The Chemistry of Life

AP Biology 2007-2008

Chemistry of Life

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

AP Biology

Hydrogen1 proton1 electron

� Everything is made of matter� Matter is made of atoms

AP BiologyProton Neutron Electron

Oxygen8 protons8 neutrons8 electrons

+ 0 –

The World of Elements

C

H

ON

P SNa

K

Mg

Ca

AP Biology

Different kinds of atoms = elementsDifferent kinds of atoms = elements

K Ca

Life requires ~25 chemical elements

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

matter: • carbon (C) • hydrogen (H)

AP Biology

• oxygen (O) • nitrogen (N)

� Four elements make up most of remaining 4%:

• phosphorus (P) • calcium (Ca)

• sulfur (S) • potassium (K)

Bonding properties

� Effect of electrons� electrons determine

chemical behavior of atomdepends on number

AP Biology

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

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

Bonding properties

� Effect of electrons� chemical behavior of an atom depends on

number of electrons in its valence shell

AP BiologyHow does this atom behave?How does this atom behave? How does this atom behave?How does this atom behave?

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

AP Biology

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)

Elements & their valence shellsElements in the same columnhave the same valence & similar chemical properties

Elements in the same columnhave the same valence & similar chemical properties

Remembersome food chains

AP Biology

some food chainswere built on

reducing O to H2O& some on

reducing S to H2S

Chemical reactivity� Atoms tend to

� complete a partially filled valence shellor

� empty a partially filled valence shell

AP Biology

–

–

–

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

and creates bondsand creates bonds

Bonds in Biology� Weak bonds

� hydrogen bonds� attraction between + and –

� hydrophobic & hydrophilicinteractions

Hydrogen bond

H2O

H2O

AP Biology

–

–

H2 (hydrogen gas)

Covalent bondinteractions

� van derWaals forces(weak attraction)

� Strong bonds� covalent bonds

Covalent bonds� Why is this a strong bond?

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

� Forms molecules (2 or more atoms)

AP Biology

� Forms molecules (2 or more atoms)

–

–

H2 (hydrogen gas)H2 (hydrogen gas)

H — H

H2O (water)H2O (water)

H

H

OxygenH

HO

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

� double bonds � 2 pairs of electrons

� triple bonds3 pairs of electrons

AP Biology

� 3 pairs of electrons

� Very strong bonds

H

H–C–H

H

––

More isbetter!

Electronegativity in covalent bonds

� Strength of bond is determined by electronegativity difference� Ionic bonds (lose/gain e-)

� So strong, e- being pulled from one to other

Covalent bonds (shared e -)

AP Biology

� Covalent bonds (shared e -)� Polar = unequally shared, non-polar = equally

Polar covalent bonds� Pair of electrons shared

unequally by 2 atoms� Water = O + H

� oxygen has stronger “ attraction ” for the + –

AP Biology

H

H

Oxygen

“ attraction ” for the electrons than hydrogen

� oxygen has higher electronegativity

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

properties of water…

+

+

––

––

Hydrogen bonding� Polar water creates molecular attractions

� positive H atom in one H 2O molecule attracted to negative O in another H 2O

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

AP Biology

an -OH exists in a larger molecule

� Weak bond

Opposites Attract!

Chemistry of Life

Properties of Water

AP Biology 2007-2008

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� + attracted to –� creates a

sticky molecule

AP Biology

sticky molecule

Elixir of Life� Special properties of water

� cohesion & adhesion� surface tension, capillary action

� good solvent� many molecules dissolve in H 2O

AP Biology

� many molecules dissolve in H 2O� hydrophilic vs. hydrophobic

� lower density as a solid� ice floats!

� high specific heat� water stores heat

� high heat of vaporization� heats & cools slowly

I like the partabout the ice!

Cohesion & Adhesion� H bonding between H 2O molecules is cohesion

� water is “sticky”� surface tension� drinking straw

� H bonding between H 2O &

AP Biology

� H bonding between H 2O & other substances is adhesion� capillary action� meniscus� water climbs up

paper towel or cloth

How does H 2O get to top of trees?Transpiration built on cohesion & adhesion

AP Biology

Let’s go to the videotape!

Water is the solvent of life� Polarity makes H 2O a good solvent

� polar H 2O molecules surround + & – ions� solvents dissolve solutes creating solutions

AP Biology

Do you dissolve in water?� Hydrophilic

�substances have attraction to H 2O�polar or non-polar ?

AP Biology

Or don’t you?� Hydrophobic

�substances that don’t have an attraction to H 2O

�polar or non-polar ?

AP Biology fat (triglycerol)

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

when they are solid, butNot water…

� Ice floats !

AP Biology

�

� H bonds form a crystal

And this hasmade all the difference!

Ice floats

AP Biology

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

AP Biology

� ponds, lakes & even oceans would freeze solid� in summer, only upper few inches would thaw

� seasonal turnover of lakes� cycling nutrients in autumn

Specific heat� H2O resists changes in temperature

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

AP Biology

� H2O moderates temperatures on Earth

AP Biology

Specific heat& climate

Heat of vaporizationEvaporative cooling

AP BiologyOrganisms rely on heat of vaporization to remove body heat

Ionization of water & pH� Water ionizes

�H+ splits off from H 2O, leaving OH–

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

AP Biology

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

� pH scale�how acid or basic solution is�1 →→→→ 7 →→→→ 14

H2O →→→→ H+ + OH–H2O →→→→ H+ + OH–

pH Scale10–1

H+ IonConcentration

Examples of Solutions

Stomach acid, Lemon juice1

pH100 Hydrochloric acid0

10–2 2

10–3 Vinegar, cola, beer3

10–4 Tomatoes4

10–5 Black coffee, Rainwater5

10–6 Urine, Saliva6Pure water, Blood

AP Biology

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

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

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

AP Biology 1001

2

3

45

6

7

89

3Amount of base added

Bufferingrange

4 52

pH

� Control pH by buffers� reservoir of H +

� donate H+ when [H+] falls

� absorb H+ when [H+] rises