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Ch’s 2*, 3, 6* LO 2.5 Chapter 2 Chemical Context What you must know: The three subatomic particles & their significance The types of bonds, how they form, and their relative strengths Matter VS Energy MATTER Has mass & takes up space Affected by gravity Consists of elements and compounds ENERGY Moves matter Potential, kinetic Ability to do work Conversions Sound, light, heat Comparison ELEMENT “Pure” substance Can’t be broken down by “ordinary means to another substance Ex. Hydrogen (H), Nitrogen (N) COMPOUND 2 or more different elements combined in a fixed ratio Ex. H2O, CO2 Elements of Life 25 elements 96%: O, C, H, N ~4%: P, S, Ca, K & trace elements (ex: Fe, I) Hint: Remember CHNOPS! Subatomic Particles Atoms are composed of smaller parts called subatomic particles Relevant subatomic particles include Neutrons (no electrical charge) Protons (positive charge) Electrons (negative charge) Neutrons and protons form the atomic nucleus Electrons form a cloud around the nucleus Subatomic Particles MASS (dalton or AMU) Location Charge Neutron 1 Nucleus 0 Proton 1 Nucleus +1 Electron Negligible Shell -1 2 Atomic number He 4.00 Atomic mass Element symbol Electron distribution diagram Helium 2He Figure 2.6 2 Hydrogen 1H Atomic number He Atomic mass First shell 4.00 Helium 2He Element symbol Electron distribution diagram Lithium 3Li Beryllium 4Be Boron 5B Carbon 6C Nitrogen 7N Oxygen 8O Fluorine 9F Neon 10Ne Sodium 11Na Magnesium 12Mg Aluminum 13Al Silicon 14Si Phosphorus 15P Sulfur 16S Chlorine 17Cl Argon 18Ar Second shell Third shell Isotopes All atoms of an element have the same number of protons but may differ in number of neutrons Isotopes are two atoms of an element that differ in number of neutrons # Neutrons varies, but same # of protons Radioactive isotopes decay spontaneously, giving off particles and energy; used as tracers Uncontrolled exposure causes harm Isotopes Carbon-12 Carbon-13 Carbon-14 Protrons 6 6 6 Neutrons 6 7 8 Electrons 6 6 6 Chemical Bonging Electronegativity- used to determine whether a given bond will be nonpolar covalent, polar covalent, or ionic. Electronegativity is a function of: the atom's ionization energy (how strongly the atom holds on to its own electrons) Strongest bonds: 1. 2. Covalent: sharing of e- a. b. Polar: covalent bond between atoms that differ in electronegativity Non-Polar: e- shared equally; eg. O2 or H2 a. b. Na+ClEffected by environment (eg. water) Ionic: 2 ions (+/-) bond (givers/takers) Chemical Bonding Chemical Bonding Weaker Bonds 3. Hydrogen: H or polar covalent molecule bonds to electronegative atom of other polar covalent molecules 4. Van der Waals Interactions: slight, fleeting attractions between atoms and molecule close together a. weakest bond b. Eg. Gecko toe hairs + wall surface Chemical Bonding Covalent Ionic Hydrogen All important to life Form cell’s molecules Quick H bonds to other reactions/responses electronegative atoms Strong bond Weaker bond (esp. in H2O Even weaker Made an broken by chemical reactions Chemical Bonding All bond affect molecule’s SHAPE affect molecule’s FUNCTION Natural endorphin Key Carbon Hydrogen Nitrogen Sulfur Oxygen Morphine Similar shapes= mimic Morphine, heroin, opiates mimic endorphin (euphoria, relieve pain) (a) Structures of endorphin and morphine Natural endorphin Brain cell Morphine Endorphin receptors Chemical Reactions Chemical reactions are the making and breaking of chemical bonds The starting molecules of a chemical reaction are called reactants The final molecules of a chemical reaction are called products Figure 2.UN02 O2 2 H2 Reactants 2 H2O Reaction Products Chemical Reactions REACTANTSPRODUCTS EG. 6CO2 + 6H2O C6H12O6 + O2 Some reactions are reversible: Eg. 3H2 + N2 2NH3 Chemical equilibrium: point at which forward and reverse reactions offset one another exactly Reactions still occurring, but no net change in concentrations of reactants/products Carbon and the molecular diversity of life What you must know The role of dehydration synthesis in the formation of organic compounds and hydrolysis in the digestion of organic compounds How to recognize the 4 biologically important organic compounds (carbs, lipids, proteins, nucleic acids) by their structural formulas The cellular functions of all 4 organic compounds The 4 structural levels of proteins Water properties Carbon Atoms Of all chemical elements CARBON is unparalleled in its ability to form molecules that are large, complex, and varied. H, O, N, S, P are other common ingredients of these compounds but it is the element C that accounts for the enormous variety of biological molecules. For reasons- compounds containing C is said to be an organic compound, and compounds associated with life contain H atoms in addition to C atoms. Biomolecules Why does it have to be CARBON? 4 available bonds! Can form single, double, and triple bonds Can form chains and rings 3 Simple Organic Molecules Carbon Bonding/Skeletons Chemical Groups Organic molecules depend not only on the arrangement of its CARBON skeleton but also on the chemical groups attached to that skeleton The number and arrangement of chemical groups help give each organic molecule its unique properties Biomolecules How can we fancy up the hydrocarbons? Functional groups! hydroxyl carboxyl sulfhydryl amine carbonyl phosphate Chemical Groups Functional Groups Hydroxyl Forms alcohols Ex: ethanol Carboxyl Double-bonded O plus an –OH Is acidic Ex: acetic acid Functional Groups Sulfhydryl An S-H group Often form bonds with each other (disulfide bridges) Ex: DNA links Amine - acts as a base - Ex: amino acids; norepinephrine Functional Groups Carbonyl Is double-bonded O Aldehyde if on end Ketone if in middle Functional Groups Phosphate Negative charge Attaches to C by one of its O’s Ex: DNA nucleotides Water Properties H-Bonds Cohesion Surface Tension Adhesion Transpiration High specific heat Evaporative Cooling Insulation Solvent pH Polarity of Water O will bond with H on a different molecule of - + water=Hydrogen bond Water can form up to 4 bonds Water Properties Adhesion: attraction between UNLIKE molecules Cohesion: attraction between TWO waters Transpiration: movement of water UP plants; water clings to each other by cohesion, cling to xylem tubes by adhesion Surface Tension: measure of how difficult it is to break or stretch surface of liquid Heat: total amount of KE in system Temperature: measure intensity of HEAT due to AVERAGE KE of molecules High Specific Heat: change temp less when absorbs/loses heat, large bodies of water absorb & sore more heat, create stable marine/land environment Water Properties Evaporative Cooling: water has high heat of vaporization, molecules with greatest KE leave as gas, stable temp in lakes & ponds, cool plants, humans sweat Insulation by ice: less dense, floats, insulates under water Universal solvent: Dissolves more substances than any others! Solution: liquid, homogenous mixture of 2+ substances Solvent: dissolving agent (liquid) Solute: dissolved substances pH: acids & bases- acids: increases H+ concentration (HCL) bases: reduces H+ concentration (NaOH) Acids & Bases Buffers: minimize changes in concentration of H+ and OH- in a solution (weak acids and bases Buffers keep blood at pH of ~ 7.4 If blood drops to 7 or up to 7.8 then DEATH Carbonic Acid-Bicarbonate System: important buffers in blood plasma Macromolecules & Polymers Macromolecules in three of the four classes of life’s organic compounds Carbohydrates, Proteins, & Nucleic Acids are chain like molecules called polymers Polymer- is a long molecules consisting of many similar or identical building blocks linked by covalent bonds, much as a train consisting of cars. The repeating units that serve as the building blocks of a polymer are similar molecules called monomers Monomers Polymers Macromolecules *Small organic *Used for building blocks of polymers *Connects with condensation reaction (dehydration synthesis) *Long molecules of monomers *With many identical or similar blocks linked by covalent bonds *Giant molecules *2 or more polymers bonded together i.e. Amino Acid peptide polypeptide protein Smaller Larger Polymers Cells make and break down polymers by the same process A dehydration reaction occurs when two monomers bond together through the loss of a water molecule Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction These processes are facilitated by enzymes, which speed up chemical reactions Figure 3.6 (a) Dehydration reaction: synthesizing a polymer Short polymer Longer polymer (b) Hydrolysis: breaking down a polymer Unlinked monomer Figure 3.6a (a) Dehydration reaction: synthesizing a polymer Short polymer Dehydration removes a water molecule, forming a new bond. Longer polymer Unlinked monomer Figure 3.6b (b) Hydrolysis: breaking down a polymer Hydrolysis adds a water molecule, breaking a bond. Diversity of Polymers Each cell has thousands of different macromolecules Macromolecules vary among cells of an organism, vary more within a species, and vary even more between species An immense variety of polymers can be built from a small set of monomers Biomolecules Critically important molecules of all living things fall into four main classes Carbohydrates Lipids Proteins Nucleic Acids The first three of these can form huge molecules called macromolecules 1. Carbohydrates Carbohydrates include sugars and the polymers of sugars The simplest carbohydrates are monosaccharides, or simple sugars Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks CHO Monosaacharides formulas that Monosaccharides have molecular are usually multiples of CH2O Glucose (C6H12O6) is the most common monosaccharide Monosaccharides are classified by the number of carbons in the carbon skeleton and the placement of the carbonyl group (C=O) Though often drawn as linear skeletons, in aqueous solutions many sugars form rings Monosaccharides serve as a major fuel for cells and as raw material for building molecules Examples: glucose, fructose, dextrose Figure 3.7 Triose: 3-carbon sugar (C3H6O3) Glyceraldehyde An initial breakdown product of glucose in cells Pentose: 5-carbon sugar (C5H10O5) Ribose A component of RNA Hexoses: 6-carbon sugars (C6H12O6) Glucose Fructose Energy sources for organisms Dehydration Synthesis Remove water to join molecules together; Is an endergonic reaction – needs energy Hydrolysis Add water to break apart a molecule Is an exergonic reaction – gives off energy Figure 3.9-2 Glucose Fructose 1–2 glycosidic linkage Sucrose Polysaccharides A disaccharide is formed when a dehydration reaction joins two monosaccharides This covalent bond is called a glycosidic linkage Polysaccharides, the polymers of sugars, have storage and structural roles The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages Examples: starch, glycogen, cellulose, chitin 2. Lipids Fats (triglycerides): store energy; 3 fatty acids + glycerol; saturated, unsaturated, & polyunsaturated Steroids: cholesterol & hormones Phospholipids: lipid bilayer of cell memebrane Examples Food – oils, butter, fatty meats, whole milk, nuts, egg yolk Cell – phospholipid, cholesterol Plant – waxy cuticles, plant oils Animal – fat, egg yolk, testosterone Other - hormones 3. Proteins Proteios=first of primary 50% dry weights of cells Contains CHONS Proteins Proteins Monomers used to build proteins: Amino Acids Properties are determined by Rgroup Determines folding pattern Protein Functions ENZYMES (lactase) DEFENSE (antibodies) STORAGE (milk protein=casein) TRANSPORT (Hemoglobin) HORMONES (insulin) MOVEMENT (motor proteins) STRUCTURE (keratin) Overview of Protein Functions Overview of Protein Functions Levels of Protein The primary structure of a protein is its unique sequence of amino acids Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain Tertiary structure is determined by interactions among various side chains (R groups) Quaternary structure results from interactions between multiple polypeptide chains Primary Structure Amino Acid: (AA) sequence, 20 different AA’s Peptide bonds- link AA’s R group- side chains Hydrophobic Hydrophilic Ion (acids & bases) Amino: -NH2 Acid: -COOH Figure 3.21a Primary structure Amino acids 1 10 5 Amino end 30 35 15 20 25 45 40 50 Primary structure of transthyretin 65 70 55 60 75 80 90 85 95 115 120 110 105 100 125 Carboxyl end Secondary Gains 3-D shape (folds, coils) by H-Bonding Alpha (α) helix, Beta (β) pleated sheet Principles of protein folding: Hydrophobic AA buried in interior of protein (hydrophobic interactions) Hydrophilic AA exposed on surface of protein (hydrogen bonds) Acidic + basic AA form salt bridges (ionic bonds) Cysteines can form disulfide bonds. Figure 3.21ba Secondary structure helix pleated sheet Hydrogen bond strand Hydrogen bond Tertiary Bonding between side chains (R groups) of AA H-Bonds, ionic bonds, disulfide bridges, van der Waals interactions Figure 3.21bb Tertiary structure Transthyretin polypeptide Quaternary 2+ polypeptides bond together Figure 3.21bc Quaternary structure Transthyretin protein Figure 3.21b Secondary structure Tertiary structure Quaternary structure Transthyretin polypeptide Transthyretin protein helix pleated sheet Chaperonins: assist in proper folding of proteins Protein structure & function are sensitive to chemical and physical conditions Unfolds or denatures if pH and temperature are not optimal Figure 3.23-2 Normal protein Denatured protein Figure 3.23-3 Normal protein Denatured protein Change in structure = change in function 4. Nucleic Acids Function: Store hereditary information Nucleic Acids Monomer: Nucleotides sugar, base, phosphate Polymers: DNA, RNA’s, NADH, NADPH, ATP The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene Genes are made of DNA, a nucleic acid made of monomers called nucleotides DNA provides directions for its own replication DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis Nucleic Acids The sugar in DNA is deoxyribose; in RNA it is ribose A prime () is used to identify the carbon atoms in the ribose, such as the 2 carbon or 5 carbon A nucleoside with at least one phosphate attached is a nucleotide Nucleotide Polymers 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 of the next These links create a backbone of sugarphosphate units with nitrogenous bases as appendages The sequence of bases along a DNA or mRNA polymer is unique for each gene © 2014 Pearson Education, Inc. Animation: DNA and RNA Structure Right click slide / Select play Figure 3.25-1 DNA 1 Synthesis of mRNA mRNA NUCLEUS CYTOPLASM Figure 3.25-2 DNA 1 Synthesis of mRNA mRNA NUCLEUS CYTOPLASM mRNA 2 Movement of mRNA into cytoplasm Figure 3.25-3 DNA 1 Synthesis of mRNA mRNA NUCLEUS CYTOPLASM mRNA 2 Movement of mRNA into cytoplasm Ribosome 3 Synthesis of protein Polypeptide Amino acids Intro to Metabolism What You Need To Know: Examples of endergonic and exergonic reactions. The key role of ATP in energy coupling. That enzymes work by lowering the energy of activation. The catalytic cycle of an enzyme that results in the production of a final product. The factors that influence enzyme activity. Chapter 8 Warm-Up 1. Define metabolism. 2. List 3 forms of energy. 3. Where does the energy available for nearly all living things on earth come from? Ch. 8 Warm-Up 1. What are the 1st and 2nd laws of thermodynamics? 2. Give the definition and an example of: A. Catabolic reaction B. Anabolic reaction 3. Is the breakdown of glucose in cellular respiration exergonic or endergonic? Ch. 8 Warm-Up 1. Draw and label the following: enzyme, active site, substrate. 2. Describe what is meant by the term induced fit. 3. What types of factors can affect an enzyme’s function? Metabolism is the totality of an organism’s chemical reactions Manage the materials and energy resources of a cell Catabolic pathways release energy by breaking down complex molecules into simpler compounds Eg. digestive enzymes break down food release energy Anabolic pathways consume energy to build complex molecules from simpler ones Eg. amino acids link to form muscle protein Energy = capacity to do work Kinetic energy (KE): energy associated with motion Heat (thermal energy) is KE associated with random movement of atoms or molecules Potential energy (PE): stored energy as a result of its position or structure Chemical energy is PE available for release in a chemical reaction Energy can be converted from one form to another Eg. chemical mechanical electrical Thermodynamics is the study of energy transformations that occur in nature A closed system, such as liquid in a thermos, is isolated from its surroundings In an open system, energy and matter can be transferred between the system and its surroundings Organisms are open systems The First Law of Thermodynamics The energy of the universe is constant Energy can be transferred and transformed Energy cannot be created or destroyed Also called the principle of Conservation of Energy The Second Law of Thermodynamics Every energy transfer or transformation increases the entropy (disorder) of the universe During every energy transfer or transformation, some energy is unusable, often lost as heat Energy Free energy: part of a system’s energy available to perform work G = change in free energy Exergonic reaction: energy is released Spontaneous reaction G < 0 Endergonic reaction: energy is required Absorb free energy G > 0 A cell does three main kinds of work: Mechanical Transport Chemical Cells manage energy resources to do work by energy coupling: using an exergonic process to drive an endergonic one ATP (adenosine triphosphate) is the cell’s main energy source in energy coupling ATP = adenine + ribose + 3 phosphates When the bonds between the phosphate groups are broken by hydrolysis energy is released This release of energy comes from the chemical change to a state of lower free energy, not in the phosphate bonds themselves How ATP Performs Work Exergonic release of Pi is used to do the endergonic work of cell When ATP is hydrolyzed, it becomes ADP (adenosine diphosphate) Pi P Motor protein Protein moved Mechanical work: ATP phosphorylates motor proteins Membrane protein ADP + Pi ATP Pi P Solute transported Solute Transport work: ATP phosphorylates transport proteins P Glu + NH2 NH3 + Glu Pi Reactants: Glutamic acid Product (glutamine) and ammonia made Chemical work: ATP phosphorylates key reactants Catalyst: substance that can change the rate of a reaction without being altered in the process Enzyme = biological catalyst Speeds up metabolic reactions by lowering the activation energy (energy needed to start reaction) Enzymes lower activation energy This allows those reactions to work more speedy Substrate Specificity of Enzymes The reactant that an enzyme acts on is called the enzyme’s substrate The enzyme binds to its substrate, forming an enzyme-substrate complex The active site is the region on the enzyme where the substrate binds Substrates Enzymes act on only one substance… the substrate Substrate binds at the enzyme’s active site which is where the reaction takes place How is the Rxn made faster? Enzyme strains bonds in reactants so they take less energy to break May also change internal environment More Substrate = Faster Rxn INDUCED FIT: ENZYME FITS SNUGLY AROUND SUBSTRATE -- “CLASPING HANDSHAKE” An enzyme’s activity can be affected by: Temperature (faster @ higher temps) pH (normal range is neutral areas) Chemicals Being too far off will denature ENZ Cofactors Cofactors are nonprotein enzyme helpers such as minerals (eg. Zn, Fe, Cu) Coenzymes are organic cofactors (eg. vitamins) Enzyme Inhibitors Competitive inhibitor: binds to the active site of an enzyme, competes with substrate Noncompetitive inhibitor: binds to another part of an enzyme enzyme changes shape active site is nonfunctional Inhibition of Enzyme Activity Regulation of Enzyme Activity To regulate metabolic pathways, the cell switches on/off the genes that encode specific enzymes Allosteric regulation: protein’s function at one site is affected by binding of a regulatory molecule to a separate site (allosteric site) Activator – stabilizes active site Inhibitor – stabilizes inactive form Cooperativity – one substrate triggers shape change in other active sites increase catalytic activity Feedback Inhibition End product of a metabolic pathway shuts down pathway by binding to the allosteric site of an enzyme Prevent wasting chemical resources, increase efficiency of cell Feedback Inhibition Negative Feedback Inhibition Many metabolic pathways regulated this way An end-product switches off a previous step in the pathway (usually as an allosteric inhibitor) Localization of Enzymes Enzymes are located where they are needed within cells…teams of enzymes that work on same pathway are together Ex: cell respiration enzymes in the mitochondria AP Lab: Enzyme Catalysis http://www.bozemanscience.com/science-videos/2010/9/5/ap-biology-lab-2-enzyme-catalysis.html FRQ Practice Describe THREE types of bonds/interactions found in proteins. For each, describe its role in determining protein structure. (2008, #1A) FRQ Practice How do each of the following illustrate the link between structure and function? Enzyme – Substrate complex Enzyme Inhibition Phospholipids Amino acid R-groups N-base component of nucleic acids Relative amounts of O in carbs vs lipids