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Biochemistry

Biochemistry. The study of chemistry as it pertains to living things. http://www.wiley.com/college/boyer/0470003790/animations/central_dogma/central_dogma.htm. Atoms. Atoms are the smallest unit of an element

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Biochemistry

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  1. Biochemistry • The study of chemistry as it pertains to living things

  2. http://www.wiley.com/college/boyer/0470003790/animations/central_dogma/central_dogma.htmhttp://www.wiley.com/college/boyer/0470003790/animations/central_dogma/central_dogma.htm

  3. Atoms • Atoms are the smallest unit of an element • Atoms consist of electrons that orbit a nuclear region containing protons and neutrons

  4. Atoms and structure • http://web.jjay.cuny.edu/~acarpi/NSC/3-atoms.htm

  5. Elements • The periodic table is a list of al known elements • The table is arranged by various properties of the elements • The four most abundant elements in living things are H, N, O and C

  6. Carbon • Carbon is found in all living organisms • Carbon is extremely important to living things because of its versatility in bonding • Carbon is able to form four bonds • The study of chemicals that contain carbon is organic chemistry • Molecules that contain carbon are called organic compounds

  7. Bonds • Elements bond together to form compounds • There are three basic types of bonds: covalent ionic hydrogen

  8. Covalent bonds • Covalent bonds occur when two atoms share electrons

  9. Ionic Bonds • Ionic bonds occur when one atom pulls electrons away from another atom

  10. Hydrogen Bonds • Hydrogen bonds occur between hydrogen atoms and another atom that is more electronegative

  11. Reactions • Reactions occur between elements or compounds • These events change the properties of the molecules involved • Two parts: the reactants and the products 6H2O + 6CO2 C6H12O6 + 6O2

  12. Water • Water is a molecule that consists of two hydrogen atoms bound to a single oxygen atom • The bonds between the hydrogen and oxygen are covalent bonds • Water is a polar molecule due to the fact that the hydrogen atoms are pulled to one end of the oxygen atom

  13. Properties of Water • Water is critical to life • Water has several important properties due to its structure: • Water – • is a polar molecule • expands when frozen • is less dense when frozen • has a high specific heat • has a high heat of vaporization • has a high surface tension

  14. Functional Groups: give specific characteristics to molecules and help determine how they react with other molecules • Amino group – makes molecules slightly basic • Found in amino acids • Group of molecules known as “amines”

  15. Carboxyl group – makes molecules slightly acidic • Also found in amino acids

  16. Carbonyl group – highly polar • 2 forms: ketones and aldehydes • Ketones are found in middle of molecule • Aldehydes are found at end of molecule

  17. Hydroxyl group – extremely polar • Dissolves easily in water • “alcohols”

  18. Phosphate group – makes molecules slightly acidic • Found in ATP and DNA

  19. Sulfhydryl Group – forms bonds between amino acids during tertiary folding stage of protein formation • Forms disulfide bridges • Molecules known as “thiols”

  20. http://www.execulink.com/~ekimmel/functional.htm

  21. Organic Compounds • There are four classes of organic compounds: • Carbohydrates • Lipids • Proteins • Nucleic Acids

  22. Polymers • Polymers are molecules made up of repeating subunits • Most organic compounds are polymers

  23. pH • pH is the measure of the hydrogen ion concentration of a solution • pH = -log [H+] • Acids = substances that release hydrogen ions in solution • Bases = substances that release hydroxide ions in solution • Buffer = weak acid or base that accepts H+ or OH- ions to regulate pH

  24. pH Scale • pH scale runs from 1 – 14 7 is neutral (water) • Below 7 is acidic • Above 7 is b basic • Human blood pH must be maintained at a range of 7.35 to 7.45 • Enzymes function best at specific pH levels • pH = -log [H+]

  25. Carbohydrates are sugars • They are polymers of monosaccharides • Simple sugars are monosaccharides, complex sugars are polysaccharides • Carbohydrates are used by living things for energy and some are also used for structure

  26. Examples of Carbohydrates • Carbohydrates are classified as structural or as functional: • Cellulose provides structure to plant cell walls • Chitin provides structure to fungal cell walls and to animal exoskeletons • Starch is a stored form in plants • Glycogen is a stored form in animals

  27. Carbohydrate Structure • Monosaccharides are bound together by glycosidic linkages • All sugars have the classic carbon ring structure

  28. Lipids • Most lipids are made up of a glycerol molecule bound to two or more fatty acid chains • Ester linkages bind fatty acids to the glycerol • Lipids are used by organisms for energy, protection and insulation • Cell membranes are made up of phospholipids

  29. Two types of lipids are unsaturated fats and saturated fats • Saturated fats have hydrogens at every possible bonding site while unsaturated fats have some double bonds between carbons that allow fewer hydrogen bonds • We often refer to unsaturated fats as oils due to their more fluid nature

  30. Steroids • Steroids are another type of lipid • Steroid structure is different that other fats and oils • Steroids act as hormones like estrogen and testosterone • Cholesterol stabilizes cell membranes

  31. Proteins • Proteins are polymers of amino acids • Amino acids are linked by peptide bonds

  32. Amino Acids • There are 20 amino acids that may be linked in varying sequences to make a protein • The function of a protein depends upon the sequence of its amino acids

  33. Protein Structure • Primary structure: sequence of amino acids • Secondary structure: α - helix or ß - pleated sheets formed by hydrogen bonds • Tertiary structure: disulfide bridges form to make loops • Quaternary structure: two or more polypeptides bind together to make functional protein

  34. Protein Function • Structural proteins: Muscle fibers • Functional proteins: enzymes transport proteins glycoproteins hormones • Proteins cause genetic traits to be expressed

  35. Nucleic Acids • Nucleic Acids are polymers of nucleotides • DNA and RNA • DNA carries genetic code • RNA translates genetic code into proteins

  36. Enzymes • Enzymes are proteins that act as catalysts • A catalyst speeds up chemical reactions • Enzymes speed up chemical reactions by lowering activation energy • Enzymes are not used up in a reaction • Enzymes are specific  one enzyme, one substrate

  37. Enzyme Catalytic Cycle

  38. Factors affecting Enzyme Reaction Rate • pH • Temperature • Concentration of enzyme • Concentration of substrate

  39. Effect of temperature on enzyme reaction rate Effect of pH on enzyme reaction rate

  40. ATP • Adenosine Triphosphate • Molecule used to do work in a cell • Phosphate breaks away from ATP making ADP , free phosphate then attaches to different molecule

  41. Review Questions and Animations http://www.lew-port.com/10712041113402793/lib/10712041113402793/Animations/Enzyme_activity.html http://www.biology.arizona.edu/biochemistry/problem_sets/large_molecules/large_molecules_problems.html http://www.wiley.com/college/boyer/0470003790/animations/enzyme_inhibition/enzyme_inhibition.htm

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