the chemical foundation of life (2)
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The Chemical Foundation of LifeTRANSCRIPT
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The Chemical Foundations of Life
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• 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
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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
Protones Neutrones
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.
Electrones
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—18 electrons
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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
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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
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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
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• 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
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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
+ +
+ +
+ +
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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
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electronegativity
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• 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
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Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
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
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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 ion(a cation)
Sodium chloride (NaCl)
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Figure 2.14 A sodium chloride crystal
Na+
Cl–
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Weak Chemical Bonds
• Hydrogen bonds
• Van der Waals interactions
• Ionic interactions
• Hydrophobic interactions
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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.+
+
+
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Unnumbered Figure p. 42
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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
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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
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Unnumbered pg. 44
Reactants Reaction Products
2 H2 +
+
O2 2 H2O
Chemical Equilibrium
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• 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
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• 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
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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
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Figure 3.3 Water transport in plants
Water conducting cells
100 µm
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Figure 3.4 Walking on water
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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
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•H2O + H2O OH– + H3O+
hydroxide ion
• H2O H+ + OH–
hydrogen ion or proton
• Chemical Equilibrium
• pH = – log [H+] acidic pH < 7 basic pH > 7
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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
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Buffer
CO2 + H2O H2CO3 H+ + HCO3
Carbon dioxide carbonic acid bicarbonate ion
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• 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
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Carbon- the Backbone of Biological Molecules
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The hydrocarbon skeleton provides a basic framework:
Biological Molecules Small and Large
Figure 3-3Figure 3-3
Saturated vs. unsaturated
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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
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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
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Figure 4.8 The pharmacological importance of enantiomers
L-Dopa
(effective against Parkinson’s disease)
D-Dopa
(biologically inactive)
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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
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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–