ChemistryChemistry

AP Biology

Chemical Bonds

Electronegativities of Common Elements

Hydrogen 2.1

Oxygen 3.5

Carbon 2.5

Nitrogen 3.0

Sulfur 2.5

Phosphorus 2.1

Sodium 0.9

Chlorine 3.0

• Electronegativity = how well an atom “holds its electrons

Bonds within a molecule

• Bonding between atoms can be organized on a continuum between covalent and ionic bonds

X X X XY Z

Increasing electronegativity difference between two atoms

Nonpolar Covalent Polar Covalent Ionic

Bonds within a molecule

• Nonpolar covalent bond = electrons are shared evenly between atoms

• Polar covalent bond = electrons are shared but are more tightly held by one atom

• Ionic bond = Electrons are not shared due to strong electronegativity differences (one atom “grabs” the electrons from the other)

Bond Type By ElectronegativityElectronegativity difference Bond Type

< 0.3 Nonpolar Covalent

Between 0.3 and 1.7 Polar Covalent

> 1.7 Ionic

Hydrogen Bonds• This is a type of bond

BETWEEN molecules (different from polar covalent bond)

• Involves the hydrogen of one molecule being attracted to a strongly electronegative atom in another molecule

H

HO

H

N

-

+

+

+

-

• Hydrogen bonds are extremely important in biological systems. We’ll see them again and again:– Proteins– DNA– Enzymes– And more!

Img taken without permission from: http://cny.new21.net/gg/images/nucleotide2.gif

Van der Waals Interactions

• Weak attractions when two molecules are very close together

• Temporary dipole moments in an atom can cause these tiny attractions

Images taken without permission from: http://news.bbc.co.uk/1/hi/sci/tech/781611.stm

Applications…

• Stickybot– uses same model as gecko feet!

• Gecko glue

Image taken without permission from http://www.sciencedaily.com/releases/2010/08/100826104135.htm

Properties of Water• Polar molecule

forms hydrogen bonds

• Hydrogen bonds give water some special characteristics (not all):– High specific heat– Evaporative cooling– Insulation of bodies of

water

Properties of water (cont.)

• High Specific Heat– Takes a lot of energy to

heat up 1 degree– Makes water very stable

• Evaporative cooling– Water has a high heat of

vaporization– Evaporative cooling

prevents overheating

Properties of water (cont.)

• Insulation of bodies of water– Solid water is less dense

than liquid water– ice floats!

– Ice on top creates a “cover” that keeps water below from freezing

– Allows fish and plants underneath to continue to exist.

Buffers

• Maintain the pH in a solution

• Typically consist of an H+ acceptor and an H+ donor

• Why might this be important in living things?

Image taken without permission from: http://www.chemistry.wustl.edu/~edudev/LabTutorials/Buffer/images/Eqn10.jpg

Carbon- a versatile element

• Each carbon atom can form 4 bonds

• Carbon is used in (for all living organisms)– Storage compounds – Cell formation

Molecular drawings

• In some molecular drawings, C and H are left out as a shortcut– Junction between lines

= C– Line that ends with

nothing at the end = C– Since C makes 4 bonds,

unless otherwise noted H is assumed to be there (to make 4 bonds total)

O

OH

OH

C

HO

HO

C

C

C

C

C

H

H

H

H

OH

H

H

H

O

OH

OH

CH2OH

HO

HO

2 ways to draw the

same molecule!

Functional Groups

• Functional groups are groups of atoms– participate in many chemical reactions– Help determine the properties of organic

molecules

• Alcohol (hydroxyl)– Other forms: HO—

• Aldehyde– Other forms: -COH– Properties: Polar, Soluble in water

• Ketone– Other forms:– Properties: Polar, Soluble in water

Functional groups

CH2C

O

CH2

Functional groups

• Carboxyl

– Other forms: -COOH, -COO-

– Properties: Acidic, Polar, Water Soluble

• Amino

– Other forms: -NH2, - NH3+

– Properties: Basic, Polar

Functional groups

• Thiol– Other forms: -SH– Properties: Polar, forms disulfide

bridges/bonds in proteins

• Phosphate

– Other forms: -PO42-

– Properties: Charged, Polar