1. LECTURE 1: Introduction to biochemistry
Historical aspect of biochemistry and applications of biochemistry in biotechnology and other branches of life sciences

2. COURSE OUTCOME (C0 1)
CO1: Ability to differentiate basic structure, properties, functions and classification of important biomolecules.

3. 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.

4. LECTURE CONTENTS 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

5. Ch.1 MEANING OF LIFE What is the meaning of life?
Life is complex and dynamic – composed of carbon-based (organic) molecules
Life is organised and self-sustaining – composed of biomolecules (linked biomolecules formed polymers- macromolecules)
Life is cellular
Life is information-based – genes
Life adapts and evolves – mutations

6. 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.

7. 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

8. 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

9. ORIGIN OF LIFE – Solar System & Earth.
SOLAR SYSTEM-Big Bang theory- one mass of matter blew apart 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.

10. 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?

11. PHASES IN ABIOGENESIS EARLY PHASE CHEMICAL EVOLUTION POLYMERIZATION
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

12. 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

13. 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 ( ) – 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

14. ALEXANDR OPARIN ( ) - 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 ( ) AND STANLEY MILLER ( ) tested Oparin and Haldane’s spectulations under laboratory conditions and obtained presence of amino acids, alanine and glysine in the tarry residue

15. 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.

16. 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

17. 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.

18. 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 domains
ARCHAEA: Halophiles and Thermophiles
BACTERIA: Cyanobacteria and Heterotrophic bacteria
EUKARYA: Flagellates, Fungi, Plants and Animals

19. 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.

20. 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

21. 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’.

22. 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:
Eubacteria / Bacteria
Archaebacteria/Archaea

23. EUKARYOTIC CELLS Organelles
Eukaryotic cells are larger than prokaryotes.
They have a variety of internal membranes and structures, they are:
Organelles
cytoskeleton composed of microtubules, microfilaments and intermediate filaments
Eukaryotic DNA is composed of several linear bundles called chromosomes.

24. Similarities between Eukaryotes and Prokaryotes
Both have DNA as their genetic material.
Both are membrane bound.
Both have ribosomes.
Both have similar basic metabolism.
Both amazingly diverse in forms.

25. 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.

26. FEATURES OF PROKARYOTIC CELL
Has five essential structural components:
genome (DNA)
ribosomes
cell membrane
cell wall
surface layer
Structurally, a prokaryotic cell has three architectural regions:
appendages (flagella and pili)
cell envelope (capsule, cell wall , plasma membrane)
cytoplasm region (cell genome (DNA) and ribosomes.

29. Ch.6 Important biochemical cell organelles (components)
Cytoskeleton
Cell wall
Nucleus
Cytoplasm
Ribosome
Mitochondrion
Chloroplast

30. 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

31. 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)

32. 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

33. Diagram of mitochondrion

34. 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.

35. 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

36. 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

37. 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

38. 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.

39. 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.

40. 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

41. 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.

42. 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.

43. 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.

44. 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.

45. 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.

46. 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.