Biochemistry: The Molecular Basis of Life - Chapter 1 PDF

TRUDY MCKEE JAMES R. MCKEE Chapter 1 Biochemistry: An Introduction  Online Video Redox Reactions Section 1.3 Reduction (gaining electrons) and oxidation (the loss of electrons) combine to form redox chemistry, which contains...

TRUDY MCKEE JAMES R. MCKEE Chapter 1 Biochemistry: An Introduction  Online Video Redox Reactions Section 1.3 Reduction (gaining electrons) and oxidation (the loss of electrons) combine to form redox chemistry, which contains the majority of chemical reactions. As electrons jump from atom to atom, they carry energy with them, and that transfer of energy is indispensible for life. From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Online Video Overview of Amino Acid Metabolism Section 1.3 Metabolism is the sum of all the enzyme-catalyzed reactions in a living organism. These reactions are organized into pathways in which an initial reactant molecule is modified in a step-by-step sequence into a product that can be used by the cell for a specific purpose. From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Biochemistry : An Introduction Chapter 1 Overview Life: It is a Mystery! Section 1.1: What Is Life? Section 1.2: Biomolecules Section 1.3: Is the Living Cell a Chemical Factory? From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Life: It is a Mystery! Life: It is a Mystery! Why study biochemistry? Foundation upon which all of the modern life sciences are built Life and its Diversity Life is Resilient  Biochemistry: is the foundation upon which all of the modern life sciences are built  Biochemistry: has provided the life sciences with biochemical knowledge for living processes at the molecular level From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.1: What Is Life? All Life Obeys the Same Chemical and Physical Laws: Life is complex and dynamic Life is organized and self- sustaining Life is cellular Life is information-based Life adapts and evolves Figure 1.1 Hierarchical Organization From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.2: Biomolecules Living organisms composed of inorganic and organic molecules Water is the matrix of life, may constitute 50 to 95% of a cell’s content Biomolecules: are organic (carbon-based) molecules synthesized by living organisms, classified as: proteins, carbohydrates, lipids, and nucleic acids  there are hundreds of biochemical reactions (divided into biochemical pathways) catalyzed by enzymes that maintain life Six principal elements: carbon (C), hydrogen (H), oxygen (O), nitrogen (N), phosphorous (P), and sulfur (S) Other elements are also important (i.e., Na+, K+, Mg2+, and Ca2+) Biomolecules are derived from hydrocarbons Carbon forms four strong covalent bonds Organic molecules can form three complex shapes: straight structures, branched chains, or rings  Biochemical properties are determined by their functional groups https://www.youtube.com/watch?v=H8WJ2KENlK0 From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.2: Biomolecules Figure 1.2 Hydrocarbon Structural Formulas Functional Groups of Organic Biomolecules Most organic molecules are derived from hydrocarbons Hydrocarbons are carbon- and hydrogen-containing compounds that are hydrophobic (water-insoluble) Their chemical properties are determined by functional groups Section 1.2: Biomolecules  Section 1.2: Biomolecules Major Classes of Small Biomolecules Many organic molecules are relatively small (less than 1000 Daltons (Da)) Families of small molecules: amino acids, sugars, fatty acids, and nucleotides Some molecules have special biological functions, e.g. ATP.  Section 1.2: Biomolecules Figure 1.3 General Formula for α-Amino Acids  Amino Acids and Proteins Examples of Nonstandard amino Acids Hundreds of naturally occurring amino acids, but only twenty amino acids occur in proteins Classified α, β, or γ according to amino group location The most common type are α-amino acids From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.2: Biomolecules Figure 1.4 Structural Formulas for Several α-Amino Acids From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.2: Biomolecules Figure 1.5 Select Examples of Naturally Occurring Amino Acids That Are Not α-Amino Acids: β- Alanine and γ-Aminobutyric Acid (GABA) Amino Acids and Proteins There are also many naturally occurring amino acids that are not α-amino acids β-Alanine: a precursor of the vitamin pantothenic acid γ-Aminobutyric acid: a neurotransmitter From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.2: Biomolecules Figure 1.6 Structure of Met-Enkephalin, a Pentapeptide Amino Acids and Proteins Amino acids are connected via peptide bonds Amino acid R groups lead to structure and function of proteins From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.2: Biomolecules Amino Acids and Proteins Chemical properties of amino acids depend on hydrophobic or hydrophilic side chains, or R groups Amino acids used to make long polymers, or polypeptides (proteins) Proteins consist of one or more polypeptides Figure 1.7 Polypeptide Structure From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.2: Biomolecules Figure 1.8 Some Biologically Important Monosaccharides Sugars and Carbohydrates Alcohol and carbonyl functional groups Two types of carbohydrates: aldoses and ketoses Range from monosaccharides to polysaccharides From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.2: Biomolecules Figure 1.9 Fatty Acid Structure Fatty Acids There are two types of fatty acids: saturated and unsaturated Very few fatty acids occur independently; most are components of lipids (e.g., triacylglycerol) From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press Figure 1.10 Lipid Molecules That Contain Fatty Acids (a) Triacylglycerol. (b) Phosphatidylcholine, a type of phosphoglyceride.  Section 1.2: Biomolecules Nucleotides and Nucleic Acids Nucleotides are composed of a five-carbon sugar, nitrogenous base, and one or more phosphate groups Two classes of base: purine and pyrimidine Nucleotides are involved in DNA and RNA biosynthesis Figure 1.11 Nucleotide Structure From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.2: Biomolecules DNA DNA (deoxyribonucleic acid) encodes the genetic information of an organism DNA structure: two antiparallel polynucleotide strands forming a right-handed double helix Four basic DNA nucleotides: adenine, guanine, thymine, and cytosine DNA strands are held together by hydrogen bonds and hydrophobic interactions An organism’s entire set of DNA sequences is called its genome From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.2: Biomolecules Figure 1.12 The Nitrogenous Bases: Purines Figure 1.14 The Nitrogenous Bases: Pyrimidines From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.2: Biomolecules Figure 1.13 DNA From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.2: Biomolecules RNA RNA is a single-stranded polynucleotide with ribose instead of deoxyribose RNA is synthesized via transcription using the four principal bases: adenine, cytosine, guanine, and uracil There are three types of RNA involved in protein synthesis: mRNA, rRNA and tRNA Several types of noncoding RNA: siRNA, miRNA, snRNA, snoRNA and IncRNA From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.2: Biomolecules Gene Expression Gene expression controls when the information encoded in a gene will be accessed A class of proteins called transcription factors that contribute to protein-coding gene expression From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.3: Is the Living Cell a Chemical Factory? The properties of even the simplest cells are remarkable Autopoiesis: living organisms are self-organizing, and self- maintaining Autopoiesis has been coined to describe the remarkable properties of living organisms The functional properties of thousands of enzymes make possible the process of metabolism Metabolism is defined as: The acquisition and utilization of energy Synthesis of molecules needed for cell structure and function Growth and development Removal of waste products From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.3: Is the Living Cell a Chemical Factory? Biochemical Reactions 1. Although the number of reactions is large, the types of biochemical reactions is relatively small. 2. Biochemical reactions have simple organic reaction mechanisms. 3. The biochemical reactions that are used in energy production and the synthesis and degradation of major cell components are relatively few  The most common reaction types in biochemical processes are: nucleophilic substitution, elimination, addition, isomerization, and oxidation-reduction reactions. From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press Section 1.3: Is the Living Cell a Chemical Factory? Biochemical Reactions 1. In a nucleophilic substitution reaction, an atom with an unshared pair of electrons displaces a leaving group where A: is the nucleophile and X: is the leaving group  nucleophiles (A:): are anions (negatively charged atoms or groups) or neutral species having nonbonding electron pairs (such as H2O)  A (nucleophile) binds to B (electrophile, electrons deficient)  Electrophile: easily attacked by a nucleophile. https://www.youtube.com/watch?v=QAyriElN-30 From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press Section 1.3: Is the Living Cell a Chemical Factory? Biochemical Reactions Nucleophilic substitution reaction: An important type is a hydrolysis (hydration) reaction - Oxygen of water molecules acts as the nucleophile. From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.3: Is the Living Cell a Chemical Factory?  a covalent bond is cleaved, group removed, cleavage site is replaced by a water molecule (hydrolysis) ATP + H2O → ADP + HPO42– (Pi) Figure 1.15 A Hydrolysis Reaction From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press Section 1.3: Is the Living Cell a Chemical Factory? Biochemical Reactions Continued 2. An elimination reaction forms a double bond when atoms in a molecule are removed - Elimination Reactions is seen in dehydration reactions  a covalent bond is formed (a double bond is formed)  https://www.youtube.com/watch?v=bWHuBmTCC60 Figure 1.17 An Elimination Reaction From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press Section 1.3: Is the Living Cell a Chemical Factory? Biochemical Reactions Continued Elimination reaction (dehydration ) Figure 1.17 An Elimination Reaction From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press Section 1.3: Is the Living Cell a Chemical Factory? Biochemical Reactions Continued 3. An addition reaction is when two molecules combine to form a single product https://www.youtube.com/watch?v=ZKjAi5BU3CE From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press Section 1.3: Is the Living Cell a Chemical Factory? Biochemical Reactions Continued Addition reaction Figure 1.18 An Addition Reaction From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.3: Is the Living Cell a Chemical Factory? Biochemical Reactions Continued 4. An isomerization reaction results in atoms or groups undergoing intramolecular shifts Figure 1.19 An Isomerization Reaction From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press Section 1.3: Is the Living Cell a Chemical Factory? Biochemical Reactions Continued 5. Electron transfer is the result of oxidation- reduction reactions The electron donor is the reducing agent and the electron acceptor is the oxidizing agent When reducing agents donate electrons they become oxidized and when oxidizing agents accept electrons they become reduced Oxidized CH3CH2-OH CH3C-OH Reduced O Ethyl Alcohol Acetic Acid From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press Section 1.3: Is the Living Cell a Chemical Factory? Biochemical Reactions Continued -Oxidation–Reduction (Redox) Reactions:  occur when there is a transfer of electrons or hydrogen from a donor (the reducing agent) to an electron or hydrogen acceptor (the oxidizing agent)  the reducing agent become oxidized , and the oxidizing agents become reduced  oxidation: is gaining oxygen or loosing hydrogen or electron  reduction: is gaining hydrogen or electron or loosing oxygen  in biological redox reactions, electrons and hydrogen are transferred from NADH (nicotinamide adenine dinucleotide) forming NAD+ (reduced/oxidized form).. + NAD NADH R R From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.3: Is the Living Cell a Chemical Factory? Energy Energy is defined as the capacity to do work Cells generate most of their energy with redox reactions The energy captured when electrons are transferred from an oxidizable molecule to an electron-deficient molecule is used to drive ATP synthesis Whenever an electron is transferred, energy is lost.  when fatty acids and sugars are oxidized, their hydrogen atoms are transferred to redox coenzymes NAD+ (nicotinamide adenine dinucleotide) or FAD (flavin adenine dinucleotide)  the reduced NADH and FADH2 then transfers the electrons to another electron acceptor in the electron transport pathway in mitochondria and energy is released, in which some is used to generate ATP From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.3: Is the Living Cell a Chemical Factory? Energy Acquiring energy from the environment happens in distinct ways: Autotrophs Heterotrophs  Plants are photoautotrophs (organisms that transform light energy (usually from the sun) into chemical bond energy (photosynthesis)  Human and animals are chemoheterotroph (organisms that use preformed organic molecules as its sole source of energy From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.3: Is the Living Cell a Chemical Factory? Overview of Metabolism Metabolic pathways come in two types: anabolic and catabolic Anabolic: large complex molecules synthesized from smaller precursors Catabolic: large complex molecules degraded into smaller, simpler products Energy transfer pathways capture energy and transform it into a usable form Signal transduction pathways allow cells to receive and respond to signals Figure 1.20 A Biochemical Pathway From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press Section 1.3: Is the Living Cell a Chemical Factory? Figure 1.21 Anabolism and Catabolism From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press  Section 1.3: Is the Living Cell a Chemical Factory? Biological Order Most living process can be classified into 4 categories. The coherent unity that is observed in all organisms: 1. Synthesis of biomolecules: many require energy, supplied by ATP 2. Transport across membranes: cell membranes regulate the passage of ions and molecules 3. Cell movement: Cell division and organelle movement, two processes that depend to a large extent on the structure and function of a complex network of protein filaments known as the cytoskeleton. 4. Waste removal - CO2 (from sugar and fatty acids metabolism) (→ carbonic acid → lungs) - NH3 (from amino acids metabolism)(→ urea cycle → urea → kidneys) From McKee and McKee, Biochemistry, 7th Edition, © 2020 by Oxford University Press