Unit 1 Study Guide
Unit 1 Study Guide BSC 2010
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UNIT 1 Study Guide THEMES IN THE STUDY OF LIFE 1 Emergent Properties a New properties emerge at each level of biological hierarchy b The study of life can be divided into different levels of organization Atoms Molecules Organelles Tissues Cells Organs and Organ Systems 2 The Power and Limitations of Reductionism a Reductionist reduction of complex systems to simpler components that are easier to study atoms making up biosphere the structure of DNA b An understanding of biology balances reductionism with the study of emergent properties i For example new understanding comes from studying the interactions of DNA with other molecules 3 Systems Biology a Combination of components that function together b Systems biology constructs models for the dynamic behavior of whole biological systems c The systems approach poses questions such as i How does a drug for blood pressure affect other organs ii How does increasing C02 alter the biosphere 4 Approaches to study biology or really anything a Reductionist b Emergent properties c Systems Biology Levels at which we study life Biosphere Systems Biology Ecosystem Community 0 Population Organism Organ system 0 Organ Tissue Cell Organelle Reductionism Molecule 0 Atom 5 The cell can perform all activities required for life a Homeostasis Regulation of the internal environment to maintain a constant state for example electrolyte concentration or sweating to reduce temperature b Organization Being structurally composed of one or more cells which are the basic units of life 9 Metabolism Transformation of energy by converting chemicals and energy into cellular components anabolism and decomposing organic matter catabolism Living things require energy to maintain internal organization homeostasis and to produce the other phenomena associated with life Growth Maintenance of a higher rate of anabolism than catabolism A growing organism increases in size in all of its parts rather than simply accumulating matter Adaptation The ability to change over a period of time in response to the environment This ability is fundamental to the process of evolution and is determined by the organism39s heredity as well as the composition of metabolized substances and external factors present Response to stimuli A response can take many forms from the contraction of a unicellular organism to external chemicals to complex reactions involving all the senses of multicellular organisms A response is often expressed by motion for example the leaves of a plant turning toward the sun phototropism and by chemotaxis Reproduction The ability to produce new individual organisms either asexually from a single parent organism or sexually from two parent organisms Cells are an organism s basic units of structure and function a b The cell is the lowest level of organization that can perform all activities required for life All cells i Are enclosed by a membrane ii Use DNA as their genetic information The ability of cells to divide is the basis of all reproduction growth and repair of multicellular organisms Cells and the domains of life a b C A eukaryotic cell has membraneenclosed organelles the largest of which is usually the nucleus By comparison a prokaryotic cell is simpler and usually smaller and does not contain a nucleus or other membraneenclosed organelles Bacteria and Archaea are prokaryotic plants animals fungi and all other forms of life are eukaryotic The continuity of life is based on heritable information in the form of DNA a b c b c Chromosomes contain most of a cell s genetic material in the form of DNA deoxyribonucleic acid DNA is the substance of genes Genes are the units of inheritance that transmit information from parents to offspring DNA gtTranscription gtRNA gtTranslation gtProtein DNA Structure and Function a Each chromosome has one long DNA molecule with hundreds or thousands of genes DNA is inherited by offspring from their parents DNA controls the development and maintenance of organisms d Each DNA molecule is made up of two long chains arranged in a double helix e Each link of a chain is one of four kinds of chemical building blocks called nucleotides f Genes i Genes control protein production indirectly ii DNA is transcribed into RNA then translated into a protein iii An organism s genome is its entire set of genetic instructions Biology The Study of Life g How do we study life i Discovery Science observe and describe some aspect of the world and use inductive reasoning to draw general conclusions ii HypothesisBased Science based on observations scientists propose hypothesis that lead to predictions If a hypothesis is correct and we test it we can expect a certain outcome CHAPTER 2 Matter consists of chemical elements in pure form and in combinations called compounds 0 An element s properties depend on the structure of its atoms 0 The formation and function of molecules depend on chemical bonding between atoms 0 Chemical reactions make and break chemical bonds 1 Overview A Chemical Connection to Biology a Biology is a multidisciplinary science b Living organisms are subject to basic laws of physics and chemistry c One example is the use of formic acid by ants to maintain devil s gardensquot stands of Duroia trees 2 Matter consists of chemical elements in pure form and in combinations called compounds a Organisms are composed of matter b Matter is anything that takes up space and has mass c Elements and Compounds i Matter is made up of elements ii An element is a substance that cannot be broken down to other substances by chemical reactions iii A compound is a substance consisting of two or more elements in a xed ratio iv A compound has characteristics different from those of its elements d Essential Elements of Life i About 25 of the 92 elements are essential to life ii Carbon hydrogen nitrogen and oxygen make up 96 of living matter CHNO think CHINO iii Most of the remaining 4 consists of calcium phosphorus potassium and sulfur iv Trace elements are those required by an organism in minute quantities 3 An element s properties depend on the structure of its atoms a Each element consists of unique atoms b An atom is the smallest unit of matter that still retains the properties of an element c Subatomic Particles i Atoms are composed of subatomic particles ii Relevant subatomic particles include 1 Neutrons no electrical charge 2 Protons positive charge 3 Electrons negative charge iii Neutrons and protons form the atomic nucleus iv Electrons form a cloud around the nucleus v Neutron mass and proton mass are almost identical and are measured in Daltons d Atomic Number and Atomic Mass i Atoms of the various elements differ in number of subatomic particles ii An element s atomic number is the number of protons in its nucleus iii An element s mass number is the sum of protons plus neutrons in the nucleus iv Atomic mass the atom s total mass can be approximated by the mass number e Isotopes i All atoms of an element have the same number of protons but may differ in number of neutrons ii Isotopes are two atoms of an element that differ in number of neutrons iii Radioactive isotopes decay spontaneously giving off particles and energy Subatomic Particle Charge Location Mass Special Neutron No Charge Atomic Nuc eus 1 Dalton varies in isotopes Proton Positive Atomic Nucleus 1 Dalton Proton atomic Electron Negative quotCloudquot 0 confer chemical char E A 22 I animatingmm v H lliiif ii Has5 r Ella 39i ii m ll I V Electron 2 minimum 39 I F I 395 Eq I F El 1 I H L T 9 ll Energy 5 Level of Electrons awnm 3 iv Energy is the capacity to cause change v Potential energy is the energy that matter has because of its location or structure vi The electrons of an atom differ in their amounts of potential energy vii An electron s state of potential energy is called its energy level or electron shell f Electron Distribution and Chemical Properties i The chemical behavior of an atom is determined by the distribution of electrons in electron shells ii The periodic table of the elements shows the electron distribution for each element iii Valence electrons are those in the outermost shell or valence shell iv The chemical behavior of an atom is mostly determined by the valence electrons v Elements with a full valence shell are chemically inert g Electron Orbitals i An orbital is the threedimensional space where an electron is found 90 of the time ii Each electron shell consists of a speci c number of orbitals Hydrogen Carbon Oxygen Chlorine Total E l 6 8 l7 Shells l 2 2 3 Valence E l 4 6 7 E Needed 1 4 2 l The formation and function of molecules depend on chemical bonding between atoms h Atoms With incomplete valence shels can share or transfer valence electrons With certain other atoms iThese interactions usually result in atoms staying close together held by attractions called chemical bonds j Covalent Bonds A covalent bond is the sharing of a pair of valence electrons by two atoms In a covalent bond the shared electrons count as part of each atom s valence shell A molecule consists of two or more atoms held together by covalent bonds iv A single covalent bond or single bond is the sharing of one pair of valence electrons v A double covalent bond or double bond is the sharing of two pairs of valence electrons vi The notation used to represent atoms and bonding is called a structural formula 0 For example HH vii This can be abbreviated further with a molecular formula 0 For example H2 viii Covalent bonds can form between atoms of the same element or atoms of different elements ix A compound is a combination of two or more different elements x Bonding capacity is called the atom s valence xi Electronegativity is an atom s attraction for the electrons in a covalent bond xii The more electronegative an atom the more strongly it pulls shared electrons toward itself xiii In a nonpolar covalent bond the atoms share the electron equally Ex CH4 Perfect Covalent NonPolar xiv In a polar covalent bond one atom is more electronegative and the atoms do not share the electron equally xv Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule H a an 0 CyJHCHaD o Hair E D Polar H13Nflltj HaNl C ltO iH3mgttlrciD Haw frag H3N l c H H H H H Glycine Alanine V Valine V Lancing lsaleucine Ely or G ma or A Val or V ar L llE or I E Hls I V EEEU fall H2 6H2 5 339 0H llI 539 N y THE Haw Ei EEHI Mans a tin CH TEETHZ till 39 EH2 LEM 5 0 39139 IT H H jg H N Hw jcg IHil nun Ech Haw 43 Hillel FD H3quot l c Ha t E GXDF 3 up 3 Cr 5 Iin D a o39 flu Rut Methionine phenyla anine Twpomhan Praline Sarina ThrEnnine Cystnine Tymsiine AsparaginE Glutamine Met or M Phe or F Trp or W Pro or P Ser nr 5 rm or T 055 nr E I39yr nir Y nan nr N Gin or Q k lonic Bonds Atoms sometimes strip electrons from their bonding partners ii An example is the transfer of an electron from sodium to chlorine iii After the transfer of an electron both atoms have charges iv A charged atom or molecule is called an ion 1 A cation is a positively charged ion 2 An anion is a negatively charged ion v An ionic bond is an attraction between an anion and a cation vi Compounds formed by ionic bonds are called ionic compounds or salts vii Salts such as sodium chloride table salt are often found in nature as crystals l Weak Chemical Bonds i Most of the strongest bonds in organisms are covalent bonds that form a cell s molecules ii Weak chemical bonds such as ionic bonds and hydrogen bonds are also important iii Weak chemical bonds reinforce shapes of large molecules and help molecules adhere to each other 1 Hydrogen Bonds a A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom b In living cells the electronegative partners are usually oxygen or nitrogen atoms 2 Van der Waals Interactions a If electrons are distributed asymmetrically in molecules or atoms they can result in hot spotsquot of positive or negative charge b Van der Waals interactions are attractions between molecules that are close together as a result of these charges c Collectively such interactions can be strong as between molecules of a gecko s toe hairs and a wall surface m Molecular Shape and Function i A molecule s shape is usually very important to its function ii A molecule s shape is determined by the positions of its atoms valence orbitals iii In a covalent bond the s and p orbitals may hybridize creating speci c molecular shapes Chemical reactions make and break chemical bonds n Chemical reactions are the making and breaking of chemical bonds The starting molecules of a chemical reaction are called reactants The nal molecules of a chemical reaction are called products Photosynthesis is an important chemical reaction Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen i 6 C02 6 H20 C6H1206 6 02 5 Some chemical reactions go to completion all reactants are converted to products t All chemical reactions are reversible products of the forward reaction become reactants for the reverse reaction u Chemical equilibrium is reached when the forward and reverse reaction rates are equal asap WATER THE MEDIUM OF LIFE Water 0 appears to be unique to our earth 0 covers threefourths of its surface constitutes 6070 wt of the living world regenerates and is redistributed through evaporation water cycle 0 exists in all three states ice water steam in the natural environment absolutely essential to life dehydration kills quickly Uhhnhded electron pair Water H20 Develop our understanding of water on three fronts ll Hydrogen Bonding lll Emergent properties IV Acid Base chemistry l Hydrogen Bonding A The structure of water is simple you must be able to draw water One 0 covalently bonded to two H Bond angle is 1050 O is electronegative it attracts electrons The electrons of the H spend more time closer to the O Unequal electron distribution gives water a polarity a 0 region is ha a slight charge b H ends have a slight quot charge U39gtJLI The polar nature allows for interactions 6 Liquid a Fragile disorganized hydrogen bonds b Last few trillionths of a second c Constantly reforming 7 Solid a Organized hydrogen bonds four neighbors in 3D space b Crystal is more spacious than disorganized liquid lce oats 8 Gas a Single molecules liberated from others by the addition of energy ll Emergent properties that make water great for sustaining life on earth A Cohesion adhesion and surface tension 2 3 4 Collectively hydrogen bonds hold water molecules together a phenomenon called cohesion Cohesion helps the transport of water against gravity in plants Adhesion is an attraction between different substances for example between water and plant cell walls Surface tension is a measure of how hard it is to break the surface of a liquid Surface tension is related to cohesion B Ability to moderate temperature 1 2 Heat and Temperature a Water absorbs heat from warmer air and releases stored heat to cooler air b Water can absorb or release a large amount of heat with only a slight change in its own temperature c The behavior of water is the basis for the metric temperature scale a The Celsius scale is a measure of temperature using Celsius degrees C b A calorie cal is the amount of heat required to raise the temperature of 1 g of water by 1 C c The calories on food packages are actually kilocalories kcal where 1 kcal 1000 cal d The joule J is another unit of energy where 1 0239 cal or 1 cal 4184 The high speci c heat of water a The speci c heat of a substance is the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 19C b The speci c heat of water is 1 calgQC c Water resists changing its temperature because of its high speci c heat d Water s high speci c heat can be traced to hydrogen bonding a Heat is absorbed when hydrogen bonds break b Heat is released when hydrogen bonds form e The high speci c heat of water minimizes temperature uctuations to within limits that permit life C Evaporative cooling 1 2 3 4 Evaporation is transformation of a substance from liquid to gas Heat of vaporization is the heat a liquid must absorb for 1 g to be converted to gas As a liquid evaporates its remaining surface cools a process called evaporative cooling Evaporative cooling of water helps stabilize temperatures in organisms and bodies of water D Expansion upon FreezingInsulation of bodies of water 1 2 3 Ice oats in liquid water because hydrogen bonds in ice are more ordered making ice less dense Water reaches its greatest density at 4 C lf ice sank all bodies of water would eventually freeze solid making life impossible on Earth E Universal solvent 1 De nitions a solution solvent solute b Hydration shell a Water is a versatile solvent due to its polarity which allows it to form hydrogen bonds easily b When an ionic compound is dissolved in water each ion is surrounded by a sphere of water molecules called a hydration shell c Water can also dissolve compounds made of nonionic polar molecules d Even large polar molecules such as proteins can dissolve in water if they have ionic and polar regions 2 Hydrophilic and Hydrophobic substances a A hydrophilic substance is one that has an af nity for water b A hydrophobic substance is one that does not have an af nity for C d water Oil molecules are hydrophobic because they have relatively nonpolar bonds A colloid is a stable suspension of ne particles in a liquid 3 Solute concentrations and Molarity a b Acid Base chemistry Most biochemical reactions occur in water Chemical reactions depend on collisions of molecules and therefore on the concentration of solutes in an aqueous solution c Molecular mass is the sum of all masses of all atoms in a molecule d Numbers of molecules are usually measured in moles where 1 mole mol 602 x 1023 molecules Avogadro s number and the unit dalton were de ned such that 602 x 1023 daltons 1 g Molarity M is the number of moles of solute per liter of solution 0 Water is in a state of dynamic equilibrium in which water molecules dissociate at the same rate at which they are being reformed Though statistically rare the dissociation of water molecules has a great effect on organisms A hydrogen atom in a hydrogen bond between two water molecules can shift from one to the other The hydrogen atom leaves its electron behind and is transferred as a proton or hydrogen ion H The molecule with the extra proton is now a hydronium ion H3O though it is often represented as H The molecule that lost the proton is now a hydroxide ion OH Changes in concentrations of H and OH can drastically affect the chemistry of a cell F The pH scale pH was originally written by Dr Soren Sorensen in 1909 as PH and it stands for pondus hydrogenii which means quotpotential hydrogenquot The terminology refers to acidity being due to a predominance of hydrogen ions in an aqueous water containing solution 10 1 In any aqueous solution at 25 C the product of H and OH is constant and can be written HOH 103914 concentration written as pH log H 3 For a neutral aqueous solution H is 10 7 7 7 4 Acidic solutions have pH values less than 7 5 Basic solutions have pH values greater than 7 G Acids and Bases The pH of a solution is de ned by the negative logarithm of H 1 What causes an imbalance in H and OH concentrations Acids and Bases Acids increases the hydrogen ion concentration Hydrochloric Acid HCI 2 3 4 HCI gt H Cl39 single arrow complete dissociation STRONG 5 Bases reduce the hydrogen ion concentration two ways a Accepting a H Ammonia NH3 H ltgt NH4 b Providing and OH which ultimately makes another molecule of water Sodium Hydroxide NaOH gt Na OH H Buffers 1 The internal pH of most living cells must remain close to pH 7 2 Buffers are substances that minimize changes in concentrations of H and OH in a solution 3 Most buffers consist of an acidbase pair that reversibly combines with H 4 The weak acid carbonic acid is formed when C02 reacts with H20 in blood plasma H2CO3 DD HCO339 H H donor H acceptor H ion acid base Electrically charged l 392 EH ACIdIC Lu r H CH Willi 3 BH HE EIIH 5 a p 39 in 2 c a 39 p 41 3 H 44 Haw 456 Haw 14 H3M r c Clng 1 chig EH 39 t Aspar Eacid Glutamic aci Lysine Arginine ai39 ls lnR Aspg DD Glu or E EH3 XE Lys or K quotEH Wg or R His er H E H3N quot CR HaNt lii C HEW C Cg H or H o L p CARBON THE BACKBONE OF LIFE Carbon 11 Enters the biosphere through plants convert C02 to sugar and biological macromolecules Unique in its ability to form molecules that are large complex and diverse Forms bonds with H N O P and S to make biological macromolecules DNA RNA and proteins Develop our understanding of carbon on three fronts 12 l The study of carbon compounds ll Carbon makes four bonds III A small number of chemical groups are key to molecular diversity The study of carbon compounds Organic chemistry A Organic compounds carbon containing compounds B Range from small molecules CH4 huge macromolecules chromosomes C Think of C as the coolest tinyest LEGO ever Carbon bonds to four other atoms A Carbon has 6 electrons 1 2 in rst shell 2 4 in second shell 4 valence electrons B Completes outer shell by sharing its 4 valence electrons with other atoms C Tetravalence is what makes carbon so versatile D Single and double bond geometry Shape and function intertwined in biology 1 Hybrid orbitals and tetravalence give methane a tetrahedral geometry Bond angles of 1095 2 Hybrid orbitals of double bonds create a trigonal planar molecule Bond angles of 120 Carbon backbones can connect diverse molecules A Carbon Backbone variation 1 Length 2 Branching 3 Double bonds 4 Circularization The electron con guration of carbon gives it covalent compatibility with many different elements The valences of carbon and its most frequent partners hydrogen oxygen and nitrogen are the building codequot that governs the architecture of living molecules B Hydrocarbons 1 Hydrocarbons are organic molecules consisting of only carbon and hydrogen 2 Many organic molecules such as fats have hydrocarbon components 3 Hydrocarbons can undergo reactions that release a large amount of energy C lsomers 1 Structural isomers have different covalent arrangements of their atoms 2 Geometric isomers have the same covalent arrangements but differ in spatial arrangements 3 Enantiomers are isomers that are mirror images of each other A small number of chemical groups make biological molecules Monomers or Polymer or larger Components molecule Type of Linkage Sugars Polysaccharides Glycosidic Monosaccharides Linkage Lipids Fatty Acids Triacylglycerols Ester Linkages Proteins Amino Acids Polypeptides Peptide Bonds Nucleic Acids Nucleotides Polynucleotides Phosphodiester Linkages Sugars Monosaccharides Polysaccharides Glycosidic Linkages MPG monopolyglyco Lipids Fatty Acids Triacylglycerols Ester Linkages FTE fattriester Proteins Amino Acids Polypeptides Peptide Bonds APP AmPoPep Nucleic Acids Nucleotides Polynucleotides Phosphodiester Linkages NPP NuPoPho Functional groups are the components of organic molecules that are most commonly involved in chemical reactions 0 The number and arrangement of functional groups give each molecule its unique properties A Hydroxyl 0H E Phosphate B Carbonyl F Sulfhyrdyl c C Carboxyl 0 ll CEO H D Amino ll G Methyl l N H BIOLOGICAL MACROMOLECULES Biological Macromolecules are polymers built from monomers 1 All living things are made up of four classes of large biological molecules a Carbohydrates b Lipids c Proteins d nucleic acids 2 Within cells small organic molecules are joined together to form larger molecules a Macromolecules are large molecules composed of thousands of covalently connected atoms b Molecular structure and function are inseparable A polymer is a long molecule consisting of many similar building blocks 1 These small buildingblock molecules are called monomers 13 a An immense variety of polymers can be built from a small set of monomers b Three of the four classes of life s organic molecules are polymers i Polysaccharides are built from monosaccharides ii Nucleic Acids DNA and RNA are built from nucleotides A TU C and G iii Proteins are built from amino acids A R N D C E Q G H l L K M F P S T W Y and V 2 Polymers are formed by dehydration synthesis a A dehydration synthesis occurs when two monomers bond together through the loss of a water molecule b Enzymes are macromolecules that speed up the dehydration process c Disassembled by hydrolysis the addition of water to break a bond 3 Polymers are disassembled to monomers by hydrolysis a Hydrolysis is essentially the reverse of the dehydration reaction CARBOHYDRATES Carbohydrates include sugars and the polymers of sugars The simplest carbohydrates are monosaccharides or single sugars Carbohydrate macromolecules are polysaccharides polymers composed of many sugar building blocks called monosaccharides Ill Monosaccharides A have molecular formulas that are usually multiples of CHZO B Numbering of monosaccharide carbons from functional group C Glucose C6H1206 is the most common monosaccharide D Monosaccharides are classi ed by 1 The location of the carbonyl group as aldose or ketose 2 The number of carbons in the carbon skeleton 3 Spatial arrangement of carbons a Though often drawn as linear skeletons in aqueous solutions many sugars form rings E Monosaccharides serve as a major fuel for cells and as raw material for building molecules F Monosaccharides may be linear chains or ring structures IV Disaccharides A A disaccharide is formed when a dehydration reaction joins two monosaccharides B This covalent bond is called a glycosidic linkage V Polysaccharides A Polymers of sugars B The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages C Roles of polysaccharides 1 Energy storage roles a Starch amylose unbranched and amylopectin i Storage polysaccharide of plants ii consists entirely of glucose monomers a Plants store surplus starch as granules within chloroplasts and other plastids b Glycogen more branched than amylopectin a Glycogen is a storage polysaccharide in animals 14 b Humans and other vertebrates store glycogen mainly in liver and muscle cells 2 Structural roles a Cellulose a The polysaccharide cellulose is a major component of the tough wall of plant cells b Like starch cellulose is a polymer of glucose but the glycosidic linkages differ c The difference is based on two ring forms for glucose alpha 0c and beta B d Structure function relationships 1 Polymers with ocglucose are helical 2 Polymers with Bglucose are straight e In straight structures cellulose H atoms on one strand can bond with OH groups on other strands f Parallel cellulose molecules held together this way are grouped into micro brils which form strong building materials for plants g Enzymes that digest starch by hydrolyzing 0c linkages can t hydrolyze B linkages in cellulose h Cellulose in human food passes through the digestive tract as insoluble ber i Some microbes use enzymes to digest cellulose j Many herbivores from cows to termites have symbiotic relationships with these microbes b Chitin a Chitin another structural polysaccharide is found in the exoskeleton of arthropods b Chitin also provides structural support for the cell walls of many fungi c Used to make dissolving stitchesquot LIPIDS Share one important trait mix poorly with water Are not true polymeric macromolecules Some polar parts but generally hydrocarbons nonpolar We will focus on Fats Phospholipids and Steroids 1 Fats a Fats are constructed from two types of smaller molecules glycerol and fatty acids i Fatty acids 1 Think about the name fatty acid Hydrocarbon Carboxylic acid 2 A fatty acid consists of a carboxyl group attached to a long carbon skeleton ii Glycerol 1 threecarbon alcohol with a hydroxyl group attached to each carbon 15 iii Three fatty acids are joined to glycerol by an ester linkage creating a triacylglycerol or triglyceride iv Fatty acids vary in 1 length number of carbons 2 number and locations of double bonds a Saturated fatty acids i have the maximum number of hydrogen atoms possible and no double bonds They are saturated with hydrogens ii solids at room temperature iii animal fats except for sh b Unsaturated fatty acids i have one or more double bonds ii liquids at room temperature iii plant and sh fats b Some points on hydrogenation i A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits ii Hydrogenation is the process of converting unsaturated fats to saturated fats by adding hydrogen iii Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds iv These trans fats may contribute more than saturated fats to cardiovascular disease c Functions in biology i The major function of fats is energy storage 1 A gram of fat stores twice as much energy as a gram of carbohydrate Remember my gasoline analogy last Thursday 2 Plants don t have to move so they can store carbohydrates animals move so need a more efficient energy storage solution ii Humans and other mammals store their fat in adipose cells iii Adipose tissue also cushions vital organs and insulates the body 2 Phospholipids a Two fatty acids and a phosphate group are attached to glycerol i Hydrophobic tail The two fatty acids ii hydrophilic head the phosphate group and its attachments b Formation into bilayers i When phospholipids are added to water they selfassemble into a bilayer with the hydrophobic tails pointing toward the interior ii The structure of phospholipids results in a bilayer arrangement found in cell membranes iii Phospholipids are the major component of all cell membranes 3 Steroids a Steroids are lipids characterized by a carbon skeleton consisting of four fused rings b Cholesterol i component in animal cell membranes ii synthesized in the liver iii essential in animals but high levels in the blood may contribute to cardiovascular disease 16 iv Precursor from which other steroids are formed estradiol testosterone c Very important biological molecules that signal gene expression PROTEINS Proteins account for more than 50 of the dry mass of most cells 0 Protein functions include structural support storage transport cellular communications movement and defense against foreign substances Polypeptides are polymers built from the same set of 20 amino acids 0 A protein consists of one or more polypeptides Amino acids are organic molecules with carboxyl and amino groups 0 Amino acids differ in their properties due to differing side chains called R groups 1 Proteins have several roles in the cell a Enzymes i Enzymes are a type of protein that acts as a catalyst to speed up chemical reactions ii Enzymes can perform their functions repeatedly functioning as workhorses that carry out the processes of life 2 Amino Acid Polymers a Amino acids are the building blocks i All have a common chemical structure with differing radical R groups ii Rgroups give speci c chemical properties 1 Nonpolar equal distribution of electrons 2 Polar Unequal distribution of electrons 3 Charged Acidic or Basic Amino acids are linked by peptide bonds A polypeptide is a polymer of amino acids Polypeptides range in length from a few to more than a thousand monomers Each polypeptide has a unique linear sequence of amino acids A functional protein consists of one or more polypeptides twisted folded and coiled into a unique shape cameos 3 Structure Function Relationships a The sequence of amino acids determines a protein s threedimensional structure b A protein s structure determines its function 4 levels of structure i The primary structure of a protein is its unique sequence of amino acids a 7m 7 Mm Acids Primary Structure Secondary structure found in most proteins consists of coils and folds in the polypeptide chain 17 Pleated sheet t Alph ahelix Seeender Structure ii Tertiary structure is determined by interactions Tertiary Structure various Side groups among chains R iii Quaternary structure results when a protein consists of multiple polypeptide chains ueterner g Structure c Primary structure i Primary structure the sequence of amino acids in a protein is like the order of letters in a long word ii Primary structure is determined by inherited genetic information d Secondary Structure i The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone ii Typical secondary structures are 1 a coil called an alpha helix 2 and a folded structure called a l pleated sheet e Tertiary Structure i Tertiary structure is determined by interactions between R groups rather than interactions between backbone constituents ii These interactions between R groups include 1 hydrogen bonds 2 ionic bonds 3 hydrophobic interactions 4 van o er Waas interactions iii Strong covalent bonds caed disul de bridges may reinforce the protein s structure f Quaternary Structure 18 i Quaternary structure results when two or more polypeptide chains form one macromolecule ii Collagen is a brous protein consisting of three polypeptides coiled like a rope iii Hemoglobin is a globular protein consisting of four polypeptides two alpha and two beta chains 4 Other Factors Play a Role in Protein Structure a In addition to primary structure physical and chemical conditions can affect structure b Alterations in pH salt concentration temperature or other environmental factors can cause a protein to unravel c This loss of a protein s native structure is called denaturation d A denatured protein is biologically inactive 5 Protein Folding in a Cell a It is hard to predict a protein s structure from its primary structure b Most proteins probably go through several states on their way to a stable structure c Chaperonins are protein molecules that assist the proper folding of other proteins 1 Protein Structures a Scientists use Xray crystallography to determine a protein s structure b Another method is nuclear magnetic resonance NMR spectroscopy which does not require protein crystallization c Bioinformatics uses computer programs to predict protein structure from amino acid sequences NUCLEIC ACIDS Store and transmit hereditary information o The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene 0 Genes are made of DNA a nucleic acid 0 There are two types of nucleic acids Deoxyribonucleic acid DNA Ribonucleic acid RNA 0 DNA provides directions for its own replication 0 DNA directs synthesis of messenger RNA mRNA and through mRNA controls protein synthesis 0 Protein synthesis occurs in ribosomes 2 Nucleic Acid Structure a Nucleic acids are polymers called polynucleotides b Each polynucleotide is made of monomers called nucleotides c Each nucleotide consists of i a nitrogenous base ii a pentose sugar iii and a phosphate group 19 d The portion of a nucleotide without the phosphate group is called a nucleoside 3 Nucleotide Monomers a Nucleoside nitrogenous base sugar b There are two families of nitrogenous bases i Pyrimidines cytosine thymine and uracil have a single sixmembered rig ii Purines adenine and guanine have a sixmembered ring fused to a fivemembered ring it if H C C Ha if ti HC N 3H Hscmd m H EH5 mHE Adenine A Guanine G Purine balsa twarings he sugars between DNA and RNA differ i DNA the sugar is deoxyribose ii RNA the sugar is ribose r2 3 E r H 39 39 Hi N 3 NH Hi EH H 39mHI allj H mx h H RN HO H H H Cytesine Thyrrine Uracil Py nidine b35525 one rings T d Nucleotide nucleoside phosphate group 4 Nucleotide Polymers a Nucleotide polymers are linked together to build a polynucleotide b 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 c These links create a backbone of sugarphosphate units with nitrogenous bases as appendages d The sequence of bases along a DNA or mRNA polymer is unique for each gene FCATGAATTC 3GTACTTAAGF 5 The DNA Double Helix a A DNA molecule has two polynucleotides spiraling around an imaginary axis forming a double helix b In the DNA double helix the two backbones run in opposite 5 gt 3 directions from each other an arrangement referred to as antiparallel c The nitrogenous bases in DNA pair up and form hydrogen bonds i adenine A always with thymine T two hydrogen bonds ii guanine G always with cytosine C three hydrogen bonds Test Questions 1 Covalent Beer 2 Starchis the storage polysaccharide 0 an storade polvsaccharide in animals saturat Ad 20 occurs when two monomers bond together through the loss of a whi Glycoge is the 3 fatty acids have the maximum number of hydrogen atoms possible and no double bond solid at room temperature 4 What is the reaction M two monomers Dehydration Synthesis 5 What is the reaction that breaks apart two joined molecules Hydrolysis YOU SHOULD NOW BE ABLE TO 0 List and describe the four major classes of molecules 1 Carbohydrates incl sugars and polymers of sugars monosaccharides and polysaccharides Glucose C6H1206 2 Lipids mix poorly with water not true polymeric macromolecules generally nonpolar hydrocarbons Fats Phospholipids Steroids saturated max hydrogen atoms no double bonds solid and unsaturated 1 double bonds liqud 3 Proteins 50 of dry mass in most cells structure storage transport consist of 1 polypeptides amino acids 4 Nucleic Acids make up genes have DNA or RNA own replication protein synthesis occurs in ribosomes Nitrogenous base pentose sugar phosphate group R 0 N H H H H H H H H H 0 l l l l l l l l l f f f f f f f i f i I H H H H H H H H saturated H H H H H H 01x l l l l l I 339 fC C C C C C Ctecf Isa D a J I D Gyloslna l H H H H H from fr 39Og g v39 H unsaturated 339 go s3 5 HH NucleicAcids l ucscwc we Vov V o gCosidic linkage anu39ci39imls ungulsn DELWEOH l monosaccharides disaccharides and polysaccharides gtGlycosidic Linkage linkage between two or more monosaccharides involving condensation polymerization hydrogen ion detached from hydroxyl that is attached to carbon atom on 1St monomer leaving free binding oxygen ion gt Monosaccharides simplest carbohydrate single sugar have molecular formula that is multiple of CH20 classi ed by carbonyl group as ALDOSE or KETOSE serve as fuel for cells or raw material for building may be linear chains or ring structures gt Disaccharides formed when a dehydration reaction joins two monosaccharides this covalent bond is called a glycosidic linkage gt Polysaccharides polymers of sugars energy storage structural storage chitin structure and function determined by sugar monomers and position of glycosidic linkages CHEDH CHEDH CI CI OH OH OH HO OH HO O CHEDH OH OH monosaccharidefglucosej HUGH CI EjH 2 disacc haride 3 ucrosej CHEDH CHEDH CHEDH CHEDH D c D D 21 1 OH OH OH DH 3 D D 2 OH OH OH OH pc lysaccharide am lose star h Distinguish between saturated and unsaturated fats and between cis and trans fat molecules SATilil liA EI t39t39t39t39 39 t39t39 t39t39 l 39 39 39 Etnari i acid Hquot quot5 EH Foundinbu v iHHHHHHlHHHHHHHHHH UHEETUEHTEE Limlleic acid MunIi is Fig EmilyII ail 7 fi m l Hrr r e quot at 39iFKsIEtIIKDEH HI H H H H Hi tmLiinzmlei acid rrrrrrrr Tm Hesstttes hum in same H H H H H H H H I mairgagrin e 39 Fl bOSE a no deoxyrl DOSE he 339 Grid and 539 Grid OT a DUCleOEIGe HE A Purines i Pia ttt ii 1 i H E xr33 39 i 7 nahJ M v E H T lea it HIDE KID F BEBE a Hill 1 251 i E I I I E i r wu mh hi39 39739quot quot NH ii DD 33 v32 glymsmlmbnncl H E l 39v I m I i HE DH 2 rlb el I Adeninequot n r Guanine l l i H denatyribauae Pyrimidinee nili2 a c HM quotJthl39H H1 V39JIL M H I f i Ii i Ii 3 39 HIE Lil Lit Hquot rill quotLec LliEDElIElE triipn zaphat a n39 4331 liarsquot 39ll39l39lllile39Ei ifil39lE Draw Amino Acid Steroid Fatty Acid cis andlitrgrisUNlucleotide purine and pyrimidine phospholipid bilayer water molecule bond angle of 104 5 degrees and partial charges Functional Group Amino Acid Steroid Fatty Acid J I cis trans Purine Pyrimidine Phospholipid Bilayer Nonpolar Tails Polar Heads Water u HIKE Jig quot I HI 1 22 1039 i519 23
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