow its growth and sunlight dictates how the plant grows. Biotic factors such as infection also can dictate how the plant acts. Plants often have the ability to completely resist a pathogen through systemic acquired resistance and harsh chemical attacks that can prevent infection from spreading past an area, however this immunity often comes at an energetic cost to the plant. The energetic cost will result in lower performance and production of other goods the plant needs. In a way the biotic factor can control, to a certain degree, the activities and actions of the plant. 632, 636.
26. Predict and justify with explanations how the stability of a population, community, and ecosystem is affected by interactions with biotic and abiotic factors. Lets assume our population of interest is a population of bees in some flower forest. The living things like the flowers, bees, herbivores, and carnivores make up our community. Everything in the flower forest makes up our ecosystem. Now, a terrible disease strikes the bees. The resistance is a recessive trait and more than half of the bee population is wiped out. Now there are less bees to pollenate flowers meaning less new flowers meaning that less herbivores get dinner meaning less herbivores in total meaning less food for carnivores and you see where this is really going. The whole ecosystem is interconnected and thus the carnivores rely on the stability of the bees so that there will be enough food. Its a simple domino effect and janga tower combined. Take out the vital piece and the whole thing can come crashing down. The disease didnt permanently effect the bees, as they would eventually reproduce offspring that were resistant, however many components of the community and ecosystem are heavily damaged, and the farther down the food chain the more amplified the effect becomes.
27. Describe how disruptions at the molecular and cellular levels affect the health of the organism. The efficiency and capability at molecular and cellular levels of an organism can affect the health of the organism in varying ways. For example, our body temperature is regulated by the hypothalamus, a region in the brain. The hypothalamus will make changes as it sees fit as a result from outside stimuli. However, if the sensors arent working properly then it wont be able to detect stimuli and signal a change. Or if the neural pathways arent working then it the signal will fail to reach the hypothalamus and no change will occur. Or if the small nuclei in a portion of the brain are defective and cant control temperature then you cant adjust. If youre too hot then the hypothalamus can promote cooling of the body by vasodilation of the vessels in the skin. If youre too cold then the hypothalamus can cause you to shiver to increase your core body temperature. You normally increase your body temperature to help fight off infection, but what if you cant? These minor disruptions and simple deficiencies and impact our health on a much larger scale. 647.
28. Describe how disruptions to ecosystems impact the homeostasis or balance of the ecosystem. Natural disasters can cause drought or flooding which screws over the flora, which in turn screws over the entire ecosystem because there isnt the transport of energy that organisms get by consuming down the food chain. A flood can drown the plants and do the exact same thing. A pesticide or earthquake or volcano eruption and destroy a vital chain in the ecosystem, where everything is heavily interdependent with each other.
29. Design a plan for collecting data to show that all biological systems are affected by complex biotic and abiotic interactions. Just simply draw an ecosystem. Start with plants and then some herbivore and then ideal carnivores and etc. Then come up with the worst possible thing to happen to one of these groups and remove it and see how badly everything else gets screwed over.
30. Analyze data to identify possible patterns and relationships between a biotic or abiotic factor and a biological system.
The Basic Elements and Their Bonding Ability, Macromolecules and Their Structures and Their Role and General Law of Thermodynamics in Biological Systems