AP Biology2007-2008

CHAPTERS 2 & CHAPTERS 2 & 3: THE 3: THE

CHEMISTRY OF CHEMISTRY OF LIFELIFE

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WHY ARE WE STUDYING CHEMISTRY…AGAIN?Chemistry is the

foundation of Biology

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CHEMISTRY LEADS TO…

Biomoleculeslead to…

Cellslead to…

Organisms…Populations…Communities…Ecosystems…

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Proton

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 = elementsDifferent 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 lifeFour 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…what’s up buddy?

= Effect of electrons (they’re at the center of it all…har har!)

electrons determine chemical behavior of atom depends on number of electrons in atom’s outermost shell

= valence shell

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

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Bonding properties

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

The most important parts of an atom interms of BIOLOGY are its…???

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Electrons!!!!Electrons!!!!

WHY?

Electrons are on the OUTSIDEThey are the parts that BUMP INTO other atoms= the parts that REACT with and BOND to other atoms

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–

–

–

CHEMICAL REACTIVITY DEPENDS ON BONDING!

Atoms tend to:complete a partially filled valence shell (take or share) = strong (non-metals)

orempty a partially filled valence shell (give) = weak (metals)

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

and creates bondsand creates bonds

Atoms “want” 8 electrons in their outer shell!

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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)

Generally, knowing how many SHELLS an atom hasIs not very useful to us (at least in ap bio)

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Why do you think the only atom other than oxygen

used in food chains on

planet Earth is SULFUR?

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Solid @ RTSolid @ RT

Liquid or Gas @ RTLiquid or Gas @ RT

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–

–

H2 (hydrogen gas)

Covalent bond

WHAT TYPES OF BONDS SHOULD YOU KNOW FOR BIOLOGY?

Weak bondsWeak bondshydrogen bonds VIDEOattraction between + and –

hydrophobic & hydrophilic interactionsinteraction with H2O

van derWaals forces disulfide bridges

Strong bondsStrong bondscovalent bondsIonic bonds

Hydrogen bond

H2O

H2O

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COVALENT BONDSWhy are covalent bonds strong

bonds? two atoms shareshare a pair of electrons both atoms holding onto the electrons very stable not always equal sharingForms molecules

–

–

H2 (hydrogen gas)H2 (hydrogen gas)

H — H

H2O (water)H2O (water)

H

H

OxygenH

HO

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NONPOLAR COVALENT BOND

Pair of electrons shared equally by 2 atomsexample: 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 = H2Ooxygen has stronger “attraction” for the electrons than hydrogen

oxygen has higher electronegativity + vs – poles leads to many interesting properties of water…

+

+

––

––

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HYDROGEN BONDINGPolar water creates external

molecular attractions between positive H in one H2O molecule to negative O in another

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

= Weak bond

HO

H

Hydrogen bonding of water has PROFOUND importance for LIFE

ON EARTH!

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KEY CONCEPTS OF CHAPTER 2 FOR AP BIO EXAM:

1. Chemical rxns are the basis of species-specific communication strategies (BIG IDEA 3)

2. Biochemistry is vital to natural selection and evolution (BIG IDEA 1)

3. Biochemistry can serve as the mechanisms by which populations interact (BIG IDEA 4)

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THE PERCENTAGES OF NATURALLY OCCURRING ELEMENTS MAKING UP THE HUMAN BODY ARE SIMILAR TO THE PERCENTAGES OF THESE ELEMENTS FOUND IN OTHER ORGANISMS. HOW COULD YOU ACCOUNT FOR THIS SIMILARITY AMONG ORGANISMS? EXPLAIN YOUR THINKING.

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DRAW LEWIS DOT STRUCTURES FOR EACH HYPOTHETICAL MOLECULE SHOWN BELOW, USING THE CORRECT NUMBER OF VALENCE ELECTRONS FOR EACH ATOM. DETERMINE WHICH MOLECULE MAKES SENSE BECAUSE EACH ATOM HAS A COMPLETE VALENCE SHELL & EACH BOND HAS THE CORRECT NUMBER OF ELECTRONS. EXPLAIN WHAT MAKES THE OTHER MOLECULES NONSENSICAL, CONSIDERING THE NUMBER OF BONDS EACH TYPE OF ATOM CAN MAKE.

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CHEMISTRY OF LIFEPROPERTIES OF WATER:

CHAPTER 3

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All life occurs in water & needs water for life

processes

inside & outside the cell

All life occurs in water & needs water for life

processes

inside & outside the cell

WHY ARE WE STUDYING WATER???

ITS ITS POLARITYPOLARITY

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CHEMISTRY OF WATERH2O molecules form H-bonds with each

other

+H attracted to –O (SLIGHT) creates a sticky molecule

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REMEMBER…

Covalent bonds are WITHIN the water molecule

Hydrogen bonds are BETWEEN water molecules

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THE ELIXIR OF LIFE

Special properties of water:1. cohesion & adhesionsurface tension, capillary action

2. good solventmany molecules dissolve in H2Ohydrophilic vs. hydrophobic

3. lower density as a solidice floats!

4. high specific heatwater stores heat

5. high heat of vaporizationheats & cools slowly

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1. COHESION & 2. ADHESION

CohesionH bonding between H2O moleculeswater is “sticky”

surface tensiondrinking straw

AdhesionH bonding between H2O & other substancescapillary actionmeniscuswater climbs uppaper towel or cloth

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TRANSPIRATION IS BUILT UPON THE CONCEPTS OF COHESION & ADHESION

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3. WATER IS THE SOLVENT OF LIFE

Polarity makes H2O a good solventpolar H2O molecules surround + & – ionssolvents dissolve solutes creating solutions

Hydrationshells

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WHAT DISSOLVES IN WATER?

Hydrophilicsubstances have attraction to H2Opolar or non-polar?

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4. WATER IS AN ORGANIZER OF NON POLAR MOLECULES

Water is attracted to things that are also polar or charged in some way.

Molecules that LACK polarity / charge cannot attract water…much like a magnet will not stick to plastic.

However, water WILL push these non polar molecules out of the way and thus organize them as it is drawn toward other polar things

WHY IS THIS IMPORTANT?

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WATER’S ABILITY TO ORGANIZE NON POLAR MOLECULES IS CRITICAL TO THE FORMATION OF CELLULAR MEMBRANES…

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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)

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SOLID WATER FLOATS?!?!...HUH??

Oceans & lakes don’t freeze solidsurface ice insulates water belowallowing life to survive the winter

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

seasonal turnover of lakessinking cold H2O cycles nutrients in autumn

Water is MOST dense at 4 deg. C

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5. SPECIFIC HEATH2O resists changes in temperature specific heat HIGH OR LOW ??

H2O moderates temperatures on Earth & homeostasis in living things!!!

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6. Water has a high heat of vaporization

= the amount of energy it takes to cause 1g of a liquid to become a gas

**It takes a lot of energy to cause water to vaporize

**Why is this important?**Why is this important?When water leaves the body, it takes a LOT of heat energy with it

= Sweat cools us down!Back to homeostasis

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7. IONIZATION OF WATER & PH

Water ionizesH+ splits off from H2O, leaving OH–

if [H+] = [-OH], water is neutralif [H+] > [-OH], water is acidicif [H+] < [-OH], water is basic

pH scalepH scalehow acid or basic solution ishow acid or basic solution is

1 1 7 acidic 7 acidic7 7 14 basic 7 neutral 14 basic 7 neutral

H2O H+ + OH–H2O H+ + OH–

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PH SCALE

10–1

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 ~7affects shape of molecules shape affects function

= pH affects cellular function

Control pH by buffers= reservoir of H+

donate H+ when [H+] falls

absorb H+ when [H+] rises

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REMEMBER ALL THESE PROPERTIES EXIST BECAUSE…

…Water hydrogen bonds with itself

Which happens because……Water molecules are polarWhich happens because……Oxygen is Elelctronegative