Unit 2B Biochemistry Part 2

1. Unit 2B Biochemistry Part 2 Proteins, Chemical Reactions, and pH

2. Proteins • Of all the organic compounds, proteins are the largest, most complex, and most diverse. • While 70% of the body is water, most of the other 30% is protein!

3. Proteins • Made of elements C, H, O, N • Made of amino acids (the monomer) • Peptide bonds link amino acids together to make polypeptides • One or more polypeptides “fold” into a Protein

4. Proteins are Diverse • 20 amino acids are used to make proteins • Different combos of amino acids lead to different functioning proteins • DNA tells the proteins how to assemble.

5. Amino Acids • Amino acids are compounds with an amino group (-NH2) on one end and a carboxyl (-COOH) group on the other end.

6. Each amino acid consists of one of each of the following, connected to each other by covalent bonds. 1) carboxyl group (-COOH) 2) amino group (-NH2) 3) one central carbon atom (-C-) • Between the amino and carboxyl groups 4) one lone hydrogen atom (-H) • Comes off the central carbon 5) 'R' (variable) group - one of 20 different side chains Central Carbon Lone Hydrogen

7. Circle each amino group, box each carboxyl group and label each R group (-R).

8. Because of their uniform structure, any amino acid can bond to any other amino acid using a covalent bond called a peptide bond. • What process will link together two individual amino acids?

9. Glycine Valine • On the two amino acids below, circle the atoms that must be removed in order to create a peptide bond. • Hint: These atoms create a __________ molecule, which is a product of the reaction.

10. Polypeptides • Segments of amino acids are called polypeptides • When they are first assembled, polypeptides are linear (straight) chains. • They are not yet functioning proteins!

11. R groups on the amino acids interact with each other causing the polypeptide to fold into a specific 3-dimentional shape or structure.

12. Once it is completely and correctly folded, it is considered a protein. • (other small changes or modifications may also occur before the protein is completely functional) • The structure of each protein in unique; Structure leads to function! Protein Folding

13. How many amino acids are shown in the polypeptide below? (Hint: count the R groups) How many peptide bonds are shown in the polypeptide below? (Hint: peptide bonds are between which two atoms?) How many water molecules were released as this polypeptide was formed? (Hint: one for each bond made!)

14. Chemical Reactions Everything that happens in an organism is based on a chemical reaction! • Change one set of chemicals into another • Chemical bonds change • Reactants- elements/compounds that enter the reaction • Products- are produced by the reaction

15. When bonds are made or broken… - Energy is absorbed (taken in) or released (given off) • Reactions releasing energy can (but not always) occur on their own, or spontaneously. • Reactions absorbing energy will not occur without a source of energy

16. Example • Paper is made of cellulose which burns in the presence of oxygen, and releases energy in the form of heat and light. But this packet is not spontaneously bursting into flames right now. Why not? What is missing?

17. Where does your body get energy for chemical reactions? Plants? Make food by photosynthesis and turn it into energy by cellular respiration. Animals? Eat food and turn it into energy by cellular respiration.

18. Activation Energy • Is the amount of energy that a reaction needs to get started • Every reaction requires a certain amount of activation energy to get started, regardless of whether it is an energy-absorbing or energy-releasing reaction.

19. Energy absorbing reactions (Endergonic) • Products have more energy than the reactants • Products are larger, less stable, and more complex than reactants • It takes more energy to break bonds in the reactants than is released by making new bonds in the products • Examples: dehydration synthesis; photosynthesis

20. Dehydration Synthesis (Energy Absorbing)

21. Energy releasing reactions (Exergonic) •Reactants have more energy than the products •Reactants are larger, less stable, and more complex than products •More energy is released when new bonds are formed in the products than was needed to break the old bonds in the reactants Examples: hydrolysis; cellular respiration

22. Dehydration Synthesis (Energy Absorbing) Hydrolysis (Energy releasing)

23. Enzymes • Some chemical reactions would be too slow or have too high of an activation energy without a little help. • Catalyst- a substance that speeds up a chemical reaction • works by lowering the activation energy • Cells make special proteins called enzymes to act as catalysts for chemical reactions. • There is one type of enzyme for each type of chemical reaction (its shape makes it specific for its job)

24. Would the hill be higher or lower with an enzyme present?

25. HOW DO ENZYMES WORK? 1. They provide a site for the reactants to be brought together to react. 2. They help to break the bonds of the reactants. • This reduces the energy needed for the reaction. “Enzyme Catalyzed Reaction”- a reaction sped up by an enzyme

26. Substrates- what the reactants are called in an enzyme catalyzed reaction. • Substrates bind to a place on the enzyme called the active site which has a specific shape.

27. 2 Models help explain how enzymes work 1. "Lock and Key Model": The substrates fit the active site of an enzyme like a key fits into a lock. A very specific interaction! • This provides the site for the reactants to come together. Substrate Enzyme

28. Example of an enzyme-catalyzed reaction: ____________ is formed by combining ___________________ and water in the presence of the enzyme “_______________________”. 2. “Induced-fit Model”: The enzyme binds the substrate(s) and slightly changes its shape to “hug” the substrate(s) tightly (like a handshake). This places “strain” on existing bonds, allowing bonds to break and the chemical reaction to go forward.

29. WHY aren’t enzymes considered a reactant or a product? • After the product is released from the enzyme, the enzyme is recycled and used again. • Enzymes are reusable!

30. Common Hydrolytic Enzymes(The suffix "–ase" commonly indicates that a protein is an enzyme) 1. protease- any enzyme that speeds hydrolysis or breakdown of proteins 2. sucrase (a disaccharidease) - an enzyme which speeds the breakdown of ___________________ 3. lipase - any enzyme which speeds the breakdown of _________________________ 4. nuclease - any enzyme which speeds the breakdown of _______________________ 5. amylase - an enzyme which speeds the breakdown of amylose (=starch!)

31. FACTORS AFFECTING ENZYME ACTIVITY • Temperature, pH, and regulatory molecules affect enzyme activity • An increase in temperature will increase the rate of a reaction to a certain point • After that point, the enzyme will no longer work

32. Denaturation - when a protein unfolds and loses its overall shape (and thus function) due to increased temp or changes in pH. • Denatured enzymes lose the shape of their active site and will no longer function. Think! Why are temperature and pH important factors in maintaining homeostasis?

33. pH • Water is one of the most important inorganic substances in living organisms. • Sometime water molecules will break apart (dissociate) to form ions. • Ion- a positively or negatively charged atom (set of atoms) due to loss or gain of electrons

34. About 1 water molecule in 550 million splits in this way. • Because the number of positive H+ ions is equal to the number of negative OH- ions, water is neutral. • pH scale- measures the concentration of H+ ions in solution [H+]

35. pH Scale • Measured 0-14 • Each step represents a factor of 10 • 7 is neutral (like water- has equal amounts of H+ and OH-) • Lower from 7 becomes more acidic (has more H+) • Higher from 7 becomes more basic/alkaline (has less H+)

36. Order these substances in order of increasing acidity: human blood, acid rain, bleach, seawater, stomach acid.

37. Acid, Base, or Neutral? Strong or Weak? • pH 7:_______ pH 13.5:_____ • pH 8:_______ pH 2:________ • Which one is more acidic pH of 2 -or- pH of 4 • How many times more?___________ • Which one is more basic? Tomato juice -or- Soap • How many times more?________

38. Definitions of acids and bases • ACID- compound that forms H+ ions in solution • Acids have more H+ than OH- • BASE- compounds that forms OH- ions in solution • Bases have more OH- than H+

39. Study the reaction below. Is this substance an ACID or BASE? (circle) Dissociation In Water HClH+ + Cl- Hydrogen Chloride Hydrogen ion Chloride ion Study the reaction below. Is this substance an ACID or BASE? (Circle) Dissociation In Water NaOH Na+ + OH- Sodium Hydroxide Sodium ion hydroxide ion

41. acid neutral Base

42. Sample acids and bases

43. BUFFERS • Controlling pH is important for maintaining homeostasis in cells. The pH of most cells in the human body must be kept between 6.5 and 7.5. • Buffers- Weak acids or bases that react with strong acids or bases to prevent sharp, sudden changes of pH. • Example: Sudden pH changes in blood are prevented by buffers such as bicarbonate and phosphate ions.