Ch. 2

AP Bio Notes

Chemistry Overview:

Matter -

Occupies space, has mass – all things are composed of matter
Matter generally is found in three different states:
- Solid - particles tend to be densely packed and move very little
- Liquid - particles tend to be less densely packed and move more rapidly
- Gas - particles tend to be loosely packed and highly moveable

Elements: pieces that we can’t break down and still keep their characteristics – periodic table (118 total)

Each element is designated by its chemical symbol (such as H, N, O, C, and Na), and possesses unique properties
Principle elements: C, H, N, O, P, Ca, K, Na, S, Cl, and Mg
Trace elements (iron, iodine, zinc, nickel, copper, chromium, manganese, selenium, etc…)

Compounds: sticking together or bonding two different elements together which will have different characteristics from the element by itself – this gives us a lot of options to mix and match and make different functions and characteristics

The Atom -

Atoms are the smallest unit of matter that still retains the properties of an element

Atoms can be broken down into subatomic particles, however if the atom is broken down further it would lose the properties that make up that element. Subatomic particles we will discuss in detail include:
- Protons (+) have a positive charge and located in the nucleus or core of the atom
- Neutrons have a neutral charge and also located in the nucleus or core of the atom
- Electrons (-) have a negative charge and are located outside the nucleus creating an electron cloud made up of levels called electron shells

Carbon dating - radiocarbon dating, or carbon-14 dating, is a scientific method that can accurately determine the age of organic materials as old as approximately 60,000 years

Atomic number - the number of protons (number placement on the periodic table like Nitrogen is number 7), however in all neutral atoms, the number of electrons is the same as the number of protons

Mass number - proton plus neutrons (EX: on PT for Carbon it would be 12.011 or Hydrogen 1.008)

Isotopes - atoms with the same number of protons but different number of neutrons (can vary) 6 protons plus 6 neutrons = carbon-12 or 6 protons plus 7 neutrons = carbon-13 – this means that the mass number can actually fluctuate

This is important because some of these isotopes can be radioactive which can help us figure out the age of things
Different isotopes of an element have essentially identical chemical properties, and so are indistinguishable except on the basis of their mass

Energy -

Allows us to get stuff done

Within our bodies we will primarily use ATP (adenosine triphosphate) as our energy molecule

Some of our energy reactions will be exothermic

Will release energy
Start with high level of energy and end up with lower level of energy so the in-between amount is released and used to do the work which allows us to get stuff done biologically

And some of our reactions will be endothermic

Absorbs energy
Need an input of energy

Energy levels -

As electrons move further away from the nucleus (that has stored energy) and as they fall back down to get closer to the nucleus they release that energy – atoms have the ability to store energy in the location of their electrons as well as release it
These energy levels are designated by a number and the symbol “n” with n1, n2, etc. Since n1 is closest to the nucleus its energy will be the lowest of the shells. The outermost shell contains the most energy

Molecules and compounds can store energy through bonding –

Wherever you break a bond you have to give it some energy and when you form a bond you release energy – these bonds play a critical role in figuring out just how much energy is stored in a molecule

Valence Electrons -

The electrons that we have on the outermost energy level of an atom – orbitals S and P

Lewis dot diagrams help us map out how many valence electrons something has (show picture)

EX: Oxygen - has six valence electrons 2 paired up and 2 single–everyone else wants 8 electrons to be stable so oxygen needs two more electrons to be stable so they can share or they can lose/gain electrons

The Bohr model shows the atom as a central nucleus containing protons and neutrons, with the electrons in circular orbitals at specific distances from the nucleus (picture)
Neutral atoms possess the same number of protons and electrons. A neutral atom of Hydrogen possesses one proton and one electron. The proton is in the nucleus while the electron is in the electron cloud
- Not all atoms are neutral. Some atoms possess a charge. These atoms are called ions. There are two types of ions:
- Cations-positively charged atoms created by the loss of one or more electrons. Examples: Na+, Ca2+, or Mg2+
- Anions-negatively charged atoms created by the gaining of one or more electrons. Examples: Cl-, SO42-, or PO42-
Shells must fill up the inner layer with electrons before moving to the next layer. The outermost shell of an atom is called the valence shell. The number of electrons in this shell determines if atoms are reactive or inert
An element can donate, accept, or share electrons with other elements to fill its outer shell and satisfy the octet rule. N1 needs 2 electrons to complete its shell. N2 and higher need 8 electrons to fill their shells
Electrons do not circle the nucleus like the earth orbits the sun, but are found in electron orbitals
- Subshells are designated by the letter s, p, d, and f
- Principal shell 1n has only a single s orbital, which can hold two electrons
- Principal shell 2n has one s and one p subshell, and can hold a total of eight electrons
- Principal shell 3n has s, p, and d subshells and can hold 18 electrons. Subshells d and f have more complex shapes and contain five and seven orbitals
- Principal shell 4n has s, p, d and f orbitals and can hold 32 electrons

Chemical Bonds -

Atoms often interact to form larger and more complex structures held together by chemical bonds

Chemical bonds are interactions that stabilize the outer energy levels of atoms
- In a chemical reaction, new chemical bonds form between atoms, or existing bonds between atoms are broken
- These changes occur as atoms in the reacting substances (reactants) are rearranged to form different substances (products)
- In a balanced chemical equation the number of atoms of each element are the same on each side of the equation

EX: 2H2O2 (hydrogen peroxide) → 2H2O (water) + O2 (oxygen)

Reversible reactions are those that can go in either direction
Molecules are chemical substances consisting of atoms of one or more elements held together by covalent bonds while compounds are chemical substances made up of atoms from two or more different elements, regardless of the type of bonds joining them together
Whether an atom forms chemical bonds is based on the number of electrons in its valence shell
- If the outer shell is not full, the atom will form chemical bonds with other atoms until it satisfies its outermost shell requirements. The atom is said to be reactive. Hydrogen, Lithium, and Sodium are all reactive because their valence shells are not full
- If the outer shell is full, the atom will not react with other atoms and is said to be inert. Helium and neon, for example, are called inert gases or noble gases

Ionic Bonds -

Chemical bonds created by the electron transfer from one atom to another atom
- The transfer of electrons creates two ionized atoms: one a cation and the other an anion
- Being of opposite charges, the two atoms attract to one another. This attraction is an ionic bond EX: Na+ + Cl- yields NaCl (table salt)
- Ionic bonds are common in the formation of inorganic compounds such as acids, bases, and salts
- Certain salts are referred to in physiology as electrolytes (including sodium, potassium, and calcium), ions are necessary for nerve impulse conduction, muscle contractions and water balance
This is where trading of the electrons will happen (loss or gain) – so one is going to give up electrons and become positive because it gave a negative charge and the other is going to gain that negative charge and will become negative
Usually occurs when one is a metal and the other is a nonmetal – this will occur because there’s a large electronegativity gap (how badly you want to grab hold of electrons and so the nonmetals have a very high electronegativity whereas the metals have a very low electronegativity)

Covalent Chemical Bonds -

Chemical bonds that form between neutral atoms rather than ionized atoms
- Covalent bonds share their electrons with each atom – they’re not trying to steal electrons because there isn’t enough of a difference in electronegativity to allow them to take the electrons away from the other so instead they line themselves up so the orbitals (contains their electrons) overlap and each get the electron that they need (they’ll basically be connected)
- Covalent bonds are usually associated with organic compounds such as starch, proteins, lipids, etc.

EX: C + 4H yields CH4 (methane)

Single covalent bonds exist when one pair of electrons are shared between two atoms while double covalent bonds exist when two pairs of electrons are shared between two atoms

Polarity - this is where there is an imbalance in electronegativity – one is more electronegative so it’s able to pull things a little closer to it so it becomes partially negative and the other will be partially positive because the electrons are further away from it

This can be important because they can interact with stuff like ions that are fully charged because they have this partial charge, so it’s a weaker interaction but it’s still there
Nonpolar covalent bonds are those where the atoms share the electrons equally

EX: would be oil or fat

Polar covalent bonds are created by unequal sharing of the electrons due to the electronegativity of the atoms. Water is an example of a molecule formed by polar covalent bonds
- Polar things don’t like to mix with nonpolar things (water and oil)
A hydrogen bond is the weak attractive force occurring when the small positive charges on the hydrogen atoms of one polar molecule can be attracted to the negative charges on another polar molecule, and this can change the shapes of the molecules or pull adjacent molecules together

Attractive Forces -

Forces between separate molecules that are not bonds, not as strong as bonds (very weak compared to covalent bonds)

We have water (covalently bound–very strong) and we have these weaker attractive forces holding them together – they are important because it keeps things in specific arrangements to try to allow separate objects/molecules to still stick closer together than they would elsewise

Molecules that have the partial charges (things that are polar) will tend to have a type of interaction called hydrogen bonding (semi-positive and partial negative region and the partially negative region attracts the partially separate positive regions – so the hydrogen of one water molecule would be attracted to the oxygen of a separate water molecule – opposites attract) (bonds can break but the partial charge is permanent)

Van der Waals forces occur for everyone

A molecule has its electrons constantly moving and sometimes those electrons happen to be on one side of the molecule so that side of the molecule becomes slightly negative for a moment and the other side becomes slightly positive and so they can get these temporary attractive forces between the different molecules

Water and Life:

Water -

Water is the most important constituent of the body, accounting for up to two-thirds of the total body weight. A change in the body’s water content can have fatal consequences because virtually all physiological systems will be affected

In solution, an ionic compound dissociates as water molecules break them apart. The anions are surrounded by the positive pole of the water molecule, and the cations are surrounded by the negative pole of the water molecule. The sheath of water molecules around an ion in solution is called a hydration sphere
- Hydration spheres also form around an organic molecule containing polar covalent bonds. If the molecule binds water strongly, as does glucose, it will dissolve. Molecules that interact readily with water are called hydrophilic
- Many organic molecules either lack polar covalent bonds or have very few. Such molecules do not have positive and negative poles and are said to be nonpolar. When nonpolar molecules are mixed in water, hydration spheres do not form and the molecules do not dissolve in the water. These molecules are said to be hydrophobic
There are fluids that surround our cells called interstitial fluid (fills the spaces between cells)

Water chemistry -

Water is very polar

All of the bonds that it has are some of the most polar that exist

Picture of water–it has a bent shape (looks like a v) – both hydrogens (slightly positive) have low electronegativity so they are not good at tugging at those electrons and oxygen (slightly negative) has one of the highest of electronegativities so it’s very good at tugging on them so that means that these electrons tend to hover closer to oxygen–the partial positive and partial negative allow it to attract other water molecules (hydrogen bonds allowing separate water molecules stick together with a powerful force)-- water has a high attraction without it being an ion so this allows for a very good job of sticking to other water molecules and other substances that have any type of full or partial charge (ionic or polar)

Water characteristics -

Cohesion - water can stick to itself (water droplets from a faucet – the water molecules (polar) like to stick to other polar water molecules and so water likes to clump together)

Adhesion - water molecules sticking to other polar substances (water droplet clinging to metal of a water faucet; water droplet sticking to a window)

Because of adhesion and cohesion you get capillarity - water can climb against gravity if you give it a optimal situation (take something like a cup, fill it with water and put a straw in it and then the water will climb up the straw just a little bit above the water level of the cup; a piece of paper towel and stick it in a cup filled with water, same thing, the water climbs up the paper towel)--this is critical for plants because they let water climb up without some complex thing to feed them

High surface tension - because water likes to stick to other waters we get to where it’s a little difficult to fall into water–if you’re small enough you can climb around on water (there are certain items that will float – paper clip, tiny insect)

Water temperature -

Water is the only substance that occurs as a solid (ice), a liquid (water), and a gas (water vapor) at temperatures compatible with life

High heat capacity: Heat capacity is the ability to absorb and retain heat
- Specific heat - the amount of heat one gram of a substance must absorb or lose to change its temperature by one degree Celsius. For water, this amount is one calorie
- A large mass of water changes temperature very slowly - thermal inertia

High specific heat - it takes quite a bit of energy to make water change temperature

Evaporate (vaporization – adding a bunch of heat to it to make it boil)
Freeze – taking a bunch of heat from it

This is useful for us for homeostasis – it means that if you walk into a freezer you won’t go in and die because it will take a while for your body to cool because water resists temperature change

Water carries a great deal of heat away with it when it finally does change from a liquid to a gas in evaporation. This feature accounts for the cooling effect of perspiration on the skin

Density and state - water floats when it’s solid (really rare amongst any chemicals)

Liquids are going to be less dense than solid but as water molecules slow down they are able to stretch out as much as possible and lock into a lattice formation
Cold water is going to be more dense – critical for things living in a lake during winter (ice will float and won’t crush the organisms underneath during the winter)

Universal solvent - mixes with pretty much anything (not everything)

Water can dissolve or dissociate things that you put into it that have any propensity to become at least partially charged but it won’t dissolve or go through things that are nonpolar
- The polar charges on water molecules gives water the ability to disrupt the bonds of other polar molecules and ionic compounds causing them to dissolve
- The individual particles become dispersed within the water, and the result is a solution - mixture of two or more substances
- The medium in which other atoms, ions, or molecules are dispersed is called the solvent
- The dispersed particles are the solutes
- The charges associated with these molecules will form hydrogen bonds with water, surrounding the particle with water molecules in a sphere of hydration
- When ionic compounds are added to water, the individual ions react with the polar regions of the water molecules and their ionic bonds are disrupted in the process of dissociation

PH -

Water can naturally breakdown to form two ions - H+ and OH- and sometimes H+ binds to a water becomes H3O+

Hydrogen ions are spontaneously generated in pure water by the dissociation (ionization) of a small percentage of water molecules into equal numbers of hydrogen (H+) ions and hydroxide (OH-) ions
Hydrogen ions are extremely reactive in solution. They will break chemical bonds, change the shapes of complex molecules, and generally disrupt cell and tissue function. The concentration of hydrogen ions dissociating from pure water is 1 × 10-7 moles H+ ions per liter of water or a pH of 7
The hydrogen ion concentration in the body fluids is measured on the pH scale. Litmus paper can tell the pH of a solution indicates its acidity or alkalinity

Acids - Acids are biological compounds that release hydrogen ions (H+) when placed in solution

Hydrochloric acid (HCl) is an important compound found in our stomachs and is necessary for the digestion of certain foods
HCl yields H+ and Cl- in solution
Acids have a low pH on the pH scale (1 - 6.9). The more H+ ions released by the substance the more acid the substance is (closer to 1)
Acids are proton donors

Bases - Bases are biological compounds that release hydroxide ions (OH-) when placed in solution. Also known as alkalinity

Sodium hydroxide (NaOH) reacts with fats in the diet and is used to make soaps in industry
NaOH yields Na+ and OH- in solution
Bases have a high pH on the pH scale (7.1 - 14). The more OH- ions released the more alkaline the substance is (closer to 14)
Bases are proton acceptors

Neutrals - Neutrals are biological compounds that release equal numbers of H+ and OH- when placed in solution

Distilled water is neutral
H2O yields an equal number of H+ and an OH- in solution
Neutrals have a pH of 7.0 on the pH scale
1 = 10^-1 or 0.1; 2 = 10^-2 2 or 0.01; 10^-13 (super small number)

Aquatic organisms have to balance their pH or else they can die and we have to watch our temperature because if it changes too much it can kill us

Buffers -

Buffers resist change in pH

This can help organisms maintain homeostasis and stay alive (if add a bunch of acid, they can absorb that H+ and if add a bunch of bases they tend to release the H+ that they absorbed earlier) – they can help balance out the concentration of H+ to prevent the pH from spiking and becoming too acidic or becoming too basic
Buffers don’t work completely (if someone injects an acid or base into your veins you will die, but if you eat something like lemon juice it will deal with something like that) (stomach has acids but the buffers that can help neutralize the acid so that it’s not eating away at your intestines)
Many organisms are sensitive to pH however they typically have some durability so long as they stay in the range that the buffers in their bodies can help them
The normal pH of blood is 7.35 to 7.45. Bicarbonate is one of the buffer systems used in the human body Ex: H+ + HCO3- ⇔ H2CO3 ⇔ H20 + CO2

Carbon and diversity -

Organic chemistry - going to be based around carbon

A lot of people initially thought that life was something that was put upon you by something else (that is not the case) – this is the idea of vitalism (something else acted upon you and turned you into something alive)
Vitalism was replaced by mechanism (this is where we started to understand the laws that rule chemistry/physics and how those applied to allowing life to function without needing something else)

EX: a living cell can make a living cell and doesn’t need somebody else to act upon it for that to work

As they studied chemistry and started to understand these natural laws they stumbled upon a special atom that makes up most of the molecules within living organisms that aren’t water: carbon-based compounds

Carbon -

Carbon has four valence electrons (tetravalent (four)) – it wants to form four covalent bonds (max that you can do as an element) so it’s very good at connecting to other things (gives it lots of possibilities)
It can bond with itself – it forms large carbon compounds (graphite, diamond) because a lot of elements don’t really like to bond with themselves OR they’ll bind together but only about two of them
Carbon doesn’t just form single bonds and double bonds but it can form triple bonds – this allows for it to have all of the bonding options that there are
The structures of carbon that bond together are called allotropes – the ability to swap out small numbers of other things that are mixed in there gives us brand new molecules and brand new characteristics
There are four types of biological macromolecules: carbohydrates, lipids, proteins and nucleic acids

Hydrocarbon -

Number one partner that we will see in organic chemistry will be Hydrogen

They are nonpolar (oil)
The bonds are high energy bonds – so when we break/reform them we give off a lot of energy (things like fats that we eat provide us with more energy than proteins or carbohydrates) (we can take things like coal, natural gas, oil and extract tons of energy from them to allow us to do a bunch of things) (if an animal is fat and then is starved they can use that fat to provide them with energy but fat can also take energy away)
Hydrocarbons are organic molecules consisting entirely of carbon and hydrogen, such as methane (CH4)
Hydrocarbons may exist as linear carbon chains, carbon rings, or combinations of both:
- Hydrocarbon chains (aliphatic hydrocarbons) are formed by successive bonds between carbon atoms and may be branched or unbranched with single, double, and triple covalent bonds
- Hydrocarbon rings (aromatic hydrocarbons) consist of closed rings of carbon atoms sometimes with double bonds ex: benzene. Some hydrocarbons have both aliphatic and aromatic portions; beta-carotene is an example of such a hydrocarbon

Isomers -

Isomers are molecules that share the same chemical formula but differ in the placement (structure) of their atoms and/or chemical bonds (glucose and fructose)
Structural isomers (ex: butane and isobutene) differ in the placement of their covalent bonds: both molecules have four carbons and ten hydrogens (C4H10), but the different arrangement of the atoms within the molecules leads to differences in their chemical properties
Geometric isomers usually have a double bond and wherever that double bond, is rotated
- When the carbons are bound on the same side of the double bond, this is the cis configuration; if they are on opposite sides of the double bond, it is a trans configuration. In the trans configuration, the carbons form a more or less linear structure, whereas the carbons in the cis configuration make a bend of the carbon backbone
- In triglycerides (fats and oils), long carbon chains known as fatty acids may contain double bonds, which can be in either the cis or trans configuration
- Fats with at least one double bond between carbon atoms are unsaturated fats
- Triglycerides with trans double bonds “trans fats”, have relatively linear fatty acids that are able to pack tightly together at room temperature and form solid fats (usually of animal origin). Triglycerides without double bonds between carbon atoms are called saturated fats, meaning that they contain all the hydrogen atoms available
Enantiomers are molecules that share the same chemical structure and chemical bonds but differ in the three-dimensional placement of atoms (mirror images) – these differences will have different properties and cause major issues

Functional groups - groups of atoms found along the “carbon backbone” that confer specific chemical properties to those molecules. Molecules with other elements in their carbon backbone are substituted hydrocarbons

Each of the four types of macromolecules (proteins, lipids, carbohydrates, and nucleic acids) has its own characteristic set of functional groups (hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl) that contributes greatly to its differing chemical properties and its function in living organisms
Hydrogen bonds between functional groups (within the same molecule or between different molecules) are important to the function of many macromolecules and help them to fold properly into and maintain the appropriate shape for functioning. Hydrogen bonds are also involved in various recognition processes, such as DNA complementary base pairing and the binding of an enzyme to its substrate

Minor changes can affect your overall end product and can do so in a predictable way – life has so many options (enzymes, dna) that we use for different purposes and all of that is possible because the molecules that we can form due to functional groups, single/double/triple bonds, it allows for life to have a tremendous diversity/adaptability