Covalent bonds – where electrons are shared

• Typically the strongest bonds in biological systems.

• Can be polar (where electrons are not equally shared) or non-polar (electrons are equally shared).

Figure 2.10

• Formation of a covalent bondHydrogen atoms (2 H)

Hydrogenmolecule (H2)

+ +

+ +

+ +

In each hydrogenatom, the single electronis held in its orbital byits attraction to theproton in the nucleus.

1

When two hydrogenatoms approach eachother, the electron ofeach atom is alsoattracted to the protonin the other nucleus.

2

The two electronsbecome shared in a covalent bond,forming an H2

molecule.

3

• A molecule

– Consists of two or more atoms held together by covalent bonds

• A single bond

– Is the sharing of one pair of valence electrons

• A double bond

– Is the sharing of two pairs of valence electrons

(a)

(b)

Name(molecularformula)

Electron-shell

diagram

Structuralformula

Space-fillingmodel

Hydrogen (H2). Two hydrogen atoms can form a single bond.

Oxygen (O2). Two oxygen atoms share two pairs of electrons to form a double bond.

H H

O O

Figure 2.11 A, B

• Single and double covalent bonds

Name(molecularformula)

Electron-shell

diagram

Structuralformula

Space-fillingmodel

(c)

Methane (CH4). Four hydrogen atoms can satisfy the valence ofone carbonatom, formingmethane.

Water (H2O). Two hydrogenatoms and one oxygen atom arejoined by covalent bonds to produce a molecule of water.

(d)

HO

H

H H

H

H

C

Figure 2.11 C, D

Covalent bonding in compounds

• 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

A nonpolar covalent bond

– The atoms have similar electronegativities

– Share the electron equally

– Common in hydrocarbons

Figure 2.12

This results in a partial negative charge on theoxygen and apartial positivecharge onthe hydrogens.

H2O

–

O

H H+ +

Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen.

– The atoms have differing electronegativities

– Share the electrons unequally

A polar covalent bond

Ionic Bonds

• Electron transfer between two atoms creates ions

• Ions

– Are atoms with more or fewer electrons than usual

– Are charged atoms

– An anion

• Is negatively charged ions

– A cation

• Is positively charged

An ionic bond

Cl–

Chloride ion(an anion)

–

The lone valence electron of a sodiumatom is transferred to join the 7 valenceelectrons of a chlorine atom.

1 Each resulting ion has a completedvalence shell. An ionic bond can formbetween the oppositely charged ions.

2

Na NaCl Cl

+

NaSodium atom

(an unchargedatom)

ClChlorine atom(an uncharged

atom)

Na+

Sodium on(a cation)

Sodium chloride (NaCl)Figure 2.13

An attraction between anions and cations

These bonds are strong in crystal form, but weak in water

Ionic compounds

Na+

Cl–

Figure 2.14

– Are often called salts, which may form crystals

Weak Chemical Bonds – form due to differences in polarity

– +

+

Water(H2O)

Ammonia(NH3)

OH

H

+

–

N

HH H

A hydrogenbond results from the attraction between thepartial positive charge on the hydrogen atom of water and the partial negative charge on the nitrogen atom of ammonia.+ +

Figure 2.15

• Hydrogen bonds

– Form when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

Van der Waals Interactions

• Van der Waals interactions

– Occur when transiently positive and negative regions of molecules attract each other

• Weak chemical bonds

– Reinforce the shapes of large molecules

– Help molecules adhere to each other

BSC 2010 - Exam I Lectures and Text Pages• I. Intro to Biology (2-29)

• II. Chemistry of Life

– Chemistry review (30-46)

– Water (47-57)

– Carbon (58-67)

– Macromolecules (68-91)

• III. Cells and Membranes

– Cell structure (92-123)

– Membranes (124-140)

• IV. Introductory Biochemistry

– Energy and Metabolism (141-159)

– Cellular Respiration (160-180)

– Photosynthesis (181-200)

Water – The Solvent of Life (Ch. 3)

Cells are made of 70-95% water, the “SOLVENT OF LIFE”. All living things require water more than any other substance.

• Solvent -

• Solute -

• Aqueous -

• Three-quarters of the Earth’s surface is submerged in water

• The abundance of water is the main reason the Earth is habitable

Figure 3.1

The water molecule is a polar molecule

• The polarity of water molecules

– Allows them to form hydrogen bonds with each other (negative O ends are attracted to positive H ends)

– Contributes to the various properties water exhibits

Hydrogenbonds

+

+

H

H+

+

–

–

– –

Figure 3.2

Emergent Properties of Water Contribute to Life

• A. cohesion: (related properties: surface tension and adhesion)

• B. Water tends to resist rupturing. (related to cohesion)

• C. Water resists changes in temperature.

• D. Water expands when it freezes.

• E. Water is a versatile solvent.

Cohesion

• Water molecules exhibit cohesion

• Cohesion

– Is the bonding of a high percentage of the molecules to neighboring molecules

– Water molecules stick together due to hydrogen bonding

– Causes surface tension and adhesion.

Cohesion

Helps pull water up through the microscopic vessels of plants. Water molecules stick to each other and to the walls of the xylem.

Water conducting cells

100 µmFigure 3.3

Surface tension

Is a measure of how hard it is to break the surface of a liquid.

Figure 3.4

Moderation of Temperature

• Water moderates air temperature

– This is very important for the maintenance of homeostasis by living organisms.

– Also - ~75% of the earth is covered with water, this helps stabilize climate.

– Water absorbs heat from air that is warmer and releases the stored heat to air that is cooler

Water’s High Specific Heat

• The specific heat of a substance

– Is the amount of heat that must be absorbed or lost for 1 gram of that substance to change its temperature by 1ºC

Water’s High Specific Heat

• Water has a high specific heat, which allows it to minimize temperature fluctuations to within limits that permit life.

– Heat is absorbed when hydrogen bonds break.

– Heat is released when hydrogen bonds form.

Evaporative Cooling

• Heat of vaporization

– Is the quantity of heat a liquid must absorb for 1 gram of it to be converted from a liquid to a gas

• Evaporative cooling

– Is due to water’s high heat of vaporization

– Allows water to cool a surface

Ice Floats

• The hydrogen bonds in ice

– Are more “ordered” than in liquid water, making ice less dense

Liquid water

Hydrogen bonds constantly break and re-form

Ice

Hydrogen bonds are stable

Hydrogen bond

Figure 3.5

Insulation of Bodies of Water by Floating Ice

• Solid water, or ice

– Is less dense than liquid water

– Floats in liquid water

• Allows life to exist in frozen lakes and ponds.

The Solvent of Life

• Water is a versatile solvent due to its polarity

• It can form aqueous solutions

Forming solutions with ionic solutes.

• The different regions of the polar water molecule can interact with ionic compounds and dissolve them.

Negative

oxygen regions

of polar water molecules

are attracted to sodium

cations (Na+).

+

+

+

+Cl –

–

–

–

–

Na+Positive hydrogen regions

of water molecules cling to chloride anions

(Cl–).

++

+

+

–

–

–

–

–

–Na+

Cl–

Figure 3.6

Forming solutions with polar solutes.

• Water can also interact with polar molecules such as proteins

This oxygen is

attracted to a slight

positive charge on

the lysozyme

molecule.This hydrogen is attracted to a slight

negative charge on the lysozyme

molecule.(a) Lysozyme molecule

in a nonaqueous

environment

(b) Lysozyme molecule (purple)

in an aqueous environment

such as tears or saliva

(c) Ionic and polar regions on the protein’s

Surface attract water molecules.

+

–

Figure 3.7

Hydrophilic and Hydrophobic Substances

• Some substances are attracted to water and others are not.

• A hydrophilic substance

– Has an affinity for water. Ions and polar molecules.

• A hydrophobic substance is not attracted to water.

– Nonpolar molecules.

Life is sensitive to pH (Acids and Bases)

• Water can dissociate

– Into hydronium ions and hydroxide ions

• Changes in the concentration of these ions

– Can have a great affect on living organisms

H

Hydroniumion (H3O+)

H

Hydroxideion (OH–)

H

H

H

H

H

H

+ –

+

Figure on p. 53 of water dissociating

Acids and Bases

• An acid

– Is any substance that increases the hydrogen ion concentration of a solution (donates protons)

• A base

– Is any substance that reduces the hydrogen ion concentration of a solution (accepts protons)

The pH Scale

• The pH of a solution

– Is determined by the relative concentration of hydrogen ions

– Is low in an acid

– Is high in a base

Most biological solutions range from pH of 6-8, but there are exceptions (stomach acids pH 1-2)

• The pH scale and pH values of various aqueous solutions

Incr

easi

ngly

Aci

dic

[H+]

> [

OH

–]

Incr

easi

ngly

Bas

ic[H

+]

< [

OH

–]

Neutral[H+] = [OH–]

Oven cleaner

0

1

2

3

4

5

6

7

8

9

10

11

12

13

14

pH Scale

Battery acid

Digestive (stomach) juice, lemon juiceVinegar, beer, wine,colaTomato juice

Black coffee RainwaterUrine

Pure waterHuman blood

Seawater

Milk of magnesia

Household ammonia

Household bleach

Figure 3.8

Buffers

• The internal pH of most living cells

– Must remain close to pH 7

Buffers

• Are substances that minimize changes in the concentrations of hydrogen and hydroxide ions in a solution

• Consist of a weak acid-base pair that reversibly combines with hydrogen ions