BIOCHEMISRY

By;- Getahun A (BSc, MSc in medical

biochemistry)
 Introduction to Biochemistry

01/23/2026 BIOCHEM 2
 Objectives
Definition of biochemistry
Discuss the relevance of biochemistry in pharmacy in disease
and health conditions
Classification of biochemistry as Descriptive and Dynamic
 Elucidate the major chemical constituents of cells
 List the elemental composition of the living system
 List and explain the cellular component
 Brief introduction to metabolism and enzymes

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Biochemistry can be defined as the science of the chemical
basis of life (Greek bios “life”).
Biochemistry is the language of biology
It is the science that study about chemical constituents of living
cells and the reactions and processes they undergo.
According to this definition, Biochemistry encompasses large
areas of cell biology, molecular biology and genetics.
Biochemistry describe & explain all biochemical processes of
living cells at molecular level.
In general Biochemistry is the study of the chemistry of life
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processes
 Role of Biochemistry

To evaluate the nutritive value of different type nutrients.

 Development and exploitation of better genotypes

 Removal and inactivation of toxic factors present in food

 Food preservation and processing technology

 Biochemistry of disease pathogenesis in human being.

 Vaccine development

 Identification receptor and mechanism of drug action

How the food we eat generate energy to maintain our daily activities

Diagnosis (BIOMARKERS) and preventive medicine

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 Role of Biochemistry

Biochemistry is important to understand basic functions of

cells at the molecular level.
e.g. How the food that we eat is digested, absorbed, and
used to make ingredients of the body?
How does the body derive energy for normal day to day
activities?
Health depends on a harmonious balance of biochemical
reactions occurring in the body,
Disease reflects abnormalities in biomolecules, biochemical
reactions, or biochemical processes
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 Role of biochemistry Cont…

Modern day medical practices are highly dependent on the

biochemical investigation of body fluids (blood, CSF, Urine,
synovial fluids etc)
The disease manifestations are reflected in the composition
of body fluids and other tissues.
Hence, the demarcation of abnormal from normal constituents
of the body is another aim of the study of biochemistry

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 Role of biochemistry Cont…
Almost all the diseases have biochemical involvement.
Biochemistry helps to understand the biochemical changes and
related physiological alteration in the body.
Pathophysiology of any disease is studied through biochemical
changes.
Figure 1: Biomolecule Basis of Different Diseases

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Classification of Biochemistry
Descriptive biochemistry: deals with qualitative and quantitative nature
of Biomolecules in the living cells, such as:

Water, Micro molecules which include Vitamins & Minerals

Macromolecules (carbohydrates, proteins, lipids & nucleic acids)

 What is it made of ? It describes what exists, not how things change

Dynamic biochemistry: deals with the reactions,

mechanisms of reactions & regulation in the cells.
What does it do and how does it work?
It shows biochemical change
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 Atoms
 Molecules (biomolecules)
 Organelles
 Cells
 Tissues
 Organs
 Organ Systems
 Organisms
 Populations
 Communities
 Ecosystems
 Biosphere
carbon DNA organelle cell
atom molecule tissue

biosphere

ecosystem

organ

organ
system

community organism
population
 Levels of structural organization in the human body.
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 Elemental Composition of the Living System
More than 99% of the elements in animals’ bodies are, carbon,
hydrogen, oxygen, and nitrogen.

Most of the H & O occur as H2O, which alone account 60-70% of

cell mass.
These elements are the major constituents of biomolecules, on
which most living organisms depend.
Proteins (10-20%), Nucleic acids (7-10%) , Polysaccharides (2-5%)
and lipids (3%) are account of weight of the cell.

The seven essential mineral elements (Na, K, Mg, Ca, Cl, S & P)
account only about 0.5% of the body mass.
 Elemental Composition of the Living System

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 Cellular Components

 Each cell has four common components:

[Link] membrane
[Link] region
[Link]
[Link] molecules and biochemical pathways
 Non-membrane-limited organelles: ribosomes,

cytoskeleton, centriole
 Membrane-limited organelles: Nucleus, ER, Golgi

apparatus (GA), lysosomes, mitochondria and peroxisomes

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Functions of Membrane-bounded Organelles in Eukaryotic Cell
 Brief introduction to Metabolism and Enzymes
 Metabolism is sum of all chemical changes in the body
 Metabolism is a highly coordinated cellular activity in which
enzymes are organized into discrete metabolic pathways that
cooperate in degrading/synthesizing energy-rich nutrients from
the environment
 There are three types of Metabolism

(Synthetic reactions)- endergonic

ANABOLIC

AMPHIBOLIC (Dual purpose), e.g.. Krebs cycle

CATABOLIC (break down- exergonic

Figure 2: Catabolic and Anabolic Pathway

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Figure 3: General Metabolic Routes for Dietary in the
Body

Essential biomolecules,
nutrient
Xenobiotic, Fuel storage,
currency of the cell,

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 Four Major Biomolecules:
Categories:

Carbohydrates (2-5%) Lipids (3%)

Proteins(10- 20%) Nucleic Acids (7%)

Table: Caloric Content of Four Major Biomolecules
BRIEF INTRODUCTION TO ENZYMES
 Introduction
 Enzymes are biological catalysts which increase the rate of chemical
reaction by lowering activation energy .

 Enzymes provide Speed, Specificity and Regulatory control to reactions

 They determine the patterns of transformations for chemicals, as well as

forms of energy in the living organisms.
 Rates of chemical reactions folds (1015) times by action of enzymes
 Without enzymes most biochemical reactions would occur much slowly to
maintain life
 Most enzymes are proteins but there are few RNA and DNA
possessing catalytic activity which are called:
 Ribozymes (ribonuclease, Peptidyl transferase(Peptide synthetase) &
Deoxyribozyme (Ligase) respectively
 Therefore biocatalysts can be proteins, ribozymes, deoxyribozyme
Enzyme Catalysis Overview
 Common Features Enzymes
1. Do not consume themselves: No changes in quantity and
quality of Enzymes before and after the reactions.

2. Do not change the equilibrium points: only enhance the

reaction rates.

3. Apply to the thermodynamically allowable reactions

(spontaneous reaction with negative ∆G)

4. Reduce the activation energy

 Nomenclature of Enzymes

 Conventional Nomenclature
 Historical or common names: Pepsin, chymotrypsin, Lysozyme

 Substrate-dependent naming: lipase (for lipids) and protease (for

protein) and glycosidase for carbohydrates

 Chemical nature/ reaction-dependent naming: Hydrolase,

Transaminases, Dehydrogenase

 Systematic Nomenclature:
 IUBMB Categorize enzymes in to 6 classes according to the general
class of organic reactions catalyzed and assigned a unique number, a
systematic name, a shorter common name to each enzyme
Systematic Nomenclature (IUB)
ENZYMES CLASSIFICATION: SIX GROUPS
 Classification of Enzymes Based on Regulatory Behavior

Key regulatory Enzymes:

 Regulate the rate and direction of a pathway

 Usually have the slowest activity, catalyze irreversible rxns

 Some catalyze rate-limiting steps: “Pace makers” / “bottleneck”

step

They are unique to particular pathway & present in small amount.

Non-key regulatory Enzymes:
 Catalyze reversible rxns

 Shared by more than one pathway

 Exhibit high activities and present in excess

 The two Structural Components of Enzymes
1. Active Center (hydrophobic region look like a cleft or a crevice)
The catalytic site: where enzyme catalyzes the chemical reaction
Substrate-binding site(active site)

2. Allosteric site: have no catalytic function but has a regulatory function

Allosteric activator site & Allosteric inhibitor site
 Components of Enzymes
 Allosteric activator site/ Allosteric activators
 Allosteric inhibitor site/Allosteric inhibitor

Allosteric Binding
Allosteric effector Substrate due to
activator site Active site + + increased
substrate
affinity

Allosteric No binding due to

inhibitor site + + lowered substrate
affinity
Allosteric enzyme
 Molecular Components of Enzymes
 Simple enzymes: consists of only peptide/proteins chain
 Conjugated enzymes:
Holoenzyme = Apoenzyme + Cofactor
(protein) (non-protein)
 Cofactors: are different types of non-proteins molecules that attached to
enzymes and enhance their activities.

 Cofactors are classified into three groups:

A coenzyme-a non-protein organic substance which is loosely
attached to the protein part.
A prosthetic group –an organic substance which is firmly attached
to the protein or apoenzyme portion.
 A metal-ion activator- these include K+, Fe++, Fe+++, Cu++, Co++,
Zn++,Mn++ ,Mg++,Ca++; :loosely bound.
Molecular Components of Enzymes
Two Models which Describe Substrate-Enzyme Interaction
Lock and key model Induced-fit
model

 Lock and key model: both E and S are rigid and fixed, so they must be
complementary to each other perfectly in order to have a right match.
 Induced-fit model: The binding induces conformational changes of both E
and S, forcing them to get a perfect match.
Factors Affecting Enzymatic Activity

Temperature

pH and the ionic strength

Enzyme concentration

Substrate concentration

Inhibitors

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Effect of Temperature
Optimum temperature
Rate of reaction

for humans is close to

37o C
Heat energy causes
more collisions
Enzymes denature at high
between enzyme and
temperatures so rate falls rapidly
substrate

30 32 34 36 38 40 42
44 46
Temperature
37o C
 Effect of pH
 Affect especially ionizable side chains

 Extremes of pH & ionic strength can

also lead to denaturation of an enzyme

pHoptimum
Most body enzymes: 6 - 8
Pepsin: 1.5 – 2
Alkaline Phosphatase: 9.8
Salivary amylase: 6.8-7;
Pancreatic amylase: 7.2
Glucose-6-phosphatase: 8.0
 stomach intestines
Rate of reaction

pepsin trypsin

2 3 4 5 6 7 8 9
10
pH
Effect of Enzyme Concentration

If product
accumulates
Initial velocity, Vo

Enzyme concentration, [E]

Effect of Substrate
Concentration
Saturation of all the available
Initial velocity, Vo

Vmax enzymes with the previously added

substrate

Substrate concentration,
[S]
 Inhibitors
 Inhibitors are certain molecules that can decrease the catalytic
rate of an enzyme-catalyzed reaction.
 Inhibitors can be normal body metabolites or foreign substances
(drugs and toxins).

 The inhibition process can be either:

 Irreversible (covalent)

 Reversible (non-covalently): the effect of an inhibitor can be reversed by

decreasing the concentration of inhibitor OR increasing substrate

I. Competitive (Active site)

II. Non-competitive (allosteric site/E-S complexes).

III. Un-competitive (only to the E-S complexes).

Thank You!