BIOCHEMISTRY The Chemical Context of Life

The Elements of Life C. HOPKINS CaFe About 20 25% of the 92 elements are essential to life Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter Most of the remaining 4% consists of calcium, phosphorus, potassium, and sulfur Trace elements are those required by an organism in minute quantities 2

Covalent Bond Review A covalent bond is the sharing of a pair of valence electrons by two atoms In a covalent bond, the shared electrons count as part of each atom s valence shell A covalent bond is formed between shared pairs of electrons: 1 pair a single bond 2 pairs a double bond 3 pairs a triple bond 3

Not all sharing is created EQUAL! In a nonpolar covalent bond, the atoms share the electron equally In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally Unequal sharing of electrons causes a slightly positive and negative pole(s) O + H H H 2 O + 4

Question Why are covalent bonds more prevalent among biological molecules than ionic bonds? A. Ionic bonds only occur between metals and non-metals, and therefore aren't usually present in biological systems. B. You can have double covalent bonds, but not double ionic bonds, so covalent bonds provide more variety consistent with the structural demands required in biological systems. C. Biological conditions are often aqueous, and the water would cause ionic bonds to dissociate. D. Ions only form under extreme conditions not compatible with the cell's environment.

IMFs There is a rift between biology and chemistry text books. The biology book often speaks of weak bonds which are really intermolecular forces (IMFs) IMFs are intermolecular whereas chemical bonds are intramolecular Inter means between molecules (molecule to molecule, like magnets) Intra means within the molecule (atom to atom, a real bond) 7

What s the big deal? With IMFs, molecules become sticky or adhere to one another. Hydrogen bonds are IMFs; aka not REAL bonds; aka WEAK bonds Collectively, IMFs can be pretty strong, as between the molecules of a gecko s toe hairs and the surface of a wall. He s not really defying gravity! 8

Hydrogen Bonding: A Special Case of IMFs A hydrogen bond is not the same as a bonded hydrogen! It s a special case of IMFs A bonded hydrogen is within a water molecule A hydrogen bond is between molecules! Bonded Hydrogens (actual chemical bonds consisting of a shared pair of electrons) Hydrogen bonds (IMFs) 9

Hydrogen Bonding: A Special Case of Dipole-Dipole IMFs Hydrogen bonding in water occurs when the positive H of one water molecule is attracted to the negative O on an adjacent molecule. (It happens in any other polar molecules too.) Bonded Hydrogens (actual chemical bonds consisting of a shared pair of electrons) (Draw one in your notes ) Hydrogen bonds (IMFs) 10

Hydrogen Bonding: A Special Case of Dipole-Dipole IMFs Hydrogen bonding is an IMF that makes molecules more attracted to each other, thus more tightly held to each other, thus more energy is required to separate them! Polar molecules have a higher melting point, boiling point, heat of vaporization, and enchanced solubility as a result of the H bonds 11

Structure and Function A molecule s shape determines its function A molecule s shape is determined by the positions of its atoms valence orbitals In a covalent bond, the s and p orbitals may hybridize, creating specific molecular shapes 12

The puzzle pieces have to fit! Biological molecules recognize and interact based on shape Molecules with similar shapes have similar effects Long ago you accepted that the 4 DNA bases pair A-T and G-C, but WHY?? Why can t the A pair with the C in DNA? 13

The puzzle pieces have to fit! Why does a molecule have shape in the first place? That has to do with IMFs holding things in place defining its 3-D shape. The big people word for shape is conformation. In the case of A-T vs. G-C, it s all about lining up that IMF called hydrogen bonding ; 2 sites for A-T and 3 for G-C

Endorphins & Pain Meds Natural endorphin Carbon Hydrogen Nitrogen Sulfur Oxygen Morphine (a) Structures of endorphin and morphine

Ta Da! Pain killer! The brain receptors bind with either with similar results. Natural endorphin Morphine Brain cell Endorphin receptors (b) Binding to endorphin receptors 16

Chemical Reactions Make and/or Break Chemical Bonds 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 17

Photosynthesis is a mighty important chemical reaction! Photosynthesis is an important chemical reaction Sunlight powers the conversion of carbon dioxide and water to glucose and oxygen 6 CO 2 + 6 H 2 O C 6 H 12 O 6 + 6 O 2 18

Water: The molecule that supports life on this planet! Water is the biological medium for all life on Earth All living organisms require water more than any other substance 19

FOUR Emergent Properties of water contribute to Earth s suitability for life 1. Water s cohesive & adhesive behavior 2. Water s ability to moderate temperature 3. Water s expansion upon freezing 4. Water s versatility as a solvent. 20

What causes water molecules to both Cohesion is when water molecules stick to each other. Adhesion is when water molecules stick to some other type of substance like plant cell walls. Both caused by H bonds cohere and adhere? Animation by scrolling over image 21

What causes water molecules to both cohere and adhere? Surface tension is a measure of how hard it is to break the surface of a liquid and a consequence of cohesion. What causes it? Go ahead, guess! Hydrogen bonding, yet again! 22

How does water moderate temperature? Water has a high heat capacity, which is the amount of heat required to raise 1 g of water by 1 o C (1 calorie = 4.184 J) What does that mean? It means water can absorb large quantities of heat without much change in its own temperature, thus it s a good thermoregulator, meaning it minimizes changes in temperature. But, why? Guess again! 23

Water is a freak! It expands upon freezing! Ice floats in liquid water because hydrogen bonds in ice are more ordered forming a hexagonal shape with a hole in the middle, making ice less dense. Water reaches its greatest density at 4 C, which is excellent news if you re a fish! If ice sank, all bodies of water would eventually freeze solid, making life impossible on Earth

Water is a freak! It expands upon freezing! Hydrogen bond Liquid water: Hydrogen bonds break and re-form Ice: Hydrogen bonds are stable

Water has Versatility as a Solvent A solution is a liquid that is a homogeneous mixture of substances A solvent is the dissolving agent of a solution or dissolver The solute is the substance that is dissolved or disolvee An aqueous solution is made with water 26

Water s Versatility as a Solvent Water is a versatile solvent due to its polarity, which allows it to form hydrogen bonds easily. When an ionic compound is dissolved in water, each ion is surrounded by a sphere of water molecules called a hydration shell 27

Water s Versatility as a Solvent Water can also dissolve compounds made of nonionic polar molecules Even large polar molecules such as proteins can dissolve in water if they have ionic and polar regions 28

But water can t dissolve everything A hydrophilic substance is one that dissolves in water A hydrophobic substance is one that does not dissolve in water; fears water Oil molecules are hydrophobic because they have relatively nonpolar bonds A colloid is a stable suspension of fine particles in a liquid (like milk fat suspended in water Yummy!) 29

Acids, Bases and Buffers. Oh, my! Simply put, An acid is any substance that increases the H + concentration of a solution; less than 7 on ph scale A base is any substance that reduces the H + concentration of a solution; greater than 7 on ph scale Bleac h 30

Acids, Bases and Buffers. Oh, my! Buffers The internal ph of most living cells must remain close to 7 Buffers RESIST changes in concentrations of H + and OH in a solution, therefore they RESIST a change in ph Most buffers are protein enzymes that consist of an acid side and base side so they can neutralize any solution 31

The ph Scale Each increase (toward more acidic or more basic away from 7 in either direction) on the ph scale increases by a factor of 10. So an acid with a ph of 2 is 100 times more acidic than an acid with a ph of 4. 32

Homework Create an annotated drawing (a doodle with notes, basically!) that demonstrates how the appropriate properties of water cause the following Trees to absorb water from their roots all the way up to the leaves Include the following terms: cohesion, adhesion, capillary action, hydrogen bonding, and transpiration. Using the internet and your notes to research before you draw is highly encouraged. 33