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Biology Notes 1 Chapter 1 Videos • biology – the scientific study of life o there are more microorganisms/more diversity than anything else that is currently alive • Characteristics of living things o order o regulation o energy processing o evolutionary adaptation o growth and development o response to the environment o reproduction • Life also… o is carbon-based o requires water o has DNA-based transfer of hereditary information o is made up of units called cells o is integrated with other organisms • Hierarchy of Biological Organization o decreases in complexity going down from biosphere to molecules 1. The biosphere § area where we find living things § most complex scale at which we can look at life § broken down into… 2. ecosystems § contains organisms that live in these ecosystems § ex: marine, forest, desert, etc. § broken down into… 3. communities § includes all different types of organisms § ex: deer, trees, plants, insects, etc. § broken down into… 4. populations § a single species § ex: maple trees § broken down into… 5. organisms § one thing § ex: one maple tree § broken down into… 6. organs and organ systems § work together to achieve all qualities that make something alive § broken down into… 1 7. tissues § units of the same type of cells § broken down into… 8. cells § bare minimum of what you have to be to be alive § broken down into… 9. organelles § means “tiny organs” § broken down into… 10.molecules/atoms § enable organelles to do their jobs, and so on • Structure and function are correlated at all levels o we can make observations at macroscopic levels (with our eyes) that go along with observations we see at microscopic levels • The cell is an organism’s basic unit of structure and function • The continuity of life is based on heritable information in the form of DNA • Evolution accounts for the unity and diversity of life o evolution is the central theory of biology o cilium o diverse families of plants - orchids • Classifying the diversity of life o we define life as being in a hierarchy § we have evermore inclusive groups • species is the most inclusive group § species --> genus --> family --> order --> class --> phylum --> kingdom --> domain o Eukaryotes – nucleus o Prokaryotes – NO nucleus • There are 3 domains: 1. Bacteria • all “bad guy” bacteria that cause diseases plus other bacteria that don’t impact humans • single-celled organisms that don’t have nuclei in their cells 2. Archaea • in shape they don’t look that different from bacteria • was split from bacteria in the past 20 years • single-celled organisms that don’t have nuclei in their cells 3. Eukarya • our own domain • almost everything we think of being alive minus bacteria • ex: Kingdom Plantae, Kingdom Animalia, Kingdom Fungi, Kingdom Protists o protists - single-celled organisms that have nuclei in their cells 2 • What about viruses…where do they fit in? o microscopic – so we can’t see them o colds are due to the human rhino virus o Alive? (no) § have nucleic acid transmission of hereditary information § composed of the same types of material as living organisms § evolve in response to selection pressure o NOT alive! § cannot reproduce independently of their host cells § do not grow or develop § do not self-regulate o NO, viruses are NOT alive § but they are of interest to biologists § they give us clues to how life on earth may have evolved from having no living things to having truly living things on it • So what is science? o Latin – “knowledge” o A way of knowing about the natural world, or the observable universe o Making observations and testing hypotheses § hypotheses – ideas about how the natural, observable universe functions • The scientific method o observations o questions o hypotheses o test prediction • The flexibility of the scientific method o different scientists have used it differently to make observations about the natural world, support hypotheses, and contribute to the theory of evolution • Theories in science o Evolutionary Theory o Atomic Theory o Plate Tectonic Theory o “Big Bang” Theory o Cell Theory o Germ Theory o Theory of Gravity o Theories of Relativity • What is a theory? o A scientific theory is a broad framework or model for explaining natural phenomena o A theory generates more specific, testable hypotheses o A theory must be supported by observational and experimental evidence o A scientific theory is NOT a wild guess 3 Chapter 2 Videos • Key Concepts: o Matter consists of chemical elements in pure form and in combinations called compounds o An element’s properties depend on the structure of its atoms o The formation and function of molecules depend on chemical bonding between atoms o Chemical reactions make and break chemical bonds • Matter: o takes up space o has mass o solid, liquid, gas (plasma) • Element – a substance that cannot be broken down by chemical means o ex: oxygen, iron, gold, etc. • Compound – substance of two or more elements in fixed ratio (always 1:1) o ex: table salt, sodium chloride, NaCl • Chemical symbols o Elements have 1 or 2 letter symbols § see periodic table o Examples: § Gold = Au § Boron = B § Uranium = U § Radon = Rn • Human body is mostly oxygen, carbon, hydrogen, and nitrogen • Subatomic particles o an element is defined by what is present in the atom of that element • Elemental properties are determined by atomic structure o Atoms – the smallest unit of matter, indivisible by chemical means o Nucleus – the central part of the atom o Proton – nuclear particle with positive charge o Neutron – nuclear particle with no charge o Mass =PMass N = 1.7 x 10 g § = 1 dalton = 1 amu (atomic mass unit) o Electron: atomic particle with negative charge, 1/2000 Mass P or N • Atomic number and atomic mass o Atomic NUMBER determined by number of protons § 1H,2 He,3 Li, etc. o Atomic MASS determined by number of protons and neutrons 1 2 4 7 § H, H, He, Li, etc. • Isotopes o Carbon (C – 12) § most common form of carbon: • atomic number = 6 4 • 6 protons & 6 neutrons § can have a carbon atom with 7 neutrons in the nucleus = Carbon – 13 • not as abundant as Carbon – 12 atoms are § can also have Carbon – 14 § unstable and will decay by radioactive decay, aka is radioactive • Atoms are mostly empty space • Nuclei are not directly involved in most chemical reactions o Chemical reactions make and break bonds o Bond are interactions between electrons o So let’s talk more about electrons and…. • Energy! o Energy: the capacity to do work or effect change, comes in many forms § Chemical, mechanical, heat, light o Potential energy: reflects position or structure o Like a water tower § storing potential energy • water pressure: the potential energy is turned into gravitational energy which is turned into water pressure • Energy levels of electrons o A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons § Third shell (highest energy level in this model) § Second shell (higher energy level) § First shell (lowest energy level) • energy absorbed – moving to higher level/shell • energy lost – moving to lower level/shell o electrons are not found between stairs (levels) § electrons want to be at the lowest potential energy level § Atomic nucleus • Electron distribution and chemical properties • Orbital shapes can get pretty weird • Strong chemical bonds forms… o Because atoms are more stable when their valence (outermost) shells are filled. • Chemical bonds o Are how molecules are formed o Atoms are more stable when their valence shell is full o Strong bond (intramolecular) § Covalent § Ionic o Weaker bonds (intermolecular) § Hydrogen bonds § Van der Waals interactions ------------------------------------------------- PICTURES 1 -------------------------------------------------- 5 • Covalent bonds o share electrons in their valence shells • Bonding capacity o Is the number of bonds an atom can form o Is dependent on the number of valence electrons § oxygen is very polar and shares electrons a lot o How many unpaired electrons required to complete valence shell? § H – 1 § C – 4 § O – 2 § N – 3 • Polar covalent bonds o some atoms are much more electronegative or have a higher affinity for electrons than others o Oxygen is the most electron-greedy atom § in H O: O has a slightly more negative charge, while the H atoms have 2 a slightly positive charge to them • Ionic bonds o not sharing electrons, but donating them § in some cases, atoms accept or donate electrons to get a stable, valence shell § cations and anions • Ions o Are charged atoms or molecules o # protons ≠ # electrons o + charged ion = cation o – charged ion = anion o Ionic compounds, generally, are SALTS o EPSOM SALT, MgSO (magnesium sulfate) 2+ 2- 4 o Mg and SO 4 § sometimes ions can have different atoms or multiple atoms participating in that ion § sulfate has covalent bonds, but it can ionically bond to the magnesium ions o Environment affects ionic bond strength! • Weak chemical bonds o Hydrogen bonds § effect of having polar-covalent bonds o Van der Waals interactions § typical in non-polar molecules § asymmetry in charge distribution § large molecules, packed together § weaker than H-bonds § strength in #s 6 • Molecular shape and function o All these types of bonds contribute to the shape of molecules o Molecules are 3-D o Shape is essential to function! • Chemical reactions make and break bonds • Chemical reactions are dynamic processes o Note: Reactions are reversible o Concentrations (amounts) of reactants affects the rate of reactions o Equilibrium: rates of forward and reverse rxns are the SAME 7 Chapter 3 Videos • Key Concepts o Polar covalent bonds in water molecules result in hydrogen bonding o Four emergent properties of water contribute to Earth’s suitability for life o Acidic and basic conditions affect living organisms • Water is covalently bonded with polar covalent bonds o Oxygen hogs the electrons, and thus has a partially negative charge o Hydrogen bonding • Four emergent properties of water o Cohesion of water molecules § Cohesion = same molecules sticking to itself o Moderation of temperature by water o Ice floats o Water is the solution (at least the solvent) • Water moderates temperature o Energy: the capacity to do work or effect change o Heat vs. Temperature o Heat – the TOTAL kinetic energy o Temperature – the AVERAGE kinetic energy § lower temp. = less movement • Temperature vs. heat o POOL vs. COFFEE o Which has greater temperature? § coffee o Which has greater heat? § pool • bc it has the volume of thousands of cups of coffee • Heat o Measured in calories o 1 calorie à amt of heat to 1 g H 2 by 1*C o Food calories are actually kcal (1000 calories) o Heat is a form of energy, so can also measure in joules 1 J = 0.239 cal • Specific heat o Amount of heat required to change temperature o water changes temperature less rapidly than other substances § aka has a very high specific heat § water molecules stick together and it takes more energy to drive them apart than a lot of other substances • Moderation of temperature o water is capable of monitoring temperature o coastal areas have much less dramatic shifts in temperature than dryer areas such as deserts • Phases of matter o Density: 8 § Gas < liquid < solid § So… • Why does ice float? o this is a property that can be traced to hydrogen bonding o Ice: hydrogen bonds are stable o Liquid water: hydrogen bonds break and re-form o so the ice is less dense than liquid water because of formation (?) • Chemical Solutions o Solution: a uniform mix of 2 or more substances o Solvent: the liquid dissolving reagent in a solution o Solute: the dissolved reagent in a solution • Ionic compounds are typically referred to as salts o in air, most ionic compounds are stable o when put in water, they can be pulled apart atom by atom o when put in a solution, the partially positive molecule portions point towards negatively charged ions, and vise versa o ions get completely surrounded by water molecules o water molecules face away from the sodium ions and the chlorine ions have the legs of the water molecules pointed toward them = hydration shell § chlorine and sodium ions cannot interact because both are surrounded by water molecules • water is a good solvent for ionic compounds o proteins are very large molecules § can still be dissolved in water because its surface has lots of charged particles on it (because of hydrogen bonding) • Hydrophilic and hydrophobic substances o Substances which attract water are hydrophilic o Substances which repel water are hydrophobic o Generally, ionic or polar substances are hydrophilic o Substances which are non-polar and non-ionic are hydrophobic § ex: oils • Concentration and Molarity o Amounts of reagents are important o Molecular weight = sum of atomic weights o Sucrose: C H12 22 11 o MW = 12*C + 22*H + 11*O = 342 Da/molecule o Avogadro’s Number à 6.02 x 10 à 1 mole § Converts Daltons to grams • 1 Dalton = weight of23 proton o 342 grams of sucrose is 6.02 x 10 molecules o Example: We want to make 5 L of a 0.2 M glucose solution. § We need to know how many g of glucose § Glucose: C 6 12 6 § Step 1: Calculate the molecular weight 9 § Step 2: Dimensional analysis § Step 3: Multiple and cancel terms • 6 x C (12.011) = 72.06 • 12 x H (1.0079) = 12.08 • 6 x O (15.999) = 95.994 • TOTAL = about 180.12 Da/molecule = g/mole • 180.12 g X0.2 moles X L = 180.12 g moles L 1 M (=moles/L) o ex: How many moles of water in 1 L? § Given 1 mL = 1 g § 1 L = 1,000 mL = 1,000 g 1Xmol = 55.49 mol 18.02 g o Moles help us fix ratios of molecules o 1 mole sucrose in 1 L of water § = 1 Molar solution § = 1M sol’n o Molarity is # moles solute per liter of solvent (usually water) • Acids and bases o Water is not all H O 2 o Can dissociate into ions o H O2<-> H + OH - o 1 molecule in 554 million typically o In pure water @ 25*C (room temp.), [H ] = 10 M -7 o Also, [OH ] = 10 M -7 § because they are happening in equal measure o Ions are more reactive than H O 2 § Hydronium and Hydroxide ions o Other ionic compounds, added to water will dissociate, like: + - § HCl <-> H + Cl § NaOH <-> Na + OH - o These will dramatically affect [H ] and [OH ] - + o Compounds which contribute H are ACIDS § aka compounds that contribute protons are acids § also compounds that absorb or take out hydroxide ions are acids o Compounds which contribute OH are BASES § aka compounds that contribute hydroxide ions are bases § also compounds that absorb protons are bases • Representation of the pH scale (measure of acidity) + o Acids donate H in aqueous solutions o Bases donate OH - o lower the number = more powerful the acid/higher concentration of protons § more acidic = higher concentration of protons than hydroxide ions § neutral pH of 7 = concentration of protons equals concentration of hydroxide ions 10 § basic/alkaline = concentration of hydroxide ions surpasses concentration of protons o scale goes from 0 – 14 § 7 is right in the middle and has to do with the 1 in 554 million number which is the molarity of ions in water • The pH scale o pH = - log [H ] + § in this case, H is protons or hydrogen ions o [H ] can vary from 10 – 10 M -14 - -14 0 o [OH ] varies reciprocally 10 – 10 M o 10 = 1M -1 o 10 = 1/10 M o 10 = 1/10000 M o pH + pOH = 14 o pH 1 = pOH 13 o pH 3 = pOH 11 § pH 3 means the concentration of protons is 1/10 M & the concentration of [OH ] is 1/10 M 11 o pH 4: [H ] = 1/10000 M o =pOH 10: [OH ] = 1/10000000000 M + o pH 10: [H ] = 1/10000000000 M o =pOH 4: [OH ] = 1/10000 M • Buffers Minimize Changes in pH o Buffers act as acids or bases or both o They are weakly ionizing o Many buffers are both acid and base at the same time, depending on pH of surrounding solution o Bicarbonate is an important buffer in vertebrate blood: + - § CO 2+ H O2<-> H CO2 <->3H + HCO 3 (Carbon dioxide) (Carbonic acid) (Bicarbonate ion) • Ecological effects of pH o Acid precipitation (rain) results from burning o Natural and human made 11 Chapter 4 Videos • Overview: Carbon: The Backbone of Life o Living organisms consist mostly of carbon-based compounds o Carbon is unparalleled in its ability to form large, complex, and diverse molecules o Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds • Concept 4.1: Organic chemistry is the study of carbon compounds o Organic chemistry is the study of compounds that contain carbon o Organic compounds range from simple molecules to colossal ones o Most organic compounds contain hydrogen atoms in addition to carbon atoms § Hydrogen is the most abundant element in the universe § Often when carbon doesn’t have anything else to bond to, it is bonded to hydrogen • Vitalism vs. Mechanism o vitalism - the idea that living organisms had some kind of a different chemistry than non-living organisms § some sort of spiritual yet observable factor that non-living things did not posses o Friedrich Wohler § 19th century German chemist who synthesized urea, which is a component of urine, by using all but one non-living feedstock or reagent that went into the production of this • he produced urea from non-living materials § meant we didn’t have to use natural resources to produce such things • Concept 4.2: Carbon atoms can form diverse molecules by bonding to four other atoms o Electron configuration is the key to an atom’s characteristics o Electron configuration determines the kinds and numbers of bonds an atom will form with other atoms • 4 elements that are the most abundant in all living tissues: o Hydrogen (H) § valence = 1 o Oxygen (O) § valence = 2 o Nitrogen (N) § valence = 3 o Carbon (C) § valence = 4 • Molecular Diversity Arising from Carbon Skeleton Variation o Carbon chains form the skeletons of most organic molecules o Carbon chains vary in length and shape 12 ------------------------------------------------- PICTURES 2 -------------------------------------------------- • “-ene” ending represents an alkene, and usually means there is a double bond in the structure somewhere • Hydrocarbons o Hydrocarbons are organic molecules consisting of only carbon and hydrogen o Many organic molecules, such as fats, have hydrocarbon components o Hydrocarbons can undergo reactions that release a large amount of energy o ex: octane – eight carbon chain completely saturated with hydrogens • Isomers o Isomers are compounds with the same molecular formula but different structures and properties 1. Structual isomers • different covalent arrangements of their atoms/different arrangement of covalent bonds • ex: a line isomer and a t-shaped isomer 2. Cis-trans isomers (Geometric isomers) • same covalent bonds but differ in spatial arrangements • around a double bond • cis isomer: the two not-H atoms are on the same side • trans isomer: the two not-H atoms are on opposite sides 3. Enantiomers • isomers that are mirror images of each other • L isomer • D isomer • left and right handed forms of same molecule • asymmetrical carbon – all 4 bonds are to different atoms/molecules (a stereo center) o ex: chlorofluorobrome methane o asymmetric carbons can’t have double bonds ------------------------------------------------- PICTURES 7 -------------------------------------------------- o “iso-“ prefix means similar or the same ------------------------------------------------- PICTURES 3 -------------------------------------------------- • Concept 4.3: A few chemical groups are key to the functioning of biological molecules o Distinctive properties of organic molecules depend on the carbon skeleton and on the molecular components attached to it o A number of characteristic groups can replace the hydrogens attached to skeletons of organic molecules • The Chemical Groups Most Important in the Processes of Life 13 o Functional groups are the components of organic molecules that are most commonly involved in chemical reactions o The number and arrangement of functional groups give each molecule its unique properties • Functional Groups (overview on Ch.4-3 & 4 videos) o 1) Hydroxyl polar alcohol o 2) Carbonyl polar ketone, aldehyde o 3) Carboxyl polar organic acids o 4) Amino polar amines o 5) Sulfhydryl polar/non-polar thiels o 6) Phosphate polar phosphates o 7) Methyl non-polar ------------------------------------------------- PICTURES 8 -------------------------------------------------- • Ketones o ex: acetone (nail polish remover), testosterone, tetracycline (antibiotic), phenylpyruvic acid (PKU) • Aldehydes o has to do with the smell of food items o formaldehyde, vanillin, cinnamaldehyde, retinal ------------------------------------------------- PICTURES 9 -------------------------------------------------- • Organic acids contain carboxyl functional group o Butyric acid § smell of rancid butter o Caproic acid § smell of goats o Omega-3 and Omega-6 Fatty Acids • ATP: An important Source of Energy for Cellular Processes • The Chemical Elements of Life: A Review o The versatility of carbon makes possible the great diversity of organic molecules o Variation at the molecular level lies at the foundation of all biological diversity • Review of Ch. 4 – Organic Chemistry o carbon o Valence of 4 N≅N o Hydrocarbon diversity § length of C – skeleton § branching of C – skeleton § rings and double bonds -C≅N (cyanide) ------------------------------------------------- PICTURES 5 -------------------------------------------------- 14 • Ch. 4 Learning Objectives - You should be able to: § Explain why carbon is such a versatile element § Describe three types of isomers • Structural • Cis/trans • Enantiomers (stereoisomers) o Recognize a stereocenter ------------------------------------------------- PICTURES 6 -------------------------------------------------- § Recognize some important functional groups • Hydroxyl, carbonyl (aldehyde and ketone), carboxyl, amino, sulfhydryl, phosphate, methyl 15 Chapter 5 Videos • Chapter 5. The Structure and Function of Large Biological Molecules – Part I. Introduction, Carbohydrates and Lipids • The Molecules of Life o All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids o Macromolecules are large molecules and are complex § “macro” – Greek for “very large” § “micro” – Greek for “very small” o Large biological molecules have unique properties that arise from the orderly arrangement of their atoms • Concept 5.1: Macromolecules are polymers, built from monomers o A polymer is a long molecule consisting of many similar building blocks § polymer means “many parts” o The repeating units that serve as building blocks are called monomers o Three of the four classes of life’s organic molecules are polymers § Carbohydrates § Proteins § Nucleic acids o Lipids is missing from the list above aka are NOT polymers • The Synthesis and Breakdown of Polymers o Enzymes are special macromolecules that speed up chemical reactions such as those that make or break down polymers o A dehydration reaction occurs when two monomers bond together through the loss of a water molecule o Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction § How many moles/L of water is there at standard temperature and pressure? –ANSWER: 55 M • water is rarely, truly limiting in these reactions • The Diversity of Polymers o Each cell has thousands of different macromolecules o Macromolecules vary among cells of an organism, vary more within a species, and vary even more between species o A huge variety of polymers can be built from a small set of monomers • Concept 5.2: Carbohydrates serve as fuel and building material o Carbohydrates include sugars and the polymers of sugars § carbohydrates are a source of energy/fuel as well as providing structure/building material o The simplest carbohydrates are monosaccharides, or simple sugars o Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks • Sugars o Monosaccharides have molecular formulas that are usually multiples of CH 2 16 o Glucose (C H 6 12is6the most common monosaccharide § carbohydrates usually have the “-ose” ending, such as in glucose, lactose, fructose, etc. o Monosaccharides are classified by: § The location of the carbonyl group (as aldose or ketose) (which have different numbers of sugar in their skeletons) • aldoses – aldehyde sugars o double-bonded Oxygen is at the end of the chain • ketoses – ketone sugars o double-bonded Oxygen is internal to the carbon skeleton § The number of carbons in the carbon skeleton o Hexoses (6-carbon sugars) are the most common type of sugars o Though often drawn as linear skeletons, in aqueous solutions many sugars form rings o Monosaccharides serve as a major fuel for cells and as raw material for building molecules § can be used to structurally build up things that will be used to make cells in organisms’ bodies o A disaccharide is formed when a dehydration reaction joins two monosaccharides o This covalent bond is called a glycosidic linkage § There are different types of glycosidic linkages § Not all glycosidic linkages are equal • Polysaccharides o “poly” = many o “saccharides” = sugars o Polysaccharides, the polymers of sugar, have storage and structural roles § long strands of sugars o The architecture and function of a polysaccharide are determined by its sugar monomers and the positions of its glycosidic linkages • Storage Polysaccharides o Starch, a storage polysaccharide of plants, consists entirely of glucose monomers o Plants store surplus starch as granules within chloroplasts and other plastids o The simplest form of starch is amylose o Glycogen is a storage polysaccharide in animals o Glycogen is stored mainly in liver and muscle cells o Hydrolysis of glycogen in these cells releases glucose when the demand for sugar increases • Structural Polysaccharides o The polysaccharide cellulose is a major component of the tough wall of plant cells 17 o Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ o The difference is based on two ring forms for glucose: alpha (α) and beta (β) o Starch (α configuration) is largely helical o Cellulose molecules (β configuration) are straight and unbranched o Some hydroxyl groups on the monomers of cellulose can hydrogen bond with hydroxyls of parallel cellulose molecules o Enzymes that digest starch by hydrolyzing α linkages can’t hydrolyze β linkages in cellulose o The cellulose in human food passes through the digestive tract as “insoluble fiber” o Some microbes use enzymes to digest cellulose o Many herbivores, from cows to termites, have symbiotic relationships with these microbes o Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods o Chitin also provides structural support for the cell walls of many fungi o The basic subunit of chitin is a modified form of glucose called N-acetyl glucosamine • Concept 5.3: Lipids are a diverse group of hydrophobic molecules o Lipids are the one class of large biological molecules that does not include true polymers o The unifying feature of lipids is that they mix poorly, if at all, with water § aka they are hydrophobic o Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bonds o The most biologically important lipids are fats, phospholipids, and steroids • Fats o Fats are constructed from two types of smaller molecules: glycerol and fatty acids o Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon o A fatty acid consists of a carboxyl group attached to a long carbon skeleton (has a long hydrocarbon chain on it) o Fats separate from water because water molecules hydrogen-bond to each other and exclude the fats o In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride o The fatty acids in a fat can be all the same or of two or three different kinds o Fatty acids vary in length (number of carbons) and in the number and locations of double bonds o Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds o Unsaturated fatty acids have one or more double bonds 18 o Fats made from saturated fatty acids (such as butter) are called saturated fats and are solid at room temperature o Most animal fats are saturated o Fats made from unsaturated fatty acids are called unsaturated fats or oils and are liquid at room temperature o Plant fats and fish fats are usually unsaturated o A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits o Hydrogenation is the process of converting unsaturated fats to saturated fats by adding hydrogen o Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds o These trans fats may contribute more than saturated fats to cardiovascular disease o Trans-fats are typically produced by artificial hydrogenation of fatty acids • Omega-3 fatty acids o Certain unsaturated fatty acids are not synthesized in the human body o These must be supplied in the diet § we don’t make them in our body because we are warm-blooded o These essential fatty acids include the omega-3 fatty acids, which are required for normal growth and are thought to provide protection against cardiovascular disease o The major function of fats is energy storage o Humans and other mammals store their long-term food reserves in adipose cells o Adipose tissue also cushions vital organs and insulates the body • Phospholipids o In a phospholipid, two fatty acids and a phosphate group are attached to glycerol o The two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head o When phospholipids are added to water, they self-assemble into double- layered structures called bilayers o At the surface of a cell, phospholipids are also arranged in a bilayer, with the hydrophobic tails pointing toward the interior o The structure of phospholipids results in a bilayer arrangement found in cell membranes o The existence of cells depends on phospholipids • Steroids o Steroids are lipids characterized by a carbon skeleton consisting of four fused rings o Cholesterol, a type of steroid, is a component in animal cell membranes and a precursor from which other steroids are synthesized 19 o A high level of cholesterol in the blood may contribute to cardiovascular disease • Chapter 5. Biological molecules – Part 2. Proteins and nucleic acids, summary o eggs are a good source of protein and nucleic acids • Concept 5.4: Proteins include a diversity of structures, resulting in a wide range of functions o Proteins account for more that 50% of the dry mass of most cells o Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances • Enzymatic proteins o Function: Selective acceleration of chemical reactions o Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecules • Storage proteins o Function: Storage of amino acids o Examples: Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants have storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo. • Hormonal proteins o Function: Coordination of an organism’s activities o Examples: Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration • Contractile and motor proteins o Function: Movement o Examples: Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contraction of muscles. • Defensive proteins o Function: Protection against disease o Example: Antibodies inactivate and help destroy viruses and bacteria. • Transport proteins o Function: Transport of substances o Examples: hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules across cell membranes. • Receptor proteins o Function: Response of cell to chemical stimuli o Example: Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells. 20 • Structural proteins o Function: Support o Examples: Keratin is the protein of hair, horns, feathers, and other skin appendages. Insects and spiders use silk fibers to make their cocoons and webs, respectively. Collagen and elastin proteins provide a fibrous framework in animal connective tissues. • Polypeptides o Polypeptides are unbranched polymers built from the same set of 20 amino acids § made of a chain of amino acids that can be bent up, folded, etc. § not considered a protein until it’s fully functioned § ex: an unassembled table o A protein is a biologically functional molecule that consists of one or more polypeptide o amino acids à polymers à polypeptides ??? • Amino Acid Monomers o Amino acids are organic molecules with carboxyl and amino groups o Amino acids can function simultaneously as both an acid and a base o Amino acids absorb protein ??? o Amino acids differ in their properties due to differing side chains, called R groups o Side chain (R group) § also called substitution § α carbon (the carbon in the middle of the molecule) is asymmetric most of the time • asymmetric – has 4 different things on it ------------------------------------------------- PICTURES 4-------------------------------------------------- • What to know about the 20 amino acids that are found in all living things: o they are grouped based on the chemistry of the R group (ex: polar or non- polar) o why they are different o 3 letter abbreviations & 1 letter abbreviations o basic components • Amino Acid Polymers o Amino acids are linked by peptide bonds o A polypeptide is a polymer of amino acids o Polypeptides range in length from a few to more than a thousand monomers o Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus) • Protein Structure and Function o A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape 21 o The sequence of amino acids determines a protein’s three-dimensional structure o A protein’s structure determines its function • Four Levels of Protein Structure o The primary structure of a protein is its unique sequence of amino acids § Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word § Primary structure is determined by inherited genetic information o Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain § The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone § Typical secondary structures are a coil called an α helix and a folded structure called a β pleated sheet o Tertiary structure is determined by interactions among various side chains (R groups) § Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents § These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions § Strong covalent bonds called disulfide bridges may reinforce the protein’s structure o Quaternary structure results when a protein consists of multiple polypeptide chains § Quaternary structure results when two or more polypeptide chains form one macromolecule § Collagen is a fibrous protein consisting of three polypeptides coiled like a rope § Hemoglobin is a globular protein consisting of four polypeptides: two alpha chains and two beta chains • Sickle-Cell Disease: A Change in Primary Structure o A slight change in primary structure can affect a protein’s structure and ability to function o Sickle-cell disease, an inherited blood disorder, results form a single amino acid substitution in the protein hemoglobin • What Determines Protein Structure? o In addition to primary structure, physical and chemical conditions can affect structure o Alteration in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel o This loss of a protein’s native structure is called denaturation § aka when a protein loses its shape o A denatured protein is biologically inactive • Protein Folding in the Cell o It is hard to predict a protein’s structure form its primary structure 22 o Most proteins probably go through several stages on their way to a stable structure o Chaperonins are protein molecules that assist the proper folding of other proteins o Diseases such as Alzheimer’s, Parkinson’s, and mad cow disease (BSE) are associated with misfolded proteins o Scientists use X-ray crystallography to determine a protein’s structure o Another method is nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization o Bioinformatics uses computer programs to predict protein structure from amino acid sequences • Concept 5.5: Nucleic acids store, transmit, and help express hereditary information o The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene o Genes are made of DNA, a nucleic acid made of monomers called nucleotides • The Roles of Nucleic Acids o There are two types of nucleic acids § Deoxyribonucleic acid (DNA) • provides directions for its own replication • the pristine copy § Ribonucleic acid (RNA) o DNA provides directions for its own replication o DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis o Protein synthesis occurs in ribosomes • The Components of Nucleic Acids o Nucleic acids are polymers called polynucleotides o Each polynucleotide is made of monomers called nucleotides o Each nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups o The portion of a nucleotide without the phosphate group is called a nucleoside o Sugars § Deoxyribose (in DNA) § Ribose (in RNA) o Nucleoside = nitrogenous base + sugar § two of the three parts that make a nucleoside o There are two families of nitrogenous bases § Pyrimidines (cytosine, thymine, and uracil) have a single six- membered ring • have 1 ring • remember: big word, small ring • Cytosine (C) & Thymine (T, in DNA) Uracil (U, in RNA) 23 § Purines (adenine and guanine) have a six-membered ring fused to a five-membered ring • have 2 rings • remember: small word, big ring • Adenine (A) & Guanine (G) o In DNA, the sugar is deoxyribose; in RNA, the sugar is ribose o Nucleotide = nucleoside + phosphate group • Nucleotide Polymers o Nucleotide polymers are linked together to build a polynucleotide o Adjacent nucleotides are joined by covalent bonds that form between the -OH group on the 3’ carbon of one nucleotide and the phosphate on the 5’ carbon on the next o These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages o The sequence of bases along a DNA or mRNA polymer is unique for each gene • The Structures of DNA and RNA Molecules o RNA molecules usually exist as single polypeptide chains o DNA molecules have two polynucleotides spiraling around an imaginary axis, forming a double helix o In the DNA double helix, the two backbones run in opposite 5’ à 3’ directions from each other, an arrangement referred to as antiparallel o One DNA molecule includes many genes o Nitrogenous bases in DNA pair up § form hydrogen bonds: § adenine (A) always with thymine (T), § guanine (G) always with cytosine (C) o Complementary base pairing § always have this exact pairing o Complementary pairing can also occur between two RNA molecules or between parts of the same molecule o In RNA, thymine is replaced by uracil (U) so A and U pair o RNA, in contrast to DNA, is single stranded o While DNA always exists as a double helix, RNA molecules are more variable in form • Concept 5.6: Genomics and proteomics have transformed biological inquiry and applications o Once the structure of DNA and its relationship to amino acid sequence was understood, biologists sought to “decode” genes by learning their base sequences o The first chemical techniques for DNA sequencing were developed in the 1970s and refined over the next 20 years o It is enlightening to sequence the full complement of DNA in an organism’s genome o The rapid development of faster and less expensive methods of sequencing was a side effect of the Human Genome Project 24 o Many genomes have been sequenced, generating reams of data o Bioinformatics uses computer software and other computational tools to deal with the data resulting from sequencing many genomes o Analyzing large sets of genes or even comparing whole genomes of different species is called genomics o A similar analysis of large sets of proteins including their sequences is called proteomics • DNA and Proteins as Tape Measures of Evolution o Sequences of genes and their protein products document the hereditary background of an organism o Linear sequences of DNA molecules are passed from parents to offspring o We can extend the concept of “molecular genealogy” to relationships between species o Molecular biology has added a new measure to the toolkit of evolutionary biology 25