Biochemistry has become the foundation for understanding all biological                              processes.It has prov...
What is Biochemistry ?    Biochemistry is the application of chemistry to the     study of biological processes at the ce...
Principles of Biochemistry Cells (basic structural units of living organisms) are highly    organized and constant source...
Cells Basic building blocks of life Smallest living unit of an organism Grow, reproduce, use energy, adapt, respond to ...
Nucleoid region contains the DNA    Contain 3 basic cell structures:•Cell membrane & cell wall          • Nucleus• Contain...
Two Main Types of   Eukaryotic Cells                                       6
Characteristic Bio-membranes and Organelles Plasma Membrane A lipid/protein/carbohydrate complex, providing a barrier and ...
.     Rough endoplasmic reticulum (RER)     A network of interconnected membranes forming channels within the     cell. Co...
Vacuoles      Membrane surrounded "bags" that contain water and storage      materials in plants.       Peroxisomes or Mic...
Biolog. NanostructuresBiochemistry                                    10
How did organic complex molecules evolved frommore simple molecules?                        CH4, H2O, NH3, HCN            ...
How did organic complex molecules evolved from   more simple molecules?• Urea was synthesized by heating the inorganic  co...
The Urey-Miller experiment (1950)                  Some amino acids could be produced:                                    ...
Many Important Biomoleculesare Polymers • Biopolymers - macromolecules created by joining many   smaller organic molecules...
15
Molecular Organisation of a cell                                   16
WaterAbout 60-90 percentof an organism is waterWater is used inmost reactions inthe bodyWater is calledthe universalsolve...
Bio-molecules   Just like cells are building blocks of tissues likewise molecules are    building blocks of cells.   Ani...
Biomolecules – Structure                            Anabolic Building block       Macromolecule   Simple sugar        ...
Linking MonomersCells link monomers by a process  called dehydration synthesis (removing a molecule of water)             ...
Breaking Down Polymers Cells break down macromolecules by a process called hydrolysis (adding a molecule of water)       ...
Sugars   Carbohydrates most abundant organic molecule    found in nature.   Initially synthesized in plants from a compl...
Monosaccharides -Polysaccharides                    Glucose - Cellulose                   Glycosidic bonds connecting     ...
Fatty acids - Lipids Are monocarboxylic acid contains even number C atoms Two types: saturated (C-C sb) and unsaturated ...
TriglycerideGlycerol     Fatty Acid Chains                                 25
Structure of a biological membrane   • A lipid bilayer with associated proteins                                           ...
SteroidsThe carbon skeleton ofsteroids is bent to form4 fused rings                                             Cholester...
Nucleic AcidsStore hereditary informationContain information for making all thebody’s proteins Two types exist --- DNA & ...
Amino acids - Proteins: Amino acids:                 •   Building blocks of proteins.                 •   R Group (side c...
Proteins as Enzymes    Many proteins act as biological catalysts or     enzymesThousands of different enzymes exist in th...
Enzymes:• Active site - a cleft or groove in an enzyme that binds the  substrates of a reaction  The nature and arrangemen...
Macromolecules                 32
Macromolecules                 33
Concepts of Life    Life is characterized by   Biological diversity: lichen, microbes,    jellyfish, sequoias, hummingbir...
Life needs 3 things:(1) ENERGY, which it mustknow how to:         Extract         Transform         Utilize            ...
The Energetics of Life• Photosynthetic  organisms capture  sunlight energy and use  it to synthesize organic  compounds• O...
Using toxic O2 to generate energy   2 H2O  O2 + 4e- + 4H+ (photosynthesis)      Glucose + 6O2  6CO2 + 6H2O + Energy     ...
Glycolysis: the preferred way for theformation of ATP                                        38
Life needs (2) SIMPLE MOLECULES,which it must know how to:          Convert          Polymerize          Degrade       ...
Life needs (3) CHEMICALMECHANISMS, to: Harness energy Drive sequential chemical reactions Synthesize & degrade macromol...
Trick #1: Life uses chemical coupling todrive otherwise unfavorable reactions                                           41
Trick #2: Life uses enzymes to speed upotherwise slow reactions                                          42
How does an enzyme do it,thermodynamically?                            43
How does an enzyme do it,mechanistically?                            44
Chemical reaction types encountered in biochemical processes1. Nucleophilic Substitution One atom of group substituted fo...
4. Isomerization Reactions. Involve intramolecular shift of atoms or groups5. Oxidation-Reduction (redox) Reactions Occu...
47
Biochemical Reactions    Metabolism: total sum of the chemical reaction happening in a     living organism (highly coordi...
Even though thousands of pathways sound very  large and complex in a tiny cell: The types of pathways are small Mechanis...
Energy for Cells Living cells are inherently unstable. Constant flow of energy prevents them from  becoming disorganized...
51
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Biochem Introduction

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  • Biochemistry has become the foundation for understanding all biological processes. It has provided explanations for the causes of many diseases in humans, animals and plants."
  • Biochem Introduction

    1. 1. Biochemistry has become the foundation for understanding all biological processes.It has provided explanations for the causes of many diseases in humans, animals and plants 1
    2. 2. What is Biochemistry ? Biochemistry is the application of chemistry to the study of biological processes at the cellular and molecular level. It emerged as a distinct discipline around the beginning of the 20th century when scientists combined chemistry, physiology and biology to investigate the chemistry of living systems by: A. Studying the structure and behavior of the complex molecules found in biological material and C. the ways these molecules interact to form cells, tissues and whole organism 2
    3. 3. Principles of Biochemistry Cells (basic structural units of living organisms) are highly organized and constant source of energy is required to maintain the ordered state. Living processes contain thousands of chemical pathways. Precise regulation and integration of these pathways are required to maintain life Certain important pathways e.g. Glycolysis is found in almost all organisms. All organisms use the same type of molecules: carbohydrates, proteins, lipids & nucleic acids. Instructions for growth, reproduction and developments for each organism is encoded in their DNA 3
    4. 4. Cells Basic building blocks of life Smallest living unit of an organism Grow, reproduce, use energy, adapt, respond to their environment Many cannot be seen with the naked eye A cell may be an entire organism or it may be one of billions of cells that make up the organism Basis Types of Cells 4
    5. 5. Nucleoid region contains the DNA Contain 3 basic cell structures:•Cell membrane & cell wall • Nucleus• Contain ribosomes (no membrane) • Cell Membraneto make proteins in • Cytoplasm with organellestheir cytoplasm 5
    6. 6. Two Main Types of Eukaryotic Cells 6
    7. 7. Characteristic Bio-membranes and Organelles Plasma Membrane A lipid/protein/carbohydrate complex, providing a barrier and containing transport and signaling systems. Nucleus Double membrane surrounding the chromosomes and the nucleolus. Pores allow specific communication with the cytoplasm. The nucleolus is a site for synthesis of RNA making up the ribosome Mitochondrion Surrounded by a double membrane with a series of folds called cristae. Functions in energy production through metabolism. Contains its own DNA, and is believed to have originated as a captured bacterium.Chloroplasts (plastids)Surrounded by a double membrane, containing stacked thylakoidmembranes. Responsible for photosynthesis, the trapping of lightenergy for the synthesis of sugars. Contains DNA, and likemitochondria is believed to have originated as a capturedbacterium. 7
    8. 8. . Rough endoplasmic reticulum (RER) A network of interconnected membranes forming channels within the cell. Covered with ribosomes (causing the "rough" appearance) which are in the process of synthesizing proteins for secretion or localization in membranes. Ribosomes Protein and RNA complex responsible for protein synthesis Smooth endoplasmic reticulum (SER) A network of interconnected membranes forming channels within the cell. A site for synthesis and metabolism of lipids. Also contains enzymes for detoxifying chemicals including drugs and pesticides. Golgi apparatus A series of stacked membranes. Vesicles (small membrane surrounded bags) carry materials from the RER to the Golgi apparatus. Vesicles move between the stacks while the proteins are "processed" to a mature form. Vesicles then carry newly formed membrane and secreted proteins to their final destinations including secretion or membrane localization. Lysosymes A membrane bound organelle that is responsible for degrading proteins and membranes in the cell, and also helps degrade materials ingested by the cell. 8
    9. 9. Vacuoles Membrane surrounded "bags" that contain water and storage materials in plants. Peroxisomes or Microbodies Produce and degrade hydrogen peroxide, a toxic compound that can be produced during metabolism. Cell wall Plants have a rigid cell wall in addition to their cell membranes Cytoplasm enclosed by the plasma membrane, liquid portion called cytosol and it houses the membranous organelles. Cytoskeleton Arrays of protein filaments in the cytosol. Gives the cell its shape and provides basis for movement. E.g. microtubules and microfilaments.http://www.biology.arizona.edu copyright © 1997 - 2004.. 9
    10. 10. Biolog. NanostructuresBiochemistry 10
    11. 11. How did organic complex molecules evolved frommore simple molecules? CH4, H2O, NH3, HCN ?Biochemical Evolution 11
    12. 12. How did organic complex molecules evolved from more simple molecules?• Urea was synthesized by heating the inorganic compound ammonium cyanate (1828)• This showed that compounds found exclusively in living organisms could be synthesized from common inorganic substances 12
    13. 13. The Urey-Miller experiment (1950) Some amino acids could be produced: 13
    14. 14. Many Important Biomoleculesare Polymers • Biopolymers - macromolecules created by joining many smaller organic molecules (monomers) • Condensation reactions join monomers (H2O is removed in the process) • Residue - each monomer in a chain 14
    15. 15. 15
    16. 16. Molecular Organisation of a cell 16
    17. 17. WaterAbout 60-90 percentof an organism is waterWater is used inmost reactions inthe bodyWater is calledthe universalsolvent 17
    18. 18. Bio-molecules Just like cells are building blocks of tissues likewise molecules are building blocks of cells. Animal and plant cells contain approximately 10, 000 kinds of molecules (bio-molecules) Water constitutes 50-95% of cells content by weight. Ions like Na+, K+ and Ca+ may account for another 1% Almost all other kinds of bio-molecules are organic (C, H, N, O, P, S) Infinite variety of molecules contain C. Most bio-molecules considered to be derived from hydrocarbons. The chemical properties of organic bio-molecules are determined by their functional groups. Most bio-molecules have more than one. 18
    19. 19. Biomolecules – Structure Anabolic Building block  Macromolecule Simple sugar  Polysaccharide Amino acid  Protein (peptide) Nucleotide  RNA or DNA Fatty acid  Lipid Catabolic 19
    20. 20. Linking MonomersCells link monomers by a process called dehydration synthesis (removing a molecule of water) Remove H H2O Forms Remove OH This process joins two sugar monomers to make a double sugar 20
    21. 21. Breaking Down Polymers Cells break down macromolecules by a process called hydrolysis (adding a molecule of water) Water added to split a double sugar 21
    22. 22. Sugars Carbohydrates most abundant organic molecule found in nature. Initially synthesized in plants from a complex series of reactions involving photosynthesis. Basic unit is monosaccharides. Monosaccharides can form larger molecules e.g. glycogen, plant starch or cellulose.Functions Store energy in the form of starch (photosynthesis in plants) or glycogen (in animals and humans). Provide energy through metabolism pathways and cycles. Supply carbon for synthesis of other compounds. Form structural components in cells and tissues. Intercellular communications 22
    23. 23. Monosaccharides -Polysaccharides Glucose - Cellulose Glycosidic bonds connecting glucose residues are in red 23
    24. 24. Fatty acids - Lipids Are monocarboxylic acid contains even number C atoms Two types: saturated (C-C sb) and unsaturated (C-C db) Fatty acids are components of several lipid molecules. E,g. of lipids are triacylglycerol, steriods (cholestrol, sex hormones), fat soluble vitamins.Functions Storage of energy in the form of fat Membrane structures Insulation (thermal blanket) Synthesis of hormones 24
    25. 25. TriglycerideGlycerol Fatty Acid Chains 25
    26. 26. Structure of a biological membrane • A lipid bilayer with associated proteins 26
    27. 27. SteroidsThe carbon skeleton ofsteroids is bent to form4 fused rings CholesterolCholesterol is the“base steroid” fromwhich your body Estrogenproduces other TestosteronesteroidsEstrogen &testosterone are alsosteroids Synthetic Anabolic Steroids are variants of testosterone 27
    28. 28. Nucleic AcidsStore hereditary informationContain information for making all thebody’s proteins Two types exist --- DNA & RNA 28
    29. 29. Amino acids - Proteins: Amino acids: • Building blocks of proteins. • R Group (side chains) determines the chemical properties of each amino acids. • Also determines how the protein folds and its biological function. • Functions as transport proteins, structural proteins, enzymes, antibodies, cell receptors. 29
    30. 30. Proteins as Enzymes  Many proteins act as biological catalysts or enzymesThousands of different enzymes exist in the bodyEnzymes control the rate of chemical reactions byweakening bonds, thus lowering the amount ofactivation energy needed for the reaction ->Catalysator-> No not interfere with the equilibrium of reaction-> Enzymes are reusable !!!! 30
    31. 31. Enzymes:• Active site - a cleft or groove in an enzyme that binds the substrates of a reaction The nature and arrangement of amino acids in the active site make it specific for only one type of substrate. (accepts just one enaniomer)Egg white lysozyme 31
    32. 32. Macromolecules 32
    33. 33. Macromolecules 33
    34. 34. Concepts of Life Life is characterized by Biological diversity: lichen, microbes, jellyfish, sequoias, hummingbirds, manta rays, gila monsters, & you Chemical unity: living systems (on earth) obey the rules of physical and organic chemistry – there are no new principles 34
    35. 35. Life needs 3 things:(1) ENERGY, which it mustknow how to:  Extract  Transform  Utilize 35
    36. 36. The Energetics of Life• Photosynthetic organisms capture sunlight energy and use it to synthesize organic compounds• Organic compounds provide energy for all organisms 36
    37. 37. Using toxic O2 to generate energy 2 H2O  O2 + 4e- + 4H+ (photosynthesis) Glucose + 6O2  6CO2 + 6H2O + Energy 37
    38. 38. Glycolysis: the preferred way for theformation of ATP 38
    39. 39. Life needs (2) SIMPLE MOLECULES,which it must know how to:  Convert  Polymerize  Degrade 39
    40. 40. Life needs (3) CHEMICALMECHANISMS, to: Harness energy Drive sequential chemical reactions Synthesize & degrade macromolecules Maintain a dynamic steady state Self-assemble complex structures Replicate accurately & efficiently Maintain biochemical “order” vs outside 40
    41. 41. Trick #1: Life uses chemical coupling todrive otherwise unfavorable reactions 41
    42. 42. Trick #2: Life uses enzymes to speed upotherwise slow reactions 42
    43. 43. How does an enzyme do it,thermodynamically? 43
    44. 44. How does an enzyme do it,mechanistically? 44
    45. 45. Chemical reaction types encountered in biochemical processes1. Nucleophilic Substitution One atom of group substituted for another2. Elimination Reactions Double bond is formed when atoms in a molecule is removed3. Addition Reactions: Two molecules combine to form a single product. A. Hydration Reactions Water added to alkene > alcohol (common addition pathway) 45
    46. 46. 4. Isomerization Reactions. Involve intramolecular shift of atoms or groups5. Oxidation-Reduction (redox) Reactions Occur when there is a transfer of e- from a donor to an electron acceptor6. Hydrolysis reactions Cleavage of double bond by water. 46
    47. 47. 47
    48. 48. Biochemical Reactions Metabolism: total sum of the chemical reaction happening in a living organism (highly coordinated and purposeful activity) a. Anabolism- energy requiring biosynthetic pathways b. Catabolism- degradation of fuel molecules and the production of energy for cellular function All reactions are catalyzed by enzymes The primary functions of metabolism are: a. acquisition & utilization of energy b. Synthesis of molecules needed for cell structure and functioning (i.e. proteins, nucleic acids, lipids, & CHO c. Removal of waste products 48
    49. 49. Even though thousands of pathways sound very large and complex in a tiny cell: The types of pathways are small Mechanisms of biochemical pathways are simple Reactions of central importance (for energy production & synthesis and degradation of major cell components) are relatively few in number 49
    50. 50. Energy for Cells Living cells are inherently unstable. Constant flow of energy prevents them from becoming disorganized. Cells obtains energy mainly by the oxidation of bio- molecules (e- transferred from 1 molecule to another and in doing so they lose energy) This energy captured by cells & used to maintain highly organized cellular structure and functions 50
    51. 51. 51

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