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Intro: Answer the best you can. We will learn all this and much more this unit. 1.What are proteins? 2.Why do we need proteins? 3.What are lipids (fats)?

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Presentation on theme: "Intro: Answer the best you can. We will learn all this and much more this unit. 1.What are proteins? 2.Why do we need proteins? 3.What are lipids (fats)?"— Presentation transcript:

1 Intro: Answer the best you can. We will learn all this and much more this unit. 1.What are proteins? 2.Why do we need proteins? 3.What are lipids (fats)? 4.Why do we need lipids? 5.What are carbohydrates? 6.Why do we need carbohydrates? 7.What are nucleic acids? 8.Why do we need nucleic acids?

2 Biochemistry Day 1

3 Elements Cannot be broken down into a simpler substance 90 occur naturally; the rest are synthetic or radioactive # of Protons gives characteristic nature – state, reactivity, etc Many are needed by Living Orgs. for 8 characteristics….

4 Periodic Table of Elements

5 A. Human Body Composition

6 Biochemistry Most of the human body is made up of water, H 2 O, with cells consisting of 65-90% water by weight. Therefore, it isn't surprising that most of a human body's mass is oxygen. Carbon, the basic unit for organic molecules, comes in second. 99% of the mass of the human body is made up of just six elements: oxygen, carbon, hydrogen, nitrogen, calcium, and phosphorus. Oxygen (65%) Carbon (18%) Hydrogen (10%) Nitrogen (3%) Calcium (1.5%) Phosphorus (1.0%)

7 96% Living things are made up of the elements C,H,N,O (Carbon, Hydrogen, Nitrogen, and Oxygen)

8 Elements: ~25 elements are essential to life Found in the body in very small amounts, yet play vital roles! What are trace elements?

9 B. Basic Atom

10 The Atom The charge of a proton = +1 (positive 1) The charge of an electron = -1 (negative 1) The charge of a neutron = 0 (neutral) The mass of a proton = about 1 amu The mass of a neutron = about 1 amu The mass of an electron is close to zero in comparison to protons and neutrons Protons and neutrons are found in the nucleus Electrons are found in orbitals outside the nucleus Atomic Number Mass Number

11 The Atom atomic number = The number of protons The Atomic Mass = The mass of all protons, neutrons, and electrons. Number of neutrons = The atomic mass rounded – The Atomic number Or since the electrons weigh near zero Number of Neutrons = Number of protons and neutrons – the number of protons The number of neutrons in Helium = = 2

12 Activity 1 How many protons neutrons and electrons in the following atoms: a. Carbon b. Oxygen c. Iron

13 Activity 2: Carbon Draw an atom of Carbon. Identify the parts of the atom

14 Carbon Draw an atom of Carbon. Identify the parts of the atom Number of Protons 6 Number of Electrons 6 Number of Neutrons = =6 If there is no charge the number of protons = the number of electrons 6P 6N

15 C. Atoms vs. Ions

16 What is the difference between an atom and an ion? An ion is a atom that has lost or gained an electron.

17 Ions have a different number of electrons than protons and therefore have a charge An atom that looses a(n) electron(s) becomes a cation or positively charged ion An atom that gains a(n) electron(s) becomes a anion or negatively charged ion

18 D. Isotopes

19 How are isotopes different?

20 Isotopes have the same number of protons but different numbers of neutrons

21 In carbon-13, the 13 stands for the number of protons plus neutrons

22 E. Atoms, Elements, Molecules, and Compounds

23 Example Atoms: H, He, Li, Be, B, C, N, O, F, Ne Example Molecules: O 2, H 2 O, CO 2 NH 3 How is an atom different than a molecule? Molecules are made up of more than one atom covalently bonded

24 Example Elements: O 2, H 2, He, N 2 Example Compounds: H 2 O, CO 2 NH 3 How is an element different than a compound? Isomer = Same chemical composition but different arrangement

25 Example Elements: O 2, H 2, He, N 2 Example Compounds: H 2 O, CO 2 NH 3 How is an element different than a compound? Elements have only one type of atom Compounds have more than one type of atom

26 F. Chemical Formulas

27 Subscripts are used to tell you how many of that atom are present Ex. CO 2 is composed of one carbon and 2 oxygen atoms Coefficients tell you how many molecules are present 2(CO 2 ) is telling you that there are two entire carbon dioxide molecules A missing subscript or superscript means that there are only 1

28 What atoms are present and how many are in each compound? O 2 = Oxygen H 2 O = Water CO 2 = Carbon dioxide

29 What atoms are present and how many are in each compound? O 2 is Oxygen 2 Oxygen atoms

30 What atoms are present and how many are in each compound? H 2 O is Water 2 Hydrogen atoms 1 Oxygen atom

31 What atoms are present and how many are in each compound? CO 2 = Carbon dioxide 1 Cabon atom 2 Oxygen atoms

32 G. Covalent, Ionic, and Hydrogen Bonds

33 In covalent bonding the electrons are _shared__ between the atoms. In Ionic bonding atoms are ____transferred____ from one atom to another. Covalent bonding forms ____molecules______. Ionic bonding forms __ions___.

34 Electrons are constantly in motion around the nucleus Electrons are attracted to the positive charges in the nucleus (protons) so they remain in orbit around the nucleusElectrons are attracted to the positive charges in the nucleus (protons) so they remain in orbit around the nucleus Electrons move around in energy levels called electron cloudsElectrons move around in energy levels called electron clouds Each can hold a certain number of electronsEach can hold a certain number of electrons -first level can hold up to 2 e - -second level can hold up to 8 e - -third level can hold up to 8 e - - 4th level – 18e-

35 The Atom: Electron clouds & dot diagrams Electron CloudCan hold a max of ___ e - s

36 Look at the periodic table to clear up any confusion…

37 The Atom: Electron clouds EXAMPLE: Carbon has 6 electrons They are arranged as: –2 in the first e - cloud –4 in the second e - cloud

38 Electrons in the outer orbital are called valence electrons. –Valence electrons determine an elements bonding potential (or reactivity) –An atoms outer orbital must be filled to be stable Example: –How many valence e - s does carbon have? –How many does it want to be stable? Valence Electrons

39 Chemical bonds: Forming a compound Bond – to join together atoms using electron energy/force Atoms are most stable when their outer e - cloud is full Elements can share electrons to fill their outer (valence) e - cloud This causes stability

40 1. Covalent bonds Figure 6.6 EXAMPLE: Oxygen alone only has 6 electrons in its outer E level If it shares 2 more it would have 8 in its outer E level and be stable CO = share

41 Single, Double and Triple Covalent Bonds 1 electron shared = single bond Ex: C - H 2 electrons shared = double bond Ex: O = O

42 Write this on your notes somewhere Organic means something is based on carbon Why is carbon important to life? Carbon has the ability to form four covalent bonds. It can bond on all sides. This allows it to form complex structures like proteins, lipids, carbohydrates, and nucleic acids

43 2. Ionic bonds Figure 6.7 When atoms give or take electrons; not sharing The atoms with extra (or less) e - are now not neutral = ION = bond forms

44 Bond Strengths How much energy is stored bond/How much energy it takes to break the bond 1. Triple Covalent 2. Double Covalent 3. Covalent Single 4. Ionic 5. Hydrogen*

45 Chemical Reactions Bonds of atoms are broken and re-formed into new substances Reactions are written as chemical equations which show reactants and products All reactions in an organism = Metabolism What does balanced mean?

46 Chemical Reactions EXAMPLE – Photosynthesis 6CO 2 + 6H 2 O C 6 H 12 O 6 + 6O 2 Elements in water become the elements in glucose! ReactantsProducts

47 End Day 1 Work on page 1 of the study guide and the first question on page 2 (5. BONDING: Compare and contrast Ionic and Covalent bonds.)

48 Day 2 Notes: Water Hydrophilic vs. Hydrophobic Hydrophilic – substances have affinity water Hydrophobic – substances that repel water; form clusters called hydrophobic interactions. –Ex: Oil and H2O Like dissolves like –Polar dissolves polar –Non-polar dissolves non-polar

49 Intro Place the following bonds based on strength in the correct order (Hydrogen Bond, Triple Covalent Bond, Double Covalent Bond, Ionic Bond, Single Covalent Bond) Write down the following with the bonds in the right place Strongest Bond Weakest Bond

50 What is polarity in a molecule? Polarity is when there are charged sides in an overall neutral molecule. Larger atoms tend to hog electrons and become slightly negative Oxygen is a neutral molecule but the oxygen side is slightly negative and the hydrogen side is slightly positive.

51 What is a hydrogen bond? A hydrogen bond is a polar bond where hydrogen is involved. There is an intermolecular attraction between positive and negatively charged sides of different molecules Hydrogen bonds in water

52 Properties of Water If there are other beings who have seen Earth, he said, they must surely call it the blue planet. The astronaut was referring to the blue appearance of the water in the oceans, which cover three fourths of Earths surface. Water is also the single most abundant compound in most living things.

53 Things to know Hydrogen bond – Because of positive and negative charges of water (polarity). Water attracts other water molecules. Cohesion- attraction between molecules of the same substance. Adhesion- attraction between molecules of different substances Adhesion- Substance to glass (capillary action)

54 9 properties of water 1.is a powerful solvent – can dissolve things 2.is very cohesive (due to H bonds holding water together) 3.Is very adhesive (due to H bonds with other things) 4.Has capillary action 5.has high surface tension 6.has high specific heat 7.has a high boiling point – a high heat of vaporization 8.is a good evaporative coolant 9.has a high freezing point and lower density as a solid than a liquid (density anomaly)

55 Water Properties 1. Powerful, versatile solvent – due to polarity. Called the universal solvent

56 Water Properties 2. Very Cohesive behavior (due to H bonds holding water together)

57 Water Properties 3. Very Adhesive behavior (due to H bonds with other things)

58 Water Properties 4. Has capillary action

59 Water Properties 5. High Surface Tension

60 Water Properties 6. High Specific Heat

61 Specific heat: The amount of energy needed to raise the temperature of one gram 1°C Water is high vs. most molecules Some common specific heats and heat capacities: SubstanceS (J/g 0C) Air1.01 Aluminum0.902 Copper0.385 Gold0.129 Iron0.450 Mercury0.140 NaCl0.864 Ice2..03 Water4.179

62 Water Properties 7. High Boiling Point – High Heat of Vaporization

63 Water Properties 8. Good evaporative coolant

64 Water Properties 9. High freezing point and lower density as a solid than a liquid (density anomaly) –Water is less dense in a frozen state Water Benzene This is unusual for most substances

65 Why is waters lower density as a solid than a liquid important for life? When water freezes it does not fall to the bottom of a lake. It stays up top allowing for life to continue below.

66 Mixtures Solutions vs. Suspensions

67 How is a solution different than a suspension? A solution is homogeneous meaning that the parts dissolve and the mixture looks all the same throughout

68 How is a solution different than a suspension? A suspension is heterogeneous meaning that the parts do not dissolve and you can see different particles in the mixture

69 What are the parts of a solution What are the parts of a solution: The solvent is the substance being dissolved in The solute is the substance being dissolved Creamer- solute Coffee- solvent

70 Worksheet Biochem Review and Practice

71 Water Lab Day

72 Day 3 Notes: Acids vs. Bases It is the presence of hydrogen ions(H + ) relative to hydroxide(OH - ) that determines a solution's pH. hydrogen ions(H + ) are not usually found alone, instead they have a tendency to attract to a H 2 O and become hydronium ions (H 3 O) +

73 Acids vs. Bases The molecules in pure water auto- dissociate into hydronium and hydroxide ions in the following equilibrium:auto- dissociate 2H 2 O OH + H 3 O + hydroxide hydronium ions

74 Acids have a high concentration of H + ions (called hydrogen ions or protons) Bases have a high concentration of OH - ion (called hydroxide ions) In pure water, there is an equal number of hydroxide and hydrogen ions, so it has a neutral pH of 7. A pH value less than 7 indicates an acidic solution, and a pH value more than 7 indicates a basic solution or alkaline.

75 pH: a measurement of hydrogen ions Figure 2.10 Acids = forms hydrogen (H + ) ions in water Bases = forms hydroxide (OH - ) ions in water Neutral substances have a pH of 7

76 Acid and Base Strength Acid and Base STRENGTH is based on how many H + are given up (acids) or attracted to (bases) OH- Water cant equalize strong acids/bases bases and acids are used to neutralize each other Neutralization reaction – acid + base water + salt (pH 7) NaOH (strong base) + HCl (strong acid) NaCl (salt) + H 2 O (water)

77 Measuring pH There are several INDICATORS to measure pH: –pH paper –litmus paper –pH meter

78 Acids in the Biology HCl in stomach – involved in digestion Acidic blood – too much CO 2 in body causes brain to speed up respiration (CO 2 out and O 2 in) blood more basic Lactic acid build up – not enough O 2 in muscles for aerobic respiration (soreness) Most food – slightly acidic

79 Bases in Biology Neutralize stomach acids (antacids) Bile salts – liver, pancreas – emulsify lipids (fats) in body for digestion Blood buffers - Blood has a pH of 7.4; bicarbonate keeps blood slightly basic Many poisons are basic…are foods? Many cleaners are basic…why?

80 Intro Quiz 1.What is a ion? 2.What is a isotope? 3.Acids have a lot of what ion? 4.Bases have a lot of what ion? 5.What is the pH of a neutral ion? 6.Draw a pH scale labeling the neutral, the acid side, the base side. 7.Place the materials we tested in yesterdays lab on this scale 8.What is a heterogeneous mixture?

81 Macromolecules Life molecules are base on big (Macro) carbon based (organic) molecules

82 Polymers are made of monomers All macromolecules Have monomers (mono means one- a single units) Polymers are large chains of these monomers Monome r

83 Monomers are put together by dehydration synthesis Monome r

84 Monomers are put together by dehydration synthesis Gives off water (H 2 O) Monome r H2OH2O

85 Monomers are broken apart by hydrolysis Takes water (H 2 O) Hydro (water) Lysis (destroying) Monome r H2OH2O

86 Monomers are broken apart by hydrolysis Takes water (H 2 O) Hydro (water) Lysis (destroying) Monome r

87 4 life macromolecules Carbohydrate Lipid (Fat) Protein Nucleic Acid

88 Carbohydrates Elements that make carbohydrates Carbon (C) Hydrogen (H) Oxygen (O) 1:2:1 ration of C:H:O Two H for every C and O

89 Monomer Monosaccharide –Ex. Glucose and Fructose are isomers –Have Same formula but different configuration –Both C 6 H 12 O 6 1:2:1 ratio

90 Carbohydrate- Function(s) in the cell 1. Quick Energy 2. Building Block –Plant Cells have cell walls made of Cellulose (a polysaccharide) Cellulose Cell Wall

91 SPECIFIC Examples Types of carbohydrates (the shorter the quicker energy) Monosaccharide: ex. glucose and fructose Disaccharide (double monomer): ex. Sucrose (table sugar), Lactose (milk sugar) Polysaccharide (multiple monomers: ex. Starch, cellulose (plant cell walls) mono sacch aride

92 Lipids Elements that make Lipids Mainly C and H Sometimes O, P, N, and S

93 Monomer(s) –Fatty acid –Sometimes glycerol Fatty Acids

94 Lipids function(s) in the cell –1. Long Term Storage –2. Cell Membranes –3. Protection (padding) Fatty Acids

95 SPECIFIC Examples Unsaturated (Commonly called oils) –Liquid at room temperature –Have double bonds Double Bonds bend molecule

96 Saturated (Commonly called Fats) –Solid at room temperature –Have only single bonds No Double Bonds Flat Molecules that melt at a higher temperature

97 Other lipids –Cholesterol –Steroids

98 Proteins Elements that make Proteins N,H,C,O

99 Monomer(s) –Amino Acid –Four levels of structure (very complex) –Start with amino acids bonded together by peptide bonds –20 types of amino acids commonly found

100 Monomer(s) –Amino Acid –Four levels of structure (very complex) –Start with amino acids bonded together by peptide bonds –20 types of amino acids commonly found Called Primary Structure (first level of four)

101 Monomer(s) –Amino Acid –Four levels of structure (very complex) –Amino Acids are bonded together by peptide bonds –20 types of amino acids commonly found

102 Protein function(s) in the cell 1.Building blocks (provide the structure of living things) 2.Catalyze reactions (make them occur easier) enzymes are proteins that serve this purpose

103 SPECIFIC Examples –Enzymes- Catalyze reactions –structural proteins- hair, nails, horns, and hooves –muscles (all meats are protein)

104 Nucleic Acids Elements that make nucleic acids O,H,C,N,P

105 Monomer(s) Nucleotides: Made of a base, sugar, and phosphate

106 Nucleic Acid Function in the cell 1. Transmit genetic material (heredity)

107 SPECIFIC Examples –DNA- deoxyribonucleic acid –RNA- ribonucleic acid

108 Energy & Reactions ENZYMES!

109 Chemical Reactions and Enzymes Enzymes are special proteins Usually end in the suffix –ase They speed up (also called catalyze) reactions

110 Chemical Reactions Reactants- react Products- produced Activation energy- energy needed to get a reaction started Energy can be gained or lost in a reaction Reactants Products A + B C

111 Types of reactions: exergonic reaction gives off energy (Ex for energy exits) endergonic reaction takes in energy (En for sounds like in) Endergonic ReactionExergonic Reaction

112 An enzyme is a (protein) catalyst A catalyzed reaction is aided by an enzyme speeds up the reaction by lowering the activation energy (energy needed to get it started) reactions involving enzymes will conserve energy because the enzyme helps lower the activation energy lower the _______energy. Activation energy (Uncatalyzed) Activation energy (Catalyzed) Normal Reaction Catalyzed Reaction Product Reactant

113 Active Site Substrate Enzyme Enzyme-Substrate Complex Products Enzymes are specific to certain substrate An enzyme like amylase only breaks down amylose (starch)

114 Enzyme at Work 1. Substrate binds at active site 2. Enzyme breaks the substrate (reactant) down 3. Products are released 4. The enzyme is unchanged (not used up and can be used again) Active Site Substrate Enzyme Enzyme-Substrate Complex Products

115 Other Terms Metabolism: The sum of all chemical processes in cells Enzymes Help Metabolism The Body Can Regulating Enzymes: Competitive Inhibitors: Bind to enzymes active site and block their intended activity Denaturing- changing shape of enzyme stops it from working

116 Active Site Substrate Enzyme Enzyme-Substrate Complex Products Competitive inhibitor: Stops the enzyme from working since the substrate no longer fits Competitive inhibitors can be used by the body to stop an enzyme from working


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