AP Biology Unit 1: the Chemistry of Life

Matter

• What organisms are composed of

• Anything that takes up space and has mass

What is matter made up of?

• Elements

Elements

• Substances that cannot be broken down to other substances by chemical reactions

Compound

• A substance consisting of two or more elements combined in a fixed ratio

• Has characteristic different from those of its elements

Essential elements

• Carbon, hydrogen, oxygen, nitrogen

• A few other elements make up the remaining 4% of living matter

Trace elements

• Elements required by an organism in only minute quantities

Atom

• The smallest unit of matter that still retains the properties of an element

• Each element consists of a certain kind that is different from those of other elements

Subatomic particles

• Smaller parts of an atom

Neutrons

• Have no electrical charge

Protons

• Positively charged

Electrons

• Negatively charged

• Surrounding the nucleus in a “cloud”

Atomic nucleus

• Composed of protons and neutrons

Atomic number

• The number of protons

• Is unique to each element

Mass number

• Sum of protons plus neutrons in the nucleus of an atom

• An approximation of the atomic mass of an atom

Isotopes

• Atoms of a given element may occur in different forms

• They differ in the number of neutrons in the atomic nucleus, but have the same number of protons

Radioactive isotopes

• Spontaneously give off particles and energy

• Can be used in biology (ex: tracers)

Energy

• Defined as the capacity to cause change

Potential energy

• The energy that matter possesses because of its location or structure

• The electrons of an atom differ in amounts of potential energy they possess

Energy levels

• Represented by electron shells

• Energy can move from one level to another only if the energy it gains or loses is exactly equal to the difference in energy between the two levels

Electron behavior and configuration determines..

• The chemical behavior of an atom

Valence electrons

• Electrons in the outermost, or valence shell

• Determine the chemical behavior of an atom

Orbital

• The three dimensional space where an electron is found 90% of the time

• Each orbital holds up to two electrons

Types of orbitals

• First shell: one 1s orbital with a maximum of 2 electrons

• Second shell: one 2s orbital, and three 2p orbitals

Covalent bond

• The sharing of a pair of valence electrons

• Ex: when two hydrogen atoms approach each other, the electron of each atom is also attracted to the proton in the other nucleus and the two electrons become shared in a covalent bond, forming an H2 molecule

Molecule

• Consists of two or more atoms held together by covalent bonds

Single bond

• The sharing of one pair of valence electrons

• Ex: two hydrogen atoms and one oxygen atom are joined by covalent bonds to produce a molecule of water

Double bond

• The sharing of two pairs of valence electrons

Electronegativity

• Attraction of a particular kind of atom for the electrons in a covalent bond

• The more electronegative an atom, the more strongly it pulls shared electrons toward itself

Nonpolar covalent bond

• Atoms have similar electronegativities

• Share the electron equally

Polar covalent bond

• Atoms have differing electronegativities

• Share the electrons unequally

Ionic bonds

• When atoms strip electrons away from their bonding partners

• An attraction between anions and cations

Ions

• Caused by electron transfer between two atoms

• Atoms with more or fewer electrons than usual

• Are charged atoms

Anion

• Negatively charged ions

Cation

• Positively charged ions

Ionic compounds

• Called salts, and may form crystals

Weak chemical bonds

• Include hydrogen and van der waals forces

• Important in living systems

Hydrogen bond

• Forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

Van der Waals interactions

• Occurs when transiently positive and negative regions of molecules attract each other

What do weak chemical bonds do?

• Reinforce the shapes of larger molecules

• Help molecules adhere to each other

Molecular shape

• Very important to its function in the living cell

• Determined by the positions of the atom’s valence orbitals

Covalent bond molecular shape

• The s and p orbitals may hybridize, creating specific molecular shapes

• They combine to form four teardrop shaped hybrid orbitals (tetrahedron)

What does molecular shapes determine?

• How biological molecules recognize and respond to one another with specificity

Chemical reaction

• The making or breaking of chemical bonds

• Leads to changes in the composition of matter

• Convert reactants to products (ex: photosynthesis)

Chemical equilibrium

• Is reached when the forward and reverse reaction rates are equal

Water

• Something that all living organisms require more than any other substance

• The biological medium on Earth

Is the water molecule polar or nonpolar?

• A polar molecule

• Allows water molecules to form hydrogen bonds with each other

Cohesion

• What water molecules exhibit

• It is the bonding of a high percentage of the molecules to neighboring molecules due to hydrogen bonding

• Helps pull water up through the vessels of plants

Surface tension

• A measure of how hard it is to break the surface of a liquid

How does water moderate air temperature?

• It absorbs heat from air that is warmer and releases the stored heat to air that is cooler

Kinetic energy

• The energy of motion

Heat

• A measure of the total amount of kinetic energy due to molecular motion

Temperature

• Measures the insanity of heat

Specific heat

• The amount of heat that must be absorbed or lost for 1 gram of that substance to change its temperature by 1 degree Celsius

Does water have a high or low specific heat?

• A high specific heat, which allows it to minimize temperature fluctuation to within limits that permit life

In water, how is heat absorbed or released?

• Absorbed when hydrogen bonds break

• Released when hydrogen bonds form

Evaporation

• The transformation of a substance from a liquid to a gas

Heat of vaporization

• The quantity of heat a liquid must absorb for 1 gram of it to be converted from a liquid to a gas

Evaporative cooling

• Due to water’s high heat of vaporization

• Allows water to cool a surface

Ice

• Less dense than liquid water

• Floats in liquid water

• Life can still exist under the frozen surface of lakes and polar seas

Hydrogen bonds in ice

• More ordered than in liquid water, making ice less dense

• The bond are more stable and less likely to constantly break and reform

Is water a solvent?

• Yes, because of its polarity

• It can form aqueous solutions

How does water interact with solutes?

• The different regions of the polar water molecules can interact with ionic compounds called solutes and dissolve them

• Ex: the negative oxygen regions of polar water molecules are attracted to sodium cations, whereas the positive hydrogen regions of water molecules cling to chloride anions

Does water interact with polar molecules?

• Yes, especially proteins

• Ex: the oxygen is attracted to a slight positive charge on lysozyme (protein)

Hydrophilic substance

• Has an affinity for water

Hydrophobic substance

• Does not have an affinity for water

Mole

• Represents an exact number of molecules of a substance in a given mass

Molarity

• The number of moles of solute per liter of solution

Can water dissociate?

• Yes, it dissociates into hydronic ions and hydroxide ions

• Changes in the concentration of these ions can have an effect on living organisms

Acid

• Any substance that increases the hydrogen ion concentration of a solution

Base

• Any substance that reduces the hydrogen ion concentration of a solution

pH of a solution

• Determined by the relative concentration of hydrogen ions

• Is low in an acid

• Is high in a base

What must the internal pH of most living cells remain close to?

• A pH of 7

Buffers

• Substances that minimize changes in the concentration of hydrogen and hydroxide ions in a solution

• Consist of an acid-base pair that reversibly combines with hydrogen ions

Acid precipitation

• Refers to rain, snow, or fog with a pH lower than pH 5.6

• Caused by mixing of different pollutants with water in the air

• Can damage life in Earth’s ecosystems

Is carbon found in living organisms?

• Yes, all living organisms are made up of chemicals based mostly on the element carbon

Vitalism

• Organic compounds arise only within living organisms

• Was disproved when chemists synthesize compound in laboratory

How many atoms does carbon typically bond with?

• Four

How many valence electrons does carbon have?

• Four valence electrons

• This allows it to form four covalent bonds with a variety of atoms

• Has high bonding versatility and covalent capability with many different elements

Carbon chains

• Form the skeletons of most organic molecules

• Vary in length or shape, from rings to branches

Hydrocarbons

• Molecules consisting of only carbon and hydrogen

• Found in many of a cell’s organic molecules

Isomers

• Molecules with the same molecular formula but different structures and properties

• Include three types: structural, geometric, and enantiomers (important in pharmaceutical industry)

Functional groups

• Chemically reactive groups of atoms within an organic molecule and give molecules distinctive chemical properties

What are the six functional groups that are important in the chemistry of life?

• Hydroxyl, carbonyl, carbohydrate, amino, sulfhydryl, phosphate

What functional group is this?

• Hydroxyl

• One in which a hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule

• Written as -OH, sometimes as HO-

What functional group is this?

• Carbonyl group

• Consists of a carbon atom joined to an oxygen atom by a double bond

• >CO

What functional group is this?

• Carboxyl group

• Consists of an oxygen atom that is double bonded to a carbon atom that is also bonded to a hydroxyl group

• -COOH

What organic compounds contain hydroxyl groups?

• Alcohols, with their specific names ending in -ol

• Ex: ethanol

What organic compounds contain carbonyl groups?

• Ketones if the carbonyl group is within a carbon skeleton

  • Ex: acetone

• Aldehydes if the carbonyl group is at the end of the carbon skeleton

  • Ex: propanal

What organic compounds contain carboxyl?

• Carboxylic acids, or organic acids

  • Ex: acetic acid

What is true about hydroxyl groups?

• Are polar as a result of the electronegative oxygen atom

• Attracts water molecules, helping dissolve organic compounds

What is true about carboxyl groups?

• Have acidic properties because it is a source of hydrogen ions

• The covalent bond between oxygen and hydrogen is so polar that hydrogen ions tends to dissociate reversibly

What functional group is this?

• Amino group

• Consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton

• -NH2

What functional group is this?

• Sulfyhdryl group

• Consists of a sulfur atom bonded to an atom of hydrogen

• -SH, or HS-

What functional group is this?

• Phosphate group

• A phosphorus atom is bonded to four oxygen atoms; one oxygen is bonded to carbon skeleton, two carry negative charges

• -OPO3H2

What organic compounds contain amino groups?

• Amine

  • Ex: glycine, but it also has a carboxyl group so is both an amine and carboxylic acid

What are compounds called who have both amine and carboxylic acids?

• Amino acids

What is true about amino functional groups?

• Acts as base and can pick up a proton from the surrounding solution to become ionized

• Name of compound: amines

What is true about sulfhydryl functional groups?

• Two sulfhydryl groups can interact to help stabilize protein sutrcutre

• Name of compound: thiol

What is true about phosphate functional groups?

• Makes the molecule of which it is a part of an anion

• Can transfer energy between organic molecules

• Name of compound: organic phosphates

Four main classes large molecules

• Carbohydrates, lipids, proteins, nucleic acids