ap biology 2007-2008 the chemistry of life ap biology fig. 2-1

AP Biology 2007-2008

The Chemistry of Life

AP Biology

Fig. 2-1

AP Biology

Fig. 2-2EXPERIMENT

RESULTS

Cedrelasapling

Duroiatree Inside,

unprotected Inside,protected

Devil’sgarden

Outside,unprotected

Outside,protected

Insectbarrier

Dea

d le

af t

issu

e (c

m2)

afte

r o

ne

day

Inside,unprotected

Inside,protected

Outside,unprotected

Outside,protected

Cedrela saplings, inside and outside devil’s gardens

0

4

8

12

16

AP Biology

Fig. 2-2a

Cedrelasapling

Duroiatree Inside,

unprotected

Devil’sgarden

Inside,protected

Insectbarrier

Outside,unprotected

Outside,protected

EXPERIMENT

AP Biology

Fig. 2-2b

Dea

d le

af t

issu

e (c

m2 )

afte

r o

ne

day

16

12

8

4

0Inside,

unprotectedInside,

protectedOutside,

unprotectedOutside,protected

Cedrela saplings, inside and outside devil’s gardens

RESULTS

AP Biology

Why are we studying chemistry?Chemistry is the foundation of Biology

AP BiologyProton Neutron Electron

Hydrogen1 proton1 electron

Oxygen8 protons8 neutrons8 electrons

+ 0 –

Everything is made of matter Matter is made of atoms

AP Biology

Elements and Compounds

Matter is made up of elements An element is a substance that cannot

be broken down to other substances by chemical reactions

A compound is a substance consisting of two or more elements in a fixed ratio

A compound has characteristics different from those of its elements

Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

AP Biology

Fig. 2-3

Sodium Chlorine Sodiumchloride

How does Sodium Chloride have emergent properties?

AP Biology

The World of Elements

C

Different kinds of atoms = elementsDifferent kinds of atoms = elements

H

ON

P SNa

K

Mg

Ca

AP Biology

Life requires ~25 chemical elements

About 25 elements are essential for life Four elements make up 96% of living

matter:

• _Carbon__ • _Hydrogen___

• _Nitrogen___ • _Oxygen_____

Four elements make up most of remaining 4%:

• phosphorus (P) • calcium (Ca)

• sulfur (S) • potassium (K)

AP Biology

Fig. 2-4a

(a) Nitrogen deficiency

AP Biology

Fig. 2-4b

(b) Iodine deficiency

AP Biology

Concept Check Is a trace element an essential

element? Iron (Fe) is a trace element required for

the proper functioning of hemoglobin, the molecule that carries oxygen in red blood cells. What might be the effects of an iron deficiency?

AP Biology

Bonding properties

Effect of electrons electrons determine

chemical behavior of atom

depends on numberof electrons in atom’s outermost shell valence shell

How does this atom behave?How does this atom behave?

AP Biology

Bonding properties

Effect of electrons chemical behavior of an atom depends on

number of electrons in its valence shell

What’s themagic number?

How does this atom behave?How does this atom behave? How does this atom behave?How does this atom behave?

AP Biology

Elements & their valence shells

Elements in the same row have the same number of shellsElements in the same row have the same number of shells

Moving from left to right, each element has a sequential addition of electrons (& protons)Moving from left to right, each element has a sequential addition of electrons (& protons)

AP Biology

Elements & their valence shells

Elements in the same column have the same valence & similar chemical properties

Elements in the same column have the same valence & similar chemical properties

Remembersome food chains

are built on reducing O to H2O

& some on reducing S to H2S

AP Biology

Concept Check A nitrogen atom has 7 protons, and the most common

isotope of nitrogen has 7 neutrons. A radioactive isotope of nitrogen has 8 neutrons. Write the atomic number and mass number of this radioactive nitrogen.

A lithium atom has 3 protons and 4 neutrons. What is its atomic mass in daltons?

How many electrons does fluorine have? How many electron shells? Name the orbitals that are occupied. How many electorns are needed to fill the valence shell?

AP Biology

–

–

–

Chemical reactivity Atoms tend to

complete a partially filled valence shell

or empty a partially filled valence shell

This tendency drives chemical reactions…This tendency drives chemical reactions…

and creates bondsand creates bonds

AP Biology

–

–

H2 (hydrogen gas)

Covalent bond

BONDS IN BIOLOGYCovalent bonds

sharing electrons

Ionic bondscation and anion (forms salts)

Hydrogen bondshydrogen is attracted to negative charge on

another already bonded atom

Van der Waals interactions

weak attractions occur when 2

atoms are close together and

have charge fluctuations

Hydrogen bond

H2O

H2O

AP Biology

Covalent bonds Why are covalent bonds strong bonds?

two atoms share a pair of electrons both atoms holding onto the electrons very stable

Forms molecules

–

–

H2 (hydrogen gas)H2 (hydrogen gas)

H — H

H2O (water)H2O (water)

H

H

OxygenH

HO

AP Biology

Multiple covalent bonds 2 atoms can share >1 pair of electrons

double bonds 2 pairs of electrons

triple bonds 3 pairs of electrons

Molecular shape

H

H–C–H

H

––

More isbetter!

AP Biology

Nonpolar covalent bond Electrons are shared equally

example: hydrocarbons = CxHx

methane (CH4 )

balanced, stable,good building block

AP Biology

H

H

Oxygen

Polar covalent bonds Electron stays closer to

more electronegative atom.

Example: water = H2O oxygen has stronger

“attraction” for the electrons than hydrogen

oxygen has higher electronegativity

Polarity_______ + vs – poles leads to many interesting

properties of water…

+

+

––

––

AP Biology

Hydrogen bonding Polar water creates molecular attractions

_Between the O and the H of adjacent water molecules.

also can occur wherever an -OH exists in a larger molecule

Let’s go to the videotape!

HO

H

AP Biology

Isotopes

All atoms of an element have the same number of protons but may differ in number of neutrons

Isotopes are two atoms of an element that differ in number of neutrons

Radioactive isotopes decay spontaneously, giving off particles and energy


AP Biology

Some applications of radioactive isotopes in biological research are: Dating fossils Tracing atoms through metabolic processes Diagnosing medical disorders


AP Biology

Fig. 2-6TECHNIQUE

RESULTS

Compounds includingradioactive tracer(bright blue)

Incubators

1 2 3

4 5 6

7 8 9

10°C 15°C 20°C

25°C 30°C 35°C

40°C 45°C 50°C

1

2

3

Human cells

Humancells areincubatedwith compounds used tomake DNA. One compound is

labeled with 3H.

The cells areplaced in testtubes; their DNA isisolated; andunused labeledcompounds areremoved.

DNA (old and new)

The test tubes are placed in a scintillation counter.

Co

un

ts p

er m

inu

te(

1,0

00)

Optimumtemperaturefor DNAsynthesis

Temperature (ºC)

0

10

10

20

20

30

30 40 50

AP Biology

Fig. 2-6a

Compounds includingradioactive tracer(bright blue)

Human cells

Incubators1 2 3

4 5 6

7 8 950ºC45ºC40ºC

25ºC 30ºC 35ºC

15ºC 20ºC10ºC

Humancells areincubatedwith compounds used tomake DNA. One compound islabeled with 3H.

1

2 The cells areplaced in testtubes; their DNA isisolated; andunused labeledcompounds areremoved.

DNA (old and new)

TECHNIQUE

AP Biology

Fig. 2-6b

TECHNIQUE

The test tubes are placed in a scintillation counter.3

AP Biology

Fig. 2-6c

RESULTSC

ou

nts

per

min

ute

( 1

,000

)

010 20 30 40 50

10

20

30

Temperature (ºC)

Optimumtemperaturefor DNAsynthesis

AP Biology

Fig. 2-7

Cancerousthroattissue

AP Biology

Van der Waals Interactions

If electrons are distributed asymmetrically in molecules or atoms, they can result in “hot spots” of positive or negative charge

Van der Waals interactions are attractions between molecules that are close together as a result of these charges


AP Biology

Collectively, such interactions can be strong, as between molecules of a gecko’s toe hairs and a wall surface


AP Biology

Molecular Shape and Function

A molecule’s shape is usually very important to 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


AP Biology

Biological molecules recognize and interact with each other with a specificity based on molecular shape

Molecules with similar shapes can have similar biological effects


AP Biology

Fig. 2-18

(a) Structures of endorphin and morphine

(b) Binding to endorphin receptors

Naturalendorphin

Endorphinreceptors

Morphine

Brain cell

Morphine

Natural endorphin

KeyCarbonHydrogen

NitrogenSulfurOxygen

AP Biology

Fig. 2-18b

Naturalendorphin

EndorphinreceptorsBrain cell

Binding to endorphin receptors

Morphine

(b)

AP Biology

Concept Check Explain what hold together the atoms in

a crystal of magnesium chloride (MgCl2).

If you were a pharmaceutical researcher, shy would you want to learn the three-dimensional shapes of naturally occurring signal molecules?

AP Biology 2007-2008

Chemistry of Life

Properties of Water

AP Biology

More about Water

Why are we studying water?Why are we studying water?

All life occurs in water inside & outside the cell

All life occurs in water inside & outside the cell

AP Biology

Chemistry of water H2O molecules form H-bonds

with each other +H attracted to –O creates a

sticky molecule

AP Biology

Concept Check What is electronegativity and how does

it affect interactions between water molecules?

What would be the effect on the properties of the water molecule if oxygen and hydrogen had equal electronegativity?

AP Biology

Elixir of Life Special properties of water

1. _Cohesion_______________ surface tension, capillary action

2. _The solvent of life ____ many molecules dissolve in H2O hydrophilic_ vs. _hydrophobic__

3. _Expansion upon freezing_____ ice floats!

4. Moderation of temperature________ water stores heat

5. _High specific heat_________ heats & cools slowly

Ice! I could use more ice!

AP Biology

1. Cohesion & Adhesion

Try that with flour…or sugar…

_Cohesion_______________ H bonding between H2O molecules water is “sticky”

surface tension drinking straw

_Adhesion________________ H bonding between H2O & other substances

capillary action meniscus water climbs up

paper towel or cloth

AP Biology

How does H2O get to top of trees?Transpiration is built on cohesion & adhesion

Let’s go to the videotape!

AP Biology

Fig. 3-3

Water-conductingcells

Adhesion

Cohesion

150 µm

Directionof watermovement

AP Biology

2. Water is the solvent of life ____________________________________

polar H2O molecules surround + & – ions solvents dissolve solutes creating solutions

AP Biology

Fig. 3-7

Cl–

Na

Cl–

+

+

+

+

+

+

++

––

–

–

–

–

––

Na+

–

––

+

AP Biology

What dissolves in water? _Hydrophilic______________

substances have attraction to H2Opolar or non-polar?

AP Biology

What doesn’t dissolve in water? _hydrophobic__________

substances that don’t have an attraction to H2O

polar or non-polar?

fat (triglycerol)

Oh, lookhydrocarbons!

AP Biology

3. The special case of ice Most (all?) substances are more dense

when they are solid, but

not water… _Water expands!

H bonds form a crystal

And this hasmade all the difference!

AP Biology

Ice floats

AP Biology

Why is “ice floats” important? Oceans & lakes don’t freeze solid

The ice acts to insulate the water below. allowing life to survive the winter

if ice sank… ponds, lakes & even oceans would freeze solid in summer, only upper few inches would thaw

Floating ice prevents the water below from freezing. ______________________________________

AP Biology

Fig. 3-6

Hydrogenbond

Liquid waterHydrogen bonds break and re-form

IceHydrogen bonds are stable

AP Biology

4. Specific heat Amount of heat to increase T of 1g by 1°C.

high specific heat takes a lot to heat it up takes a lot to cool it down

H2O moderates temperatures on Earth

AP Biology

Specific heat& climate

AP Biology

5. Heat of vaporizationEvaporative cooling

Organisms rely on heat of vaporization to remove body heat

AP Biology

Concept Check Describe how properties of water contribute to the upward

movement of water in a tree.

Explain the saying, “It’s not the heat, it’s the humidity.”

What if a water strider’s legs are coated with a hydrophobic substance. What might be the benefit? What would happen if the substance were hydrophilic?

AP Biology

Ionization of water & pH Water ionizes

H+ splits off from H2O, leaving OH–

if [H+] = [-OH], water is neutral if [H+] > [-OH], water is acidic if [H+] < [-OH], water is basic

pH scalehow acid or basic solution is1 7 14

H2O H+ + OH–H2O H+ + OH–

AP Biology

pH Scale10–1

H+ IonConcentration

Examples of Solutions

Stomach acid, Lemon juice

1

pH100 Hydrochloric acid0

10–2 2

10–3 Vinegar, cola, beer3

10–4 Tomatoes4

10–5 Black coffee, Rainwater5

10–6 Urine, Saliva6

10–7 Pure water, Blood7

10–8 Seawater8

10–9 Baking soda9

10–10 Great Salt Lake10

10–11 Household ammonia11

10–12 Household bleach12

10–13 Oven cleaner13

10–14 Sodium hydroxide14

tenfold changein H+ ions

pH1 pH210-1 10-2

________________

pH8 pH710-8 10-7

________________

pH10 pH810-10 10-8

________________

AP Biology 1001

2

3

4

5

6

7

8

9

3Amount of base added

Bufferingrange

4 52

pH

Buffers & cellular regulation pH of cells must be kept ~7

pH affects shape of molecules shape of molecules affect function pH affects cellular function

______________________ reservoir of H+

donate H+ when [H+] falls

absorb H+ when [H+] rises

AP Biology

Threats to Water Quality on Earth 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 and can fall at some distance from the source of pollutants

Acid precipitation can damage life in lakes and streams

Effects of acid precipitation on soil chemistry are contributing to the decline of some forests

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

AP Biology

Fig. 3-10

Moreacidic

0

AcidrainAcidrain

Normalrain

Morebasic

123456789

1011121314

AP Biology

Human activities such as burning fossil fuels threaten water quality

CO2 is released by fossil fuel combustion and contributes to: A warming of earth called the “greenhouse”

effect Acidification of the oceans; this leads to a

decrease in the ability of corals to form calcified reefs

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

AP Biology

Fig. 3-11

EXPERIMENT

RESULTS

Cal

cif

icat

ion

rat

e(m

mo

l C

aCO

3

per

m2 p

er d

ay)

[CO32–] (µmol/kg)

150 200 250 3000

20

40

AP Biology

Surface tension lab

AP Biology

Fig. 3-UN6

Surface of EarthSurface of Mars

ap biology 2007-2008 the chemistry of life ap biology fig. 2-1

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