1. THE CHEMISTRY OF LIFE

1. THE CHEMISTRY OF LIFE

DR. AYAT B. AL-GHAFARI Biochemistry

What is

Biochemistry?

ةيويحلا ءايميكلا ملع

• Biochemistry= chemistry of life.

• Bios= life.

•

Biochemistry is the science concerned with studying the various molecules

that occur in living cells and organisms

and with their chemical reactions.

Chemistry of life

• Element: simplest form of a substance - cannot be broken down any further

without changing what it is.

• Atom: the actual basic unit of the matter - composed of protons, neutrons, and

electrons. They are very small. The atom is made up of 3 particles:

Charge Particle

+ Proton

Neutral Neutron

- Electron

ISOTOPES رئاظنلا

• Atoms of the same element that HAVE A DIFFERENT NUMBER OF NEUTRONS

• Some isotopes are radioactive. This

means that their nuclei is unstable and will break down over time.

• There are several practical uses for radioactive isotopes:

1. TRACERS

2. KILL BACTERIA / CANCER CELLS

COMPOUNDS تابكرملا

• A substance formed by the chemical combination of 2 or more elements in

definite proportions for example : water, salt, glucose, carbon dioxide

TWO TYPES OF COMPOUNDS

1. Organic - Contain C, H, O,

Sand N in some ratio (usually referred to as chemicals of life)

Ex.: Carbohydrates, Proteins, Lipids, Nucleic Acids

2. Inorganic - usually "support"

life - no specific ratio of C, H, and O

Ex.: Water (H₂O), Carbon Dioxide (CO₂)

CHEMICAL BONDS ةيئايميكلا طباورلا

• Chemical bonds hold the

atoms in a molecule together.

• There are 2 types of chemical bonds:

IONIC and COVALENT

IONIC BONDS ةينويلأا طباورلا

• Occur when 1 or more electrons are

TRANSFERRED from one atom to another.

• When an atom loses an electron it is a POSITIVE charge.

• When an atom gains an electron it is a NEGATIVE charge.

• These newly charged atoms are now called IONS.

COVALENT BONDS ةيمهاستلا طباورلا

• Occur when electrons are SHARED by atoms.

• These new structures that result from covalent bonds are called MOLECULES.

• In general, the more chemical bonds a

molecule has the more energy it contains.

SOLUTIONS ليلاحملا

Two parts:

• SOLUTE – Substance that is being dissolved (sugar/salt).

• SOLVENT - the substance in which the solute dissolves.

• Materials that do not dissolve are known as SUSPENSIONS. Blood is the most common example of a suspension where Cells & other particles remain in suspension.

FORMULA ةغيصلا

• The chemical symbols and numbers that compose a compound ("recipe")

• Structural Formula – Line drawings of the compound that shows the elements in

proportion and how they are bonded

• Molecular Formula – the ACTUAL formula for a compound

C H O

ACIDS & BASES

ACIDS ضامحلأا

• Acids: always (almost) begin with "H"

because of the excess of H⁺ ions (hydrogen).

• Acids turn litmus paper RED and usually taste SOUR.

• Examples of acidic foods (coffee, vinegar, soda, AND spicy foods)

BASES دعاوقلا

• Bases or alkaline: always (almost) end with -OH because of the excess of

hydroxide ions (Oxygen & Hydrogen)

o EX: oven cleaner, bleach, ammonia, sea water, blood.

• Bases turn litmus BLUE.

• Bases usually feel SLIPPERY to touch and taste BITTER.

• When an acid reacts with a base they produce a salt and water.

• This process known as Neutralization (ةلداعملا )

WATER (H 2 O)

Overview

• Water is the predominant chemical component of living organisms, making up 70% or more of the weight of most organisms.

• Water has a higher melting and freezing points (0 C), ͦ boiling point (100 C). ͦ

• There is a specific chemical bond called hydrogen bond formed between polar molecules in which hydrogen (H) is bound to a highly electronegative

atom, such as nitrogen (N), oxygen (O) or fluorine (F).

This bond is responsible for the unique characteristics of water.

• Water is a polar solvent. It can dissolve most biomolecules.

• Compounds that dissolve easily in water are hydrophilic (water- loving).

• Compounds that do not dissolve in water are hydrophobic (water- hating) such as waxes and lipids.

• Compounds contain regions that are polar (charged) and regions that are nonpolar are known as amphipathic compounds e.g.,

Van der Waals interaction or

force

• When two uncharged

atoms are come close to each other, their

surrounding electrons influence each other.

• Also known as London forces.

• This interaction is weak

Water Dissociation ئزج ككفت ءاملا

• Atoms can gain or lose electrons in order to form ions in a process called ionization.

• When ionic compounds dissolve in water, their ions separate from one another in a process called dissociation.

• Substances dissociate to different degrees, ranging from substances that dissociate very

slightly, such as water, to those that dissociate

• The ability to conduct electricity is based on the ionic composition of a substance. The more ions a substance contains, the better it will

conduct electricity.

• A substance that dissociates only slightly (weak acid like vinegar) is a weak electrolyte, as it

conducts electricity poorly.

• A substance that is almost completely

dissociated (NaCl, or hydrochloric acid, HCl) conducts electricity very well.

• When water dissociates, one of the hydrogen nuclei leaves its electron behind with the oxygen atom to become a hydrogen ion (H⁺), while the oxygen and other hydrogen atoms become a hydroxide ion

(OH^-).

• The hydrogen ion (proton) attaches to the oxygen

atom of a second un-ionized water molecule to form a hydronium ion (H3O +).

Hydrogen (Yellow)

Oxygen (Purple)

• Equilibrium constant or ion product constant of water is:

K

_W

= [H

⁺

][OH

^-

] / [H

₂

O]

• Water is not involved in the equilibrium expression because it is a pure liquid.

• Value for K

_w

= [H

⁺

][OH

^-

] = 1x 10

^-14

• On the P scale: pK

_w

= pH + pOH= 14

• Definitions of acidic, basic, and neutral solutions based on [H

⁺

] acidic: if [H

⁺

] is greater than 1 x 10

^-7

M

basic: if [H

⁺

] is less than 1 x 10

^-7

M

neutral: if [H

⁺

] if equal to 1 x 10

^-7

M

Example (1)

• Example 1: What is the [H⁺] of a sample of lake water with [OH^-] of 4.0 x 10^-9 M? Is the lake acidic, basic, or neutral?

• Solution:

K_w = [H⁺][OH^-] = 1x 10^-14

[H⁺] = 1 x 10^-14 / 4 x 10^-9 = 2.5 x 10^-6 M Therefore the lake is slightly acidic

Example (2)

• Example 2: What is the [H⁺] of human saliva if its [OH^-] is 4 x 10^-8 M? Is human saliva acidic, basic, or neutral?

• Solution:

[H⁺] = 1.0 x 10^-14 / 4 x 10^-8 = 2.5 x 10^-7 M

Therefore, The saliva is pretty neutral or acidic.

Power of hydrogen (pH) سلأا ينيجورديهلا

• Is a measure of the acidity and basicity of an aqueous solution.

• In a more technical definition: it is the negative logarithm of the activity of the (solvated)

hydrogen ion, more often expressed as the

measure of the hydronium ion concentration.

pH = -log [H⁺]

• The [H⁺] can be calculated from the pH by taking the antilog of the negative pH

The pH scale ranges from 0-14, where

0-5 Acidic 6-7 Neutral 8-14

• The pH can be determined experimentally by using pH paper or a pH meter

Example (1)

• Example 3: calculate the [OH^-] of a solution of baking soda with a pH of 8.5.

• Solution:

1. First calculate the [H⁺]

2. if pH is 8.5, then the antilog of -8.5 is 3.2 x 10^-9. Thus the [H⁺] is 3.2 x 10^-9 M

3. Next calculate the [OH^-]

4. Apply K_w = [H⁺][OH^-] = 1x 10^-14

5. 1.0 x 10^-14 / 3.2 x 10^-9 = 3.1 x 10^-6 M

• Example: Calculate the pH of a solution of

household ammonia whose [OH^-] is 7.93 x 10^-3 M.

• Solution:

1. First calculate the [H⁺] from the [OH^-] 2. 7.93 x 10^-3 M OH^- = 1.26 x 10^-12 M H⁺ 3. Then find the pH

4. -log[1.26 x 10^-12] = 11.9

Example (2)

Example (3)

• Question: What is the pH of a 0.025 M solution of Hydrobromic Acid?

• Solution

Hydrobromic Acid, is a strong acid and will dissociate completely in water to H⁺ and Br^-. So the concentration of H⁺ will be the same as the concentration of HBr.

Therefore, [H⁺] = 0.025 M.

pH is calculated by the formula pH = - log [H⁺]

Enter the concentration found before pH = - log (0.025)

Practice (1)

• What is the pH of a solution of NaOH that has a [OH^-] of 3.5 x 10^-3 M?

• Answer:

1. Apply K_w = [H⁺][OH^-] = 1x 10^-14

2. [H+]= 1x10^-14 /3.5x10^-3 = 2.86x10^-12

3. pH= - log [2.86x10^-12 ]= - (-11.5)=11.5

• The H⁺ of vinegar that has a pH of 3.2 is what?

• Answer:

• if pH is 3.2, then the antilog of -3.2 is 6.3 x 10^-4. Thus the [H⁺] is 6.3 x 10^-4 M

Practice (2)

The Henderson- Hasselbalch Equation

• Buffers are aqueous solutions that tend to resist changes in pH when small amounts of acid [H⁺] or base [OH^-] are added.

• A buffer system consists of a weak acid (the proton donor) and its conjugate base (the proton acceptor).

• The Henderson- Hasselbalch Equation describes the derivation of pH as a measure of acidity by

using pK_a, the negative log of the acid dissociation constant.

The generalized weak acid HA ionizes as follows:

HA <===> H⁺ + A¯

The equilibrium constant for this dissociation is:

K_a=[H⁺] [A^-]/ [HA]

Cross-multiplication gives

36

Divide both sides by [A^-] [H⁺]= K_a [HA]/ [A^-]

Take the log of both sides:

Log [H⁺]= log (K_a [HA]/ [A^-])

= log K_a + log [HA]/ [A^-] Multiply through by -1:

- Log [H⁺]= - log K_a - log [HA]/ [A^-]

Substrate pH and pK_a for - Log [H⁺] and - log K_{a ,} respectively then

pH= pK_a - log [HA]/ [A^-]

Inversion of the last term removes the minus sign and gives the Henderson- Hasselbalch

equation:

pH = pK_a + log ([A^-]/[HA])

Example (1)

• Example: Calculate the pH of a buffer solution made from 0.20 M HC₂H₃O₂ and 0.50 M C₂H₃O₂^- that has an acid dissociation constant for

HC₂H₃O₂ of 1.8 x 10^-5?

• _Solution:

pH = pK_a + log ([A^-]/[HA])

pH = pK_a + log ([C₂H₃O₂^-] / [HC₂H₃O₂])

pH = -log (1.8 x 10^-5) + log (0.50 M / 0.20 M) pH = -log (1.8 x 10^-5) + log (2.5)

pH = 4.7 + 0.40 pH = 5.1

REFERENCES

1. Murray, R., Bender, D., Botham, K.,

Kennelly, P., Rodwell, V., Weil., P. (2012) Harper’s illustrated biochemistry, 29^th edition. Publisher: McGraw Hill Lange.

2. Nelson, D. and Cox, M. (2008) Lehninger principles of biochemistry, 5^th edition.

Publisher: W.H. Freeman and company, New York.

3. Harvey, R. and Ferrier, D. (2011) Lippincott’s illustrated reviews:

4. Moorthy, K. (2008) Fundementals of Biochemical Calculations, 2^nd edition. Publisher: CRC Press.