AP Biology 2007-2008

The Chemistry of Life

Living organisms and their environments are subject to basic laws of physics and chemistry. The use of formic acid by ants to protect themselves against predators and microbial parasites

AP Biology

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

AP Biology

Evolution of Tolerance to Toxic Elements:§ Some species can become adapted to

environments containing toxic elementsu For example, some plant communities are

adapted to serpentine rock

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How did these green sea turtles show up in the San Gabriel River (Los Angeles river bed), and what could they possibly be eating?http://www.ocregister.com/2015/03/01/how-

did-these-green-sea-turtles-show-up-in-the-san-gabriel-river-and-what-could-they-

possibly-be-eating/

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

HON

P SNaK

MgCa

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Life requires ~25 chemical elements§ About 25 elements are essential for life

u Four elements make up 96% of living matter: • carbon (C) • hydrogen (H)• oxygen (O) • nitrogen (N)

u Four elements make up most of remaining 4%:• phosphorus (P) • calcium (Ca)• sulfur (S) • potassium (K)

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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 that are detectable

Radiometric Dating: scientists measure the ratio of different isotopes and calculate how many half-lives have passed since the fossil or rock was formed

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Radioactive Tracers:§ Radioactive isotopes are often used as

diagnostic tools in medicine§ Radioactive tracers can be used to track atoms

through metabolism§ They can also be used in combination with

sophisticated imaging instruments

A PET scan, a medical use for radioactive isotopes

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Bonding properties:§ Effect of electrons

u electrons determine chemical behavior of atom

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

How does this atom behave?

AP Biology

Bonding properties:§ Effect of electrons

u 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?

AP Biology

First shell

Second shell

Third shell

Hydrogen1H

Lithium3Li

Sodium11Na

Beryllium4Be

Magnesium12Mg

Boron5B

Aluminum13Al

Carbon6C

Silicon14Si

Nitrogen7N

Phosphorus15P

Oxygen8O

Sulfur16S

Fluorine9F

Chlorine17Cl

Neon10Ne

Argon18Ar

Helium2He

2He

4.00Mass number

Atomic number

Element symbolElectrondistributiondiagram

a) How many electrons fit on each orbital?b) How does the proton number compare to the electron number?

C) How do you think the number of electrons on the outer orbital of each atom relates to how stable the element is?d) Which elements are the most stable? e) Which elements are the most reactive?

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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 columnhave 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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Draw and label a Hydrogen atom with protons, neutrons, and electrons (show valence shells) using different colors.Jot down in your notes what this atom would be called if the proton, electron or neutron numberchanged.

a. a change in the number of protons?b. a change in the number of electrons?c. a change in the number of neutrons?

Draw and label a Carbon atom with protons, neutrons, and electrons (show valence shells) using different colors.

AP Biology

–

–

–

Chemical reactivity:§ Atoms tend to

u complete a partially filled valence shellor

u empty a partially filled valence shellThis tendency drives chemical reactions…

and creates bonds

How do the valence electrons influence molecular bonding?

AP Biology

AP Biology

–

–

H2 (hydrogen gas)

Covalent bond

Bonds in Biology: Hydrogen bond

H2O

H2O

1. Hydrogen bonds (intermolecular forces between molecules)attraction between + and – parts of the molecule.

2. Covalent Bond – (intramolecular forces) sharing of electrons.

3. Ionic Bond - (intramolecular forces) transfer of electrons from one atom to the other. + ion attracted to – ion.

ionic bond

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Covalent bonds:§ What causes a covalent bond?

u two atoms share a pair of electronsu both atoms holding onto the electronsu 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

u single bonds § 1 pair of electrons

u double bonds § 2 pairs of electrons

u triple bonds§ 3 pairs of electrons

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Hydrogen bonding:§ Polar water molecules

creates molecular attractionsu attraction between positive H

in one H2O molecule to negative O in another H2O

§ Weak bond compared to covalent and ionic bonds

Let’s go ou

tside!

HO

H

AP Biology

Natural endorphin

(a) Structures of endorphin and morphine

Morphine

KeyCarbonHydrogen

OxygenSulfurNitrogen

MorphineNatural endorphin

EndorphinreceptorsBrain cell

(b) Binding to endorphin receptors

Molecular Shape & Function:• Molecular shape is crucial in

biology because it determines how biological molecules specifically recognize and respond to one another

• Biological molecules often bind temporarily to each other by forming weak bonds, but only if their shapes are complimentary

• Opiates, such as morphine, and naturally produced endorphins have similar effects because their shapes are similar and they bind the same receptors in the brain

AP Biology

While waiting at the airport, Neil Campbell overhears this claim: “It’s paranoid and ignorant to worry about industry or agriculture contaminating the environment with their chemical wastes. After all, this stuff is just made of the same atoms that were already present in our environment.” Drawing on your knowledge of electron distribution, bonding, and emergent properties, either defend or counter this argument.