The Chemical Context of Life

Chemical Basis of Biology

Elements :

Matter : made up of elements, substances that cannot be broken down to other substances by chemical reactions

Compounds

Molecular

Atom

• Each element

– Consists of a certain kind of atom that is different from those of other elements

• An atom

– Is the smallest unit of matter that still retains the properties of an element

• The atomic number of an element– Is the number of protons– Is unique to each element

Secondshell

Helium

2He

Firstshell

Thirdshell

Hydrogen

1H

2He

4.00Atomic mass

Atomic number

Element symbol

Electron-shelldiagram

Lithium

3LiBeryllium

4BeBoron

3BCarbon

6CNitrogen

7NOxygen

8OFluorine

9FNeon

10Ne

Sodium

11NaMagnesium

12MgAluminum

13AlSilicon

14SiPhosphorus

15PSulfur

16SChlorine

17ClArgon

18Ar

The periodic table of the elements

• A few other elements

– Make up the remaining 4%

of living matter

• major elements

Essential Elements of Life (25/92)

O, C, H, N (96%)

• Trace elements (<0.01%)

(a) Nitrogen deficiency (b) Iodine deficiency

The effects of essential element deficiencies

0.15mg/per day

Neutrons: no electrical charge

Protons: positively charged

Electrons: negatively charged

Atoms

Nucleus

Cloud of negativecharge (2 electrons)

Electrons

orbital

Valence electrons

Are those in the outermost, or valence shell

Determine the chemical behavior of an atom

Isotopes

• Isotopes

differ in the number of neutrons

same number of protons

• Radioactive isotopes

– Spontaneously give off particles and energy

32P 3H 14C

Incubators

Human cells

1 2 3

4 5 6

987

10°C 15°C 20°C

25°C 30°C 35°C

40°C 45°C 50°C

DNA (old and new)

1 2 3 4 5 6 7 8 9

Radioactive isotopesIngredients includingRadioactive tracer (bright blue)

3H

scintillation fluid

Whether temperature affects the rate of DNA synthesis?

Nitrogenousbase

Nucleoside

O

O

O

O P CH2

5’C

3’CPhosphate

group Pentosesugar

O

HRNA

DNA-OH

32P 3H 14C

Temperature (°C)

10 20 30 40 50

Optimumtemperaturefor DNAsynthesis

30

20

10

0

Cou

nts

per

min

ute

(x 1

,000

)

scintillation counter

*DNA (3H)

Temperature affects the rate of DNA synthesis—the most DNA was made at 35°C.

– Can be used in biology

Cancerous throat tissue

Radioactive isotopes

*glucose

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Isotopes

12C 13C 14C

stable stable radioactive

Proton number Neutron number

6 6 6

e- number

6 7 8 6 6 6

Chemical properties: the samePhysical properties: different

Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

How atom combine to form molecular and ionic compounds?

Covalent bond

Ionic bond

2 or more atoms

2 or more atoms

molecular

Ionic compoundsor salts

Strong chemical bonds:

Sodium Chloride (Cl) Sodium Chloride

+

• ionic compounds (or salts)

– two or more elements combined in a fixed ratio

– In nature as crystals of various shape and size

(see fig2.14)

NaCl

(Na)

–characteristics different from those of its elements

–

Na NaCl Cl

+

Cl–

Chloride ion(an anion)Na

Sodium atomCl

Chlorine atom

Na+

Sodium on(a cation)

Sodium chloride (NaCl)

– an attraction between anions and cations

– Environment affects the strength of ionic bonds

ionic bond in compound

An anion: negatively charged ions

A cation: positively charged ion

(c)

Methane (CH4).

Water (H2O).

(d)

HO

H

H H

H

H

C

Covalent bond in compounds

-sharing of a pair of valence electrons

• In a nonpolar covalent bond

– The atoms have similar electronegativities

– Share the electron equally

Hydrogen (H2).

Oxygen (O2).

H H

O O

• Electronegativity

– Is the attraction of a particular kind of atom for the electrons in a covalent bond

• The more electronegative an atom

– The more strongly it pulls shared electrons toward itself

O2The most electronegative of the 92 elements:

H2O

–

O

H H+ +

In a polar covalent bond

The atoms have differing electronegativities

Share the electrons unequally

( O>H )

Delta minus

Delta plus

Partial negative

Partial positive

Weak chemical bonds are important in living systems

Hydrogen Bonds

Van der Waals Interactions

ReversibilityInter-molecular interaction:

Intra-molecular interaction in the large biological molecular

ex. Protein

Ionic bond

(3D structure)

Hydrogen Bonds

– +

+

Water(H2O)

Ammonia(NH3)

OH

H

+

–

N

HH H

+ d+

When a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

Partial positive charge

Partial negative charge

H…..OH…..N

Insects walk on water.

Van der Waals Interactions

Help molecules adhere to each other

•Weak•Occur only when atom and molecular are very close together•Occur when transiently positive and negative regions of molecules attract each other

Gecko lizard

Tiny hairsIncrease surface area

Molecular Shape and Function

• The precise shape of a molecule

– Is usually very important to its function in the living cell

– Is determined by the positions of its atoms’ valence orbitals

Electron Orbitals• An orbital

– Is the three-dimensional space where an electron is found 90% of the time

• Each electron shell– Consists of a specific number of orbitals

1s orbital 2s orbital Three 2p orbitals1s, 2s, and 2p orbitals

(a) First shell (maximum 2 electrons)

(b) Second shell (maximum 8 electrons)

(c) Neon, with two filled shells (10 electrons)

x

Z

Y

s orbital

ZThree p orbitals

X

Y

Four hybrid orbitals

Tetrahedron

In a covalent bond

The s and p orbitals may hybridize, creating specific molecular shapes

Molecular Shape and Function

determined by the positions of its atoms’ valence orbitals

Space-fillingmodel

Hybrid-orbital model(with ball-and-stick

model superimposed)UnbondedElectron pair

104.5°

O

HWater (H2O)

Methane (CH4)

H

H H

H

C

O

H

H

H

C

Ball-and-stickmodel

H H

H

H

The positions of the hybrid orbital determine the shapes of the molecules

Morphine

Carbon

Hydrogen

Nitrogen

Sulfur

OxygenNaturalendorphin

Naturalendorphin

Endorphinreceptors

Morphine

Brain cell

specificity

Structures of endorphin and morphine

drugs

Molecular Shape and Function

Reactants

Reaction

Product

2 H2 O2 2 H2O

+

+

– Convert reactants to products

Reactants

– making and breaking of chemical bonds

– changes in the composition of matter

A chemical reaction

Photosynthesis

6CO2+ 6H2O C6H12O6 + O2

glucose

Sunlight

the forward and reverse reaction rates are equal

Chemical equilibrium

dynamic process

3H2+ N22NH3

reversible

Relative concentration of product and reactants stop to change