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LECTURE 1. LIFE & CELLS
 Introduction to biochemistry
 REVIEW and DISCUSS the origin of life.
EXPLAIN the evolution of cells.
INTRODUCE the laws of
thermodynamics.
 Living cells
 DISCUSS and COMPARE the structure
of prokaryotes and eukaryotes cells.
COURSE OUTCOME (C0 1)
 CO1: Ability to define the biochemical concepts
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and terms associated with life
Terms used in Course Outcome and
Teaching
Knowledge: Define, introduce, describe,
name, relate, explain, identify and Remember
concepts and principles.
Repetition: Repeat and discuss concepts and
principles.
Application: Apply, demonstrate, interpret and
illustrate concepts and principles.
WHAT IS BIOCHEMISTRY?
 A combination of the words biology and
chemistry.
 Biology is the study of cells that form the
fundamental units of all living organisms.
 Whereas, chemistry is the science that deals
with the composition, structure, and
properties of substances and the
transformations that they undergo.
LECTURE CONTENTS
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MEANING OF LIFE
HISTORY AND ORIGIN OF LIFE
ABIOGENESIS
SCIENTISTS’ CONCEPTS AND
EXPERIMENTS ON ABIOGENESIS
THE LIVING WORLD – CELLS
IMPORTANT CELL COMPONENTS
ASSOCIATED WITH BIOCHEMISTRY
COMPARING DIFFERENT CELLS
(Prokaryotes and Eukaryotes)
STATING LAWS OF THERMODYNAMICS
Ch.1 MEANING OF LIFE
 What is the meaning of life?
 Life is complex and dynamic –
composed of carbon-based molecules
 Life is organised and self-sustaining –
composed of biomolecules
 Life is cellular
 Life is information-based – genes
 Life adapts and evolves – mutations
CELLS
Cells are fundamental units of biology,
and building block of all organisms
Organisms range from:
Unicellular: 1 cell = 1 organism e.g.
Paramecium & Amoeba
Multicellular: 1036 cells = 1
organism, different cells for different
functions, exhibit division of labor
e.g. muscle, skeletal, immune, lungs,
epithelium, etc...)
Ch. 2 HISTORY OF LIFE
 Study of history - based on geological
(fossil record), biological and chemical
evidence
 Earth formed from a cloud of condensing
cosmic dust and gas 4.5 billion years
ago
 Earliest organisms stromatolites
(compressed layers of bacterial remains)
existed 3.6 billion years ago.
STRATEGIES IN ORIGIN OF
LIFE STUDIES
 TOP-DOWN APPROACH – phylogenetic
(evolutionary) history of modern organisms
based on the similarities and differences among
organisms that are clues to their evolutionary
past
 BOTTOM-UP APPROACH –
abiogenesis ( mechanism of reconstructing
and transformation of early earth into the first
primitive living organisms), and analyzing
biomolecules as vestigial remanants of the
prebiotic world
ORIGIN OF LIFE -Gaseous
 Started with the formulation of carbon
and higher elements
 Smaller H and He atoms fused to form
heavier elements - stars huge masses of
interstellar gases
 Then followed by the formation of the
Solar system and Earth
ORIGIN OF LIFE – Solar System
& Earth.
 SOLAR SYSTEM-Big Bang theory- one
mass of matter blew apart 12-15 billion
years ago
 Sun formed 6 billion years ago
 Planets formed 4.6 billion years ago by
the condensing of peripheral gases and
matter around the sun.
Ch. 3 ABIOGENESIS
Essential issues
 How were simple organic molecules
(sugars, amino acids, and nucleotides)
formed?
 How did these primordial molecules link
up to form proteins and nucleic acids?
 How did the first cells originate?
PHASES IN ABIOGENESIS
EARLY PHASE
Energy in the form of light, lightning and heat promoted the
formation of organic molecules from inorganic precursors
CHEMICAL EVOLUTION
Primitive cell-like structures enclosed by lipid precursors molecules
possessed a richer diversity of organic molecules
POLYMERIZATION
Certain monomer molecules polymerized to form polypeptides and
nucleic acids
PRIMORDIAL CELL
Once the protocells became enclosed in a membrane-like barrier,
their evolution proceeded over time
ASSUMPTIONS EXPLAINING
ABIOGENESIS
 The first form of life was simple in both
structural and functional capabilities
 The basic requirements of any form of
life is the presence of one or more
molecules that are able to duplicate
themselves using raw materials available
in their environment
Ch.4 SCIENTISTS’ CONCEPTS
AND EXPERIMENTS ON
ABIOGENESIS
 CHARLES DARWIN – suggested that life might
have arisen in a ‘warm little pond’ speculated to
contain ammonia, phosphate and other
molecules
 J.B.S. HALDANE (1892-1962) – coined term
‘primordial soup’. He and other scientists
spectulated that life arose from hot ocean water
into which washed inorganic and organic
molecules from volcanic eruptions and
asteroids from space
 ALEXANDR OPARIN (1894-1980) - proposed about
early earth containing hydrogen, methane, ammonia,
and water vapour, but with no oxygen. He viewed (1924)
early earth as a reducing atmosphere. He also talked
about the first cells and ‘vesicular membrane’.
 HAROLD UREY (1893-1981) AND STANLEY MILLER
(1930 - ) tested Oparin and Haldane’s spectulations
under laboratory conditions and obtained presence of
amino acids, alanine and glysine in the tarry residue
 Miller (1953) – duplicated the early conditions in the
lab by :
(1) creating an artificial ‘atmosphere’ and ‘ocean’ (2)and
introducing hydrogen, methane, ammonia, and water into
the system (3)with electric spark as energy supply, (4) to
obtain after one week, the formation of amino acids and
small organic molecules
 The molecules that make up living organisms are referred
to as biomolecules.
 Other scientists repeated Oparin & Miller’s work,
eventually producing amino acids, ATP, glucose and
other sugars, lipids, and the bases which form RNA and
DNA, and adenine the key component of ATP and NAD.
THE RNA WORLD CONCEPT
 RNA was the first information molecule
 It possess genetic info and also can
behave as an enzyme
 Formation of peptide bonds during
protein synthesis is catalysed by an RNA
component of ribosomes
 In certain conditions in living cells, DNA
can be synthesized from an RNA
molecule by an enzyme reverse
transcriptase
HYPOTHETICAL SCENARIO OF ORIGIN OF
LIFE
 Short RNA segments may have originally
encoded short peptides
 As protocells became more stable and complex
form of genetic info, a reverse trascriptase
started copying RNA sequences into DNA
 This resulted in the role of DNA as the major
info macromolecule in all modern organisms
 Hence DNA is the genetic blueprint;
PROTEINS, the devices that perform the tasks
of all living processes; and RNA, the carrier of
info used to manufacture protein.
Ch.5 THE LIVING WORLD
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A protocell could have contained only RNA to
function as both genetic material and
enzymes.
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First protocells were heterotrophs using
ATP as energy and carrying out a form of
fermentation.
Domains of Life on Earth: 3 domains
1. ARCHAEA: Halophiles and Thermophiles
2. BACTERIA: Cyanobacteria and Heterotrophic
bacteria
3. EUKARYA: Flagellates, Fungi, Plants and
Animals
PROTOCELLS
 PROTOCELL – cell-like structure with a lipid-
protein membrane developed from coacervate
droplets.
What are coacervate droplets ?
Coacervate droplets – are complex spherical
units formed spontaneously when concentrated
mixtures of macromolecules (like RNA, DNA,
amino acids, phospholipids, clay etc.) are held
at the right temperature, ion composition, and
pH. They absorb and incorporate various
substances from the surrounding solution.
EARLY CELLS
 Bacteria and Archaea are termed as
PROKARYOTES –organisms whose DNA is not
enclosed in a nucleus of the cell.
 EUKARYOTIC cells are aerobic and arose 2.1
billion years ago. They contain nuclei and
organelles.
 PLANTS appeared on land (mud flats) during
the ‘Paleozoic’ period, about 440 million years
ago. They provided food for higher animals to
evolve
EARLY BACTERIA
 PRECAMBRIAN ERA encompasses
87% of geological time scale and based
on this, life began from 570 million to 4.6
billion years ago.
 Early bacteria resembled archaea that
live in hot springs today.
 Archaeans resemble bacteria but
developed separately from common
ancestor nearly 4 billion years ago. They
thrive under extreme conditions and are
labeled as ‘extremophiles’.
PROKARYOTES
Prokaryotes are single-celled microorganisms
characterized by:
• the lack of a membrane-bound nucleus
and
• membrane bound organelles.
There are two domains of prokaryote:
1. Eubacteria / Bacteria
2. Archaebacteria/Archaea
EUKARYOTIC CELLS
 Eukaryotic cells are larger than
prokaryotes.
 They have a variety of internal
membranes and structures, they are:
1. Organelles
2. cytoskeleton composed of
microtubules, microfilaments and
intermediate filaments
 Eukaryotic DNA is composed of several
linear bundles called chromosomes.
Similarities between
Eukaryotes and Prokaryotes
 Both have DNA as their genetic
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material.
Both are membrane bound.
Both have ribosomes.
Both have similar basic metabolism.
Both amazingly diverse in forms.
DIFFERENCES BETWEEN BACTERIA AND
ARCHAEA
Eubacteria have cell walls composed of
peptidoglycan, Archaebacteria have cell
walls composed of various different substances.
Eubacteria have ester-linked straight-chain
membrane lipids (fatty acids). Archaebacteria
have ether-linked branched-chain member
lipids.
Eubacteria and Archaebacteria have differences
in their DNA replication and transcription
systems that suggest independent elaboration
in these two groups
Bacteria translation apparatus inhibited by
antibiotics (e.g. streptomycin, tetracycline etc.).
Archaea not affected by antibiotics.
FEATURES OF PROKARYOTIC CELL
 Has five essential structural components:
genome (DNA)
2. ribosomes
3. cell membrane
4. cell wall
5. surface layer
 Structurally, a prokaryotic cell has three architectural
regions:
1. appendages (flagella and pili)
2. cell envelope (capsule, cell wall , plasma
membrane)
3. cytoplasm region (cell genome (DNA) and
ribosomes.
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Ch.6 Important biochemical
cell organelles (components)
 Cytoskeleton
 Cell wall
 Nucleus
 Cytoplasm
 Ribosome
 Mitochondrion
 Chloroplast
Functions of important
biochemical cell components
 Cytoskeleton:
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Helps to maintain cell shape.
The primary importance of the cytoskeleton is in cell
motility.
Provides a supporting structure for the internal
movement of cell organelles, as well as cell
locomotion and muscle fiber contraction could not
take place without the cytoskeleton.
It is composed of proteinaceous fibers
 Cell-wall: Every cell is enclosed in a membrane, a double
layer of phospholipids (lipid bilayer) composed of
peptidoglycan
 Nucleus: is enclosed in a double membrane and communicates
with the surrounding cytosol (semi-liquid portion of cytoplasm)
via numerous nuclear pores. Within the nucleus is the DNA
providing the cell with its unique characteristics.
 Ribosome: is
the site of protein synthesis
 Cytoplasm: This is a collective term for the cytosol plus the
organelles suspended within the cytosol. The cytosol is full of
proteins that control cell metabolism including signal
transduction pathways, glycolysis, intracellular receptors, and
transcription factors.
 Mitochondria (membrane-bound organelles (double membrane):
are power centers of the cell. The different sections in a
mitochodrion are: outer membrane; intermembrane space;
inner membrane (where oxidation phosphorylation takes place)
and matrix (where the Kreb Cycle takes place)
CHLOROPLAST IN PLANTS
 Chloroplast:
This organelle contains the plant cell's chlorophyll
responsible for the plant's green color.
 Structurally it is very similar to the mitochondrion
except it is larger than the mitochondrion, not folded
into cristae, and not used for electron transport
It contains:
A permeable outer membrane,
A less permeable inner membrane,
Inter membrane space
A third membrane containing the light-absorbing system,
the electron transport chain, and ATP synthetase, that
forms a series of flattened discs, called the thylakoids
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Diagram of mitochondrion
Ch. 7 COMPARING PROKARYOTES AND
EUKARYOTES
SIZE
Prokaryotes are usually much smaller than
eukaryotic cells
Eukaryotic cells are, on average, ten times the size
of prokaryotic cells.
CELL WALL
Prokaryotes have cell wall composed of peptidoglycan (a
single large polymer of amino acid and sugar). Cell wall of
eukaryotes is not made up of this polymer.
SURFACE AREA
Prokaryotes have a large surface area /volume ratio giving
them the advantage of having a higher metabolic and growth
rate with smaller generation time as compared to the
eukaryotes.
3. Differentiating Prokaryotes and Eukaryotes
SUPPORT
In Eukaryotes provided by cytoskeleton;
none in Prokaryotes
PROTEIN SYNTHESIS
In Eukaryotes (animals) Rough Endoplasmic
Reticulum (Rough ER) is involved
In Prokaryotes ribosomes are involved
FAT SYNTHESIS
In Eukaryotes – Smooth ER involved
No fat synthesis in Prokaryotes
4. Differentiating Prokaryotes and Eukaryotes
ENERGY PRODUCTION
In Eukaryotes – chloroplasts (plants);
mitochondrion (Kreb’s cycle)
In Prokaryotes – chlorophyll (if present) but has no
covering or chloroplast; no mitochondrion and
Kreb’s cycle replaced by fermentation
ENERGY DIGESTION
Lysosomes involved in aging process of cell in
Eukaryotes
No lysosomes in Prokaryotes
5. Differentiating Prokaryotes and Eukaryotes
MOVEMENT
In Eukaryotes – cilia, flagella and
pseudopod movement
In Prokaryotes – flagella of different
structure involved in locomotion
REPRODUCTION - DNA control
In Eukaryotes – DNA in chromosomes
inside nucleus
In Prokaryotes – DNA in single strand and
floating freely without a nucleus
Ch.8 THERMODYNAMICS
 DEFINITION: The investigation of energy
transformations that accompany physical and
chemical changes in matter is called
thermodynamics. It is the science of energy
transformations.
 The principles of thermodynamics are used to
evaluate the flow and interchanges of matter
and energy.
 Bioenergetics is the study of energy in living
organisms. It is useful in determining the
direction and extent to which specific
biochemical reactions occur.
LAWS OF THERMODYNAMICS
 FIRST LAW: In all physical and chemical changes,
energy is neither created or destroyed.
The total amount of energy in the universe is constant.
 SECOND LAW: The disorder “S” or entropy in the
universe always increases. All chemical and physical
occur spontaneously when disorder is increased.
The universe equals, the system + the surrounding,
where according to the Second Law, a spontaneous
change in a system proceeds in the direction of
decreasing free energy.
 THIRD LAW: As the temperature of a perfect crystalline
solid approaches absolute zero (0o K), disorder
approaches zero.
FACTORS AFFECTING
BIOCHEMICAL REACTIONS
 ENTHALPY (Total heat content)- related
to the First Law of Thermodynamics
 ENTROPY (Disorder)- related to the
second Law of Thermdynamics
 FREE ENERGY (Energy available to do
chemical work)- is derived from the
mathematical relationship between
enthalpy and entropy
GIBBS FREE ENERGY
 GIBBS FREE ENERGY: the maximum amount
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of energy available to do work in a system;
symbolized by “G”.
The Second Law can be stated in terms of: the
universe: disorder (S) in universe is increasing
The system: free energy (G) decreases during
a spontaneous change in a system.
If a spontaneous change proceeds in the
direction of decreasing free energy, the delta G
is negative and energy is given off.
At equilibrium, the change in free energy (delta
G) is zero.
Rections Associated with
Thermodynamic Laws
Associated with the First Law:
Exothermic: In a reaction or process, heat is given off.
Endothermic: In a reaction or process, heat is absorbed
from the surrounding.
Isothermic: In a reaction or process, heat is not exchanged
with the surrounding.
Associated with the Third Law
In a chemical reaction, we have the reactants which react to
produce the products.
In exergonic reaction (energy released): The products
have a lower free energy than the reactants. The reaction
proceeds spontaneously and yields energy.
In endergonic reaction (energy dependent): The products
have a higher free energy than the reactants and the
reaction does not proceed spontaneously and requires
energy to occur.
METABOLISM
LIFE OBEYS THE LAWS OF
THERMIDYNAMICS
Principles of Metabolism: Reactions in cells are
catalyzed by enzymes, which are proteins
catalysts. The reactions are grouped together in
sequences called pathways.
Types of pathways:
Catabolism: reactions which break down
molecules; delta G is negative. Energy is given
off and can be captured as ATP.
Anabolism: synthetic reactions; delta G is
positive; energy input is required.
SUMMARY
Origin of life
 A model for the origin of life proposes
that organisms arose from simple
organic molecules that polymerized to
form more complex molecules capable
of replicating themselves.
 Compartmentation gave rise to cells that
developed metabolic reactions for
synthesizing biological molecules and
generating energy.
Cells
 All cells are prokaryotic or eukaryotic.
 Eukaryotic cells contain a variety of
membrane-bound organelles.
 Phylogenetic evidence groups
organisms into 3 domains: archaea,
bacteria, eukarya.
 Natural selection determines the
evolution of species.
Themodynamics
 Life obeys the laws of thermodynamics.
 Energy is conserved in the First Law.
 (Second Law) Spontananeous
processess increase the disorder
(entropy) of the universe which affects
the biochemical processess.
 The equilibrium constant for a process is
related to the standard free energy
change for that process.
 Living organisms are open systems that
maintain a steady state.