CHEMICAL CONTEXT OF LIFE CHAPTER 2

Chemical Benefits and Costs Understanding of chemistry provides fertilizers, medicines, etc. Chemical pollutants damage ecosystems

Bioremediation Use of living organisms to withdraw harmful substances from the environment

Fundamental forms of matter Can’t be broken apart by normal means Elements Fundamental forms of matter Can’t be broken apart by normal means 92 occur naturally on Earth

Most Common Elements in Living Organisms Oxygen Hydrogen Carbon Nitrogen

About 20 of the 92 elements are essential to life Trace elements are required only in minute quantities Deficiencies can be harmful

Nitrogen Deficiency in Tomato Plants

Iodine Deficiency – Enlarged Thyroid Gland Thyroid grows to abnormal size Can be reversed with iodine rich diet Daily intake of 0.15mg Iodized salt has reduced incidence Trace Elements

Chemical Terminology Matter – anything that takes up space and has mass Element - substances that cannot be broken down to by chemical reactions

Atomic Structure Determines the Behavior of an Element

Atoms are the smallest unit having properties of an element. Elements made of Atoms... Atoms are the smallest unit having properties of an element. 3 Particles of an Atom Protons (+ charge) Electrons (- charge) Neutrons (neutral charge)

Smallest particles that retain properties of an element What are Atoms? Smallest particles that retain properties of an element Made up of subatomic particles: Protons (+) Electrons (-) Neutrons (no charge)

Protons and Neutrons packed tightly in core - Atomic Nucleus Electrons move along outer orbit (speed of light)

Isotopes - differ in # neutrons Lighter Heavier Mass Difference

Radioisotopes Have an unstable nucleus that emits energy and particles Radioactive decay transforms radioisotope into a different element Decay occurs at a fixed rate

Radioisotopes Carbon-12 and Carbon-14 are isotopes Both types very common Carbon-12 is very stable Carbon 14 is unstable Will disintegrate 5600 yrs Emit radiation as it decays

Radioisotopes as Tracers Tracer is substance with a radioisotope attached to it Emissions from the tracer can be detected with special devices Following movement of tracers is useful in many areas of biology

Thyroid Scan Measures health of thyroid by detecting radioactive iodine taken up by thyroid gland normal thyroid enlarged cancerous

Other Uses of Radioisotopes Drive artificial pacemakers Radiation therapy Emissions from some radioisotopes can destroy cells. Some radioisotopes are used to kill small cancers.

What Determines Whether Atoms Will Interact? The number and arrangement of their electrons

Electrons Carry a negative charge Repel one another Are attracted to protons in the nucleus Move in orbitals - volumes of space that surround the nucleus y Z X When all p orbitals are full

Electron Cloud

Electron Orbitals Orbitals can hold up to two electrons Atoms differ in the number of occupied orbitals Orbitals closest to nucleus are lower energy and are filled first

Electron Vacancies Unfilled shells make atoms likely to react Hydrogen, carbon, oxygen, and nitrogen all have vacancies in their outer shells CARBON 6p+ , 6e- NITROGEN 7p+ , 7e- HYDROGEN 1p+ , 1e-

2 elements bond together to form compounds

Sodium + Chlorine = Table Salt Compound... Substance consisting of 2 or more elements chemically combined Sodium + Chlorine = Table Salt

Chemical Bonds, Molecules, & Compounds Bond is union between electron structures of atoms Atoms bond to form molecules Molecules may contain atoms of only one element - O2 Molecules of compounds contain more than one element - H2O

Chemical Bookkeeping Use symbols for elements when writing formulas Formula for glucose is C6H12O6 6 carbons 12 hydrogens 6 oxygens

Reactants ---> Products Chemical Bookkeeping Chemical equation shows reaction Reactants ---> Products Equation for photosynthesis: 6CO2 + 6H2O ---> + C6H12O12 + 6H2O

Ionic Bonds Covalent Bonds Hydrogen Bonds Important Bonds in Biological Molecules Ionic Bonds Covalent Bonds Hydrogen Bonds

Ion Formation Atom has equal number of electrons and protons - no net charge Atom loses electron(s), becomes positively charged ion Atom gains electron(s), becomes negatively charged ion

Ionic Bonding One atom loses electrons, becomes positively charged ion Another atom gains these electrons, becomes negatively charged ion Charge difference attracts the two ions to each other

Formation of NaCl Sodium atom (Na) Outer shell has one electron Chlorine atom (Cl) Outer shell has seven electrons Na transfers electron to Cl forming Na+ and Cl- Ions remain together as NaCl

Formation of NaCl electron transfer SODIUM ATOM 11 p+ 11 e- CHLORINE 7mm electron transfer SODIUM ATOM 11 p+ 11 e- CHLORINE ATOM 17 p+ 17 e- CHLORINE ION 17 p+ 18 e- SODIUM ION 11 p+ 10 e- Fig. 2.10a, p. 26

Atoms share a pair or pairs of electrons to fill outermost shell Covalent Bonding Atoms share a pair or pairs of electrons to fill outermost shell Single covalent bond Double covalent bond Triple covalent bond

Nonpolar Covalent Bonds Atoms share electrons equally Nuclei of atoms have same number of protons Example: Hydrogen gas (H-H)

Polar Covalent Bonds Number of protons in nuclei of participating atoms is NOT equal Electrons spend more time near nucleus with most protons Water - Electrons more attracted to O nucleus than to H nuclei

Hydrogen Bonding Molecule held together by polar covalent bonds has no NET charge However, atoms of the molecule carry different charges Atom in one polar covalent molecule can be attracted to oppositely charged atom in another such molecule

Examples of Hydrogen Bonds one large molecule another large molecule a large molecule twisted back on itself Fig. 2.12, p. 27

Polarity Solvent Temperature-Stabilizing Cohesive Properties of Water Polarity Solvent Temperature-Stabilizing Cohesive

1. Water Structure Water is a polar molecule. Oxygen has a partial negative charge Hydrogen has a partial positive charge.

Water Is a Polar Covalent Molecule Oxygen and hydrogen share electrons forming a covalent bond Two molecules of water are joined by Hydrogen bonds O H H

Liquid Water H + + _ H + O H + O _ + H +

2. Water as a Solvent Background information: Solution: a homogenous mixture of two or more substances Solvent: the dissolving agent Solute: the dissolved substance Aqueous solution: a solution where water is the solvent.

Water as a Solvent Water dissolves a lot of things!! Why?? The polarity of water separates and dissolves ions (positive or negatively charged!) Other polar molecules behave in the same way!

Keeping Ions Separate = Dissolving Power Spheres of Hydration Na+ Cl– – + Keeping Ions Separate = Dissolving Power

To Dissolve or Not to Dissolve? Hydrophilic: A substance with an affinity/able to dissolve in water. What kind of substances? Hydrophobic: A substance that repels water/don’t dissolve.

Hydrophilic & Hydrophobic Substances Hydrophilic substances Polar Hydrogen bond with water Example: sugar Hydrophobic substances Nonpolar Repelled by water Example: oil

Cell Membrane

3. Temperature-Stabilizing Effects Liquid water can absorb much heat before its temperature rises Why? Much of the added energy disrupts hydrogen bonding rather than increasing the movement of molecules

Moderation of Temperature Water is able to stabilize temperature because it has a HIGH specific heat. Specific heat: the amount of heat that must be absorbed or lost for 1 g to change its temperature by 1º. (water takes a lot of energy) Think of specific heat as a measure of how well a substance resists changing its temperature when it absorbs or releases heat.

Evaporation of Water Large energy input can cause individual molecules of water to break free into air As molecules break free, they carry away some energy (lower temperature) Evaporative water loss is used by mammals to lower body temperature, cool oceans, etc.

Why Ice Floats In ice, hydrogen bonds lock molecules in a lattice keeping them apart Water molecules in lattice are spaced farther apart then those in liquid water Ice is less dense than water

4. Water Cohesion Hydrogen bonding holds molecules in liquid water together Creates surface tension Allows water to move as continuous column upward through stems of plants

Hydrogen Ions: H+ Unbound protons Have important biological effects Form when water ionizes

0---------------------7-------------------14 The pH Scale Measures H+ concentration of fluid Change of 1 on scale means 10X change in H+ concentration Highest H+ Lowest H+ 0---------------------7-------------------14 Acidic Neutral Basic

Examples of pH Pure water is neutral with pH of 7.0 Acidic Basic Stomach acid: pH 1.0 - 3.0 Lemon juice: pH 2.3 Basic Seawater: pH 7.8 - 8.3 Baking soda: pH 9.0

Acids & Bases Acids Bases Donate H+ when dissolved in water Acidic solutions have pH < 7 Bases Accept H+ when dissolved in water Acidic solutions have pH > 7

Weak and Strong Acids Weak acids Strong acids Reluctant H+ donors Can also accept H after giving it up Carbonic acid (H2CO3) is example Strong acids Completely give up H+ when dissolved Hydrochloric acid (HCl) is example

Buffer Systems Minimize shifts in pH Partnership between weak acid and base it forms when dissolved Two work as pair to counter shifts in pH

Carbonic Acid-Bicarbonate Buffer System When blood pH rises, carbonic acid dissociates to form bicarbonate and H+ H2C03 -----> HC03- + H+ When blood pH drops, bicarbonate binds H+ to form carbonic acid HC03- + H+ -----> H2C03