Biol 210 General Biology 1

Lecture 2

Review

Chemical Bonds

Atomic Structure

• Nucleus– Protons, mass = 1, charge = +1

– Neutrons, mass = 1, charge = 0

• Electrons– Mass = negligible

– Charge = -1

– # e– = # protons

– Outer shell (most energenic) e–’s form chemical bonds

Isotopes

• Some isotopes are stable, such as 1H2

• Other isotopes are unstable, such as 1H3.

• When tritium decays, it gives off particle.

• Because the mass of an element includes the average isotope abundance, the mass and the atomic weight differ slightly

• Helium, He, atomic number 4, mass 4.003

Important Elements• C HOPKINS CaFe Mg

– C = carbon– H = hydrogen– O = oxygen– P = phosphorous– K = potassium– I = iodine– N = nitrogen– S = sulfur– Ca = calcium– Fe = iron– Mg = magnesium

Na = sodiumCl = chloride

•Every atom has a characteristic total number of covalent bonds that it can form = an atom’s valence.

•The valence of hydrogen is 1.

•Oxygen is 2.

•Nitrogen is 3.

•Carbon is 4.

•Phosphorus should have a valence of 3, based on its three unpaired electrons, but in biological molecules it generally has a valence of 5, forming three single covalent bonds and one double bond.

Chemical Bonds

• Two atoms share one or more pairs of valence electrons

• Four kinds of chemical bonds– Covalent– Hydrogen– Ionic– Van der Waals

• You must know the first 3 kinds

Covalent Bonds

• Two atoms share one or more pairs of electrons

Covalent Bonds

• Two atoms share one or more pairs of electrons

• Strongest chemical bond

Covalent Bonds

• Two atoms share one or more pairs of electrons

• Strongest chemical bond

• 50-110 kcal/mol

Hydrogen molecule

• Hydrogen atoms have one valence electron each

• Innermost shell can accommodate two electrons

• Each atom contributes an electron

• Electrons effectively fill valence shell for both atoms

Oxygen

• Oxygen has 2 valence electrons• Can share two pairs of electrons• Two O atoms can form 2 covalent bonds

Oxygen + Hydrogen

• Oxygen can form bonds with hydrogen atoms

Oxygen + Hydrogen

• Oxygen can form bonds with hydrogen atoms• Since H can only form one covalent bond

Oxygen + Hydrogen

• Oxygen can form bonds with hydrogen atoms• Since H can only form one covalent bond• O must bond two H atoms

Oxygen + Hydrogen

• Oxygen can form bonds with hydrogen atoms• Since H can only form one covalent bond• O must bond two H atoms• H2O = water

Carbon

• Carbon has a valence of 4 electrons

Carbon

• Carbon has a valence of 4 electrons• Can form 4 covalent bonds

Carbon

• Carbon has a valence of 4 electrons• Can form 4 covalent bonds• Biological molecules are largely carbon-

containing molecules

Carbon

• Carbon has 4 valence electrons• Can form 4 covalent bonds• Biological molecules are largely carbon-containing

molecules• Organic = derived from organisms

s orbital

ZThree p orbitals

X

Y

Four hybrid orbitals

(a) Hybridization of orbitals. The single s and three p orbitals of a valence shell involved in covalent bonding combine to form four teardrop-shaped hybrid orbitals. These orbitals extend to the four corners of an imaginary tetrahedron (outlined in pink).

Tetrahedron

Figure 2.16 (a)

H—H

O=O

H—O—H

CH4

Morphine

Carbon

Hydrogen

Nitrogen

Sulfur

OxygenNaturalendorphin

(a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds toreceptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match.

(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine.

Naturalendorphin

Endorphinreceptors

Morphine

Brain cell

Ionic Bond

• Covalent bonds result from two atoms sharing electrons

Ionic Bond

• Covalent bonds result from two atoms sharing electrons

• Sometimes one atom “takes” the electron from another atom.

Ionic Bond

• One atom has more protons than electrons = +1

Ionic Bond

• One atom has more protons than electrons = +1• Other atom has one more electron than protons = -

1

Ionic Bond

• One atom has more protons than electrons = +1• Other atom has one more electron than protons = -

1• Opposite charges attract weakly (3-7 kcal/mol)

Hydrogen Bond

• We have studied two bonding extremes

Hydrogen Bond

• We have studied two bonding extremes• Covalent bond = atoms share electrons

Hydrogen Bond

• We have studied two bonding extremes• Covalent bond = atoms share electrons• Ionic bond = one atom “take”s electrons

Hydrogen Bond

• Unequal e- sharing = partial charges on molecule

Hydrogen Bond

• Unequal e- sharing = partial charges on molecule• Oxygen nucleus more attractive to electrons

Hydrogen Bond

• Unequal e- sharing = partial charges on molecule• Oxygen nucleus more attractive to electrons • Hydrogen nucleus less attractive

Hydrogen Bond

• Unequal e- sharing = partial charges on molecule• Oxygen nucleus more attractive to electrons • Hydrogen nucleus less attractive• Partial charges, O more neg, H more pos

Hydrogen Bond

• Water = polar molecule

Hydrogen Bond

• Water = polar molecule• Can interact weakly with other polar molecules

Hydrogen Bond

• Water = polar molecule• Can interact weakly with other polar molecules• H-bond 3-7 kcal/mol

Comparative Bond Strength

• Covalent bond = 50-110 kcal/mol

• Ionic bond = 3-7 kcal/mol

• H-bond = 3-7 kcal/mol

• van der Waals bond = ~1 kcal/mol

Predicted BP for water = -76°C

Predicted BP for water = -76°CPredicted MP for water = -87°C

Predicted BP for water = -76°CPredicted MP for water = -87°CTemp. range for liquid water = 11°

Predicted BP for water = -76°CPredicted MP for water = -87°CPredicted temp. range for liquid water = 11°Actual: 0–100°C

Predicted BP for water = -76°CPredicted MP for water = -87°CPredicted temp. range for liquid water = 11°Actual: 0–100°CRationale: H-bonds

Hydrogenbonds

+

+

H

H+

+

–

–

– –

Figure 3.2

•The polarity of water molecules

Hydrogenbonds

+

+

H

H+

+

–

–

– –

Figure 3.2

•The polarity of water molecules

–Allows them to form hydrogen bonds with each other

Hydrogenbonds

+

+

H

H+

+

–

–

– –

Figure 3.2

•The polarity of water molecules

–Allows them to form hydrogen bonds with each other

–Contributes to the various properties water exhibits

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

+

+

+

+Cl –

–

–

–

–

Na+

++

+

+

–

–

–

–

–

–Na+

Cl–

Figure 3.6

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

Negative

oxygen regions

of polar water molecules

are attracted to sodium

cations (Na+).

+

+

+

+Cl –

–

–

–

–

Na+

++

+

+

–

–

–

–

–

–Na+

Cl–

Figure 3.6

• The different regions of the polar water molecule can interact with ionic compounds called solutes 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

• Water can also interact with polar molecules such as proteins

This oxygen is

attracted to a slight

positive charge on

the lysozyme

molecule.

This oxygen 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

pH

• Water can dissociate

H

Hydroniumion (H3O+)

H

Hydroxideion (OH–)

H

H

H

H

H

H

+ –

+

Figure on p. 53 of water dissociating

pH

• Water can dissociate– Into hydronium ions and hydroxide ions

H

Hydroniumion (H3O+)

H

Hydroxideion (OH–)

H

H

H

H

H

H

+ –

+

Figure on p. 53 of water dissociating

pH

• Water can dissociate– Into hydronium ions and hydroxide ions

• Changes in the concentration of these ions

H

Hydroniumion (H3O+)

H

Hydroxideion (OH–)

H

H

H

H

H

H

+ –

+

Figure on p. 53 of water dissociating

pH

• 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

• 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

• 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

—pH 7.4