1. Biochemistry and Enzymes Test date:9/23 (A) 9/24 (B)

2. Overview Atoms, elements, compounds Bonding Properties of Water Solution, solvent, and solute pH, acids, and bases Monomer, polymer, macromolecules Chemical reactions Enzymes

3. Atoms An atom is the smallest basic unit of matter – In other words, it cannot be broken down any further without damaging it A period on a piece of paper would contain millions of atoms!!! It would take more than one trillion years to count the number of atoms in a grain of sand!

4. Parts of an atom Proton  (+) – Center of the atom – More dense – Same number of protons and neutrons (electrically neutral) Neutron  (neutral=no charge) – Center of the atom – More dense Electron  (-) – Lie outside the atom – Never come into contact with the nucleus (electron cloud) – Much smaller than protons and neutrons

5. Drawing of an atom

6. Atomic number and atomic mass Atomic number  number of protons, which is unique for every element. – Located to the left of the symbol for most periodic tables – In an atom that has no charge (electrically neutral) the number of protons is the same as electrons – Ex: 2 He has an atomic number of 2 Atomic Mass  sum of protons plus neutrons – Ex: 2 He would have an atomic mass of 4 – How many neutrons does it have? 4

7. Isotopes An element whose atoms have a different number of neutrons, same number of electrons and protons You name them by their atomic mass, which is the sum of neutrons, electrons, and protons EX: Carbon has 6 neutrons, 6 protons, and 6 electrons (Carbon12) Isotopes of carbon  Carbon13 (7 neutrons, 6 protons, and 6 electrons) and Carbon14 (8 neutrons, 6 protons, and 6 electrons) – Radioactive isotope  Carbon14 is used for radioactive dating to determine half life of particular substances, fossils, and rocks

8. Periodic Table Organized by atomic number that goes from 1 to 118 Dmitri Mendeleev Abbreviations

9. Organization Groups  the vertical columns – Gives the type of element, the number of valence electrons, behavior like volatility, and electronegativity – All in group one are called alkali metals – All in group 18 are called noble gases Period  horizontal row – Determine ionization energy, electronegativity, and electron affinity (likeness of other molecules)

10. Electron An orbital is a “shell” around the nucleus where the electrons are traveling Different orbitals can hold various amounts of electrons. – Ex: the first shell can only hold 2 electrons, but the second shell can hold 8 The left-to-right sequence of elements in each row corresponds to the sequential addition of electrons (and protons)

11. Valence Electrons The term for the amount of electrons in the outermost shell

12. Element Two different possibilities – A group of atoms of the same type – One particular type of atom that cant be broken down – Name some elements: Hydrogen, oxygen, nitrogen, carbon, gold, iron, nickel, aluminum, helium are all common elements If all atoms are made up of protons, neutrons, and electrons, are all elements the same? – If not, what makes one element different than the other

13. Elements All elements have a different number of protons in each atom – For example, hydrogen atoms have only one proton, while oxygen atoms have 8 protons Electrons of each atom of an element determine the properties of that element The electrons move around in their “clouds” forming energy levels Different energy levels can hold a different number of electrons The different energy levels are sometimes called orbitals Most atoms are more stable when the orbital is full

14. Elements in biology Of all the 91 elements that naturally occur on earth only 25 are found in organisms Just 4 elements make up 96% of humans – Carbon, oxygen, nitrogen, and hydrogen The other 4% comes from trace amounts of many other elements – Even if they are in small amounts, it is essential for your body to have them – Ex: Iron, Calcium, Phosphorous, Magnesium, Potassium, Sulphur, Sodium

15. Compounds Substance made of atoms of different elements bonded together in a very specific ratio Impt compounds: – Water (H 2 O) – Carbon Dioxide (CO 2 ) Compounds properties are very different than the elements they are made up of – Ex: Hydrogen and Oxygen are both gases, but together form a liquid at room temperature – Ex: A diamond is pure carbon, but it is black Carbon is also in sugars, proteins, and almost all compounds

16. Ions and ionic bonding Ion  an atom that has gained or lost an electron – An atom cannot lose protons An ion is formed and is less stable than the original atom An ion that loses electrons becomes (+) because it has more protons than electrons (cation) An ion that gains electrons becomes (-) because it has less protons than electrons (anion) Ionic compounds are compounds created when both atoms are ions (one positive and one negative) We have some names for this, ionic compound or salt To summarize, one atom gains, the other loses an electron creating a polar compound Ex: NaCl (table salt)=sodium chloride

17. Drawing of ionic bonding

18. Covalent Bonding Some atoms do not like to gain or lose electrons easily Some can only bond covalently  when two or more compounds share a pair of valence electrons Covalent bonds are much stronger than ionic bonds Two atoms may form several covalent bonds to share several pairs of electrons When shared, all atoms have to have a full outer orbital (shell) Resulting is not called a compound, instead it is called a molecule Some elements occur naturally this way – Hydrogen, nitrogen, and oxygen are usually seen in pairs that share electrons (O 2, H 2, and N 2 ) Ex: Carbon dioxide (CO 2 )

19. Structural formula Represented by all atoms involved in the bond with “lines” between them The line is representing the bond Single bond= single line Double bond=double line Triple bond=triple line Molecular formula  the formula without the lines for bonds

20. Drawing of covalent bonding

21. Van der Waals Forces With covalent bonds, electrons are shared equally Van der Waals forces are like covalent bonds in that they share electrons, but they are different because it is unequal sharing When molecules are close together, they can be attracted to a neighboring molecule without bonding to it – Geckos “sticking” to smooth vertical surfaces – Van der Waals forces form between molecules on the surface of the geckos foot and molecules on the surface of the wall

22. Properties of Water Hydrogen Bonding Adhesion Cohesion Surface tension Polarity Specific heat Heat of vaporization “the calorie”

23. Properties of Water Group Lab activity Black Pepper Paper Clip Pour on table Drops on a penny Celery

24. Water H 2 O Your body has to have water: – Gives cells structure – Allows for transport – All processes necessary for life take place in an aqueous environment-water Why does ice float in water? – Less dense as a solid than as a liquid-very few compounds behave this way Contains hydrogen bonds Polar Opposite charges of two polar molecules can form hydrogen bonds

25. Polar vs Non-polar Polar  one atom has a partial positive charge, and the other atom has a partial negative charge Water is polar, so only polar molecules dissolve in water – Few exceptions if they are very small (O 2 ) Non-Polar  usually covalent bonds that do not have any polarity (no negatives or positive charges)

26. Drawing of ionic, polar, and non polar Ionic Bonding Polar bonding Non-Polar bonding

27. Hydrogen Bonding An attraction between a slightly negative atom and a slightly positive atom Usually forms many bonds with many of the same type of molecule – Ex: very many water molecules all bound together in unison Very weak as individual bonds, but are very strong as a whole Why is hydrogen bonding important: – Adhesion, cohesion, surface tension, specific heat

28. Adhesion Comes from the word adhere  to stick to Adhesion is the ability of water to stick to other things “Trickle” on sides of water bottle The water is actually sticking to the sides of the water bottle The reason for a meniscus inside a test tube or graduated cylinder This is very important for plants Celery

29. Cohesion Comes from the latin prefix “co” which means together The ability for water molecules to stick to each other using hydrogen bonds Water “beading” up on your windshield when it rains or when it has been washed Reason for surface tension  top layer of water that is “harder” than the underneath layers Why it hurts when you dive into water “Jesus Lizard”

30. Dehydration Synthesis De-Hydra-tion Synthesis Chemical Reaction that involves the loss of water (water gets used up) in order to combine two or more reactants Ex: Glucose and fructose can combine together to make table sugar, the reaction uses up water

31. Hydrolysis Hyro-Lysis Breaking apart chemical bonds by using water to do so, which in turn breaks apart the water Salts of weak acids or bases are dissolved in water, breaking apart the water and breaking apart the salt Ex: dissolving sulfuric acid and water uses hydrolysis, because the sulfuric acid dissociates into hydronium and bisulfate

32. Dissolving in water Solution  is what is created when one substance is dissolved in another Solvent  the liquid that dissolves the solid; usually water Solute  the solid that gets dissolved The amount of solute that gets dissolved in a certain amount of solvent is called the concentration of the solution If you are mixing Kool-Aid, and put a small amount of mix, it will taste very weak, but as you put more mix into the solution, it will taste more like Kool-Aid and less like water Biology ex: bloodplasma  is 95% water, so the solvent is water, the sugars, proteins, etc. in plasma are solutes, and plasma is the solution

33. Heat and Water Water has a high specific heat Specific heat  the amount of heat that must be absorbed or lost for 1g of that substance to change its temperature by 1 degree celsius The specific heat of water is measured in Calories Kilocalorie  1000 calories The “calories” on food packages are actually kilocalories

34. Heat of Vaporization The amount of heat a liquid must absorb for 1g of it to be converted from the liquid to the gaseous state Water has a high heat of vaporization Both of these properties changes weather and climate patterns globally In what climate region does the temperature change the most? Least?

35. Suspensions When molecules do not dissolve when placed in water, they instead break apart into smaller pieces The movement of water molecules keeps the small particles suspended Important biological fluids are suspensions Blood is a very important suspension – Mostly water, with many dissolved compounds, but also a lot that get broken down into tiny pieces (iron, calcium, salt)

36. Acids/Bases When compounds are dissolved in a solvent, they often break down into ions What is an ion? An acid  compound that releases a proton (H+) when it is dissolved in water – Higher concentration of H+ in the solution A Base  compound that removes H+ from the solution – Low concentration of H+ in the solution A solutions acidity is based off of the pH scale

37. pH scale Stands for potential hydrogen (H+) A solution with pH of 0 is very acidic with a high concentration of H+ A solution with a pH of 14 is very basic with a low concentration of H+ A solution with a pH of 7 is neutral, neither basic or acidic Most living organisms need to keep their pH around 7 – Exception: Azalea bush needs a pH of around 4.5 Buffers  compound that can bind to an H+ ion when the ion concentration increases, and can release an H+ ion when the H+ concentration decreases – In simple terms, it keeps the pH around 7 – Normal pH of blood is around 7.4, anything above 7.8 and below 6.8, causes fatalities

38. Drawing of pH scale

39. – What color is carbon? – When you burn wood, what color are the ashes? – If you burnt an orange, what color would the ashes be? – If you burned a person, what color would the ashes be?

40. Carbon-based molecules Carbon is the basis for all life, anything living is made up of carbon People say that anything living makes good compost, because it breaks down into carbon, which is the basis for soil, hence the black color Carbon is so important because of its atomic structure – Has four valence electrons, therefore, it can form covalent bonds with up to four other molecules at once – Draw picture – Organic chemistry  the study of carbon compounds

41. Types of carbon formations Ring Branched Straight

42. Important Vocab Monomer: subunits of a complex molecule – One – “What can the macromolecule be broken down into?” Polymer: – Many monomers bound together in a chain or strand – Can be all the same monomer (starch) or all be different monomers (proteins) – “If you put the monomers together, what do you get?”

43. Picture of monomer and polymer

44. Four Macromolecules Carbohydrates Lipids Proteins Nucleic Acids

45. Carbohydrates Molecules composed of carbon, hydrogen, and oxygen Can be broken down into starches, and starches into sugars Carbohydrates get broken down into useable energy=ATP Basic carbohydrates are called monosaccharides=one sugar Simple sugars usually have five or six carbons in a chain – Ex: fructose, glucose These simple sugars can bind together in repeating units creating a polysaccharide=many sugars – Ex: table sugar  sucrose=glucose + fructose

46. Complex carbohydrates Starch – Branched chains of glucose – Can be broken down into simple glucose sugars and used for energy by plants and animals Glycogen – Used and stored only in animal cells – Highly branched Cellulose – Used by only plants, animals cannot break down cellulose – This is why it is stored as “butt dimples” in humans – Makes up the cell wall in plants and helps plants stand up by themselves Ex: celery

47. Uses for carbohydrates In animals, provide energy In plants, is the product of photosynthesis Foods – Corn, potatoes, rice, pasta, any other starch Real life application – Why does the food pyramid suggest that we eat more carbs than any other type of food?

48. Drawing of carbohydrates

49. Lipids Non-polar molecules, what does that mean? Fats, oils, cholesterols, and steroids Some lipids can be broken down into usable energy for cells, others help out with the structure of the cell (later chapter) Fats and oils actually contain much more energy than carbohydrates – Animal fats  meat and butter – Plant fats  vegetable and peanut oil

50. Structure of lipids Contain repeating units of three fatty acids bonded to a glycerol, which is called a triglyceride Saturated fatty acids  no double bonds – Not so good fats – Usually true animal fats such as lard and butter – Solid at room temperature Unsaturated fatty acids  contain at least one double bond – Better fats for you health wise – Usually in the form of oils (double bond makes them liquid)

51. Uses for lipids Cell membrane=phospholipids A phospholipid contains two fatty acids and a phosphate group bonded to a glycerol Have head and tail region Very unique structure that we will discuss more when we get to parts of the cell

52. Steriods Cholesterol – Is bad if your body has too much, but it is essential for life – A lot of steroid based hormones such as estrogen and testosterone are made from cholesterol – Also is part of the cell membrane, and helps it be more fluid – Real life application  when you have a fever, it is your bodies way of “melting” the cholesterol to allow the pathogens to escape out the cell membrane Hormones such as estrogen, progesterone, and testosterone are also considered steriods

53. Drawing of fatty acid chains

54. Proteins NOT repeating units, instead they vary depending on structure and function A protein is a polymer made up of monomers called amino acids Amino acids are molecules that contain carbon, hydrogen, nitrogen, oxygen, and sometimes sulfur There are 20 different amino acids that can combine together in any order to create millions of different proteins Your body can make 12 of these naturally, the others we have to eat

55. Structure of amino acids All amino acids have similar structure – Carbon bonded to Hydrogen atom Amino group Carboxyl group Amino acids differ only in their side group Amino acids form covalent bonds with each called peptide bonds Many amino acids bond together forming polypeptides More than one peptide bound together is called a protein

56. Important info about proteins Proteins differ in the particular amino acids used to make them Also they differ in the number of amino acids These two things determine the structure and function of the protein Functions of proteins: – Cellular transport into and out of the cell – Cellular transport from organelle to organelle – Helps make DNA and genes – Enzymes are a specific type of protein that has many functions

57. Four levels of protein structure Primary Secondary Tertiary Quaternary

58. Protein Folding Chaperonins  molecules that assist the protein in folding itself – They basically make sure the structure is not damaged by outside forces and molecules Takes several steps that scientists do NOT know all of at this point in time X-ray crystallography is the best method for examining the final three dimensional structure of a protein

59. Drawing of protein/amino acids

60. Nucleic Acids Polymers that are made up of monomers of nucleotides Basis for DNA and RNA Instructions for building proteins Nucleotide  sugar, phosphate group, and a nitrogenous base Unlike all the others who have many functions, nucleic acids only have one, to make proteins You will learn a lot more about nucleic acids later in the year

61. Chemical Reactions Change substances by breaking and reforming chemical bonds – Burning wood Physical reactions, just alters the state of the chemical involved – Ice melting Important vocab: – Reactant, Product, bond energy, activation energy, equilibrium, exothermic, and endothermic Important tools – Balancing equations

62. Basics of chemical reactions Reactants  what goes into the reaction – “ingredients” – What gets broken down Products  what comes out of the reaction – Final outcome – What gets reformed

63. Some examples

64. Bond energy Bond energy is the amount of energy needed to break a bond between two atoms This is different and unique for each type of atom A certain amount of energy is needed to break bonds between two oxygen atoms A certain amount of energy is needed to break hydrogen bonds in water Energy is also needed to form a bond The energy needed to form a bond is equal to the amount of energy needed

65. Chemical Equilibrium Some reactions continue until all the reactants are used up, and you are left with only product However, other reactions can also work in reverse, and turn the product back into reactant Actually what happens is that reactants are being turned into products at the same rate as products are turning into reactants We call this chemical equilibrium= state of equality (amount of reactants=amount of products; 50% of each)

66. Drawing and examples

67. Energy in chemical reactions All chemical reactions involve changes in energy – Energy is never created or destroyed Energy that is added to the reaction breaks down their chemical bonds – Can be in the form of heating the reaction up, cooling it down Energy is released at the end of the reaction when the product is formed – Can be heat, steam, cold, etc. All chemical reactions do both, it takes some energy to start the reaction and also energy gets released – The ratio of absorbtion vs. releasing is determined by bond energy

68. Activation energy The amount of energy that needs to be absorbed for the reaction to occur – Can think of it like the energy it takes to roll a rock up a hill, once it gets to the top, it will roll down by itself

69. Exothermic Releases more energy than it absorbs Products have lower bond energy than the reactants The excess energy is released as heat or light Ex: fireflies, squids Cellular respiration is an example of an exothermic reaction that keeps your body warm EXO=Exit Endothermic Absorbs more energy than gets released Takes more energy to start the reaction than gets released Products have higher bond energy than the reactants Photosynthesis is an example of an endothermic reaction, because it needs sunlight to start the reaction ENDO=Into

70. Drawings and examples

71. Enzymes Vocab: – Enzymes – Catalysts – Substrates – Active site – Lock and key model – Induced fit model

72. Catalysts Some reactions take a long time to absorb enough energy to break the activation energy threshold Other reactions, even after threshold has been reached, takes a long time to form products Catalysts fix both problems, enzymes are used to lower the activation energy required to start the reaction, therefore, speeding up the reaction

73. Drawing

74. Enzyme (almost always end in “ase”) Catalysts for chemical reactions produced in living organisms (known as biocatalysts) Specific types of proteins They act just like a catalyst in a chemical reaction, they lower activation energy speeding up the chemical reaction In reactions that are reversible, enzymes do not affect chemical equilibrium They DO NOT change direction, only rate of reaction

75. Enzymes in biology Involved in almost every process in living organisms Help break down food (saliva) Build proteins Your body could not break down food without the enzyme in saliva called amylase Still long chains of amino acids Function of enzyme depends on order and structure of amino acids

76. Changes in enzyme function All enzymes have a specific temp, pH, and concentration that they work the best Temperature – When temps are decreased, enzyme will work, but much slower – When temps are increased, enzyme will become denatured  break down pH – Increases or decreased in pH can cause the enzyme to work slowly, or too quickly – Also, changes in pH can cause the enzyme to become denatured Enzyme concentration – All enzymes have a specific substrate/enzyme ratio in concentration, and deviations from that ratio causes enzyme to not work or become denatured

77. Enzyme Structure Enzyme structure is very important because each enzyme’s shape determines what reactants can bind to the enzyme The specific reactant in which an enzyme can bind is called its substrate Ex: Amylase only breaks down starch and turns it into sugar. – Enzyme=amylase – Substrate=starch – Product=sugar

78. How do enzymes work? 1.Enzyme is specific to certain substrate 2.Substrates bind to the enzyme at active site 3.The enzyme brings substrates together, lowers activation energy, and weakens their bonds 4.The catalyzed reaction forms a product that is released from the enzyme

79. Picture and Video

80. Lock-and-Key model The theory that a substrate and enzyme fit together like a lock and key The fit must be perfect, and that some substrates may fit, but if they are not perfect, then the enzyme wont react with the substrate Original accepted model until more recently

81. Drawing

82. Induced Fit The idea that substrates are still specific for certain enzymes, but they do not fit perfectly Instead they fit good, and go through a conformational change in order to make it fit better The best analogy is like a glove, it fits, but never fits perfectly, you have to stretch it to make it fit better My analogy is like an adjustable (one size fits all) hat Now more accepted than lock-and-key model

83. Drawing

84. Inhibitors Inhibitors do exactly as the name says, they inhibit In other words, they block the active site, and prevent the substrate from binding to the enzyme Many different types – Reversible Inhibitors  only change for that one time Competitive, uncompetitive, non-competitive, and mixed – Irreversible inhibitors  changes that enzyme forever Also known as suicide inhibitors

85. Competitive The inhibitor and substrate are both trying to bind at the same time, and both cannot One will outcompete the other  depends on the concentration

86. Uncompetitive The inhibitor binds to the enzyme after the substrate has already bound to it This causes the enzyme to not work properly

87. Mixed The Inhibitor binds to the enzyme at a different spot than the active site, and causes the enzyme to go through a conformational change that results in the substrate no longer fitting/working

88. Non-competitive The inhibitor binds to a different spot other than the active site, but does not prevent the enzyme from working, but instead makes it work less

89. Suicide Inhibitors Irreversible Inhibitor binds to the active site instead of the substrate causing a permanent conformational change to the enzyme therefore destroying it from ever binding to the substrate again. Looks just like competitive

90. Real Life Applicaiton Most drugs are inhibitors They inhibit neurotransmitters and hormones (substrates) They can also prevent the body from destructive damage  when the body is attacking itself Suicide Inhibitor  example is chemotherapy- which completely kills the cells and the enzymes involved