Lecture 1 - MOL1.pptx.PDF - Molecules of Life

The Molecules of Life 1 Textbook chapters 2-4 pollev.com/barbaraakum216 Images from Campbell Biology 10th, 11th or 12th edition, © 2014, 2017 or 2020 Pearson Education Inc. unless otherwise indicated 1 Topics to be covered Some chemistry of life Valence, covalent bonds Noncovalent bo...

The Molecules of Life 1 Textbook chapters 2-4 pollev.com/barbaraakum216 Images from Campbell Biology 10th, 11th or 12th edition, © 2014, 2017 or 2020 Pearson Education Inc. unless otherwise indicated 1 Topics to be covered Some chemistry of life Valence, covalent bonds Noncovalent bonds, hydrogen bonds Basic organic chemistry Molecular shape, isomers, 2 The chemical composition of a human being One way of thinking about a human being “What % of a human being is oxygen?” We will not ask exam questions like this 3 Each of us developed from a single cell Human body - trillions of cells with many specialized functions In PoB1, you will learn the details of: How simple chemical building blocks make cells, How these cells communicate and cooperate to make organs and organisms. Image credit: genius.com, giphy.com 4 What chemistry knowledge are we assuming? Assumed knowledge: What are atoms, ions, protons, electrons and neutrons? What is an element? What is a compound? But we will review these today 5 What determines the properties of a compound? 6 Elements and Compounds Matter is made up of elements An element - substance that cannot be broken down to other substances by chemical reactions A compound - substance consisting of two or more elements in a fixed ratio ○ characteristics (emergent properties) different from those of its elements 7 The Elements of Life 92 natural elements Essential elements required for life (20–25%) Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter Remaining 4% consists of calcium, phosphorus, potassium, and sulfur Trace elements needed in minute quantities 8 Properties of Elements Each element consists of unique atoms Atom - smallest unit of matter that still retains the properties of an element ○ Composed of subatomic particles Neutrons (no electrical charge) - nucleus Protons (positive charge) - nucleus Electrons (negative charge) - around the nucleus Atomic nucleus Neutrons + protons 9 Simplified models of a helium (He) atom Electron Distribution and Chemical Properties Electrons are found in different electron shells, each with a characteristic average distance and energy level The chemical behavior of an atom is determined by the distribution of electrons in the electron shells The periodic table of the elements shows the electron distribution for each element 10 Properties of elements Mass number or A ○ sum of the number of protons and neutrons Atomic Number or Z ○ number of protons in the nucleus Carbon 11 Periodic table displays all of the known elements and is arranged in order of increasing atomic number The left-to-right sequence of elements in each row corresponds to the sequential addition of electrons and protons 12 Valence Valence electrons - outermost shell, or valence shell The chemical behavior of an atom is mostly determined by the number of valence electrons Elements with a full valence shell - chemically inert An atom’s valence is the number of bonds it can form This is determined by how many electrons it takes to fill (or empty) its outer shell 13 Goal: completes the valence shells Atoms interact in a way that completes their valence shells First shell - max is 2 electrons Second shell - max is 8 electrons 14 Poll Questions Atoms whose outer electron shells contain 8 electrons tend to A) form ionic bonds in aqueous solutions. B) form covalent bonds in aqueous solutions. C) be stable and chemically nonreactive, or inert. D) be unstable and chemically very reactive pollev.com/barbaraakum216 15 Chemical reactions Making and breaking of chemical bonds Reactants - starting molecules of a chemical reaction Products - resulting molecules of a chemical reaction 16 Chemical Bonding Atoms with incomplete valence shells can interact with other atoms by ○ Sharing valence electrons ○ Transferring valence electrons These interactions usually result in atoms staying close together, held by attractions called chemical bonds Type of chemical bonds ○ Covalent bonds ○ Ionic bonds ○ Hydrogen bonds ○ Van der Waals interactions 17 Type of chemical bonds ○ Covalent bonds ○ Ionic bonds ○ Hydrogen bonds ○ Van der Waals interactions https://www.brainkart.com/article/Types-of-chemical-bond_39889/ 18 1. Covalent Bonds Between atoms of the Name Electro Lewis Spa same or different elements and n Dot ce- The total number of Molec Distrib Structur Filli covalent bonds must add (a)ular ution e and ng Formu Hydrogen Diagra Structur Mo up to an atom’s valence (H2)la H H m al del Formula (b) Oxygen O O A single bond - sharing of (O2) one pair of valence (c) Water (H2O) O H electrons H A double bond - sharing of two pairs of valence (d) H Methane electrons (CH4) H C H A triple bond - sharing of H three pairs of valence electrons 19 Notation Molecular formula - abbreviation further with a For example, H2 (hydrogen) and O2 (oxygen) Condensed formula CH3CH2 Structural formula - used to represent atoms and bonding is For example, H—H represents a single bond O═O represents a double bond Bond line or skeletal carbon atoms are often omitted at the corners of lines, and hydrogen atoms attached to carbon are usually not explicitly shown unless necessary for clarity 20 Electronegativity Atoms in a molecule attract electrons to varying degrees Electronegativity - tendency of an atom to pull electrons towards itself The more electronegative an atom is, the more strongly it pulls shared electrons toward itself 21 Types of covalent bonds Nonpolar covalent bond - equal sharing of electrons Polar covalent bond - unequal sharing of electrons ○ one atom is more electronegative ○ causes a partial positive or partial negative charge for each atom or molecule 22 Polar covalent bonds Electrons of the polar covalent bonds spend more time near the oxygen than the hydrogen 23 Nonpolar covalent bonds 24 2. Ionic bonds One atom donates one or more electrons to another The two resulting oppositely charged atoms or molecules are called ions ○ A positively charged ion is called a cation ○ A negatively charged ion is called an anion Anions and cations attract each other; this attraction is called an ionic bond 25 2. Ionic bonds Compounds formed by ionic bonds are called ionic compounds, or salts Salts, such as sodium chloride (NaCl; table salt), are often found in nature as crystals ○ NaCl itself is not a molecule; ○ The formula for an ionic compound indicates the ratio of elements in a crystal of the salt ○ Stable when dry, but dissociate quite easily in water 26 3. Hydrogen Bonds A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom In living cells, the electronegative partners are usually oxygen or nitrogen atoms Polarity allows water molecules to form hydrogen bonds with each other 27 Water: The Solvent of Life A solution is a liquid that is a completely homogeneous mixture of substances The solvent is the dissolving agent of a solution The solute is the substance that is dissolved An aqueous solution is one in which water is the solvent Water is a versatile solvent due to its polarity When an ionic compound is dissolved in water, each ion is surrounded by a sphere of water molecules called a hydration shell 28 Water: The Solvent of Life Water can also dissolve compounds made of nonionic polar molecules Large polar molecules such as proteins can dissolve in water if they have ionic and polar regions Hydrophilic substance - has affinity for water Hydrophobic substance - NO affinity for water What if we mix water with something non-polar? 29 Non-polar molecules are hydrophobic Oil forms spherical droplets in water Droplets merge to produce larger spheres, which merge, (etc), until the total Area of the oil-water interface is minimized. This maximizes the # of strong polar interactions between H2O molecules This concept is really important for protein folding and membrane transport30 Acidic and basic conditions A hydrogen atom in a hydrogen bond between two water molecules can shift from one to the other ○ The hydrogen atom leaves its electron behind and is transferred as a proton, or hydrogen ion (H+) ○ The molecule that lost the proton - hydroxide ion (OH–) ○ The molecule with the extra proton - hydronium ion (H3O+) often represented as H+ + – ○ H and OH are very reactive ○ Changes in their concentrations can drastically affect the chemistry of a cell 31 Acidic and basic conditions Water is in a state of dynamic equilibrium in which water molecules dissociate at the same rate at which they are being reformed Pure water - Equal concentrations of H+ and OH– Adding certain solutes, called acids and bases, modifies the concentrations of H+ and OH– + ○ Acid - substance that increases the H concentration of a solution + ○ Base is a substance that reduces the H concentration of a solution 32 The pH Scale + pH = –log [H ] Acid pH < 7 In any aqueous Neutral pH =7 solution at 25ºC, [H+] x [OH–] = 10–14 Most biological fluids Base pH > 7 pH of a solution is –log [H+] the higher the H+, the more acidic 33 4. Van der Waals Interactions If electrons are not evenly distributed, they may accumulate by chance in one part of a molecule Van der Waals interactions are attractions between molecules that are close together as a result of these charges Van der Waals interactions are individually weak but can be cumulatively strong 34  Molecular shape and Function A molecule’s size and shape are key to its function A molecule’s shape is determined by the positions of its atoms’ orbitals In a covalent bond, the s and p orbitals may hybridize, creating specific molecular shapes 35 Carbon the basis for all biological molecules 36 Organic chemistry Carbon valence = 4 Carbon atoms can bond to 4 other atoms Carbon can form large, complex molecules 37 Drawing Organic Structures Reminder: 3 Note that the carbons and hydrogens are often implied especially in complex structures 38 Drawing Organic Structures Organic molecules tend to have a lot of carbon and hydrogen 3 structural isomers of pentane Also drawn as: So chemists often just draw molecules with C as corners/ends, and the H implicit 39 Valences of C, H, O, N The number of unpaired electrons in the valence shell of an atom is generally equal to its valence, the number of covalent bonds it can form 40 Carbon Skeletons Carbon atoms can partner with atoms other than hydrogen, such as the following: Carbon dioxide: CO 2 41 Functional groups Each carbon can bond to: Up to 4 other carbons Up to 4 hydrogens Up to 4 functional groups 7 functional groups that are most important in the chemistry of life Hydroxyl group Carbonyl group Carboxyl group Amino group Sulfhydryl group Phosphate group Methyl group You should know these groups 42 Carbon Skeletons Carbon atoms can also be linked into chains Hydrocarbons are organic molecules consisting of only carbon and hydrogen Four ways that carbon skeletons can vary 43 Isomers Compounds with: same molecular formula different structures and properties Type of Isomers ○ Structural isomers have different covalent arrangements of their atoms ○ Cis-trans isomers (also called geometric isomers) have the same covalent bonds but differ in their spatial arrangements ○ Enantiomers - mirror images of each other 44 1. Structural Isomers have the same molecular formula, but different connectivity between atoms C5H12 can be arranged in three different ways: here are two of them 45  2. Geometric isomers C-C single bonds make tetrahedral, and can rotate C=C double bonds impose a flat structure: These bonds do not rotate 46 2. Geometric isomers: cis-trans isomers at C=C double These are two isomers of 2-butene cis isomer has the larger functional groups on the same side of the C=C double bond; in the trans isomer they are on opposite sides 47  2. Geometric isomers: cis-trans isomers at C=C double A molecule can have multiple C=C double bonds ○ In a large molecule, this can produce dramatic shape changes These are two isomers retinal cis isomer has the larger functional groups on the same side of the C=C double bond; in the trans isomer they are on opposite sides 48 Tetrahedral structure A carbon with four single bonds has a Four single covalent bonds make a tetrahedron 49 3. Chiral Carbons and Stereoisomers Chiral carbon = asymmetric carbon Carbon atom is bonded to 4 distinct functional groups Note: 3-dimensional structure notations Two arrangements are possible at each chiral carbon. The resulting molecules, known as stereoisomers, cannot be superimposed Image credit:Wedge-hash diagrams 43 Why care about stereoisomers? Many of the building blocks of life contain chiral carbons e.g. proteins are composed exclusively of L- amino acids Enantiomers/stereoisomers are sometimes called R and S; sometimes D and L. Don’t worry about naming 51 Image credit: me.me Why care about stereoisomers? Biological systems are exquisitely sensitive to molecular shape Enantiomers can have very different properties This This smells like smells like spearmint * * caraway (rye bread) Carvone Ibuprofen This dulls the pain * This does nothing * Image credit: wikipedia.com