Biochemistry and Chemistry: Water, Reactions, Bonds, and Functional Groups

Water

Water is the most abundant molecule in cells, accounting for 70% or more of total cell mass.

Polarity

The critical property of water is that it is a polar molecule.

Hydrophobic

Water fearing molecules (Nonpolar).

Hydrophilic

Water loving molecules (Polar).

Amphiphilic

Both water loving and fearing (Both polar/nonpolar).

Dehydration Synthesis (Condensation)

Joins monomers to form dimers/polymers.

Hydrolysis (Decomposition)

A reaction that breaks down compounds by the addition of water.

Redox

A type of reaction involving the transfer of electrons.

Phosphorylation

The addition of a phosphate group to a molecule.

Monomer

A single unit of a molecule.

Dimer

Two joined units of monomers.

Oligomer

A small molecule made of a few monomers (approximately 4-12).

Polymer

A large molecule made of many monomers.

Polymerization

The process of creating a polymer.

Joint Lubrication

Water lubricates and cushions joints.

Waste Removal

Water helps get rid of wastes through urination, perspiration, and bowel movements.

Cell Composition

Cells are composed of water, ions, and organic molecules.

Interactions of Water

Interactions between water and all other constituents of cells are of central importance.

Creation of Polymer

Creation of polymer is done by polymerization.

Water's Effect on Cells

Since most molecules are dissolved in water in the body, water has a profound effect on the cell.

Functional Groups

Certain functional groups may affect a molecule's polarity.

Bond Formation

Making and breaking bonds is important to forming molecules.

Dehydration Synthesis Reaction (DSR)

Joins monomers to form dimers/polymers.

Hydrolysis Reactions (HR)

Breaks a polymer into dimers/monomers.

Redox Reactions

Reduction-oxidation - Transfer of electrons between molecules.

Organic compounds

A large class of chemical compounds in which one or more atoms of carbon are covalently linked to atoms of other elements, most commonly hydrogen, oxygen, or nitrogen.

Hydrocarbon

An organic chemical compound composed exclusively of hydrogen and carbon atoms.

Hydrocarbons occurrence

Hydrocarbons occur naturally and form the basis of crude oil, natural gas, coal.

Hydrocarbon chain

A molecule that consists of hydrogen and carbon.

Structural formulas

A method of drawing hydrocarbons that shows the arrangement of atoms in the molecule.

Skeletal formulas

A method of drawing hydrocarbons where every 'kink' represents a carbon atom and hydrogen 'side groups' are not drawn.

Bonds in atoms

Every atom has the proper number of necessary bonds: Carbon: 4, Oxygen: 2, Hydrogen: 1.

Reactivity of functional groups

Functional groups are more reactive than hydrocarbons.

Hydrophilic functional groups

Functional groups that are polar and increase solubility in water.

Hydrophobic functional groups

Functional groups that are nonpolar and decrease solubility in water.

Functional groups in molecules

In a molecule, there may be multiple functional groups present.

Methyl group

A functional group represented as H3C- or -CH3 depending on its position in the molecule.

ATP

A molecule that contains numerous functional groups, important in energy transfer.

Electronegativity

A measure of the tendency of an atom to attract a bonding pair of electrons.

Polar molecule

A molecule that has a net dipole moment due to the presence of polar bonds.

Nonpolar molecule

A molecule that does not have a net dipole moment, typically due to symmetrical distribution of electron density.

Covalent bond

A chemical bond that involves the sharing of electron pairs between atoms.

Overall polarity of a molecule

Determined by the sum of the individual bond polarities and the molecular geometry.

Polarity symbols

Symbols used to indicate the direction of polarity in a molecule.

Hydrocarbons

M.E.P.B pentane hexane septane octane nonane decane

Electronegativity scale

A scale that ranks elements based on their ability to attract electrons. 0-0.5 non polar, 0.5-1.7 polar covalent, 1.7+ ionic

Chemical Bond

Force of attraction (FOA) between atoms, ions or molecules that enables the formation of chemical compounds.

Intramolecular Bonds

Bond(s) that holds atoms within a molecule together.

Intermolecular Bonds

Forces between molecules that allow them to (potentially) interact.

Intermolecular Forces

Three types collectively referred to as Van der Waals forces.

Dipole - Dipole Forces

FOA between the positive part of one polar molecule and the negative part of another polar molecule.

Dipole

A molecule with a partially positively charged end (δ+) and a partially negatively charged end (δ-).

Hydrogen Bonds

FOA between a H atom which is covalently bound to a more electronegative atom.

London Dispersion Forces (LDF)

Weak attractive force between any (and all) molecules caused by electrons randomly being on one side of an atom/molecule.

Dipole-Dipole Forces vs Hydrogen Bonds

Hydrogen bonds are usually stronger than dipole-dipole forces.

Temporary Dipole

A dipole that occurs due to the random distribution of electrons.

Ranking Intermolecular Force

LDF weakest, then it is dipole-dipole, then hydrogen bonds

Nonpolar Molecules and LDF

If a molecule is nonpolar, LDF are the only intermolecular forces.

Opposites Attract

In dipole-dipole interactions, δ+ is attracted to δ- between molecules.

Strong Intermolecular Force

Hydrogen bonds are a strong intermolecular force.

All Molecules Have LDF

All molecules have LDF, but if they can have DD or HB, those forces usually 'overpower' LDF.

Hydrophobic Forces

Another term for London Dispersion Forces.

Effect of Intermolecular Forces

Intermolecular forces only have an effect when molecules are close together.

London Dispersion

A type of intermolecular force that occurs between non-polar molecules.

Like dissolves like

Substances with similar chemical characteristics will dissolve in each other.

Polar solvents

Solvents that tend to dissolve polar solutes.

Non-polar solvents

Solvents that tend to dissolve non-polar solutes.

Polar substances

Substances that have a distribution of electrical charge leading to partial positive and negative charges.

Non-polar substances

Substances that do not have a significant charge distribution.

Intra- and intermolecular bonds

Intra- refers to bonds within a molecule, while inter refers to bonds between molecules.

Types of intermolecular bonds

Includes hydrogen bonds, dipole-dipole interactions, and London dispersion forces.

Strongest intermolecular bond

Hydrogen bonding is typically the strongest type of intermolecular bond.

Weakest intermolecular bond

London dispersion forces are typically the weakest type of intermolecular bond.

Always occurring intermolecular force

London dispersion forces occur regardless of the polarity of molecules.

Hydrogen bonding in water

Water molecules can do hydrogen bonding due to the presence of hydrogen atoms bonded to oxygen.

Hydrogen bonding in hexane

Hexane cannot do hydrogen bonding as it is a non-polar molecule.

Nonpolar Covalent Bonds

Equal sharing of valence electrons between two non-metal atoms.

Polar Covalent Bonds

Unequal sharing of valence electrons between two non-metal atoms.

Ionic Bonds

Bonds formed through the transfer of electrons from one atom to another.

Metallic Bonds

Bonds formed by the attraction between metal ions and delocalized electrons.

Solubility of polar molecules

Polar molecules tend to be soluble in polar solvents.

Solubility of non-polar molecules

Non-polar molecules tend to be soluble in non-polar solvents.

Intermolecular forces in water

Hydrogen bonds hold water molecules together.

Intermolecular forces in hexane

London dispersion forces hold hexane molecules together.

Drawing intermolecular forces

Intermolecular forces can be represented as dotted lines between molecules.

Polar Covalent Bonds (PC)

Unequal sharing of valence e-s between two non-metal atoms.

Differences in electronegativity (∆EN)

Can be used to predict bond type.

Small ∆EN

Expected when two atoms share electrons.

Large ∆EN

Expected when one atom steals an electron.

Electronegativity difference (∆EN)

Difference in electronegativities between two atoms.

NPC

Nonpolar covalent bond, indicated by a ∆EN of 0 - 0.5.

PC

Polar covalent bond, indicated by a ∆EN of 0.5 - 1.7.

I

Ionic bond, indicated by a ∆EN greater than 1.7.

KF

Example calculation of ∆EN resulting in 3.18.

O2

Example with ∆EN of 0, indicating a nonpolar covalent bond.

KCl

Example with ∆EN of 2.38, indicating an ionic bond.

CCl

Example with ∆EN of 0.6, indicating a polar covalent bond.

HCl

Example with ∆EN of 1.0, indicating a polar covalent bond.

OH

Example with ∆EN of 1.2, indicating a polar covalent bond.

Water (O-H Bond)

Example with ∆EN of 1.2, indicating a polar covalent bond.