Introduction into

biochemistry
PROF. NAFEZ ABU TARBOUSH
NURSING SUMMER 2022 -2023
What is biochemistry?
It is the chemistry of living organisms.
It describes the structure, organization, and functions of living matter in molecular terms.
It describes the flow of energy inside a living cell/organism.
 Hydrogen

Important terms
Electronegativity Oxygen
Nitrogen Carbon
Covalent bonds
◦ Polar vs. non-polar covalent
bonds
Non-covalent interactions
◦ Electrostatic interactions
◦ Hydrogen bonds (donor and
acceptor)
◦ Hydrophobic interactions
◦ Hydrophobic versus hydrophilic
molecules
Carbon
Why can carbon form complex molecules?
 Properties of carbon (1)
It can form four covalent bonds, which can be
single, double, or triple bonds (example: fatty
acids).
Each bond is very stable.
◦ strength of bonds: triple > double > Single)
They link C atoms together in chains and rings
(example: sugars).
◦ These serve as a backbones
Properties of carbon (2)
Carbon bonds have angles giving
molecules distinct three-
dimensional structures.

In a carbon backbone, some

carbon atoms rotate around a
single covalent bond producing
molecules of different shapes.
Properties of carbon (3)
The electronegativity of carbon is between other atoms.
◦ It can form polar and non-polar molecules
Pure carbon is not water soluble, but when carbon forms covalent bonds with
other elements like O or N, the molecule that makes carbon compounds to be
soluble.
Nonpolar
Properties of water (1)
Water is a polar molecule as a whole
because of
◦ the different electronegativity
between Hydrogen and oxygen
◦ It is angular
Water is highly cohesive.
Water molecules produce a network.
Properties of water (2)
Water is an excellent
solvent because It is small,
and it weakens electrostatic
forces and hydrogen
bonding between polar
molecules.
Properties of water (3)
It is reactive because it is a nucleophile.
◦ A nucleophile is an electron-rich molecule that is attracted to positively-
charged or electron-deficient species (electrophiles)
Properties of water (4)
A water molecule is ionized to become a positively-charged hydronium ion (or
proton), and a hydroxide ion:
Acids versus bases - 1
Acid: a substance that produces H+ when dissolved in water (HCl, HNO3,
CH3COOH, H2SO4, H3PO4)
◦ H+ Reacts with water producing hydronium ion (H3O+)

Base: a substance that produces OH- when dissolved in water (NaOH, KOH)
Acids and bases - 2
Acid: any substance (proton donor) able to give a hydrogen ion (H+-a proton) to
another molecule
◦ Monoprotic acid: HCl, HNO3, CH3COOH
◦ Diprotic acid: H2SO4
◦ Triprotic acid: H3PO4

Base: any substance that accepts a proton (H+) from an acid

◦ NH3
Water: acid or base?
Both
Products: hydronium ion (H3O+) and hydroxide
 amphi- = “both”
Amphoteric substances
Substances that can act as an acid in one reaction and as a base in another are
called amphoteric substances
◦ Example: water
With ammonia (NH3), water acts as an acid because it donates a proton
(hydrogen ion) to ammonia
NH3 + H2O ↔ NH4+ + OH–
With hydrochloric acid, water acts as a base water is acting as a bas
HCl+ H2O → H3O+ + Cl-
Acid/base strength
Acids differ in their ability to release
protons.
◦ Strong acids dissociate 100%.
Bases differ in their ability to accept
protons.
◦ Strong bases have strong affinity for
protons.
For multi-protic acids (H2SO4, H3PO4), each
proton is donated at a different strength.
 Rule
The stronger the acid, the weaker the conjugate base

Reactions favor formation of a weak acid.

◦ Strong acids and bases are one-way reactions.
HCl → H+ + Cl-
NaOH → Na+ + OH-
◦ Weak acids and bases do not ionize completely.
HC2H3O2 ↔ H+ + C2H3O2-
NH3 + H2O ↔ NH4+ + OH-
Equilibrium constant
Acid/base solutions are at constant equilibrium.
We can write equilibrium constant (Keq) for such reactions:

The value of the Keq indicates direction of reaction

◦ When Keq is greater than 1 the product side is favored The strength of
an acid or base
◦ When Keq is less than 1 the reactants are favored
is measure by
Equilibrium constant for acids is Ka and for bases Kb. its Keq.
◦ Note: H3O+ = H+
Expression
A solutions can be expressed in terms of its concentration or molarity (M).
Acids and bases can also be expressed in terms of their equivalence (Eq).
Molarity of solutions
We know that moles of a solution are the amount in grams in relation to its
molecular weight (MW).
moles = grams / MW
A molar solution is one in which 1 liter of solution contains the number of grams
equal to its molecular weight.
M = moles / volume
Since (mol = grams / MW), you can calculate the grams of a chemical you need
to dissolve in a known volume of water to obtain a certain concentration (M)
using the following formula:
grams = M x vol x MW
Exercise
How many grams do you need to make 5M NaCl solution in 100 ml (MW 58.4)?

grams = 58.4 x 5 M x 0.1 liter = 29.29 g

Equivalents
When it comes to acids, bases and ions, it is useful to think of them as
equivalents.
An equivalent is the amount of moles of hydrogen ions that an acid can donate .
◦ or a base can accept.
A 1 g-Eq of any ion is defined as the molar mass of the ion divided by the ionic
charge.
Examples
For acids:
1 mole HCl = 1 mole [H+] = 1 equivalent
1 mole H2SO4 = 2 moles [H+] = 2 equivalents
◦ 1 eq of H2SO4 = ½ mol (because 1 mole gives two H+ ions)

Remember: One equivalent

For ions:
of any acid neutralizes one
One equivalent of Na+ = 23.1 g equivalent of any base.
One equivalent of Cl- = 35.5 g
One equivalent of Mg+2 = (24.3)/2 = 12.15 g
 Molarity and equivalents
Equivalents = n x M x volume (L)
One equivalent of any acid neutralizes one equivalent of base.

Based on the equation above, since x eq of an acid is neutralized by the same x eq

of a base, then (n x M x vol) of an acid is neutralized by (n x M x vol) of a base.
Problem 1
Note that each one produces 1 mole of H+ or OH-, so 1M of HCl is equal to 1M of
NaOH, so 1M HCl produces 1M of H+, which is neutralized by 1M NaOH, which
produces 1M OH-

Eq of acid = Eq of base
N x M1 x Vol1 = n x M2 x Vol2
1 x 0.12 x 22.4 = 1 x M2 x 12
M2 = (0.12 x 22.4) / 12
M2 = 0.224 M
Problem 2
Note that 1 mole of HNO3 produces 1 mole of H+, but 1 mole of Ba(OH)2
produces 2 moles of OH-. In other words, the n is different.
Eq of acid = Eq of base
N x M1 x Vol1 = n x M2 x Vol2
1 x 0.085 x Vol = 2 x 0.12 x 15
Vol = (2 x 0.12 x 15) / 1 x 0.085
Vol = 42.35 mL
Ionization of water
Water dissociates into hydronium (H3O+) and hydroxyl (OH-) ions
For simplicity, we refer to the hydronium ion as a hydrogen ion (H+) and write
the reaction equilibrium as
 Equilibrium constant
The equilibrium constant Keq of the dissociation of water is

The equilibrium constant for water ionization under standard conditions is 1.8 x 10-16 M
Kw
Since there are 55.6 moles of water in 1 liter, the product of the hydrogen and
hydroxide ion concentrations results in a value of 1 x 10-14 for:

This constant, Kw, is called the ion product for water

[H+] and [OH-]
For pure water, there are equal concentrations of [H+] and [OH-], each with a
value of 1 x 10-7 M
Since Kw is a fixed value, the concentrations of [H+] and [OH-] are inversely
changing
If the concentration of H+ is high, then the concentration of OH- must be low,
and vice versa. For example, if [H+] = 10-2 M, then [OH-] = 10-12 M
What is pH?
Changes in [H+] have significant effects on many biochemical processes
A logarithmic quantity, pH, was developed as a convenient scale for working
with levels of [H+] The pH of a solution is a measure of its concentration of H+
(acidity)
The pH is defined as
Acidic and basic pH
On the pH scale, pH of 7.0 is considered neutral
pH values below 7.0 indicate acidic solutions
pH values above 7.0 indicate basic (alkaline) solutions
Strong acids
A strong acid dissociates completely, while a strong base completely binds to a
proton.
HA  H+ + A-
In a 0.1 M solution of hydrogen chloride (HCl) in water, [H+] = 0.1 M because all
the HCl has dissociated into H+ and Cl- ions
For this solution pH = log 0.1 = 1.0
Strong bases
Similarly, a 0.01 M solution of NaOH will have an OH- concentration of 1 x 10-2
The pH is calculated as shown below:
[H+] = 1 x 10-14 / 1 x 10-2
= 1 x 10-12
The pH will be 12
Otherwise, if [OH-] = 10-2, then [H+] = 10-12 and the pH = 12
Weak acids and bases
Many acids, such as the amino acids and acetic acid, do not dissociate
completely in water
Such acids are called weak acids, and similarly, some bases do not completely
dissociate and are called weak bases
The ionization equilibrium of a weak acid is given as
Acid dissociation constant
Ka, the acid dissociation constant, is the equilibrium constant for the reaction of
a weak acid (HA) converting into a proton and the conjugate base (A-).
What is pKa?
As with pH, a logarithmic scale is useful for working with Ka values. pKa is
defined as:

pKa: the tendency of an acid to dissociate into H+ and its conjugate base A-
Each weak acid and base have their own fixed pKa values

Note: if Ka is very large, pKa is very small

The Henderson-Hasselbalch equation
What is the relation between pH, pKa, and the ratio of acid to base?
A useful expression can be derived
When pKa = pH
At the point of the dissociation where the concentration of the conjugate base
[A-] is equal to that of the acid [HA]:
pH = pKa + log[1]
The log of 1 = 0
pKa = pH

pKa is the pH where 50% of acid is dissociated into conjugate base.

Maintenance of equilibrium
Because a weak acid (or base) can exist in equilibrium with its conjugate base,
the equilibrium can be maintained even when small amounts of [H+] or [OH-] are
added to it.
Example
If a small amount of [H+] is added to a solution of weak acid, then the [H+] can
combine with it to produce [HA], maintaining [H+] level

If a small amount of [OH-] is added, then [OH-] will bind to [H+] producing H2O,
[HA] will dissociate to [H+] and [A-] to compensate for the loss of [H+],
maintaining [H+] level
What is a buffer?
The shift in equilibrium will then maintain the pH of the solution.
A solution with the ability to resist changes in pH is called a buffer.
Titration
The pKa values of weak acids are
determined by titration.
This involves adding small amounts of
a strong acid or base to the solution
and measuring the resulting changes in
pH generating a plot of titration curve.
Midpoint
For example, titration of acetic acid gives the
curve shown to the right. Note that the pKa
value is the midpoint of the curve.
At this point, pH is equal to the pKa since there
are equal concentrations of HA and A-.
Buffering capacity
The ability of a buffer to minimize changes in
pH is known as its buffering capacity.
The buffering capacity of weak acids and bases
is one pH unit from their pKa values.
In other words, a buffer is effective at resisting
changes in pH at pH +/- 1 of the pKa.
For example, since the pKa of acetic acid is 4.7,
then the buffering capacity ranges 3.7-5.7.
 What are the ratios of [A-]/(HA] of the
acetate buffer at point X and point Y?
At point X, it is the end of the buffering capacity where the pH = pKa – 1. pKa = 4.8.
so, pH = 3.8. Use the Henderson-Hasselbalch equation to solve for [A-]/[HA]. Y

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

3.8 = 4.8 = [A-]/[HA]
log [A-]/[HA] = 3.8 – 4.8
X
log [A-]/[HA] = -1
[A-]/[HA] = 1/10
For point Y, it is the other end of the buffering capacity where the pH = 5.8. If you
solve it, [A-]/[HA] = 10/1.
Conjugate bases
Acid Conjugate base
CH3COOH CH3COONa (NaCH3COO)
H3PO4 NaH2PO4
H2PO4- (or NaH2PO4) Na2HPO4
H2CO3 NaHCO3
Properties of buffers
They all have the same function.
Their pKa’s are different.
Buffering capacities are same.

We choose a buffer based on its pKa, which should

be close to the desired pH.
Problems and solutions
the Henderson-Hasselbalch (HH) equation is useful for determining the pH of a
solution if the molar proportion of A- to HA and the pKa of HA are known.

Example:
Consider a solution of 0.1 M acetic acid and 0.2 M acetate ion. The pKa of acetic
acid is 4.8. Hence, the pH of the solution is given by

Similarly, the pKa of an acid can be calculated if the molar proportion of A- to HA

and the pH of the solution are known.
 Exercise
What is the pH of a buffer containing 0.1M HF and 0.1M NaF? (Ka = 3.5 x 10-4)?
HF is a weak acid meaning that it does not dissociate into the ions H+ and F-. The
concentration of the acid (HF) = 0.1. The concentration of the conjugate base (NaF) = 0.1.
There are two ways to solve it. The first is to calculate [H+}, then calculate the pH
The other way is to convert Ka to pKa, then use the
[H3O+] = Ka x [HF]/[F-] Henderson-Hasselbalch equation to solve for pH.
= 3.5 x 10-4 x (0.1/ 0.1) pKa = -log Ka

= 3.5 x 10-4 pKa = -log 3.5 x 10-4

pKa = 3.46
pH = -log 3.5 x 10-4
pH = pKa + log (F-]/[HF]
= 3.46 pH = 3.46 + (0.1/0.1)
pH = 3.46
Polyprotic weak acids
Some weak acids (buffers) can donate more than one proton.
An example is phosphoric acid (H3PO4).
Phosphoric acid can donate up to three protons.
Different pKa’s
These protons do not dissociate at the same time.
Each proton has a certain pKa.
and…
Each proton dissociates at a
certain pH.
 What is the pH of a lactate buffer that contains 75%
lactic acid and 25% lactate? (pKa = 3.86)
Problem 1
Remember, lactic acid is HA that has the proton to donate and lactate is the conjugate base
that does not have a proton and carries a negative charge. Use the Henderson-Hasselbalch
equation to solve for the pH:
pH = pKa + log (lactate]/[lactic acid]
pH = 3.86 + log 25/75
pH = 3.86 + (-0.48)
pH = 3.38
You can guess the answer as well. Since you have more acid than the conjugate base and it
Is not by more than 10 times (the ratio between conjugate base to acid is not less than 10
times), the pH should be lower than the pKa.
Problem 2
What is the pKa of a dihydrogen phosphate buffer when pH of 7.2 is obtained
when 100 ml of 0.1 M NaH2PO4 is mixed with 100 ml of 0.1 M Na2HPO4?

NaH2PO4 is acid and Na2HPO4 is its conjugate base because NaH2PO4 has an extra
proton.
Use the Henderson-Hasselbalch equation to solve for the pH:
pH = pKa + log (Na2HPO4]/[ NaH2PO4]
7.2 = pKa + (0.1/0.1)
7.2 = pKa
Buffers in human body
Carbonic acid-bicarbonate system (blood)

Dihydrogen phosphate-monohydrogen phosphate system

Proteins (via the amino acids)

Blood buffering
Blood pH must be maintained at around 7.4.
Any dramatic change (up or down) can be dangerous.
By far the most important buffer for maintaining acid-base balance in the blood
is the carbonic-acid-bicarbonate buffer.
How?
During metabolism, cells produce CO2. This CO2 is dissolved in blood and is
converted to carbonic acid, which dissociates into bicarbonate ion (conjugate
base) and H+.

Dissolved CO2 is in equilibrium with pressure of CO2 (pCO2) in lungs.

If blood pH changes, then the body changes the rate of breathing in order to
balance blood pH.
The equation
Relationships of the bicarbonate buffer system to the lungs and the kidneys.
Roles of lungs and kidneys
Maintaining blood is balanced by the kidneys and the lungs
Kidneys control blood HCO3- concentration ([HCO3-])
Lungs control the blood CO2 concentration (PCO2)