Chapter 5: Microbiology Basics Chapter 5: Microbiology Basics.
Chapter 5
description
Transcript of Chapter 5
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Chapter 5The Structure and
Function of Macromolecules
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The Molecules of Life• Overview:
– Another level in the hierarchy of biological organization is reached when small organic molecules are joined together
– Atom ---> molecule --- compound
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Macromolecules– Are large molecules composed of
smaller molecules– Are complex in their structures
Figure 5.1
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Macromolecules•Most macromolecules are polymers, built from monomers• Four classes of life’s organic molecules are polymers
– Carbohydrates– Proteins– Nucleic acids– Lipids
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• A polymer– Is a long molecule consisting of many
similar building blocks called monomers– Specific monomers make up each
macromolecule– E.g. amino acids are the monomers for
proteins
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The Synthesis and Breakdown of Polymers
• Monomers form larger molecules by condensation reactions called dehydration synthesis
(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
Figure 5.2A
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The Synthesis and Breakdown of Polymers
• Polymers can disassemble by– Hydrolysis (addition of water
molecules)
(b) Hydrolysis of a polymerHO 1 2 3 H
HO H1 2 3 4
H2O
HHO
Hydrolysis adds a watermolecule, breaking a bond
Figure 5.2B
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• 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
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Carbohydrates• Serve as fuel and building
material• Include both sugars and
their polymers (starch, cellulose, etc.)
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Sugars• Monosaccharides
– Are the simplest sugars– Can be used for fuel– Can be converted into other
organic molecules– Can be combined into polymers
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• Examples of monosaccharidesTriose sugars
(C3H6O3)Pentose sugars
(C5H10O5)Hexose sugars
(C6H12O6)
H C OHH C OHH C OHH C OHH C OH
H C OHHO C H
H C OHH C OHH C OH
H C OHHO C HHO C H
H C OHH C OH
H C OH
H C OH
H C OH
H C OHH C OHH C OH
H C OHC OC O
H C OHH C OHH C OH
HO C H
H C OHC O
H
H
H
H H H
H
H H H H
HH H
C C C COOOO
Aldo
ses
GlyceraldehydeRibose
Glucose Galactose
Dihydroxyacetone
Ribulose
Keto
ses
FructoseFigure 5.3
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• Monosaccharides– May be linear– Can form rings
H
H C OH
HO C H
H C OH
H C OH
H C
OC
H
12
3
4
5
6
H
OH
4C
6CH2OH 6CH2OH
5C
HOH
CH OH
H2 C
1CH
O
H
OH
4C
5C
3 CH
HOH
OH
H2C
1 C
OH
HCH2OH
H
H
OHHO
H
OH
OH
H5
3 2
4
(a) Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5.
OH 3
O H OO6
1
Figure 5.4
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• Disaccharides–Consist of two monosaccharides
–Are joined by a glycosidic linkage
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Dehydration reaction in the synthesis of maltose. The bonding of two glucose units forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide.
Dehydration reaction in the synthesis of sucrose. Sucrose is a disaccharide formed from glucose and fructose.Notice that fructose,though a hexose like glucose, forms a five-sided ring.
(a)
(b)
H
HOH
HOH H
OH
O H
OH
CH2OH
H
HO
H
HOH H
OH
O HOH
CH2OH
H
O
H
HOH H
OH
O H
OH
CH2OH
H
H2O
H2O
H
H
O
H
HOH
OH
O HCH2OH
CH2OH HO
OHH
CH2OH
HOH H
H
HO
OHH
CH2OH
HOH H
O
O H
OHH
CH2OH
HOH H
O
HOH
CH2OH
H HO
O
CH2OH
H
H
OH
O
O
1 2
1 41– 4
glycosidiclinkage
1–2glycosidic
linkage
Glucose
Glucose Glucose
Fructose
Maltose
Sucrose
OH
H
H
Figure 5.5
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Polysaccharides• Polysaccharides
– Are polymers of sugars– Serve many roles in organisms
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Storage Polysaccharides• Starch
– Is a polymer consisting entirely of glucose monomers
– Is the major storage form of glucose in plants
Chloroplast Starch
Amylose Amylopectin
1 m
(a) Starch: a plant polysaccharideFigure 5.6
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• Glycogen– Consists of glucose monomers– Is the major storage form of glucose in
animals Mitochondria Giycogen granules
0.5 m
(b) Glycogen: an animal polysaccharide
Glycogen
Figure 5.6
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Structural Polysaccharides
• Cellulose– Is a polymer of glucose
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– Has different glycosidic linkages than starch
(c) Cellulose: 1– 4 linkage of glucose monomers
H O
O
CH2OH
HOH H
H
OHO
HH
H
HO
4
CCCCCC
H
H
H
HO
OH
HOHOHOH
H
O
CH2OH
HH
H
OH
OHH
H
HO4 O
H
CH2OH O
OH
OH
HO
41O
CH2OH O
OH
OH
O
CH2OH O
OH
OH
CH2OH O
OH
OH
O O
CH2OH O
OH
OH
HO
4O
1
OH
O
OH O
HO
CH2OH O
OH
O OH
O
OH
OH
(a) and glucose ring structures
(b) Starch: 1– 4 linkage of glucose monomers
1
glucose glucose
CH2OH
CH2OH
1 4 41 1
Figure 5.7 A–C
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Plant cells
0.5 m
Cell wallsCellulose microfibrils
in a plant cell wall
Microfibril
CH2OH
CH2OHOH
OH
OO OHO
CH2OHO
OOH
OCH2OH OH
OH OHO
O
CH2OHO
O OH
CH2OH
OO
OH
O
O
CH2OHOHCH2OHOH
OOH OH OH OH
O
OH OHCH2OH
CH2OHOHO
OH CH2OH
OO
OH CH2OHOH
Glucose monomer
O
O
O
OO
O
Parallel cellulose molecules areheld together by hydrogenbonds between hydroxyl
groups attached to carbonatoms 3 and 6.
About 80 cellulosemolecules associate
to form a microfibril, themain architectural unitof the plant cell wall.
A cellulose moleculeis an unbranched glucose polymer.
OH
OH
O
OOH
Cellulosemolecules
Figure 5.8
– Is a major component of the tough walls that enclose plant cells
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• Cellulose is difficult to digest– Cows have microbes in their stomachs
to facilitate this process
Figure 5.9
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• Chitin, another important structural polysaccharide– Is found in the exoskeleton of
arthropods– Can be used as surgical thread
(a) The structure of the chitin monomer.
OCH2O
H
OHHH OH
HNHCCH3
O
H
H
(b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emergingin adult form.
(c) Chitin is used to make a strong and flexible surgical
thread that decomposes after the wound or incision heals.
OH
Figure 5.10 A–C
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Lipids• Lipids are a diverse group of
hydrophobic molecules• Lipids
– Are the one class of large biological molecules that do not consist of polymers
– Share the common trait of being hydrophobic
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Fats– Are constructed from two types of smaller
molecules, a single glycerol and usually three fatty acids
– Vary in the length and number and locations of double bonds they contain
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Fats– Are constructed from two types of smaller
molecules, a single glycerol and usually three fatty acids
– Vary in the length and number and locations of double bonds they contain
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Fats• Are constructed from two types of smaller
molecules, a single glycerol and usually three fatty acids
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Fats• Vary in the length and number and
locations of double bonds they contain
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• Saturated fatty acids– Have the maximum number of
hydrogen atoms possible– Have no double bonds
(a) Saturated fat and fatty acid
Stearic acid
Figure 5.12
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• Unsaturated fatty acids– Have one or more double bonds
(b) Unsaturated fat and fatty acidcis double bondcauses bending
Oleic acid
Figure 5.12
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• Phospholipids– Have only two fatty acids– Have a phosphate group instead of
a third fatty acid
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• Phospholipid structure– Consists of a hydrophilic “head”
and hydrophobic “tails”CH2
OPO OOCH2CHCH2
OOC O C O
Phosphate
Glycerol
(a) Structural formula (b) Space-filling model
Fatty acids
(c) Phospholipid symbol
Hyd
r oph
obic
tai
ls
Hydrophilichead
Hydrophobictails
–
Hyd
r oph
ilic
h ead CH2 Choline+
Figure 5.13
N(CH3)3
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• The structure of phospholipids– Results in a bilayer arrangement found
in cell membranes
Hydrophilichead
WATER
WATERHydrophobictail
Figure 5.14
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Steroids• Steroids
– Are lipids characterized by a carbon skeleton consisting of four fused rings
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• One steroid, cholesterol– Is found in cell membranes– Is a precursor for some hormones
HO
CH3
CH3
H3C CH3
CH3
Figure 5.15
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Proteins• Proteins have many
structures, resulting in a wide range of functions
• Proteins do most of the work in cells and act as enzymes
• Proteins are made of monomers called amino acids
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• An overview of protein functions
Table 5.1
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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
H2OFructose
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.
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4 Products are released.Figure 5.16
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Polypeptides• Polypeptides
– Are polymers (chains) of amino acids
• A protein– Consists of one or more
polypeptides
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• 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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Twenty Amino Acids• 20 different amino acids make up proteins
O
O–
H
H3N+ C CO
O–H
CH3
H3N+ C
H
CO
O–
CH3 CH3
CH3
C CO
O–
H
H3N+
CHCH3
CH2
C
H
H3N+
CH3CH3
CH2
CH
C
H
H3N+ C
CH3
CH2
CH2
CH3N+
H
CO
O–
CH2
CH3N+
H
CO
O–
CH2
NH
H
CO
O–
H3N+ C
CH2
H2C
H2N C
CH2
H
C
NonpolarGlycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)
Methionine (Met) Phenylalanine (Phe)
CO
O–
Tryptophan (Trp) Proline (Pro)
H3C
Figure 5.17
S
O
O–
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O–
OHCH2
C CH
H3N+
O
O–
H3N+
OH CH3
CHC CH O–
O
SHCH2
CH
H3N+ C
O
O–
H3N+ C C
CH2
OH
H H H
H3N+
NH2
CH2
OC
C CO
O–
NH2 OCCH2
CH2
C CH3N+
O
O–
OPolar
Electricallycharged
–O OCCH2
C CH3N+
H
O
O–
O– OCCH2
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 bonds
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Protein Conformation and Function
• A protein’s specific conformation (shape) determines how it functions
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Four Levels of Protein Structure
• Primary structure– Is the unique
sequence of amino acids in a polypeptide
Figure 5.20–
Amino acid
subunits
+H3NAmino
end
oCarboxyl end
oc
GlyProThrGlyThr
GlyGluSeuLysCysProLeu
MetVal
LysVal
LeuAspAlaValArgGlySerPro
Ala
GlylleSerProPheHisGluHis
AlaGlu
ValValPheThrAlaAsnAsp
SerGlyProArg
ArgTyrThr lleAla
AlaLeu
LeuSerProTyrSerTyrSerThr
ThrAlaVal
ValThrAsnProLysGlu
ThrLysSer
TyrTrpLysAlaLeu
GluLleAsp
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O C helix
pleated sheetAmino acid
subunitsNCH
CO
C NH
CO H
RC N
H
CO H
CR
NHH
R CO
RCH
NH
CO H
NCO
RCH
NH
HCR
CO
CO
CNH
H
RC
CO
NH H
CR
CO
NH
RCH C
ONH H
CR
CO
NH
RCH C
ONH H
CR
CO
N H
H C RN H O
O C NC
RC
H O
CHR
N HO C
RC H
N H
O CH C R
N H
CC
NR
HO C
H C R
N HO C
RC H
HCR
NH
CO
C
NH
RCH C
ONH
C
• Secondary structure– Is the folding or coiling of the
polypeptide into a repeating configuration
– Includes the helix and the pleated sheet
H H
Figure 5.20
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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
OHOCHOCH2
CH2 NH3+ C-O CH2
O
CH2SSCH2
CH
CH3CH3
H3CH3C
Hydrophobic interactions and van der Waalsinteractions Polypeptid
ebackbone
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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Review 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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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 structureFunction
Red bloodcell shape
Hemoglobin SMolecules 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 . . .. . .
Figure 5.21
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
• Temperature, pH, etc. affect protein structure
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•Denaturation is when a protein unravels and loses its native conformation(shape) Denaturation
Renaturation
Denatured proteinNormal protein
Figure 5.22
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The Protein-Folding Problem• Most proteins
– Probably go through several intermediate states on their way to a stable conformation
– Denaturated proteins no longer work in their unfolded condition
– Proteins may be denaturated by extreme changes in pH or temperature
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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.
CorrectlyfoldedproteinPolypeptide
2
1
3
Figure 5.23
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• X-ray crystallography– Is used to determine a protein’s three-
dimensional structure X-raydiffraction pattern
Photographic filmDiffracted X-
raysX-raysource
X-ray
beam
CrystalNucleic acid Protein
(a) X-ray diffraction pattern(b) 3D computer modelFigure 5.24
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Nucleic Acids• Nucleic acids store and
transmit hereditary information• Genes
– Are the units of inheritance– Program the amino acid
sequence of polypeptides– Are made of nucleotide
sequences on DNA
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The Roles of Nucleic Acids• There are two types of nucleic acids
– Deoxyribonucleic acid (DNA)– Ribonucleic acid (RNA)
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Deoxyribonucleic Acid• DNA
– Stores information for the synthesis of specific proteins
– Found in the nucleus of cells
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DNA Functions– Directs RNA synthesis (transcription)– Directs protein synthesis through RNA
(translation)1
2
3
Synthesis of mRNA in the nucleus
Movement of mRNA into cytoplasm
via nuclear pore
Synthesisof protein
NUCLEUSCYTOPLASM
DNA
mRNARibosome
AminoacidsPolypeptide
mRNA
Figure 5.25
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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
Figure 5.26
O
O
O
O
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• Each polynucleotide– Consists of monomers called nucleotides– Sugar + phosphate + nitrogen base
Nitrogenousbase
Nucleoside
O
O
O
O P CH2
5’C
3’CPhosphategroup Pentose
sugar
(b) NucleotideFigure 5.26
O
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Nucleotide Monomers• Nucleotide
monomers – Are made up of
nucleosides (sugar + base) and phosphate groups
(c) Nucleoside componentsFigure 5.26
CHCH
Uracil (in RNA)U
Ribose (in RNA)
Nitrogenous bases Pyrimidines
CNNC
OH
NH2
CHCH O C N
HCH
HN CO
C CH3
NHN
C
CH
O
O
CytosineC
Thymine (in DNA)T
NHC
N CC N
C
CHN
NH2 ON
HCNHH
C C
N
NHC NH2
AdenineA
GuanineG
Purines
OHOCH2
HH H
OH
H
OHOCH2
HH H
OH
H
Pentose sugars
Deoxyribose (in DNA)Ribose (in RNA)OHOH
CHCH
Uracil (in RNA)U
4’
5”
3’OH H
2’
1’
5”
4’
3’ 2’
1’
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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
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Gene• 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
Figure 5.27
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A,T,C,G• The nitrogenous bases in DNA
– Form hydrogen bonds in a complementary fashion (A with T only, and C with G only)
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DNA and Proteins as Tape Measures of Evolution
• Molecular comparisons – Help biologists sort out the
evolutionary connections among species
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The Theme of Emergent Properties in the Chemistry of
Life: A Review• Higher levels of organization
– Result in the emergence of new properties
• Organization– Is the key to the chemistry of
life
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