The Chemical Basis of Life PDF

1.The Chemical Basis of Life 1.1 Introduction  What is Biochemistry? ❑ Biochemistry is the scientific discipline that seeks to explain life at the molecular level. It offers answers to such fundamental questions as: ✔ “What are we made of ?” and ✔ “How do we work?” ❑ Biochemist...

1.The Chemical Basis of Life 1.1 Introduction  What is Biochemistry? ❑ Biochemistry is the scientific discipline that seeks to explain life at the molecular level. It offers answers to such fundamental questions as: ✔ “What are we made of ?” and ✔ “How do we work?” ❑ Biochemistry is also a practical science: ✔ It generates powerful techniques that underlie advances in other fields, such as genetics, cell biology, and immunology; ✔ It offers insights into the treatment of diseases such as cancer and diabetes; and ✔ It improves the efficiency of industries such as wastewater treatment, food production, and drug manufacturing. ❑ Biochemistry has traditionally been a science of  Elements found in biological systems ❑ An element is a pure substance which cannot be broken down by chemical means, consisting of atoms (the basic chemical units). ❑ Only a small subset of the known elements are found in living systems. ❑ The most abundant of these elements are: C, N, O, and H, followed by Ca, P, K, S, Cl, Na, and Mg. ❑ Certain trace elements are also present in very small quantities. ❑ Virtually all the molecules in a living organism contain carbon, in addition they are also constructed from H, N, O, P, and S. Most of these molecules belong to one of a few structural classes, known as functional groups.  The most abundant elements are most darkly shaded; trace elements are most lightly shaded. Figure Courtesy: Essential Biochemistry  Biological ❑ Biological molecules are Molecules composed of a subset of all possible elements and functional groups. ❑ Cells contain four major types of biological molecules: 1. Amino Acids The simplest compounds are the amino acids, so named because they contain an amino group (-NH2) and a carboxylic acid group (-COOH). 2. Carbohydrates Simple carbohydrates (also called monosaccharides or just sugars) have the formula (CH2O)n. 3. Nucleotides A five-carbon sugar, a nitrogen-containing ring (bases), and one or more phosphate groups are the components of nucleotides. For example, adenosine triphosphate (ATP) contains the nitrogenous group adenine linked to the monosaccharide ribose, to which a  Figure courtesy: Essential Biochemistry ❑ The most common nucleotides are mono-, di-, and triphosphates containing the nitrogenous ring compounds (or “bases”) adenine, cytosine, guanine, thymine, or uracil (abbreviated A, C, G, T, and U). 4. Lipids The fourth major group of biomolecules consists of the lipids. These compounds cannot be described by a single structural formula since they are a diverse collection of molecules. However, they all have in common a tendency to be poorly  Biological Polymers ❑ The universal feature of nature: A few kinds of building blocks can be combined in different ways to produce a wide variety of larger structures. These larger structures are known as “Macromolecules”. ❑ Generally, macromolecules are “polymers”-made up of “monomers”-the building block, or subunit of a large molecule. ❑ Amino acids, monosaccharides, and nucleotides each form polymeric structures with widely varying properties. In most cases, the individual monomers become covalently linked in head-to-tail fashion. ❑ The linkage between monomeric units is characteristic of each type of polymer. The monomers are called residues after they have been incorporated into the polymer. ❑ Lipids do not form polymers, although they do tend to aggregate to Figure courtesy: Essential Biochemistry  There are three major kinds of biological polymers 1. Proteins Polymers of amino acids are called polypeptides or proteins. The amino acid residues are linked to each other by amide bonds called peptide bonds. Proteins are the most structurally variable and therefore, the most functionally versatile of all the biopolymers.  There are three major kinds of biological polymers 2. Nucleic Acids ❑ Polymers of nucleotides are termed polynucleotides or nucleic acids, better known as DNA and RNA. ❑ Each nucleic acid is made from just four different nucleotides: the residues in RNA contain the bases adenine, cytosine, guanine, and uracil, whereas the residues in DNA contain adenine, cytosine, guanine, and thymine. ❑ Polymerization involves the phosphate and sugar groups of the nucleotides, which become linked by phosphodiester bonds. ❑ Nucleic acids tend to have more regular structures than proteins. This is in keeping with their primary role as carriers  There are three major kinds of biological polymers 3. Polysaccharides ❑ Polysaccharides usually contain only one or a few different types of monosaccharide residues. ❑ As polysaccharides are homogeneous in nature, tends to limit their potential for carrying genetic information in the sequence of their residues (as nucleic acids do) or for adopting a large variety of shapes and mediating chemical reactions (as proteins do). Polysaccharides perform essential cell functions by serving as fuel-storage molecules and by providing structural support. 1.The Chemical Basis of Life 1.2 Energy and Metabolism  Purpose of ❑ In order to stay alive Energy and to reproduce themselves--living organisms and cells must need to perform work. In fact, cells require energy for all the functions of living, growing, and reproducing. ❑ They require energy to assemble small molecules into polymeric macromolecules. ❑ And unless the monomeric units are readily available, a cell must synthesize the monomers, which also requires energy. ❑ Cellular processes such as the building and breaking down of complex molecules occur through stepwise chemical reactions. Some of these chemical reactions are spontaneous and release energy, whereas others require energy to proceed. ❑ All of the chemical reactions that take place inside cells, including those that use energy and those that release energy, are collectively known as the cell’s metabolism.  Evolution of Metabolic Pathways ❑ Metabolism is a complex process, and the complexity varies from organism to organism. ❑ The origin and evolution of metabolic pathways allowed primitive cells to become more chemically independent from the prebiotic sources of essential molecules. ❑ The mechanism of emergence of new metabolic processes would imply recycling and modifying of old molecular entities, e.g., oxygenic from anoxygenic photosyntheses or aerobic from anaerobic respirations.  Metabolic Pathways: Anabolic & Catabolic There are two types of metabolic pathways that are characterized by their ability to either synthesize molecules with the utilization of energy (anabolic pathway) or break down of complex molecules by releasing energy in the process (catabolic pathway).  Anabolic Pathway ❑ Requires an input of energy to synthesize complex molecules from simpler ones. ❑ Examples: ✔ Synthesizing sugar from CO2 ✔ Synthesis of large proteins from amino acid building blocks, and ✔ The synthesis of new DNA strands from nucleic acid building blocks. ❑ All these biosynthetic processes are critical to the life of the cell, take place constantly, and demand energy provided by ATP and other high-energy molecules like NADH (nicotinamide adenine dinucleotide) and NADPH  Catabolic Pathway ❑ Catabolic pathways involve the degradation (or breakdown) of complex molecules into simpler ones. ❑ Molecular energy stored in the bonds of complex molecules is released in catabolic pathways and harvested in such a way that it can be used to produce ATP (adenosine ❖ ATP is the primary energy currency triphosphate, or ATP). of the cell. It has an adenosine backbone with three phosphate ❑ Other energy-storing groups attached. molecules, such as fats, are also broken down through similar catabolic reactions to release energy Figure Courtesy:  Evolution of Organism Despite the differences between organisms and the complexity of metabolism, researchers have found that all branches of life share some of the same metabolic pathways, suggesting that all organisms evolved from the same ancient common ancestor. Evidence indicates that over time, the pathways diverged, adding specialized enzymes to allow organisms to better adapt to their environment, thus increasing their chance to survive. However, the underlying principle remains that all organisms must harvest energy from their environment and convert it to ATP to carry out cellular functions. 1.The Chemical Basis of Life 1.3 The origin and Evolution of Life Subcellular fractionation of cells Figure 1-8: Subcellular fractionation of tissue. ✔ Mechanically homogenize tissue to break the cell components,. ✔ Cell components dispersed into the buffer solution. ✔ Different speed of centrifugation isolate differentare Microsomes cell component. artificial structures derived from pieces of endoplasmic reticulum formed during tissue homogenization.  Cells are the structural and functional units of all living organism Fig 1-3: The universal features if living cells. ❖ All cells have a nucleus or nucleoid, a plasma membrane and cytoplasm. ❖ The cytosol is the portion of cytoplasm that remains in the supernatant after breakage of plasma membrane. ❖ Centrifugation of the resulting extract at 150,000 g for 1 hour. g is the relative centrifugal force The Earth’s Present Life- The earth’sForms present-day life-forms are of two types, which are distinguished by their cellular architecture: 1. Prokaryotes are small unicellular organisms that lack a discrete nucleus and usually contain no internal membrane systems. This group comprises two subgroups : the eubacteria (usually just called bacteria), exemplified by E. coli, and the archaea (or archaebacteria), best known as organisms that inhabit extreme environments. 2. Eukaryotic cells are usually larger than prokaryotic cells and contain a nucleus and other membrane-bounded cellular compartments (such as mitochondria, chloroplasts, and endoplasmic reticulum). Eukaryotes may be unicellular or multicellular. This group (also called the eukarya) includes microscopic organisms as well as familiar macroscopic plants and animals  Three Domains of Life Differences in cellular and molecular level define three distinct domains of life. The basis of this tree is the nucleotide sequence of ribosomal RNA. The more similar the sequence the more closer the branch Phylogeny of the three domains of life  Characteristics Eukaryotic cells Prokaryotic cells Definition Any cell that contains a clearly Any unicellular organism that defined nucleus and membrane does not contain a membrane bound organelles bound nucleus or organelles Examples Animal, plant, fungi and protist cells Bacteria and Archaea Nucleus Present (membrane bound) Absent (nucleoid region) Cell size Large (10-100 micrometers) Small ( less than a micrometer to 5 micrometers) DNA Replication Highly regulated with selective Replicates entire genome at origins and sequences once Organism type Usually multicellular Unicellular Chromosomes More than one One long single loop of DNA and plasmids Ribosomes Large (70s and 80s) Small (70s only) Growth Rate/ Generation Slower Faster Time Organelles Present Absent Characteristic Prokaryotic cell Eukaryotic cell Size Generally small (1-10 μm) Generally large (5-100 μm) Genome DNA with nonhistone protein: DNA complexed with histone and nonhistone Genome in nucleoid, not proteins in chromosomes: Chromosomes in surrounded by membrane nucleus with membranous envelope Cell division Fission or budding: no mitosis Mitosis, including mitotic spindle; centrioles in many species Membrane bound Absent Mitochondria, chloroplasts (in plants, some organelles algae), endoplasmic reticulum, Golgi complexes, lysosomes (in animals) etc. Nutrition Absorption; some Absorption, ingestion; photosynthesis in some photosynthesis species Energy No mitochondria; oxidative Oxidative enzymes packaged in mitochondria; metabolism enzymes bound to plasma more unified pattern of oxidative metabolism membrane; great variation in metabolic patter Cytoskeleton None Complex, with microtubules. intermediate filaments, actin filaments Intracellular None Cytoplasmic streaming, endocytosis, movement phagocytosis, mitosis, vesicle transport  Components of Bacterial Structure Cell Composition Function Cell Wall Peptidoglycan Mechanical support Cell membrane Lipid + Protein Permeability barrier Nucleoid DNA + Protein Genetic information Ribosomes RNA + Protein Protein synthesis Pili Protein Adhesion, conjugation Flagella Protein Motility Cytoplasm Aqueous solution Site of metabolism ❖ There are two subunits of prokaryotic ribosomes (50-S and 30-S type). 50-S and 30-S are the large and small subunits of bacteria that colloquially constitute the 70-S type of ribosome. ❖ Eukaryotic ribosomes have two unequal subunits, designated small subunit (40S) and large subunit (60S), combinedly 80 S. ❖ The variation is due to the variation in sedimentation while centrifugation.  ❑ Eukaryotic cells may have evolved when multiple cells joined into one. They began to live in what we call symbiotic relationships. The theory that explains how this could have happened is called endosymbiotic theory. ❑ The mitochondrion and the chloroplast are both organelles that were once free-living cells. They were prokaryotes that ended up inside of other cells (host cells). They may have joined the other cell by being eaten (a process called phagocytosis), or perhaps they were parasites of that host cell. ❑ During the 1950s and 60s, scientists found that both mitochondria and plastids inside plant cells had their own DNA. It was different from the rest of the plant cell DNA. ❑ A scientist named Lynn Margulis put all this information together and published it in 1967. Her paper is called “On the origin of mitosing cells”. Two main Endosymbiotic tenets of Margulis’s theory, that Theory mitochondria are the descendants of  Endosymbi osis Endosymbiosis a type of symbiosis in which one organism lives inside the other, the two typically behaving as a single organism. ❖ The hypothesised process by which prokaryotes gave rise to the first eukaryotic cells is known as endosymbiosis. ❖ Endosymbiosis also explains the origin of mitochondria and chloroplast. ❖ Eukaryotic cells are believed to have evolved from early prokaryotes that were engulfed by phagocytosis.  Evolution of eukaryotes through endosymbiosis. Figure courtesy: Principle of  Evide ❑ Membrane: Mitochondria nce and chloroplast have their own cell membranes, just like a prokaryotic cell does. ❑ Ribosomes: Ribosomes found in eukaryotic organelles such as mitochondria or chloroplasts have 70S ribosomes—the same size as prokaryotic ribosomes. ❑ DNA: Each mitochondrion and chloroplast has its own circular DNA genome, like a bacteria's genome, but much smaller. This DNA of the chloroplast is very similar to photosynthetic blue-green bacteria, Binary while the mitochondrion DNA is very fission similar to the aerobic bacteria. ❑ Replication: Mitochondria and chloroplast reproduce by pinching in half (binary  The Prebiotic World ❑ A combination of theory and experimental data leads to several plausible scenarios for the emergence of life from non-biological (prebiotic) materials on the early earth. ❑ One theory holds that Earth's early atmosphere was highly reduced, rich in methane (CH4), ammonia (NH3), water (H2O), and hydrogen (H2), and that this atmosphere was subjected to large amounts of solar radiation and lightning.  The Miller-Urey Experiment ❑ In the 1930s, Oparin and Haldane independently suggested that ultraviolet radiation from the sun or lightning discharges caused the molecules of the primordial atmosphere to react to form simple organic (carbon-containing) compounds. ❑ This process was replicated in 1953 by Stanley Miller and Harold Urey, who subjected a mixture of H2O, CH4, NH3, and H2 to an electric discharge for about a week. The resulting solution contained water-soluble organic compounds, including several amino acids (which are components of proteins) and other biochemically significant compounds. Courtesy: Problem Associated With Miller- Urey Experiment ❑ The gases they used (a reactive mixture of methane and ammonia) did not exist in large amounts on early Earth. On the other hand, modern scientists believe the primeval atmosphere contained an inert mix of carbon dioxide and nitrogen. ❑ In 1983, Miller repeated the experiment with correct combo and the resulted mixture created a colorless brew containing few amino acids. ❑ Miller’s student, Jeffry Bada noticed that the reaction actually produced chemicals like nitrites which, ✔ destroy amino acids as quickly as they form. ✔ water acidic—which prevents amino acids from forming. ❑ Bada reran the experiment adding iron and carbonate minerals, thought to neutralize nitrites and acids in primitive earth. He still got the same watery liquid as Miller did in 1983, but this time it was chock-full of amino acids. ❑ So, this result moves toward more realism in terms of what the conditions were on early Earth." ❑ A new study, titled “Selective prebiotic formation of RNA pyrimidine and DNA purine nucleosides,” appeared June 3 in Nature. ❑ According to the new finding, “The nucleic acids, RNA and DNA, are clearly related,” and they both derive from a hybrid ancestor, rather than one preceding the other.  MCQ (Practice) Select one answer only 1. General formulae for 2. Which one is the universal ce glucose – component? a) (CH2O)n a) Nucleus b) (C2H2O)n b) Nucleoid c) (CH2O2)n c) Cell wall and cytoplasm d) None of the above d) Plasma membrane 3. Which of the following organelles 4. A living that come to eukaryotic cells via organism is an endosymbiosis? a) Open system a) Mitochondria and ribosome b) Closed system b) Chromosome and cell wall c) Isolated system c) Lysosome and plastid d) All of the above d) Chloroplast and mitochondria  Summa 1. rymake it a central part of The unique properties of carbon biological molecules. 2. Carbon binds to oxygen, hydrogen, and nitrogen covalently to form the many molecules important for cellular function. 3. Cells perform the functions of life through various chemical reactions. 4. A cell’s metabolism refers to the chemical reactions that take place within it. 5. There are two metabolic pathways: catabolism and anabolism. 6. Catabolism is associated with release of energy. On the other hand, anabolic processes require energy. 7. Energy comes in many different forms. 8. System refers to the matter and its environment involved in energy transfers. Everything outside of the system is called the surroundings. Single cells are biological systems. 9. The first law of thermodynamics states that the total amount of energy in the universe is constant. 10. The second law of thermodynamics states that every energy transfer involves some loss of energy in an unusable form, resulting in a more disordered system. 11. The free energy of a system is determined by its enthalpy and entropy. 12. Living organisms obey the laws of thermodynamics.