Chemistry of life

AP Biology 2007-2008

The Chemistry of Life

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

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The World of Elements

C

Different kinds of atoms = elements

H

ON

P SNa

K

Mg

Ca

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Life requires ~25 chemical elements

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

matter:

• carbon (C) • hydrogen (H)

• oxygen (O) • nitrogen (N) Four elements make up most of

remaining 4%:

• phosphorus (P) • calcium (Ca)

• sulfur (S) • potassium (K)

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Bonding properties

Effect of electrons electrons determine

chemical behavior of atom

depends on numberof electrons in atom’s outermost shellvalence shell

How does this atom behave?

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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?

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Elements & their valence shells

Elements in the same row have the same number of shells

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

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Elements & their valence shells

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

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–

–

–

Chemical reactivity Atoms tend to

complete a partially filled valence shell

or empty a partially filled valence shell

This tendency drives chemical reactions…

and creates bonds

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–

–

H2 (hydrogen gas)

Covalent bond

Bonds in Biology Weak bonds

hydrogen bonds attraction between + and –

hydrophobic & hydrophilic interactions interaction with H2O

van der Waals forces (ionic)

Strong bonds covalent bonds

Hydrogen bond

H2O

H2O

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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)

H — H

H2O (water)

H

H

OxygenH

HO

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

double bonds 2 pairs of electrons

triple bonds 3 pairs of electrons

Very strong bonds

H

H–C–H

H

––

More isbetter!

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Nonpolar covalent bond Pair of electrons shared equally by 2 atoms

example: hydrocarbons = CxHx

methane (CH4 )

balanced, stable,good building

block

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H

H

Oxygen

Polar covalent bonds Pair of electrons shared

unequally by 2 atoms example: water = H2O

oxygen has stronger “attraction” for the electrons than hydrogen

oxygen has higher electronegativity

water is a polar molecule + vs – poles leads to many interesting

properties of water…

+

+

––

––

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Hydrogen bonding Polar water creates molecular attractions

attraction between positive H in one H2O molecule to negative O in another H2O

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

Weak bond

Let’s go to the videotape!

HO

H


Properties of Water

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More about Water

Why are we studying water?

All life occurs in water inside & outside the cell

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Chemistry of water H2O molecules form H-bonds

with each other +H attracted to –O creates a

sticky molecule

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Elixir of Life Special properties of water

1. cohesion & adhesion surface tension, capillary action

2. good solvent many molecules dissolve in H2O hydrophilic vs. hydrophobic

3. lower density as a solid ice floats!

4. high specific heat water stores heat

5. high heat of vaporization heats & cools slowly

Ice! I could use more ice!

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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

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

Let’s go to the videotape!

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2. Water is the solvent of life Polarity makes H2O a good solvent

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

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What dissolves in water? Hydrophilic

substances have attraction to H2Opolar or non-polar?

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What doesn’t dissolve in water? Hydrophobic

substances that don’t have an attraction to H2O

polar or non-polar?

fat (triglycerol)

Oh, lookhydrocarbons!

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

when they are solid, but

not water… Ice floats!

H bonds form a crystal

And this hasmade all the difference!

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Ice floats

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

surface ice insulates 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

seasonal turnover of lakes sinking cold H2O cycles nutrients in autumn

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4. Specific heat H2O resists changes in temperature

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

H2O moderates temperatures on Earth

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Specific heat& climate

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5. Heat of vaporizationEvaporative cooling

Organisms rely on heat of vaporization to remove body heat

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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–

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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

10 times less H+

pH8 pH710-8 10-7

10 times more H+

pH10 pH810-10 10-8

100 times more H+

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

Control pH by buffers reservoir of H+

donate H+ when [H+] falls

absorb H+ when [H+] rises


He’s gonnaearn a

Darwin Award!

Do one brave thing today…then run like hell!

AnyQuestions?


Chemistry of Life

Building Blocks of Life

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Macromolecules Smaller organic molecules join together

to form larger molecules macromolecules

4 major classes of macromolecules: carbohydrates lipids proteins nucleic acids

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Why study Carbon? All of life is built on carbon Cells

~72% H2O ~25% carbon compounds

carbohydrates lipids proteins nucleic acids

~3% salts Na, Cl, K…

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Chemistry of Life Organic chemistry is the study of

carbon compounds C atoms are versatile building blocks

bonding properties 4 stable covalent bonds

HHC

H

H

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Complex molecules assembled like TinkerToys

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Hydrocarbons Combinations of C & H

non-polar not soluble in H2O hydrophobic

stablevery little attraction

between molecules a gas at room temperature

methane(simplest HC)

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Hydrocarbons can grow

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Isomers Molecules with same molecular formula

but different structures (shapes) different chemical properties different biological functions

6 carbons

6 carbons

6 carbons

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Form affects function Structural differences create important

functional significance amino acid alanine

L-alanine used in proteins but not D-alanine

medicines L-version active but not D-version

sometimes withtragic results…

stereoisomers

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Form affects function Thalidomide

prescribed to pregnant women in 50s & 60s reduced morning sickness, but… stereoisomer caused severe birth defects

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Diversity of molecules

Substitute other atoms or groups around the carbon ethane vs. ethanol

H replaced by an hydroxyl group (–OH) nonpolar vs. polar gas vs. liquid biological effects!

ethane (C2H6) ethanol (C2H5OH)

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Functional groups Parts of organic molecules that are

involved in chemical reactions give organic molecules distinctive

properties hydroxyl amino

carbonyl sulfhydryl

carboxyl phosphate

Affect reactivity makes hydrocarbons hydrophilic increase solubility in water

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Viva la difference! Basic structure of male & female

hormones is identical identical carbon skeleton attachment of different functional groups interact with different targets in the body

different effects

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H2O

HO

HO H

H HHO

Polymers Long molecules built by linking repeating

building blocks in a chain monomers

building blocks repeated small units

covalent bonds

Dehydration synthesis

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H2O

HO

HO H

H HHO

How to build a polymer Anabolism

joins monomers by “taking” H2O out one monomer donates OH–

other monomer donates H+ together these form H2O

requires energy & enzymes

enzymeDehydration synthesis

Condensation reaction

You gotta be open to“bonding!

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H2O

HO H

HO H HO H

How to break down a polymer

Catabolism use H2O to breakdown polymers

reverse of dehydration synthesis cleave off one monomer at a time

H2O is split into H+ and OH–

H+ & OH– attach to ends requires enzymes releases energy

Breaking upis…easy to do!

Hydrolysis

Digestion

enzyme


Any Questions??

Chemistry of life

Education

Transcript of Chemistry of life