Basic Chemistry Review

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.