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 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

1. MEANING OF LIFE2. HISTORY AND ORIGIN OF LIFE3. ABIOGENESIS4. SCIENTISTS’ CONCEPTS AND

EXPERIMENTS ON ABIOGENESIS5. THE LIVING WORLD – CELLS6. IMPORTANT CELL COMPONENTS

ASSOCIATED WITH BIOCHEMISTRY 7. COMPARING DIFFERENT CELLS

(Prokaryotes and Eukaryotes)8. 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 PHASEEnergy in the form of light, lightning and heat promoted the

formation of organic molecules from inorganic precursors

CHEMICAL EVOLUTIONPrimitive cell-like structures enclosed by lipid precursors molecules

possessed a richer diversity of organic molecules

POLYMERIZATIONCertain monomer molecules polymerized to form polypeptides and

nucleic acids

PRIMORDIAL CELLOnce 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 A protocell could have contained only RNA to

function as both genetic material and enzymes.

First protocells were heterotrophs using ATP as energy and carrying out a form of fermentation.

Domains of Life on Earth: 3 domains1. ARCHAEA: Halophiles and Thermophiles2. BACTERIA: Cyanobacteria and Heterotrophic

bacteria3. 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 microorganismscharacterized 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 material.

1. Both are membrane bound.

2. Both have ribosomes.

3. Both have similar basic metabolism.

4. 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: 1. genome (DNA)2. ribosomes3. cell membrane4. cell wall5. 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.

Ch.6 Important biochemical cell organelles (components)

Cytoskeleton Cell wall Nucleus Cytoplasm Ribosome Mitochondrion Chloroplast

Functions of important biochemical cell components Cytoskeleton:

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: 1. A permeable outer membrane, 2. A less permeable inner membrane, 3. Inter membrane space4. 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

Diagram of mitochondrion

Ch. 7 COMPARING PROKARYOTES AND EUKARYOTES

SIZEProkaryotes are usually much smaller thaneukaryotic cells Eukaryotic cells are, on average, ten times the sizeof prokaryotic cells.CELL WALLProkaryotes have cell wall composed of peptidoglycan (asingle large polymer of amino acid and sugar). Cell wall ofeukaryotes is not made up of this polymer.SURFACE AREAProkaryotes have a large surface area /volume ratio givingthem the advantage of having a higher metabolic and

growthrate with smaller generation time as compared to theeukaryotes.

3. Differentiating Prokaryotes and Eukaryotes

SUPPORTIn 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 PRODUCTIONIn 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

EukaryotesNo lysosomes in Prokaryotes

5. Differentiating Prokaryotes and Eukaryotes

MOVEMENT In Eukaryotes – cilia, flagella and

pseudopod movementIn Prokaryotes – flagella of different

structure involved in locomotionREPRODUCTION - DNA controlIn Eukaryotes – DNA in chromosomes

inside nucleusIn 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

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 LawIn 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.

METABOLISMLIFE OBEYS THE LAWS OF THERMIDYNAMICSPrinciples 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.

SUMMARYOrigin 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.