WEEK 2 BIOCHEM NOTES
Chapter 2: Water: The Solvent for Biochemical Reactions
Water is 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 - refers to a bond in which two atoms share electrons evenly
Dipoles - molecules with positive and negative ends due to an uneven distribution of electrons in bonds
Salt bridge - an interaction 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 and covalent bonds - are the strongest bonds, being many times stronger than the next weakest one.
Ion-dipole Interaction - An Ion in solution can also interact with molecules that have dipoles; a charged ion will interact with the corresponding opposite partial charge on the water.
Ion-dipole and Dipole-Dipole interaction - helps ionic and polar compounds dissolve in water
Van der Waals forces - noncovalent associations based on the weak attraction of transient dipoles for one another
Dipole-dipole - these forces occur between molecules that are dipoles, with the partial positive side of one molecule attracting the partial negative side of another molecule
Dipole-Induced Dipole Interactions - a permanent dipole in a molecule, when it comes into close contact with any molecule, even those that have no dipoles, can induce a transient dipole in the other.
Induced Dipole-Induced Dipole interactions - when two molecules lacking dipoles bump into each other, they distort each other’s electron cloud, thereby creating a brief interaction between these induced dipoles.
London Dispersion force - an attraction between transient induced dipoles
Hydrophilic - tending to dissolve in water
Hydrophobic - tending not to dissolve in water
Hydrophobic interactions - attractions between molecules that are nonpolar; also called hydrophobic bonds
Amphipathic - refers to a molecule that has one end with a polar, water-soluble group and another end with a nonpolar hydrocarbon group that is insoluble in water.
Hydrogen bonding - a noncovalent association formed between a hydrogen atom covalently bonded to one electronegative atom and a lone pair of electrons on another electronegative atom
Nonlinear bonds are weaker than bonds in which all three atoms lie in a straight line.
Acids and Bases
Acid strength - the tendency of an acid to dissociate to a hydrogen ion and its conjugate base
Acid dissociation constant - a number that characterizes the strength of an acid
Ion product constant for water - a measure of the tendency of water to dissociate to give hydrogen ions and hydroxide ions
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
In biochemistry, most of the acids encountered are weak acids. These have a Ka well below 1
Henderson-Hasselbalch equation - a mathematical relationship between the pKa of an acid and the pH of a solution containing the acid and its conjugate base
Titration - an experiment in which a measured amount of base is added to an acid
Equivalence point - the point in a titration where an acid is exactly neutralized
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
Buffering capacity - a measure of the amount of acid or base that can be absorbed by a given buffer solution.
Zwitterions - molecules that have both a positive and a negative charge
Acidosis - a condition in which blood pH drops below 7.35
Alkalosis - a condition in which blood pH rises above 7.45
Summary:
Water and polarity
When two atoms with the same electronegativity form a bond, the electrons are shared equally between the two atoms.
If atoms with differing electronegativity form a bond, the electrons are shared equally, and more of the negative charge is found closer to one of the atoms.
The polar nature of water largely determines its solvent properties
Ionic compounds with full charges and polar compounds with partial charges tend to dissolve in water
The underlying physical principle is electrostatic attraction between unlike charges. The negative end of a water dipole attracts a positive ion or the positive end of another dipole
The positive end of a water molecule attracts either a negative ion or the negative end of another dipole
Oil molecules are amphipathic - having both polar (hydrophilic) heads and nonpolar (hydrophobic) tail portions
When oil and water separate ion layers, the polar head groups of the oil molecules are in contact with the aqueous environment, and the nonpolar tails are sequestered from the water
Van der Waals interactions between nonpolar molecules provide the energetic basis for this spontaneous molecular arrangement
Hydrogen bonds
Water has unique properties for a molecule of its size, such as a very high boiling point and melting point.
This is due to the extensive hydrogen bonding possible between water molecules.
Each water molecule has two sources of partial positive charge and two of partial negative charge. This allows water to form an array in a solid form and to bond with many other water molecules in a liquid form.
The extensive hydrogen bonding requires large amounts of energy to disrupt, and therefore, it melts and boils at higher temperatures than other molecules of its relative size.
Acids, Bases, and pH
Acids are compounds that release hydrogen ions (protons) when dissolved in aqueous solution. In other words, they are proton donors.
Bases are compounds that are proton acceptors.
The mathematical definition of pH is the negative of the logarithm of the hydrogen ion concentration
pH is a measure of the acidity of the solution. The lower the pH, the more acidic the solution
Because of the term, a pH change of one unit means a tenfold change in hydrogen ion concentration
It is important to know the pH because many biological reactions require a very tight range of pH values
For example, an enzyme that is active at pH 7.0 may be completely inactive at pH 8.0
Solutions used in science often must have their pH controlled in order to have an experiment function correctly
Although local variation in pH may occur in certain subcellular organelles, a cell must maintain a pH near neutrality in order to stay alive
Buffers
It works based on the nature of weak acids and their conjugate bases that compose the buffer.r
If a source of extra hydrogen ions is added to a buffer solution, it reacts with the conjugate base ot form the weak acid.
If a source of hydroxide ions is added to the buffer, it reacts with the weak acid to form water and the conjugate base.
In this way, either added H+ or OH- is “used up” by adding it to a buffer. This keeps the pH much more stable than if the same acid or base had been added to an unbuffered system.
We choose a buffer primarily by knowing the pH that we wish to maintain
For example, if we are performing an experiment and we want the solution to stay at pH 7.5, we look for a buffer that has a pKa of 7.5 because buffers are most effective when the pH is close to the buffer's pKa
The most efficient way to make a buffer in the laboratory 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
The pH will be either too low or too high
We then add strong acid or strong base until the pH is the desired buffer pH.
Then we bring the solution up to the final volume so that the concentration is correct.
Buffers are not just an artificial system used in the laboratory. Living systems are buffered by naturally occurring compounds.
Naturally occurring phosphate and carbonate buffers help maintain physiological pH near 7.0
Amino Acids and Peptides
Amino group - the NH2 functional group
Carboxyl group - the COOG functional group that dissociates to give the carboxylate anion, COO-, and a hydrogen ion
Side chain group - the portion of an amino acid that determines its identity
Stereochemistry - the branch of chemistry that deals with the three-dimensional shape of molecules
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
Sterioisomers - molecules that differ from each other only in their configuration (three-dimensional shape); also called optical isomers
L- and D-amino acids - amino acids whose stereochemistry is the same as the stereochemical standards L- and D-glyceraldehyde, respectively
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
One group of amino acids has nonpolar side chains:
This includes glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan, and methionine
On several members of this group - namely, alanine, valine, leucine, and isoleucine - each side chain 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
Basic Amino Acids
Three amino acids - histidine, lysine, and arginine - have basic side chains, and the side chain in all three is positively charged at or near neutral pH.
Lysine - the side-chain amino group is attached to an aliphatic hydrocarbon tail
Arginine - the side-chain basic group, the guanidino group, is a more complex structure than the amino group, but it is also bonded to an aliphatic hydrocarbon tail.
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 - the carboxylate portion negatively and the amino group positively.
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
Residues - portions of monomer units included in polymers after splitting out water between the linked monomers
Peptide bond - an amide bond between amino acids in a protein
Peptides - molecules formed by linking two to several dozen amino acids by amide bonds
Polypeptide chain - the backbone of a protein; it is formed by linking amino acids by peptide (amide) bonds
Resonance structures - structural formulas that differ from each other only in the position of electrons
Summary
Amino Acids are three-dimensional
The amino acids that are the monomer unit of proteins have a general structure in common, with an amino group and a carboxyl group bonded to the same carbon atom.
The nature of the side chains, which are referred to as R groups, is the basis of the differences among amino acids.
Except for glycine, amino acids can exist in two forms, designated L and D. These two stereoisomers are non-superimposable mirror images of each other
The amino acids found in proteins are of the L form; some D-amino acids occur in nature.
Structures and Properties of Amino Acids
A classification scheme for amino acids can be based on the properties of their side chains.
Two particularly important criteria are the polar or non-polar nature of the side chain and the presence of an acidic or basic group in the side chain.
Nonpolar Amino Acids
One group of amino acids has nonpolar side chains
The side chains are mostly aliphatic or aromatic hydrocarbons or their derivatives
Polar-neutral Amino acids
A second group of amino acids has side chains that contain electronegative atoms such as oxygen, nitrogen, and sulfur
Acidic Amino Acids
Two amino acids, glutamic acid and aspartic acid, have carboxyl groups in their side chains.
Best Amino Acids
Three amino acids - histidine, lysine, and arginine - have basic side chains.
Uncommon Amino Acids
Some amino acids are found only in a few proteins
They are formed from the common ones after the protein has been synthesized in the cell.
Titration of Amino Acids
In free amino acids at neutral pH, the carboxylate group is negatively charged (acidic) and the amino group is positively charged (basic)
Amino acids without charged groups on their side chains exist in neutral solution as zwitterions with no net charge.
Titration curves of amino acids indicate the pH ranges in which titratable groups gain or lose a proton.
Side chains of amino acids can also contribute titratable groups; the charge (if any) on the side chain must be taken into consideration in determining the net charge on the amino acid.
The Peptide Bond
Peptides are formed by reacting the carboxyl group of one amino acid with the amino group of another amino acid in a covalent (amide) bond.
Proteins consist of polypeptide chains; the number of amino acids in a protein is usually 100 or more
The peptide group is planar; this stereochemical constraint plays an important role in determining the three-dimensional structures of peptides and proteins.
Small Peptides with Physiological Activity
Small peptides, containing two to several dozen amino acid residues, can have marked physiological effects in organisms.
Oxytocin and vasopressin each have nine amino acids and only differ in two positions.
They both have marked biological effects in vertebrates
Oxytocin stimulates uterine contractions, lactation, mother-child bonding, pair bonding, feelings of trust, and altruistic behavior
Vasopressin is involved in the control of blood pressure, as well as being implicated in male behavior of territoriality, aggression, pair bonding, and social group defense