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Lecture Outline
1. Macromolecules are polymers, built frommonomers
2. Carbohydrates serve as fuel and building material
3. Lipids are a diverse group of hydrophobic
molecules4. Proteins include a diversity of structures, resulting
in a wide range of functions
5. Nucleic acids store, transmit, and help expresshereditary information
6. Genomics and proteomics have transformedbiological inquiry and applications
3
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Macromolecules are polymers, built
from monomers
4
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The Diversity of Mcromolecules
Monomers Polymer
5
A polymeris a long molecule consisting of many similar
building blocks.
The repeating units that serve as building blocks are called monomers
Three of the four classes of lifes organic molecules are polymers:
Carbohydrates
, Proteins
,Nucleic acids
Each cell has thousands of different macromolecules, which vary among
cells of an organism, vary more within a species, and vary even more
between species.
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(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 3
The Synthesis and Breakdown of Polymers
Fig 5.2
Dehydration reaction/
Condensation reaction
Hydrolysis
Enzymesrequired
Diverse Polymers
6
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Carbohydrates serve as fuel and
building material
7
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(Carbonyl group)
8
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Aldoses (Aldehyde Sugars) Ketoses (Ketone Sugars)
Glyceraldehyde
Trioses: 3-carbon sugars (C3H6O3)
Dihydroxyacetone
Pentoses: 5-carbon sugars (C5H10O5)
Hexoses: 6-carbon sugars (C6H12O6)
Ribose Ribulose
Glucose Galactose Fructose
aldoseketose
D- form
epimers at C-4
dextrose = D-(+)-Glc
Figure 5.3 The structure and
classification of some monosaccharides
Sugars
Monosaccharides molecular formulas:
(CH2O)n Glucose (C6H12O6):
the most common
classification
The location of thecarbonyl group: aldose
ketose
number of carbons
9
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-
-
anomer, anomeric carbon
(~ 2/3)
(a) Linear and ring forms of glucose
10
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11
-D-glucopyranose-D-glucopyranose
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Disaccharide
nonreducing end reducing endGal
(14)Glc
reducing sugarhydrolyzed by lactase (human), -galactosidase (bacteria)
Lactose intolerance
The covalent bond joins two monosaccharides is
called a glycosidic linkage
12
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(a) Dehydration reaction in the synthesis of maltose
(b) Dehydration reaction in the synthesis of sucrose
Glucose Glucose
Glucose
Maltose
Fructose Sucrose
14glycosidiclinkage
12glycosidic
linkage
1 4
1 2
Examples of disaccharide synthesis(glycosidic linkage)
reducing sugar
non-reducing sugar13
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Polysaccharides (Glycans)
Serve as storage and structural roles
The architecture and function of a polysaccharide
are determined by its sugar monomers and the
positions of its glycosidic linkages
14
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Storage Polysaccharides
Starch,polymers of glucoses in plants: (14)
amyloseThe simplest form,& amylopectin
Plants store surplus starch as granules within chloroplasts
and other plastids
Glycogen, polymers of glucosesin animals
Is stored mainly in liver and muscle cells
They are hydrolyzed to release glucose when the demandfor sugar increases
Structural Polysaccharides
Cellulose,polymers of glucoses in plant cell walls. but the glycosidic linkages differ from starch; (14)
Chitin, in the exoskeleton of arthropods and cell walls
of many fungi
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Amylopectin, glycogen: (14) & (16) linkage,
branched
Cellulose:(14)
(14)
(16)
Amylases
Cellulases
16
( glucose monomer)
( glucose monomer)
Figure 5 6
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Figure 5.6
Storage structures(plastids)containing starchgranules in a potatotuber cell
50 m
(a) Starch
Amylose (unbranched)
Amylopectin(somewhatbranched)
Glucosemonomer
Glycogengranules inmuscletissue Glycogen (branched)
1 m
(b) Glycogen
Cellwall
Plant cell,surroundedby cell wall
10 m
0.5 m
(c) Cellulose
Microfibril
Cellulose microfibrilsin a plant cell wall Cellulose molecule (unbranched)
Hydrogen bonds
18
largely helical
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The cellulose in human food passes through the digestivetract as insoluble fiber
Many herbivores, from cows to termites, have symbiotic
relationships with some microbes that use enzymes
(cellulases) to digest cellulose
What would happen if a cow were given antibiotics
that killed all the prokaryotes in its stomach?
19
Figure 5 8
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Figure 5.8
The structureof the chitinmonomer
Chitin, embedded in proteins,
forms the exoskeleton ofarthropods
.
Chitin is used to
make a strongand flexiblesurgicalthread.
N-acetylglucosamine
units, in -1,4 linkage
20
Chitin also provides
structural support for the
cell walls of many fungi
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N-link (Asn) & O-link (Ser)
21
Glycoproteins
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proteoglycan glycosaminoglycan, GAG )
heparin
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proteoglycan
glycosaminoglycanGAG
(Hyaluronic acid)
23
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Lipids are a diverse group of
hydrophobic molecules
24
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25
Energy storage
Cell membrane Signaling molecule
Lipid Functions
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26
Lipids
the one class of large biological molecules that does not
include true polymers
consist mostly of hydrocarbons; hydrophobic
The most biologically important lipids are fats, phospholipids,
and steroids
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Fats separate from water because watermolecules hydrogen-bond to each other andexclude the fats
In a fat, three fatty acids are joined to glycerolby an ester linkage, creating a triacylglycerol,or triglyceride
The fatty acids in a fat can be all the same or of
two or three different kinds Fatty acids vary in length (number of carbons)
and in the number and locations of double bonds
Saturated fatty acidshave the maximum number
of hydrogen atoms possible and no double bonds Unsaturated fatty acidshave one or more double
bonds
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Fats are
constructedfrom glycerol
and fatty acids
A fatty acid
consists of a
carboxyl group
attached
to a long carbon
skeleton
(a) One of three dehydration reactions in the synthesis ofa fat
(b) Fat molecule (triacylglycerol)
Fatty acid
(in this case, palmitic acid)
Glycerol
Ester linkage
Fig 5.10
The synthesis and
structure of a fat, or
triacylglycerol
28
Fats
(,or triglyceride
F tt id i l th ( b f b ) d
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Figure 5.11
(a) Saturated fatStructuralformula of asaturated fatmolecule
Space-filling model of stearicacid, a saturated fatty acid
Structuralformula of anunsaturated fatmolecule
Cisdouble bondcauses bending.
29
Fatty acids vary in length (number of carbons) and
in the number and locations of double bonds
(b) Unsaturated fat
Space-filling model of oleicacid, an unsaturated fatty acid
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Nomenclatures of fatty acids
Trans-fatty acid cis-fatty acid
monounsaturated fatty acids, MUFA
polyunsaturated fatty acids, PUFA
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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
Essential fatty acids
These must be supplied in the diet, not
synthesized in the human body 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 long-
term food reserves in adipose cells Adipose tissue also cushions vital organs and
insulates the body
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A diet rich in saturated fats may contribute to
cardiovascular disease through plaque deposits
Hydrogenationis the process of convertingunsaturated fats to saturated fats by adding
hydrogen
Hydrogenating vegetable oils also creates
unsaturated fats with transdouble bonds
These t rans fatsmay contribute more than
saturated fats to cardiovascular disease
Successful diets usually involve three things:
decreasing the amounts of carbohydrates
and fats; exercise; and behavior modification.
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Phospholipids
Choline
Phosphate
Glycerol
Fatty acids
Hydrophilichead
Hydrophobictails
(c) Phospholipid symbol(b) Space-filling model(a) Structural formula
Hydrophilichead
Hydrophobictails
Fig 5.12 The structure of a phospholipid.
In a phospholipid, two
fatty acids and a
phosphate group areattached to glycerol
The two fatty acid tails
are hydrophobic, but the
phosphate group and its
attachments form a
hydrophilic head
34
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When phospholipids are added to water, they
self-assemble into double-layered structures
called bilayers At the surface of a cell, phospholipids are also
arranged in a bilayer, with the hydrophobic tails
pointing toward the interior
The structure of phospholipids results in a
bilayer arrangement found in cell membranes
The existence of cells depends on phospholipids
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The structure of phospholipids results in a bilayer
arrangement found in cell membranes
36
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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
Fig 5.14 Cholesterol, a steroid
37
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Cholesterol and Membrane Fluidity
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39
Sex hormones
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Proteins include a diversity of structures,
resulting in a wide range of functions
40
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Proteins are all constructed from the same set of
20 amino acids
Polypeptidesare unbranched polymers built
from these amino acids
A proteinis a biologically functional molecule
that consists of one or more polypeptides Proteins account for more than 50% of the dry
mass of most cells.
Diverse protein functions
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42
Classification
A i f t i f ti
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Enzymatic proteins Defensive proteins
Storage proteins Transport proteins
Enzyme Virus
Antibodies
Bacterium
Ovalbumin Amino acidsfor embryo
Transportprotein
Cell membrane
Function: Selective acceleration ofchemical reactions
Example: Digestive enzymes catalyze thehydrolysis of bonds in food molecules.
Function: Protection against disease
Example: Antibodies inactivate and help destroy
viruses and bacteria.
Function: Storage of amino acids Function: Transport of substances
Examples: Casein, the protein of milk, is the major
source of amino acids for baby mammals.
Plants have storage proteins in their seeds.
Ovalbumin is the protein of egg white, used as
an amino acid source or the developing embryo.
Examples: Hemoglobin, the iron-containing
protein of ertebrate blood, transports oxygen
from the lungs to other parts of the body. Other
proteins transport molecules across
cell membranes.
An overview of protein functions
Figure 5.15
Figure 5.15-b
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Hormonal proteins
Function: Coordination of an organisms activities
Example: Insulin, a hormone secreted by the
pancreas, causes other tissues to take up glucose,
thus regulating blood sugar concentration
Highblood sugar
Normalblood sugar
Insulinsecreted
Signalingmolecules
Receptorprotein
Muscle tissue
Actin Myosin
100 m 60
m
Collagen
Connectivetissue
Receptor proteinsFunction: Response of cell to chemical stimuli
Example: Receptors built into the membrane of a
nerve cell detect signaling molecules released by
other nerve cells.
Contractile and motor proteinsFunction: MovementExamples: Motor proteins are responsible for the
undulations of cilia and flagella. Actin and myosin
proteins are responsible for the contraction of
muscles.
Structural proteinsFunction: SupportExamples: Keratin is the protein of hair, horns,
feathers, and other skin appendages. Insects and
spiders use silk fibers to make their cocoons and
webs,respectively. Collagen and elastin proteins
provide afibrous framework in animal connective
tissues.
Enzymes are a type of protein that acts as a catalyst to
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Enzyme(sucrase)
Substrate(sucrose)
Fructose
Glucose
OH
HO
H2O
Products
Active site
The catalytic cycle
of an enzyme
Enzymes are a type of protein that acts as a catalyst to
speed up chemical reactions
Enzymes can perform their functions repeatedly, functioning
as workhorses that carry out the processes of life.
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Amino Acid Monomers
Amino acids are
organic molecules
with carboxyl and
amino groups
Amino acids differ inside chains, called R
groups
Side chain (R group)
Aminogroup
Carboxylgroup
carbon
Figure 5.16
Nonpolar side chains; hydrophobic
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p ; y p
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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Polypeptides (Amino Acid Polymers)
Amino acids are linked by covalent bondscalled peptide bonds
A polypeptide is a polymer of amino acids
Polypeptides range in length from a few tomore 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)
Making a
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Peptide bond
New peptidebond forming
Side chains
Back-bone
Amino end
(N-terminus)
Peptidebond
Carboxyl end
(C-terminus)
Figure 5.17 Making a
polypeptide chain
Peptide bond
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Protein Structure and Function
The specific activities of proteins result from theirintricate three-dimensional architecture
A functional protein consists of one or morepolypeptides precisely twisted, folded, and coiled
into a unique shape The sequence of amino acids determines a
proteins three-dimensional structure
A proteins structure determines its function
The function of a protein usually depends on itsability to recognize and bind to some othermolecule
Figure 5.16
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(a) A ribbon model (b) A space-filling model (c) A wireframe model
GrooveGroove
Targetmolecule
Structure of a protein, the enzyme lysozyme
Figure 5.17
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Antibody protein Protein from flu virus
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Levels of Protein Structure
The primary structureof a protein is itsunique sequence of amino acids
Secondary structure, found in most proteins,consists of coils and folds in the polypeptide
chain Tertiary structureis determined byinteractions among various side chains (Rgroups)
Quaternary structureresults when a proteinconsists of multiple polypeptide chains
Primary structure
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Aminoacids
Amino end
Carboxyl end
Primary structure of transthyretin
the sequence ofamino acids in a
protein
is determined by
inherited genetic
information
Primary structure
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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 helixand a folded structure called a pleated sheet
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Tertiary structure, the overall shape of a
polypeptide, results from interactions between
R groups, rather than interactions between
backbone constituents
These interactions include hydrogen bonds,
ionic bonds, hydrophobic interactions, andvan der Waals interactions
Strong covalent bonds called disulfidebridges
may reinforce the protein
s structure
Four Levels of Protein Structure
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Four Levels of Protein Structure
Secondary
structure
Tertiary
structure
Quaternary
structureHydrogen bond
helix
pleated sheet
strand
Hydrogenbond
Transthyretinpolypeptide
Transthyretinprotein
Secondary structure
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Secondary structure
Hydrogen bond
helix
pleated sheet
strand, shown as aflat arrow pointingtoward the carboxyl end
Hydrogen bond
Figure 5.20c
Figure 5.20e
T ti t t
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Tertiary structure
Transthyretin
polypeptide
Hydrogen
bond
Disulfide
bridge
Polypeptidebackbone
Ionic bond
Hydrophobic
interactions and
van der Waals
interactions
Quaternary structure results when two or more
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Transthyretin protein(four identical polypeptides)
Collagen-- triple helix structure
Quaternary structureresults 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.
Heme
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Hemoglobin
Iron
subunit
subunit
subunit
subunit
Si kl C ll Di A Ch i P i
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Sickle-Cell Disease: A Change in Primary
Structure
A slight change in primary structure can affect
a proteins structure and ability to function
Sickle-cell disease, an inherited blood
disorder, results from a single amino acid
substitution in the protein hemoglobin
A single amino acid substitution in a protein causes sickle-cell disease
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PrimaryStructure
Secondaryand TertiaryStructures
QuaternaryStructure
FunctionRed BloodCell Shape
subunit
subunit
Exposedhydrophobicregion
Molecules do notassociate with oneanother; each carriesoxygen.
Sickle-cellhemoglobin
Normalhemoglobin
10 m
10 m
Sickle-cellhemo
globin
No
rmalhemoglobin
1
23
4
5
6
7
1
2
3
4
5
6
7
Molecules interact withone another andcrystallize into a fiber;capacity to carryoxygen is reduced.
What Determines Protein Structure?
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What Determines Protein Structure?
Alterations in pH, salt concentration, temperature, or other
environmental factors can cause a protein to unravel This loss of a proteins native structure is called
denaturation (2, 3, 4)
A denatured protein is biologically inactive
Figure 5.22
Denaturation
and renaturation
of a protein.
Protein Folding in the Cell
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Protein Folding in the Cell
Chaperonins are proteinmolecules that assist the proper
folding of other proteins
Diseases such as Alzheimers,
Parkinsons, and mad cowdisease are associated with
misfolded proteins
Cap
Chaperonin(fully assembled)
Hollow
cylinder
Fig 5.23
It is hard to predict a proteins
structure from its primary structure
Most proteins probably go through
several stages on their way to a
stable structure
Figure 5.23 A chaperonin in action.
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The cap attaches, causingthe cylinder to changeshape in such a way thatit creates a hydrophilicenvironment for thefolding of the polypeptide.
Polypeptide
Correctlyfoldedprotein
Steps of ChaperoninAction:
An unfolded poly-peptide enters thecylinder fromone end.
The cap comesoff, and theproperly foldedprotein isreleased.
32
1
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Scientists use X-ray crystallographyto
determine a proteins structure
Another method is nuclear magnetic resonance(NMR) spectroscopy, which does not require
protein crystallization
Bioinformatics is another approach to prediction
of protein structure from amino acid sequences
EXPERIMENTDetermine a
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DiffractedX-rays
X-ray
source X-raybeam
Crystal Digital detector X-ray diffractionpattern
RNA DNA
RNApolymerase II
RESULTS
Figure 5.24 Inquiry: What
can the 3-D shape of the
enzyme RNA polymerase II
tell us about its function?
X-ray
crystallography
nuclear magnetic
resonance (NMR)
spectroscopy Bioinformatics
proteins
structure
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Nucleic acids store, transmit, andhelp express hereditary information
69
Nucleic acids store transmit and help
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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 consist of DNA, a nucleic acidmade ofmonomers called nucleotides
There are two types of nucleic acids
Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)
The Roles of Nucleic Acids
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The Roles of Nucleic Acids
DNA provides directions for its own replication
DNA directs synthesis of messenger RNA (mRNA)and, through mRNA, controls protein synthesis
This process is called gene expression
Each gene along a DNA molecule directs synthesisof a messenger RNA (mRNA)
The mRNA molecule interacts with the cellsprotein-synthesizing machinery to direct
production of a polypeptide
The flow of genetic information can besummarized as DNA RNA protein
DNA DNA: Genetic materials
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Synthesis of
mRNA mRNA
NUCLEUS
CYTOPLASM
mRNA
Ribosome
AminoacidsPolypeptide
Movement ofmRNA intocytoplasm
Synthesisof protein
1
2
3
DNA RNA Protein
RNA: Gene expression
r-RNA, mRNA, rRNA,
& others
(some as enzymes)
Figure 5.25-3
The Components of Nucleic Acids
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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
Nucleotide Monomers
The Components of Nucleic Acids
Components of nucleic acidsSugar-phosphate backbone Nitrogenous bases
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Sugar phosphate backbone5end
5C
3C
5
C
3C
3end
(a) Polynucleotide,or nucleic acid
(b) Nucleotide
Phosphategroup Sugar
(pentose)
NucleosideNitrogenous
base
5C
3
C
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
Figure 5.26
Nucleotide Polymers
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Nucleotide Polymers
Nucleotides are linked together to build a
polynucleotide Adjacent nucleotides are joined by a
phosphodiester linkage, which consists of aphosphate group that links the sugars of two
nucleotides These links create a backbone of sugar-phosphate
units with nitrogenous bases as appendages
The sequence of bases along a DNA or mRNApolymer is unique for each gene
The Structures of DNA and RNA Molecules
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e St uctu es o a d o ecu es
DNA molecules have two polynucleotides spiralingaround an imaginary axis, forming a double helix
The backbones run in opposite 5 3directionsfrom each other, an arrangement referred to asantiparallel
One DNA molecule includes many genes Only certain bases in DNA pair up and formhydrogen bonds: adenine (A) always with thymine(T), and guanine (G) always with cytosine (C)
This is called complementary base pairing This feature of DNA structure makes it possible togenerate two identical copies of each DNAmolecule in a cell preparing to divide
RNA i t t t DNA i i l t d d
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RNA, in contrast to DNA, is single stranded
Complementary pairing can also occur
between two RNA molecules or between partsof thesame molecule
In RNA, thymine is replaced by uracil (U) soA and U pair
While DNA always exists as a double helix,RNA molecules are more variable in form
Figure 5.27
The structures of DNA and tRNA molecules
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Sugar-phosphatebackbones
Hydrogen bonds
Base pair joinedby hydrogen bonding
Base pair joinedby hydrogen
bonding
(b) Transfer RNA(a) DNA
5
3
5
3
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Genomics and proteomics have
transformed biological inquiry and
applications
Figure 5.26
MAKE CONNECTIONSC t ib ti f G i d P t i t Bi l
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Contributions of Genomics and Proteomics to Biology
Paleontology Evolution
Hippopotamus Short-finned pilot whale
Medical Science Conservation BiologySpeciesInteractions
80
Genomics and proteomics have transformed
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biological inquiry and applications
Once the structure of DNA and its relationship toamino acid sequence was understood, biologistssought to decode genes by learning their basesequences
The first chemical techniques for DNA sequencing were
developed in the 1970s and refined over the next 20years
It is enlightening to sequence the full complement ofDNA in an organisms genome
The rapid development of faster and less expensivemethods of sequencing was a side effect of the HumanGenome Project
Many genomes have been sequenced, generatingreams of data
Bioinformatics uses computer software and
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Bioinformatics uses computer software andother computational tools to deal with thedata resulting from sequencing manygenomes
Analyzing large sets of genes or evencomparing whole genomes of different
species is called genomics A similar analysis of large sets of proteins
including their sequences is called proteomics
DNA and Proteins as Tape Measures
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p
of Evolution
Sequences of genes and their protein productsdocument the hereditary background of anorganism
Linear sequences of DNA molecules arepassed from parents to offspring
We can extend the concept of moleculargenealogy to relationships between species
Molecular biology has added a new measureto the toolkit of evolutionary biology
DNA and Proteins as Tape Measures
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of Evolution
Human GibbonRhesusmonkey
Summary
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Summary
An immense variety of biological polymers with
diverse functions can be built from a small numberof specific class of monomers.
Carbohydrates, lipids, proteins, and nucleic acids
are four major categories of biological
macromolecules in living organisms.
Can you compare the common and diverse
characteristics of the four major large biological
molecules in terms of structure and function? Importance of genomics and proteomics
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(1)
(2)DNAdouble helix Helix Sheetconformation
(3)
(4)
(5)