Chemistry AP Biology Chemical Bonds Electronegativities of Common Elements Hydrogen2.1 Oxygen3.5...

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