Download Figure 3-1. Structures of several small, biologically important organic

Environmental Biology
for Engineers and Scientists
D.A. Vaccari, P.F. Strom, and J.E. Alleman
© John Wiley & Sons, 2005
Chapter 3 –
The Substances of Life
Figure 3-1. Structures of several small, biologically important organic molecules.
CH2
CH3
CH2
H2C
Ethylene
OH
Ethanol
HC
CH2
Proprionic
acid
COOH
COOH
Oxalic acid
CH3
OH
COOH
COOH
COOH
Acetic acid
CH3
CH3
CH3
Lactic
acid
HC
O
NH2
HC
OH
CH2
H2C
OH
COOH
Glyceraldehyde Glycine
H2C
OH
O
HC
OH
COOH
H2C
OH
Pyruvic
acid
Glycerol
C
NH2
NH2
HC
CH3
C
O
COOH
NH2
Alanine
Urea
Figure 3-2. Electronegativity of biologically important elements. This shows the
portion of the periodic table containing many of the elements that are important to
life. The numbers indicate the electronegativity of the corresponding elements.
(From Pauling, Linus, 1960)
H
2.1
Li
1.0
Na
0.9
K
0.8
Be
1.5
Mg
1.2
Ca
1.0
Sc
1.3
Ti
1.5
V
1.6
Cr
1.6
Mo
1.8
W
1.7
Mn
1.5
Fe
1.8
Co
1.8
Ni
1.8
Cu
1.9
Zn
1.6
B
2.0
Al
1.5
Ga
1.6
C
2.5
Si
1.8
Ge
1.8
Sn
1.8
N
3.0
P
2.1
As
1.9
O
3.5
S
2.5
Se
2.4
F
4.0
Cl
3.0
Br
2.8
I
2.5
Figure 3-3. Fraction of undissociated acid for acetic acid (pKa = 4.5).
Points shown are for pH 3.5, 4.5, and 5.5.
Fraction Undissociated
1.25
1.00
0.75
0.50
0.25
pKa
0.00
0.0
2.0
4.0
pH
6.0
8.0
Figure 3-4. Tetrahedral structure of carbon bonding,
and a methane molecule. (Based on Gaudy)
H
C
H
H
H
Figure 3-5. Three-dimensional view of glyceraldehyde structure. (a) Mirror-image views;
(b) views showing orientation with hydrogen of central carbon pointed towards viewer.
(a)
d(+)-glyceraldehyde:
(b)
l(-)-glyceraldehyde:
Monosaccharide structures
H
C
O
H
C
O
H
C
O
CH2OH
HO
C
H
H
C
OH
H
C
OH
C
O
H
C
OH
HO
C
H
H
C
OH
HO
C
H
H
C
OH
HO
C
H
H
C
OH
H
C
OH
H
C
OH
H
C
OH
H
C
OH
CH2OH
d(+)-glucose
CH2OH
CH2OH
d(+)-galactose
CH2OH
d(+)-ribose
d(-)-fructose
Ring structures of glucose and fructose.
CH2OH
CH2OH
O
O
OH
OH
OH
CH2OH
OH
OH
OH
d-glucose
OH
d-fructose
A common disaccharide
CH2OH
CH2OH
O
O
OH
OH
OH
O
OH
CH2OH
OH
sucrose
OH
Figure 3-6. Polymers of glucose: (a) starch or glycogen showing maltose
repeating disaccharide unit; (b) cellulose with cellobiose repeating unit.
CH2OH
O
CH2OH
O
O
O
CH2OH
CH2OH
O
CH2
O
O
CH2OH
O
O
CH2OH
O
O
O
O
CH2OH
O
O
CH2OH
O
CH2OH
O
O
CH2OH
CH2OH
O
O
O
O
Figure 3-7. Structures of some of the more common fatty acids.
Basic structure:
R-COOH
Saturated fatty acids:
Formic HCOOH
Acetic CH3COOH
Proprionic
CH3CH2COOH
n-Butyric
CH3(CH2)2COOH
Caproic CH3(CH2)4COOH
Palmitic CH3(CH2)14COOH
Stearic CH3(CH2)16COOH
Unsaturated fatty acids
Oleic
CH3(CH2)7CH=CH(CH2)7COOH
Linoleic CH3(CH2)4CH=CHCH2CH=CH(CH2)7COOH
Arachidonic CH3(CH2)4-(CH=CH-CH2)4-(CH2)2-COOH
Figure 3-8. Formation of triglyceride from glycerol and fatty acids.
O
H2C
H2C
OH
HC
OH
H2C
OH
O
3
R
O
O
+
C
C
R
HC
O
C
R
O
HO
H2C
O
C
R
+ 3H2O
Phospholipid structure.
OH
R
O
P
H
O
C
H
O
O
HC
O
C
O
H2C
O
C
Figure 3-9. Surfactant structures formed in solution.
a. Behavior of surfactants in solution.
Polar head
Nonpolar tail
Monolayer
Micelle
Monomers
b. Phospholipid bilayer structure.
Phospholipid
Steroid structure, example of cholesterol.
HO
Structure of poly-β-hydroxybutyric acid. The repeating unit is outlined.
O
CH3
C
O
CH
O
CH3
C
C
H2
O
CH
O
C
C
H2
O
Amino acid structure
COO-
COOH
R
C
H
R
C
H
NH3+
NH2
Peptide bond formation.
H
R1
C
NH2
H
O
+ R
2
C
OH
C
NH2
O
C
R1
OH
H
O
C
C
NH2
COOH
N
C
H
H
R2 + H2O
Ser
Figure 3-10. Tertiary
and quarternary
protein structure as
shown in bovine
insulin. This protein
consists of two
polypeptide chains
joined by two disulfide
bonds. Another
disulfide bond within
the smaller chain
contributes to the
molecule’s shape.
Gly
Leu
Val
Glu Glu
Cys
S
S
Cys
Leu
Tyr
Glu
Val
Leu
Ser
Glu
Cys
Ala
Asp
S
S
Val
Asp
Glu
His Leu
Tyr
Cys
Cys
Gly
Asp
S
S
Ser
His
Tyr Leu Val Cys Gly Glu
Leu
Leu
Val
Glu
Arg
Gly
Ala
Phe
Phe
Thr Tyr
Ala
Lys
Pro
Figure 3-11. Enzyme control of proximity and orientation of substrates.
A
Product
+
B
+
+
Enzyme
Enzyme-substrate
complex
Figure 3-12. A hypothetical enzyme mechanism involving a cofactor.
Substrate
+
+
Cofactor
+
Enzymesubstratecofactor
complex
Enzyme
PURINES
PYRIMIDINES
NH2
O
N
H3 C
N
NH
N
OH
N
N
P
O
CH2
O
O
OH
O
OH
5'
O
4'
P
O
CH2
O
1'
OH
Figure 3-13.
Nucleotide
structure.
H
3'
2'
OH
OH
Adenine
Thymine
O
NH2
N
NH
N
N
OH
N
NH2
N
O
P
O
OH
CH2
O
O
O
OH
P
O
CH2
O
OH
OH
Guanine
OH
Cytosine
O
NH
N
OH
O
P
O
CH2
O
OH
OH
OH
Uracil
O
Figure 3-14. DNA molecule section showing phosphate-sugar “backbone”.
3' end
5' end
CH3
O
O
H
O
O
H
N
P
N
N
OH
H
N
N
5'
CH2
Thymine
N
CH2
N
O
O
4'
H
O
O
O
1'
3'
Adenine
HO
2'
O
O
H
O
P
N
H
O
P
O
OH
N
N
H
N
O
N
O
CH2
O
H
N
CH2
O
N
H
Guanine
O
3' end
Cytosine
O
N
HO
P
O
5' end
O
Figure 3-15. Schematic of a two-dimensional thin layer chromatograph separation
of amino acids. [Based on White, et. al., 1973.]
1.0
Arg
Phe
Pro
Met
Ile
Lys
Val
Leu
Trp
His
Gln
1.0
Ala
Thr
Asn
Tyr
Gly
Ser
Glu
0.3
Asp
CySSCy
0.0
0.0
0.3
0.6
1.0