Chapter 2 Essential Chemistry for Biology 0
 
Start with Atoms <ul><ul><li>Atoms </li></ul></ul><ul><ul><ul><li>Fundamental building blocks of matter </li></ul></ul></u...
Nucleus Protons Neutrons Electrons Nucleus Cloud of negative charge   2 electrons  2 2 2
Proton •  Positive charge •  Determines  element Neutron •  No charge •  Determines  isotope Electron •  Negative charge •...
Elements <ul><ul><li>A pure substance consisting of atoms with the same number of protons </li></ul></ul><ul><ul><li>_____...
H Rb K Na Li Fr Cs Sr Ca Mg Be Ra Ba Y Sc Ac La Zr Ti Rf Hf Nb V Db Ta Mo Cr Sg W Tc Mn Bh Re Ru Fe Hs Os Rh Co Mt Ir Pd N...
Elements <ul><ul><li>There are 92 naturally occurring elements on Earth. </li></ul></ul><ul><ul><li>25 elements are essent...
Carbon   C  : 18.5% Hydrogen   H  : 9.5% Nitrogen   N  : 3.3% Calcium   Ca  : 1.5% Trace elements: less than 0.01%...
Trace Elements <ul><ul><li>Occur in smaller amounts and are essential for life </li></ul></ul><ul><ul><li>Deficiencies cau...
Isotopes <ul><ul><li>Atoms of the same element that differ in the number of neutrons </li></ul></ul><ul><ul><li>Example : ...
H Rb K Na Li Fr Cs Sr Ca Mg Be Ra Ba Y Sc Ac La Zr Ti Rf Hf Nb V Db Ta Mo Cr Sg W Tc Mn Bh Re Ru Fe Hs Os Rh Co Mt Ir Pd N...
Radioactive Isotopes <ul><ul><li>_______________ – atoms with the same # protons, but different # neutrons </li></ul></ul>...
Positron-Emission Tomography (PET) Scan
Electron Arrangement and the Chemical Properties of Atoms <ul><ul><li>Atoms acquire, share and donate electrons </li></ul>...
Electrons and Energy Levels <ul><ul><li>Atoms have the same # electrons as protons </li></ul></ul><ul><ul><li>Electrons or...
Shell Models First electron shell  can hold 2 electrons  Outer electron shell  can hold 8 electrons  Hydrogen   H  A...
Electron Interactions <ul><ul><li>Atoms whose outermost shell is not completely full tends to interact with other atoms </...
Electrical Charge <ul><ul><li>An atom with equal numbers of protons and electrons has  no net charge </li></ul></ul><ul><u...
Sodium atom 11p +  11e - no net Charge  (weakly  electro- negative) Sodium ion 11p +  10e - net positive charge electron l...
Molecules and Mixtures <ul><ul><li>Molecule  – forms when  >  2 atoms join in chemical bonds </li></ul></ul><ul><ul><li>Ch...
Chemical Bonding and Molecules <ul><ul><li>Chemical reactions enable atoms to donate, acquire or share electrons to comple...
Ionic Bonds <ul><ul><li>Strong association between a positive ion and a negative ion (attraction of opposite charges) </li...
Outer shell has 1 electron Outer shell has 7 electrons The outer electron is stripped from sodium and completes the chlori...
See Animation on Ionic Bonds (Posted to MyCourses)
Covalent Bonds <ul><ul><li>Form when two atoms share  >  1 pairs of outer-shell electrons </li></ul></ul><ul><ul><li>_____...
Two hydrogen atoms, each with one proton, share two electrons in a  single nonpolar covalent bond . Molecular hydrogen  (H...
See Animation on Covalent Bonds (Posted to MyCourses)
Hydrogen Bonds <ul><ul><li>Attraction between a  _______________  atom and another atom </li></ul></ul><ul><ul><ul><li>Bot...
Hydrogen Bonds <ul><ul><li>Water is a compound in which the electrons in its covalent bonds are shared unequally. </li></u...
Hydrogen Bonds <ul><ul><li>The polarity of water results in weak electrical attractions between neighboring water molecule...
Water – The Most Important Molecule <ul><ul><li>Without water, there would be no life </li></ul></ul><ul><ul><li>Life on E...
Polarity of the Water Molecule <ul><ul><li>Water molecules are  polar </li></ul></ul><ul><ul><ul><li>Form hydrogen bonds w...
See Animation on Water Structure (Posted to MyCourses)
Water’s Life-Giving Properties <ul><ul><li>The polarity of water molecules and the hydrogen bonding that results explain m...
The Cohesion of Water <ul><ul><li>Hydrogen bonding provides  _______________  (resistance of molecule separation) </li></u...
Microscopic tubes Cohesion due to hydrogen bonds between water molecules Evaporation from leaves drives the flow of water ...
See Animation on Water Transport (Posted to MyCourses)
Water Moderates Temperature <ul><ul><li>Because of hydrogen bonding, water has a strong resistance to temperature change. ...
<ul><ul><li>Earth’s giant water supply causes temperatures to stay within limits that permit life. </li></ul></ul><ul><ul>...
The Biological Significance of Ice Floating <ul><ul><li>When water molecules get cold enough, they move apart, forming ice...
<ul><ul><li>If ice did not float, ponds, lakes, and even the oceans would freeze solid. </li></ul></ul><ul><ul><li>Life in...
Water as the Solvent of Life <ul><ul><li>A  _______________  is a liquid consisting of a  homogeneous mixture  of two or m...
Sodium ion in solution Chloride ion in solution Salt crystal Na  Na  Cl – Cl –
Solvents  form “ spheres of hydration ”  around  solutes
Acids, Bases, and pH <ul><ul><li>Ions are dissolved in fluids both inside and outside each living cell </li></ul></ul><ul>...
How do Acids and Bases Differ? <ul><ul><li>A chemical compound that releases H +  to solution is an  _______________ . </l...
Acids, Bases, and pH <ul><ul><li>pH scale </li></ul></ul><ul><ul><ul><li>Indicates hydrogen ion (H + ) concentration of a ...
Buffers Against Shifts in pH <ul><ul><li>Enzymes and biological molecules function properly only in a narrow range of pH <...
<ul><ul><li>A set of chemicals (an acid or base AND its salt) that keeps the pH of a solution stable </li></ul></ul><ul><u...
<ul><ul><li>Buffers help maintain homeostasis </li></ul></ul><ul><ul><li>Most biological processes proceed only within a n...
Evolution Connection: The Search for Extraterrestrial Life <ul><ul><li>If life similar to ours has evolved elsewhere in th...
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  1. 1. Chapter 2 Essential Chemistry for Biology 0
  2. 3. Start with Atoms <ul><ul><li>Atoms </li></ul></ul><ul><ul><ul><li>Fundamental building blocks of matter </li></ul></ul></ul><ul><ul><ul><li>Composed of three smaller subatomic particles </li></ul></ul></ul><ul><ul><ul><ul><li>Positively charged _______________ </li></ul></ul></ul></ul><ul><ul><ul><ul><li>Uncharged (neutral) _______________ </li></ul></ul></ul></ul><ul><ul><ul><ul><li>Negatively charged _______________ </li></ul></ul></ul></ul><ul><ul><ul><li># _______________ = # _______________ </li></ul></ul></ul><ul><ul><ul><li>Protons and neutrons are part of the nucleus </li></ul></ul></ul><ul><ul><ul><li>Electrons move around the nucleus </li></ul></ul></ul>
  3. 4. Nucleus Protons Neutrons Electrons Nucleus Cloud of negative charge  2 electrons  2 2 2
  4. 5. Proton • Positive charge • Determines element Neutron • No charge • Determines isotope Electron • Negative charge • Participates in chemical reactions • Outer-shell electrons determine chemical behavior Nucleus • Consists of neutrons and protons Atom
  5. 6. Elements <ul><ul><li>A pure substance consisting of atoms with the same number of protons </li></ul></ul><ul><ul><li>_______________ _______________ = quantity of protons (unique for each element) </li></ul></ul><ul><ul><ul><li>Ex: Carbon = 6 </li></ul></ul></ul>Mercury  Hg  Copper  Cu  Lead  Pb 
  6. 7. H Rb K Na Li Fr Cs Sr Ca Mg Be Ra Ba Y Sc Ac La Zr Ti Rf Hf Nb V Db Ta Mo Cr Sg W Tc Mn Bh Re Ru Fe Hs Os Rh Co Mt Ir Pd Ni Uun Pt Xe Kr Uuo Rn Ag Cu Uuu Au Cd Zn Uub Hg Ar Ne In Ga Tl Al B Sn Ge Uuq Pb Si C Sb As Bi P N Te Se Uuh Po S O I Br At Cl F He Th Ce Pa Pr U Nd Np Pm Pu Sm Am Eu Lr Lu Cm Gd Bk Tb Cf Dy Es Ho Fm Er Md Tm No Yb 6 C 12
  7. 8. Elements <ul><ul><li>There are 92 naturally occurring elements on Earth. </li></ul></ul><ul><ul><li>25 elements are essential to life. </li></ul></ul><ul><ul><li>Four elements make up about 96% of the weight of the human body: </li></ul></ul><ul><ul><ul><li>Oxygen </li></ul></ul></ul><ul><ul><ul><li>Carbon </li></ul></ul></ul><ul><ul><ul><li>Hydrogen </li></ul></ul></ul><ul><ul><ul><li>Nitrogen </li></ul></ul></ul>
  8. 9. Carbon  C  : 18.5% Hydrogen  H  : 9.5% Nitrogen  N  : 3.3% Calcium  Ca  : 1.5% Trace elements: less than 0.01% Boron  B  Manganese  Mn  Oxygen  O  : 65.0% Magnesium  Mg  : 0.1% Phosphorus  P  : 1.0% Potassium  K  : 0.4% Sulfur  S  : 0.3% Sodium  Na  : 0.2% Chlorine  Cl  : 0.2% Cobalt  Co  Chromium  Cr  Iron  Fe  Iodine  I  Fluorine  F  Copper  Cu  Silicon  Si  Zinc  Zn  Vanadium  V  Tin  Sn  Molybdenum  Mo  Selenium  Se 
  9. 10. Trace Elements <ul><ul><li>Occur in smaller amounts and are essential for life </li></ul></ul><ul><ul><li>Deficiencies cause disease </li></ul></ul><ul><ul><ul><li>Example: An Iodine deficiency causes goiter </li></ul></ul></ul>
  10. 11. Isotopes <ul><ul><li>Atoms of the same element that differ in the number of neutrons </li></ul></ul><ul><ul><li>Example : 12 C (6p and 6n), 13 C (6p and 7n), 14 C (6p and 8n) </li></ul></ul><ul><ul><li>_______________ _______________ = protons plus neutrons </li></ul></ul>
  11. 12. H Rb K Na Li Fr Cs Sr Ca Mg Be Ra Ba Y Sc Ac La Zr Ti Rf Hf Nb V Db Ta Mo Cr Sg W Tc Mn Bh Re Ru Fe Hs Os Rh Co Mt Ir Pd Ni Uun Pt Xe Kr Uuo Rn Ag Cu Uuu Au Cd Zn Uub Hg Ar Ne In Ga Tl Al B Sn Ge Uuq Pb Si C Sb As Bi P N Te Se Uuh Po S O I Br At Cl F He Th Ce Pa Pr U Nd Np Pm Pu Sm Am Eu Lr Lu Cm Gd Bk Tb Cf Dy Es Ho Fm Er Md Tm No Yb 6 C 12
  12. 13. Radioactive Isotopes <ul><ul><li>_______________ – atoms with the same # protons, but different # neutrons </li></ul></ul><ul><ul><li>Radioactive isotopes are not stable </li></ul></ul><ul><ul><ul><li>Nucleus (protons and neutrons) spontaneously decays into other elements and electrons are emitted </li></ul></ul></ul><ul><ul><li>Can be used as tracers and attached to molecules </li></ul></ul><ul><ul><ul><li>Example: Attach a tracer to glucose to monitor brain activity (PET scan) </li></ul></ul></ul>
  13. 14. Positron-Emission Tomography (PET) Scan
  14. 15. Electron Arrangement and the Chemical Properties of Atoms <ul><ul><li>Atoms acquire, share and donate electrons </li></ul></ul><ul><ul><li>Some atoms do so easily, others do no </li></ul></ul><ul><ul><ul><li>The number and arrangement of electrons in atoms dictate acquisition, sharing and donation </li></ul></ul></ul>
  15. 16. Electrons and Energy Levels <ul><ul><li>Atoms have the same # electrons as protons </li></ul></ul><ul><ul><li>Electrons orbit the nucleus of an atom in specific electron shells </li></ul></ul><ul><ul><li>The farther an electron is from the nucleus, the greater its energy </li></ul></ul><ul><ul><li>The number of electrons in the outermost shell determines the chemical properties of an atom </li></ul></ul>
  16. 17. Shell Models First electron shell  can hold 2 electrons  Outer electron shell  can hold 8 electrons  Hydrogen  H  Atomic number = 1 Carbon  C  Atomic number = 6 Nitrogen  N  Atomic number = 7 Oxygen  O  Atomic number = 8 Electron
  17. 18. Electron Interactions <ul><ul><li>Atoms whose outermost shell is not completely full tends to interact with other atoms </li></ul></ul><ul><ul><ul><li>They donate, accept, or share electrons to eliminate vacancies </li></ul></ul></ul><ul><ul><ul><li>Those with the outermost shell filled are chemically inactive and very stable </li></ul></ul></ul>sodium 11p+ , 11e - chlorine 17p+ , 17e - argon 18p+, 18e -
  18. 19. Electrical Charge <ul><ul><li>An atom with equal numbers of protons and electrons has no net charge </li></ul></ul><ul><ul><li>_______________ are atoms that carry a charge </li></ul></ul><ul><ul><ul><li>Have either gained (negatively charged) or lost (positively charged) electrons </li></ul></ul></ul>
  19. 20. Sodium atom 11p + 11e - no net Charge (weakly electro- negative) Sodium ion 11p + 10e - net positive charge electron loss Chlorine atom 17p + 17e - no net Charge (highly electronegative) Chlorine ion 17p + 18e - net negative charge electron gain
  20. 21. Molecules and Mixtures <ul><ul><li>Molecule – forms when > 2 atoms join in chemical bonds </li></ul></ul><ul><ul><li>Chemical Bond – attractive force between atoms due to interactions of electrons </li></ul></ul><ul><ul><li>Compounds – molecules consisting of > 2 elements (Ex: water is 2H bound to 1O) </li></ul></ul><ul><ul><li>Mixture – elements intermingle but do not bind (Ex: Sugar into water – sugar dissolves, no bonds formed) </li></ul></ul>
  21. 22. Chemical Bonding and Molecules <ul><ul><li>Chemical reactions enable atoms to donate, acquire or share electrons to complete their outer shells. </li></ul></ul><ul><ul><li>Chemical reactions usually result in atoms interacting through three types of bonds </li></ul></ul><ul><ul><ul><li>Ionic bond </li></ul></ul></ul><ul><ul><ul><li>Covalent Bond </li></ul></ul></ul><ul><ul><ul><li>Hydrogen Bond </li></ul></ul></ul>
  22. 23. Ionic Bonds <ul><ul><li>Strong association between a positive ion and a negative ion (attraction of opposite charges) </li></ul></ul>
  23. 24. Outer shell has 1 electron Outer shell has 7 electrons The outer electron is stripped from sodium and completes the chlorine atom’s outer shell Na Sodium atom Cl Chlorine atom Complete outer shells The attraction between the ions—an ionic bond—holds them together Na  Sodium ion Cl  Chlorine ion Sodium chloride (NaCl)
  24. 25. See Animation on Ionic Bonds (Posted to MyCourses)
  25. 26. Covalent Bonds <ul><ul><li>Form when two atoms share > 1 pairs of outer-shell electrons </li></ul></ul><ul><ul><li>_______________ covalent bond </li></ul></ul><ul><ul><ul><li>Atoms share electrons equally </li></ul></ul></ul><ul><ul><li>_______________ covalent bond </li></ul></ul><ul><ul><ul><li>Electrons are shared unequally </li></ul></ul></ul><ul><ul><ul><li>Produces polar molecules – one end slightly negative, other slightly positive </li></ul></ul></ul>
  26. 27. Two hydrogen atoms, each with one proton, share two electrons in a single nonpolar covalent bond . Molecular hydrogen (H—H) Two oxygen atoms, each with eight protons, share four electrons in a nonpolar double covalent bond . Molecular oxygen (O=O) Two hydrogen atoms each share an electron with an oxygen atom in two polar covalent bonds . The oxygen exerts a greater pull on the shared electrons, so it has a slight negative charge. Each hydrogen has a slight positive charge. Water molecule (H—O—H)
  27. 28. See Animation on Covalent Bonds (Posted to MyCourses)
  28. 29. Hydrogen Bonds <ul><ul><li>Attraction between a _______________ atom and another atom </li></ul></ul><ul><ul><ul><li>Both have their own separate covalent bonds </li></ul></ul></ul><ul><ul><li>Are not chemical bonds </li></ul></ul><ul><ul><ul><li>Do not make atoms into molecules </li></ul></ul></ul><ul><ul><ul><li>Weaker than ionic or covalent, and easily form or break </li></ul></ul></ul><ul><ul><ul><li>Used to stabilize structures of large molecules </li></ul></ul></ul>
  29. 30. Hydrogen Bonds <ul><ul><li>Water is a compound in which the electrons in its covalent bonds are shared unequally. </li></ul></ul><ul><ul><ul><li>This causes water to be a polar molecule , one with opposite charges on opposite ends. </li></ul></ul></ul>2 H 2 2 H 2 O O 2 Hydrogen gas Oxygen gas Water  
  30. 31. Hydrogen Bonds <ul><ul><li>The polarity of water results in weak electrical attractions between neighboring water molecules. </li></ul></ul><ul><ul><ul><li>These interactions are called hydrogen bonds . </li></ul></ul></ul>Hydrogen bond
  31. 32. Water – The Most Important Molecule <ul><ul><li>Without water, there would be no life </li></ul></ul><ul><ul><li>Life on Earth began in water and evolved there for 3 billion years </li></ul></ul><ul><ul><ul><li>Modern life remains tied to water </li></ul></ul></ul><ul><ul><ul><li>Your cells are composed of 70%–95% water </li></ul></ul></ul><ul><ul><li>The abundance of water is a major reason Earth is habitable </li></ul></ul>
  32. 33. Polarity of the Water Molecule <ul><ul><li>Water molecules are polar </li></ul></ul><ul><ul><ul><li>Form hydrogen bonds with each other and with other polar molecules </li></ul></ul></ul><ul><ul><ul><li>Hydrophilic (water-loving) substances are polar </li></ul></ul></ul><ul><ul><ul><li>Hydrophobic (water-dreading) substances are nonpolar (ex. Oils) </li></ul></ul></ul>+ + H H O - − slight negative charge on the oxygen atom The positive and negative charges balance each other; overall, the molecule carries no charge. slight positive charge on the hydrogen atoms
  33. 34. See Animation on Water Structure (Posted to MyCourses)
  34. 35. Water’s Life-Giving Properties <ul><ul><li>The polarity of water molecules and the hydrogen bonding that results explain most of water’s life-supporting properties: </li></ul></ul><ul><ul><ul><li>Water molecules stick together. </li></ul></ul></ul><ul><ul><ul><li>Water has a strong resistance to change in temperature. </li></ul></ul></ul><ul><ul><ul><li>Frozen water floats. </li></ul></ul></ul><ul><ul><ul><li>Water is a common solvent for life. </li></ul></ul></ul>
  35. 36. The Cohesion of Water <ul><ul><li>Hydrogen bonding provides _______________ (resistance of molecule separation) </li></ul></ul>
  36. 37. Microscopic tubes Cohesion due to hydrogen bonds between water molecules Evaporation from leaves drives the flow of water up and through the plant SEM Flow of water
  37. 38. See Animation on Water Transport (Posted to MyCourses)
  38. 39. Water Moderates Temperature <ul><ul><li>Because of hydrogen bonding, water has a strong resistance to temperature change. </li></ul></ul><ul><ul><li>Heat and temperature are related, but different. </li></ul></ul><ul><ul><ul><li>_______________ is the amount of energy associated with the movement of the atoms and molecules in a body of matter. </li></ul></ul></ul><ul><ul><ul><li>_______________ measures the intensity of heat. </li></ul></ul></ul><ul><ul><li>Water can absorb and store large amounts of heat while only changing a few degrees in temperature. </li></ul></ul>
  39. 40. <ul><ul><li>Earth’s giant water supply causes temperatures to stay within limits that permit life. </li></ul></ul><ul><ul><li>Evaporative cooling removes heat from the Earth and from organisms. </li></ul></ul>
  40. 41. The Biological Significance of Ice Floating <ul><ul><li>When water molecules get cold enough, they move apart, forming ice. </li></ul></ul><ul><ul><li>A chunk of ice has fewer molecules than an equal volume of liquid water. </li></ul></ul><ul><ul><li>Ice floats because it is less dense than the liquid water around it. </li></ul></ul>Hydrogen bond Liquid water Ice
  41. 42. <ul><ul><li>If ice did not float, ponds, lakes, and even the oceans would freeze solid. </li></ul></ul><ul><ul><li>Life in water could not survive if bodies of water froze solid. </li></ul></ul>The Biological Significance of Ice Floating
  42. 43. Water as the Solvent of Life <ul><ul><li>A _______________ is a liquid consisting of a homogeneous mixture of two or more substances. </li></ul></ul><ul><ul><ul><li>The dissolving agent is the _______________ . </li></ul></ul></ul><ul><ul><ul><li>The dissolved substance is the _______________ . </li></ul></ul></ul><ul><ul><li>When water is the solvent, the result is an aqueous solution . </li></ul></ul>
  43. 44. Sodium ion in solution Chloride ion in solution Salt crystal Na  Na  Cl – Cl –
  44. 45. Solvents form “ spheres of hydration ” around solutes
  45. 46. Acids, Bases, and pH <ul><ul><li>Ions are dissolved in fluids both inside and outside each living cell </li></ul></ul><ul><ul><li>_______________ ions are the most influential </li></ul></ul><ul><ul><ul><li>Chemically active </li></ul></ul></ul><ul><ul><ul><li>Tons of them – they are everywhere </li></ul></ul></ul>
  46. 47. How do Acids and Bases Differ? <ul><ul><li>A chemical compound that releases H + to solution is an _______________ . </li></ul></ul><ul><ul><li>A compound that accepts H + and removes it from solution is a _______________ . </li></ul></ul>Basic solution Neutral solution Acidic solution
  47. 48. Acids, Bases, and pH <ul><ul><li>pH scale </li></ul></ul><ul><ul><ul><li>Indicates hydrogen ion (H + ) concentration of a solution </li></ul></ul></ul><ul><ul><ul><li>Ranges from 0 (most acidic , most H + ) to 14 (most basic or alkaline , least H + ) </li></ul></ul></ul><ul><ul><ul><li>At pH 7 ( neutral ) H + and OH - concentrations are equal </li></ul></ul></ul>Neutral Basic Acidic pH scale 14 7 0 Lower H + concentration H + = OH – Greater H + concentration
  48. 49. Buffers Against Shifts in pH <ul><ul><li>Enzymes and biological molecules function properly only in a narrow range of pH </li></ul></ul><ul><ul><li>Cells must quickly respond to pH shifts otherwise cellular processes halt </li></ul></ul><ul><ul><li>Most cells and body fluids are buffered in order to maintain a constant pH </li></ul></ul>
  49. 50. <ul><ul><li>A set of chemicals (an acid or base AND its salt) that keeps the pH of a solution stable </li></ul></ul><ul><ul><li>A “salt” is any compound that dissolves easily in water, and releases ions other than H + and OH - </li></ul></ul><ul><ul><ul><li>Form when an acid interacts with a base (Ex: NaCl) </li></ul></ul></ul><ul><ul><ul><li>HCl + NaOH NaCl + H 2 0 </li></ul></ul></ul><ul><ul><ul><li>Na + + Cl - + H 2 O </li></ul></ul></ul>Buffer System
  50. 51. <ul><ul><li>Buffers help maintain homeostasis </li></ul></ul><ul><ul><li>Most biological processes proceed only within a narrow pH range, usually near neutrality (blood pH = 7.3 – 7.5) </li></ul></ul><ul><ul><ul><li>Acidosis: decline in blood pH </li></ul></ul></ul><ul><ul><ul><li>Alkalosis: increase in blood pH </li></ul></ul></ul><ul><ul><ul><li>Both are potentially lethal </li></ul></ul></ul>Functions of Buffer Systems
  51. 52. Evolution Connection: The Search for Extraterrestrial Life <ul><ul><li>If life similar to ours has evolved elsewhere in the universe, then it too would depend upon water. </li></ul></ul><ul><ul><li>Recent NASA missions to Mars have detected evidence that liquid water flowed over the planet’s surface. </li></ul></ul>

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