Water & Carbon: The Chemical Basis of Life

Chapter 2

Biology 11

Overview Basic Definitions

Radioactive isotopes – not in chapter 2 text Understanding the four types of bonding

Ionic Covalent Polar covalent hydrogen

Water’s special properties Solvent Adhesion/cohesion Surface tension Specific heat

Overview

Acid-Base Reactions and pH Chemical Energy

Kinetic energy Potential energy Gibbs free-energy

Chemical Evolution Functional Groups

Basic Definitions

Elements – metals vs. nonmetals Atomic number – number of protons Mass number – protons and neutrons

Isotopes

Atomic mass unit – amu Orbitals – 3D shapes which holds electrons

s, p, d, & f

Valence electrons – outermost electrons Number of valence electrons determines chemical

properties and chemical reactivity

Isotopes

Isotopes are atoms that have the same number of protons but differ in the number of neutrons

Not all isotopes are radioactive Radioactive means that the atom is trying to

decay or reach a more stable state Three types of energy emission

Alpha, beta, & gamma

Radioactive Isotopes

Four Types of Chemical Bonds

Ionic Covalent Polar Covalent Hydrogen

Ionic Bonding

Ionic Between a metal and a non metal Greatly different values of electronegativity Involves a complete transfer of electrons Held together by an electrostatic interaction

between a + charge and a – charge Metal is always giving electrons Non metal is always accepting electrons

In solution become “ions”

Ionic Bonding

Covalent Bonding

Covalent Always between two non-metals No difference in electronegativity No charges present Strong bond Held together by the attraction of an electron of

one atom to the nucleus of the other atom Equal sharing of electrons

Covalent Bonding

Polar Covalent Polar Covalent

Two non metals Differences in electronegativity

Electronegativity is the ability of an atom to pull an electron to itself in a chemical bond

One atom is more greedy than the other and therefore the electron of the less greedy atom spends more time around the nucleus of the greedy atom

Creates a dipole moment Partial positive charge δ+ and δ-

Bonding and Solubility

Like dissolves like Solubility is the ability of water to “coat” another molecule

or to interact chemically with that molecule

Molecules with a great deal of covalent bonding and not much polar covalent bonding are hydrophobic Waxes, oils, fats

Molecules with many polar covalent bonds are easily soluble in water glucose

Bonding Summary

Hydrogen Bonding

All of the bonds this far have been intramolecular Hydrogen bonding is an intermolecular force Week interaction always involving a hydrogen atom

on one molecule and either an oxygen, or nitrogen on another atom

Responsible for water’s special properties Holds together

DNA double helix tRNA structure 3D protein structure (alpha helix & beta sheets)

Hydrogen Bonding in DNA

Water Universal Solvent

Water easily dissolves ionic and polar molecules

To be dissolved in water is to be surrounded and coated by water molecules

Water Universal Solvent

Hydrophobic molecules repel water

Cohesion

Binding between like molecules Transpiration in trees Meniscus Surface tension

Adhesion

Binding between unlike molecules Usually between a liquid and solid surface

Density of Ice and Water

When water freezes each water molecule must form four hydrogen bonds

This forms a regular and repeating structure which has air space between the molecules

This is why ice is less dense than liquid water

Specific Heat

Water has a high capacity for absorbing heat Specific heat

Amount of energy required to raise the temperature of 1 gram of a substance by one degree C.

Before heat can be transferred so that the water molecules can move faster (increased kinetic energy increased heat) the hydrogen bonds must be broken

Heat of Vaporization

Energy required to change one gram of liquid water to water vapor (gas)

Why is water such an efficient coolant Water molecules have to absorb a great deal of

energy from your body in order to evaporate You loose heat

Acids and Bases

In chemical reality protons do not exist by themselves

Protons associate with water to form hydronium ions

H2O + H2O H3O+ + OH-

H2O H+ + OH-

Acids and Bases

Substances that give up protons during chemical reaction and raise the hydrogen ion concentration are acids

Substances that acquire protons during chemical reactions and lower the hydrogen ion concentration are bases

Acid base reactions require a proton donor and a proton acceptor

HCl + H2O H3O+ + Cl-

pH Calculations & pH Scale

pH = -log[H+]

Basic Terms of Chemical Reactions Reactants Products Chemical Equilibrium

Forward and reverse reactions occur at the same rate

The amount of reactant and product are not necessarily the same

Exothermic – energy given out to system Endothermic – energy consumed

Energy Dynamics

Potential Energy Kinetic energy Thermal energy

kinetic energy of molecular motion

1st law of thermodynamics

2nd law of thermodynamics

Spontaneous Reactions

∆G = ∆H – T∆S ∆G negative = spontaneous

Exergonic energy releasing ∆G positive = not spontaneous

Endergonic energy consuming Reactions are spontaneous when ∆H is

negative and ∆S is positive We have to use the combined contributions

of changes in heat and disorder to determine spontaneity

Understanding ∆H Enthalpy

∆H is the difference in potential bond energy between the products and reactants

∆H reflects the number and kinds of chemical bonds in reactants and products

When heat content of the product is less than the reactant ∆H is negative and exothermic Gives off heat to surroundings - ∆H

When heat content of the reactants is less than the products ∆H is positive and endothermic Takes heat in from surroundings + ∆H

Bond Enthalpy

You can also think of this as the bonds in methane hold more energy than the bonds of CO2 or it takes more energy to form methane bonds than CO2 bonds

Understanding ∆S Entropy

Measurement of disorder

Reactions are spontaneous when the products molecules are less ordered than the reactant molecules

Chemical Evolution

First molecules on a hot earth CH4, NH3, H2O, CO2, N2

Spontaneous generation must have occurred at some point in earth’s history

Chemical evolution Early in earth’s history simple inorganic molecules

in the atmosphere and oceans combined to form larger more complex molecules

Chemical Evolution

Kinetic energy and heat from sunlight was converted into chemical bonds

Larger molecules accumulated and reacted with one another to produced more complex molecules

One of these complex molecules was able to self replicate

The big shift As the molecule multiplied evolution by natural selection

replaced chemical evolution

Formation of Early Complex Molecules

Using only the chemical precursors of the early atmosphere could these molecules form Formaldehyde H2CO Hydrogen cyanide HCN

Reaction between CO2 and H2 is endergonic Formaldehyde and water have more potential

energy and are more ordered

Energy Inputs and Chemical Evolution

When earth’s early inorganic substances are placed in a test tube nothing happens

But what happens when these molecules are struck by sunlight or lightening?

In the early earth’s atmosphere many high energy photons would have reached the planet? Why

Energy Inputs and Chemical Evolution

Energy from photons can break molecules apart by knocking electrons off

Free radicals form which are highly reactive

Temperature and Early Chemical Reactions

For the complex molecules to form from the inorganic molecules one chemical bond must break and one chemical bond must form

Reactants must collide When temperature are high reactants move

faster (increased kinetic energy) and collide more frequently

Chemical Evolution

Sunlight was converted into chemical energy Potential energy now held in chemical bonds Why was HCN and H2CO so important

The formation of C – C bonds was possible Heat alone can link to formaldehyde molecules

into acetaldehyde Reactions between acetaldehyde and

formaldehyde produce sugars Crucial step towards production of the types of

molecules found in living organisms

Step 1Chemical Evolution

Step 2Chemical Evolution

Step 3 Chemical Evolution

Water’s Specific Heat & Chemical Evolution

Water’s high specific heat insulated dissolved substances from sources of energy like intense sunlight which could have broken the chemical bonds apart

Water’s heat of vaporization would have kept land masses near water cool for further chemical evolution

Importance of Carbon

Because carbon can form 4 bonds it can form has a limitless array of molecular shapes

The carbon atoms in an organic molecule furnish a skeleton that gives the molecule its overall shape

However, the type of macromolecule and the types of reactions that a molecule can participate in is dictated by functional groups

Review Table 2.3 of your text