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Biochemistry Chemical Bonds • An Atom is the smallest unit of matter that CANNOT be broken down by CHEMICAL means. • Atoms are made of a nucleus containing PROTONS and NEUTRONS • And an ELECTRON CLOUD containing electrons. • The electrons available for bonds are called VALENCE ELECTRONS. Elements • Elements are pure substances. Atomic Number and Mass • The atomic number is the number of Protons in an atom. It is the Blue number on our Periodic Table Chart. • The atomic mass is the total mass of the atom. This includes the protons and neutrons. The electrons are so small they don’t really count. electron Proton Nucleus ee+ +/- Xx +/- + Neutron Do you know what element this is? How do I Identify the Element • The Number of……………. PROTONS Soooooo…. The element is……. HELIUM Isotopes • An isotope has the same atomic number as the parent atom, but has a different atomic mass. This is because it has more or less neutrons. • Example: Carbon (C) has an atomic number of 6 and a mass of 12 according to the Periodic table. This means it has 6 protons and 12 – 6 = 6 neutrons. • But scientists often use Carbon-14. This is because it still has 6 protons, but it has 14 – 6 = 8 neutrons So back to an ATOM (in this case Hydrogen—1 proton, no neutrons.) e- + Just like seating at a stadium… All atoms have “seats” for electrons: All atoms want to have a Full outer ring. • Ring one has room for only 1 or 2 electrons. • Ring two and three can have up to 8 electrons. The Outer Ring Electrons Are Called If an atom does NOT have enough electrons to fill its outer ring… It may try to: 1) Share valence electrons with another atom Or 2) Grab a valence electron from another atom. Covalent Bonds—sharing of Valence Electrons e- H H e- Covalent Bonds in H2O (water) Have a LITTLE CHARGE so they are called POLAR COVALENT BONDS. + H + e- e- ee- O e- e- ee- e- e- _ H Hydrogen Bonding HYDROGEN BONDS BETWEEN MOLECULES Polar Waters tend be Cohesive ClClClNa+ Na+ Na+ HYDROGEN BONDS BETWEEN MOLECULES NaCl ions can fit between the Polar water molecules. When EVENLY dispersed they are said to be IN SOLUTION. Polar Waters tend be Cohesive, Adhesive ClClClNa+ Na+ Na+ HYDROGEN BONDS BETWEEN MOLECULES NaCl ions can fit between the Polar water molecules. When EVENLY dispersed they are said to be IN SOLUTION. Special Characteristics of Water • https://www.youtube.com/watch?v=QqjcCvzWwww • Demo + - Na Cl Now the two IONS are attracted by charge to each other + Na+ ION _ Cl- ION Video of Bonding https://www.youtube.com/watch?v=QqjcCv zWwww Acids and Bases Acids Bases 14 1 H3O+ =hydronium ion 7 H2O OH - = Hydroxide ion https://www.youtube.com/watch?v=tsAHt0FiwN M http://www.teachertube.com/v ideo/science-lab-safetyvideo-rap-194405 Enzymes, which are “proteins that do something” require specific pH levels to work • Stomach enzymes like to work in ACIDS • Intestinal enzymes like to work in BASES. Organic Chemistry—the Chemistry of Life • All life on earth is CARBON BASED. • Carbon atoms have 4 valence electrons. C Organic Chemistry—the Chemistry of Life • Because they have 4 valence electrons they can interact and BOND with 4 different atoms or molecules. H C H H H Organic Chemists leave out the electrons in a molecule. • For example • Is written H O • And 2 becomes just C H C H H H Carbons can form many molecules. Scientists who draw organic molecules Write them so many times that they stop even writing the C’s and H’s. H H H C C C H H H Becomes H H C C C CARBOHYDRATES Molecules made of Carbon, Hydrogen and Oxygen in a 1:2:1 ratio. CH2OH OH H H C O C OH OH H Glucose C6H12O6 H C OH CH2OH OH O H OH C OH C C H H H OH Fructose These are Simple Sugars or Monosaccharides Monosaccharides become Disaccharides A CHAIN OF 2 SIMPLE SUGARS CH2OH OH H H C O H CH2OH C C OH OH Glucose O OH O H OH C C C H OH H H Fructose H CH2OH O C OH H O H C OH H CH2 OH C O O H OH C C C H OH H H POLYSACCHARIDES ARE LONGER CHAINS OF SUGARS H H CH2 OH H O C OH H CHOH 2 C C H Forming Chains That make up Complex Carbohydrates Such as Starches, Glycogen and cellulose. H H OH O OH O H OH C C C H OH H O For example a long chain of Glucose molecules makes a STARCH. •All Carbohydrates store ENERGY from the SUN. •Plants make Glucose and store excess as Starches. •Animals and Humans eat the starch and Glucose for their energy needs. •Animals store excess glucose as Glycogen. LIPIDS • Lipids are made of carbon and hydrogen. • They are HYDROPHOBIC, ie they float on Water. • Common lipids include Fats, Oils, Waxes, Phospholipids, and Steroids. • One of the building blocks of lipids is… Glycerol C C C The thick gooey stuff that hand creams are made of. O A Fatty Acid is a long chain of Carbon and hydrogen… C OH Etc… With a Polar end (Hint: remember that the points on the line Indicate C and H) And a Non-polar Hydrophobic end Add Glycerol to the Fatty acid and it becomes… There are 3 types of fatty acids: O Saturated Fatty Acid (solid at room T like butter or meat fat) O Mono-unsaturated Fatty Acid Polyunsaturated Fatty Acid (liquid at room T, so doesn’t clog arteries. O Example: olive oil) Hydrophyllic end Phospholipids Form membranes OH C O Glycerol Hydrophobic end Cell membrane OUTSIDE THE CELL IS HYDROPHYLLIC PHOSPHOLIPIDS INSIDE THE MEMBRANE IS HYDROPHOBIC INSIDE THE CELL IS HYDROPHYLLIC Triglycerides are another important lipid group. Tri means 3 Glyceride refers to Glycerol Glycerol One more type of LIPID. Steroids— made of 3 6-member rings and one 5 member ring. Carbohydrates (polysaccharides) Building Block Monosaccharides (sugars) Lipids Glycerol and Fatty Acids Proteins Nucleic Acids Amino Acids Nucleotides--held together by HYDROGEN bonds. P Structure N Important elements C:H:O 1:02:01 Uses energy energy (Structure and support membranes Cell recognition) steroids Examples word endings monosaccharides glucose, fructose (Disaccharides:) sucrose polysaccharides starch glycogen cellulose ends in -ose Just C and H lipids triglycerides fats waxes phospholipids steroids C ------ N C NH2 side and COOH side Peptide bonds N Phosphate groups ribose or deoxyribose sugar Nitrogenous base structures, enzymes heredity (movement, communication, transportation) (lactase dehydrogenase hemoglobin) DNA, RNA ATP is also a nucleotide, but is NOT a nucleic acid. ATP transfers energy ends in -ase Amino Acids (there are 20 common AA’s) R H N C C H H O NH 2 COOH (Carboxyl group) (amino group) Examples of R groups: H or CH OH 3 A chain of AA’s forms a polypeptide… And ultimately, a PROTEIN. Enzymes are proteins that Catalyze reactions. Protein Substrate Enzyme A The Substrate is modified but the Enzyme is unchanged. Enzymes are proteins that Catalyze reactions. Protein Substrate Enzyme A The Substrate is modified but the Enzyme is unchanged. Energy Activation Energy With enzyme Time PO4 Base Sugar A nucleotide Sugar= Deoxyribose (DNA) or Ribose (RNA DNA is a string of nucleotides that are hydrogen bonded to each other. PO4 Base PO4 Base Sugar Sugar PO4 Base PO4 Base Sugar Sugar The strands form a Double Helix. Carbohydrates (polysaccharides) Building Block Monosaccharides (sugars) Lipids Glycerol and Fatty Acids Proteins Nucleic Acids Amino Acids Nucleotides--held together by HYDROGEN bonds. P Structure N Important elements C:H:O 1:02:01 Uses energy energy (Structure and support membranes Cell recognition) steroids structures, enzymes monosaccharides glucose, fructose (Disaccharides:) sucrose polysaccharides starch glycogen cellulose ends in -ose (lactase dehydrogenase hemoglobin) Examples word endings Just C and H C ------ N lipids triglycerides fats waxes phospholipids steroids C NH2 side and COOH side Peptide bonds N Phosphate groups ribose or deoxyribose sugar Nitrogenous base heredity (movement, communication, transportation) DNA, RNA ATP is also a nucleotide, but is NOT a nucleic acid. ATP transfers energy ends in -ase