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Page 1: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

1 04/20/23

ATOMS

Page 2: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

2 04/20/23

Major atoms in biology

Major atoms in biology

C H O N S P# of atoms in outer shell–H, 1–C 4–N, P 5–O, S 6

Page 3: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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C

N P

S

Atoms are sociable

HO

HChemical bonds

Page 4: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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Chemical bonds.....Chemical bonds.....

CovalentNoncovalent

Strong

Puny but important

Page 5: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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Atoms attached via shared electrons in outer shells

H O HH HO

Covalent bonds

CC

C

C C

C

Page 6: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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e.g. CH3-CH3, ethane

Covalent bonds

• stable (strong)

Page 7: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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Covalent bond cleavage

CH3:CH3--> CH3 + CH3

Reactant Products

(Methyl radicals)

(EthaneCH3-CH3)

Page 8: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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Covalent bond cleavage

CH3:CH3--> CH3 + CH3Reactant Products

E = +83 kcal/mol

E is the difference between the energy of reactants and products

Page 9: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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Covalent bond strengths

High bond strength confers stability

0-H 110

C-H 99

C-C 83

C=C 146

Page 10: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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Double bonds restrict rotation

H

H

H

H

Molecule is planar (flat)

e.g. Ethylene (CH2=CH2)

Page 11: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

11 04/20/23

Covalent bonds are orientated in space

H

H

O104.5 deg

Page 12: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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Covalent Non-covalent

1-5

• 4 kinds.....

Bond strength(kcal/mol) 50-195

Page 13: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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Non-covalent bonds

• Hydrogen bonds

• ionic bonds

• van der Waal's interactions

• hydrophobic interactions

Page 14: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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Non-covalent bonds

• Hydrogen bonds

e.g. in liquid water

oxygen,

hydrogen,

Page 15: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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Hydrogen bond

In liquid water

Each molecule may be H-bonded to

4 others. Bonds are transient

Page 16: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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Typical Hydrogen bonds

H Oor

H N

Page 17: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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Ionic bonds

Non-covalent bonds (cont.)

Result of attraction between + and - charges of ionized atoms

e.g. Na+ Cl-

Page 18: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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Ionic bonds

NaCl dissolved in H2O

Na+ Cl

Note the tight shells of water molecules

Hydrated diameter of ions is important in permeability

Page 19: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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Van der Waals interactions

Non-covalent interactions (cont.)

Due to electron fluxes any atom can become a

transient dipole

Page 20: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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Van der Waals interactions

Non-covalent interactions (cont.)

2 atoms in van der Waals contact

Page 21: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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Van der Waals interactions

Atoms are very close

But not close enough so that their electron shells overlap. If so, they repel each other

You’re disgusting!

Page 22: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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Our next AttractionOur next Attraction

HydrophobiHydrophobiaaStarring a cast of thousandsof greasy characters

Hydrocarbons

Page 23: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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Non-covalent interactions (cont)

Hydrophobic interactions

CH

HCH

HCH

HCH

HCH

HH

Hydrocarbons

CH

HCH

HCH

HH

Combined hydrophobic and van der Waals interactions

Page 24: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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O

NH3 O

CH3

CH2

NH2

CH2

O H C

CH2 C

OCH2 CH2

CH2

CHCH3 CH3

CH3 CH CH2

Bonds at work, H-bonds, ionic

and vd Waals+ hydrophobic bonds

Protein

Protein

Page 25: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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How many water molecules in a teaspoonful?

As many as the teaspoonfuls of water present in the Atlantic Ocean

Trivia Time

A one, a two, a three...

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An everyday protein molecule, hemoglobin

All your hemoglobin alpha chains are

identical with 574 amino acids chained

together in precise sequence

In the past second you have just assembled 400 million million of them

Page 27: 1 11/9/2015 ATOMS. 2 11/9/2015 Major atoms in biology n C H O N S P n # of atoms in outer shell – H, 1 – C4 – N, P5 – O, S 6

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