Introduction to biochemistry
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This document provides an introduction to biochemistry, including definitions and key concepts. It discusses biochemistry as the study of the structure and function of biomolecules in living organisms. The document outlines that living things are composed of common elements like carbon, hydrogen, oxygen, nitrogen and complex macromolecules including carbohydrates, proteins, nucleic acids and lipids. It also describes important cellular structures like the cell membrane, nucleus, mitochondria and chloroplasts. Finally, the document provides overviews of the four major macromolecule classes and how pH and buffers are important concepts in biochemistry.
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Introduction to biochemistry
- 1. Introduction to biochemistry Moshtaghi-Kashanian Associated professor Kerman University of Medical Sciences
- 2. What is Biochemistry Biochemistry is mother of different field in medicine 1. 2. 3. 4. 5. 6. 7. 8. Anatomy Physiology Pharmacology Genetic Immunology Bacteriology Immunology Parasitology 1. 2. 3. 4. 5. 6. 7. Internal medicine Surgery Endocrinology Dentistry Psychology Sociology Nursing
- 4. Definition of Biochemistry “Chemistry of Life” Living Things are composed of lifeless molecules Doesn’t fully take into account what chemistry is Biochemistry- Study of the structure, properties and changes of bio-matter
- 5. Special Considerations 1. Complex and highly ordered 2. Everything has a function 3. Living things transform their environment (extract energy) 4. Self-replicating 5. Reactions occur at constant temperature, pressure and pH; in an aqueous environment
- 6. Biomolecules - Elements C, H, O, N 99% of mass of most cells P, S Mg2+, Na+, K+, Ca2+, ClFe, Zn, Mn, Co, Cu
- 7. Biomolecules - Macromolecules 1. Carbohydrates- made up mostly of 7 monosaccharides 2. Proteins - 5 × 106, made up of 20 amino acids 3. Nucleic Acids - 1,000, made up of 4 nucleotides 4. Lipids
- 8. Water • • 70% of most organisms polar • • favors solubility directionality holds macromolecules in given conformations
- 9. Water • hydrogen bond • • • • • half-life < 1/1,000,000 sec holds water together without being viscous high specific heat colligative properties weakly ionizable
- 10. Sizes of living things
- 11. Cell Structure
- 12. Cell Membrane Appears as 3 layers by EM • 7.5-10 nm thick • “Unit membrane” These three things are explained on a molecular level as a phospholipid bilayer Function: osmotic barrier Present in all cells Further consideration in lipid material. •
- 13. Nucleus Bounded by a porous nuclear membrane Function: contain DNA Present in all eukaryotic cells • 1 per cell • Often 1-4 nucleoli •
- 14. The nucleus and the nuclear envelope
- 15. Cell Wall & cell membrane Thick, tough wall Function: rigidity Present in plant and prokaryotic cells
- 18. Mitochondria • • Shape varies, size varies 500-2,000 per cell
- 19. Mitochondria Function: “powerhouse of the cell” Present in all eukaryotic cells Structure: compartments Further consideration in metabolism.
- 21. Endoplasmic Reticulum Rough and Smooth Phospholipid bilayer surrounding a lumen ± ribosomes Function: protein synthesis (rough) lipid synthesis (smooth) Present in all eukaryotic cells (lots)
- 22. Rough Endoplasmic Reticulum Surface looks rough because of the presence of ribosomes, another organelle (present in all cells)
- 25. Golgi Apparatus Historically cis, medial and trans: trans-golgi network Function: protein processing and secretion Present in all eukaryotic cells (lots)
- 26. Lysosomes About as big as a mitochondrion • not much to see Function: degradation of proteins Present in animal cells, plant cells have similar organelle called peroxisome Number per cell varies enormously •
- 27. Chloroplasts Stacks of “grana” • grana composed of thylakoid disks Function: photosynthesis Present in photosynthetic cells 50-200 per cell •
- 28. Cytoplasm Aqueous, solute-containing contents within the plasma membrane Contains soluble proteins, salts, organelles Cytosol- is the supernate of a centrifugation process
- 29. Microtubules • • Polymer of a protein called actin Gives shape to cell, also functions in transport around the cell
- 30. 4 classes of macromolecules Carbohydrates: Energy, structure Lipids: Energy, membranes Proteins: Catalysts, structure, etc. Nucleic Acids: Information
- 34. Making & breaking polymers
- 36. Cellulose: A structural polysaccharide
- 37. Chitin: a structural polysaccharide
- 40. Polar & charged amino acids
- 44. Protein Structure: 4 Levels Primary Secondary Tertiary Quaternary
- 45. Primary structure of protein: the amino acid sequence lysozyme
- 46. Amino Acid Structure R is different for different amino acids.
- 48. Primary structure of protein: the amino acid sequence Primary structure is due to strong covalent peptide bonds joining amino acids together. lysozyme
- 49. Secondary structure: group of amino acids folded repetitively to make a discrete shape. lysozyme
- 50. Secondary structure: group of amino acids folded repetitively to make a discrete shape. due to hydrogen bonds between amino acids’ backbones. lysozyme
- 51. Tertiary structure: the overall 3-d conformation of a polypeptide. lysozyme
- 52. Tertiary structure involves several kinds of bonds.
- 53. Tertiary Structure Most proteins are hydrophilic outside, hydrophobic inside.
- 57. Nucleic Acids are Polymers
- 58. pH and Buffers
- 59. Water is Weakly Ionizable • • • • 2 H2O <===> OH– + H3O+ Weakly means this doesn’t happen often [OH–] = [H3O+] = 1 × 10-7 M, [OH–] × [H3O+] = 1 × 10-14, the basis of the pH scale
- 60. Equilibrium Constants Mathematically Represent Degree of Dissociation in biochemistry to Keq’ is used denote modified standard state.
- 61. pKa’ Values are Used to Describe Ionization of Acids • • • • CH3COOH + H2O <===> CH3COO– + H3O+ Keq’ = Ka’ = 1.74 x 10-5 = pKa’ = 4.76
- 62. Graphical Determination of pKa’ • The pKa’ is the pH at the point where buffering occurs
- 63. Buffers Buffer- a compound that does not allow the pH to change even if acid or base is added to the system. Amphiprotic compounds are also good buffers. Amphiprotic compound- a compound that can act as a proton donor or as a proton acceptor.
- 64. The Henderson-Hasselbalch Equation is Used to Determine the pH of Buffered Solutions pH = pKa’ + log [A–] [HA] or pH = pKa’ + log [salt] [acid]
- 65. When pH = pKa’, There is Equal Amounts of A– and HA • Proof on board
- 66. pH Problems What will the pH of a solution be if 0.1 mL of 6 M HCl is added to 100. mL of H2O? What will the pH of a solution be if 0.1 mL of 6 M HCl is added to 100. mL of 1 M HEPES initially at pH 7.6? What will the pH of a solution be if 0.1 mL of 6 M HCl is added to 100. mL of 50 mM HEPES initially at pH 7.6?
- 67. Choosing a Buffer • • • pKa ± 0.5 pH units ionic strength: use 50 or 100 mM metal ion chelation, etc.