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