Chemicals common in biology

Carbon, Oxygen, Hydrogen and Nitrogen most abundant

Phosphorus, Calcium, Sodium, Magnesium, Potassium and Sulfur are also common

Most organic material comprises only 25 elements

Table 2-1

Cloud of negativecharge (2 electrons)

Fig. 2-5

Nucleus

Electrons

(b)(a)

Atomic Structure Protons and

neutrons in nucleus Protons +

charge Neutrons are

neutral

Electrons “orbit” nucleus in electron shell Electrons -

charge

Atomic characteristics

Number of protons and electrons is equal under most conditions (no net charge)

Atomic number=number of protons Atomic mass=combined number of protons

plus neutrons in nucleus Isotopes=atom that contains the same number

of protons, but different numbers of neutrons

Fig. 2-9

Hydrogen

1H

Lithium

3LiBeryllium

4BeBoron

5BCarbon

6CNitrogen

7NOxygen

8O

Fluorine

9FNeon

10Ne

Helium

2HeAtomic number

Element symbol

Electron-distributiondiagram

Atomic mass

2He

4.00Firstshell

Secondshell

Thirdshell

Sodium

11NaMagnesium

12Mg

Aluminum

13AlSilicon

14SiPhosphorus

15PSulfur

16S

Chlorine

17ClArgon

18Ar

Shell configurations of electrons

Chemical Bonding Atoms or molecules with full valence shells are

very stable (inert gases) Chemical Bonding takes place to allow filling

of valence shells Two types of chemical bonds

Covalent bonds Ionic bonds

New molecule often has characteristics unique from parent atoms (NaCl)

Fig. 2-12

Name andMolecularFormula

Electron-distribution

Diagram

Lewis DotStructure and

Structural Formula

Space-fillingModel

(a) Hydrogen (H2)

(b) Oxygen (O2)

(c) Water (H2O)

(d) Methane (CH4)

Multiple atoms share electrons to fill outer shell.

Can take place between two identical atoms (O2 or H2)

Carbon-based molecules are typically covalently linked

Covalent Bonding

Fig. 2-13

–

+ +H H

O

H2O

Attraction of atom for electrons is called electronegative force

In some compounds the difference in electronegative force is large enough that one atom pulls shared electrons to itself

Results in a molecule with slightly charged regions

Polar Covalent Bonds

Fig. 2-14-2

Na Cl Na Cl

NaSodium atom Chlorine atom

Cl Na+

Sodium ion(a cation)

Cl–Chloride ion

(an anion)

Sodium chloride (NaCl) Caused by strong electronegative differences between atoms One atom donates an electron to another Both atoms become charged and their opposite charges

causes an attractive force Strong bonds outside of aqueous solution, weak in solution

Ionic Bonds

Hydrogen bonding Weak bonds that are

made and broken easily

Hydrogen of a polar, covalent molecule has attraction to Nitrogen or Oxygen of similar molecule

Results from weak charge of regions on polar molecules

Fig. 2-17

s orbital Three porbitals

(a) Hybridization of orbitals

Tetrahedron

Four hybrid orbitals

Space-fillingModel

Ball-and-stickModel

Hybrid-orbital Model(with ball-and-stick

model superimposed)

Unbondedelectronpair

104.5º

Water (H2O)

Methane (CH4)

(b) Molecular-shape models

z

x

y

Molecular Shape

Determined by electron shells and the size of atoms included

Space-filling models attempt to demonstrate the shape of a molecule

s orbital Three porbitals

(a) Hybridization of orbitals

Tetrahedron

Four hybrid orbitals

Space-fillingModel

Ball-and-stickModel

Hybrid-orbital Model(with ball-and-stick

model superimposed)

Unbondedelectronpair

104.5º

Water (H2O)

Methane (CH4)

(b) Molecular-shape models

z

x

y

Biological Activity

Biological activity of molecules is largely determined by: Shape of molecule

3D structure allows molecule to interact with other molecules

Charge of molecule of on portions of molecule Charged regions often interact with oppositely

charged molecules Bond type

Covalent bond is more easily broken and assembled

Molecular Mimicry One molecule

has a shape that is similar to another molecule

The similarity in shape often results in a similarity in function

Seen in pharmaceutical development and pathogenic microbiology