BIOL 111 - Unit 1

(Ch. 1-4)

Matter

anything that takes up spa

Element

a substance that cannot be further broken down by chemical reactions

Compound

a substance made up of 2 or more elements combined

Which four elements make up 96% of all living matter?

Oxygen, Carbon, Hydrogen, and Nitrogen

Why are these four elements so abundant ?

Few other organisms account for the remaining 4% of an organism’s mass

In which compounds are these elements (O, C, H, N) found?

organic compounds

Essential elements

elements required for an organism to survive grow and \n reproduce.

Trace elements

elements that indispensable for life but required in extremely \n minute amounts.

Atom

smallest unit of matter that retains the properties of an element.

Dalton

a measure of mass for atoms and subatomic particles; the same as atomic mass unit (amu).

radioactive isotope

an unstable isotope whose nucleus spontaneously decays and \n gives off energy and particles

Valence Electrons

electron(s) on the outermost electron shell

Valence shell

the outermost energy shell of an atom containing electrons involved in the chemical reactions of that atom.

Electron orbital

a 3D space where electrons are found 90% of the time.

Chemical bonds

an attraction between two atoms leading to, the two atoms sharing outer-shell \n electrons, or the presence of opposite charges on the atoms

Covalent bonds

the sharing of a pair of valence electrons by two atoms

Molecule

two or more atoms held together by covalent bonds

Electronegativity

the attraction of a given atom for the electrons of a covalent bond

Nonpolar covalent bonds

a type of covalent bond in which electrons are shared equally \n between two atoms of similar electronegativity

Polar covalent bonds

a type of covalent bond in which electrons are shared equally between \n two atoms of differing electronegativity

cation

positively charged ion

anion

negatively charged ion

ionic bond

chemical bond resulting from the attraction between oppositely charged ions

Hydrogen bond

a weak chemical bond formed when a slightly positive hydrogen atom is attracted to \n a slightly negative atom of a polar covalent bond in another molecule or region of the same \n molecule

Van der Waals interactions

weak attractions between molecules of parts of molecules that \n result from ever-changing local partial charges

Why do atoms form bonds?

Atoms bond in an attempt to complete their valence shells.

What determines whether a covalent bond is non-polar or polar?

whether or not the \n atoms bonded have similar or differing electronegativity.

Why are hydrogen bonds not true bonds?

The atoms can come together but separate after affecting each other.

What causes molecules to have different shapes?

Molecules have different shapes due to the positioning of their atoms’ orbitals.

Why is different molecular shapes biologically important?

Molecular shape determines how biological molecules recognize and respond to one another with specificity; Biological molecules only bind if their shapes are complimentary

Chemical reactions

the making and breaking of chemical bonds leading to changes in \n composition of matter.

Chemical equilibrium

the state in a chemical reaction when the rate of the forward reaction \n equals the rate of the reaction in reverse.

What does it mean that a reaction has reached equilibrium?

\n It means the rate of the reaction going forward is equal to the rate of the reverse \n reaction, so the relative concentration of reactants and products don’t change over \n time.

Polar molecule

a molecule with an uneven distribution of charges in different regions.

What kind of bonds link each atom in a water molecule?

Polar covalent

How many hydrogen bonds can each water atom form?

Each water molecule can hydrogen bond with up to four other water molecules

Why is liquid water denser than frozen water (ice)?

Cohesion

the linking together of like molecules, often by hydrogen bonds

Surface tension

a measure of how difficult it is to stretch or break the surface of a liquid

Adhesion

the linking together of different molecules by means of hydrogen bonds

Specific heat:

the amount of heat that must be absorbed/lost for 1g of a substance to change its temperature by 1 degree Celsius.

Heat of vaporization

the quantity of heat a liquid must absorb for 1g of it to be converted from \n liquid into a gas.

Evaporative cooling

the process in which the surface of an object becomes cooler during evaporation as a result of molecules with the greatest kinetic energy changing from a liquid to gas

Hydrophilic

having an affinity for water; if water molecules are too big ma not dissolve

Hydrophobic

having no affinity for water/ tending to coalesce and form droplets in water

What are the four emergent properties of water that are important for life?

Cohesion, Moderation of temperature, Expansion Upon Freezing, Versatility as a Solvent

Does water have a low or high specific heat relative to most other molecules? Why?

Water has a high specific heat is because much of the heat absorbed by water is used to disrupt the hydrogen bonds before water molecules that to move fast enough.

Why is the floating of frozen water important?

The expansion of water upon freezing allow to life to continue under frozen surfaces of lake and polar seas.

Why is water a good solvent?

Water makes a good solvent because its polar molecules it’s attracted to ions and other polar molecules that it can form hydrogen bonds with.

How is hydrogen bonding is important to each of water’s emergent properties?

Cohesion → allows water molecules to drag each other up

Mod. of temp. → water’s resistant to temp. change b/c heat goes towards breaking H bonds

Expansion upon freezing → molecules expand ice as not to break H bonds

Versatility as Solvent → form H bonds with polar/ionic molecules thus separating them

Expansion Upon Freezing

H bonds stabilize in cold temp. and thus can form up to 4 bonds

Organic compounds

the study of carbon compounds

How can only a handful of different elements (e.g. C, H, O, N) form so many different molecules?

Carbon has the ability to form four bonds (the maximum possible), it can form an inexhaustible variety of organic molecules with the handful of major elements (C, H, O, N, S, P).

Hydrocarbon

an organic molecule made up of only carbon and hydrogen

Isomer

one of two compounds that have the same numbers of atoms of the same elements but \n different structures and hence different properties.

Structural isomer

isomers that differ in the covalent arrangement of their atoms

Geometric isomer (cis-trans isomer)

an isomer that has the same molecular formula and covalent bonds between atoms but differ in the spatial arrangements of their atoms owing to the inflexibility of double bonds

Enantiomer

one of two compounds that mirror each other but differ in shape due to the presence of an asymmetric carbon

How can the carbon skeletons differ?

Carbon skeletons can very in length, branching, double bond position, presence of rings, and/or presence of other elements.

Functional group

a specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and involved in chemical reactions

List the 7 important functional groups in biology.

hydroxyl, carboxyl, carbonyl, amino, sulfhydryl, phosphate, methyl

Hydroxyl (OH)

Alcohol

Polar, reactive, forms hydrogen bonds

Carboxyl (COOH)

Carboxyl/organic acid

Polar, reactive, acts as an acid, its ionized form found in cells

Carbonyl (CO)

Ketone/Aldehyde

polar, reactive, sugars

Amino (NH2)

Amine

Polar, reactive, act as a base

Sulfhydryl (SH)

Thiol

Polar, reactive, forms cross-links to stabilize protein structures

phosphate

Organic phosphate

Polar, reactive, contributes to negative charge, releases energy when in contact with water

methyl

Methylated compound

nonpolar, nonreactive, affects expression of genes when bonded to DNA or proteins that do

What is ATP?

An adenine containing nucleoside triphosphate that releases free energy when its phosphate bonds are hydrolyzed.

When ATP reacts with water, it undergoes hydrolysis. What are the products of the \n hydrolysis reaction?

\n ADP (adenosine diphosphate)