the chemical foundations of life. the chemical foundations of life what is chemistry? chemistry is...

The Chemical Foundations of Life

The Chemical Foundations of LifeWhat is Chemistry?

ChemistryChemistry is the study of the properties of is the study of the properties ofMatter—living and nonliving , and the Matter—living and nonliving , and the transformation of all forms of mattertransformation of all forms of matter

BiochemistryBiochemistry is the study of chemical is the study of chemical reactions that occur in organismsreactions that occur in organisms

The Chemical Foundations of LifeWhat is Matter?

Matter is the substantive portion of our Universe. Matter is the substantive portion of our Universe. Having material form, it occupies space and has Having material form, it occupies space and has a property we know as mass.a property we know as mass.

Matter can exist in several physical states.Matter can exist in several physical states.What are these physical states?What are these physical states?

SolidsLiquids

Gases

• 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

The Chemical Foundations of Life

The first three periods of the Periodic TableThe first three periods of the Periodic Table

Figure 2-7Figure 2-7

同位素─中子數不同

• 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 Life

Salt crystal formation,Salt crystal formation,the result of bonding.the result of bonding.

Ionic bondIonic bondformation.formation.

Figure 2-9Figure 2-9

• 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

electronegativity

• 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

• 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

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

•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

• 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

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 hydrocarbon skeleton provides a basic framework:

Biological Molecules Small and Large

Figure 3-3Figure 3-3

Saturated vs. unsaturated

Four Classes of Building Blocks

• Lipids

• Sugars – polysaccharides

• Nucleotides – nucleic acids

• Amino acids – proteins

Biological Molecules

The hydrocarbon skeleton provides a basic framework:

Biological Molecules Small and Large

Figure 3-3Figure 3-3

One of the key concepts associated with the One of the key concepts associated with the chemistry of carbon that will help us here is chemistry of carbon that will help us here is saturationsaturation..

Carbon has an Atomic Number of 6. How Carbon has an Atomic Number of 6. How many valence electrons does it have?many valence electrons does it have?

44

Biological Molecules Small and Large

That means that carbon can formThat means that carbon can formup toup to 4 separate bonds 4 separate bonds

The simplest organic moleculeThe simplest organic moleculeis methane, with a formula ofis methane, with a formula ofCHCH44..

Biological Molecules Small and Large

The way a typical methane The way a typical methane molecule would appear would molecule would appear would be:be:

HH

HH CC HH

HH

With 4 separate bonds to With 4 separate bonds to 4 separate atoms, carbon 4 separate atoms, carbon is said to be is said to be saturatedsaturated..

Biological Molecules Small and Large

If two methane molecules are If two methane molecules are joined together, they formjoined together, they forma molecule known ethane.a molecule known ethane.

HH

HH CC

HH

HH

CC HH

HH

Biological Molecules Small and Large

HH

HH CC

HH

HH

CC HH

HH

How many carbons are present How many carbons are present in ethane?in ethane?

22

Is each of these carbons saturated?Is each of these carbons saturated? Yes.Yes.

Biological Molecules Small and Large

Are these carbons Are these carbons saturated?saturated?

HH

HH CC

HH

HH

CC HH

HH

Does thisDoes thiscarbon havecarbon havefour bondsfour bondsto four separateto four separateatoms?atoms?

YesYes

Biological Molecules Small and Large

HH

HH CC

HH

HH

CC HH

HH

Does this carbon have fourDoes this carbon have fourbonds to four separate atoms?bonds to four separate atoms?

YesYesSo both areSo both aresaturatedsaturated..

Biological Molecules Small and Large

This molecule looks very This molecule looks very similar to the previous molecule.similar to the previous molecule.Do the two carbons each have 4 Do the two carbons each have 4 bonds to 4 separate atoms?bonds to 4 separate atoms?

HH

HH CC

HH

CC HH

No, this a double bondNo, this a double bondand each of the carbons and each of the carbons is is unsaturatedunsaturated as a result. as a result.

Biological Molecules Small and Large

So, if a molecule has a point of unsaturaSo, if a molecule has a point of unsaturation, the carbons at that point have how tion, the carbons at that point have how many bonds?many bonds?

Three or fewer*Three or fewer* single bonds to single bonds to differentdifferent or separate atoms (we don’t or separate atoms (we don’t count the double bond as two separate count the double bond as two separate bonds). (*Triple bonds are also bonds). (*Triple bonds are also possible.)possible.)

Biological Molecules Small and Large

Therefore, if a carbon atom has less Therefore, if a carbon atom has less than four separate single bonds, we say than four separate single bonds, we say it is it is unsaturatedunsaturated..

Biological Molecules Small and Large

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–

Four Classes of Building Blocks

• Lipids

• Sugars – polysaccharides

• Nucleotides – nucleic acids

• Amino acids – proteins

Condensation : monomer oligomer polymer

Four Classes of Building Blocks

• Lipids

• Sugars - polysaccharides

• Nucleotides – nucleic acids

• Amino acids – proteins

三酸甘油酯

膽固醇