chemical bldg blocks of life chapter 3
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The Chemical Building
Blocks of Life
1
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Organic Chemistry
Organic molecules contain carbon
Abundant in living organisms
Macromolecules are large, complex organic
molecules
2
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3
Carbon
Framework of biological moleculesconsists primarily of carbon bonded to
Carbon
O, N, S, P or H
Can form up to 4 covalent bonds
Hydrocarbonsmolecule consisting only
of carbon and hydrogen Nonpolar
Functional groups add chemical properties
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4
Hydroxyl
Carbonyl
Carboxyl
Amino
Sulfhydryl
Phosphate
Methyl
Example
OH
O
C
O
OH
C
H
H
N
S H
O
proteins
proteins
H
H
Glycerol phosphate
Alanine
Cysteine
Alanine
Acetic acid
Acetaldehyde
Ethanol
COOH
NH2
HH
H
HH
C OHC
O
H C C
H
H
H
H C
O
OHH
C
O H
N
H
HCH3
H C HSCH2
NH2
OH OH H
P
O
P O
O
O
OCCCH
H H H
O H
HO C C
H C H
H
O
O
H
C
HO C C
H
Found
In
carbo-
hydrates,
proteins,
nucleic
acids,
lipids
carbo-
hydrates,
nucleic
acids
proteins,
lipids
proteins,
nucleic
acids
nucleic
acids
Functional
Group
Structural
Formula
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Isomers
Molecules with the same molecular or
empirical formula
Structural isomers
Stereoisomersdiffer in how groups attached
Enantiomers
mirror image molecules
chiral
D-sugars and L-amino acids
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Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
C
W
Y
W
Y
C
Z
X
Z
X
Mirror
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Macromolecules
Polymerbuilt by linking monomers
Monomersmall, similar chemical subunits
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Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
O
P
P
OH
HO
H
OH
H
OHOH
H
H
H
O
Cellular Structure Polymer Monomer
Chromosome DNA strand Nucleotide
MonosaccharideStarchStarch grains in a chloroplast
5-carbon sugar
Phosphate
group
Nitrogenous base
CH2OH
Carbohydrate
Nuc
leicAcid
P
P
P
PP
P
P
G
C
T
A
A
T
P
A
P
P
P
P
G
C
P
P
T
A
G
C
P
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AlaAla
ValVal
Ser O
NH
C
H
OHH
C
CH3
Intermediate filament Polypeptide Amino acid
Protein
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
HO H H H H H H H H H H
HHO C C C C C C C C C C C C
H H H H H H H H H H H
Adipose cell with fat dropletsTriglyceride
Fatty acid
Lipid
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Dehydration synthesis
Formation of large molecules by the removal of water
Monomers are joined to form polymers
Hydrolysis
Breakdown of large molecules by the addition of
water
Polymers are broken down to monomers
HO
HO H
HO HH HHO
HO H HHO
a.Dehydration reaction b .Hydrolysis reaction
H2O H2O
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Carbohydrates
Molecules with a 1:2:1 ratio of carbon,
hydrogen, oxygen
Empirical formula (CH2O)
n
CH covalent bonds hold much energy
Carbohydrates are good energy storage
molecules
Examples: sugars, starch, glucose
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H
CH2OH
H
OH
OH HH
H
C
CC
C
C
C
C
H
C H
HO
OHH
OHH C
OHH C
OHH C
H
O H
C HH
OH
H
OH
H
O H
H
OH
H
OH HH
H
C
CC
C
C O
OH
OH HH
H
C
CC
C
OC
OH
OH
O
H23
5
14
6
5
4
3
2
1
23
5
6
14
23
5
14
-glucoseor
-glucose
OO
CH2OH
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Fructose Glucose Galactose
H OH
O
C
C
C
C
C
C
H
H
HO H
H OH
H OH
H OH
H
OC
C
C
C
C
H
H
HO H
OH
H OH
H OH
OC
C
C
C
C
C
H
H
H
HO H
OH
H OH
H OH
CH OH HO H
Stereo-
isomer
Structural
isomer
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Disaccharides
2 monosaccharides linked together by
dehydration synthesis
Used for sugar transport or energy storage
Examples: sucrose, lactose, maltose
OH
SucroseFructose-glucose
HO
CH2OH
H
OH
H
OHH
H
H
O
H
OH H
HO
HO
H
OH
H
OH OHH
H
O
H OH
OH H
HO
+
a. b.
Maltose
HO
H
OH
H
OH OH
H
H
O H
OH
H
OH
OH
HH
H
O
OHHO
H2O
CH2OH CH2OH CH2OH CH2OH CH2OH
CH2OH CH2OH
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Polysaccharides
Long chains of monosaccharides
Linked through dehydration synthesis
Energy storage
Plants use starch
Animals use glycogen
Structural support Plants use cellulose
Arthropods and fungi use chitin
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Glycogen
Amylose + Amylopectin
b .
a. c. 3.3 m
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
-glucose
HO
CH2OH
H
OH
H
OH H
H
H
O
OH
4 1
-1 4 linkages
CH2OH
OH
H
OH H
H
O
CH2OH
OH
H
OH H
H
O
CH2OH
OH
H
OH H
H
O
O O
H
-1 4 linkage
a -1
CH2OH
O
H
OH
H
OH H
H
H
O
CH2
H
OH
H
OH H
H
H
O
O
CH2OH
H
OH
H
OH H
H
H
O
6 linkage
b: Asa Th oresen/Photo Researchers, Inc .; c: J. Carson/Custom Medical Stock Photo
7.5 m
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HO
CH2OH
H
OH
H
OH HH
H
OCH2OH
H H
OH
H
OH HH
H
O
O
CH2OH
H
OH
H
OH HH
H
O
OHH
HO H H
H
CH2OH
O
-1 4 linkages
OHO O
O
4 1
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
b: Science VU/Visuals Unlimited
-glucose
500 mb.
a.
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Nucleic acids
Polymernucleic acids
Monomersnucleotides
sugar + phosphate + nitrogenous base
sugar is deoxyribose in DNA or ribose in RNA
Nitrogenous bases include Purines: adenine and guanine
Pyrimidines: thymine, cytosine, uracil
Nucleotides connected by phosphodiesterbonds
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5
3
P
P
P
P
OH
Phosphate group
O
O
NH2CC
NN
N
C
HN
C
CH
O
H
H
OC
NC
H
N
C
NH2
H
CH
a.
b .O
O
O
C
NC
H
N
CH3C
CH
H
O
O
C
NC
H
N
CH
CH
CC
NN
N
C
HN
C
CHH
O
4
5
1
3 2
4
5
1
3 2
4
5
1
3 2
4
5
1
32
Phosphodiester bonds
5-carbon sugar
Nitrogenous
base
NH2
GuanineAdenine
Purines
Pyrimidines
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Cytosine
(both DNA and RNA)
Thymine
(DNA only)
Uracil
(RNA only)
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Deoxyribonucleic acid (DNA)
Encodes information for amino acid
sequence of proteins
Sequence of bases
Double helix2 polynucleotide strands
connected by hydrogen bonds
Base-pairing rules
A with T (or U in RNA)
C with G
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Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
5 end
P
P
P
P
P
C
G
A
A
OH
T
T
Phosphodiesterbonds
3 end
Sugarphosphatebackbone
Hydrogenbonds
between
nitrogenous bases
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Ribonucleic acid (RNA)
RNA similar to DNA except
Contains ribose instead of deoxyribose
Contains uracil instead of thymine
Single polynucleotide strand
RNA uses information in DNA to specify
sequence of amino acids in proteins
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Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
P
P
P
P
PP
P
P
P
P
P
P
P
P
P
G
C
G
C
T
A
A
A
A
T
T
G
Bases
Hydrogen bonding
Occurs between base-pairs
P
P
PP
P
P
P
G
G
C
A
A
U
U
Bases
Deoxyribose-phosphate
backbone
Ribose-phosphatebackbone
RNA
DNA
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Other nucleotides
ATP adenosine triphosphate
Primary energy currency of the cell
NAD+and FAD+
Electron carriers for many cellular reactions
4
56
2
394
8
7
1
3 2
5
1
CH2
OOO
O
OH OH
NH2
N
N
N
N
O
O O O OP P P
Triphosphate group
5-carbon sugar
O
Nitrogenous base
(adenine)
O O
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Proteins
Protein functions include:
1. Enzyme catalysis
2. Defense
3. Transport
4. Support
5. Motion
6. Regulation
7. Storage
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Proteins are polymers
Composed of 1 or more long, unbranched
chains
Each chain is a polypeptide
Amino acids are monomers
Amino acid structure
Central carbon atom
Amino group
Carboxyl group
Single hydrogen
Variable R group
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Amino acids joined by dehydration
synthesis
Peptide bond
RH
H
R
H O
R
OH
RH
OH
H2O
H
O
H
OH OH
O HH
CC C C
CC CC
N
N N
NH H
Amino acid
Dipeptide
Amino acid
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4 Levels of structure
The shape of a protein determines its
function
1. Primary structuresequence of amino acids
2. Secondary structureinteraction of groups
in the peptide backbone
helix
sheet
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4 Levels of structure
3. Tertiary structurefinal folded shape of a
globular protein
Stabilized by a number of forces
Final level of structure for proteins consisting
of only a single polypeptide chain
4. Quaternary structurearrangement of
individual chains (subunits) in a protein with2 or more polypeptide chains
32
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Primary Structure
Secondary Structure Secondary Structure
Tertiary Structure Quaternary Structure
N
H
H H
C C C N C C NC
O
O H
OH H
R
R
R
-pleated sheet -helix
C
H
R
The primary structure can foldInto a pleated sheet, or turn into a helix
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Additional structural characteristics
Motifs
Common elements of secondary structure
seen in many polypeptides
Useful in determining the function of unknownproteins
Domains
Functional units within a larger structure Most proteins made of multiple domains that
perform different parts of the proteins function
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Domain 3 Domain 2
Domain 1
DomainsMotifs
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--motif
Helix-turn-Helix
motif
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Once thought newly made proteins folded
spontaneously
Chaperone proteins help protein fold
correctly
Deficiencies in chaperone proteins
implicated in certain diseases
Cystic fibrosis is a hereditary disorder
In some individuals, protein appears to have
correct amino acid sequence but fails to fold
Chaperones
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Chance for protein to refold
ADP + P
Cap
ATP
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Correctly
folded
protein
Misfolded
protein
Chaperoneprotein
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Denaturation
Protein loses
structure and function
Due to environmental
conditions pH
Temperature
Ionic concentration of
solution
38
Properly folded protein
Denaturation
Denatured
protein
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Lipids
Loosely defined group of molecules with
one main chemical characteristic
They are insoluble in water
High proportion of nonpolar CH bonds
causes the molecule to be hydrophobic
Fats, oils, waxes, and even some vitamins
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Fats
Triglycerides Composed of 1 glycerol and 3 fatty acids
Fatty acids
Need not be identical Chain length varies
Saturatedno double bonds between carbonatoms
Higher melting point, animal origin
Unsaturated1 or more double bonds Low melting point, plant origin
Trans fats produced industrially
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C
C
H
H
C
H
H
C
H
H
O
C
H
CH C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
C
H H
C
H
C C
HH H H
C
H
C C
H
O
H
HH H
CH
H
CH
H
O
C
H
CH CH
H
CH
H
CH
H
CH
H
CH
H
CH
H
CH
CH
C
H
CH
CHH H
C
H
CH
CH H
O
H
H H
C
H
H
C
H
H
O
C
H
CH C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
C
H H
C
H H
C
H
C
H
H
C
H H
C
HH
C
H H
CO
O
C
H
C
H
H
C
H
H
C
H
H
CH C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
O
O
C
H
C
H
H
C
H
H
C
H
H
CH C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
O
O
C
H
CH
H
CH
H
CH
H
CH CH
H
CH
H
CH
H
CH
H
CH
H
CH
H
CH
H
CH
H
CH
H
CH
H
CH
H
CH
H
C
H
H
C
H
H
H
C
H
H
C
H
H
H
CH
H
CH
HO
H
H
Structural Formula Structural Formula
Space-Filling Model Space-Filling Model
a. b.
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Phospholipids
Composed of
Glycerol
2 fatty acidsnonpolar tails
A phosphate grouppolar head
Form all biological membranes
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Nonpolar
HydrophobicTails
PolarHydrop
hilicHeads
Choline
Phosphate
Glycerol
a. b. c. d.
CH2
CH2
CH2H2C
O
OO P
C
O O
OO
C
H
C
O-
N+(CH3)3
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
F
attyacid
F
attyacid
CH
CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3
CH
CH2CH2CH2CH2CH2CH2CHCHCH2CH2CH2CH2CH2CH2CH2CH3
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