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Transcript of B.tech biotech i bls u 3 building blocks of life
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Building blocks of Life
Course: B.Tech BiotechSubject: Basic of Life Science
Unit: III
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Overview: The Molecules of Life
• All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids
• Macromolecules are large molecules composed of thousands of covalently connected atoms
• Molecular structure and function are inseparable
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Macromolecules are polymers, built from monomers
• A polymer is a long molecule consisting of many similar building blocks
• These small building-block molecules are called monomers
• Three of the four classes of life’s organic molecules are polymers
– Carbohydrates– Proteins– Nucleic acids
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• A dehydration reaction - when two monomers bond together through the loss of a water molecule
• Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction
The Synthesis and Breakdown of Polymers
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Animation: Polymers
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Figure 5.2(a) Dehydration reaction: synthesizing a polymer
Short polymer Unlinked monomer
Dehydration removesa water molecule,forming a new bond.
Longer polymer
(b) Hydrolysis: breaking down a polymer
Hydrolysis addsa water molecule,breaking a bond.
1
1
1
2 3
2 3 4
2 3 4
1 2 31.
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1. Carbohydrates serve as fuel and building material
• Carbohydrates - sugars and the polymers of sugars
• simplest carbohydrates -monosaccharide, or single sugars
• Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks
• Definition : “Carbohydrates may be defined as
polyhydroxy alcohols with aldehydes or ketone and their derivatives.”
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Classification:
• 1. Monosaccharide::• Simple sugars• Not hydrolyzed
• Cn(H2O)n
• Glucose (C6H12O6)-most common monosaccharide
• Monosaccharide are classified by – The location of the carbonyl group (as aldose
or ketose)– The number of carbons in the carbon skeleton
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Figure 5.3a
Aldose (Aldehyde Sugar) Ketose (Ketone Sugar)
Glyceraldehyde
Trioses: 3-carbon sugars (C3H6O3)
Dihydroxyacetone
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Tetrose: 4-carbon sugars
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Figure 5.3b
Pentoses: 5-carbon sugars (C5H10O5)
Ribose Ribulose
Aldose (Aldehyde Sugar) Ketose (Ketone Sugar)
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Figure 5.3c
Aldose (Aldehyde Sugar) Ketose (Ketone Sugar)
Hexoses: 6-carbon sugars (C6H12O6)
Glucose Galactose Fructose
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Heptose : 7-carbon sugars
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Figure 5.4
(a) Linear and ring forms
(b) Abbreviated ring structure
1
2
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4
5
6
6
5
4
32
1 1
23
4
5
6
1
23
4
5
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• 2. disaccharide : formed when a dehydration reaction joins two monosaccharide
• This covalent bond is called a glycosidic linkage
• Two molecules of the same or of different monosaccharide
• Cn(H2O)n-1
• Examples: Lactose, Maltose, Sucrose
© 2011 Pearson Education, Inc.
Animation: Disaccharide
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Figure 5.5
(a) Dehydration reaction in the synthesis of maltose
(b) Dehydration reaction in the synthesis of sucrose
Glucose Glucose
Glucose
Maltose
Fructose Sucrose
1–4glycosidic
linkage
1–2glycosidic
linkage
1 4
1 2
3.
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4.
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• 3. Oligosaccharides:• Yield 2-10 monosaccharide units on hydrolysis• Example: Maltotriose composed of three
glucose molecules which are linked with α-1,4 glycosidic bonds.
5.
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Polysaccharides
• 4. Polysaccharides, the polymers of sugars, have storage and structural roles
• The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages
• Yield more than 10 molecules of polysaccharides
• (C6H10O5)x
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• The long chain polymers are either straight chain or branched. They are also called glycanes.
• Classification of Polysaccharides:• 1) On the Basis of Function:• a) Storage e.g. Starch, glycogen
b) Structural e.g. Cellulose, Pectin• 2) On the Basis of Composition:• a) Homo polysaccharides(same type of
monosaccharide)b) Hetero polysaccharides.(different type)
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Storage Polysaccharides
• Starch, a storage polysaccharide of plants, consists entirely of glucose monomers
• Plants store starch as granules within chloroplasts and other plastids
• The simplest form of starch is amylose
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Figure 5.6
(a) Starch: a plant polysaccharide
(b) Glycogen: an animal polysaccharide
Chloroplast Starch granules
Mitochondria Glycogen granules
Amylopectin
Amylose
Glycogen
1 m
0.5 m 6.
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• Glycogen is a storage polysaccharide in animals
• Humans and other vertebrates store glycogen mainly in liver and muscle cells
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Structural Polysaccharides
• The polysaccharide cellulose is a major component of the tough wall of plant cells
• Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ
• The difference is based on two ring forms for glucose: alpha () and beta ()
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Animation: Polysaccharides
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Figure 5.7
(a) and glucose ring structures
(b) Starch: 1–4 linkage of glucose monomers (c) Cellulose: 1–4 linkage of glucose monomers
Glucose Glucose
4 1 4 1
4141
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• Polymers with glucose are helical• Polymers with glucose are straight• In straight structures, H atoms on one
strand can bond with OH groups on other strands
• Parallel cellulose molecules held together this way are grouped into microfibrils, which form strong building materials for plants
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Cell wall
Microfibril
Cellulosemicrofibrils in aplant cell wall
Cellulosemolecules
Glucosemonomer
10 m
0.5 m
Figure 5.8
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2. Lipids are a diverse group of hydrophobic molecules
• Lipids are the one class of large biological molecules that do not form polymers
• having little or no affinity for water• Lipids are hydrophobic because they consist
mostly of hydrocarbons, which form nonpolar covalent bonds
• The most biologically important lipids are fats, phospholipids, and steroids
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Fats
• Fats are constructed from two types of smaller molecules: glycerol and fatty acids
• Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon
• A fatty acid consists of a carboxyl group attached to a long carbon skeleton
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Figure 5.10a
(a) One of three dehydration reactions in the synthesis of a fat
Fatty acid(in this case, palmitic acid)
Glycerol
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• Fats separate from water because water molecules form hydrogen bonds with each other and exclude the fats
• In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride
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Figure 5.10b
(b) Fat molecule (triacylglycerol)
Ester linkage
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• Fatty acids vary in length (number of carbons) and in the number and locations of double bonds
• Saturated fatty acids - maximum number of hydrogen atoms possible and no double bonds
• Unsaturated fatty acids - one or more double bonds
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Animation: Fats
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(a) Saturated fat
Structuralformula of asaturated fatmolecule
Space-fillingmodel of stearicacid, a saturatedfatty acid
Figure 5.11a
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Figure 5.11b(b) Unsaturated fat
Structuralformula of anunsaturated fatmolecule
Space-filling modelof oleic acid, anunsaturated fattyacid
Cis double bondcauses bending. 12.
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• Fats made from saturated fatty acids are called saturated fats, and are solid at room temperature
• Most animal fats are saturated• Fats made from unsaturated fatty acids are
called unsaturated fats or oils, and are liquid at room temperature
• Plant fats and fish fats are usually unsaturated
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• A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits
• Hydrogenation - converting unsaturated fats to saturated fats by adding hydrogen
• Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds
• These trans fats may contribute more than saturated fats to cardiovascular disease
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• Certain unsaturated fatty acids are not synthesized in the human body
• These must be supplied in the diet
• These essential fatty acids include the omega-3 fatty acids, required for normal growth, and thought to provide protection against cardiovascular disease
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• The major function of fats is energy storage• Humans and other mammals store their fat in
adipose cells• Adipose tissue also cushions vital organs and
insulates the body
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Phospholipids
• In a phospholipid, two fatty acids and a phosphate group are attached to glycerol
• The two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head
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Figure 5.12
Choline
Phosphate
Glycerol
Fatty acids
Hydrophilichead
Hydrophobictails
(c) Phospholipid symbol(b) Space-filling model(a) Structural formula
Hyd
rop
hil
ic h
ead
Hyd
rop
ho
bic
tai
ls
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• When phospholipids are added to water, they self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior
• The structure of phospholipids results in a bilayer arrangement found in cell membranes
• Phospholipids are the major component of all cell membranes
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Figure 5.13
Hydrophilichead
Hydrophobictail
WATER
WATER
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Steroids
• Steroids are lipids characterized by a carbon skeleton consisting of four fused rings
• Cholesterol, an important steroid, is a component in animal cell membranes
• Although cholesterol is essential in animals, high levels in the blood may contribute to cardiovascular disease
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Figure 5.14
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3: Proteins include a diversity of structures, resulting in a wide range of functions
• Proteins account for more than 50% of the dry mass of most cells
• functions - structural support,
• -storage,
- transport,
- cellular communications,
-movement,
-defense against foreign substances
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Polypeptides
• Polypeptides unbranched polymers built from the same set of 20 amino acids
• A protein is a biologically functional molecule that consists of one or more polypeptides
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Amino Acid Monomers
• Amino acids - organic molecules with carboxyl and amino groups
• Amino acids differ in their properties due to differing side chains, called R groups
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Figure 5.UN01
Side chain (R group)
Aminogroup
Carboxylgroup
carbon
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Figure 5.16Nonpolar side chains; hydrophobic
Side chain(R group)
Glycine(Gly or G)
Alanine(Ala or A)
Valine(Val or V)
Leucine(Leu or L)
Isoleucine (Ile or I)
Methionine(Met or M)
Phenylalanine(Phe or F)
Tryptophan(Trp or W)
Proline(Pro or P)
Polar side chains; hydrophilic
Serine(Ser or S)
Threonine(Thr or T)
Cysteine(Cys or C)
Tyrosine(Tyr or Y)
Asparagine(Asn or N)
Glutamine(Gln or Q)
Electrically charged side chains; hydrophilic
Acidic (negatively charged)
Basic (positively charged)
Aspartic acid(Asp or D)
Glutamic acid(Glu or E)
Lysine(Lys or K)
Arginine(Arg or R)
Histidine(His or H)
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Figure 5.16a
Nonpolar side chains; hydrophobic
Side chain
Glycine(Gly or G)
Alanine(Ala or A)
Valine(Val or V)
Leucine(Leu or L)
Isoleucine(Ile or I)
Methionine(Met or M)
Phenylalanine(Phe or F)
Tryptophan(Trp or W)
Proline(Pro or P)
GAVLI PPTM18.
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Figure 5.16b
Polar side chains; hydrophilic
Serine(Ser or S)
Threonine(Thr or T)
Cysteine(Cys or C)
Tyrosine(Tyr or Y)
Asparagine(Asn or N)
Glutamine(Gln or Q) TAG CTS
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Figure 5.16c
Electrically charged side chains; hydrophilic
Acidic (negatively charged)
Basic (positively charged)
Aspartic acid(Asp or D)
Glutamic acid(Glu or E)
Lysine(Lys or K)
Arginine(Arg or R)
Histidine(His or H)
HAL AG
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Amino Acid Polymers
• Amino acids are linked by peptide bonds• A polypeptide is a polymer of amino acids• Polypeptides range in length from a few to
more than a thousand monomers • Each polypeptide has a unique linear
sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus)
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Figure 5.17
Peptide bond
New peptidebond forming
Sidechains
Back-bone
Amino end(N-terminus)
Peptidebond
Carboxyl end(C-terminus)
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Protein Structure and Function
• A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape
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• The sequence of amino acids determines a protein’s three-dimensional structure
• A protein’s structure determines its function
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Four Levels of Protein Structure
• The primary structure of a protein is its unique sequence of amino acids
• Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain
• Tertiary structure is determined by interactions among various side chains (R groups)
• Quaternary structure results when a protein consists of multiple polypeptide chains
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Animation: Protein Structure Introduction
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Figure 5.20aPrimary structure
Aminoacids
Amino end
Carboxyl end
Primary structure of transthyretin
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• Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word
• Primary structure is determined by inherited genetic information
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Animation: Primary Protein Structure
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Figure 5.20b
Secondarystructure
Tertiarystructure
Quaternarystructure
Hydrogen bond
helix
pleated sheet
strand
Hydrogenbond
Transthyretinpolypeptide
Transthyretinprotein
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• The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone
• Typical secondary structures are a coil called an helix and a folded structure called a pleated sheet
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Animation: Secondary Protein Structure
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• Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents
• These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions
• Strong covalent bonds called disulfide bridges may reinforce the protein’s structure
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Animation: Tertiary Protein Structure
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Hemoglobin
Heme
Iron
subunit
subunit
subunit
subunit
Figure 5.20i
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• Quaternary structure results when two or more polypeptide chains form one macromolecule
• Collagen is a fibrous protein consisting of three polypeptides coiled like a rope
• Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains
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Animation: Quaternary Protein Structure
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Sickle-Cell Disease: A Change in Primary Structure
• A slight change in primary structure can affect a protein’s structure and ability to function
• Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin
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Figure 5.21
PrimaryStructure
Secondaryand TertiaryStructures
QuaternaryStructure Function Red Blood
Cell Shape
subunit
subunit
Exposedhydrophobicregion
Molecules do notassociate with oneanother; each carriesoxygen.
Molecules crystallizeinto a fiber; capacityto carry oxygen isreduced.
Sickle-cellhemoglobin
Normalhemoglobin
10 m
10 m
Sic
kle-
cell
hem
og
lob
inN
orm
al h
emo
glo
bin
1
23
456
7
1
23
456
7
25.
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What Determines Protein Structure?
• In addition to primary structure, physical and chemical conditions can affect structure
• Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to untie.
• This loss of a protein’s native structure is called denaturation
• A denatured protein is biologically inactive
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4: Nucleic acids store, transmit, and help express hereditary information
• The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene
• Genes are made of DNA, a nucleic acid made of monomers called nucleotides
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The Roles of Nucleic Acids
• There are two types of nucleic acids– Deoxyribonucleic acid (DNA)– Ribonucleic acid (RNA)
• DNA provides directions for its own replication
• DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis
• Protein synthesis occurs on ribosomes
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Figure 5.25-3
Synthesis ofmRNA
mRNA
DNA
NUCLEUSCYTOPLASM
mRNA
Ribosome
AminoacidsPolypeptide
Movement ofmRNA intocytoplasm
Synthesisof protein
1
2
3
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The Components of Nucleic Acids
• Nucleic acids are polymers called polynucleotides
• Each polynucleotide is made of monomers called nucleotides
• Each nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups
• The portion of a nucleotide without the phosphate group is called a nucleoside
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Figure 5.26
Sugar-phosphate backbone5 end
5C
3C
5C
3C
3 end
(a) Polynucleotide, or nucleic acid
(b) Nucleotide
Phosphategroup Sugar
(pentose)
Nucleoside
Nitrogenousbase
5C
3C
1C
Nitrogenous bases
Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA)
Adenine (A) Guanine (G)
Sugars
Deoxyribose (in DNA) Ribose (in RNA)
(c) Nucleoside components
Pyrimidines
Purines
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• Nucleoside = nitrogenous base + sugar
• There are two families of nitrogenous bases– Pyrimidines (cytosine, thymine, and uracil)
have a single six-membered ring– Purines (adenine and guanine) have a six-
membered ring fused to a five-membered ring
• In DNA, the sugar is deoxyribose; in RNA, the sugar is ribose
• Nucleotide = nucleoside + phosphate group
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Nucleotide Polymers
• Nucleotide polymers are linked together to build a polynucleotide
• Adjacent nucleotides are joined by covalent bonds that form between the —OH group on the 3 carbon of one nucleotide and the phosphate on the 5 carbon on the next
• These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages
• The sequence of bases along a DNA or mRNA polymer is unique for each gene
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The Structures of DNA and RNA Molecules
• RNA molecules usually exist as single polypeptide chains
• DNA molecules have two polynucleotides spiraling around an imaginary axis, forming a double helix
• In the DNA double helix, the two backbones run in opposite 5→ 3 directions from each other, an arrangement referred to as antiparallel
• One DNA molecule includes many genes
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• The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C)
• Called complementary base pairing• Complementary pairing can also occur between
two RNA molecules or between parts of the same molecule
• In RNA, thymine is replaced by uracil (U) so A and U pair
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The Structure of DNAWatson and Crick,
Nature, 1953
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Figure 5.27
Sugar-phosphatebackbones
Hydrogen bonds
Base pair joinedby hydrogen bonding
Base pair joinedby hydrogen
bonding
(b) Transfer RNA(a) DNA
5 3
53
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Watson and Crick’s DNA Model
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Key Concepts: DISCOVERY OF DNA’S FUNCTION
In all living cells, DNA molecules store information that governs heritable traits
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12.2 Discovery of DNA Structure
DNA consists of two strands of nucleotides, coiled into a double helix
Each nucleotide has • A five-carbon sugar (deoxyribose)• A phosphate group• A nitrogen-containing base (adenine, thymine,
guanine, or cytosine)
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DNA Nucleotides
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Base Pairing
Bases of two DNA strands pair in only one way• Adenine with thymine (A-T)• Guanine with cytosine (G-C)
The DNA sequence (order of bases) varies among species and individuals
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31
2-nanometer diameter overall
0.34-nanometer distancebetween each pair of bases
3.4-nanometerlength of eachfull twist of thedouble helix
In all respects shown here, theWatson–Crick model for DNAstructure is consistent with theknown biochemical and x-raydiffraction data.
The pattern of basepairing (A with T,and G with C) isconsistent with theknown compositionof DNA (A = T,and G = C).
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Key Concepts: THE DNA DOUBLE HELIX
A DNA molecule consists of two chains of nucleotides, hydrogen-bonded together along their length and coiled into a double helix
Four kinds of nucleotides make up the chains: adenine, thymine, guanine, and cytosine
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12.3 Watson, Crick, and Franklin
Rosalind Franklin’s research produced x-ray diffraction images of DNA• Helped Watson and Crick
build their DNA model, for which they received the Nobel Prize
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DNA and Proteins as Tape Measures of Evolution
• The linear sequences of nucleotides in DNA molecules are passed from parents to offspring
• Two closely related species are more similar in DNA than are more distantly related species
• Molecular biology can be used to assess evolutionary relationship
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Book and Web References
• Book Name : Genome by T.A.Brown
: Biotechnology by B.D.Singh
• http://askabiologist.asu.edu/explore/building-blocks-life
• http://www-nmr.cabm.rutgers.edu/labdocuments/projectrpts/jessica/Thesis_JLau_Jan2005.pdf
• http://www.physicsoftheuniverse.com/topics_life_early.html
• http://www.foothill.edu/attach/1578/chapter_21.1-21.9.pdf
89
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Image References
• 1.http://www.yellowtang.org/images/formation_of_peptid_c_la_784.jpg• 2.http://bio1151.nicerweb.com/Locked/media/
ch05/05_04aGlucoseLinearRing-L.jpg• 3.http://bealbio.wikispaces.com/file/view/disaccharides.JPG/
364413582/disaccharides.JPG• 4. http://www.medbio.info/horn/time%201-2/CarbCh4.gif• 5.http://patentimages.storage.googleapis.com/
EP1340770A1/00060001.png• 6.https://classconnection.s3.amazonaws.com/866/flashcards/1866866/
jpg/get_it_right1347646144294.jpg• 7.http://3.bp.blogspot.com/S3A94J8n2sE/T3dd27ceY7I/
AAAAAAAAAIg/XlLgHcPzh5M/s640/045glu4.gif• 8.http://www.goldiesroom.org/Multimedia/Bio_Images/
04%20Biochemistry/13%20Polysaccharides.GIF
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• 9.http://plantcellbiology.masters.grkraj.org/html/Plant_Cell_Biochemistry_And_Metabolism3-Lipid_Metabolism_files/image021.gif
• 10.http://plantcellbiology.masters.grkraj.org/html/Plant_Cell_Biochemistry_And_Metabolism3-Lipid_Metabolism_files/image022.gif
• 11.http://www.smartkitchen.com/assets/kcfinder/upload/images/fat%20and%20fatty%20acid.jpg
• 12. http://yourbestyou90.com/wp-content/uploads/2011/07/saturated_unsaturat_c_la_784.jpg
• 13.http://www.ias.ac.in/meetings/myrmeet/18mym_talks/mjswamy/img2.jpg• 14. http://www2.fiu.edu/~pitzert/F03070.JPG• 15. http://www.quia.com/files/quia/users/lmcgee/biochemistry/steroid-structure-
chol_L.gif• 16. to 21. Book Principles of Biochemistry by Lehninger.• 22.http://www.foodnetworksolution.com/uploaded/primary%20structure.gif
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• 23.http://sphweb.bumc.bu.edu/otlt/MPHModules/PH/PH709_BasicCellBiology/ProteinStructure.jpg
• 24.http://xray.bmc.uu.se/Courses/bioinformatik2003/Intro/quat_struc.jpg• 25.http://thumb1.shutterstock.com/display_pic_with_logo/
636694/195789230/stock-photo-anemia-195789230.jpg• 26. http://compbio.pbworks.com/f/central_dogma.jpg• 27. & 28. Book Principles of Biochemistry by Lehninger.• 29. http://schnapzer.com/uploaded_images/original/91ced-H4000039-
Watson-and-Crick_cropped-by-CM-v1-1440x866.jpg• 30. http://www.di.uq.edu.au/sparq/images/ssDNA.JPG• 31. http://passel.unl.edu/Image/siteImages/DNAdhStructureLG.jpg