Mdm Khadijah Hanim bt Abdul Rahman

Sem I: 2013/2014khadijahhanim@unimap.edu.my

CO 1: Ability to differentiate basic structure,

properties, functions and classification of important biomolecules.

- Demonstrate types of biomolecules, chemical nature and biological roles of water, buffer and its importance.

Living organisms: organic and inorganic molecules.

Composed of water- inorganic molecules. 50-95% of cell’s content.

Other ions: Na+, K+, Mg2+ and Ca2+ = 1%

Other molecules are organic: composed of 6 elements: C, H, N, P and S.

Simplest type of biomolecules are derived from hydrocarbons

Hydrocarbon: H and C containing molecules that are hydrophobic.

Eg: CH4, C2H6, C6H12

The chemical properties are determined by their functional groups. (alcohol, aldehyde, ketone, acids, amines etc).

Organic compounds are relatively small found in the cells.

4 families of small molecules: amino acids, sugars, fatty acids and nucleotides.

Several functions:- Used to synthesis larger molecules;

polymers- proteins, carbohydrates and nucleic acids.

- Special biological functions; nucleotide adenosine triphosphate (ATP) serve as cellular reservoir of chemical energy

- Involved in complex reaction pathways.

Small molecule Polymer General functions

Amino acids Proteins Catalysts and structural elements

Sugars Carbohydrates Energy sources and structural elements

Fatty acids N.A Energy sources and structural elements of complex lipid molecules

Nucleotides DNA, RNA Genetic information, protein synthesis

Hundreds of naturally occurring amino acids.

Each contain amino and hydroxyl group. Most common type: α-amino group R group: side chain- determined the

chemical properties of amino acid. Hydrophobic/hydrophilic.

20 standard a-amino acids that occur in proteins.

Some like glycine and glutamic acid: neurotransmitters in animal

Amino acids are used primarily in the synthesis of long, complex polymers: polypeptides.

Molecules that composed of polypeptides: enzymes, structural proteins and transport proteins.

Individual amino acids are connected in peptides by peptide bond involving a carbonyl group which occurs between amino group and carboxyl group of another molecule. NH-CO

Sugars: alcohol and carbonyl groups. Sugars with aldehyde group: aldoses Sugars with ketone group: ketoses Eg: 6 carbons sugar glucose: aldohexose Fructose: ketohexose Sugars are basic units for carbohydrates:

monosaccharides (glucose and fructose); polysaccharides (starch and cellulose)

Functions:- glucose: principle energy source in

animals and plants- Sucrose: use by plants as efficient means

to transport energy- Cellulose: structural component of wood- Chitin: protective outer coatings of

insects - Some biomolecules contain carbohydrate

components: nucleotides contain sugar ribose or deoxyribose.

Monocarboxylic acids that contain an even no of carbon atoms.

They serve as energy sources. Fatty acids chemical formula R-COOH; R

is alkyl group that contain Cand H atoms. 2 types: saturated (no double bond) and

unsaturated F.A (contain double bond; 1 or more)

F.A occur as independent molecules and only in trace amounts in living organisms

Most often they are components of lipid molecules.

Lipids are diverse groups that are soluble in organic solvents but are insoluble in water.

Eg: triacylglycerols are esters containing glycerol.

Each nucleotides contain 3 components: a 5-carbon sugar (ribose or deoxyribose), nitrogenous base and 1 or more phosphate groups

Functions: Energy generating reactions: energy obtained

from food is used to form a high-energy ATP Building block molecules of nucleic acids: 2

types of nucleic acids.- DNA- genetic infromation.- Structure: 2 polynucleotide strands wound

around each other to form a right-handed double helix.

- 4 types of base: purines adenine and guanine. Pyrimidines thymine and cytosine.

RNA: different from DNA. Contain ribose sugar and base uracil instead of thymine.

RNA is single stranded. 3 major types of RNA: rRNA, tRNA and

mRNA.

More than 70% of the earth’s surface is covered with the molecule of water.

Cell components and molecules (protein, poly sacharides, nucleic acid,

membranes) assume their shape in response to water

Water acts as a solvent & substrate for many cellular reactions

Water is a common chemical substance that is essential for the survival of all known

forms of life. (In typical usage, water refers only to its liquid form or state, but the substance also has a solid state, ice, and a gaseous state,

water vapor. )

Water is the chemical substance with chemical formula H2O: one molecule of water has two hydrogen atoms covalently bonded to a single oxygen atom.

Water is a tasteless, odorless liquid at ambient temperature and pressure, and appears colorless in small quantities, although it has its own intrinsic very light blue hue.

Oxygen attracts electrons much more strongly than hydrogen, resulting in a net positive charge on the hydrogen atoms, and a net negative charge on the oxygen atom.

The presence of a charge on each of these atoms gives each water molecule a net dipole moment.

Electrical attraction (hydrogen bonding) between water molecules due to this dipole pulls individual molecules closer together, making it more difficult to separate the molecules and therefore raising the boiling point.

Water can be described as a polar liquid that dissociates disproportionately into the hydronium ion (H3O+(aq)) and an associated hydroxide ion (OH−(aq))

Water is in dynamic equilibrium between the liquid, gas and solid states at standard temperature and pressure (0°C, 100.000 kPa) , and is the only pure substance found naturally on Earth.

Exist in all three physical states of matter: solid, liquid, and gas.

Has high specific heat Water conducts more easily than any

liquid except mercury Water has a high surface tension Water is a universal solvent Water in a pure state has a neutral pH.

The oxygen in water is sp3 hybridized. Therefore water has tetrahedral geometry. Consequently the water molecule is bent. The H-O-H angle is 104.5o.

The bent structure indicate water is polar coz linear structure is nonpolar.

Phenomenon where charge is separated to partial –ve charge and partial +ve charge is called dipoles.

Becoz of the large difference in electronegativity of H and O, the electron-deficient H are attracted to the unshared pairs of electrons of another H2O molecule.

Interaction- hydrogen bonding

Ionic interactions

Hydrogen bonding

Van der Waals forcesDipole-dipoleDipole-induced dipoleInduced dipole-induced dipole

Ionic interactions occur between charged atoms or groups.

Oppositely charged ions are attracted to each other. In proteins, the attraction of positively and

negatively charged amino acid side chains sometimes form ionic salt bridges.

CH2CH2COO-

CH2CH2NH3

+

Salt bridge

Repulsive forces created when similarly charged species come into close proximity

Important features in protein folding and enzyme catalysis

Most salt bridges rarely form in the presence of water- attraction between biomolecules decreases.

Salt bridges normally occur in free water or at molecular interfaces where water is excluded.

Water molecules can perform hydrogen bond with one another. Four hydrogen bonding attractions are possible per molecule:

2 through the hydrogens and

2 through the nonbonding

electron pairs.

HO

H

HO

H

HO

H

HO

HH

OH

hydrogen attached to an O becomes very polarized and highly partial plus (δ+). This partial positive charge interacts with the nonbonding electrons on another O giving rise to the very powerful hydrogen bond.

Water has an abnormally high boiling point due to intermolecular hydrogen bonding.

HO

H

HO

H

HO

H

H bonding is a

weak attraction between an electronegative atom in one molecule and an H(on an O) in another.

These forces are electrostatic interactions. Relatively weak.

These interactions occur among permanent and/or induced dipoles

The magnitude of Van der Waals forces depends on how easily an atom is polarized.

Electronegative atoms with unshared pairs of electrons are easily polarized.

Interactions among permanent dipoles such as carbonyl groups are much weaker than ionic interactions

Van der Waal’s forces

a. Dipole-dipole: occur between molecules containing electronegative atoms, cause molecules to orient themselves (positive end is directed toward negative end of another molecule)

b. Dipole-induced dipole: permanent dipole induces transient dipole in a nearby molecule by distorting its electron distribution.

C O C O+-

+-

C O H

H

HH

+- +

-

c. Induced dipole-induced dipole: the electron motion in nearby non polar molecules result in charge imbalance in adjacent molecules.

H

H

HH

H

H

HH

+-

+-

Hydrogen bonding keeps water in the liquid phase between 0oC and 100oC.

Liquid water has a high:Heat of vaporization - energy to vaporize

one mole of liquid at 1 atm

Heat capacity - energy to change the temperature by 1oC

Water plays an important role in thermal regulation in living organisms.

Max number of hydrogen bonds form when water has frozen into ice.

Hydrogen bonds is approximately 15% break when ice is warmed.

Liquid water consists of continuously breaking and forming hydrogen bonds.

The rising tempt. The broken of hydrogen bonds are accelerating.

When boiling point is reached, the water molecules break free from one another and vaporize.

Water easily dissolves a wide variety of the constituents of living organisms.

Water also unable to dissolve some substances: lipids and certain amino acid- lead to formation of membrane and protein folding.

This behavior is called hydrophilic and hydrophobic properties of water.

The polar nature of water makes it an excellent solvent for polar and ionic materials that are water loving (hydophillic)

Salts such as NaCl are held together by ionic forces>

Ionic interactions in aqueous solution- hydration of ions.

Water molecules are polar, therefore attracted to charged ions. Shells of water molecules refered to as solvation spheres cluster around these ions.

Ions become hydrated and the attractive force between them is reduced- dissolved in water.

Nonpolar molecules tend to coalesce into droplets in water. The repulsions between the water molecules and the nonpolar molecules cause this phenomenon.

The water molecules form a “cage” around the small hydrophobic droplets.

Water forms hydrogen-bonded cage like structures around hydrophobic molecules, forcing them out of solution.

Amphipathic molecules contain both polar and nonpolar groups.

Ionized fatty acids are amphipathic. The carboxylate group is water soluble and the long carbon chain is not.

Amphipathic molecules tend to form micelles, colloidal aggregates with the charged “head” facing outward to the water and the nonpolar “tail” part inside.

Osmosis is a spontaneous process in which solvent (e.g. water) molecules pass through a semi permeable membrane from a solution of lower solute (e.g. chemical) concentration to a solution of higher solute concentration.

Osmosis is the movement of solvent from a region of high concentration (here, pure water) to a region of relatively low concentration (water containing dissolved solute).

Water moves by osmosis and solutes by diffusion.

Osmotic pressure is the pressure required to stop osmosis or the influx of water (22.4 atm for 1M solution).

Because cells have a higher ion concentration than the surrounding fluids, they tend to pick up water through the semi permeable cell membrane.

The cell is said to be hypertonic relative to the surrounding fluid and will burst (hemolyze) if osmotic control is not effected.

Cells placed in a hypotonic solution will lose water and shrink (crenate).

If cells are placed in an isotonic solution (conc. same on both sides of membrane) there is no net passage of water.

Hypotonic solution: A solution with a lower salt concentration than in normal cells of the body and the blood.

Hypertonic solution: A solution with a higher salt concentration than in normal cells of the body and the blood.

Isotonic solution: A solution that has the same salt concentration as the normal cells of the body and the blood. An isotonic beverage may be drunk to replace the fluid and minerals which the body uses during physical activity.

Liquids move from high osmotic pressure (high conc. solvent and low conc. solute) to low osmotic pressure (high conc. solute and low conc. of solvent)

The self-ionization of water is the chemical reaction in which two water molecules react to produce a hydronium (H3O+) and a hydroxide ion (OH−).

Water ionization occurs endothermically due to electric field fluctuations between molecules caused by nearby dipole librations resulting from thermal effects, and favorable localized hydrogen bonding.

Ions may separate but normally recombine within a few min. to seconds. Rarely (about once every eleven hours per molecule at 25°C, or less than once a week at 0°C) the localized hydrogen bonding arrangement breaks before allowing the separated ions to return, and the pair of ions (H+, OH-) hydrate independently and continue their separate existence.

Water dissociates. (self-ionizes) H2O = H+ + OH-

Ka=[H+][OH-]/[H2O] Ka: equilibrium constant for the

reaction

The conditions for the water dissociation equilibrium must hold under all situations at 25o C. equib. constant for ionization of water is, Ka =1.8 x10-16 M and conc of pure water is 55. 5 M

Kw= [H+][OH-]=1 x 10-14

Kw= ion product of water. This means that the product of [H+] and [OH-] in any water solution is always 1x10-14.

Since [H+] is equal to [OH-] when pure water dissociates:

[H+ ] = [OH-] = 1 x 10-7 M

When solution contains equal amount of [H+] and [OH-] : neutral

Sol with excess [H+] : acidic Sol with excess [OH-] : basic H+ ion conc varies over a wide range :

provides the basis of pH scale : pH = - log [H+]

An acid is a substance that can donate a proton

A base is a substance that can accept a proton

H+ ions (called a protons, since a H+ ion has neither electrons nor neutrons).

Weak acids do not completely dissociates in water

The dissociation of organic acid is decribed below

HA ↔ H+ + A- (conjugate base of HA) Deprotonated product of the dissociation

reaction : conjugate base The strength of a weak acid (capacity to

release H ions): Ka = [H+][A-]/[HA] Ka is the acid dissociation constant, the

larger value of Ka, the stronger the acid. pKa = - log Ka

Added acids increase the concentration of hydronium ion and bases the concentration of hydroxide ion.

In acid solutions [H+] > 1 x 10-7 M [OH-] < 1 x 10-7 M

In basic solutions [OH-] > 1 x 10-7 M [H+] < 1 x 10-7 M

pH scale measures acidity without using exponential numbers.

Ka pKa

CH3COCOOH 3.2x10-3 2.5

CH3CHOHCOOH 1.4x10-4 3.9

CH3COOH 1.8x10-5 4.8

Larger Ka and smaller pKa values indicate stronger acids.

Buffer : a solution that resists change in pH when small amounts of strong acid or base are added. Help maintain a relatively constant H ion conc.

A buffer consists of:a weak acid and its conjugate base ora weak base and its conjugate acid

The capacity of a buffer to maintain a specific pH depends on 2 factors:

- The molar conc of the acid-conjugate base pair

- The ratio of their conc. The more molecules of buffer present,

the more H+ and OH- can be absorbed without changing the pH.

The Henderson-Hasselbalch (HH) equation is derived from the equilibrium expression for a weak acid.

pH = pKa + log [A-] [HA]

The HH equation enables us to calculate the pH during a titration and to make predictions regarding buffer solutions.

What is a titration?It is a process in which carefully measured volumes of a base are added to a solution of an acid in order to determine the acid concentration.

When chemically equal (equivalent) amounts of acid and base are present during a titration, the equivalence point is reached.

The equivalence point is detected by using an indicator chemical that changes color or by following the pH of the reaction versus added base, ie. a titration curve.

Water is essential for all living things.

Water molecules can form hydrogen bonds with other molecules because they have 2 H atoms that can be donated ans 2 unshared electron pairs that can act as acceptors.

Liquid water is an irregular network of water molecules that each form 4 hydrogen bonds with neighbouring water molecules.

Summary contd. Hydophilic substances such as ions

and polar molecules dissolve readily in water.

The hydrophobic effect is the tendency of water to minimizeits contact with nonpolar substances.

Water molecules move from regions of high concentration to regions of low concentration by osmosis.

Solutes move from regions of high conc. to regions of low conc. by diffusion.

Summary contd. Water ionizes to H+ (which represents the

hydronium ion H3O) and OH-. The concentration of H+ ions in solutions

is expressed as a pH value. Acids can donate protons and bases

accept protons. The strength of an acis is expressed as its

pK. Henderson-Hasselbalch equation relates

the pH of a solution to the pK and concentration of an acid to its conjugate base.

Buffered solutions resist changes in pH within about one pH unit of the pK of the buffering species.

1. Noncovalent bonding of water has play a vital role in determining the properties of water. Describe types of those bonding and

water properties they determined.2. Differentiate polar and nonpolar

molecule.Explain how polar nature of water makes it an excellent solvent for polar and ionic materials.