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• The Structure and Function of
Nucleic Acids and Proteins
Macromolecules
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 1
• Macromolecules
– Are large molecules composed of smaller
molecules
– Are complex in their structures
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 2
Concept 1: Most macromolecules are polymers,
built from monomers
Three of the classes of life’s organic
molecules are polymers
– Carbohydrates
– Proteins
– Nucleic acids
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 3
The Synthesis and Breakdown of Polymers
• A polymer is a long molecule consisting of
many similar building blocks called monomers
• Monomers form larger molecules by
condensation reactions called dehydration
reactions
HO
1
3
2
H
Unlinked monomer
Short polymer
Dehydration removes a water
molecule, forming a new bond
HO
1
2
H
HO
3
H2O
4
H
Longer polymer
(a) Dehydration reaction in the synthesis of a polymer
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 4
• Polymers can disassemble by
– Hydrolysis
HO
1
2
3
4
Hydrolysis adds a water
molecule, breaking a bond
HO
1
2
3
H
H
H2O
HO
H
(b) Hydrolysis of a polymer
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 5
The Diversity of Polymers
• Each class of polymer
– Is formed from a specific set of monomers
1
2
3
H
HO
• Although organisms share the same limited
number of monomer types, each organism is
unique based on the arrangement of
monomers into polymers
• An immense variety of polymers can be built
from a small set of monomers
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 6
Concept 2: Nucleic acids store and transmit
hereditary information
• Genes
– Are the units of inheritance
– Program the amino acid sequence of
polypeptides
– Are made of nucleic acids
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 7
The Roles of Nucleic Acids
• There are two types of nucleic acids
– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)
• DNA
– Stores information for the synthesis of specific
proteins
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I-2- 8
– Directs RNA synthesis
– Directs protein synthesis through RNA
DNA
1 Synthesis of
mRNA in the nucleus
mRNA
NUCLEUS
CYTOPLASM
mRNA
2 Movement of
mRNA into cytoplasm
via nuclear pore
Ribosome
3 Synthesis
of protein
Polypeptide
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Amino
acids
I-2- 9
The Structure of Nucleic Acids
• Nucleic acids
– Exist as polymers called polynucleotides
5’ end
5’C
O
3’C
O
O
5’C
O
3’C
OH
3’ end
(a) Polynucleotide,
or nucleic acid
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 10
• Each polynucleotide
– Consists of monomers called nucleotides
Nucleoside
Nitrogenous
base
5’C
O

O
P
O
CH2
O
O
Phosphate
group
3’C
Pentose
sugar
(b) Nucleotide
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 11
Nucleotide Monomers
• Nucleotide monomers
– Are made up of nucleosides and phosphate
groups
Pyrimidines
Nitrogenous bases
Pyrimidines
NH2
O
O
C
C
CH
C
3
N
CH
C
CH HN
HN
CH
C
CH
C
C
CH
N
N
O
N
O
O
H
H
H
Cytosine Thymine (in DNA) Uracil
(in
RNA)
Uracil (in RNA)
U
C
U
T
Purines
O
NH2
N C C
N CC
NH
N
HC
HC
C
CH
N C
N
NH2
N
N
H
H
Adenine
Guanine
A
G
5”
Pentose sugars
HOCH2 O OH
4’
Purines
H H
1’
5”
HOCH2 O OH
4’
H H
1’
H
H
H 3’ 2’ H
3’ 2’
OH H
OH OH
Deoxyribose (in DNA) Ribose (in RNA)
(c) Nucleoside components
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 12
Nucleotide Polymers
• Nucleotide polymers
– Are made up of nucleotides linked by the–OH
group on the 3´ carbon of one nucleotide and
the phosphate on the 5´ carbon on the next
• The sequence of bases along a nucleotide
polymer
– Is unique for each gene
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I-2- 13
The DNA Double Helix
• Cellular DNA molecules
– Have two polynucleotides that spiral around an
imaginary axis
– Form a double helix
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I-2- 14
• The DNA double helix
– Consists of two antiparallel nucleotide strands
5’ end
3’ end
Sugar-phosphate
backbone
Base pair (joined by
hydrogen bonding)
Old strands
A 3’ end
Nucleotide
about to be
added to a
new strand
5’ end
3’ end
5’ end
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
New
strands
3’ end
I-2- 15
• The nitrogenous bases in DNA
– Form hydrogen bonds in a complementary
fashion (A with T only, and C with G only)
Nucleoside
Nitrogenous
base
5’C
O

O
P
O
CH2
O
O
Phosphate
group
3’C
Pentose
sugar
(b) Nucleotide
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 16
Light absorption and temperature in DNA denaturation
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 17
James Watson and Francis Crick with a model of
the DNA molecule, the double helix.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 18
X-Ray Diffraction Photograph of a Hydrated DNA
Fiber
Rosalind Franklin: The
Dark Lady of DNA
(Brenda Maddox, 2002)
Photograph 51
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Dr. Rosalind Franklin
I-2- 19
Dark Lady of DNA
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I-2- 20
Electron Micrograph of Part of the E. coli genome
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I-2- 21
討論：
•DNA有何特徵？
– １
– ２
– ３
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 22
The chemical structure of RNA
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I-2- 23
The conformation of an RNA molecule
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Transfer RNA (tRNA)
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RNA secondary and tertiary structures
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I-2- 26
Complex Structure of an RNA Molecule
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I-2- 27
討論：
•RNA有何特徵？
– １
– ２
– ３
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 28
Concept 3: Proteins have many structures,
resulting in a wide range of functions
– Proteins
• Have many roles inside the cell
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I-2- 29
An overview of protein functions
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 30
• Enzymes
– Are a type of protein that acts as a catalyst,
speeding up chemical reactions
1 Active site is available for
a molecule of substrate, the
reactant on which the enzyme acts.
Substrate
(sucrose)
2 Substrate binds to
enzyme.
Glucose
OH
Enzyme
(sucrase)
H2O
Fructose
H O
4 Products are released.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
3 Substrate is converted
to products.
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Polypeptides
• Polypeptides
– Are polymers of amino acids
• A protein
– Consists of one or more polypeptides
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 32
Amino Acid Monomers
• Amino acids
– Are organic molecules possessing both
carboxyl and amino groups
– Differ in their properties due to differing side
chains, called R groups
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 33
• 20 different amino acids make up proteins
CH3
CH3
H
H3N+
C
CH3
O
H3N+
C
H
Glycine (Gly)
O–
C
H3N+
C
H
Alanine (Ala)
O–
CH
CH3
CH3
O
C
CH2
CH2
O
H3N+
C
H
Valine (Val)
CH3
CH3
O–
C
O
H3N+
C
H
Leucine (Leu)
H3C
O–
CH
O
C
C
O–
H
Isoleucine (Ile)
Nonpolar
CH3
CH2
S
NH
CH2
CH2
H3N+
C
H
CH2
O
H3N+
C
O–
Methionine (Met)
C
H
H3 N+
C
C
O–
Phenylalanine (Phe)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
CH2
O
H
O
H2C
CH2
H2N
C
O
C
O–
H
C
O–
Tryptophan (Trp)
Proline (Pro)
I-2- 34
OH
OH
Polar
CH2
H3N+
C
CH
O
H3N+
C
O–
H
Serine (Ser)
C
CH2
O
H3N+
C
O–
H
C
CH2
O
C
H
O–
H3N+
C
O
H3N+
C
O–
H
Electrically
charged
H3N+
CH2
C
H3N+
O–
C
NH3+
O
C
CH2
C
CH2
CH2
CH2
CH2
CH2
CH2
O
CH2
C
O–
H
H3N+
C
O
CH2
C
H
O–
H3N+
C
H
O–
H
Glutamic acid
(Glu)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
NH+
C
O–
Lysine (Lys)
NH2+
H3N+
CH2
O
CH2
H3N+
C
H
Aspartic acid
(Asp)
O
C
Glutamine
(Gln)
NH2
C
C
C
Basic
O–
O
O
Asparagine
(Asn)
Acidic
–O
CH2
CH2
H
Tyrosine
(Tyr)
Cysteine
(Cys)
Threonine (Thr)
C
NH2 O
C
SH
CH3
OH
NH2 O
NH
CH2
O
C
C
O–
H
O
C
O–
Arginine (Arg)
Histidine (His)
I-2- 35
Amino Acid Polymers
• Amino acids
– Are linked by peptide bonds
Peptide
bond
OH
CH2
SH
CH2
H
N
H
OH
CH2
H
C C
H
N C C OH H N C
H O
H O
H
(a)
C OH
O DESMOSOMES
H2O
OH
DESMOSOMES
DESMOSOMES
SH
OH
Peptide
CH2 bond CH2
CH2
H
H N C C
H O
(b)
Amino end
(N-terminus)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
H
H
N C C
H O
N C C OH
Side
chains
Backbone
H O
Carboxyl end
(C-terminus)
I-2- 36
Determining the Amino Acid Sequence of a Polypeptide
• The amino acid sequences of polypeptides
– Were first determined using chemical means
– Can now be determined by automated
machines
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I-2- 37
Protein Conformation and Function
• A protein’s specific conformation
– Determines how it functions
• Two models of protein
Groove
• conformation:
(a) A ribbon model
Groove
(b) A space-filling model
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 38
Four Levels of Protein Structure
• Primary structure
– Is the unique sequence of amino acids in a
polypeptide
HN
Amino acid
+
Gly ProThr Gly
Thr
3
Amino
end
Gly
Glu
Cys LysSeu
LeuPro
Met
Val
Lys
subunits
Val
Leu
Asp
AlaVal Arg Gly
Ser
Pro
Ala
Glu Lle
Leu Ala
Gly
Asp
Thr
Lys
Ser
Lys Trp Tyr
lle
Ser
ProPhe
His Glu
Ala Thr PheVal
Asn
His
Ala
Glu
Val
Asp
Tyr
Arg
Ser
Arg
Gly Pro
Thr Ser
Tyr
Thr
lle
Ala
Ala
Leu
Leu
Ser
Pro
SerTyr
Thr
Ala
Val
Val
LysGlu
Thr
AsnPro
c
o
o–
Carboxyl end
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I-2- 39
• Secondary structure
– Is the folding or coiling of the polypeptide into a
repeating configuration
– Includes the  helix and the  pleated sheet
 pleated sheet
O H H
C C N
Amino acid
subunits
C N
H
R
R
O H H
C C N
C C N
O H H
R
R
O H H
C C N
C C N
OH H
R
R
R
O
R
C
H
H
R
O C
O C
N H
N H
N H
O C
O C
H C R H C R
H C R H C
R
N H O C
N H
O C
O C
H
C
O
N H
N
C
C
H
R
H
R
N
C
C
H
O H H
C C N
C C N
OH H
R
O
C
H
H
H C N HC
C N HC N
C
N
H
H
C
O
C
C
O
R
R
O
R
O
C
H
H
NH C N
C
H
O C
R
C C
O
R
R
H
C
N HC N
H
O C
H
 helix
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 40
• Tertiary structure
– Is the overall three-dimensional shape of a
polypeptide
– Results from interactions between amino acids
and R groups
Hydrophobic
Hyrdogen
bond
CH22
CH
O
H
O
CH
H3C
CH3
H3C
CH3
CH
interactions and
van der Waals
interactions
Polypeptide
backbone
HO C
CH2
CH2 S S CH2
Disulfide bridge
O
CH2 NH3+ -O C CH2
Ionic bond
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I-2- 41
• Quaternary structure
– Is the overall protein structure that results from
the aggregation of two or more polypeptide
subunits
Polypeptide
chain
Collagen
 Chains
Iron
Heme
 Chains
Hemoglobin
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I-2- 42
• The four levels of protein structure
+H
3N
Amino end
Amino acid
subunits
helix
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I-2- 43
Sickle-Cell Disease: A Simple Change in
Primary Structure
• Sickle-cell disease
– Results from a single amino acid substitution in
the protein hemoglobin
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Hemoglobin structure and sickle-cell disease
Primary
structure
Normal hemoglobin
Val
His Leu Thr
1 2 3 4 5 6 7
Secondary
and tertiary
structures
Red blood
cell shape
Val
His
Leu Thr


Molecules do
not associate
with one
another, each
carries oxygen.


Quaternary
structure
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Val Glu
...




10 m
Red blood
cell shape
Exposed
hydrophobic
region
 subunit
Function
10 m
Normal cells are
full of individual
hemoglobin
molecules, each
carrying oxygen
Pro
structure 1 2 3 4 5 6 7
Secondary
 subunit and tertiary
structures
Quaternary Hemoglobin A
structure
Function
Pro Glul Glu
Sickle-cell hemoglobin
. . . Primary
Hemoglobin S
Molecules
interact with
one another to
crystallize into a
fiber, capacity to
carry oxygen is
greatly reduced.
Fibers of abnormal
hemoglobin
deform cell into
sickle shape.
I-2- 45
What Determines Protein Conformation?
• Protein conformation
– Depends on the physical and chemical
conditions of the protein’s environment
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I-2- 46
Denaturation
• Is when a protein unravels and loses its native
conformation
Denaturation
Normal protein
Denatured protein
Renaturation
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I-2- 47
Flexibility and Function: the protein lactoferrin
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I-2- 48
The Protein-Folding Problem
• Most proteins
– Probably go through several intermediate
states on their way to a stable conformation
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I-2- 49
Chaperonins
– Are protein molecules that assist in the proper
folding of other proteins
Polypeptide
Cap
Correctly
folded
protein
Hollow
cylinder
Chaperonin
(fully assembled)
Steps of Chaperonin
Action:
1 An unfolded polypeptide enters the
cylinder from one end.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
2 The cap attaches, causing
3 The cap comes
the cylinder to change shape in off, and the properly
such a way that it creates a
folded protein is
hydrophilic environment for the released.
folding of the polypeptide.
I-2- 50
X-ray crystallography
• Is used to determine a protein’s threedimensional structure
X-ray
diffraction
pattern
Photographic film
Diffracted X-rays
X-ray
source
X-ray
beam
Crystal
(a) X-ray diffraction pattern
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Nucleic acid
Protein
(b) 3D computer model
I-2- 51
An overview of protein functions
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 52
討論：
•蛋白質有何特徵？
– １
– ２
– ３
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
I-2- 53