LECTURE - 2

Water & Carbon

Quiz Answers

The Carboxyl functional group:

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Epigenetics: The structural adaptation of chromosomal regions so as to register, signal or perpetuate altered activity states.

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Outline

Water Structure Important properties

Carbon Structure Important properties Functional Groups

Water

The molecule that supports all life (as we know it)

• It is the biological medium on Earth• 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

Water is a polar molecule

Polar covalent bonds allow for extensive hydrogen bonding Polar – the opposite ends have opposite

charges

Four Important Properties of Water

1. Cohesive behavior2. Ability to moderate temperature3. Expansion upon freezing4. Versatility as a solvent

#1 - Cohesion

Cohesion Hydrogen bonds hold water molecules

together Adhesion

An attraction between different substances

Water molecules bind together to form the water column (cohesion)

They also bind to the cell walls to help resist gravity (adhesion)

Example of Cohesion & Adhesion

#1 - Cohesion

Surface tension Related to cohesion A measure of how hard it is to break the

surface of a liquid

#2 – Moderation of Temperature Kinetic energy is the energy of motion Heat = the total amount of kinetic

energy due to molecular motion Temperature measures the intensity of

heat due to the average kinetic energy of molecules

#2 – Moderation of Temperature Measuring temperature

Celsius scale to indicated temperature 0 degrees Celsius is freezing, 100 degrees is

boiling Room Temp is about 20 - 25 degrees Why would most biochemical experiments be

run at 37 degrees? Calorie

The amount of heat it takes to raise the temperature of 1g of water by 1 degree celcius

#2 – Moderation of Temperature Specific Heat - The amount of heat that

must be absorbed or lost for 1g of substance to change its temperature 1 degree C.

Water has a high specific heat.

#2 – Moderation of Temperature Water has a High Specific Heat

allows it to minimize temperature fluctuations

Heat is absorbed when hydrogen bonds break Example: Liquid water steam

Heat is released when hydrogen bonds form Water vapor in clouds raindrops Formation of raindrops or ice actually raises the

surrounding air temperature by a slight amount!

#2 - Moderation of Temperature Oceans stabilize the temperature of the

air. 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

#2 – Moderation of Temperature Oceans can absorb heat during the day

and release it back at night while the ocean temp remains relatively constant.

Santa Barbara 73°

Los Angeles(Airport) 75°

Pacific Ocean 68°

Santa Ana 84°

Burbank90°

San Bernardino100°

Palm Springs106°

Riverside 96°

San Diego 72° 40 miles

70s (°F)80s90s100s

#2 – Moderation of Temperature Evaporation is transformation of a

substance from liquid to gas Heat of vaporization

The heat a liquid must absorb for 1 g to be converted to gas – water has a high heat of vaporization

As a liquid evaporates, its remaining surface cools, a process called evaporative cooling

Evaporative cooling of water helps stabilize temperatures in organisms and bodies of water

# 3 – Expansion Upon Freezing Ice Floats on Water

As H-bonds stabilize, the resulting crystal becomes less dense.

H-bonds are breaking and re-forming in liquid water, therefore there are more molecules per volume

#3 – Expansion Upon Freezing

Hydrogen bond

Ice:Hydrogen bonds

are stable

Liquid water:Hydrogen bonds

break and re-form

#3 – Expansion Upon Freezing Major benefit of Ice floating on water –

Insulation Insulates living organisms under ice pack in

lakes and frozen seas. Snow insulates seeds and roots under

ground in winter.

#4 – Solvent Properties

Water is a versatile solvent due to its polarity It can easily for hydrogen bonds with other

molecules including ionic compoundsFigure 3.7

Cl Cl

Na

Na

#4 – Solvent Properties

Large molecules such as proteins can dissolve in water if they have ionic and polar regionsFigure 3.8

+

+

#4 – Solvent Properties

Hydrophilic - substance that has an affinity for water.

Hydrophobic – substance that does not have an affinity for water.

Some molecules are both.

#4 – Solvent Properties

Water can disassociate into hydronium and hydroxide ions

2 H2O Hydroxideion (OH)

Hydroniumion (H3O

+)

+

#4 Solvent Properties: Acids & Bases

The dissociation of water molecules has a great effect on organisms

Changes in concentrations of H+ and OH– can drastically affect the chemistry of a cell

#4 Solvent Properties: Acids & Bases

Acid – donates a proton Increases the number of Hydronium Ions in

an aqueous solution Base –

Accepts a proton Reduces the number of Hydronium Ions in

an aqueous solution

#4 – Solvent Properties: The pH scale

pH is a measure of the relative concentration of protons. 0 < pH < 7 is an Acid ([H30+] > 10-7M) 7 < pH < 14 is a Base ([H30+] < 10-7M) pH 7 is neutral ([H30+] = [OH-] = 10-7M)

Figure 3.10pH Scale

Battery acid

Gastric juice, lemon juice

Vinegar, wine,cola

BeerTomato juice

Black coffee

Rainwater

Urine

SalivaPure waterHuman blood, tears

Seawater

Inside of small intestine

Milk of magnesia

Household ammonia

Householdbleach

Oven cleaner

Basicsolution

Neutralsolution

Acidicsolution

0

1

2

3

4

5

6

7

8

9

10

Neutral

[H+] = [OH]In

cre

asin

gly

Basic

[H+]

< [

OH

]

Incre

asin

gly

Acid

ic

[H+]

> [

OH

]

H+ H+

H+

H+H+

H+

H+

H+

OH

OH

H+

OH

H+

OH

OH

OHOH

H+H+

H+

H+

OHOH

OH

OH OHOH

OHH+

11

12

13

14

#4 – Solvent Properties: Buffers

Buffers are substances that minimize changes in concentrations of H+ and OH– in a solution. They resist a change in pH when a small

amount of acid or base is added to a solution.

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

Buffers work within a specific pH range.

#4 – Solvent Properties: Buffers Carbonic Acid – contributes to pH

stability in blood and other biological solutions.

H2CO3 is formed when CO2 reacts with water.

Carbon

Carbon

The backbone of life Living organisms consist

mostly of carbon-based compounds.

Really good at forming large, complex, and diverse molecules.

Proteins, DNA, carbohydrates, and other molecules - all composed of carbon compounds.

Carbon

Electron configuration determines the kinds and number of bonds an atom will form with other atoms

Four valence electrons – Four covalent

Allows for the formation of large, complex molecules possible

Figure 4.3

Name andComment

MolecularFormula

(a) Methane

(b) Ethane

CH4

Ball-and-Stick Model

Space-FillingModel

(c) Ethene (ethylene)

C2H6

C2H4

StructuralFormula

Carbon bonds determine molecular shape

Diversity of carbon molecules Carbon chains form the skeletons of most organic

molecules Carbon chains vary in length and shapeFigure 4.5

(a) Length

Ethane 1-Butene

(c) Double bond position

2-ButenePropane

(b) Branching (d) Presence of rings

Butane 2-Methylpropane(isobutane)

Cyclohexane Benzene

Valence Electrons

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

Figure 4.4

Hydrogen(valence 1)

Oxygen(valence 2)

Nitrogen(valence 3)

Carbon(valence 4)

Isomers

Compounds with the same molecular formula but different structures and properties

Structural isomers have different covalent arrangements of their atoms (constitutional)

Cis-trans isomers have the same covalent bonds but differ in spatial arrangements

Enantiomers are isomers that are mirror images of each other (they are chiral)

Isomers – Three typesFigure 4.7 (a) Structural isomers

(b) Cis-trans isomers

(c) Enantiomers

cis isomer: The two Xsare on the same side.

trans isomer: The two Xsare on opposite sides.

CO2HCO2H

CH3

H NH2

L isomer

NH2

CH3

H

D isomer

Isomers - EnatomersFigure 4.8

Drug

Ibuprofen

Albuterol

Condition EffectiveEnantiomer

IneffectiveEnantiomer

Pain;inflammation

Asthma

S-Ibuprofen R-Ibuprofen

R-Albuterol S-Albuterol

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Functional Groups

The components of organic molecules that are most commonly involved in chemical reactions

The number and arrangement of functional groups give each molecule its unique properties

The importance of functional groups

CH3

OH

HO

O

CH3

CH3

OH

Estradiol

Testosterone

Female lion

Male lion

7 most biologically important functional groups

Figure 4.9a

STRUCTURE

EXAMPLE

Alcohols(Their specificnames usuallyend in -ol.)

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

(may be written HO—)

Ethanol

• Is polar as a resultof the electronsspending moretime near theelectronegativeoxygen atom.

• Can form hydrogenbonds with watermolecules, helpingdissolve organiccompounds suchas sugars.

Hydroxyl

Figure 4.9b

Carbonyl

STRUCTURE

EXAMPLE

Ketones if the carbonylgroup is within acarbon skeleton

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

Aldehydes if the carbonylgroup is at the end of thecarbon skeleton

• A ketone and analdehyde may bestructural isomerswith different properties,as is the case foracetone and propanal.

Acetone

Propanal

• Ketone and aldehydegroups are also foundin sugars, giving riseto two major groupsof sugars: ketoses(containing ketonegroups) and aldoses(containing aldehydegroups).

Carboxyl

STRUCTURE

EXAMPLE

Carboxylic acids, or organicacids

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

Acetic acid

Polar; can form H-bonds

Weak acids; reversible dissociation in H2O

• Found in cells in the ionizedform with a charge of 1– andcalled a carboxylate ion.

Nonionized Ionized

Figure 4.9c

Amino

Amines

Glycine

STRUCTURE

EXAMPLE • Acts as a base; canpick up an H+ from thesurrounding solution(water, in livingorganisms):

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

• Found in cells in theionized form with acharge of 1.

Nonionized Ionized

Figure 4.9d

Sulfhydryl

Thiols

(may bewritten HS—)

STRUCTURE

EXAMPLE • Two sulfhydryl groups canreact, forming a covalentbond. This “cross-linking”helps stabilize proteinstructure.

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

• Cross-linking of cysteinesin hair proteins maintainsthe curliness or straightnessof hair. Straight hair can be“permanently” curled byshaping it around curlersand then breaking andre-forming the cross-linkingbonds.

Cysteine

Figure 4.9e

Figure 4.9f

Phosphate

STRUCTURE

EXAMPLE

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

Organic phosphates

Glycerol phosphate

• Contributes negativecharge to the moleculeof which it is a part(2– when at the end ofa molecule, as at left;1– when locatedinternally in a chain ofphosphates).

• Molecules containingphosphate groups havethe potential to reactwith water, releasingenergy.

Figure 4.9g

Methyl

STRUCTURE

EXAMPLE

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

Methylated compounds

5-Methyl cytidine

• Addition of a methyl groupto DNA, or to moleculesbound to DNA, affects theexpression of genes.

• Arrangement of methylgroups in male and femalesex hormones affects theirshape and function.