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Molecules of Life Sections of chapters 2, 3, 4, 5, 6, 22 Quiz II Oct. 5th Exam II Oct. 14th Atoms and Molecules What are living things made of? TRACING LIFE DOWN TO THE CHEMICAL LEVEL • Biology includes the study of life at many levels • In order to better understand life, in the next slide we’ll look at the macroscopic level, the ecosystem, and work our way down to the microscopic level of cells • Cells consist of enormous numbers of chemicals that give the cell the properties we recognize as life Ecosystem (African savanna) Community (All the organisms in the savanna) Organism (A Zebra) Population (Herd of zebras) Organ systems (Circulatory system) Organs (Heart) Cells (Heart muscle cell) Tissues (Heart muscle tissue) Molecules (DNA) Chemicals Atoms (Oxygen atom) SOME BASIC CHEMISTRY • Take any physical or biological system apart and you eventually end up at the chemical level Chapter 2 Molecules • Everything in the universe is made of atoms (Atomic theory of matter). • Atoms can bond together to make molecules. • Living things are made of atoms and molecules, just like any non-living thing. Matter: What is it? • Matter is anything that occupies space and has mass • Matter is found on the Earth in three physical states – Solid – Liquid – Gas • All the elements are listed in the periodic table Atomic number Element symbol Mass number Figure 2.2 • The most common elements in living things are: – Carbon – Hydrogen – Phosphorous – Nitrogen The Structure of Atoms • What is an atom? • Atoms are composed of subatomic particles – A proton is positively charged – An electron is negatively charged – A neutron is electrically neutral Chemical Bonding and Molecules • Chemical reactions enable atoms to lose, gain, or share electrons in order to complete their outer shells – These interactions usually result in atoms staying close together – The atoms are held together by chemical bonds Chemical Bonds: Ionic Bonds • When an atom loses or gains electrons, it becomes electrically charged – Charged atoms are called ions – Ionic bonds are formed between oppositely charged ions Sodium atom (Na) Chlorine atom (Cl) Complete outer shells Sodium ion (Na) Chloride ion (Cl) Sodium chloride (NaCl) Chemical Bonds: Covalent Bonds • A covalent bond forms when two atoms share one or more pairs of outer-shell electrons Figure 2.9 The Structure of Water • Studied in isolation, the water molecule is deceptively simple – Its two hydrogen atoms are joined to one oxygen atom by single covalent bonds H H O The Structure of Water: Polarity • But the electrons of the covalent bonds are not shared equally between oxygen and hydrogen – This unequal sharing makes water a polar molecule () () () () The Structure of Water: Hydrogen Bonds • The polarity of water results in weak electrical attractions between neighboring water molecules – These interactions are called hydrogen bonds () Hydrogen bond () () () () () () () (b) Figure 2.11b Water’s Life-Supporting Properties • The polarity of water molecules and the hydrogen bonding that results explain most of water’s lifesupporting properties – Water’s cohesive nature – Floating ice The Cohesion of Water • Water molecules stick together as a result of hydrogen bonding – This is called cohesion – Cohesion is vital for water transport in plants Microscopic tubes • Surface tension is the measure of how difficult it is to stretch or break the surface of a liquid – Hydrogen bonds give water an unusually high surface tension • When water molecules get cold, they move apart, forming ice – A chunk of ice has fewer molecules than an equal volume of liquid water • The density of ice is lower than liquid water – This is why ice floats Hydrogen bond Ice Liquid water Stable hydrogen bonds Hydrogen bonds constantly break and re-form Figure 2.15 Water as the Solvent of Life • Table salt, NaCl, is the result of an ionic bond between Na+ and Cl- ions. • When salt mixes with water, this ionic bond breaks, and the separated Na+ and Cl- ions are attracted to the polar water molecules. Ion in solution Salt crystal • Elements in the Human Body – Four elements make up about 96% of the weight of the human body.... – Oxygen, Carbon, Hydrogen, Nitrogen – Trace elements occur in smaller amounts Molecules: what are living things made of? Chapter 3 What is the main element that living things are made of? Carbon Chemistry An atom of C – Has four electrons in an outer shell (can hold eight) – Carbon can share its electrons with other atoms to form up to four covalent bonds • Carbon can use its bonds to Carbon skeletons vary in length – Attach to other carbons – Form an endless diversity of carbon skeletons Carbon skeletons may be unbranched or branched Carbon skeletons may have double bonds, which can vary in location Figure 3.2 Carbon skeletons may be arranged in rings • The simplest organic compounds are hydrocarbons – These are organic molecules containing only carbon and hydrogen atoms – The simplest hydrocarbon is methane Structural formula Ball-and-stick model Space-filling model Figure 3.3 • Larger hydrocarbons – Are the main molecules in the gasoline we burn in our cars – The hydrocarbons of fat molecules provide energy for our bodies Figure 3.4 Molecules • Most molecules in living things are polymers • What type of reaction creates polymers of sugars? • What type creates polymers of amino acids? • What is the name of the reaction that breaks polymers into monomers? Molecules • There are 4 classes of compounds that are the building blocks of cells – Carbohydrates – Lipids (fats and oils) – Proteins – Nucleic acids Carbohydrates • Repeating subunit is H–C–O–H which is CH2O. • Hence carbo-hydrate • Can occur as ring or chain • Monosaccharides include simple sugars like glucose and fructose Carbohydrates • Repeating subunit is H–C–O–H which is CH2O. Polysaccharides • Starch: long-term energy storage in plants • Hence carbo-hydrate • Glycogen: short-term energy storage in animals • Can occur as ring or chain • Cellulose: structure in plants • Monosaccharides include simple sugars like glucose and fructose • Chitin: structure in animals • Disaccharides (sucrose, maltose, lactose). • Polysaccharides Glucose monomer Starch granules in potato tuber cells (a) Starch Glycogen Granules In muscle tissue (b) Glycogen Cellulose fibril in a plant cell wall Cellulose molecules (c) Cellulose Figure 3.13 Carbohydrates • Carbohydrates are polar, that is, they have an uneven charge distribution across molecule. Makes them soluble in water (hydrophilic). • Diet: No carbohydrates are essential (you can create them in your body from other compounds you eat.) • Energy density: 4 Cal/g. Lipids (Fats and oils) • 4 types – Fatty acids –Triglycerides –Phospholipids –Steroids Lipids (fats, oils, waxes) • The repeating subunit of a lipid is CH2: H–C–H • Called hydrocarbons because they are composed of mostly C and H. • Lipids are nonpolar and are thus hydrophobic. • Energy density: 9 Cal/g, because in carbohydrates, the O adds mass and removes high energy bonds. Fatty Acids Fatty Acids • Fatty acids are used for energy, or stored • Store a lot of energy. Why? • Evolutionary Theory can provide a plausible explanation for why we crave fats. Saturated fats • Saturated fats are molecules in which the C atoms are saturated with H’s. • Because the hydrocarbon chains line up uniformly, saturated fats are solid at room temperature (and gummy in your arteries). • If there were any C=C (carboncarbon double bond), it would be unsaturated. Unsaturated fats • Unsaturated fats are liquid at room temperature. • Monounsaturated fats (such as olive oil) are GOOD for you, as they reduce LDL (details to follow). Trans fats • Partially hydrogenated oils (i.e., trans fats) are just as bad as saturated fats (if not worse)! • Start with a perfectly healthy vegetable oil and hydrogenate it (i.e., force H’s on it), making a new type of saturated fat. • Crisco shortening was previously soybean oil. Lipids Lipids are stored primarily as triglycerides: three fatty acids attached to a small glycerol molecule. Creating triglycerides ? • When 3 fatty acids are joined to a glycerol molecule, this reaction is called ______ and produces ______. Lipids in membranes • Membranes are composed primarily of phospholipids. • Glycerol attached to 2 fatty acids and a polar phosphate group. • Phosphate is hydrophilic while 2 hydrocarbon chains are hydrophobic. • Thus they form bilayers in cells, as the hydrocarbons avoid water while the phosphate heads turn towards water… http://telstar.ote.cmu.edu/biology/downloads/membranes/index.html Lipids: Steroids Interconnected rings of carbon atoms Small molecule, but big effects Cholesterol is another example of a steroid Lipids as messengers • Lipids can act as messengers in the body. • These steroid hormones are ring structures. • Hormones send long sustained messages, regulating slow transitions (as opposed to fast nervous system) • Ex. Puberty • Cholesterol is important in membranes (to maintain stability) Testosterone Proteins • Composed of C, H, O, and N. • The repeating subunit is an amino acid. • Central C is attached to – amine group – carboxyl group (acid) – H atom – R-group (varies depending on amino acid) Peptide bonds • When 2 amino acids are joined, the N from one’s amino group attaches to the C of the other’s carboxyl group. • Forms a peptide bond. • What is this process called? • What is released? • To join 3 amino acids, how many water are released? • When many amino acids are joined in a chain, a protein (polypeptide) is formed. • Your body has tens of thousands of different kinds of proteins • Proteins do many different jobs, some are hormones, some are enzymes, some are structural • The arrangement of amino acids makes each one different, differently shaped proteins have different functions. • Primary structure 5 1 30 35 – The specific sequence of amino acids in a protein 15 10 20 25 45 40 50 55 65 60 70 85 80 75 95 90 100 110 105 115 120 125 129 Figure 3.21 Amino acid • A slight change in the primary structure of a protein affects its ability to function – The substitution of one amino acid for another in hemoglobin causes sickle-cell disease 1 2 (b) Sickled red blood cell 6 7. . . 146 4 5 Normal hemoglobin (a) Normal red blood cell 1 3 2 3 6 7. . . 146 4 5 Sickle-cell hemoglobin Figure 3.22 Protein Structure • The shape (structure) of a protein is intimately linked to its function. • Tertiary structure: how those sheets or coils form a 3dimensional structure. • In their role as enzymes, they act as keys to make reactions occur. • Quaternary structure: using 2 or more tertiary structures to create a more complex 3-D structure. • Primary structure: the linear sequence of amino acids in a chain. • Secondary structure: the shape the chain takes (sheet or coil). • One more visual example… Proteins have four levels of structure Hydrogen bond Pleated sheet Polypeptide (single subunit) Amino acid (a) Primary structure Complete protein, with four polypeptide subunits Hydrogen bond Alpha helix (b) Secondary structure (c) Tertiary structure (d) Quaternary structure http://www.stolaf.edu/people/giannini/flashanimat/proteins/protein%20structure.swf Figure 3.23 http://www.stolaf.edu/people/giannini/flashanimat/proteins/hydrophobic%20force.swf Facts about proteins • Enzymes (proteins) are very fragile: If you change just one amino acid in the linear sequence (primary structure), you may impair the function of the enzyme. • Proteins are affected by pH and temperature. If subjected to high stress (extreme temperature or pH), and protein may denature (permanently change its shape). The structure of proteins is very important! • Diet: Proteins include eight essential amino acids – Different vegetables contain different ones; BUT no single vegetable contains all eight of them – Meats, however, do contain all eight Essential amino acids Methionine Valine (Histidine) Threonine Corn and other grains Phenylalanine Leucine Isoleucine Tryptophan Lysine Beans and other legumes Summarizing Proteins • Composed of 20 different amino acids • Amino acids joined by peptide bonds • Very complex 3dimensional structure • Extremely important as enzymes • Energy density: 4 calories/gram Nucleic Acids • Not important in nutrition, but famous because of DNA, RNA, and ATP. • Composed of nitrogenous base (5 types), pentose sugar (2 types), and a phosphate group. • They form chains of sugars attached to phosphates (with the nitrogenous base dangling. • DNA is double-stranded: the nitrogenous bases in adjacent strands attach to each other. • Some nucleic acids are also important in energetics. ATP is the ‘currency’ used in the cell to get things done. Nucleic acids • Nucleic acids are polymers of nucleotides • Nucleotides have three parts: – Sugar – Phospate – Nitrogen base • ATP (adenosine triphosphate) Energetics and Respiration How do living things work? Order and Physical Laws • Organisms require energy to maintain order in their bodies. • Without using energy to maintain order, life would be impossible. • Why? • Because of the 2nd Law of Thermodynamics: • Entropy (disorder) increases. Order and Physical Laws • 2nd Law of Thermodynamics: • Entropy (disorder) increases. • Restated in terms of chemical reactions: No energy transformation is 100% efficient. • What does that mean? • It means energy is lost as heat every time it changes forms. • For example… when: Sugar ATP glycogen fat fat glycogen Example of 2nd Law of Thermodynamics • Consider a car that is powered by gasoline. • Most of the energy in the gasoline is not used to propel the car forward, play the stereo, AC, etc. • Rather it is wasted (lost) as heat. • Much of the machinery under your hood is designed to cool the engine, not propel it! Example #2 • Consider breakfast. • If you eat a 500 calorie breakfast, less than 200 calories are actually used to produce ATP’s. • The rest is lost as heat. • Living cells and automobile engines use the same basic process to make chemical energy do work Fuel rich in chemical energy Gasoline Waste products poor in chemical energy Heat energy Carbon dioxide Combustion Kinetic energy of movement Oxygen Water (a) Energy conversion in a car Figure 5.3a Fuel rich in Chemical energy Waste products poor in chemical energy Heat energy Gasoline Carbon dioxide Combustion Kinetic energy of movement Oxygen Water (a) Energy conversion in a car Heat energy Food Oxygen Cellular respiration Energy for cellular work (b) Energy conversion in a cell Carbon dioxide Water Types of energy • kinetic energy (moving objects) 1. moving car, moving baseball 2. hits something, stops, energy converted in sound, heat, light, etc. 3. fire burning • potential energy (stored energy) 1. E.g. coiled spring, object at high location, gasoline 2. chemical energy is form of potential energy Metabolism • Living things maintain order through essential chemical reactions called metabolism. – Organic molecules are converted into other organic molecules. – Energy is released by oxidizing reduced carbon compounds (that is, breaking lots of C-H bonds). Metabolism Oxidation • Both living creatures and fire consume oxygen. The oxygen reacts with the fuel (wax in the candle, or sugars in us) to produce CO2 and H2O. This process is called oxidation. In our bodies we oxidize glucose: • C6H12O6 (glucose) + 6O2 6CO2 + 6H20 Differences between fire and metabolism • Fire consumes everything: with enough oxygen, everything is oxidized randomly and chaotically. • But Metabolism is controlled and ordered. Energy is stored in ATP molecules in your cells as the food molecules are oxidized slowly in many small steps. And each small step requires an enzyme. • How does your body control which molecules get oxidized, when, and where? • By producing the enzymes capable of certain reactions ONLY when those reactions are needed. What enzymes do • Chemical reactions require a push to get going. • The push is called activation energy. • Enzymes reduce the activation energy needed. •http://www.lewport.wnyric.org/jwanamaker/animations/Enzyme%20activity.html Facts about enzymes • Lock and key idea: enzymes must have their own perfect 3-D shape. Example: alcohol dehydrogenase Facts about enzymes • Enzymes are not used up in chemical reactions. They can be reused over and over, and will continue to exist until your body destroys them. • Enzymes have very specific functions. Each step of a chemical pathway requires a different enzyme. Facts about enzymes • Enzymes cannot get more energy out of a reaction, they just make reaction more likely to occur. Facts about enzymes Enzyme activity • Enzymes are temperature sensitive, since proteins denature at high temperatures and lose their shape. Facts about enzymes • Enzymes are sensitive to pH for the same reason. Metabolism • Living things require energy and materials to stay alive. – Energy and materials to maintain their structure and function – Energy and materials to reproduce • Where does that energy come from? Food webs and energy pyramids Autotrophs and heterotrophs • Autotrophs – Make their own food/fuel • Heterotrophs – Need to consume food/fuel produced by autotrophs • All organisms need to acquire materials from their environment, but each type needs different materials Autotrophs • Most make their own fuel by a process called photosynthesis • Have chlorophyll • Convert CO2 and H2O to C6H12O6 + O2 • Use solar energy to do this Heterotrophs • Must consume food for fuel Respiration • All eukaryotic cells burn fuel (glucose) to make ATP • ATP can then be used as an energy source anywhere in the cell or body. • Burning fuel requires O2 • In cells the process is called respiration Respiration • Respiration occurs in mitochondria • Respiration occurs in controlled steps each step requires an enzyme • Glycolysis: Glucose is split into 2 molecules – can occur without O2, produces 2 ATP molecules • Krebs Cycle and Electron transport chain: Require O2, produce 34 ATP molecules. •C6H12O6 + O2 + ADP + P → CO2 + H2O + 36 ATP Respiration Overview Glucose Glycolysis (sugar-breaking) No O2 Fermentation If O2 is present Aerobic Respiration Krebs Cycle Electron Transport Chain Respiration • Other food we eat can also be burned for energy Oxygen Cycle • Respiration C6H12O6 + O2→ CO2 + H2O • Photosynthesis CO2 + H2O → C6H12O6 + O2 • What’s wrong with this picture? • Do plants use Oxygen? If so, what for? Energy vs. Materials • Common elements in living things? • Where do living things get these? – Plants – Animals Energy vs. Materials • It takes energy to stay alive • What is the ultimate source of energy for all living things?