the chemical foundations of life. element vs. molecule ionic bond vs. covalent bond polar vs....

The Chemical Foundations of Life

• Element vs. molecule

• Ionic bond vs. covalent bond

• Polar vs. nonpolar

• Hydrogen bond vs. van der Waals force

• Hydrophilic vs. hydrophobic vs. amphipathic

• Water – cohesion vs. adhesion

solvent vs. solute

acid vs. base vs. buffer

The Chemical Foundations of LifeHere we can see the nucleus with Here we can see the nucleus with protonsprotons and and neutrons.neutrons.

1/10000

質子中子

ElectronsElectrons can be seen (much larger than they should can be seen (much larger than they shouldbe) orbiting around the nucleus.be) orbiting around the nucleus.

電子

—18 electrons

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

Figure 2.7 Energy levels of an atom’s electrons

A ball bouncing down a flightof stairs provides an analogyfor energy levels of electrons,because the ball can only reston each step, not betweensteps.

Third energy level (shell)

(a)

Second energy level (shell)

First energy level (shell)

Energyabsorbed

Energylost

An electron can move from one level to another only if the energyit gains or loses is exactly equal to the difference in energy betweenthe two levels. Arrows indicate some of the step-wise changes inpotential energy that are possible.

(b)

Atomicnucleus


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

Figure 2.8 Electron-shell diagrams of the first 18 elements in the periodic table


Figure 2.9 Electron orbitals

Electron orbitals.Each orbital holds

up to two electrons.

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

(a) First shell (maximum 2 electrons)

(b) Second shell (maximum 8 electrons)

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

Electron-shell diagrams.Each shell is shown withits maximum number of

electrons, grouped in pairs.

x

Z

Y







solvent vs. solute



Figure 2.10 Formation of a covalent bond

Hydrogen atoms (2 H)

Hydrogenmolecule (H2)

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

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

+ +

+ +

+ +


Secondshell

Helium

2He

Firstshell

Thirdshell

Hydrogen

1H

2He

4.00Atomic mass

Atomic number

Element symbol


Lithium

3LiBeryllium

4BeBoron

3BCarbon

6CNitrogen

7NOxygen

8OFluorine

9FNeon

10Ne

Sodium

11NaMagnesium

12MgAluminum

13AlSilicon

14SiPhosphorus

15PSulfur

16SChlorine

17ClArgon

18Ar


electronegativity







solvent vs. solute



Secondshell

Helium

2He

Firstshell

Thirdshell

Hydrogen

1H

2He

4.00Atomic mass

Atomic number

Element symbol


Lithium

3LiBeryllium

4BeBoron

3BCarbon

6CNitrogen

7NOxygen

8OFluorine

9FNeon

10Ne

Sodium

11NaMagnesium

12MgAluminum

13AlSilicon

14SiPhosphorus

15PSulfur

16SChlorine

17ClArgon

18Ar



Figure 2.13 Electron transfer and ionic bonding

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 uncharged

atom)

ClChlorine atom(an uncharged

atom)

Na+

Sodium on(a cation)

Sodium chloride (NaCl)


Figure 2.14 A sodium chloride crystal

Na+

Cl–


Weak Chemical Bonds

• Hydrogen bonds

• Van der Waals interactions

• Ionic interactions

• Hydrophobic interactions


Figure 2.15 A hydrogen bond

Water(H2O)

Ammonia(NH3)

– +

O

H

H

+

–

N

H

H 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.+

+

+


Unnumbered Figure p. 42


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

(b) Molecular shape models. Three models representing molecular shape are shown for two examples; water and methane. The positions of the hybrid orbital determine the shapes of the molecules


Figure 2.17 A molecular mimic

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


Unnumbered pg. 44

Reactants Reaction Products

2 H2 +

+

O2 2 H2O

Chemical Equilibrium







solvent vs. solute


Copyright 2001 by Harcourt, Inc.

The Chemical Foundations of LifeThe Chemical Foundations of Life

So there is an So there is an attraction betweenattraction betweenthe positive andthe positive andnegative sides of negative sides of a water moleculea water molecule……this is this is hydrogenhydrogenbondingbonding..

Figure 2Figure 2--1212


Figure 3.3 Water transport in plants

Water conducting cells

100 µm


Figure 3.4 Walking on water


Figure 3.5 Ice: crystalline structure and floating barrier

Liquid water

Hydrogen bonds constantly break and re-form

Ice

Hydrogen bonds are stable

Hydrogen bond

•H2O + H2O OH– + H3O+

hydroxide ion

• H2O H+ + OH–

hydrogen ion or proton

• Chemical Equilibrium

• pH ＝ – log [H+] acidic pH < 7 basic pH > 7

The Chemical Foundations of LifeThe The pH scalepH scale is the log is the log1010 of the hydrogen of the hydrogen

ion concentration in a solution. ion concentration in a solution.

Water is considered a reference or neutral pointWater is considered a reference or neutral pointwith a pH of 7.0.with a pH of 7.0.

Figure 2-20Figure 2-20

Buffer

CO2 + H2O H2CO3 H+ + HCO3

Carbon dioxide carbonic acid bicarbonate ion







solvent vs. solute


Carbon- the Backbone of Biological Molecules

The hydrocarbon skeleton provides a basic framework:

Biological Molecules Small and Large

Figure 3-3Figure 3-3

Saturated vs. unsaturated


Figure 4.5 Variations in carbon skeletons

HH H HH C

H H H HH

H

HH

H

H

H H H

H

H

H

H H H

H H H

H H

H

H

H

H

H

H

HH

H

H H H H

H H

H H

H H H H

H H

H H

HH

HH

H

H

H

C C C C C

C C C C C C C

CCCCCCCC

C

CC

C

C

C

C

CC

C

C

C

H

H

H

HH

H

H

(a) Length

(b) Branching

(c) Double bonds

(d) Rings

Ethane Propane

Butane 2-methylpropane(commonly called isobutane)

1-Butene 2-Butene

Cyclohexane Benzene


Figure 4.7 Three types of isomersH

H

H

H H

H

H

H

H

H

CO2H

CH3

NH2

C

CO2H

H

CH3

NH2

X X

X

X

H H H H H

H

H H H H

HC C C C C

HH C

HH

HH

H

C

C C C

C C C C

C

(a) Structural isomers

(b) Geometric isomers

(c) Enantiomers

H

L isomer D isomer


Figure 4.8 The pharmacological importance of enantiomers

L-Dopa

(effective against Parkinson’s disease)

D-Dopa

(biologically inactive)


Figure 4.9 A comparison of functional groups of female (estradiol) and male (testosterone) sex hormones

CH3

OH

HO

O

CH3

CH3

OH

Estradiol

Testosterone

Female lion

Male lion

Functional Groups• Hydroxyl group R-OH

• Carbonyl group R-C-H (or R)

• Carboxyl group R-C

• Amino group R-N

• Sulfhydryl group R-SH

• Phosphate group R-O-P-O–

O

O

OH

H

H

O

O–

the chemical foundations of life. element vs. molecule ionic bond vs. covalent bond polar vs....

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shell hydrogen

shell maximum

shell helium

energy levels of electrons

electrons b

buffer slide

atoms electrons

b atomic nucleus slide