Introduction to biomolecules

PREMIER o RECOGNISED o TRUSTED


BCH 1023 S1 JAN 2012

THE LEADER

In Nursing & Allied Health Education in Malaysia

MASTERSKILLUNIVERSITY COLLEGE OF HEALTH SCIENCES



BCH 1023 S2 JAN 2012

Chapter 1

INTRODUCTION TO BIOMOLECULES

BACHELOR IN BIOMEDICAL SCIENCE (HONS)BCH 1023 BIOCHEMISTRY

SEM 2



BCH 1023 S3 JAN 2012

LEARNING OUTCOMES

At the end of the lesson students should be able to:

1. Define study of biochemistry.

2. Describe the structure of water.

3. Describe the properties of water.

4. Describe acid-base reaction and buffer system



BCH 1023 S4 JAN 2012

INTRODUCTION Cell is the basic unit and building block of

biology. Biochemistry is the science concerned

with the various molecules that occur in living cells.

Cell biochemistry is the study of chemical substances and vital processes in living organism.

Modern cell biology involves the combination of three area of studies:1. Cytology – concerned with cellular structure.2. Biochemistry – understanding of cellular

functions.3. Genetics and molecular biology.



BCH 1023 S5 JAN 2012

1)WATER In human tissues the percentage of water

ranges from 20% in bones to 85% in brain cells.

Water made up 70% of human body weight. Water is important as solvent for most

biological reactions and a product or reactant for many chemical reactions.

Water’s unique combination of physical and chemical properties is considered to have been essential to the origin of life, continuing survivality and evolution of life on Earth.



BCH 1023 S6 JAN 2012

CHEMISTRY OF WATER Molecular structure: Water is composed of one

oxygen atom and two hydrogen atoms. Each hydrogen atom is covalently bonded to the

oxygen through a shared pair of electrons. Oxygen atom consist of two unshared pairs of

electrons/lone pair of electrons. Water is a tri-atomic molecule, H2O The arrangement of hydrogen

and oxygen atoms in water molecule is nonlinear with an H-O-H

Bond angle of water 104.5oC



BCH 1023 S7 JAN 2012

WATER MOLECULES HYDROGEN BONDING

Hydrogen bonding is of electrostatic origin and can be considered as a special case of dipole-dipole interaction.

Hydrogen bonding of water molecules results from the O-H bond of one water molecule (positive end, δ+) points towards one of electron pairs of another water molecule(negative end, δ-)

Each water molecule is involved in four hydrogen bond – two hydrogen-bond donor and two hydrogen-bond acceptor.

The ability to form strong hydrogen bonding contribute to the high melting point and boiling point of water.



BCH 1023 S8 JAN 2012

Hydrogen bonding of water molecules

H HO

d+

d+

d-

H HO

d+

d-

d+



BCH 1023 S9 JAN 2012

PROPERTIES OF WATER

1)Physical states of

water

2)Polarity of water

3)Water as a universal solvent

4)High specific heat

5)High surface tension

6)Solid expansion



BCH 1023 S10 JAN 2012

1)Physical states of water The physical states of water are solid,

liquid and gas. Melting point is 0°C (32°F). Boiling point is 100°C (212°F). Pure water are colorless, tasteless and

odorless. Pure water is neutral (pH 7) In pure water the content of OH- and H+

are balances at 25°C with the value of 1.0x10-7 moles/L.



BCH 1023 S11 JAN 2012

2)Polarity of water The bond form by atoms with differing

electronegativity will cause unequal electron sharing.

In the O-H bonds in water, O is more electronegative than H.

The different electronegativity between O and H gives rise to the partial positive (δ+) and partial negative (δ-) of water molecule.

The O-H bonding of water molecule are polar bond.



BCH 1023 S12 JAN 2012

3)Water as a universal solvent Water is called universal solvent because

it dissolves more substances than any other liquid.

The ability of ions and other molecules to dissolve in water is due to polarity of water.

Ionic compounds with full charges (e.g KCL, K+ and Cl- in solution) and polar compounds with partial charges or dipoles (e.g alcohol or acetone) tend to dissolves in water.

The physical principle is due to the electrostatic attraction between unlike/different charges.



BCH 1023 S13 JAN 2012

Ion-dipole and dipole-dipole interactions help ionic and polar compound dissolve in water.

a) Ion – dipole interaction

b) Dipole – dipole interaction



BCH 1023 S14 JAN 2012

3)Water as a universal solvent Hydrophilic or “water-loving” compound have

the ability to dissolve in water because they have polar functional groups that form favorable attraction toward water molecules

Polar covalent compound, ionic compounds, sugars and amino acids hydrophilic in nature.

Hydrophobic or “water-hating” compounds are is not water soluble because they have no charge or non-polar functional groups.

Non-polar covalent compound (hydrocarbon), fatty acids and cholestrol are hydrophobic compounds.



BCH 1023 S15 JAN 2012

Homework /Tutorial What is ion-dipole and dipole-dipole

interaction? Sodium chloride in its crystalline

form is dissolve in water. Explain how does this happened.

Explain why oil and water when mixed together separate into layers?



BCH 1023 S16 JAN 2012

4)HIGH SPECIFIC HEAT Water has high specific heat which means that

water can absorb a lot of heat before it begins to get hot.

Heat is used to break down the hydrogen bonding of water molecules but it does not increase the kinetic energy of the water molecules.

Water releases heat energy slowly causing cooling effect.

This properties explain why:1. Water is used as coolant.2. Large change in temperature does not takes place

when heat is produced by chemical reactions in the cells.

3. Body temperature can be regulates effectively.



BCH 1023 S17 JAN 2012

5)HIGH SURFACE TENSION Water molecules at the liquid surface are pulled

laterally and towards the bulk by the remaining stronger hydrogen bonds and resulting the high surface tension of water.

Thus water tends to clump together in drops rather than spread out in a thin film.

Surface tension along with adhesion is responsible for capillary action.

Capillary action is the tendency of water to move in narrow tubes against the force of gravity.

Capillary action allows water (and its dissolved substances) to move through the roots of plants and through tiny blood vessels.



BCH 1023 S18 JAN 2012

Surface tension of water enable water striders to walk on the

surface of the water.

Capillary action shows that the colored water

move through plant stem to leaves.



BCH 1023 S19 JAN 2012

5)HIGH SURFACE TENSION

Hydrogen bonding of water molecules makes water cohesive and adhesive.1. Cohesive tendency to stick to each other2. Adhesive adhesive forces explain how water

makes things wet. Cohesive and adhesive forces accounts for the

phenomenon of capillary action. Cohesiveness of water molecules contribute to

the high degree of surface tension.



BCH 1023 S20 JAN 2012

6)SOLID EXPANSION Ice has lower density than liquid

water because the fully hydrogen bonded array in an ice crystal is less densely packed that the liquid water.

Liquid water is less extensively hydrogen-bonded and thus is denser than ice.

This explain why ice cubes and iceberg floats.

Most substances contract when freeze but the opposite occur to water.



BCH 1023 S21 JAN 2012

a) Picture of ice cubes float in water.

b) Ice form on the lake surface.



BCH 1023 S22 JAN 2012

OSMOSIS AND DIFFUSION Osmosis is the movement of solvent from

a region of high concentration to a low concentration.

Diffusion is the transport of molecules through their random movement.

Osmotic pressure is the pressure that must be applied to the solution to prevent the inward flow of water.

In 1M solution, the osmotic pressure is 22.4atm.



BCH 1023 S23 JAN 2012

IONIZATION OF WATER Water is a neutral molecule with very slight

tendency to ionize.Pure water ionizes slightly can act as an acid (proton donor) or base (proton acceptor).

2H2O H3O+ + OH- but usually written as

H2O H+ + OH-

This generate the hydronium ion (H3O+) and hydroxide ion (OH-)

Equilibrium of water:Keq= [H+][OH-] = 1.8 x 10-16 M at 25oC

[H2O]



BCH 1023 S24 JAN 2012

Equilibrium Constant Keq represent equilibrium constant for the

reaction and the brackets for each chemical entity indicate concentration units in moles per liter (M).

Keq = [H+] [OH-] / [H2O] Calculation of Keq of pure water from

experimental measurements enable calculation of quantity for [H+] and [OH-].

Thus enable estimation of the extent of pure water self dissociation.

Keq for pure water at 25°C is 1.8 x 10-16 M



BCH 1023 S25 JAN 2012

Equilibrium constant The value of [H2O] can be estimated by:

[H2O] = Weight of water in 1L / Molecular weight of water

= 1000g / 18 = 55.5 M

Thus,[H+] [OH-] = Keq [H2O]

[H+] [OH-] = (1.8 x 10-16 M) (55.5 M)[H+] [OH-] = 1.0 x 10-14 M2

[H+] = [OH-] = √ (1.0 x 10-14 M2) = 1.0 x 10-7 M



BCH 1023 S26 JAN 2012

pH Hydrogen ion concentration

expressed in exponential form are difficult to utilize.

Thus, negative logarithm of [H+] or pH is used.

pH = -log 10 [H+] A different of 1 pH unit indicates a

tenfold different in ion concentration, [H+].

For example, a solution at pH 7 have 10x greater [H+] than a solution at pH 8.



BCH 1023 S27 JAN 2012



BCH 1023 S28 JAN 2012

ACID-BASE A biological definition of acid and base

are, acid is a molecule that acts as a proton (H+) donor and base is defined as proton (H+) acceptor.

The degree of acid losing proton or base gaining proton depends on the chemical nature of the compound.

Acid strength is the amount of H+ released when a given amount of acid is dissolved in water.

The numerical measurement of acid strength is expressed as acid dissociation constant, Ka



BCH 1023 S29 JAN 2012

ACID-BASE Ka can be written as HA for any acid.

HA H+ + A-

Ka = [H+] [A-] / [HA] The greater the Ka value mean the stronger the

acid. Acid-base reaction is a proton-transfer reaction

in which water acts as a base as well as the solvent.

The equation are,

HA (aq) + H2O (l) H3O+ (aq) + A- (aq)

(Acid) (Base) (Conjugate acid) (Conjugate base)

to H2O to HA



BCH 1023 S30 JAN 2012

BUFFERS Buffers is something that able to resists change. Buffer solutions tend to resist change in pH when

a small to moderate amounts of a strong acid or strong base is added.

Buffer solution is a mixture of either a weak acid and its salt or a weak base and its salt.

Example of buffer solution:A mixture of acetic acid (CH3COOH) and sodium acetate (CH3COONa) dissolve in water.

This buffer solution consist of high concentration of acidic (e.g CH3COOH) and basic (e.g CH3COO-) components.



BCH 1023 S31 JAN 2012

BUFFERS When a small amount of strong acid e.g H3O+ is

added, H3O+ will react with CH3COO- to produce CH3COOH and water.

CH3COO- + H3O+ CH3COOH + H2O

(Buffer component ) (Added strong acid)

The added H3O+ is removed from the solution thus, the pH hardly change.

When strong base e.g OH- is added the buffer solution reacts with CH3COOH forming CH3COO- ion and water CH3COOH + OH- CH3COO- + H2O

(Buffer component ) (Added strong acid) Added OH- are removed from the solution thus,

thus the pH remain unchanged.



BCH 1023 S32 JAN 2012

Buffer system in living organism The pH of various body fluids is maintained by

buffers. The H2PO4/HPO4

- pair is the principle buffer in cell.

In blood the buffering system is based on the dissociation of carbonic acid (H2CO3)

The pH of human blood is 7.4. Acidic condition of blood is signifies by pH less

than 7.35 where the condition is known as acidemia

Alkaline condition of blood is signifies by the pH greater than 7.45 where the condition is known as alkalemia.

Death occurs when the pH of blood is more acidic than 6.8 or more basic than 7.8



BCH 1023 S33 JAN 2012

Buffer system in living organism The process of respiration plays an important

role in the buffering of blood. An increase of [H+] can be dealt with raising the

rate of respiration. Hyperventilation (excessively deep and rapid

breathing) removes CO2 from blood that it raises the pH of blood.

The increase of blood pH are dangerous as it bring weakness and fainting.

Athletes overcome hyperventilation by performing short burst of strenuous exercise to produce high levels of lactic acid in blood.

Lactic acid in blood results in anaerobic breakdown of glycogen.



BCH 1023 S34 JAN 2012

Buffer system in living organism

The presence of lactic acid tends to lower the pH of blood.

Exposure to high altitude has a similar effects as hyperventilation at sea level.

In response to the tenuous atmosphere, the rate of respiration will increase.

At high altitude more CO2 is expired from blood, lowering the H+ and raising the pH level of blood.

The rise of pH level occur at high altitude are temporary until they become acclimated.



BCH 1023 S35 JAN 2012

TUTORIAL1. Ingestion of large dosage of aspirin can

cause aspirin poisoning. Explain this condition toward the buffer system of the blood.

2. Lactic acid causes muscle pain and muscle fatigue. However in recent study, lactic acid actually has a positive effect on fatiguing muscle. Discuss.

3. A frequently recommended treatment for hiccups is to hold one’s breath. The resulting condition, hyperventilation causes buildup of CO2 in the lungs. Discuss about the effect of pH of blood.



BCH 1023 S36 JAN 2012

1.M.K Campbell & S.O Farrell (2009). Biochemistry 6th Edition. Thomson Higher Education. USA.

2.D.Voet, JG Voet & CW Pratt (1999). Fundamentals of Biochemistry. John Wiley & Sons. Inc

3.M.Shahjahan (2006). Cell Biochemistry & Basic Genetics. PPSK,USM.

REFERENCES



BCH 1023 S37 JAN 2012

End of Chapter 1

End of Chapter 1

I run, they run, everybody run and we’re all just having fun,

Sleigh ride, boat ride, piggy back and ride, I’m gonna tell them all how I can

ride.~Foster the People~

Introduction to biomolecules

Technology

Transcript of Introduction to biomolecules