copyright © 2005 pearson education, inc. publishing as benjamin cummings i-2- 1 the structure and...
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Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings I-2- 1
• The Structure and Function of Nucleic Acids and Proteins Macromolecules
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings I-2- 2
• Macromolecules
– Are large molecules composed of smaller molecules
– Are complex in their structures
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Concept 1: Most macromolecules are polymers, built from monomers
Three of the classes of life’s organic molecules are polymers
– Carbohydrates
– Proteins
– Nucleic acids
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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
(a) Dehydration reaction in the synthesis of a polymer
HO H1 2 3 HO
HO H1 2 3 4
H
H2O
Short polymer Unlinked monomer
Longer polymer
Dehydration removes a watermolecule, forming a new bond
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• Polymers can disassemble by
– Hydrolysis
(b) Hydrolysis of a polymer
HO 1 2 3 H
HO H1 2 3 4
H2O
HHO
Hydrolysis adds a watermolecule, breaking a bond
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The Diversity of Polymers
• Each class of polymer
– Is formed from a specific set of monomers
• 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
1 2 3 HOH
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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
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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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– Directs RNA synthesis
– Directs protein synthesis through RNA
1
2
3
Synthesis of mRNA in the nucleus
Movement of mRNA into cytoplasm
via nuclear pore
Synthesisof protein
NUCLEUSCYTOPLASM
DNA
mRNA
Ribosome
AminoacidsPolypeptide
mRNA
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The Structure of Nucleic Acids
• Nucleic acids
– Exist as polymers called polynucleotides
(a) Polynucleotide, or nucleic acid
3’C
5’ end
5’C
3’C
5’C
3’ endOH
O
O
O
O
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• Each polynucleotide
– Consists of monomers called nucleotides
Nitrogenousbase
Nucleoside
O
O
O
O P CH2
5’C
3’CPhosphate
group Pentosesugar
(b) Nucleotide
O
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Nucleotide Monomers
• Nucleotide monomers
– Are made up of nucleosides and phosphate groups
(c) Nucleoside components
CHCH
Uracil (in RNA)U
Ribose (in RNA)
Nitrogenous bases Pyrimidines
CN
NC
OH
NH2
CHCH
OC
NH
CH
HNC
O
CCH3
N
HNC
C
HO
O
CytosineC
Thymine (in DNA)T
NHC
N C
CN
C
CH
N
NH2 O
NHC
NHH
CC
N
NH
C NH2
AdenineA
GuanineG
Purines
OHOCH2
H
H H
OH
H
OHOCH2
HH H
OH
H
Pentose sugars
Deoxyribose (in DNA) Ribose (in RNA)OHOH
CH
CH
Uracil (in RNA)U
4’
5”
3’OH H
2’
1’
5”
4’
3’ 2’
1’
Pyrimidines
Purines
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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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The DNA Double Helix
• Cellular DNA molecules
– Have two polynucleotides that spiral around an imaginary axis
– Form a double helix
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• The DNA double helix
– Consists of two antiparallel nucleotide strands3’ end
Sugar-phosphatebackbone
Base pair (joined byhydrogen bonding)
Old strands
Nucleotideabout to be added to a new strand
A
3’ end
3’ end
5’ end
Newstrands
3’ end
5’ end
5’ end
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• The nitrogenous bases in DNA
– Form hydrogen bonds in a complementary fashion (A with T only, and C with G only)
Nitrogenousbase
Nucleoside
O
O
O
O P CH2
5’C
3’CPhosphate
group Pentosesugar
(b) Nucleotide
O
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Light absorption and temperature in DNA denaturation
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James Watson and Francis Crick with a model of the DNA molecule, the double helix.
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X-Ray Diffraction Photograph of a Hydrated DNA Fiber
Dr. Rosalind FranklinPhotograph 51
Rosalind Franklin: The Dark Lady of DNA
(Brenda Maddox, 2002)
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Dark Lady of DNA
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Electron Micrograph of Part of the E. coli genome
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討論:
•DNA有何特徵?– 1
– 2
– 3
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The chemical structure of RNA
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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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Complex Structure of an RNA Molecule
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討論:
•RNA有何特徵?– 1
– 2
– 3
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Concept 3: Proteins have many structures, resulting in a wide range of functions
– Proteins
• Have many roles inside the cell
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An overview of protein functions
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• Enzymes
– Are a type of protein that acts as a catalyst, speeding up chemical reactions
Substrate(sucrose)
Enzyme (sucrase)
Glucose
OH
H O
H2O
Fructose
3 Substrate is convertedto products.
1 Active site is available for a molecule of substrate, the
reactant on which the enzyme acts.
Substrate binds toenzyme.
22
4 Products are released.
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Polypeptides
• Polypeptides
– Are polymers of amino acids
• A protein
– Consists of one or more polypeptides
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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
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• 20 different amino acids make up proteins
O
O–
H
H3N+ C C
O
O–
H
CH3
H3N+ C
H
C
O
O–
CH3 CH3
CH3
C C
O
O–
H
H3N+
CH
CH3
CH2
C
H
H3N+
CH3
CH3
CH2
CH
C
H
H3N+ C
CH3
CH2
CH2
CH3N+
H
C
O
O–
CH2
CH3N+
H
C
O
O–
CH2
NH
H
C
O
O–
H3N+ C
CH2
H2C
H2N C
CH2
H
C
Nonpolar
Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)
Methionine (Met) Phenylalanine (Phe)
C
O
O–
Tryptophan (Trp) Proline (Pro)
H3C
S
O
O–
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O–
OH
CH2
C C
H
H3N+
O
O–
H3N+
OH CH3
CH
C C
HO–
O
SH
CH2
C
H
H3N+ C
O
O–
H3N+ C C
CH2
OH
H H H
H3N+
NH2
CH2
OC
C C
O
O–
NH2 O
C
CH2
CH2
C CH3N+
O
O–
O
Polar
Electricallycharged
–O O
C
CH2
C CH3N+
H
O
O–
O– O
C
CH2
C CH3N+
H
O
O–
CH2
CH2
CH2
CH2
NH3+
CH2
C CH3N+
H
O
O–
NH2
C NH2+
CH2
CH2
CH2
C CH3N+
H
O
O–
CH2
NH+
NHCH2
C CH3N+
H
O
O–
Serine (Ser) Threonine (Thr)Cysteine
(Cys)Tyrosine
(Tyr)Asparagine
(Asn)Glutamine
(Gln)
Acidic Basic
Aspartic acid (Asp)
Glutamic acid (Glu)
Lysine (Lys) Arginine (Arg) Histidine (His)
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Amino Acid Polymers
• Amino acids
– Are linked by peptide bondsOH
DESMOSOMES
DESMOSOMESDESMOSOMES
OH
CH2
C
N
H
C
H O
H OH OH
Peptidebond
OH
OH
OH
H H
HH
H
H
H
H
H
H H
H
N
N N
N N
SHSide
chains
SH
OO
O O O
H2O
CH2 CH2
CH2 CH2CH2
C C C C C C
C CC C
Peptidebond
Amino end(N-terminus)
Backbone
(a)
(b) Carboxyl end(C-terminus)
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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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Protein Conformation and Function
• A protein’s specific conformation
– Determines how it functions
• Two models of protein
• conformation:
(a) A ribbon model
(b) A space-filling model
Groove
Groove
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Four Levels of Protein Structure
• Primary structure
– Is the unique sequence of amino acids in a polypeptide
–
Amino acid subunits
+H3NAmino
end
oCarboxyl end
oc
GlyProThrGlyThr
Gly
GluSeuLysCysProLeu
MetVal
Lys
ValLeu
AspAlaVal ArgGly
SerPro
Ala
Gly
lle
SerProPheHisGluHis
Ala
GluVal
ValPheThrAlaAsn
AspSer
GlyProArg
ArgTyrThr
lleAla
Ala
Leu
LeuSer
ProTyrSerTyrSerThr
Thr
Ala
ValVal
ThrAsnProLysGlu
ThrLys
SerTyrTrpLysAlaLeu
GluLle Asp
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O C helix
pleated sheet
Amino acidsubunits NC
H
C
O
C N
H
CO H
R
C NH
C
O H
C
R
N
HH
R C
O
R
C
H
NH
C
O H
NCO
R
C
H
NH
H
C
R
C
O
C
O
C
NH
H
R
C
C
O
N
HH
C
R
C
O
NH
R
C
H C
ON
HH
C
R
C
O
NH
R
C
H C
ON
HH
C
R
C
O
N H
H C R
N HO
O C N
C
RC
H O
CHR
N H
O C
RC
H
N H
O CH C R
N H
CC
N
R
H
O C
H C R
N H
O C
RC
H
H
C
RN
H
CO
C
NH
R
C
H C
O
N
H
C
• Secondary structure
– Is the folding or coiling of the polypeptide into a repeating configuration
– Includes the helix and the pleated sheet
H H
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• Tertiary structure
– Is the overall three-dimensional shape of a polypeptide
– Results from interactions between amino acids and R groups
CH2CH
OH
O
CHO
CH2
CH2 NH3+ C-O CH2
O
CH2SSCH2
CH
CH3
CH3
H3C
H3C
Hydrophobic interactions and van der Waalsinteractions
Polypeptidebackbone
Hyrdogenbond
Ionic bond
CH2
Disulfide bridge
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• Quaternary structure
– Is the overall protein structure that results from the aggregation of two or more polypeptide subunits
Polypeptidechain
Collagen Chains
ChainsHemoglobin
IronHeme
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• The four levels of protein structure
+H3NAmino end
Amino acidsubunits
helix
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Sickle-Cell Disease: A Simple Change in Primary Structure
• Sickle-cell disease
– Results from a single amino acid substitution in the protein hemoglobin
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• Hemoglobin structure and sickle-cell disease
Fibers of abnormalhemoglobin deform cell into sickle shape.
Primary structure
Secondaryand tertiarystructures
Quaternary structure
Function
Red bloodcell shape
Hemoglobin A
Molecules donot associatewith oneanother, eachcarries oxygen.
Normal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen
10 m 10 m
Primary structure
Secondaryand tertiarystructures
Quaternary structure
Function
Red bloodcell shape
Hemoglobin S
Molecules interact with one another tocrystallize into a fiber, capacity to carry oxygen is greatly reduced.
subunit subunit
1 2 3 4 5 6 7 3 4 5 6 721
Normal hemoglobin Sickle-cell hemoglobin. . .. . . Exposed
hydrophobic region
Val ThrHis Leu Pro Glul Glu Val His Leu Thr Pro Val Glu
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What Determines Protein Conformation?
• Protein conformation
– Depends on the physical and chemical conditions of the protein’s environment
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Denaturation
• Is when a protein unravels and loses its native conformation
Denaturation
Renaturation
Denatured proteinNormal protein
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Flexibility and Function: the protein lactoferrin
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The Protein-Folding Problem
• Most proteins
– Probably go through several intermediate states on their way to a stable conformation
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Chaperonins
– Are protein molecules that assist in the proper folding of other proteins
Hollowcylinder
Cap
Chaperonin(fully assembled)
Steps of ChaperoninAction: An unfolded poly- peptide enters the cylinder from one end.
The cap attaches, causing the cylinder to change shape insuch a way that it creates a hydrophilic environment for the folding of the polypeptide.
The cap comesoff, and the properlyfolded protein is released.
Correctlyfoldedprotein
Polypeptide
2
1
3
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X-ray crystallography
• Is used to determine a protein’s three-dimensional structure X-ray
diffraction pattern
Photographic film
Diffracted X-rays
X-raysource
X-ray beam
Crystal Nucleic acid Protein
(a) X-ray diffraction pattern (b) 3D computer model
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An overview of protein functions
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討論:
•蛋白質有何特徵?– 1
– 2
– 3