Biochemistry study of the molecular basis of life

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1 Biochemistry : An Introduction Biochemistry study of the molecular basis of life n Study of the chemistry of living organisms Studies organic molecules & organic reactions in living organisms n Living organisms complex and diverse All use same type of biomolecules; all use energy Biomolecules come from organic molecules; bio-reactions are organic reactions n Bedrock on which modern life sciences are built Biochemistry along with Molecular Biology greatly influenced the study of life sciences

2 Life: It is a Mystery! Life: It is a Mystery! 19 th century it was believed that Vital Forces existed only in living organisms 1828 Friedrich Wohler produced urea NH 4 OCN à H 2 NCONH 2 Ammonium Cyanate Urea Fundamental similarity of cells causes speculation on the origins of life Both cells and biomolecules must have arisen from very simple molecules H 2 O, CH 4, CO 2 NH 3, N 2 H 2 Activities in cells Formation and degradation of molecules Molecular transportation and signaling Metabolic processes

3 Life: It is a Mystery! qlife is complex and dynamic q Composed of C, N, O, H, S, P q Biomolecules organic based q Life is organized and self-sustaining q Hierarchically organized systems q Biochemical reactions catalyzed by enzymes q Metabolism sum total of all reactions q Homeostasis capacity to regulate metabolic processes q Life is cellular q Basic units of living organisms q Life is information-based q Organization requires information q Life adapts and evolves q Mutations

4 Life: It is a Mystery!

5 Section 1.2: Biomolecules Composed of inorganic and organic molecules Water critical to life 50% to 95% of cell content Trace elements (i.e., Na +, K +, Mg 2+, and Ca 2+ ) 1% cell content Six principal elements: carbon, hydrogen, oxygen, nitrogen, phosphorous, and sulfur Biomolecules derived from hydrocarbons Carbon and hydrogen only Hydrophobic Functional groups determine chemical properties

6 Section 1.2: Biomolecules

7 Section 1.2: Biomolecules Four major classes of small biomolecules monomers build polymers Amino acids à proteins; chemical processes Monosaccharides à carbohydrates; energy source Fatty acids à lipids; cell walls Nucleotides à nucleic acids (DNA,RNA); gene expression ü Largest molecule in living organism

8 Section 1.2: Biomolecules Amino Acids Hundreds of naturally occurring amino acids; most common type are a-amino acids; 20 standard amino carboxyl Classified a, b, or g according to amino group location Chemical properties determined by side-chain, R

9 Section 1.2: Biomolecules Figure 1.4 Structural Formulas for Several a-amino Acids

10 Section 1.2: Biomolecules Amino Acids and Proteins Many naturally occurring amino acids that are not a-amino acids a-glycine & a-glutamic acid function as neurotransmitters b-alanine: a precursor of the vitamin pantothenic acid g-aminobutyric acid (GABA): a neurotransmitter

11 Section 1.2: Biomolecules Amino Acids to Proteins Amino acids are connected via peptide bonds Amino acid R groups lead to structure and function of proteins Structure of Met-Enkephalin, a Pentapeptide Long chain polymers, polypeptides

12 Section 1.2: Biomolecules Sugars or monosaccharides Smallest; most abundant organic molecule in nature Alcohol(-OH) and carbonyl (C=O) functional groups Two types: aldoses (CHOR) and ketoses (CH 2 OHCOR) Range from monosaccharides to oligosaccharides to polysaccharides

13 Section 1.2: Biomolecules Fatty Acids monocarboxylic acids (R-COOH) Two types of fatty acids: saturated and unsaturated Very few fatty acids occur independently; most are components of lipids (e.g., triacylglycerol)

14 Section 1.2: Biomolecules Nucleotides à 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

15 Section 1.2: Biomolecules DNA - (deoxyribonucleic acid) Encodes the genetic information of an organism Structure: two antiparallel polynucleotide strands forming a right-handed double helix Four basic DNA nucleotides: adenine, guanine, thymine, and cytosine Strands are held together by hydrogen bonds and hydrophobic interactions Organism s entire set of DNA sequences is called its genome

16 Section 1.2: Biomolecules Figure 1.13 DNA

17 Section 1.2: Biomolecules RNA Single-stranded polynucleotide with ribose instead of deoxyribose Synthesized via transcription using the four principle bases: adenine, cytosine, guanine, and uracil Three main types: mrna, rrna, and trna Several types of noncoding RNA: sirna, mirna, snrna, and snorna

18 Section 1.2: Biomolecules Gene Expression Controls when the information encoded in a gene will be accessed Class of proteins called transcription factors regulates the expression of protein-encoding genes

19 Section 1.3: Is the Living Cell a Chemical Factory? Primary functions of metabolism: Acquisition and utilization of raw materials, energy, & information from environment Synthesis of molecules needed for cell structure and function Growth and development of an organism Discharging wast and heat into environment Autopoiesis system capable of reproducing and maintaining itself

20 Biochemical Reactions Nucleophilic substitution reaction: an atom with an unshared pair of electrons displaces a leaving group A: + B-X à A-B + X: A: is nucleophile; B is electrophile; X: is the leaving group Hydrolysis reaction is an example R C O R + H 2 O à R C OH + R OH II II O O

21 Section 1.3: Is the Living Cell a Chemical Factory? Figure 1.15 A Hydrolysis Reaction

22 Section 1.3: Is the Living Cell a Chemical Factory? Elimination reaction forms a double bond when atoms in a molecule are removed Figure 1.17 An Elimination Reaction

23 Section 1.3: Is the Living Cell a Chemical Factory? Addition reaction is when two molecules combine to form a single product Figure 1.18 An Addition Reaction

24 Section 1.3: Is the Living Cell a Chemical Factory? Isomerization reaction results in atoms or groups undergoing intramolecular shifts Figure 1.19 An Isomerization Reaction

25 Section 1.3: Is the Living Cell a Chemical Factory? Electron transfer is the result of oxidationreduction reactions Electron donor is the reducing agent and the electron acceptor is the oxidizing agent When reducing agents donate electrons they become oxidized; when oxidizing agents accept electrons they become reduced CH 3 CH 2 -OH Ethyl Alcohol Oxidized Reduced CH 3 C-OH O Acetic Acid

26 Section 1.3: Is the Living Cell a Chemical Factory? Energy sun is ultimate energy source for life Energy is defined as the capacity to do work Cells generate most of their energy with redox reactions Energy captured when electrons are transferred from an oxidizable molecule to an electron-deficient molecule is used to drive ATP synthesis Acquiring energy from the environment happens in distinct ways: Autotrophs synthesis of food from inorganic substances using light or chemical energy Heterotrophs derives nutritional requirements from complex organic substances

27 Section 1.3: Is the Living Cell a Chemical Factory? Metabolism sum of al enzyme catalyzed reactions Two types of metabolic pathways: anabolic and catabolic Catabolic: large complex molecules degraded into smaller, simpler products; release energy Anabolic: large complex molecules synthesized from smaller precursors; require energy 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

28 Section 1.3: Is the Living Cell a Chemical Factory? Figure 1.21 Anabolism and Catabolism

29 Section 1.3: Is the Living Cell a Chemical Factory? Biological Order - highly organized complexity with coherent unity observed in all living organisms Synthesis of biomolecules Transport across membranes Cell movement Waste removal

30 Section 1.4: Systems Biology Systems Biology regards living organisms as Integrated Systems Emergence: new & unanticipated properties emerge from interactions among parts Amino acids protect Fe +2 from oxidation Robustness: system remains stable despite diverse perturbations Degeneracy: capacity of structurally different parts performing same or similar functions; Genetic code 61 codons code for 20 amino acids Modularity: system consists of modules that perform specific functions

31 Section 1.4: Systems Biology Systems Biology Model Concepts System: interconnected & interacting assembly of biomolecules Network: group of interconnected molecules performing one or more functions Metabolic network: interconnected biochemical reaction pathways Signaling network: receptor proteins and signaling pathways Regulatory networks: switch genes on and off Module: subsystems that perform specific functions Motif: regulatory circuits via feedback control Negative feedback: product shuts down pathway Positive feedback: product increases itself Figure 1.22 Feedback Mechanisms

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