Biology PDF - Chapter 1

-rice : Helper Biology HELDE5 the C-4pm) study horrs : & (10am + 2) Pr offic Wed email : sfletcher & bio tam edy...

-rice : Helper Biology HELDE5 the C-4pm) study horrs : & (10am + 2) Pr offic Wed email : sfletcher & bio tam edy , , RUF : (7a) 845-3927 of - Int name - Digital textbook course & ser in Syllabus and renson ~ ↑ fill in note  Chapter 1 types of science ↓ Astronomy Chem Physical Science - Natural - physics Science I Lit - Biology a Basic Us. applied Science "Pure" bain of Isnowledge Technology · · · no insinuation of · science applied to real world product or service /Problems needs · curiosity Product/service · in mind to solve. issue or need  Types of scientific reasoning Discovery science uses inductive I inductive reasoning, DescribesNatural Processes structures deductive · uses observation and data analysis. generalization -all living Hypothesis-based Science things made of CellS Utilizes Deductive reasoning hypothesis the cells is of beging with a general understanding dog struct red similar which is then used to ask specific to a. cat -testable questions and test a hypothesis - falsifiable testable must be used in it/them false Fiabl.  Tissues do not fossilize leading to imperfect descriptions of Previous creatures Experiment Control · design. -variable remain constant at a Set of parameters -> Experimental - all variables remain constant except the independent variable of interest. hypothes A that scientific Theories - has been is repeatedly not tested and · Broad Scope finished by large of evidence · supported a body Theories in Bio II Chromosome Ocell Theory & The Breits phor gene.  Cell theory All of I or living organisms made one a more Chemical 2 life takes reaction place necessary within cell for ③ all cellsarize from Pre-existing calls ↑ Cells contain heredity into in DNAom , Ganz Georg - Gene) are He basic unit of function and inheritance , Hey are Composed of Specific DNA sequences. Chapter 1: THE STUDY OF LIFE What does it mean to study Biology?  Chapter 1 Outline Part 1: Understanding Science Types of Science Discovering Answers Part 2: Understanding Life Organizing Life Exploring Cells 02  Part 1 Understanding Science Learning Objectives: Types of Science Loading… Discovering Answers Diagram the relationship between Basic and Compare and Contrast the concepts of hypothesis & Applied Science. scientific theory. Explain the importance of designing controlled experiments. Compare and Contrast discovery science and hypothesis-driven science. Describe the steps of the Scientific Method and their limitations. Summarize each of 4 theories. Chapter 1 03  Types of Science – Natural Science The field of science that is related to the physical world and its phenomena and process Natural Science Math Natural Science Life Science Biology Physical Science Life Science Physics Chemistry Astronomy Chemistry Physics Biology Physical Earth Astronomy Science Science Chapter 1 4 Types of Science – Basic vs. Applied Basic/ “Pure” Science Applied Science Gain of Knowledge Technology Loading… No insinuation of product Science applied to real world or service problems/needs Curiosity Product/Service in mind to solve the issue or need. Chapter 1 5 Types of Scientific Reasoning – Discovery Science Utilizes Inductive Reasoning Describes natural structures & processes. Use of observation & data analysis Specific observations lead to generalizations Observations: All known living organisms are made of cells. Generalization/Conclusion: All living organisms are made of Chapter 1 cells. 6 Types of Scientific Reasoning – Hypothesis-based Science Generalization: All known living organisms are made Utilizes Deductive Reasoning of cells. Begins with a general understanding which is then used to Hypothesis ask specific questions and test a hypothesis. The cell of a dog contains the same Hypothesis: structures as the cell of a cat. tentative answer to a well-framed question or observation. Requirements for a good hypothesis: Testable Falsifiable Can NOT be proven, only supported or refuted. Chapter 1 7 Discovering Answers – The Scientific Method Ask a Question Research that Question Form a Hypothesis Experiment Supports Collect Data null hypothesis Analyze Data Support Form Conclusion Refutes Hypothesis Hypothesis Communicate 8 In deductive reasoning the logic flows from the general to the specific and if a hypothesis can be supported then we can expect a particular outcome Discovering Answers – Designing an Experiment Design to test the effect of ONE variable. Broken down into: Groups Control – all variables remain constant at a set of parameters Provide the baseline Experimental - all variables remain constant except the independent variable of interest. Variables Independent – the variable that is being manipulated and/or altered. We want to see what this variable does, controls, etc. Dependent – the variable that is being measured. We want to see if this variable changes from the baseline as a result of the independent variable’s differences. Controlled – all other variables that remain constant in both the experimental and control groups. Chapter 1 10 Discovering Answers – Scientific Theories A hypothesis that has been repeatedly test and not yet falsified. Broad in Scope Supported by a large body of evidence. Many repeated and similar experiments by many different scientists Loading… Constantly challenged, tested, and modified. Modification occurs with new information and new repeatable data. “You can disprove a theory by finding even a single observation that disagrees with the predictions of the theory“ --Stephen Hawking (A Brief History of Time, 1988) 11  “Our” Theories The Chromosome Theory The Theory of The Cell Theory The Gene Theory of Heredity Evolution 1839 1863 1902 1859 Chapter 1 12 The Cell Theory Tenets of the Cell Theory 1. All living organisms are made of one or more cells.* 2. Chemical reaction necessary for life take place within the cell. 3. All cells arise only from pre-existing cells. 4. Cells contain hereditary information in the form of DNA. Chapter 1 13  Genes are the basic unit of function and inheritance. They Chromosomes containing are comprised of specific DNA specific genes are passed from sequences. parent to offspring. The Gene Theory The Chromosome Theory of Heredity Different versions of the same gene, alleles exist Genome and cause variation “The book” “chapters” Mutations/crossing over during reproduction also produce variation Utilizes Mendel’s Laws of Inheritance to “letters” explain the role of the chromosome. Gregor Mendel set “words” the foundation for heredity in the 1850s. He became “sentences” known as the father of genetics. Chapter 1 14  Evolution – Change over time in a population Requires variation in the population Decent with modification The Theory of Change in allele frequency Evolution Typically leads to the development of new species At the time Darwin proposed this theory, Evolution was not a new concept…. His work hasn’t been refuted Charles Darwin (natural selection) Jean-Baptiste Lamarck (acquired characteristics) Chapter 1 15  Evolution – Change over time in a population The Theory of Evolution Chapter 1 16  Evolution – Change over time in a population Darwin was credited with developing this theory…. Explained it in his book On the Origin of Species in 1859 Outlined his 2 definitions for evolution: The Theory of Decent with modification Evolution Natural Selection – differential reproductive success Decent with Modification Natural Selection The idea of a common ancestor. Differential reproductive success Defines the need for heritable variation for Requires variation evolution to occur. The idea that individuals in a population will pass on to see here their traits and produce offspring more frequently variation easy than others in the population. natural selection is not just surrial of the fittest Chapter 1 17 Chapter 1 18  Part 2 Understanding Life Learning Objectives: Organizing Life Exploring Cells Summarize the levels of biological organization Describe the basic functions all organisms must accomplish. from cell to biome. Compare and Contrast Eukaryotic and Prokaryotic cell types. Accurately interpret a phylogenetic tree to determine relationship of species. Chapter 1 19  Organizing Life - Taxonomy Branch of biology that names and classifies what is difference species. between species and she species reproduction DNA , environment , Chapter 1 20 Organizing Life - The evolutionary history and relationship of an Phylogeny organism and groups of organisms & 1 I Withou timeline the - - I Most recent - Dont common ancestor of length of lines matter badger & otter Phylogeny sets out to answer: Most recent 1. What species did an common ancestor of 4 organism evolve from? all 5 species 2 2. What species is an organism most closely related Most recent to? 3 common ancestor of badger & wolf 1 Most recent common ancestor of coyote & wolf - Chapter 1 21 Organizing Life – Nature’s Order Biological organization is based on a hierarchy of structural levels Chapter 1 22  Emergent properties cells - brain new get when abilizes in arranged tisbil form which would'nt they getin form basicallyre course title nower together. 23 Organizing Life – Emergent Properties Novel properties that develop at eat level upward in the biological hierarchy Result from the interactions between components. A cell is more than a bag of molecules. The whole is greater than the sum of its parts.  Exploring Cells – The Cell Subunit for all of life as we know it. Single Cell and Multicellular organisms All organisms must accomplish the same key functions: 1. Response to environmental stimuli 2. Uptake and processing of nutrients/energy (we will talk a lot about this Ch. 7 & 8) 3. Regulation/Homeostasis 4. Growth & Development 5. Reproduction Evolution & adaptation 6. Order 7. ~ Evolution & Adaptation Chapter 1 26 Exploring Cells – Cell two major groups of cells Types Prokaryotes YI Eukaryotes Both Prokaryotes and Eukaryotes have Plasma membranes Prokaryotes Eukaryotes Chromosome structure Circular Linear Organelles (including nucleus) No cremprandona) Yes crembranebordt Reproduction Binary fission Mitosis/Meiosis Size 0.1µm – 5µm 10µm – 100µm Age 3.5 BYA 1.5 BYA Chapter 1 Diversity Little Great 27 Plasma Membrane Yes Yes 28 Exploring Cells – Why Size Matters… Cell Surface area vsvolume ratio - Loading… - must have a good ratio to maintain life Exploring Cells – Animal vs. Plant Cells Plantonly since plant wall. is very rigid nucleoriors d regiou condence where rinosomesmed are ↑ Plunt only 30 Exploring Cells – Cell Small Numbers Low Type Diversity Diversity and Elkaryotes Archea ↑ are the most closely related Large Numbers High Diversity Chapter 1 31 Exploring Cells – Eukaryotic Origin Story Endosymbiotic Theory – “Within same life form” Carnivorous anerotic Anaerobic Without prokaryote oxuger Small Aerobic prokaryote Small Photosynthetic prokaryote Chromosome 2 Membranes Reproduction & Ribosomes Chapter 1 32 Exploring Cells – Unity in Diversity As diverse as life is, there is also evidence of remarkable unity. All life shares: The same genetic material (DNA, mRNA, tRNA) Nearly universal genetic code (A, C, G, T) The same basic process of gene expression (transcription & translation) The same molecular building blocks (proteins made of 20 amino acids) The presence of ribosomes 33 Chapter 2: THE CHEMICAL FOUNDATION OF LIFE How does Chemistry influence Biology?  Chapter 2 Outline Part 1: Atoms, Isotopes, ions, & Molecules Atoms and Elements in Nature Bonds in Nature Part 2: Water Importance of Water Water’s Emergent Properties Influencing Cellular Function Part 3: Carbon Understanding Carbon Carbon as a Backbone  Part 1 Atoms, Isotopes, ions, & Molecules Learning Objectives Atoms and Elements in Nature Loading… Bonds in Nature Diagram the structure of an atom. Describe the relationship between electronegativity and chemical bonds. Explain how the atomic structure changes as you move through the periodic table. Compare and Contrast covalent and ionic bonds. Explain how isotopes differ from each other and Compare and Contrast polar and nonpolar covalent bonds. how they are used in biology. Explain the importance of weak bonds/interactions for biology 3 Atoms and Elements in Nature – The Element Substances that cannot be broken down to other substances by chemical reactions Consists of a certain kind of atom that is different from those of other elements. Designated by a 1 or 2 letter symbol Atom smallest unit of matter that still retains the properties of an element. 4  Atoms and Elements in Nature – Elements in the Living World Oxygen, Carbon, Hydrogen, & Nitrogen are essential to life. Make up 96% of living matter. Element Life Atmosphere Earth’s (Humans) Crust Loading… Oxygen (O) 65% 21% 46% Carbon (C) 18% trace trace Hydrogen (H) 10% trace 0.1% Nitrogen (N) 3% 78% trace 5 6  Atoms and Elements in Nature – Subatomic Particles Atoms of each element are composed of these smaller parts The Nucleus of an Atom Contains Protons (+) & Neutrons (neutral charge) The outermost region/cloud Contains Electrons (--)  Atoms and Elements in Nature – Defining an Element Atomic Number = number of protons Defines an atom as a specific element Atomic Mass = sum of proton and neutron mass Each have close to 1 Dalton/amu Electrons have a mass of 1/2000 Dalton (negligible) The Periodic Table shows the relationship among elements. Most of the biologically important elements are in the 1st four rows. Mass Number 8  Atoms and Elements in Nature – Isotopes An element that differs in the number of neutrons Radioactive Isotopes Emit neutrons, protons, & electrons Unstable – spontaneous expulsion of particles and energy 9  Bonds in Nature – The Electron’s Role The chemical behavior of an atom is defined by its electron configuration and distribution Can vary in the amount of energy they possess. Usually found at their lowest possible energy state. Electrons fill orbitals closest to nucleus first, then those further away in order Typically, equal to the number of protons in an atom. 10  Bonds in Nature – Valence Electrons Electrons in the outermost/valence shell of an atom Determine the chemical behavior of an atom. Atoms interact with other atoms to complete their Loading… valence shell. Full valence shell = unreactive/stable atom Valency = number of unpaired valence electrons Unique to each element/atom Hydrogen = 1 Oxygen = 2 Nitrogen = 3 This is Neon Carbon = 4 Neon has a valence/valency of 0 Neon has 8 valence electrons Neon is a noble gas (“group 0”) Neon is inert or unreactive 11  Bonds in Nature – Using Electrons in Chemical Bonds The attractive force that links atoms together to form molecules and compounds Molecule = 2 or more atoms covalently bonded together. A molecular formula: Indicates the number & types of Compound = 2 or more different elements bonded in a fixed ratio. atoms in a molecule. H2 is the molecular formula for Emergent properties (Sodium + Chloride = Sodium Chloride) hydrogen gas. jonir command tool A structural formula: Has a line to represent each pair of mos ine I compound shared electrons. H-H is a molecule of hydrogen gas. Chemical reactions = changes in distribution of electrons b/w atoms. O=O is a molecule of oxygen gas. Form and Function of molecules depend on the chemical bonds formed. Different types of bonds differ in their bond strength. The reactivity of atoms is due to unpaired electrons in their valence shell. Atoms interact by either sharing or transferring valence electrons. 12  Bonds in Nature – Bonds in Chemical Reactions Bonds of reactants must be broken, then the new bonds of the product can form Reversible Irreversible Hydrogen gas Oxygen gas Water Reactants Reaction Product 2 H2O O2 2 H2 Water Oxygen gas Hydrogen gas Reactant Reaction Products 13  Bonds in Nature – The Covalent Bond The sharing of a pair of valence electrons that results in a biological strong Thesebond. bonds are used to complete valence shells. This produces stable, relatively unreactive molecules. H H C H H H H 14  Bonds in Nature – Electronegativity affects Covalent bonds The attraction of a particular kind of atom to the electrons in a covalent bond Based on 3 factors: The number of protons in the nucleus. More protons = more electronegative The number of electrons. More electrons = more electronegative 15  The distance of the outer electrons 16  Bonds in Nature – The Types of Covalent Bonds Both bond type and molecule shape determine polarity. Nonpolar Covalent Bond Polar Covalent Bond The atoms have similar electronegativities. The atoms have different electronegativities. Equal sharing of electrons Unequal sharing of electrons For example: H2, O2, CH4 For example: H2O, NH3 17  Bonds in Nature – Ionic Bonds electrical attraction between the charges of anions and cations Atoms are so electronegative that they transfer electrons from their bonding partners. Electron transfer to complete the valence shells causes the creation of ions. Atoms with more or fewer electrons than number of protons, resulting in a charge. Anion – negatively charged Cation – positively charged 18  Bonds in Nature – Weak Chemical “Bonds”/ Intermolecular Forces s Hydrogen Bonds is betwee↓ O puthi hydrogen atom covalently bonded to a more electronegative atom in a molecule is also attracted to another electronegative atom/atom in another molecule. O Common between water molecules and DNA. Dynamic 19  Bonds in Nature – Molecular Shape & Function Shape of a Molecule: Determined by the positions of its atoms’ valence orbitals Determines how biological molecules recognize and respond to one another with specificity. Allow structures to self assemble. Carbon Nitrogen Shape = Function Hydrogen Sulfur Wrong Shape = Wrong/No Function Natural Oxygen endorphin Morphine Natural endorphin Morphine (a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds to Endorphin Brain cell receptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close receptors match. (b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine. 20  Part 2 Water Learning Objectives Nature of Water Properties of Water Explain how hydrogen bonds affect the structure Summarize the 4 emergent properties of water. and behavior of water. Calculate quantities and concentrations of atoms and Define hydrophobic and hydrophilic. molecules for solution concentrations and pH. Be able to convert units Define acid, base, weak acid, and weak base. Explain how buffers work in nature and homeostasis. 21  Nature of Water – Importance The molecule that supports and sustains all life!!! The biological medium on Earth. molecules ¾ of the Earth’s surface is water. most 4 All living organisms require water to survive. with Human body is 60-70% water. roundr Paramount e to lief Most (if not all) cellular activity occurs in an aqueous environment. thin , flow easily Low Viscosity - without resistance Polar Molecule - Molecule with opposing partial charges on opposite sides. The attraction of (+) and (-) charges allow cohesion among water molecules. Cohesion utilizes hydrogen bonding! Up to 4 hydrogen bonds possible. Contributes to the various properties water exhibits 22  Nature of Water – Attraction Hydrophilic Or Hydrophobic Escared) Affinity FOR water. (water loving) NO affinity for water. (water repelling) int Ions Noncharged & Nonpolar molecules Polar molecules ↳ Fats & oils Containing O-H or N-H covalent bonds. Scenario Oxygen gas & Carbon dioxide Presenta and ask to ask Only going C H 0:N about.. 23  Nature of Water – 3 States of Water Gas Hydrogen bonds are completely broken. Highest level of kinetic energy Molecules escape into the air Liquid Hydrogen Bonds constantly break and reform Solid Crystalline Structure maintained Too low of energy to break hydrogen bonds Less dense than the liquid state (RARE!) 24  Properties of Water – 4 Emergent Properties Cohesion Moderation of Temperature Expansion upon Versatility as a freezing solvent 25  Properties of Water – Cohesion & Adhesion Cohesion Adhesion The attraction between water The attraction of a water molecule to a non- molecules due to hydrogen bonds. water molecule due to hydrogen bonds. di Capillary Action The action that allows water to flow Surface Tension The tendency of liquid surfaces to against gravity. shrink to the smallest area. 26  Properties of Water – Moderation of Temperature Water moderates air temperature by absorbing & releasing heat from the air. Temperature - The measure of the average kinetic energy. Allows water to minimize Air is cooler than water = water releases stored thermal energy. temp. fluctuations to within Air is warmer than water = water absorbs thermal energy. limits that permit life. High Thermal Capacity & High Specific Heat Amount of heat for 1g of substance to change its temperature by 1°C. Land cools faster than sea Warm blooded animals use water to disperse heat in bodies Water in blood. High Heat of Vaporization (liquid to gas) Heat sink/Heat Reservoir Evaporation of sweat = cooling & homeostasis 27  Properties of Water – Expansion upon Freezing Water transitioning from liquid to solid results in the formation of a lattice structure of water molecules held together by stable hydrogen bonds. Stable lattice structure Less dense solid structure = solid state floats in the liquid state. ICE Liquid Water Environment Cold Environments would be drastically different if this property were reversed. 28  Properties of Water – Solvent of Life Water is the universal solvent and can dissolve more different substances than most other solvents. Solute – substance that is dissolved Solvent – liquid which dissolved a solute Loading… Solution – mixture of a solute & solvent 29  Properties of Water – Solvent of Life Water’s molecular properties make it a versatile & excellent solvent. Polarity Salts Different regions of the polar water molecule can interact with and dissolve: Amino Acids Ionic compounds Sugars Polar molecules Using Different Methods And more… Results in an aqueous solution consisting of an extensive variety of charged and polar solutes. Sphere of Hydration notes Charges associated with the solutes form hydrogen bonds with the water to create a water barrier. Keeps solute dissolved. Dissociation Occurs when ionic bonds are disrupted. Atoms break off from molecules to form ions in solution. 30  Properties of Water – Solvent of Life Most biochemical reactions occur in Water. Solute Concentration in Aqueous Solutions Chemical Reactions are affected by the concentrations of reactants and products. Concentration – the amount of solute in a defined volume. Mole (not the animal ) Represents an exact number of molecules/atoms/something. Similar to a dozen = 12 Avogadro’s number = 6.023 x 1023 molecules/atoms/something Mass - Mass of 1 mole of a substance is determined by its atomic/molecular mass. Atomic = element Molecular = molecule Carbon has an atomic mass of 12 Daltons 1 mole of carbon = 12g/mol 12g/mol of carbon contains 6.023 x 1023 atoms of 31  Properties of Water – Molarity A solution has a concentration of 1 Molar (M) when it has 1 mole of a solute in 1-liter total volume (1mole/L) You must be able to convert units!!! You did/are doing this in Lab 1. Mass ( g, mg, g, kg) Think multiples of Volume ( L, mL, L) 1000 1 L = 0.001 mL Concentration ( M, mM, M, %) 1 L = 1000 mL = 106 l 10 mL = 10,000 L 1 mL = 1,000 L = 10-6 mL Calculate the # of grams needed of NaCl to make 1L of a 2M solution. to 1. 2. Steps for Solution Calculations Calculate the molecular weight of your molecule. Calculate the number of grams need to get the requested number of moles per liter. 3. Calculate the number of grams needed to get the 32  Properties of Water – Understanding pH pH stands for the potential of hydrogen and measures the concentration of hydrogen ions in solution. Water dissociates into high reactive ions. Reversible reaction Dynamic Equilibrium Dissociates & reforms at the same rate pH Scale – measures acidity/alkalinity by describing H+ concentration. More H+ = low pH value lower OH- concentration Less H + = high pH value higher OH- concentration Changes in the concentration of these ions (and thus pH) Affect biological chemistry Affect the weak bonds of proteins and cell structures Results in the formation of acids and bases 33  Properties of Water – Understanding pH pH scale is logarithmic and predictable due to the inverse relationship between H+ and OH- ions. The concentrations of H+/OH- are inversely related… Meaning the concentration of one ion is higher or lower in relation to the other ion. The product of the concentration of these 2 ions is always 10-14 Pure water = [H+] = 10-7 and [OH-] = 10-7 [H+] x [OH-] = 10-14 pH = -log [H+] pH is the negative of the base 10 logarithm of the [H+] The log10 of 1 X 10-7 is -7, and the negative of that number is 7 Each pH unit represents a tenfold difference in H+ concentrations. 35  Properties of Water – Acids and Bases Phy Hi Cells & biological molecules are sensitive to changes in pH, this is the reason we wear gloves and goggles during experiments. acid Acids and Bases change pH in different ways. Strong ↓ X Acids – break down and donate H+ into solution. HCl H+ + Cl+- - Bases – break down and donate OH- into solution. NaOH → Na+ OR OH- OH strong bind with H+ to remove them from solution. NH3 + H+ NH4 bases TpH - 36  Properties of Water – Buffers Substances that minimize change in the concentrations of hydrogen and hydroxide ions in a solution. Buffers play a key role in maintaining the internal solutions of an organism at near neutral pH. They are important in reducing the pH change. They consist of a weak acid-base pair. These are dynamic reversible pairs that will interact with hydrogen ions. O Binds H+ from the solution when the concentration is too high. Donates H+ into the solution when concentrations are too low. It & you Bicarbonate Carbonic acid carbonic acid H+ acceptor H+ donor (weak base) (weak acid) 37  Part 3 Carbon Learning Objectives Understanding Carbon Carbon as the Backbone Compare and Contrast structural isomers, cis/trans Explain why carbon is important for life. (geometric) isomers and stereoisomers. Identify common functional groups in a compound. Explain the role of each of the 7 biologically relevant functional groups. Describe what functional groups are found in which of the 4 classes of biological molecules 38  Understanding Carbon – Why Carbon Carbon serves as the backbone in the 4 big macromolecules of life (proteins, carbohydrates, lipids, and nucleic acid) Carbon is a unique element due to the ability to: Utilize its 4 valence electrons. Form covalent bonds with up to 4 different atoms. 39  Understanding Carbon – Hydrocarbons Simplest organic molecules that consist of only Carbon and Hydrogen. Contain nonpolar covalent bonds that store energy. This energy is release when the molecule is burned. think Cars and Homes Not present as pure form in most living organisms. Can be a part of the larger macromolecules. Many of a cell’s organic molecules have large chains of only hydrogen + carbon. Think lipids. Hydrocarbon Rings are common in biological organisms. Benzene found in some amino acids & Cholesterol Mostly found as Aromatic rings with 5 or 6 carbons. Single and double bonds are common Nitrogen can be a substitute for Carbon. 40  Understanding Carbon – Dopamine A chemical messenger released by neurons, called a neurotransmitter, that functions as part of the reward-motivated behavior. Half Peridol - antipsychotic used to treat Schizophrenia and Dipolar Disorder Chlorpromazine-unt: Psychotic Benzene ring used to treat sinizophrenia and DHA 41  Carbon as the Backbone – Isomers Compounds that the same number and types of atoms of an element but are arranged differently. Isomers Structural Stereoisomers Isomers Differ in covalent arrangement of bonds Geometric Enantiomers/Optical isomers Isomers Differ in spatial arrangement Chiral molecules that are bonded to the around double bonds same 4 unique partners. 42  Carbon as the Backbone – Enantiomers Chiral molecules that contain 4 different groups boned to an asymmetric carbon. Chiral – mirror images that CANNOT be superimposed on another. Biological Chemistry and Regulation depends on molecular interactions. Molecular interactions depend on the shape of the molecule. 43  Carbon as the Backbone – Functional Groups Chemical/Functional Groups allow hydrocarbon chains to exist and have molecular interactions in an aqueous environment. Carbohydrates Proteins Lipids Nucleic Acid Hydroxyl Sulfhydryl Phosphate Phosphate Carbonyl Amino Methyl Methyl Carboxyl Carboxyl 44  Carbon as the Backbone – Carbohydrate Groups The two most common functional groups seen in carbohydrates are Hydroxyl and Carbonyl. Hydroxyl (O-H) Carbonyl (C=O) Found in alcohols & sugars 2 types found in carbs: Aldehydes - terminal Polar – due to electronegative oxygen Ketones - internal Increases solubility. Hydrophilic One or the other on every monosaccharide Polar - due to electronegative oxygen Hydrophilic 45  Carbon as the Backbone – Protein Groups The two of the most common functional groups seen in proteins are Sulfhydryl and Amino. Sulfhydryl (S-H) = bodytat Amino (NH2) Found in amino acids 32 Found in EVERY amino acid Helps to form a cross link to stabilize protein Polar – Hydrophilic structure. Acts as a base and will bind free H+ ions. Polar – due to electronegative sulfur Hydrophilic 46  Carbon as the Backbone – Protein & Lipid Groups A common functional group in both Proteins and Lipids is the Carboxyl. Carboxyl (COOH) Found in fatty acids & amino acids Polar – due to electronegative oxygens Hydrophilic Acts as an acid and will release a free H+ ion. 47  Carbon as the Backbone – Lipid & Nucleic Acids Groups Two common functional groups in both Lipids and Nucleic Acids are the Methyl and Phosphate. Phosphate (OPO32-) Methyl (CH3) Found in every nucleotide & phospholipids Common in DNA gene expression regulation Also seen in ATP Nonpolar – Hydrophobic Hydrophilic – due to the negative charge Nonreactive Also important in sex hormones (lipids) 48  Functional groups help organic compounds dissolve in water – that means they are polar! If they are polar, that means they can form hydrogen bonds. x + Y X Hydrogen bonding between functional groups is extremely important for X - * ↳ biological molecules. functional groups up moechs f ractional Chapter 3 Macromolecules What molecules dominate the cell and its function? Chapter 3 Outline Part 1: Synthesis Understanding the Molecules of Life Building Macromolecules Part 2: Carbohydrates Understanding Carbohydrates Levels of Carbs Part 3: Nucleic Acids Understanding Nucleic Acids Types of Nucleic Acids Part 4: Proteins Understanding Proteins Protein Folding Part 5: Lipids Understanding Lipids Types of Lipids 2  Part 1: Synthesis Loading… Understanding the Molecules of LifeBuilding Macromolecules Name the 4 macromolecules of Identify Dehydration Synthesis and life. Hydrolysis reactions. Describe the difference between Polymers and Monomers. Describe how polymers are built Determine which macromolecule and broken down. is not a true polymer. 3 Understanding the Molecules of Life - Molecules of Life Another level of hierarchy in biological organization: Small organic molecules are joined together Creates macromolecules Macromolecules: Emergent properties Ability to form large structures Catalyze chemical reactions Signal and record information 4 Major Biological Classes Carbohydrates Proteins Nucleic Acids Lipids Understanding the Molecules of Life - Monomers and Polymers 3 classes of life’s organic macromolecules are polymers Most macromolecules are polymers Carbohydrates Built from monomers (individual subunits/building blocks) Proteins Specific sets for each class Nucleic Acids Linked by covalent bonds. Loading… Lipids are the exception Organisms share the same limited numbers of monomer types 40-50 common monomers An immense variety of polymers can be built from a small set of monomers The great diversity is the result of the arrangement of monomers into polymers  Building Macromolecules- Dehydration Synthesis The reaction of joining monomers creating a polymer by removing a water molecule and forming a covalent bond. Monomers form larger molecules by dehydration (condensation) reactions Building Macromolecules- Hydrolysis The reaction of breaking the covalent bonds in a polymer reforming its monomer (disassembly). Hydro – water; lysis – loosen/break  Part 2: Carbohydrates Understanding Carbohydrates Levels of Carbs Explain how carbohydrates are Describe the 3 different classes of formed. carbohydrates. Describe the structural and functional properties of Identify important carbohydrates. monosaccharides, disaccharides, Explain the benefits of and polysaccharides. 8  carbohydrates. Understanding Carbohydrates- The Basics Found in grains, fruits, and veggies. Provide energy to the body in the form of glucose General formula:(CH2O)n Ratio of Carbon:Hydrogen:Oxygen is 1:2:1 3 Main subtypes: 1. Monosaccharides 2. Disaccharides 3. Polysaccharides Insanely economically important! Just looking at sugarcane: $10.4 Billion in US (2018) ~35 million ton in US (2018)  Monosaccharides Mono = one => Simplest Sugars Used for Fuel or converted into organic molecules Carbohydrate monomers Generally have molecular formulas that are a multiple of CH2O For example, glucose has the formula C6H12O6 Linked together through glycosidic linkages Most names for sugars end in –ose Like glucose  Disaccharides Consist of 2 monosaccharides (di = two) Joined by a glycosidic linkage (glycol = sugar) Loading…  Polysaccharides Long chain of monosaccharides joined & identified by glycosidic linkages May be branched or unbranched May consist of multiple types of monosaccharides Molecular weight could be > 10,000 Daltons Colossal molecules  Storage Polysaccharides Starch A polymer consisting entirely of glucose monomers Composed of: Amylose (unbranched) & Amylopectin (branched) glucose monomers joined by α glycosidic bonds Major storage form of glucose in plants. Storage Polysaccharides Glycogen Consists of glucose monomers The major storage form of glucose in animals  Structural Polysaccharides Cellulose polymer of glucose, but has different glycosidic linkages than starch unbranched chains by β glycosidic linkages Major component of the tough walls that enclose plant cells Most organisms cannot digest cellulose however cows have microbes in their stomachs to facilitate this process Structural Polysaccharides Chitin Found in the exoskeleton of arthropods and in fungal cell walls Contains nitrogen! Can be used as surgical thread  Part 3: Nucleic Acids Understanding Nucleic Acids Types of Nucleic Acids Explain how nucleic acids are Compare and Contrast the concept formed. of polarity in the context of chemical bonds and nucleic acids. Describe the structural and functional properties of nucleic acids. Compare and Contrast DNA and RNA. 17  Nucleic Acids Constitute the genetic material of living organisms 2 types of nucleic acids Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) Location Eukaryotic Cells Nucleus (DNA and RNA) Cytoplasm (RNA only) Mitochondria (their own genome!) Chloroplasts (their own genome!) Prokaryotic Cells Cytoplasm (DNA and RNA)  The Structure and Function of Nucleic Acids Nucleotides (monomers) are linked together into Polynucleotides (polymers) Covalent bonds known as Phosphodiester bonds Nucleic acids store and transmit hereditary information Polymer(s) Monomer(s) Complexity  “Genome” “Transcriptome” DNA (all base pairs) mRNA (coding only)  DNA Stores information in the sequences of bases for the synthesis of specific proteins Encodes thousands of genes (each unique sequences) Directs RNA synthesis Directs protein synthesis through mRNA Double Helix 2 polynucleotides that spiral around an imaginary axis. Consists of 2 antiparallel polynucleotides. 5’ 3’ 3’ 5’ DNA  RNA RNA is primarily involved in protein synthesis Types of RNA 1. Messenger RNA (mRNA) – intermediary nucleic acid that leaves the nucleus and contains blueprint for protein synthesis (transcription & translation) 2. Transfer RNA (tRNA) – serves as a bridge between nucleotides and amino acids (translation) 3. Ribosomal RNA (rRNA) – assists in protein synthesis (translation) Summary of the key features: DNA versus RNA DNA RNA Function Carries and stores genetic Involved in protein synthesis information Structure Double helix Usually single-stranded Sugar 2-Deoxyribose Ribose Nitrogenous Cytosine, Thymine Cytosine, Uracil bases (Pyrimidines) Nitrogenous Adenine, Guanine Adenine, Guanine bases (Purines) Use the table to better understand the differences and similarities between DNA and RNA  Part 4: Proteins Protein Folding Understanding Proteins Explain the relationship between Explain how proteins are formed. protein sequence and structure. Describe the structural and functional properties of proteins. Compare and Contrast alpha helices Identify the components of an and beta pleated sheets. amino acid. Compare and Contrast the concept of 26  Proteins The most abundant organic molecule of life. Very diverse range of functions including: Regulatory Structural Protective Transport Enzymes Toxins Amino acids Polypeptides Proteins Simple Intermediate Complex  Amino Acids – Protein Monomer There are 20 common amino acids that make up proteins 9 of the 20 are called “essential” amino acids the human body cannot synthesize them and we need to get them from our diet Amino group (-NH2) Carboxyl group (-COOH) Central carbon atom (α-carbon) determines the chemical nature of Side chain (R-group) each amino acid Nonpolar  Proteins - Consists of 1 or more Polypeptides Loading… Amino acids are Linked by peptide bonds  Proteins 4 levels of structure 1. Primary structure 2. Secondary structure 3. Tertiary structure 4. Quatenary structure  1. Primary Structure The unique sequence of amino acids in a polypeptide Protein function can be compromised if alterations in the order of amino acids is made. Amino acid sequence is based upon a gene encoding a protein β-hemoglobin MVHLTPEEKSAVTALWGKVNVDEVGGEALG α1 collagen MFSFVDLRLLLLLAATALLTHGQEEGQVEGQ  2. Secondary structure The folding or coiling of the polypeptide into a repeating configuration. Includes: helixes Formed by hydrogen bond between the oxygen in the carbonyl group and an amino acid 4 positions down the chain. pleated sheets Hydrogen bonding between atoms on the backbone of the polypeptide chain.  3. Tertiary Structure The overall unique 3-D shape of a polypeptide Results from chemical Determined by a variety of chemical interactions Hydrophobic interactions Ionic bonding Hydrogen bonding Disulfide linkages interactions between amino acids and R groups  4. Quaternary Structure The overall protein structure that results from the aggregation of 2 or more polypeptides Protein Shape/Conformation determine how a protein functions.  Sickle Cell Anemia Change in a single amino acid From glutamic acid (normal) to valine (sickle cell) 1 change out of 600 amino acids  What Determines Protein Conformation? Depends on the physical and chemical conditions of the proteins environment. pH Temperature Denaturation Occurs when a protein unravels and loses its native/stable conformation Part 5: Lipids Types of Lipids Compare and Contrast the structure of Understanding Lipids a triglyceride with a phospholipid. Explain how the presence of double Explain how lipids are formed. bonds or changes in the length of Describe the structural and fatty acids affect the physical functional properties of lipids. properties of triglycerides. Recall and Define the terms hydrophilic and hydrophobic. Relate these to amphipathic. 37  Lipids: More than just Fats! Diverse group of hydrophobic molecules. Dominated by nonpolar covalent bonds (ester linkages) The only class of large biological molecules that does not consist of polymers Lipids have many diverse functions: Long term energy stores Includes: fats, oils, waxes, phospholipids, Insulation and steroids from environment for both plants and animals Building blocks for some hormones Important component of cellular membranes  Fats Constructed from: 1 glycerol + 3 fatty acids Glycerol molecules are attached to the fatty acids via an ester linkage Fatty acids Vary in double bond number and location Vary in their overall length 2 major types of Fatty Acids Saturated Unsaturated Essential Fatty Acids Omega-3 and Omega-6  Saturated Fatty Acids Unsaturated Fatty Acids Straight hydrocarbon chains, with no Kinked chains where double C=C bonds occur, double bonds, kinks prevent molecules from tightly packing between double bonds causes “saturation” of H Liquid at room temp Solid at room temperature (most plants and fish fats) (most animal fats, butter, dairy) Increase HDL and decrease LDL by transporting Tightly packed structure to liver for removal increases the amount of LDL cholesterol (“bad” cholesterol) LDL is the cause of plaque build up in arteries  Phospholipids Only have 2 fatty acids Has a phosphate group instead of a 3rd fatty acid May be modified by the addition of charged or polar chemical groups (R group) Still attached to a glycerol backbone Amphipathic molecule Has both hydrophobic & hydrophilic parts Hydrophilic “head” Hydrophobic “tail”  Steroids Lipids characterized by a carbon skeleton consisting of 4 fused rings Much different structure than other lipids! Amphipathic too! Cholesterol – waxy metabolite found naturally throughout the body Most common steroid & very diverse in its functions: Found in cell membranes of animals as a buffer In adrenal glands, testes, and ovaries it is converted to steroid hormones In the liver, it helps form bile to aid in digestion Also synthesized in the liver Precursor for Vitamin D Transported via lipoproteins High amounts can damage the cardiovascular system LDL-C: forms plaque HDL-C: sends LDL-C to liver for breakdown and removal