Chapter 2 The Chemical Level of Organization - PDF

Chapter 2 The Chemical Level of Organization  #Goals 1. With respect to the structure of an atom: a) Describe the charge, mass, and relative location of electrons, protons, and neutrons. b) Relate the number of electrons in an electron shell to an atom’s ch...

Chapter 2 The Chemical Level of Organization  #Goals 1. With respect to the structure of an atom: a) Describe the charge, mass, and relative location of electrons, protons, and neutrons. b) Relate the number of electrons in an electron shell to an atom’s chemical stability and its ability to form chemical bonds. c) Explain how ions are produced by changing the relative number of specific subatomic particles. 2. Compare and contrast the terms atoms, molecules, elements, and compounds. 3. With respect to non-polar covalent, polar covalent, and hydrogen bonds: a) List each type of bond in order by relative strength. b) Explain the mechanism of each type of bond. c) Provide biologically significant examples of each. 4. Discuss the physiologically important properties of water. 5. Distinguish among the terms solution, solute, solvent, colloid suspension, and emulsion. 6. Define the term salt and give examples of physiological significance. 7. Define the terms pH, acid, base, and buffer and give examples of physiological significance.  #Goals 8. State acidic, neutral, and alkaline pH values. 9. Define the term organic molecule. 10. Explain the relationship between monomers and polymers. 11. With respect to carbohydrates, proteins, lipids, and nucleic acids: a) Identify the monomers and polymers. b) Compare and contrast general molecular structure. c) Provide specific examples. d) Identify dietary sources. e) Discuss physiological and structural roles in the human body. 12. Discuss the importance of protein shape for protein function. 13. Demonstrate factors that affect enzyme activity, including denaturation. 14. Describe the generalized reversible reaction for release of energy from ATP and explain the role of ATP in the cell. Atoms and Elements Matter and Mass } Matter: anything that takes up space and has mass } There are 3 states of matter: Solid, Liquid, & Gas. } Mass: amount of material contained in a substance } Determines weight } Atom: building block of all matter } Smallest stable non-living unit The Atom } Composed of three major types of subatomic particles } Protons: in nucleus } Mass: one amu } Charge: +1 } Neutrons: in nucleus } Mass: one amu } Charge: 0 } Electrons: orbit nucleus } Mass: ~1/1800th amu } Charge: -1 } Arranged into “clouds” or “shells” Elements } Possess only one kind of atom } Consistent chemical properties } Differ in the # of subatomic particles atoms contain } Named by unique symbols Elements in the Human Body Major Elements Minor Elements } Oxygen (O) } Sulfur (S) } Carbon (C) } Potassium (K) } Hydrogen (H) } Sodium (Na) } Nitrogen (N) } Chlorine (Cl) } Calcium (Ca) } Magnesium (Mg) } Phosphorus (P) } Iron (Fe) Atomic Number, Mass, and Weight } Atomic number: # of protons } Atomic mass: # protons + neutrons } Atomic weight: average mass of all elemental isotopes } Isotope: atom with same # of protons, but different # of neutrons – Variant Forms (such as carbon-12 ) Atomic Charge and Electron Shells } All atoms have 0 charge } # protons = # electrons } Electrons arranged into shells } Each has a different energy level } Each holds a set # of electrons } First shell: 2 electrons } All others: 8 or more electrons (octet rule) } Inner shells must be filled before outer shells Chemical Stability } Outermost shell: valence shell } Full with 8 electrons = chemically stable } Anything less, and atom is reactive } Reactive atoms form bonds with other atoms } Atoms work towards obtaining a full valence shell } Gain, lose, share electrons } Try to reach 8 electrons in outer shell : octet rule Think Pair Share… Pick one or Both Questions 1. What makes ISOTOPES different? 2. What are the parts of an atom and what are their charges? Chemical Bonds Ionic, Covalent, Hydrogen Chemical Bonds and Molecules } Reactive elements form bonds to become stable } Molecule: two or more atoms held together by a bond } Ex: O2, H2, N2 } Compound: atoms of two or more elements held together by a bond } Ex: H2O, NaCl } Molecules or compounds may have different properties than their individual elements } H and O are gasses, but together can form liquid water Ions } Reminder: atoms have 0 charge } However: atoms can gain or lose electrons! } Ion: an atom or molecule with a charge } Cations: lost one or more electrons } (+ charge) } Atoms with 1-3 valence electrons } Anions: gained one or more electrons } (- charge) } Atoms with 4-7 valance electrons Ionic Bonds } Two atoms: } Electron donor: loses electron(s) à cation } Electron acceptor: gains electron(s) à anion } New ions attracted to each other (opposites attract) } Form ionic bond } Resulting molecule called an ionic compound } Weaker than covalent bonds } Can break up in water Covalent Bonds } Atoms share electrons } Both need electrons to complete valence shells } Common and strong } Not easily broken } Atoms can share multiple pairs } One pair: single bond H-H } Two pairs: double bond O=O } Three pairs: triple bond N≡N Nonpolar vs. Polar Covalent } Electronegativity: the “pull” that an atom has on electrons } Varies with element } Nonpolar covalent: electrons shared equally } Atoms of the same element } Atoms of similar/identical electronegativities } Polar covalent: electrons shared unequally } Atoms with different electronegativities } Atoms have slight + or – charge (δ) } Molecules with polar bonds are polar molecules } Water is an important polar molecule Hydrogen Bonds } Attraction between a δ+ H and a δ- N, O, or F } Weak individually, strong collectively } Weaker than ionic, if singular } Cannot form molecules } Can change molecule shape and position } Helps form 3D shape of molecules } Responsible for many of water’s properties Review When table salt, sodium chloride (NaCl), is placed in water __________. } A. Na+ and Cl- form ionic bonds with each other } B. Na+ and Cl- form polar covalent bonds with each other } C. Na+ and Cl- form hydrogen bonds with water } D. Ionic bonds between Na+ and Cl- are broken Oxygen has an atomic number of eight. When two oxygen atoms come together, they form a(n) __________ bond. } A. hydrogen } B. nonpolar covalent } C. polar covalent } D. ionic } Na (atomic no. 11) reacts with Cl (atomic no. 17) to become stable. In the reaction, Na will ____________, while Cl will ____________. } A. accept one electron; give up one electron } B give up one electron; accept one electron } C. share one electron with chlorine; share one electron with sodium } D. become an anion; become a cation  Chemical Reactions, Energy, and Enzymes A Very Brief Overview Organic Vs. Inorganic Compounds } Organic compounds: contain carbon and hydrogen } Covalent bonds only } Often large, complex } Inorganic compounds: typically do not contain carbon } If C is present, bonded to other atoms besides H } Can contain covalent or ionic bonds } Includes water, oxygen, and carbon dioxide Chemical Reactions } Occur when new bonds are formed or existing bonds broken } Reactants: substances present at start of reaction } Products: substances present at end of reaction } Cells constantly form and break chemical bonds } Metabolism: sum of all chemical reactions in a cell (or organism)  Patterns of Chemical Reactions Combination reactions: Synthesis reactions which always involve bond formation. A+B AB Decomposition reactions: Molecules are broken down into smaller molecules AB A+B Exchange reactions: Bonds are made and broken down. AB + C AC + B Factors Influencing Rate of Chemical Reactions Temperature – Chemical reactions proceed quicker at higher temperatures Particle Size – The smaller the particle, the faster the chemical reaction. Concentration – Higher reacting particle concentrations produce faster reactions Catalysts – Increase the rate of a reactions without being chemically changed. Enzymes - Biological Catalysts. All the following affect the rate of a reactions except__________. } A. Temperature } B. Concentration } C. Particle size } D. Types of Bonds Present Energy and Work } Energy: capacity to do work } Work: movement or change } Potential energy: energy of position (stored energy) } Has the potential to do work } Kinetic energy: energy of motion } Performs work } Energy can be converted between forms } Energy cannot be destroyed } Converting energy “costs”: some lost as heat Forms of Energy } Chemical – Stored in the bonds of Chemical Substances } Electrical – Results from the movement of charged particles. } Mechanical – Directly involved in moving matter. } Radiant or Electromagnetic – Energy traveling in waves (i.e., visible light, ultraviolet light, and X rays) Enzymes } Chemical reactions require energy to start: activation energy } Enzymes lower the energy cost for starting a reaction } Catalysts } Also speed up reactions (change rate) } A single molecule of carbonic anhydrase can break down carbonic acid into H2O and CO2 at 36 million molecules per minute } Never consumed or changed } Reusable Characteristics of Enzymes 1. Specificity } Enzymes have an active site } Can fit specified substances (substrate) 2. Saturation Limits } Enzymes require substrate } Add more substrate à faster rate } When all enzymes are busy = saturation } Need to add more enzyme if you want to keep going faster 3. Regulation } Enzymes work as long as active site is open } Can be “turned off” by adding inhibitors } Change the shape of (or block) the active site, enzyme won’t function } Enzymes can be denatured } Lose shape, lose function } Occurs with extremes of temperature/pH } Can be reversible or permanent Properties of Water Basic Water Facts } Up to 2/3rds of body weight } Formula: H2O } Polar molecule } Vital to life and health } Water has several properties important to physiology } Primarily due to hydrogen bonds Reactivity and Lubrication } Water is reactive } Many reactions occur within or involve water } Water is a good lubricant } Little friction between water molecules } Even a small amount of water will reduce friction Dehydration synthesis & Hydrolysis High Specific Heat } Heat capacity: the quantity of heat required to raise temperature of a mass of a substance by 1° C } Water = high specific heat } Due to hydrogen bonds holding H2O molecules close } Need LOTS of heat to break bonds } Results: 1. Liquid water requires large amounts of heat to become a gas or solid } Freezing and boiling point are far apart } Allows water to stay liquid at a wide range of temperatures 2. When water evaporates it removes a great deal of heat } Sweat cools you down! 3. Water changes temperature slowly } Thermal inertia } Stabilizes body temperature Solubility: Water as the Universal Solvent } Dissolve: disperse in a liquid or “break up” } Solvent: substance that dissolves other substances } Solute: substance that dissolves into other substances } Water can dissolve most substances } Forms a solution: uniform mixture of two or more substances } Solute + solvent } Salt water, sugar water  Will it Dissolve? A Quick Guide Will Dissolve: Hydrophilic Won’t Dissolve: Hydrophobic } Ionic compounds } Nonpolar molecules } Polar molecules } “Like dissolves like” Some substances only partially dissolve in water: amphipathic Have polar and nonpolar regions Water Mixtures } Suspension: } Does not remain mixed when left alone } Scatters light, cloudy/opaque } Very large particles (>100 nm) } Too large to pass through selectively permeable membrane } Particles “settle” } Colloid: } Remains mixed when left alone } Scatters light, cloudy/opaque } Often contains proteins } Large particles (1-100 nm) } Too large to pass through selectively permeable membrane } Solution: } Substances (solute) dissolves } Particles remain mixed when left alone } Does not scatter light, clear } Substance is homogenous } Small particles ( OH- Acidic } 7= H+ = OH- Neutral } 8-14: H+ < OH- Basic } Neutralization: adding an acid to a base (or vice- versa) to return to neutral pH (7) } Buffer: substances that help prevent pH changes when acids or bases are added to a solution } Accepts H+ from acid } Adds H + to base } Often help to maintain blood pH Acids/Bases in Blood } Normal pH: 7.35 - 7.45 } Acidosis: low blood pH } Alkalosis: high blood pH } Why would these conditions be dangerous? } Enzymes would denature } H+ ions would disrupt bonds and chemical structure Biological Macromolecules Organic Chemistry Lipids, Proteins, Carbohydrates, Nucleic Acids General Characteristics of Biomolecules } Biomolecules always contain } Carbon: individually or in a carbon skeleton: https://study.com/academy/lesson/what-is-a-carbon-skeleton.html } Hydrogen } Carbon + Hydrogen = hydrocarbon (always nonpolar) } Carbon is not following the Octet rule with only 4 electrons on it’s outer shell, so it likes to bond to everything. } Biomolecules usually contain } Oxygen } Biomolecules may contain } Nitrogen } Sulfur } Phosphorus } Iron } Possibly others Monomers and Polymers } Polymers: molecules made of repeating subunits (monomers) Biomolecule Monomer Carbohydrate Simple Sugars (monosaccharide) Protein Amino Acids Nucleic acid Nucleotides Lipid N/A (not a polymer) Carbohydrates } “Hydrated Carbon”: –H and –OH are attached to every carbon } 1:2:1 ratio } Primary source of chemical energy } Short-term, easy access } Converted into fat for long term storage } Sugars and starches } Broken in to groups based on how many monomers are in the carbohydrate } Monosaccharides: one simple sugar (not a polymer) } Disaccharides: two simple sugars } Polysaccharides: more than two sugars Carbohydrates: Monosaccharides } Simple sugars } Glucose: primary metabolic fuel } Levels carefully maintained: homeostasis } Possesses isomers (fructose, galactose) } Stored as a polymer called glycogen } Ribose: component of RNA } Deoxyribose: component of DNA Carbohydrates: Disaccharides } Composed of two monosaccharides joined together } Sucrose (table sugar): glucose + fructose } Lactose (milk sugar): glucose + galactose } Maltose (malt sugar): glucose + glucose Carbohydrates: Polysaccharides } More complex carbohydrates } Straight or branched } Glycogen: glucose based “animal starch” } Storage form of glucose } Produced by liver, muscles, brain, etc. } Starch: glucose based “plant starch” } From plants } Digestible by humans } Cellulose: } From plants } Indigestible by humans (lack enzyme) } Good for roughage (fiber) Lipids } Not composed of monomers } Carbon to hydrogen in 1:2 ratio } Multiple functions } Energy source/storage } Cell structural components } Hormones/signaling molecules } Hydrophobic, insoluble in water – include fats, oils, and waxes } Five classes } Fatty acids, triglycerides, phospholipids, eicosanoids, and steroids Lipids: Fatty Acids } Hydrocarbon chains } “Head” end possesses a carboxyl group (-COOH) } Head is hydrophilic } “Tail” is a long chain of carbons } Saturated: no double bonds } Unsaturated: only one double bond } Polyunsaturated: two or more double bonds } Tail is hydrophobic Lipids: Triglycerides } Glycerol (modified sugar)+ fatty acid chain(s) } Glycerides come in three forms - Mono (1), di (2), tri (3) } Triglycerides: most common in diet/body } Functions } Energy source/storage (long term) } Insulation } Protection Lipids: Phospholipids } Phospholipid: glycerol + phosphate group + 2 fatty acid chains } Tails: nonpolar & hydrophobic } Heads (non-lipid): polar & hydrophilic } Structural component of cells } Plasma membrane } Used for lipid transportation } Micelles (droplets) Lipids: Eicosanoids } Derived from arachidonic acid } Dietary, no synthesis } Function } Serve as chemical messengers } Local signaling molecules } Prostaglandins: coordinate/direct local cell activities } Produced in most tissues } Effects vary: pain sensation, initiate labor, inflammation, clotting } Leukotrienes: coordinate response to injury/disease Lipids: Steroids } Four hydrocarbon rings } Functional groups differ } Cholesterol: component of cell membrane, precursor to all steroids } Can be ingested (egg yolk, meat, liver, shellfish) } Can be synthesized } Other steroids include } Sex hormones (estrogen, testosterone) } Metabolic/mineral regulation hormones (corticosteroids, calcitrol) } Bile salts (break down lipids Liver/Gallbladder) Proteins } Most abundant organic molecules } Contain carbon, hydrogen, oxygen, and nitrogen } May contain sulfur and phosphorus } Shape determines function } Complex 3D shapes Proteins: Function } Support: structural proteins } Movement: contractile proteins } Transport: transport proteins } Buffering: serve as buffers for body fluids } Metabolic regulation: enzymes } Coordination/Control: hormones } Defense: antibodies, clotting proteins, keratin Proteins: Structure } Monomer: amino acids } 20 in humans } C-terminal end: carboxyl (-COOH) group } N-terminal end: amine (-NH2) group } R group: varies (aka side chain) } Determines whether aa is hydrophilic or hydrophobic Proteins: Structure } Amino acids joined by peptide bonds } Polar covalent bonds } Amino acids strands are classified based on how many amino acids are present } Dipeptide: two aa } Tripeptide: three aa } Polypeptide: three or more aa } Protein: 100 or more aa Protein Shape } Primary structure: sequence of amino acid chain } Secondary: alpha helix or beta sheet } Result of hydrogen bonds } Tertiary: globular or fibrous } Result of hydrophobic/philic R groups } Disulfide bonds between cysteine amino acids (strong) } Quaternary: addition of extra polypeptide subunits Nucleic Acids: Structure } Monomer: nucleotide 1. Pentose sugar (ribose or deoxyribose) 2. Phosphate functional group 3. Nitrogenous base } Pyrimidines (single ring): cytosine, thymine (DNA only), uracil (RNA only) } Purine (double ring): adenine, guanine } A binds with T or U } G binds with C Nucleic Acids: DNA and RNA } Deoxyribonucleic acid (DNA) } Stores genetic information: directs protein synthesis } Double stranded } Uses AGCT only } Found in nucleus } Ribonucleic acid (RNA) } Participates in protein synthesis } mRNA, tRNA, rRNA } Single stranded } Uses AGCU only } Found in nucleus and cytoplasm Nucleotides: ATP } Adenosine triphosphate: contains high-energy bonds } Formation of bonds requires high energy } Breakage of bonds releases high energy } Requires addition/removal of phosphate group (PO43-) } ADP + P à ATP } Most important method of cellular energy transfer } ATP à ADP + P } Most important form of energy release } Reactions require adenosine triphosphatase (enzyme)  Up Next: Chapter 3 The Cellular Level of Organization