PTYS 214 Spring Announcements. Midterm #1 on Tuesday! Be on time! No one enters after the first person leaves! Do your homework!

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1 PTYS 214 Spring 2018 Announcements Midterm #1 on Tuesday! Be on time! No one enters after the first person leaves! Do your homework! 1

2 Last time - Properties of Life Organization, energy utilization, homeostasis, reproduction, evolution,... - Definitions of Life Sagan, NASA. - Necessities of Life Building blocks, energy, solvent, environment. 2

3 Building Blocks: Carbon Carbon is abundant in the Universe but Earth is depleted in carbon So why did life choose carbon? 3

Neutron: 0 charge; mass = 1 amu Chemical element: Atom distinguished by the number of

4 Atoms Proton: +1 charge; mass=1amu Electron: -1 charge; mass = 0 Like charges repel; opposite charges attract! Neutron: 0 charge; mass = 1 amu Chemical element: Atom distinguished by the number of protons in the nucleus (atomic number) Ion: atom with a net charge, # electrons # protons Chemical elements are uniquely identified by their atomic number 4

Modern Atom Discrete electron levels are arranged in shells, each with a maximum occupancy: - First shell has the lowest energy (maximum 2 electrons) -

5 Modern Atom Discrete electron levels are arranged in shells, each with a maximum occupancy: - First shell has the lowest energy (maximum 2 electrons) - Second and third shells have room for 8 electrons - Fourth and fifth shells have room for 18 electrons - Etc. Atoms are most stable if their outer shell is full 5

6 Atoms are most stable if their outer shell is full 1e- in the outer shell 1 electron missing to fill the outer shell Complete outer shells 6

7 The Periodic Table (Mendeleev, 1869) Atoms grouped in columns have similar chemical properties. They have same number of electrons in the outer shell, except for He 1 Alkali metals 2 Halogens Transition Metals Inert Gases 7

8 Chemical bonds Typically only electrons from the outer shell (valent electrons) engage in chemical bonds Each atom prefers a full outer shell Hydrogen Outer shell/orbits Carbon Helium 8

9 Chemical bonds Atoms combine to form molecules in various ways Most important chemical bonds for organic molecules are: Covalent bond ( strongest ) Ionic bond ( strong ) Hydrogen bond ( weak ) 9

10 Covalent bond Electrons are shared between atoms Water Hydrogen Gas 10

11 Ionic bond One atom gives its valent electron to another atom (e.g., alkali and halogens) Cl is very electronegative; Na is not 2Na+ + Cl2-2NaCl 11

12 Electronegativity Tendency for an atom to attract electrons 12

13 Polar vs. Non-polar covalent bonds Polar Non-polar + H O H + μ Water Hydrogen Polar bonds have a net dipole moment 13

Hydrogen bond Bond between polar molecules (molecules with polar covalent bonds) The charged part of a molecule is attracted to the opposite charged part of

14 Hydrogen bond Bond between polar molecules (molecules with polar covalent bonds) The charged part of a molecule is attracted to the opposite charged part of another molecule It is much weaker than the other two Example: Hydrogen bonding between water molecules makes the boiling point higher than it would otherwise be. 14

Water as a polar solvent Ionic compounds can be dissolved in water Organic molecules with polar covalent bonds also dissolve in water and are called hydrophilic

15 Water as a polar solvent Ionic compounds can be dissolved in water Organic molecules with polar covalent bonds also dissolve in water and are called hydrophilic Organic molecules without polar covalent bonds do not dissolve in water and are called hydrophobic Some organic molecules have hydrophylic and hydrophobic components 15

16 Why Carbon? Carbon atoms can form up to 4 chemical bonds with many other atoms, including itself (C-C bond is very strong) Carbon forms more compounds than any other element (almost a million pure organic compounds to date!), including long molecular chains via polymerization Carbon can form compounds that readily dissolve in water 16

17 Polymerization A polymer is molecules with large molecular mass composed of repeating structural units, or monomers, connected by covalent chemical bonds Examples: plastics, proteins, DNA 17

18 Organic and Inorganic Carbon Carbon compounds can be in reduced or oxidized forms Organic carbon Inorganic carbon C-H and C-C bonds C-O bonds only CH2O Glucose -- C6H12O6 Ethanol -- C2H5OH CO 2 carbon dioxide H2CO3 carbonic acid Life gets energy by breaking C-H bonds 18

19 Inorganic carbon Seashells (CaCO3) Coral (CaCO3)

20 Organic carbon JENNY HAGER/ THE IMAGE WORKS Coal Oil 20

21 Looking for alternatives to C What would you pick? 21

22 Looking for alternatives to C What would you pick? 1. Si is right below C (slightly larger) 2. Similar chemistry, 4 bonds 22

23 Silicon life? Si bonds are much weaker Si-based complex molecules are more fragile Si does not form double bonds less variety, smaller molecules Si-O bonds (e.g., SiO2) form very stable molecules hard to break and manipulate CO2 (product of respiration) is a gas; SiO2 is a solid, more difficult to work with (unless very high T) BUT: Si-chemistry could be much more favorable than Cchemistry in very different environmental conditions (low temperature, liquid nitrogen or methane instead of liquid water) 23

24 Organic macromolecules in living systems Most of the molecules in living systems are water (H2O) and large organic macromolecules: Lipids Carbohydrates Amino Acids Proteins Nucleic Acids 24

25 Lipids (fats and oils) Representatives: fatty acids, waxes, cholesterol Poorly soluble Good (concentrated) energy storage source Flexible (cell membrane material) Main structural component of biological membranes 25

carbohydrates has little to do with water molecules Soluble in water Good energy

26 Carbohydrates (sugars, starches) Representatives: Glucose, Fructose General form: (CH2O)n sort of "hydrated carbon, even though the arrangement of atoms in carbohydrates has little to do with water molecules Soluble in water Good energy source (energy-rich chemical bonds) Structural support for organisms (such as cellulose) Glucose 26

27 Example: Glucose and Fructose: C6H12O6 Table sugar (sucrose: C12H22O11) 27

28 Carbohydrates can polymerize, e.g.: Glucose polymerization H2O Polysaccharides Linked by dehydration reaction Starch molecules (potato) contains thousands of glucose units 28

left-handed and right-handed ones carboxyl group Chirality: property of molecules that are are

29 Amino Acids amino group amine Hundreds of amino acids are known in nature, but only 20 are used in proteins Distinguished by different side-chains Amino acids arise abiotically are a mix of both left-handed and right-handed ones carboxyl group Chirality: property of molecules that are are non-superposable with their mirror image Biological amino acids are only left-handed What might be the implication? 29

$Proteins Basic building blocks of all cells \ antibody hemoglobin insulin enzymes Chains of amino acids that fold into unique 3-dimensional structures (different proteins have different$

30 Proteins Basic building blocks of all cells \ antibody hemoglobin insulin enzymes Chains of amino acids that fold into unique 3-dimensional structures (different proteins have different sequences of amino acids) Some provide structure (muscle, cartilage, fingernails, hair) Unique capacity to bind to other molecules (transport) Enzymes are proteins that catalyze chemical reactions 30

31 Catalysts in Chemistry Substances that alter the rate of a chemical reaction but are chemically unchanged at the end of the reaction Suppose chemical reaction A + B AB is a slow reaction The same reaction can be accelerated with catalyst (D): A + D AD fast step B + AD AB + D fast step net reaction: A + B + D AB + D The net result is still A + B AB but it is much faster 31

32 Amino Acids to Proteins L-Alanine Linked by dehydration reaction (peptide bond) 32

33 Nucleic Acids Complex, organic macromolecules composed of long chains of molecules known as nucleotides that convey genetic information What is the best known example of nucleic acid? 33

34 Nucleotides Composed of 3 parts: 1. Five-carbon sugar molecule (deoxyribose for DNA, ribose for RNA) 2. One or more phosphate groups (ionized phosphoric acid) 3. Nitrogen-containing compound nitrogenous base 34

35 Nucleotide Structure The three components of a nucleotide are joined by two dehydration reactions: - one between the sugar and the phosphate - one between the sugar and the nitrogenous base Phosphate Base Sugar 35

36 Polynucleotides Chains of nucleotides linked together by dehydration reactions between the phosphate group of one and the sugar residue of the next Example: RNA Bases used: - Adenine - Guanine - Cytosine - Uracil 36

37 Overview Carbon and Polymerization Organic vs. Inorganic Compounds Alternatives to Carbon Organic Molecules / Building Blocks of Life Lipids, Carbohydrates, Proteins, Nucleic Acids 37

38 Homework Homework #3 available shortly on the web site Do the QuaRCS survey Midterm #1 next class! Do your homework! Come to office hours! 38

Chapter 2 The Chemistry of Biology. Dr. Ramos BIO 370

Chapter 2 The Chemistry of Biology Dr. Ramos BIO 370 2 Atoms, Bonds, and Molecules Matter - all materials that occupy space and have mass Matter is composed of atoms. Atom simplest form of matter not divisible