Lecture 1

Introduction: - Acid-Base Balance and Buffers

1. What is Biochemistry?
Biochemistry is the science related to an understanding of the chemical structure of
living organisms and the chemical processes which take place in them.

Clinical Biochemistry
 Clinical Biochemistry is the application part of Biochemistry for diagnosis of
the clinical conditions by determining various constituents in different body
fluids.
 Different body fluids used for diagnosis include blood (plasma, serum), urine,
cerebrospinal fluid (CSF), sputum, stools, semen etc.
 For example, quantitative determination of glucose in blood, help in the
diagnosis of diabetes millets.

4. Biomolecules:
All living things are made of cells and all cells are made of a set of molecules
known as biomolecules.
Biomolecules are made up of chemical elements.
Although slightly more than 100 elements exist in the universe, only 24 are known
to be essential for the structure and function of the human body.

The chemical elements found in humans can be classified as :

1) Nonmetallic elements (Major elements):
 They make up organic matter and water and include oxygen (O), carbon (C),
hydrogen (H), nitrogen (N), phosphorus (P), and sulfur (S).
 They account for more than 97% of the weight of most organisms, but the
relative amounts of these six elements vary among organisms.
 Four elements (O, C, H, and N) represent more than 99% of the atoms in the
animals, which form the organic molecules (macromolecules).
 Human body is composed of about 60% water, 15% protein, 15 % lipids, 2%
carbohydrates, and 8% minerals.

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2) Mineral Elements (Abundant minerals):
 These minerals are present, almost, in the form of inorganic ions.
 Example: calcium is the most abundant minerals in humans.

3) Trace elements:
 These elements are also important for life.
 These are present in small quantities. Iron represents the most abundant
element in this group.
 all of the elements except fluoride are essential

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1. Water Dissociation (Ionization):
The degree of water ionization at equilibrium is small. For example, at 25°C only
about two of every 109 molecules in pure water are ionized at any instant.

(1)

Degree of ionization can be expressed by the equilibrium constant (Keq)

The equilibrium constant for the reversible ionization of water is

(2)

1.1 Calculation of pH of a pure water

 at 25oC, the concentration of pure water is 55.5 M (grams of H2O in 1L divided

by its gram molecular weight: (1000 g/L)/(18.015 g/mol))
 Accordingly, we can substitute 55.5 M in the equilibrium constant expression at
equation (2) to yield

= Kw (3)

 where Kw designates the product (55.5 M)(Keq), the ion product of water at
25°C.
 The value for Keq, determined by electrical-conductivity measurements of pure
water, is 1.8 X 10-16 M at 25oC. Then, substituting this value for Keq in Equation
(3) gives the value of the ion product of water (seen in Equation 4):

= Kw (4)

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  Thus the product [H+] [OH-] in aqueous solutions at 25oC always equals 1 X 10-
14
M2
 When there are exactly equal concentrations of H+ and OH- (as in pure water),
the solution is said to be at neutral pH.

For pure water [H+]=[OH-] then [H+] = 1.0 X 10-7

 From the concentration of H ions [H+], the pH of pure water can be calculated as
follows:

pH = –log [H+] = – log (1 X 10-7)

= – [log 1 + log 10-7)]
= – log 1 – log10-7
= – log 1 – (–7) log10

 Remembering that by looking up in log tables, log1=0 and log 10=1, and pH
calculation becomes :

pH = 0 +7(1)= 7

 It is easier to say pH = 7 than to do the mathematics every time.

 Therefore, the pH of pure water is 7.
 Addition of an acid to water increases the [H+] and decreases the [OH-].
 Addition of a base to water decreases the [H+] by increasing the [OH-].

2. The pH Scale:
The ion product of water dissociation (Kw) is the basis for the pH scale.
Biochemical reactions are often defined in terms of hydrogen ion (H+)
concentrations.
Soren Sörensen defined pH of a solution as the negative logarithm of the
concentration (in moles/litre) of hydrogen ions, OR.

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 The pH scale specifies how acidic or how basic a solution is. For precisely, the
number of hydrogen ions present in a solution is a measure of the acidity of the
solution.
The pH scale has values that range from 0 (very acidic) to 14 (very basic).
A pH of 7, the middle of the scale, is neutral, neither acidic nor basic.

2.1 Measuring pH:

 The pH of aqueous solutions can be measured by a pH meter.

Figure 1.1. A pH meter

2.2. Calculating pH:

 The pH of a solution can be calculated when the hydrogen or hydroxide ion
concentration is known, then we can calculate [H+] or [OH-] from the pH.

2.3. Importance of measuring pH:

 Measurement of pH is a common procedure to be used in Biochemistry.
 The pH affects the structure and activity of biological macromolecules; for
example, the catalytic activity of enzymes.
 Measurements of the pH of the blood and urine are commonly used in
diagnosing disease.

3. Acids and Bases:

The properties of acids and bases are related to their chemical structure:
All acids increase the hydrogen ion concentration in water.
All bases lower the hydrogen ion concentration in water.

3.1 Definitions:
 Compounds containing hydrogen atoms that can release hydrogen ions in
solutions are referred to as an acid (a proton donor) such as hydrochloric acid.
 Bases are compounds that can accept a hydrogen ion (a proton accepter) such as
the bicarbonate ion (HCO3-).

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  Acids and bases are classified as strong when the reaction with water is virtually
100% complete and as weak when the reaction with water is much less than
100% complete (perhaps as little as 2–3%).

Important strong acids include:

Hydrochloric acid HCl + H2O H3O+ + Cl-

Nitric acid HNO3 + H2O H3O+ + NO3-

Sulfuric acid H2SO4 + H2O H3O+ + HSO4-

Important strong bass include:

Sodium hydroxide NaOH Na+ + OH-

Potassium hydroxide KOH K+ + OH-

Note that the above equations are written with a single arrow. This
indicates that the reaction has little or no tendency to proceed in the
reverse direction to establish equilibrium.

3.2. Dissociation of Weak Acids and Bases:

 As mentioned before, pH is a measure of the concentration of H+ in a solution.
An acid is a proton donor; a base is a proton acceptor.

(Conjugate base)

 Ionization of an acid yields its conjugate base, and the two are termed a
conjugate acid–base pair, for example acetic acid (CH3COOH) and acetate
(CH3COO-) are a conjugate acid–base pair

(Conjugate base)

 The species formed by the ionization of an acid is its conjugate base.

Conversely, protonation of a base yields its conjugate acid.

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 Equation 5

The pK of an acid is the pH at which it is half dissociated. i.e. when [A-] =[HA].

4. Henderson–Hasselbalch equation
The Henderson–Hasselbalch equation expresses the relationship between pH, pK and
the ratio of acid to base, and can be used to calculate these values.

[conjugate base]
[acid]

Henderson–Hasselbalch equation

The Henderson–Hasselbalch equation indicates that the pK of an acid is equal to the

pH of the solution when the molar concentration of the acid is equal to that of its
conjugate base.
The pH of a solution can be calculated from the Henderson–Hasselbalch equation if
the molar concentrations of A- and HA, and the pK of HA are known.

Example:
A solution containing acetic acid and acetate with a pKa of 4.8 can resist a change in pH from
3.8 to 5.8 with maximum buffering capacity at pH = 4.8.

Figure 1.2. The titration of acetic acid

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5. Buffers
A buffer is a mixture of an undissociated acid and its conjugate base (the form of the
acid having lost its proton).
It causes a solution to resist changes in pH when either H+ or OH- is added.
A buffer has its greatest buffering capacity in the pH range near its pKa
The buffering capacity of the acid–base pair can be defined as the pK ± 1 pH unit.
Two factors determine the effectiveness of a buffer, its pKa relative to the pH of the
solution and its concentration.

6. Buffer systems in the body

In biological fluids, the phosphate and carbonate ions act as buffers. Amino acids,
proteins, nucleic acids and lipids also have some buffering capacity.

Biological fluids such as blood are buffered. For example, in healthy individuals the
pH of the blood is carefully controlled at pH 7.4.

The major buffering components in most biological fluids are the phosphate ion
(H2PO4- , pK 6.82) and the carbonate ion (HCO3-, pK 6.35) because they have pK
values in this range.

Enzymes need an optimum pH (buffer the pH) to work properly and to avoid their
denaturation (loss of activity).

6.1 The Bicarbonate Buffer System of Blood Plasma

 The important buffer system of blood plasma is the bicarbonate/carbonic acid
couple:

Example: Sodium Bicarbonate/Carbonic acid (NaHCO3/H2CO3):

Normal ratio in the blood = NaHCO3/H2CO3 = 20/1
They are the chief buffers of blood and constitute the so called alkali reserve.
Bicarbonate buffer system is directly linked with respiration because HCO 3- is
eliminated through diffusion of CO2 through alveoli of lungs.

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 Advantages: It is efficient as compared to other buffer systems because:
a) It is present in higher concentration than other buffer systems (26-28
mmol/l)
b) It produces H2CO3 which is a weak acid and volatile and CO2 is exhaled
out.

Disadvantage:
a) Its pKa value is away from the physiological pH, and thus the plasma
b) It appears to be poorly protected against an influx of OH- ions.

6.2 Phosphate Buffer System

 Normal ratio in the blood = Alk PO4/ acid PO4 = 4/1
 This ratio becomes or kept constant with the help of kidneys. Thus, phosphate
buffer system is directly linked to the kidney.
 The phosphate system serves to buffer the intracellular fluid of cells at
physiological pH because pK2 lies near this pH value
 The intracellular pH of most cells is maintained in the range between 6.9 and 7.4.
 Advantage: - Its pKa value approaches physiological pH
 Disadvantages: - Low concentration
- Less efficient

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 Lecture 2- Carbohydrates Chemistry (Part 1)

1. Definition
Carbohydrates (sugars) are polyhydroxy compounds with a functional aldehyde or
ketone group or they are organic molecules formed from C, O, and H with a general
formula of (CH2O)n.
They are also represented with general formula Cn(H2O)n and according to this formula
carbohydrates are also called “hydrate of carbon”.

2. Functions
(i) Carbohydrates act as a major source of energy for all tissues. Sugars represent the
primary source of energy in the brain, red blood cells (RBCs), and retinal cells.
(ii) They represent a storage form of energy (starch in plants and glycogen in animals).
(iii) Carbohydrates are components of cell membranes for cell-cell interaction
(glycoproteins and glycolipids).
(iv) They can form molecules that are essential for medical and biological purposes:
a) Carbohydrates are components of nucleic acids and blood group substances.
b) Some drugs are derivatives of carbohydrates such as streptomycin (an antibiotic).
c) Ascorbic acid (vitamin C) is a derivative of carbohydrates.

3. Classifications
i. Monosaccharides: such as glucose and fructose.
ii. Disaccharides: including sucrose and lactose, consist of two monosaccharide units
joined through bridging oxygen atoms. Such a bond is called a glycosidic bond.
iii. Oligosaccharides: consist of three to ten monosaccharide units joined by glycosidic
bonds such as Raffinose "α-Galactose (1–6) α-Glucose (1–2) β-Fructose".
iv. Polysaccharides: the largest and most complex carbohydrates, which are long, often
highly branched, chains of monosaccharides. Starch, glycogen, and cellulose are all
examples of polysaccharides.

4. Natural Sources
Carbohydrate can be obtained from grains rice, potatoes, breads, cereals, sugar cane,
fruits, milk, and honey are an important source of energy for animals.
A healthy diet should contain all types. The quantity of sucrose should be minimized
because its large quantities in the diet promote obesity and tooth decay.
Deficiency: Low intake associated with inadequate total energy intake causes
starvation.
Excessive intake: High concentrations can lead to increased risk of obesity, diabetes
mellitus, and atherosclerosis.

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5. Monosaccharides
They are the simplest sugars and cannot be hydrolyzed into smaller units under mild
conditions.
The most abundant monosaccharide in nature and certainly the most important
nutritionally is the 6-carbon sugar glucose. Glucose (C6H12O6) often called “blood
sugar” because it is the major monosaccharide found in the blood.
Most monosaccharides in the body contain five or six carbon atoms and are called
pentoses and hexoses, respectively.

5.1 Subdivisions:
Monosaccharides can be subdivided into two groups:
On the basis of the functional groups they contain:
For example, a monosaccharide with an internal ketone group (–C=O) is a ketose.
If a terminal aldehyde group (–CHO) is present, it is called an aldose.
Depending on the number of carbon atoms:
For example, trioses have three carbons, pentoses have five carbons, and hexoses
have six carbons

An aldose A ketose

Table 2.1: Different forms of monosaccharides

No. of Carbons Name Formula Aldoses Ketoses

(Aldo sugars) (Keto sugars)

3 Trioses C3H6O3 Glycerol Dihydroxyacetone

4 Tetroses C4H8O4 Erythrose Erythrulose
5 Pentoses C5H10O5 Ribose Ribulose
6 Hexoses C6H12O6 Glucose Fructose

5.2 Structures of Monosaccharides

A) Open chain --(Fischer's projection):
Less than 1% of each of the monosaccharides with five or more carbons exists in
the open chain. The open form of monosaccharides have the following properties:
(i) Isomers: They are different compounds with the same chemical formula
(CH2O)6. For example: glucose and fructose are isomers

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 D-Glucose D-Fructose

Figure 2.1 Glucose and fructose as examples for isomers

(ii) Asymmetric carbon: All monosaccharides except dihydroxyacetone contain at

least one asymmetric carbon atom. A carbon atom that has four different groups
bonded to it is called an asymmetric (or chiral) carbon atom.

Figure 2.2 The asymmetric carbon in D– and L– forms of glyceraldehyde

(iii) Enantiomers: Any molecule containing a chiral carbon can exist as a pair of enantiomers
either D- or L- optical isomers. Both D- and L- forms are mirror images. In dextrorotatory
(D) form, the –OH is to the right hand while in levorotatory (L) form, the –OH is to the left.
Most of the monosaccharides found in living systems belong to the D series of optical
isomers. The chiral carbon exists farthest from the oxidized end (figures 2.2 and 2.3).

D-Glucose L-Glucose D-Fructose L-Fructose

Figure 2.3 Enantiomers of glucose and fructose with D- and L- forms.

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 (iv) Epimers: They are two isomers differ in the configuration of –OH group
around one carbon atom. For example, galactose and glucose are C-4 epimers
because configuration of hydroxyl group on 4th carbon atom of galactose is
different from glucose. Similarly, mannose and glucose are C-2 are epimers.

Figure 2.4 Different types of epimers

(v) Hemiacetals and Hemiketals:

= They are linear compounds that occur when alcohol reacts with an aldehyde or
ketone groups.
= Cyclic forms: the molecules cyclize by a reaction between the carbonyl group
and a hydroxyl group. If the sugar contained an aldehyde, the product is called
a hemiacetal; if the sugar contained a keto group, it is called a hemiketal.

Figure 2.5 Formation of hemiacetal and hemiketal

B) Cyclic form --(Haworth's Projection formulas):

In solution, the monosaccharides do not exist in an open chain form, but they
cyclize to form ring structures which are more stable. For example, cyclic glucose
forms when carbonyl group on C-1 reacts with hydroxyl group on C-5.

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 α-D-Glucose β-D- Glucose

Properties of Haworth's Projection formulas:

(i) Ring structure: a reaction of a ketose sugar such as fructose yields a cyclic
hemiketal, thus; a five-membered ring formed and is referred to as a furanose.
Pentose such as ribose can also form a five-membered ring (furanose). Glucose
cyclization will lead to formation of a six-membered ring (pyranose). A six-
membered ring is indicated by -pyran-, and a five-membered ring is indicated
by -furan-.

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 (ii) Anomeric carbon: Anomers are those monosaccharides that differ in
configuration of OH group on anomeric carbon. The anomeric carbon of an
aldose is carbon 1; and in ketoses carbon 2. Formation of ring structure
generates α- and β- forms. For example, in the α-glucose anomer, the hydroxyl
group of C-1 (anomeric carbon) is below the ring, and in the β-glucose anomer,
the C-1 hydroxyl group is above the ring.

Free aldehyde

β -D-Glucopyranose α -D-Glucopyranose
(β -D-Glucose) (α -D-Glucose)
-------------------------------------------------------------------------------------

α -D-Fructofuranose D-Fructose β -D-Fructofuranose

(α -D-Fructose) (β -D-Fructose)

(iii) Reducing sugars: All monosaccharides containing free aldehyde or ketone

group are considered reducing sugars. (Details will come later).

(iv) Glycosidic bond: The bond between the anomeric carbon atom and any of the
hydroxyl groups on the second monosaccharide is called glycosidic bond.

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