Introduction to Biochemistry

What is Biochemistry?

• It is the chemistry of the living cell.
• Biochemistry describes the structures, mechanisms, functions, and chemical processes in molecular terms.
• It provides a fundamental and broad understanding of the molecular basis of life and the function of living things.
• Biochemistry explains how disease is produced.
• The term "Biochemistry" was introduced by Carl Neuberg in 1903.
• Biochemistry deals with the chemistry of life and living processes.
• The scope of biochemistry encompasses every aspect of life, including birth, growth, reproduction, aging, and death.
• Every movement of life is packed with hundreds of biochemical reactions.
• Has become the most rapidly developing and innovative subject in medicine
• The major share of Nobel Prizes earmarked for Medicine and Physiology has gone to biochemistry researchers.
• Biochemistry serves as a guiding light to trace the intricacies of biology and unravel the chemical mysteries of life.
• All living things are closely related at the molecular level.
• Is the subject of unity in the diversified living kingdom.
• Advances in biochemistry have had a tremendous impact on human welfare.
• Benefits include the application of biochemistry in the laboratory for disease diagnosis, genetic engineering products like insulin, interferon, and growth hormone, and the potential use of gene therapy.

Elements of Life

• Living matter consists mainly of carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur.
• These elements constitute about 90% of the dry weight of the human body.
• Other functionally important elements found in cells include Ca, K, Na, Cl, Mg, Fe, Cu, Co, I, Zn, F, Mo, and Se.

Examples of Biochemistry

• The chemical structures of biomolecules.
• Interactions leading to the formation of supermacro-molecules, cells, multicellular tissues, and organisms.
• Bioenergetics of reactions in the cell.
• Storage and transmission of information.
• Chemical changes during reproduction, aging, and cell death.
• Regulation of chemical reactions inside living cells.

Principal Areas of Biochemistry

• Concerned with the structure-function relationship

Structural Chemistry

• Focuses on proteins, carbohydrates, DNA/RNA, lipids, and every other component in the cell.
• Examining the functions of these components
• Understanding the relationship between structure and function

Metabolism

• Processes and pathways
• Catabolism: Pathways of chemical reactions leading to the breakdown of molecules
• Anabolism: Pathways of chemical reactions leading to the synthesis of molecules.
• Involves the bioenergetics of reactions and the management of cellular energy.

Cellular Communication

• The storage, transmission, and expression of genetic information
• DNA replication and protein synthesis.
• How cells communicate and interact
• Signal Transduction.

History of Biochemistry

• Biochemistry is a relatively young science, only about 100 years old.
• 1828: Wohler synthesized urea from ammonium cyanate, bridging inorganic and organic chemistry.
• 1869: Miescher isolated nucleic acids
• 1897: Buchner: in vitro experiment with cell extracts.
• 1925: The glycolytic pathway was revealed.
• 1926: Sumner crystallized urease.
• 1937: Krebs elucidated the citric acid cycle.
• 1944: Avery, MacLeod, and McCarty showed DNA to be the agent of genetic transformation.
• 1953: Watson and Crick proposed the double helix for DNA.
• 1959: Determined the 3-D structure of hemoglobin.
• 1966: The genetic codes were unveiled.
• 1970: PCR & Recombinant DNA technologies developed.
• 1990: Gene Therapy emerged.

The Origin of Life

• Living matter consists of chemical elements that bind together to form molecules.
• Most compounds in biological systems are organic, containing carbon.
• Chemical compounds have reactive functional groups that participate in biological structure and biochemical reactions.
• Polymerization of organic molecules forms more complex structures through condensation reactions, removing water.
• Membranes are key to the origin of living matter, separating critical molecules needed for replication and energy capture.
• Larger polymers form macromolecules, providing biological specificity to living matter, e.g., carbohydrates, proteins, lipids, DNA, and RNA.

Biological Hierarchies

• Simple molecules are used to build complex structures.
• The hierarchy includes elements, molecules, cells, tissues, organs, organisms, populations, species, and the biosphere.
• Relative sizes vary for biological entities, with tools used to resolve them.
• The scale is logarithmic.
• 1 m = 10 dm = 100 cm = 1000mm = 10⁶ m = 10⁹ nm = 10¹⁰ Å

The Cell Theory

• Developed in the 1600-1800s, describes the basic principles of cells.
• The cell is the smallest structural and functional unit of living matter.
• All organisms are composed of one or more types of cells.
• All cells come from pre-existing cells by division, rejecting spontaneous generation.
• Cells are capable of reproduction.
• Cells contain hereditary information passed from cell to cell during cell division.
• All energy flow (metabolism and biochemistry) of life occurs within cells.

Typical Cells

• Cells from different organisms have different shapes, structures, and sizes.
• All cells have protoplasm.
• Cells are usually divided into two broad groups: Eukaryotes and Prokaryotes.

Eukaryotic Cells

• Possess a membrane-bound nucleus and a variety of organelles and internal membranes.
• Have a true nucleus.

Prokaryotic Cells

• Smaller (generally)
• Lack much of the internal compartmentalization and complexity of eukaryotic cells.
• Have no membrane-bound nucleus or other organelles.

Viruses

• Do not always conform to cell theory
• One or more of the basic cell components is missing
• Inside the host cell, viruses are living matters.

Prokaryotes

• Exhibit a limited range of morphologies but diverse metabolic capabilities.
• Are often single-celled organisms.
• Lack a true nucleus or organelles.
• Most have circular or "looped” DNA, lack internal membranous compartmentalization
• Are divided into two major lineages: Eubacteria and Archaebacteria.

Eubacteria

• Inhabit soils, surface waters, and the tissues of other living or decaying organisms
• Includes well-studied bacteria like Escherichia coli.

Archaebacteria

• Inhabit extreme environments-salt lakes, hot springs, highly acidic bogs, and the ocean depths.
• Includes:
  • Methanogens (oxygen-free milieus)
  • Halophiles (require high concentrations of salt)
  • Thermophiles (live in hot regions, 80°C, in a pH< 2)

Eukaryotic Cells

• Found in Animal, Plant, Protists, and Fungi kingdoms
• Few are single-celled; the majority are multicellular
• Are complex cells.
• Specialized in different sizes, shapes, and structures.
• Have a membrane-bound nucleus that contains the cell's genetic material (DNA).
• Contain organelles, each surrounded by a membrane or two (e.g., lysosome, Golgi bodies, endoplasmic reticulum, mitochondria).
• DNA is organized in linear structures (chromosomes) associated with proteins (histones)
• Not all unicellular organisms are eukaryotes because bacteria are unicellular prokaryotic organisms
• All multicellular organisms are eukaryotes