BIO 2, Lecture 4 THE CHEMISTRY OF LIFE II: THE SPECIAL PROPERTIES OF WATER AND CARBON.

BIO 2, Lecture 4BIO 2, Lecture 4BIO 2, Lecture 4BIO 2, Lecture 4THE CHEMISTRY OF LIFE II: THE CHEMISTRY OF LIFE II:

THE SPECIAL PROPERTIES OF THE SPECIAL PROPERTIES OF WATER AND CARBONWATER AND CARBON

WATER

• Water is life’s universal solvent• All living organisms require water• Most cells are surrounded by water,

and cells themselves are about 70–95% water

• The abundance of water is the main reason the Earth is habitable

• “Oh, ugly bags of mostly water”

• The water molecule is a polar molecule: One side is slightly positively charged and one is slightly negative charged

• Polarity allows water molecules to form hydrogen bonds with each other

• Hydrogen bonds are weak and constantly break and reform, giving water its fluidity

Hydrogenbond

–H

+

H

O

——

——

+

+

+

–

–

–

• Water has 4 special properties that facilitate an environment for life:

– Cohesive behavior– Ability to moderate temperature– Expansion upon freezing– Versatility as a solvent

• Collectively, hydrogen bonds hold water molecules together, a phenomenon called cohesion

• Cohesion helps the transport of water against gravity in plants

• Adhesion is an attraction between different substances, for example, between water and plant cell walls

COHESIVE BEHAVIOR

Water-conductingcells

Adhesion

Cohesion

150 µm

Directionof watermovement

• Surface tension is a measure of how hard it is to break the surface of a liquid

• Surface tension increases with cohesion

The high surface tension of water allows

some organisms to

crawl across it

• Water absorbs heat from warmer air and releases stored heat to cooler air

• Water can absorb or release a large amount of heat with only a slight change in its own temperature

MODERATES TEMPERATURE

• The specific heat of a substance is the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1ºC

• The specific heat of water is 1 cal/g/ºC, which is very high

• Water resists changing its temperature because of its high specific heat

• Water’s high specific heat can be traced to hydrogen bonding– Heat is absorbed when hydrogen bonds

break– Heat is released when hydrogen bonds

form

• The high specific heat of water minimizes temperature fluctuations to within limits that permit life• Cyclical nature of the ice ages may be

partly explained by this property of water

San Diego 72°

40 miles

Pacific Ocean

70s (°F)

80s

90s

100s

Santa Barbara 73°

Los Angeles (Airport) 75°

Burbank90°

San Bernardino100°

Riverside 96°Santa Ana 84° Palm Springs

106°

• Ice floats in liquid water because hydrogen bonds in ice are more stable and ordered, making ice less dense

• Water reaches its greatest density at 4°C

• If ice sank, all bodies of water would eventually freeze solid, making life impossible on Earth

Hydrogenbond

Liquid waterHydrogen bonds break and re-form

IceHydrogen bonds are stable

• A solution is a liquid that is a homogeneous mixture of substances

• A 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, 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

Cl–

Na

Cl–

+

+

+

+

+

+

++

–

–

–

–

–

–

––

Na+

–

––

+

• Water can also dissolve compounds made of nonionic polar molecules

• Even large polar molecules (including some proteins or parts of proteins) can dissolve in water if they have ionic and/or polar regions

(a) Lysozyme molecule in a nonaqueous environment

(b) Lysozyme molecule (purple) in an aqueous environment

(c) Ionic and polar regions on the protein’s surface attract water molecules.

• A hydrophilic substance is one that has an affinity for water

• A hydrophobic substance is one that does not have an affinity for water

• Oil molecules are hydrophobic because they have relatively non-polar bonds

• Hydrogen bonds are weak and constantly break and reform between water molecules

• When they break, the proton of the hydrogen atom from one of the water molecules is transferred to the other molecule

– The water molecule with the extra proton is now a hydronium ion (H3O+), though it is often represented as H+

– The water molecule that lost the proton is now a hydroxide ion (OH–)

• Water is in a state of dynamic equilibrium in which water molecules dissociate (hydrogen bonds break) at the same rate at which they are being reformed

• In any aqueous solution at 25°C the product of [H+] and [OH–] is constant and can be written as [H+][OH–] = 10–14

• The pH of a solution is defined by the negative logarithm of H+

concentration, written as pH = –log [H+]

• For a neutral aqueous solution [H+] is 10–7 = –(–7) = 7

• Concentrations of H+ and OH– are equal in pure water and are both very low • Only 1 in 10 million water molecules are

dissociated at any one time

• Adding certain solutes, called acids and bases, modifies the concentrations of H+ and OH–

• Biologists use the pH scale to describe whether a solution is acidic or basic

Firstshell

Second

shell

Thirdshell

• An acid is any substance that increases the H+ concentration of a solution• Acids typically dissociate (fully or partly) in

water, forming [H+] and an anion• As [H+] increases, [OH-] decreases

• A base is any substance that reduces the H+ concentration of an aqueous solution• Bases dissociate (fully or partly) in water into

OH- and a cation (e.g. NaOH); as [OH-] increases, [H+] decreases

• Alternatively, they may accept (bind up) H+ from the solution, thereby reducing pH directly

Bases donate OH–

or bind up H+ inaqueous solutions,thereby increasing pH

Acids donate H+ toaqueous solutions, thereby lowering pH

Acidic[H+] > [OH–]

Neutral[H+] = [OH–]

Basic[H+] < [OH–]

14

7

0

Neutral solution

Acidic solution

Basic solution

OH–

OH–

OH–

OH–

OH–OH–OH–

H+

H+

H+

OH–

H+ H+

H+ H+

OH–

OH–

OH–OH–

H+

OH–

H+

H+

H+

H+

H+

H+

H+

OH–

Neutral [H+] = [OH–]

Incre

asin

gly

Acid

ic [

H+]

> [

OH

– ]

Incre

asin

gly

Basic

[H

+]

< [

OH

– ]

pH Scale0

1

2

3

4

5

6

7

8

Battery acid

Gastric juice,lemon juice

Vinegar, beer,wine, cola

Tomato juice

Black coffee

Rainwater

Urine

SalivaPure water

Human blood, tears

Seawater

9

10Milk of magnesia

Household ammonia

Household bleach

Oven cleaner

11

12

13

14

• Acid precipitation refers to rain, snow, or fog with a pH lower than 5.6

• Acid precipitation is caused mainly by the mixing of different pollutants with water in the air

• Acid precipitation can damage life in lakes and streams as well as on land

Moreacidic

0

AcidrainAcidrain

Normalrain

Morebasic

123456789

1011121314

• The internal pH of most living cells must remain close to pH 7

• Buffers are substances that minimize changes in concentrations of H+ and OH– in a solution

• Most buffers consist of an acid-base pair that reversibly combines with H+

• A buffer solution contains a weak acid and its conjugate base

HA + H2O H3O+ + A−

• When an acid is added to the solution, the dissociated H+ is consumed to drive the equilibrium backwards

• When a base is added, the loss of H+ drives the equilibrium forward

• Thus, the pH changes less than it would if the acid or base had been added to a solution of pure water

CARBON

• Although cells are 70–95% water, the rest consists mostly of carbon-based compounds

• Carbon is unparalleled in its ability to form large, complex, and diverse molecules

• Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds

• Although cells are 70–95% water, the rest consists mostly of carbon-based compounds

• Carbon is unparalleled in its ability to form large, complex, and diverse molecules

• Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds

• Organic chemistry is the study of compounds that contain carbon

• Organic compounds range from simple molecules to colossal ones

• Most organic compounds contain hydrogen atoms in addition to carbon atoms

• Vitalism, the idea that organic compounds arise only in living organisms, was disproved when chemists synthesized these compounds in the laboratory from non-living substances

• Mechanism is the view that all natural phenomena (including life) are governed by the same physical and chemical laws

Water vapor

H2NH

3

“Atmosphere”

Electrode

Condenser

Coldwater

Cooled watercontainingorganicmolecules

Sample forchemical analysis

H2O“sea”

CH4

• With four valence electrons, carbon can form four covalent bonds with a variety of atoms

• This tetravalence makes large, complex molecules possible

• In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape

• However, when two carbon atoms are joined by a double bond, the molecule has a flat shape

NameMolecula

r Formula

Structural

Formula

Ball-and-StickModel

Space-FillingModel(a)

Methane

(b) Ethane

(c) Ethene (ethylene)

• The electron configuration of carbon gives it covalent compatibility with many different elements

• The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the “building code” that governs the architecture of living molecules

• Carbon chains form the skeletons of most organic molecules

• Carbon chains vary in length and shape

Ethane Propane1-Butene 2-Butene

(c) Double bonds

(d) RingsCyclohexane Benzene

Butane 2-Methylpropane(commonly called isobutane)

(b) Branching

(a) Length

• Hydrocarbons are organic molecules consisting of only carbon and hydrogen

• Many organic molecules, such as fats, have hydrocarbon components

• Hydrocarbons require a lot of energy (from sunlight) to make and therefore also store a lot of potential energy

(a) Mammalian adipose cells

(b) A fat molecule

Fat droplets (stained red)

100 µm

• Isomers are compounds with the same molecular formula but different structures and properties:– Structural isomers have different covalent

arrangements of their atoms– Geometric isomers have the same

covalent arrangements but differ in spatial arrangements

– Enantiomers are isomers that are mirror images of each other

(a) Structural isomers

2-methyl butanePentane

(b) Geometric isomers

cis isomer: The two Xs areon the same side.

trans isomer: The two Xs areon opposite sides.

(c) Enantiomers

L isomer D isomer

• Enantiomers are important in the pharmaceutical industry

• Two enantiomers of a drug may have different effects

• Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules

Drug

Ibuprofen

Albuterol

Condition

Pain;inflammatio

n

Asthma

EffectiveEnantiomer

S-Ibuprofen

R-Albuterol

R-Ibuprofen

S-Albuterol

IneffectiveEnantiomer

• Distinctive properties of organic molecules depend not only on the carbon skeleton but also on the molecular components attached to it

• A small number of characteristic groups, or functional groups, are often attached to skeletons of organic molecules

• The seven 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

Hydroxyl

CHEMICALGROUP

STRUCTURE

NAME OF COMPOUND

EXAMPLE

FUNCTIONALPROPERTIES

Carbonyl

Carboxyl

(may be written HO—)

In a hydroxyl group (—OH), ahydrogen atom is bonded to anoxygen atom, which in turn isbonded to the carbon skeleton ofthe organic molecule. (Do notconfuse this functional groupwith the hydroxide ion, OH–.)

When an oxygen atom isdouble-bonded to a carbonatom that is also bonded toan —OH group, the entireassembly of atoms is calleda carboxyl group (—COOH).Carboxylic acids, or organicacids

Ketones if the carbonyl group iswithin a carbon skeletonAldehydes if the carbonyl groupis at the end of the carbonskeleton

Alcohols (their specific namesusually end in -ol)

Ethanol, the alcohol present inalcoholic beverages

Acetone, the simplest ketone

Acetic acid, which gives vinegarits sour taste

Propanal, an aldehyde

Has acidic propertiesbecause the covalent bondbetween oxygen and hydrogenis so polar; for example,

Found in cells in the ionizedform with a charge of 1– andcalled a carboxylate ion (here,specifically, the acetate ion).

Acetic acid Acetate ion

A ketone and an aldehyde maybe structural isomers withdifferent properties, as is thecase for acetone and propanal.These two groups are alsofound in sugars, giving rise totwo major groups of sugars:aldoses (containing analdehyde) and ketoses(containing a ketone).

Is polar as a result of theelectrons spending more timenear the electronegative oxygen atom.Can form hydrogen bonds withwater molecules, helpingdissolve organic compoundssuch as sugars.

The carbonyl group ( CO)consists of a carbon atomjoined to an oxygen atom by adouble bond.

CHEMICALGROUP

STRUCTURE

NAME OFCOMPOUND

EXAMPLE

FUNCTIONALPROPERTIES

Amino Sulfhydryl Phosphate Methyl

A methyl group consists of acarbon bonded to threehydrogen atoms. The methylgroup may be attached to acarbon or to a different atom.

In a phosphate group, aphosphorus atom is bonded tofour oxygen atoms; one oxygenis bonded to the carbon skeleton;two oxygens carry negativecharges. The phosphate group(—OPO3

2–, abbreviated ) is anionized form of a phosphoric acidgroup (—OPO3H2; note the twohydrogens).

P

The sulfhydryl groupconsists of a sulfur atombonded to an atom ofhydrogen; resembles ahydroxyl group in shape.

(may bewritten HS—)

The amino group(—NH2) consists of anitrogen atom bondedto two hydrogen atomsand to the carbon skeleton.

Amines Thiols Organic phosphates Methylated compounds

5-Methyl cytidine

5-Methyl cytidine is acomponent of DNA that hasbeen modified by addition ofthe methyl group.

In addition to taking part inmany important chemicalreactions in cells, glycerolphosphate provides thebackbone for phospholipids,the most prevalent molecules incell membranes.

Glycerol phosphate

Cysteine

Cysteine is an importantsulfur-containing aminoacid.

Glycine

Because it also has acarboxyl group, glycineis both an amine anda carboxylic acid;compounds with bothgroups are called amino acids.

Addition of a methyl groupto DNA, or to moleculesbound to DNA, affectsexpression of genes.Arrangement of methylgroups in male and femalesex hormones affectstheir shape and function.

Contributes negative chargeto the molecule of which it isa part (2– when at the end ofa molecule; 1– when locatedinternally in a chain ofphosphates).

Has the potential to reactwith water, releasing energy.

Two sulfhydryl groupscan react, forming acovalent bond. This“cross-linking” helpsstabilize proteinstructure.Cross-linking ofcysteines in hairproteins maintains thecurliness or straightnessof hair. Straight hair canbe “permanently” curledby shaping it aroundcurlers, then breakingand re-forming thecross-linking bonds.

Acts as a base; canpick up an H+ fromthe surroundingsolution (water, in living organisms).

Ionized, with acharge of 1+, undercellular conditions.

(nonionized) (ionized)

• One phosphate molecule, adenosine triphosphate (ATP), is the primary energy-transferring molecule in the cell

• ATP consists of an organic molecule

called adenosine attached to a string of three phosphate groups

Adenosine

P P P P i P PAdenosine

Adenosine

ADP

ATP Inorganic phosphate

Reacts with H2O

+

ENERGY!