Chapter 3
description
Transcript of Chapter 3
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The Structure and Function of
Macromolecules
Chapter 3
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Are large molecules (polymers) composed of smaller molecules (monomers)
Are complex in their structures
Macromolecules
Protein
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Most macromolecules are polymers, built from monomers Four classes of life’s organic molecules are polymers
CarbohydratesProteinsNucleic acidsLipids
Macromolecules
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A polymerIs a long molecule consisting of
many similar building blocks called monomers
Specific monomers make up each macromoleculeAmino acids are the monomers for
proteinsMonosaccharides make up
carbohydratesGlycerol and Fatty acids for LipidsNucleotides for Nucleic acids
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Monomers form larger molecules by condensation reactions called Dehydration synthesis or Condensation
Is an anabolic reaction (building up)
The Synthesis and Breakdown of Polymers
(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 5.2ACondensation of amino acids
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Dehydration Synthesis of Carbohydrates
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Polymers can disassemble byHydrolysis (addition of water molecules)Is a catabolic or breakdown reaction
The Synthesis and Breakdown of Polymers
(b) Hydrolysis of a polymer
HO 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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Hydrolysis of a Disaccharide
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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
How many words can be made using the English alphabet?
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C, H, O w/ a H:O ratio of 2:1Serve as fuel and building material
Sugars and their polymers (starch, cellulose, etc.)
Tend to end in “ose”
Carbohydrates
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MonosaccharidesAre the simplest sugarsMost are: C6H12O6Can be used for fuelCan be converted into other organic molecules
Can be combined into polymers
Glucose, Galactose, Fructose, Ribose…
Sugars
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Examples of monosaccharides
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Triose 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
Glyceraldehyde
RiboseGlucose Galactose
Dihydroxyacetone
Ribulose
Keto
ses
Fructose
Figure 5.3
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MonosaccharidesMay be linearCan form rings in solution
H
H C OH
HO C H
H C OH
H C OH
H C
OC
H
12
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5
6
H
OH
4C
6CH2OH
6CH2OH5C
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 O O6
1
Figure 5.4
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DisaccharidesC12H22O11Consist 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.
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
1– 2glycosidic
linkage
MaltoseGlucose Glucose
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PolysaccharidesAre polymers of sugars
Serve many roles in organisms
Starch, glycogen, cellulose, chitin
Polysaccharides
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Starch - AmyloseIs a polymer consisting entirely of glucose monomers
Is the major storage form of glucose in plants
in amyloplasts
Storage PolysaccharidesChloroplas
t Starch
Amylose Amylopectin
1 m
(a) Starch: a plant polysaccharideFigure 5.6
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GlycogenConsists of glucose monomersIs the major storage form of glucose in animal
livers Mitochondria Giycogen granules
0.5 m
(b) Glycogen: an animal polysaccharide
Glycogen
Figure 5.6
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CelluloseIs a polymer of glucose
Structural Polysaccharides
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Has different glycosidic linkages than starch
(c) Cellulose: 1– 4 linkage of glucose monomers
H O
OCH2OH
HOH H
H
OHOHH
H
HO4
CCCCCC
H
H
H
HOOHHOHOHOH
H
OCH2OH
HH
H
OH
OHH
H
HO4 OH
CH2OHO
OH
OH
HO41
O
CH2OHO
OH
OH
O
CH2OHO
OH
OH
CH2OHO
OH
OH
O O
CH2OHO
OH
OH
HO 4O
1
OH
OOH OHO
CH2OHO
OH
O OHO
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
– C6 is on the top left on both monomers– C6 is flipped from top to bottom
OH OH
OH OH
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Plant cells
About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall.
A cellulose moleculeis an unbranched glucose polymer.
Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6.
Cellulosemolecules
Is a major component of the tough walls that enclose plant cells
21Hydrogen bonds
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Cellulose is difficult to digestCows have microbes in their stomachs to
facilitate this process
Figure 5.9
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Chitin, another important structural polysaccharideIs found in the exoskeleton of arthropodsCan 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 are a diverse group of hydrophobic molecules
LipidsAre the one class of large biological molecules
that do not consist of polymersNot considered a true macromoleculesMade up mostly of chains of hydrocarbonsShare the common trait of being hydrophobicFats, oils, waxes, phospholipids and steroidsCarbon, Hydrogen & Oxygen with
H:O ratio >2:1Involved in long term energy storage
Lipids
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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
Fats
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Saturated fatty acidsHave the maximum number of hydrogen atoms
possibleHave no double bondsLard, butter, animal fat, palm oil, coconut oil, palm
kernel oil
(a) Saturated fat and fatty acid
Stearic acid
Figure 5.12
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Unsaturated fatty acidsHave one or more double bondsOlive oil
(b) Unsaturated fat and fatty acid
cis double bondcauses bending
Oleic acid
Figure 5.12
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The following foods are high in monounsaturated fats: peanut butter olives nuts – almonds, pecans, pistachios, cashews avocado seeds – sesame oils – olive, sesame, peanut, canola
The following foods are high in polyunsaturated fats:walnuts seeds – pumpkin, sunflower flaxseed fish – salmon, tuna, mackerel oils – safflower, soybean, corn
What to eat?
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PhospholipidsHave only two fatty acidsHave a phosphate group instead of a
third fatty acidTypical of a cell membrane
***The kink in the H-C chain due to a double bond is what gives the cell membrane its fluidity
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Phospholipid structureConsists of a hydrophilic “head”
and hydrophobic “tails”CH2
OPO OOCH2CHCH
2OO
C 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 phospholipidsResults in a bilayer arrangement found in cell
membranes
Hydrophilic head
WATER
WATER
Hydrophobic tail
Figure 5.14
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SteroidsAre lipids characterized by a carbon skeleton
consisting of four fused rings
Steroids
One steroid, cholesterolIs found in cell membranesIs a precursor for some hormones like estrogen
& testosterone
HO
CH3
CH3
H3C CH3
CH3
Figure 5.15
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Proteins have many structures, resulting in a wide range of functionsBuilding and regulatory functions
Proteins do most of the work in cells and act as enzymes
Most hormones are protein derivedProteins are made of monomers called amino
acidsMade up of Carbon, Hydrogen, Oxygen,
Nitrogen & sometimes Sulfur
Proteins
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An overview of protein functions
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EnzymesAre a type of protein that acts as a catalyst,
speeding up chemical reactions (by reducing the amount of activation energy needed)
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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PolypeptidesAre polymers (chains) of amino acids
A proteinConsists of one or more polypeptides
Polypeptides
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Amino acidsAre organic molecules possessing both
carboxyl and amino groupsDiffer in their properties due to differing
side chains, called R groups
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20 different amino acids make up proteins
Twenty Amino Acids (you do not need to memorize these!!)
O
O–
H
H3N+ C CO
O–
H
CH3
H3N+ C
H
CO
O–
CH3 CH3
CH3
C CO
O–
H
H3N+
CH
CH3
CH2
C
H
H3N+
CH3
CH3
CH2
CH
C
H
H3N+ C
CH3
CH2CH2
CH3N+
H
CO
O–
CH2
CH3N+
H
CO
O–
CH2
NH
H
CO
O–
H3N+ C
CH2H2C
H2N C
CH2
H
C
Nonpolar -
Hydrophobic
Glycine (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–
OH
CH2
C C
H
H3N+
O
O–
H3N+
OH CH3
CH
C C
H O–
O
SH
CH2
C
H
H3N+ CO
O–H3N+ C C
CH2
OH
H H H
H3N+
NH2
CH2
OC
C CO
O–
NH2 OC
CH2
CH2
C CH3N+O
O–
O
Polar - Hydrophili
c
Electrically
Charged - Ionic
–O OC
CH2
C CH3N+
H
O
O–
O– OC
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 acidsAre linked by peptide bonds through Dehydration
synthesis
Amino Acid Polymers
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A protein’s specific conformation (shape) determines how it functions
Protein Conformation and Function
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The specific order of amino acids in a polypeptide interacts with the environment to determine the overall structure of the protein.
The interactions of the R group of the amino acid determines structure and function of the R region of the protein.Hydrophobic, hydrophilic or
ionic
Primary structure Is the unique sequence of
amino acids in a polypeptide Linear
Four Levels of Protein Structure
Figure 5.20
–
Amino acid
subunits
+H3NAmino
end
oCarboxyl end
oc
GlyProThrGlyThr
GlyGluSeuLysCysProLeu
MetVal
LysVal
LeuAspAlaValArgGlySerProAla
GlylleSerProPheHisGluHis
AlaGlu
ValValPheThrAlaAsnAsp
SerGlyProArg
ArgTyrThr lleAla
AlaLeu
LeuSerProTyrSerTyrSerThr
ThrAlaVal
ValThrAsnProLysGlu
ThrLysSer
TyrTrpLysAlaLeu
GluLleAsp
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Secondary structureIs the folding or coiling of the
polypeptide into a repeating configuration due to Hydrogen bonds
Includes the helix and the pleated sheet
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
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 - Disulfide bridge formed
CH2CH
OHOCHOCH2
CH2NH3+ C-O CH2
O
CH2SSCH2
CH
CH3CH3
H3CH3C
Hydrophobic interactions and van der Waalsinteractions Polypepti
debackbone
Hyrdogenbond
Ionic bond
CH2
Disulfide bridge
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Quaternary structureIs 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 diseaseResults from a single
amino acid substitution in the protein hemoglobin
Valine for Glutamic acidCaused by a point
mutation
Sickle-Cell Disease: A Simple Change in Primary Structure
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Primary structure
Secondaryand tertiarystructures
Quaternary structure
Function
Red bloodcell shape
Hemoglobin A
Molecules donot associatewith oneanother, eachcarries oxygen.
Normal cells are full 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
. . .. . .
Figure 5.21
Exposed hydrophobic
region
Val ThrHis Leu ProGlulGlu Val His Leu Thr Pro Val Gl
u
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Fibers of abnormalhemoglobin deform cell into sickle shape.
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Protein conformation depends on the physical and chemical conditions of the protein’s environment
Temperature, pH, [salt], etc. influence protein structure
What Determines Protein Conformation?
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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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Amino acid sequences of 875,000 proteins are known.
3D shapes of 7,000 are known.aka, Scientists don’t know the structure of most
proteinsMost 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
The Protein-Folding Problem
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Chaperonins (aka, chaperone proteins)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 Rosalind Franklin & DNA X-ray
diffraction pattern
Photographic film
Diffracted X-rays
X-raysource
X-ray
beam Crystal
Nucleic acidProtein
(a) X-ray diffraction pattern(b) 3D computer modelFigure 5.24
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Nucleic acids store and transmit hereditary informationPolymers of nucleotides
GenesAre the units of inheritanceProgram the amino acid sequence of polypeptidesAre made of nucleotide sequences on DNA
Nucleic Acids
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There are two types of nucleic acidsDeoxyribonucleic acid (DNA)Ribonucleic acid (RNA)
The Roles of Nucleic Acids
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DNAStores information for the synthesis of specific
proteinsFound in the nucleus of cells
Deoxyribonucleic Acid
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Directs RNA synthesis (transcription)Directs protein synthesis through RNA
(translation)
DNA Functions
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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Nucleic acidsExist as polymers called
polynucleotides
The Structure of Nucleic Acids
(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 polynucleotideConsists of monomers called
nucleotides5C Sugar + phosphate group +
nitrogen base
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Nucleotide monomers Are made up
of nucleosides (sugar + base) and phosphate groups
64Nucleotide Monomers
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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
Nucleotide Polymers5`
5`3`
3`
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The sequence of bases along a nucleotide polymerIs unique for each gene
Gene
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Cellular DNA moleculesHave two polynucleotides that spiral around an
imaginary axisForm a double helix
The DNA Double Helix
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The DNA double helixConsists of two antiparallel nucleotide strandsLook at the C’s on the ribose molecule. The 5th
C bonded to the Phosphate group is the 5` end.
3’ 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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The nitrogenous bases in DNAForm hydrogen bonds in a complementary
fashion (A with T only, and C with G only)
A,T,C,G
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Molecular comparisons Help biologists sort out the
evolutionary connections among species
DNA and Proteins as Tape Measures of Evolution