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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.

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slide2

How Did Life Originate?Understanding what life is and how it originated from non-living matter requires some understanding of basic chemistry

chemical behavior results from two tendencies of atoms
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)
slide6

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).

slide7

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

8

8

8

2

nucleus

slide8

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.

8

8

8

2

nucleus

He

2

Ne

2+8 = 10

Ar

2+8+8 = 18

Kr

2+8+8+8 = 26

slide9

Inert elements

Non-inert elements will interact with one another in ways that fill their outer

electron shells or cancel charges

slide10

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

lost an electron

has a filled outer shell

charged ion

SALT:

outer shells filled

charges cancelled

stable now

unfilled

outer shell,

almost empty

uncharged

atom

Na+

Na

11 p+

11 n

10 e-

11 p+

11 n

11 e-

Ionization: transfer of electron creates ions

Ionic

Bond

NaCl

stole an electron

has a filled outer shell

charged ion

17 p+

17 n

17 e-

unfilled

outer shell,

almost full

uncharged

atom

17 p+

17 n

18 e-

Cl-

Cl

slide15

outer shells almost empty

cations (+) form

outer shells almost full

anions (-) form

slide18

A hydrogen atom (H) with 1 electron

An unfilled outer electron shell; capacity of 2 electrons

slide19

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)

slide20

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.

oxygen molecule o 2

Shared electrons in molecular orbitals

Unshared electrons in atomic orbitals

Oxygen Molecule: O2

nucleus

nucleus

Shared electrons orbit both atoms,

although they are sometimes diagrammed as if they were between

slide25

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

P

P

P

Atomic

number

1

6

7

8

15

16

Capacity of

outer 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

Atom

Hydrogen

Carbon

Nitrogen

Oxygen

Phosphorus

Sulfur

Numbers of Covalent Bonds an Atom Can Form
polar covalent bonds water
Polar Covalent Bonds: Water

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.

O

H2O

H

H

slide31

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 interactions1
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 interactions2

-

+

-

-

-

+

+

+

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 interactions3
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 interactions4
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
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.