Chemistry, Biomolecules, and Enzymes

1. Chemistry, Biomolecules, and Enzymes Table 3

2. Basic Chemistry Elements and the Periodic Table Structure of an Atom Isotopes Chemical Bonds Covalent Bonds Ionic Bonds Hydrogen Bonds Chemical Reactions Properties of Water Macromolecules Lipids Proteins Carbohydrates Nucleic Acids Enzymes General Substrate Specificity Allosteric Regulation Inhibitors Credits Menu Denotes a Review Song!

3. Element- one of 92 substances that cannot be broken down by chemical reactions Atomic number- number of protons, equal to the number of electrons Mass number- number of protons +the number of neutrons Elements and the Periodic Table Element Name Atomic Number Chemical Symbol Atomic Mass, Mass Number would be 23 Structure of an Atom Menu

4. Atom- smallest unit of matter that still retains the properties of a specific element Proton- positively charged, 1 AMU (atomic mass unit) Neutron- neutral charge, 1 AMU Electron- negatively charged, 1/2000 AMU Structure of an Atom Elements/Table Isotopes Menu

5. Isotope- atom with the same number of protons, but different number of neutrons Radioactive Isotope- nucleus decays spontaneously, releasing particles and energy, may lead to a change in the number of protons, useful in radioactive dating (Carbon 14), following atoms through metabolism (PET scanners), diagnoses, but can damage cellular molecules Isotopes Atomic Structure Covalent Bonds Menu

6. Covalent Bond- Sharing of one or more pairs of valence electrons between two atoms (Single Bond- one pair, Double Bond- two pairs) Molecule- 2 or more atoms held together by covalent bonds Electronegativity- how much an atom attracts electrons Covalent Bonds Click to start video: Isotopes Covalent (cont.) Menu

7. Non-Polar- between two atoms with the same electronegativity, electrons are shared equally Polar- between two atoms with different electronegativity, electron pair shared unequally between the two atoms, giving one a δ+ (slight positive charge), and one a δ- (slight negative charge) Covalent Bonds Covalent Bonds Ionic Bonds Menu

8. Ionic Bond- the transfer of a valence electron to a more electronegative atom Ion- a charged atom or molecule (cation is positive, and anion is negative) Ionic Compounds/Salts- formed by ionic bonds, don’t consist of molecules, form a crystal with a definite ratio of atoms Overview of Bonding Ionic Bonds/ Overview Click to start video: Covalent Bonds Hydrogen Bonds Menu

9. Hydrogen Bond- attraction between a slightly positive hydrogen of one molecule and a slightly negative oxygen (or other electronegative atom) of another molecule, individually weak, but strong when grouped together Hydrogen Bonds Quick Review of Bonding: Time for a Song! Ionic Bonds Chemical Reactions Menu

10. Chemical Reaction- the making and breaking of chemical bonds, leading to a change in the composition of matter, most are reversible Reactants- starting materials Products- ending materials Will tend to reach equilibrium, products and reactants are in a fixed ratio Chemical Reactions Equilibrium Diagram Hydrogen Bonds Properties of H2O Menu

11. Good solvent (can dissolve other things) because it is polar and can form hydrogen bonds Is cohesive (can stick to other water) and adhesive (can stick to other molecules) because of hydrogen bonds Good medium for reaction, often an important reactant or product High specific heat (takes a lot of energy to change its heat) and High heat of vaporization (takes a lot of energy to go from a liquid to a gas, easy cooling by evaporation) Density is highest at 4ｰ C because hydrogen bonds make the solid form of water create a crystalline lattice structure that takes up space, means that ice floats and because ice is a good insulator, water underneath it will stay warm High surface tension because of hydrogen bonds Low friction/ is a good lubricant Properties of Water Chemical Reactions Lipids Menu

12. Examples: phospholipids, cholesterol, estrogen, wax Made up of glycerol and fatty acids or a steroid core (4 rings) Store energy, build membranes, insulate, serve as hormones, some are vitamins (example: vitamin E) Cholesterol used to build all other steroid molecules Lipids Glycerol Fatty Acid Tails Properties of H2O Proteins Menu

13. Made up of amino acids, which all have an amino group, carboxyl group, and one of 20 possible different R groups Joined together by peptide bonds between carboxyl and amino groups Levels of Structure Primary (1ｰ) - sequence and types of amino acids used in a protein Secondary (2ｰ)- shape (α –helix, β- pleated sheet) that different sections of the protein strand will take based on hydrogen bonds (between R- groups) Tertiary (3ｰ)- 3D shape of protein caused by hydrogen bonds and other bonds between R-groups Quaternary (4ｰ)- how 2+ protein strands (polypeptides) wrap together to form 1 large complex Make up many functional and structural parts of cells, also are enzymes to do chemical reactions Proteins Lipids Protein Diagrams Menu

14. Proteins (Diagrams) Proteins Carbohydrates Menu

15. Carbohydrates • Examples: glucose, starch, cellulose, sucrose • Made up of monosaccharides (single sugars such as glucose and fructose), form dissacharides (double sugars such as sucrose and lactose) or polysaccharides (many sugars such as cellulose, starch (plant= amylose, animal= glycogen, chitin)) • Store short and long term energy, form structures such as cell walls Amylose, a form of starch found in plants, a polysaccharide Protein Diagrams Nucleic Acids Menu

16. Nucleic Acids Quick Review of Biomolecules: Time for a Song! • Made up of nucleotides, which are made of a phosphate group, a 5 carbon sugar, and one of 4 possible nitrogenous bases (for DNA= adenine, guanine, cytosine, thymine, for RNA= adenine, guanine, cytosine, uracil) • Hold/ transfer instructions of how to build proteins (genetic information) • ATP transfers/stores energy (for a few seconds Carbohydrates Nucleic Acids (cont.) Menu

17. Nucleic Acids • Form chains when the phosphate of one nucleotide joins to the sugar of another nucleotide • Another chain is held to the first by hydrogen bonds between the bases, and the two strands twist into a double helix • Strands are antiparallel Nucleic Acids Enzymes (General) Menu

18. Enzymes (General) • Speed up metabolic reactions by lowering energy barriers • Enzyme = macromolecule that acts as a catalyst • Catalyst = chemical agent that speeds up a reaction without being consumed • Activation Energy = initial energy required for starting a reaction, often supplied as heat • Transition state = unstable form of reactants once they have absorbed enough energy for bonds to break • An enzyme catalyzes a reaction by lowering the Activation Energy Barrier, enabling the reactant molecules to reach their transition state more often Nucleic Acids Diagram of Reaction Menu

19. Diagram of a Reaction Enzymes (General) Substrate Specificity Menu

20. Substrate Specificity • Substrate = reactant an enzyme acts on, converts substrate to product • Enzyme-Substrate Complex = forms when enzyme and substrate join • Enzyme will only act on its specific substrate – dependent on shape • Active Site = region of enzyme that substrate binds to • Induced fit = enzyme changes shape to fit more snugly into substrate Click to start video: Diagram of Reaction Allosteric Regulation Menu

21. Allosteric Regulation • A protein’s function at one site is affected by the binding of a regulatory molecule to a separate site • Allosteric Activator = binds to regulatory site and stabilizes the shape that has functional active sites • Allosteric Inhibitor = binds to regulatory site and stabilizes inactive form of enzyme • Cooperativity = mechanism that amplifies the response of enzymes to substrates by triggering shape change (and thus catalysis) in all subunits of an enzyme • Feedback Inhibition = metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme that acts early in the pathway Substrate Specificity Regulation (cont.) Menu

22. Allosteric Regulation allosteric inhibitor Allosteric Regulation Inhibitors Menu

23. Quick Review of Enzymes: Time for a Song! Inhibitors • Competitive Inhibitors= mimic normal substrate molecules and block substrate from active site by binding to active site • Noncompetitive Inhibitors= impede enzymatic reactions by binding to another part of the enzyme, altering its shape Allosteric Regulation Credits Menu

24. Back Menu Biomolecule Review Song Chorus: Carbohydrates, Nucleic Acids, Proteins, Lipids, Are your passes To keep you working properly These are the molecules that you need There’s 4 types 4 types 4 types of biomolecules you need Verse 1: Lipids they’re your body’s fats You saw them when we dissected cats The phosphate heads of the bilayer They sure like to touch water They’re on the outside of the cell The fatty acid tails are protected well Verse 2: Proteins are the building blocks Of your body’s many parts They’ve got carboxyl and amino groups And 20 possible R groups too If amino acids make a chain Primary structure is its name Secondary they fold up Tertiary is a 3D clump Quaternary they join together To build the final protein structure Verse 3: Mono and disaccharrides Are carbohydrates in disguise They store short term energy From foods that are very sugary Nucleic Acids have a phosphate 5 carbon sugar and nitrogen base They make up your DNA ATP and RNA They’ve got two strands antiparallel And carry genetic info as well

25. Back Menu Enzyme Review Song Chorus: Enzymes They can catalyze Chemical reactions When they bind at their active site And substrates Have a specific shape For the enzyme That fits into them the right way Verse 1: Activation energy a reaction needs To start forcefully It forms a barrier of energy required To break the bonds that hold reactants together But then the enzyme It comes just in time And saves the day It lowers the barrier To reach the transition state Reactants unstable Reaction underway Verse 2: Enzyme inhibitors They attempt to block The enzyme-substrate lock Some compete directly And some do not With the enzyme that they want to stop Enzymes they regulate Inhibit or activate Allosterically They can change the shape Of a protein so that it may Stabilize its active sites Or just inactivate

26. Back Menu Bonding Review Song Verse: Just an ionic bond Transfer of electrons It lets atoms fill Those last valence spots Electronegativity To the higher one electrons flee Ionic bonds oh they can give Metallic properties And then there’s covalent bonds They can share electrons They make non-metals strong To last on and on and on and on Some bonds are polar Electrons shared unequally Due to different Electronegativities Hydrogen bonds They are weak one-on-one But together They are strong! Chorus: Don’t stop bonding Hold on to those electrons To keep that molecule Holding strong Ionic, Covalent And Hydrogen bonding they make Molecules stay In their place

27. Atom Cover Art: http://www.presentermedia.com/files/clipart/00001000/1474 Structure of a Carbon Atom: http://www.universetoday.com/wp-content/uploads/2010/02/c-atom_e1.gif Helium Isotopes: http://www.green-planet-solar-energy.com/images/helium-isotopes-5-to-8.gif Covalent Bond Video: http://www.youtube.com/watch?v=1wpDicW_MQQ Picture of Water Molecule: http://media.wiley.com/Lux/33/168033.image0.jpg Electronegativity Video: http://www.youtube.com/watch?v=Kj3o0XvhVqQ Hydrogen Bond Diagram: http://academic.brooklyn.cuny.edu/biology/bio4fv/page/image12.gif Equilibrium Diagram: http://www.bbc.co.uk/scotland/learning/bitesize/higher/chemistry/images/process_of_equilibrium.jpg Protein Structure Diagram: http://www.umass.edu/molvis/workshop/imgs/protein-structure2.png Nucleotide Diagram: http://www.buzzle.com/img/articleImages/387160-1237-22.jpg Amylose Diagram: http://www.mansfield.ohio-state.edu/~sabedon/071amylo.gif Antiparallel DNA Diagram: http://www.tokresource.org/tok_classes/biobiobio/biomenu/dna_structure/dsDNA.jpgD Diagram of a Reaction: http://www4.nau.edu/meteorite/Meteorite/Images/activation-energy.png Enzyme-Substrate Video: http://www.youtube.com/watch?v=V4OPO6JQLO Allosteric Regulation Diagram: http://2.bp.blogspot.com/-CQucyJGm-Nw/Ta-cyJu7E0I/AAAAAAAAACs/1ARDfnqIYac/s1600/7-10.gif Competitive vs. Non Competitive Inhibitors Diagram: http://www.tokresource.org/tok_classes/biobiobio/biomenu/enzymes/competitive_inhibit_c_la_784.jpg Musical Note: http://wwwcdn.net/ev/assets/images/vectors/afbig/musical-note-3-clip-art.jpg Credits