WEEK 2 BIOCHEM NOTES

Water

The principal component of most cells.

Electronegativity

The tendency of an atom to attract electrons to itself in a chemical bond.

Polar bonds

Bonds in which two atoms have an unequal share in the bonding electrons.

Nonpolar bonds

Bonds where two atoms share electrons evenly.

Dipoles

Molecules with positive and negative ends due to an uneven distribution of electrons.

Salt bridge

An interaction that depends on the attraction of unlike charges.

Van der Waals radius

The distance between an atom’s nucleus and its effective electronic surface.

Ionic bonds

The strongest type of bond, significantly stronger than covalent bonds.

Ion-dipole Interaction

An ion in solution interacts with molecules that have dipoles.

Dipole-Dipole interaction

Forces occurring between dipoles, attracting positive and negative sides.

Dipole-Induced Dipole Interactions

When a permanent dipole induces a transient dipole in another molecule.

Induced Dipole-Induced Dipole interactions

Interactions between two nonpolar molecules that create brief induced dipoles.

London Dispersion force

Attraction between transient induced dipoles.

Hydrophilic

Tending to dissolve in water.

Hydrophobic

Tending not to dissolve in water.

Hydrophobic interactions

Attractions between nonpolar molecules, also known as hydrophobic bonds.

Amphipathic

A molecule with one polar water-soluble group and one nonpolar group.

Hydrogen bonding

A noncovalent association between a hydrogen atom and an electronegative atom.

Acid strength

The tendency of an acid to dissociate into a hydrogen ion and its conjugate base.

Acid dissociation constant (Ka)

A number that characterizes the strength of an acid.

Ion product constant for water

A measure of water's tendency to dissociate into hydrogen ions and hydroxide ions.

pH

A measure of the acidity or basicity of a solution.

Henderson-Hasselbalch equation

Mathematical relationship between the pKa of an acid and the pH of its solution.

Titration

An experiment where a measured amount of base is added to an acid.

Equivalence point

The point in a titration where an acid is exactly neutralized.

Buffer

A substance that resists changes in pH.

Buffer solution

A solution maintaining constant pH despite the addition of acids or bases.

Buffering capacity

The measure of how much acid or base a buffer solution can absorb.

Zwitterions

Molecules with both positive and negative charges.

Acidosis

A condition where blood pH drops below 7.35.

Alkalosis

A condition where blood pH rises above 7.45.

Amino group

The NH2 functional group found in amino acids.

Carboxyl group

The COOH functional group that gives off hydrogen ions.

Side chain group

The portion of an amino acid that determines its identity.

Stereochemistry

The branch of chemistry dealing with molecular shapes.

Chiral

An object that is not superimposable on its mirror image.

Achiral

An object that is superimposable on its mirror image.

Sterioisomers

Molecules differing in their three-dimensional shapes.

L- and D-amino acids

Amino acids with stereochemistry corresponding to glyceraldehyde standards.

Basic Amino Acids

Amino acids like histidine, lysine, and arginine with positively charged side chains.

Peptide bond

An amide bond formed between amino acids.

Polypeptide chain

The backbone of a protein made by linking amino acids.

Isoelectric pH (pI)

The pH at which a molecule has no net charge.

Electrophoresis

A method for separating molecules based on charge to size ratio.

Nonpolar

refers to a bond in which two atoms share electrons evenly

Ionic bonds and covalent bonds

are the strongest bonds, being many times stronger than the next weakest one.

Van der Waals forces

noncovalent associations based on the weak attraction of transient dipoles for one another

Amphipathic

refers to a molecule that has one end with a polar, water

Nonlinear bonds

are weaker than bonds in which all three atoms lie in a straight line.

Acid dissociation constant

a number that characterizes the strength of an acid

pH of 7

When a solution has a pH of 7, it is said to be neutral, like pure water

Acidic solutions

have pH values lower than 7, and basic solutions have pH values higher than 7

Weak acids

In biochemistry, most of the acids encountered are weak acids.

Buffer

something that resists change

Buffer solution

a solution that resists a change in pH on the addition of moderate amounts of strong acid or strong base

Water and polarity

When two atoms with the same electronegativity form a bond, the electrons are shared equally between the two atoms.

Electrostatic attraction

the underlying physical principle that describes the attraction between unlike charges.

Van der Waals interactions

interactions between nonpolar molecules that provide the energetic basis for spontaneous molecular arrangement.

Hydrogen bonds

the extensive bonding possible between water molecules that contributes to water's unique properties.

Boiling point of water

Water has a very high boiling point due to extensive hydrogen bonding.

Melting point of water

Water has a very high melting point due to extensive hydrogen bonding.

Acids

compounds that release hydrogen ions (protons) when dissolved in aqueous solution.

Bases

compounds that are proton acceptors.

pH

a measure of the acidity of the solution, defined as the negative of the logarithm of the hydrogen ion concentration.

pH Change

A pH change of one unit means a tenfold change in hydrogen ion concentration.

Biological Reactions and pH

Many biological reactions require a very tight range of pH values.

Enzyme Activity and pH

An enzyme that is active at pH 7.0 may be completely inactive at pH 8.0.

pH Control in Experiments

Solutions used in science often must have their pH controlled in order to have an experiment function correctly.

Cellular pH Maintenance

A cell must maintain a pH near neutrality in order to stay alive.

Buffers

Buffers work based on the nature of weak acids and their conjugate bases that compose the buffer.

Buffer Reaction with Hydrogen Ions

If a source of extra hydrogen ions is added to a buffer solution, it reacts with the conjugate base to form the weak acid.

Buffer Reaction with Hydroxide Ions

If a source of hydroxide ions is added to the buffer, it reacts with the weak acid to form water and the conjugate base.

Buffer Stability

Buffers keep the pH much more stable than if the same acid or base had been added to an unbuffered system.

Choosing a Buffer

We choose a buffer primarily by knowing the pH that we wish to maintain.

Buffer pKa

Buffers are most effective when the pH is close to the buffer's pKa.

Making a Buffer in Laboratory

The most efficient way to make a buffer is to add either the weak acid form or the weak base form of the buffer compound to a container, add water, and then measure the pH with a pH meter.

Adjusting Buffer pH

We then add strong acid or strong base until the pH is the desired buffer pH.

Final Volume of Buffer

Then we bring the solution up to the final volume so that the concentration is correct.

Natural Buffers

Living systems are buffered by naturally occurring compounds.

Physiological pH

Naturally occurring phosphate and carbonate buffers help maintain physiological pH near 7.0.

Amino Group

The NH2 functional group.

Carboxyl Group

The COOH functional group that dissociates to give the carboxylate anion, COO

Side Chain Group

The portion of an amino acid that determines its identity.

Stereochemistry

The branch of chemistry that deals with the three

Chiral

Refers to an object that is not superimposable on its mirror image.

Achiral

Refers to an object that is superimposable on its mirror image.

Stereoisomers

Molecules that differ from each other only in their configuration (three

L

and D

Acidic Amino Acids

Two amino acids, glutamic acid and aspartic acid, have carboxyl groups in their side chains in addition to the one present in all amino acids.

Nonpolar Side Chains

A group of amino acids that includes glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan, and methionine.

Aliphatic Hydrocarbon Group

Each side chain of alanine, valine, leucine, and isoleucine is an aliphatic hydrocarbon group.

Aliphatic

refers to the absence of a benzene ring or related structure

Proline

has an aliphatic cyclic structure, and the nitrogen is bonded to two carbon atoms

Amino Acids

can act as both acids and bases; in a free amino acid, the carboxyl group and amino group of the general structure are charged at neutral pH

Titration of Amino Acids

When an amino acid is titrated, its titration curve indicates the reaction of each functional group with a hydrogen ion.

Low pH

meaning acidic, and has H+

pH < pKa

protonate

pH > pKa

deprotonate

Electrophoresis

a method for separating molecules on the basis of the ratio of charge to size

Isoelectric pH (pI)

the pH at which a molecule has no net charge; also known as the isoelectric point