The Chemical Context of Life

How Did Life Originate?

Understanding what life is and how it originated from non-living matter requires some understanding of

basic chemistry

In Terms of How They Function,Living Things Are Literally

Biochemical Machines

So why do atoms interact?

How do they interact?

Chemical behavior results from two tendencies of atoms:

• Atoms tend to fill their outer electron shells …the Octet Rule

• Atoms interact with other atoms in ways that cancel electrostatic charges (+ and - charges)

There are 92 kinds of atoms in nature, called elements. Each element has a characteristic set of protons, neutrons, and electrons (indicated by the atomic number in each block).

Electrons are distributed in concentric regions outside the nucleus called electron shells. Each electron shell has a limited capacity, as shown by

the numbers below:

An atom’s inner shells fill first because negatively charged electrons are

attracted to the positively charged nucleus

nucleus

2222

8888

8888

8888

He2 Ne

2+8 = 10 Ar2+8+8 = 18 Kr

2+8+8+8 = 26

2222

8888

8888

8888

Atoms whose outer shells are filled because they have just the right number of electrons will be stable and not interact with other atoms.

These are called the inert elements, or noble gases.

nucleus

Inert elements

Non-inert elements will interact with one another in ways that fill their outer electron shells or cancel charges

For example, consider the two smallest elements: hydrogen (1) and helium (2).

(a) Hydrogen atoms have an unfilled shell and will interact with other atoms in ways that fill the shell.

(b) Helium atoms are non-reactive (and therefore solitary) because their only (and therefore outer) electron shell is filled to capacity.

Kinds of Attractions Among Atoms• Ionic Bonds (attraction between oppositely charged ions)

• Covalent Bonds (sharing electrons to fill outer shells), two kinds:

Non-polar Covalent Bonds (electrons shared equally by identical or very similar atoms, so no partial charges are produced)

Polar Covalent Bonds (electrons shared unequally by different kinds of atoms, producing + and - partial charges in participating atoms)

• Hydrogen Bonds (attraction between partially charged atoms that are also involved in a polar covalent bonds with additional atoms)

• Van der Waals attractions (attraction between atoms that induce transient, opposite, partial charges in one another)

• Hydrophyllic (water loving) and Hydrophobic (water hating) Influences (charged regions of molecules are attracted to water molecules, whereas uncharged regions are repelled from watery environments)

Ionic Bonds

Ionic Bonds, e.g., sodium (Na, 11) and chlorine (Cl, 17)

unfilledouter shell,

almost empty

unchargedatom

unfilledouter shell,almost full

unchargedatom

lost an electronhas a filled outer shell

charged ion

stole an electronhas a filled outer

shellcharged ion

Na+

SALT:outer shells filled

charges cancelledstable now

Ionization: transfer of electron creates ions

Ionic

Bond

11 p+

11 n11 e-

11 p+

11 n11 e-

17 p+

17 n17 e-

17 p+

17 n17 e-

11 p+

11 n10 e-

11 p+

11 n10 e-

17 p+

17 n18 e-

17 p+

17 n18 e-

Cl-

Na

Cl

NaCl

outer shells almost emptycations (+) form

outer shells almost full

anions (-) form

Covalent Bonds

A hydrogen atom (H) with 1 electron

An unfilled outer electron shell; capacity of 2 electrons

A hydrogen Molecule (H2)

A non-polar covalent bond: 2 equally shared electrons

The electrons are shared equally because the two atoms are identical and therefore have the same ability to attract electrons (electronegativity)

A hydrogen Molecule (H2)

Because the electrons are shared equally, the positive charges of each nucleus are cancelled out by the electrons. Therefore hydrogen molecules are uncharged

or non-polar.

The Hindenberg DisasterReactive versus Invert Gasses

Oxygen Molecule: O2

Unshared electrons in

atomic orbitals

Shared electrons in molecular orbitals

Shared electrons orbit both atoms,

although they are sometimes diagrammed as if they were between

nucleus nucleus

Atoms that are 2 or more electrons short of a filled outer shell are likely to fill the shell by sharing electrons from

other atoms, forming covalent bonds.

Carbon has 4 electrons in its outer shell, needing 4 more

Oxygen has 6 electrons in its outer shell, needing 2 more

Numbers of Covalent Bonds an Atom Can Form

Atom

Hydrogen

Carbon

Nitrogen

Oxygen

Phosphorus

Sulfur

Atomicnumber

1

6

7

8

15

16

Capacity ofouter shell

2

8

8

8

8

8

Electrons in outer shell

1

4

5

6

5

6

Number of covalent bonds

1

4

3

2

3

2

P P P

Polar Covalent Bonds

Polar Covalent Bonds: Water

H H

O

H2O

Atoms with different electronegativities share electrons unequally. The more electronegative atom gets more than its fair share of the electron’s time and therefore has a slightly negative charge. The other atom will have a partial + charge because it gets less of the electron’s time than is required to cancel the positive charges in its nucleus.

Hydrogen Bonds

Hydrogen Bonds:

Attraction between oppositely charged atoms engaged in polar covalent bonding with other atoms

water tension: numerous hydrogen bonds can be very strong

Van der Waals Interactions

Van der Waals Interactions

+

-

-+

+-

Electrons are constantly on the move, mostly in random directions around the atom’s nucleus.

Even when the number of electrons equals the number of protons, there will be brief events where an atom’s electrons tend to be bunched together a little.

This leaves one side of those atoms + charged and the other - charged until the electrons spread out again.

3 charged atoms (“dipoles”)

Van der Waals Interactions

+

-

-+

-+-+

(a) as two dipoles approach one another...

(b) their electron clouds interact (opposite charges repel) and the two atoms face each other with opposite charges.

+- +-

(c) now they attract each other

Van der Waals Interactions

The two atoms will attract one another until their electron clouds begin to overlap and repel the two atoms …which remain suspended at a distance where attraction and repulsion are balanced

Van der Waals Interactions

Van der Walls interactions are very weak. The movement of atoms at room temperature breaks them apart almost immediately, except...

Biological molecules that interact often have complementary shapes, which brings large numbers of atoms into position for Van der Waals interaction …the cumulative effect of which is very strong

Hydrophyllic/Hydrophobic Interactions

Many molecules have polar (charges) and non-polar (uncharged) regions. The polar regions tend to orient toward the water that the molecule is suspended in, whereas the no-polar parts fold up within the interior of the molecules, hidden from water.