Introduction to Biochemistry

• Biochemistry is the "chemistry of life".
• Biochemistry is a laboratory-based science that combines biology and chemistry to understand and solve biological problems.
• Biochemistry explores chemical processes within and related to living organisms.
• Biochemistry focuses on the structure, function, and interactions of biomolecules that drive biological processes.

Biochemistry is an Interdisciplinary Science

• Biochemistry leans toward chemistry while being deeply integrated with biology.
• Biochemistry is chemistry-driven but biology-oriented.
• Biochemistry is one of the five major branches of chemistry; the other four are inorganic, organic, analytical, and physical chemistry.
• Biochemistry was once a subfield of organic chemistry but later became a distinct field.
• Biochemistry became broader as it incorporated concepts from other fields.

Biochemistry is the Study of Biomolecules and their Functions

• Biomolecules include lipids, nucleic acids, carbohydrates, and proteins.
• Carbohydrates are used for energy and as structural components.
• Proteins are used for catalysis, transport, and structural roles.
• Lipids are used for membrane formation and energy storage.
• Nucleic acids are used for genetic information storage and transmission.

Metabolic Processes

• Metabolic pathways, catabolism, and anabolism are all metabolic processes.

Signaling In Cells

• Cell signaling entails hormones, receptors, and signal transduction.

Enzyme Kinetics

• Enzyme kinetics includes enzyme activity and mechanisms.

Biochemical Techniques

• Biochemical techniques include chromatography and spectroscopy.

ATP Production and Bioenergetics

• Bioenergetics and ATP production include cellular respiration and photosynthesis.

Clinical Biochemistry

• Clinical biochemistry includes disease markers and drug metabolism.

Molecular Biology

• Molecular biology includes DNA replication, transcription, and gene regulation.

Biochemistry is Molecular and Cellular in Nature

• At the molecular level, it examines the chemical structures of biomolecules, molecular interactions, and biochemical reactions.
• At the cellular level, it examines how molecules function within the complex environment of a cell.
• Examples of function within a cell are cellular metabolism, cell signaling, gene expression, and enzymatic activities.

Biochemistry is Experimental and Analytical

• Biochemistry relies on experimentation and therefore follows the scientific method (observation, hypothesis, experimentation, data collection, and conclusion) in studying biomolecules.
• Biochemistry uses analytical techniques to study and quantify biomolecules.
• Analytical techniques ensure accuracy and reproducibility in biochemical studies.

Common techniques used in Biochemistry

• Spectroscopy measures UV-Vis, NMR, and Mass Spectrometry.
• Chromatography measures HPLC, Gas Chromatography.
• Electrophoresis measures SDS-PAGE, Western Blotting.
• Molecular Cloning & Recombinant DNA.

Biochemistry is Dynamic and Evolving

• These areas help biochemistry evolve; Lipidomics, Genomics, Metabolomics, Synthetic Biology, Nanobiotechnology, Bioinformatics and Proteomics.
• DNA was once thought to be a simple molecule, but the Human Genome Project revealed its complexity.
• Enzymes were once believed to be rigid catalysts, but the induced-fit model shows their flexibility and adaptability.
• Cancer was once viewed as uncontrolled cell growth, but now it's understood to involve mutations in biochemical pathways.
• Insulin was once extracted from animals but is now produced through genetic engineering in bacteria.

Biochemistry is Fundamental to Life Sciences

• Biochemistry is fundamental to medicine, clinical applications, agricultural science, food science, biotechnology, industrial applications, environmental applications and forensic science.
• Medical and clinical applications of biochemistry include disease diagnosis, treatment, drug development & pharmacology, and genetics & molecular medicine.
• Biotechnology and industrial applications of biochemistry include genetic engineering & recombinant DNA technology, enzyme technology in industry, and biofuels & renewable energy.
• Agricultural and food science applications of biochemistry include soil & plant biochemistry, pesticides & herbicides, and food preservation & nutrition.
• Environmental applications of biochemistry include bioremediation, climate change & carbon cycle, and wastewater treatment.
• Forensic science applications of biochemistry include DNA fingerprinting in criminal investigations, toxicology tests, blood & tissue analysis for medical & legal purposes.

Early Ideas in Biochemistry

• Hippocrates' Humoral Theory stated that the body needed balanced bodily fluids, known today as homeostasis.
• Aristotle suggested that living organisms have a unique vital force or principle that separates them from nonliving matter.
• Jöns Jacob Berzelius' Vital Force Theory (Vitalism) (1779–1848) proposed that compounds found in living organisms (organic compounds) can only be produced by living organisms.

Significant Discoveries in Biochemistry

• In 1828, Friedrich Wohler synthesized urea from ammonium cyanate, disproving the theory on vitalism.
• Louis Pasteur showed that fermentation is a biological process carried out by living organisms (yeast & bacteria) rather than just a chemical reaction that occurred spontaneously.
• Pasteur's work on fermentation laid the foundation for biochemistry by demonstrating that life processes had a chemical basis.
• Carl Neuberg coined the term “biochemistry” in 1903 and made contributions particularly in carbohydrate biochemistry and enzyme function.
• Neuberg is often referred to as the Father of Modern Biochemistry.
• Discoveries by Neuberg include carboxylase, elucidation of alcoholic fermentation and hydrotropy, also known as the "Neuberg Effect".

Origin of Life

• The Universe began with the Big Bang Theory.
• All matter was originally confined to a comparatively small, extremely hot and dense state before it started to expand about 13.8 billion years ago.
• As the universe expanded, the temperature cooled allowing formation of subatomic particles, first elements, galaxies, stars, nucleosynthesis and heavier elements, leading to the formation of planets & eventually life.
• Hubble's Law was discovered in 1929 by Edwin Hubble.
• CMB; a faint, uniform radiation coming from all directions in the universe (Arno Penzias & Robert Wilson.
• The Solar System & The Earth formed via the Nebular Hypothesis.
• The solar system began as a giant molecular cloud that began to collapse under its own gravity or possibly triggered by a nearby supernova explosion.
• As it collapsed, a disk-shaped structure formed with the Sun at the center, with other materials forming planetesimals which formed planets including the Earth 4.5 billion years ago.
• The early Earth was molten and exhibited harsh conditions.
• Very little or no free oxygen was present.
• The earth was constantly irradiated by UV light from the Sun without the ozone layer.
• Under these conditions, the chemical reactions that produced simple biomolecules took place.
• Early gases present; NH3, H2S, CO, CO2, CH4, N2, H2, H₂O
• The first life forms may have emerged on the surfaces of clay minerals, which acted as catalysts and templates for the assembly of complex organic molecules, potentially providing the necessary conditions for the development of early life forms.

Six Theories and Hypotheses on how Life Started.

• Primordial Soup Theory
• Hydrothermal Vent Hypothesis
• Panspermia Hypothesis
• RNA-World Hypothesis
• Double Origin Theory
• Clay-Particle Theory
• The Primordial Soup Theory suggests that life on Earth originated from a prebiotic soup of organic compounds in the ocean.

Those organic compounds were produced when;

• Energy from lightning
• UV rays
• Heat acted on the gases in Earth's early atmosphere (abiogenesis).
• Alexander Oparin created the theory in 1924.
• Stanley Miller & Harold Urey performed an experiment on the theory in 1952.
• Early Earth conditions were simulated by passing electric sparks (lightning) through a mixture of NH3, CH4, H2, and H2O to produce amino acids.
• Hydrothermal Vent Hypothesis suggests that HVs are fissures in the ocean floor that release hot, mineral-rich water.
• HVs are formed from tectonic plate movements.
• Environmental conditions at the vents created a gradient that powered the chemical transformation of carbon dioxide and hydrogen into organic molecules.
• The fluid in HVs is acidic and contains metals like Fe, Zn, Cu, Pb, and Co.
• Panspermia Hypothesis suggests life's building blocks came from space via meteorites or comets.
• Amino acids and nucleotides and other organic molecules were found on meteorites like the Murchison meteorite.
• The Rosetta mission found methyl chloride in comet 67P, which is an organic compound.
• RNA World Hypothesis suggests that RNA was the first self-replicating molecule and that it stores genetic information and catalyzes chemical reactions.
• Proteins better catalyze reactions.
• Eventually encoded proteins and DNA formed and DNA took over as primary genetic material carrier.
• Today, RNA's role became intermediary directing protein synthesis.
• Formation of first RNA: 2-aminooxazole reacts w/ phosphates to produce nucleotides.
• Double Origin Theory suggests that the development of catalysis and the development of a coding system may have come about separately, and the combination of the two produced life as we know it and that one protocell could have developed the ability to store genetic material and other protocell would have developed ability to perform chemical reactions.
• Both systems eventually combined to create a fully functional living cell.
• Clay-Particle Theory / Hypothesis suggests first life forms on Earth may have emerged on the surfaces of clay minerals, which acted as catalysts and templates for the assembly of complex organic molecules, potentially providing the necessary conditions for the development of early life forms.
• Alexander Graham Cairns-Smith believed clay crystals could have served as a primitive form of genetic material before the evolution of DNA and RNA.
• Clay minerals have a naturally occurring surface structure with active sites that can facilitate chemical reactions, potentially allowing for the polymerization of simple organic molecules into larger, more complex ones.

Cell Structures

• Cells are the basic and smallest structural and functional units of all living organisms.
• All cells contain DNA.
• All living things are made up of cells.
• Total DNA = genome.
• Individual units of heredity = genes.
• The word "cell" comes from the Latin word, "cellula"”, meaning small room.
• Robert Hooke found small box-like structures in 1665.

Prokaryotes (Prokaryotic Cell)

• Prokaryotes resemble the earliest cells and are single-celled organisms that are 1 to 3 um in diameter.
• Prokaryotes lack membrane-bound organelles.
• Prokaryotes have no well-defined nucleus, the only nucleoid present.
• Prokaryotes have granular cytosol due to ribosomes and possess a cell membrane and cell wall.
• Bacteria and cyanobacteria are examples of prokaryotes.

Eukaryotes (Eukaryotic Cell)

• Eukaryotes can be unicellular or multicellular and have a well-defined nucleus with membrane-bound organelles.
• Eukaryotes are larger than prokaryotes, with a diameter in the range of 10 to 100 um and there are examples of single celled organisms like yeasts & Paramecium.

Common to Plant and Animal Cells

• Mitochondrian
• Golgi apparatus
• Rough and smooth endoplasmic reticulum
• Nucleus
• Cytoplasm
• Ribosomes

Plant Cells only

• Cell wall
• Large vacuole
• Chloroplasts
• Flagella only in gametes

Animal Cells only

• No cell wall
• Small or no vacuole
• No chloroplasts
• Flagella

Prokaryotic vs Eukaryotic Cells

• Prokaryotes have a simple structure with no prominent nucleus, of a small size and posses a cell wall has peptidoglycan and small ribosomes and that can be unicellular
• Prokaryotes have no organelles.
• Prokaryotes have examples like bacteria and Archaea.
• Eukaryotes have a complex structure with a prominent nucleus, of a large size and posses cellulose or chitin cell walls and large ribosomes, being unicellular or multicellular.
• Eukaryotes have membrane bounded organelles.
• Eukaryotes types are Human, plant, fungi, and protists.
• All cells contain DNA, cytoplasm, ribosomes with cell membrane

Cell Organelles

• Organelles are membrane-bounded structures within a cell that have distinct functions.
• Organelles enable the cell to live, grow and reproduce.
• The plasma membrane is the cell's defining boundary, provides a barrier, and contains transport and signaling systems.
• The nucleus is the repository of genetic information as contained within the linear sequences of nucleotides in the DNA of chromosomes.
• Almost all DNA undergo replication and RNA synthesis there.
• The nucleolus is a site for synthesis of RNA making up the ribosome.
• The cell wall is commonly found in plant cells & bacteria and its function is to support & protect cells.
• The nuclear membrane surrounds the nucleus, is made of two layers, and openings allow material to enter and leave the nucleus.
• The chromosomes are commonly found in plant cells & bacteria and its function is to support & protect cells.
• The nucleolus is inside the nucleus and contains RNA to build proteins.
• The Endoplasmic reticulum (ER) is the transport network for molecules.
• The rough endoplasmic reticulum (RER) is covered w/ ribosomes (causing the "rough" appearance).
• Ribosomes synthesize proteins for secretion or localization in membranes and are protein and RNA complex responsible for protein synthesis.
• The smooth endoplasmic reticulum (SER) is a site for synthesis and metabolism of lipids.
• Mitochondria are the "power plants" of cells and are surrounded by a double membrane with a series of folds called cristae.
• Mitochondria function in energy production through metabolism.
• The Golgi Apparatus processes and packages macromolecules and contains a series of stacked membranes.
• Vesicles carry materials from the RER to the Golgi apparatus, moving between the stacks while the proteins are being "processed" to a mature form.
• Lysosomes contain digestive enzymes which are membrane bound organelles that degrade proteins and membranes in the cell.
• The cytoplasm is enclosed by the plasma membrane.
• The liquid substance within the cytoplasm is cytosol.
• The cytosol contains membranous organelles.
• Chloroplasts are usually found in plant cells, contain green chlorophyll, and is where photosynthesis takes place.

Classification systems

Five-Kingdom Classification

• Monera
• Protista
• Fungi
• Plantae
• Animalia
• Organisms can be prokaryotic or eukaryotic.
• Prokaryotic organisms are unicellular.
• Eukaryotic organisms are multicellular.
• Organisms can have a cell wall or have no cell wall
• With or without a cell wall, organisms can be phototrophic or heterotrophic.

Three-Domain System

• Bacteria
• Archaea
• Eukarya

Common Elements in Living Organisms

• Most abundant, essential for all organisms: C, N, O, P, S, Η
• Less abundant, essential for all organisms : Na, Mg, K, Ca, CI
• Trace levels, essential for all organism: Mn, Fe, Co, Cu, Zn
• Trace levels, essential for some organisms: V, Cr, Mo, B, Al, Ga, Sn, Si, As, Se, I

Structural Hierarchy in the Molecular Organization of Cells

• Level 1: monomeric units.

• Level 2: macromolecules.

• Level 3: supramolecular complexes.

• Level 4: the cell and its organelles.

• There are many important biomolecules are polymers.

• Lipids consist of a monomer fatty acid forms a polymer phospholipid builds into a supramolecular structure known as membrane.

• Proteins are built of amino acid monomer to form a protein subunit polymer and further to form protein complex supramolecular structure.

• Carbohydrates built of a glucose monomer and cellulose chains polymer forming cell wall supramolecular structure.

• Nucleic acids built of nucleotide monomers and DNA polymer forming chromosome supramolecular structure.

Functional Groups of Biochemical Importance

• Alkenes; General Structure of RCH=CH₂, RCH=CHR, R₂C=CHR, R₂C=CR₂ with C=C Characteristic Functional Group bond.
• Alcohols; General Structure of ROH with Hydroxyl group (-OH) is the Characteristic Functional Group.
• Ethers; General Structure of ROR with Ether group (-O-) is the Characteristic Functional Group.
• Amines; General Structure of RNH₂, R₂NH, RN with Amino group (N) is the Characteristic Functional Group.
• Thiols; General Structure of RSH with Sulfhydryl group (-SH) is the Characteristic Functional Group.
• Aldehydes; General Structure of R-C-H with Carbonyl group (C) is the Characteristic Functional Group.
• Ketones; General Structure of R-C-R with Carbonyl group (C) is the Characteristic Functional Group.
• Carboxylic acids; General Structure of R-C-OH with Carboxyl group (C-OH) is the Characteristic Functional Group.
• Esters; General Structure of R-C-OR with Ester group (C-OR) is the Characteristic Functional Group.
• Amides; General Structure of R-C-NR₂, R-C-NHR, R-C-NH₂ with Amide group (C-N) is the Characteristic Functional Group.
• Phosphoric acid esters; General Structure of R-O-P-OH with Phosphoric ester group (O-P-OH) is the Characteristic Functional Group.
• Phosphoric acid anhydrides; General Structure of R-O-P-O-P-OH with Phosphoric anhydride group P or HO-P-O-P-OH is the Characteristic Functional Group.

Hydrocarbon Functional Groups

• Alkane: Single carbon-carbon bonds (C-C)
• Alkene: Carbon-carbon double bond (C=C)
• Alkyne: Carbon-carbon triple bond (C=C)
• Aromatic (Arene): Benzene ring (C6H5), with alternating single and double bonds in a ring structure.

Other Functional Groups

• Alcohol: Hydroxyl group (-OH) bonded to a carbon atom
• Ether: Oxygen atom bonded to two carbon atoms (-O-)
• Peroxide: Two oxygen atoms bonded to each other (-O-O-)
• Amine: Nitrogen atom bonded to one, two, or three alkyl or aryl groups (-NH2, -NHR, -NR2).
• Nitrile: Carbon-nitrogen triple bond (-C=N)
• Imine: Carbon-nitrogen double bond (-C=N)
• Thiol (Mercaptan): Sulfhydryl group (-SH) bonded to a carbon atom
• Thioether (Sulfide): Sulfur atom bonded to two carbon atoms (-S-)
• Disulfide: Two sulfur atoms bonded to each other (-S-S-)
• Phosphate: Phosphorus atom bonded to four oxygen atoms (-PO₄³¯)
• Phosphoric Acid Ester (Phosphoester): Phosphate group bonded to an organic group
• Halide: Carbon bonded to a halogen (F, Cl, Br, I)
• Azide: Nitrogen chain (-N3)
• Epoxide: Three-membered cyclic ether
• Isocyanate: -N=C=O group
• Aldehyde: Carbonyl group (C=O) bonded to at least one hydrogen atom
• Ketone: Carbonyl group bonded to two carbon atoms
• Carboxylic Acid: Carbonyl group bonded to a hydroxyl group (-COOH).
• Ester: Carbonyl group bonded to an alkoxy group (-COOR)
• Amide: Carbonyl group bonded to a nitrogen atom (-CONH2, -CONHR, -CONR2)
• Acid Anhydride: Two carbonyl groups bonded to an oxygen atom (-CO-O-CO-)
• Acyl Chloride (Acid Chloride): Carbonyl group bonded to a chlorine atom (-COCI)

Common Types of Reactions in Living Organisms

• Synthesis Reactions (ANABOLISM)
• Decomposition Reactions (CATABOLISM)
• Reduction - Oxidation Reactions (REDOX)
• Condensation Reactions (DEHYDRATION SYNTHESIS)
• Hydrolysis Reactions
• Phosphorylation Reactions
• Isomerization Reactions

Anabolism (Synthesis Reactions)

• Smaller molecules (monomers) combine to form larger, more complex molecules (polymers).
• These reactions are typically endergonic (require energy input), and the energy is often derived from adenosine triphosphate (ATP)
• e.g. Protein Synthesis (Peptide Bond Formation), DNA Synthesis
• Anabolism is useful for building cellular structures & growth and development

Catabolism

• Catabolism (Decomposition Reactions) are also known as catabolic reactions and they involve the breakdown of larger, more complex molecules into smaller, simpler ones.
• Examples of reactions are typically exergonic because they release energy.
• Cells use exergonic reactions for various functions such as movement, growth, and repair.
• For example Glycolysis.
• Catabolism is critical for energy production, recycling of cellular components, and providing substrates for biosynthesis

Reduction – oxidation Reactions (REDOX)

• Involve the transfer of electrons between molecules
• These reactions are vital for cellular respiration, photosynthesis, and other metabolic pathways
• In redox reactions, one molecule loses electrons (oxidized), while another gains electrons (reduced)
• Key to energy conversion, maintaining oxidative balance and regulating metabolic pathways, and antioxidant defense and cellular signaling

Condensation Reactions

• Involve the joining of two molecules with the removal of a water molecule.
• Condensation is a type of synthesis reaction
• Condensation is important for building polymers from monomers and in peptide bond formation, glycosidic bond formation.
• Condensation is useful in polymerization and storage of energy in cells.

Hydrolysis Reactions

• The reverse of condensation reactions include breaking down complex molecules into simpler ones with the addition of water
• Essential in digestion and metabolic breakdown processes eg ATP Hydrolysis, Digestion of carbohydrates
• Necessary for enzyme regulation, metabolic regulation and nutrient absorption, and the breaking down of macromolecules for energy or recycling

Phosphorylation Reactions

• Involve the addition of a phosphate group (PO4³¯) to a molecule
• Phosphorylation is often used to activate or deactivate enzymes, transport molecules, or store energy.
• An example of phosphorylation is ATP Formation & Protein Phosphorylation
• Phosphorylation is critical for energy storage and transfer, cellular signaling, and enzyme regulation and metabolic control.

Isomerization Reactions

• Involve the rearrangement of atoms within a molecule to form isomers.
• Reactions in this process have the same molecular formula but a different structure
• An example is the conversion of Glucose-6-Phosphate to Fructose-6-Phosphate and the isomerization of Cis- and Trans- Fatty Acids
• Essential for metabolic pathways, structural diversity, and regulating the function of biologically active molecules