chapter 1 bio molecules
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Bio MoleculesTRANSCRIPT
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Chapter 1Chapter 1The Structure and The Structure and
Function of BiomoleculesBiomolecules
(Macromolecules)
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The Molecules of LifeThe Molecules of Life• Overview:Overview:
– Another level in the hierarchy of biological organization is of biological organization is reached when small organic molecules are joined togethermolecules are joined together
– Atom ---> molecule ---dcompound
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MacromoleculesMacromolecules– Are large molecules composed of smaller Are large molecules composed of smaller
molecules– Are complex in their structuresmp
3Figure 5.1
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MacromoleculesMacromolecules
M l l l •Most macromolecules are polymers, built from monomers
F l f lif ’ i• Four classes of life’s organicmolecules are polymers
Carbohydrates– Carbohydrates– Proteins
N l i id– Nucleic acids– Lipids
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• A polymer– Is a long molecule consisting of Is a long molecule consisting of
many similar building blocks called monomersmonomers
– Specific monomers make up each macromoleculemacromolecule
– E.g. amino acids are the monomers f t ifor proteins
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The Synthesis and Breakdown of Polymers
• Monomers form larger molecules by Monomers form larger molecules by condensation reactions called dehydration synthesis
HO H1 2 3 HOH
Short polymer Unlinked monomer
H2O
Short polymer Unlinked monomer
Dehydration removes a watermolecule, forming a new bond
(a) Dehydration reaction in the synthesis of a polymer
HO H1 2 3 4
Longer polymerFigure 5.2A
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The Synthesis and Breakdown of Polymers
• Polymers can disassemble byPolymers can disassemble by– Hydrolysis (addition of water molecules)
HO H1 2 3 4
H2OHydrolysis adds a watermolecule, breaking a bond
(b) Hydrolysis of a polymer
HO 1 2 3 H HHO
Figure 5 2B
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(b) Hydrolysis of a polymerFigure 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 p ysmall set of monomers
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CarbohydratesCarbohydrates• Serve as fuel and building Serve as fuel and building
materiall d b h d • Include both sugars and
their polymers (starch, p y (cellulose, etc.)
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SugarsSugars
Monosaccharides• Monosaccharides– Are the simplest sugars
C b d f f l– Can be used for fuel– Can be converted into other
i l lorganic molecules– Can be combined into polymers
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Ex mpl s f m n s h id s• Examples of monosaccharidesTriose sugars
(C H O )Pentose sugars
(C H O )Hexose sugars
(C H O )(C3H6O3) (C5H10O5) (C6H12O6)
H C OHH C OH
H C OH
H C OH
HO C H
H C OH
HO C H
H C OH
H H H HC C C C
OOOO
es H C OH H C OH
H C OH
H C OH
HO C H
H C OH
H C OH
H C OH
HO C H
HO C H
H C OH
H C OH
H
H
H HAldos
e
Glyceraldehyde
Ribose
H C OH H C OH
C OC O
H C OH
C O
H H H
HGlucose Galactose
H C OH
H C OH
H C OHH C OH
H C OHH C OH
H C OHHO C H
H
HDihydroxyacetone
b l
Keto
ses
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HRibuloseFructoseFigure 5.3
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• MonosaccharidesMonosaccharides– May be linear– Can form rings– Can form rings
H OC1
2
6CH2OH 6CH2OHCH OHH C OH
HO C H
H C OH
2
3
4
H
OH
4C
5C
HOH H
1CH
O
H
OH
4C
5C
HOH H
1 C
HCH2OH
HOH
HO
H
OH
H5
3 2
4
O H OO
6
1
H C OH
H C
H
5
6
OH C
H OH
2 C OH 3 C
H OH
2C OHH OH
OH 3
(a) Linear and ring forms. Chemical equilibrium between the linear and ringstructures greatly favors the formation of rings. To form the glucose ring,carbon 1 bonds to the oxygen attached to carbon 5.
Figure 5.4
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D h d• Disaccharides– Consist of two Consist of two
monosaccharidesA j i d b l sidi – Are joined by a glycosidic linkage
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Dehydration reaction in the synthesis of maltose. The bonding of two glucose units
(a)
OCH2OH
OCH2OH CH2OH
OCH2OH
Oof 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.
H
HO
H
HOH H
OH
O H
OH
H
O
H
HOH H
OH
O H
OHH
H
HO
OHH
HOH H
O H
OHH
HOH H
O H
OHO
1 41–4
glycosidiclinkage
OH
H
gJoining the glucose monomers in a different way would result in a different disaccharide. CH2O
H
H2O
CH OHCH2OH CH OH
Glucose Glucose Maltose
Dehydration reaction in the synthesis of sucrose. Sucrose is a disaccharide f rmed
(b)
H
HO
H
HOH
H
O
O H
OH
H
H
H
O
H
HOH
OH
O HCH2OH
CH2OH HO
OHH
HOH H
O
HOH
CH2OH
H HO
O
CH2OH
H
O
1 21–2
glycosidiclinkage
H
a disaccharide formed from glucose and fructose.Notice that fructose,though a hexose like glucose, forms a five-sided ring.
H OH
H2OHOH OHH HOH
Glucose Fructose Sucrose
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Figure 5.5
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PolysaccharidesPolysaccharides• PolysaccharidesPolysaccharides
– Are polymers of sugars– Serve many roles in organisms– Serve many roles in organisms
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Storage PolysaccharidesStorage Polysaccharides• Starch
Chloroplast Starch
Starch– Is a polymer
consisting consisting entirely of glucose
1 μmgmonomers
– Is the major
1 μm
storage form of glucose in plants
Amylose Amylopectin
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(a) Starch: a plant polysaccharideFigure 5.6
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• Glycogen• Glycogen– Consists of glucose monomers
Is th j st f f l s i – Is the major storage form of glucose in animals Mitochondria Giycogen
granules
0.5 μm
Glycogen
17(b) Glycogen: an animal polysaccharideFigure 5.6
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Structural PolysaccharidesStructural Polysaccharides• CelluloseCellulose
– Is a polymer of glucose
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– Has different glycosidic linkages than starch
H O
O
CH2OH
HHH
C
CHH
OH O
CH2OH
HOH
HHOH H O
HOHH
HO
4 C
C
C
C
H
H
HO
HHOHOHO
H
HH
H
H
OHH
HO
4 OH
1
α glucose β glucoseCH H
CH2OH
O
CH2OH
O
CH2OH
O
CH2OH
O
(a) α and β glucose ring structures
α glucose β glucose
OOH
OH
HO
41O
OOH
OH
O
OOH
OH
OOH
OH
O O
(b) Starch: 1 4 linkage of α glucose monomers
1 4 41 1
CH2OH
OOHH
O4
O1
OH
O
OH
OHO
CH2OH O
O OH
O
OH
OH
(b) Starch: 1– 4 linkage of α glucose monomers
19(c) Cellulose: 1– 4 linkage of β glucose monomers
OH
O OOH
O HCH2O
HCH2O
HFigure 5.7 A–C
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– Is a major component of the tough walls that enclose plant cells
Cell walls
Cellulose microfibrils in a plant cell wall Microfibril
About 80 cellulosemolecules associate
to form a microfibril, themain architectural unitof the plant cell wall.
0.5 μm
Plant cells
CH2OH
OHO
OO
OHOCH OH
OO
OHO
CH2OH OH
OH OHO
CH OHOHO
O
C ll l
CH2OH
OH
CH2OH
O
CH2OHO
O OH
CH2OHO
O
CH2OHOH
CH2OHOHOOH OH OH OH
OH OH
CH2OHOHO O
OH CH2OH
OH
O
O
O
OParallel cellulose molecules areheld together by hydrogenbonds between hydroxyl
groups attached to carbon
OH
OH
O
OH
Cellulosemolecules
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OOH
OOH OH
CH2OH
OH
OH CH2OHO
β Glucose monomer
Ogroups attached to carbon
atoms 3 and 6. A cellulose moleculeis an unbranched βglucose polymer.
OOH
Figure 5.8
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• Cellulose is difficult to digestCellulose is difficult to digest– Cows have microbes in their stomachs to
facilitate this processfacilitate this process
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Figure 5.9
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• Chitin, another important structural , mp u upolysaccharide– Is found in the exoskeleton of arthropodsIs found in the exoskeleton of arthropods– Can be used as surgical thread
OCH2O
H
OHHH OHOH
HNHCCH3
O
H
HOH
(a) The structure of thechitin monomer.
(b) Chitin forms the exoskeleton of arthropods. This cicada is molting shedding its old
(c) Chitin is used to make a strong and flexible surgicalthread that decomposes after
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is molting, shedding its old exoskeleton and emergingin adult form.
thread that decomposes afterthe wound or incision heals.
Figure 5.10 A–C
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LipidsLipids
Lipids are a diverse group of • Lipids are a diverse group of hydrophobic moleculesLi id• Lipids– Are the one class of large biological
l l h d i f molecules that do not consist of polymersSh th t it f b i – Share the common trait of being hydrophobic
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Fats d f f ll – 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 d f f ll – 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 , g g y y yacids
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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• Saturated fatty acids– Have the maximum number of
hydrogen atoms possiblehydrogen atoms possible– Have no double bonds
Stearic acid
28(a) Saturated fat and fatty acidFigure 5.12
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• Unsaturated fatty acids– Have one or more double bonds
Oleic acid
(b) Unsaturated fat and fatty acidcis double bondcauses bendingFigure 5.12
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• Phospholipidsp p– Have only two fatty acids– Have a phosphate group instead of a Have a phosphate group instead of a
third fatty acid
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• Phospholipid structurep p– Consists of a hydrophilic “head” and
hydrophobic “tails”hydrophobic tailsCH2
OPO O Phosphate–
CH2 Choline+N(CH3)3
PO OOCH2CHCH2
OO
C O C O
Glycerol
Fatty acids
Hydrophilichead
Hydrophobictails
31(a) Structural formula (b) Space-filling model (c) Phospholipid
symbolFigure 5.13
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• The structure of phospholipidsu u f p p p– Results in a bilayer arrangement found in
cell membranes
H d hiliWATER
Hydrophilichead
WATER
Hydrophobic
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y ptail
Figure 5.14
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SteroidsSteroids• SteroidsSteroids
– Are lipids characterized by a carbon skeleton consisting of four fused ringsskeleton consisting of four fused rings
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On st id h l st l• One steroid, cholesterol– Is found in cell membranes
f h– Is a precursor for some hormones
H3C CH
CH3
H3 CH3
CH3
CH3
HOFigure 5.15
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ProteinsProteins• Proteins have many structures Proteins have many structures,
resulting in a wide range of functionsfunctions
• Proteins do most of the work in cells and act as enzymescells and act as enzymes
• Proteins are made of monomers ll d i idcalled amino acids
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• An overview of protein functionsAn overview of protein functions
Table 5.1
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• EnzymesE zym– Are a type of protein that acts as a
catalyst, speeding up chemical reactionsy , p g p
Substrate(sucrose)
1 Active site is available fora molecule of substrate, the
reactant on which the enzyme acts.
Substrate binds toenzyme.
22
(sucrose)
GlucoseEnzyme (sucrase)
Glucose
OH H2OFructose
H O
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3 Substrate is convertedto products.
4 Products are released.Figure 5.16
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PolypeptidesPolypeptides• PolypeptidesPolypeptides
– Are polymers (chains) of amino acidsA protein• A protein– Consists of one or more polypeptides
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• Amino acidsm– Are organic molecules possessing both carboxyl and amino groupsy g p
– Differ in their properties due to differing side chains, called R groupsg g p
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Twenty Amino AcidsTwenty Amino Acids• 20 different amino acids make up CH3CH3
CH320 different amino acids make up proteinsH
H3N+ C CO
O–
CH3
H3N+ C C
O
O–
CH3 CH3
CH3
C C
O
O–
H3N+
CH
CH3
CH2
CH3N+
CH3
CH2
CH
CH3N+ CC
O
O–
H3C O
O–OH H
O OH H H
Nonpolar
Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)
O O
O
O–
CH3
CH2
CH CH CH
NH
CH2
H2C
H2N C
CH2
C
S
OCH2
CH3N+
H
C
O
O–
CH2
CH3N+
H
CO
O–
CH2
H
CO
O–
H3N+ CH
Methionine (Met) Phenylalanine (Phe) Tryptophan (Trp) Proline (Pro)
40Figure 5.17
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OH OH CH3SH
OH
NH2 OC
NH2 OC
CH2Polar
O–
CH2
C C
H
H3N+
O
O–
H3N+
3
CH
C C
H O–
O CH2
C
H
H3N+ C
O
O–
H3N+ C C
CH2
H H H
H3N+
CH2
C CO
O–
CH2
C CH3N+
O
O–
OPolar
Serine (Ser) Threonine (Thr) Cysteine (Cys)
Tyrosine(Tyr)
Asparagine(Asn)
Glutamine(Gln)
NH + NH NH+
( ) ( ) (Cys) (Tyr) (Asn) (Gln)
Acidic Basic
Electricallycharged
–O OC
CH2
C CH3N+
O
O–
O– OC
CH2
C CH3NOCH2
CH2
CH2
CH2
NH3
CH2 O
NH2
C NH2+
CH2
CH2
CH
NH
NHCH2
C CH3N+
H
O
O–
HC C3
+
HO–
CH2
C CH3N+
H
O
O–
CH2
C CH3N+
H
O
O–
CH2
H
Aspartic acid Glutamic acid Lysine (Lys) Arginine (Arg) Histidine (His)
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p(Asp) (Glu)
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Amino Acid PolymersAmino Acid Polymers• Amino acidsAmino acids
– Are linked by peptide bonds
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Protein Conformation and Protein Conformation and Function
• A protein’s specific conformation (shape) determines how it functions( p )
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Four Levels of Protein StructureFour Levels of Protein Structure• Primary structure Amino +H3N
GlyProThrGlyThrPrimary structure
– Is the unique sequence of amino
acid subunits
H3NAmino end
Gly
GluSeuLysCysProLeu
MetVal
Lys
ValLeuAsp
AlaValArgGlySer
ProAlasequence of amino
acids in a polypeptide
GlylleSerProPheHisGluHis
AlaGlu
ValValPheThrAl
ThrLysSer
TyrTrpLysAlaLeu
GluLle Asp
–oo
c
ValPheThrAlaAsn
AspSer
GlyProArgArgTyrThrlle
AlaAlaLeu
LeuSerProTyrSerTyrSerThr
ThrAlaVal
ValThrAsnProLysGlu
44
Figure 5.20o
Carboxyl end
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• Secondary structureSecondary structure– Is the folding or coiling of the polypeptide
into a repeating configurationinto a repeating configuration– Includes the α helix and the β pleated
sheetβ pleated sheet
Amino acidsubunits NC
H
CO
C NH
CO H
RC N
H
CO H
CR
NHH
R CO
RCH
NH
CO H
NCO
RCH
NH
H
CR
CO H
CR
NH
CO
C
sheet
H O H H O H H O H H
CO
C
NH
H
RC
CO
NH
H
CR
CO
NH
RCH C
ONH H
CR
C
ONH
RCH C
ONH H
CR
CO
R H R H
O
NH
RCH C
ONH
C
O C α helixN H
H C RN H O
O C N
CH O
CHR
N HO C
RC H
N H
O CH C R
N H
C N HO C
H C R
N HO C
RC
H
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O C N
RC
H O CC
N
R
H
H H
Figure 5.20
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• Tertiary structureTertiary structure– Is the overall three-dimensional shape of
a polypeptidep yp p– Results from interactions between amino
acids and R groupsg p
CH2CH
O CH3H3C
Hydrophobic interactions and van der Waalsinteractions CH2
OHOCHOCH2 CHSSCH
CH
CH3CH3
3
H3C Polypeptidebackbone
Hyrdogenbond
2
CH2 NH3+ C-O CH2
O
CH2SSCH2
Ionic bond
Disulfide bridge
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• Quaternary structureQu y u u– Is the overall protein structure that
results from the aggregation of two or gg gmore polypeptide subunits
Polypeptidechain
Collagenβ Ch iβ Chains
IronH
47α Chains
Hemoglobin
Heme
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Review of Protein StructureReview of Protein Structure
+H3NAmino end
Amino acidsubunits
α helix
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Sickle-Cell Disease: A Simple Change Sickle-Cell Disease: A Simple Change in Primary Structure
• Sickle-cell diseaseSickle cell disease– Results from a single amino acid
substitution in the protein substitution in the protein hemoglobin
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P i Normal hemoglobin Sickle-cell hemoglobinPrimary
structure
Secondaryand tertiary
Primary structure
Secondaryand tertiaryβ subunit β subunit
1 2 3 4 5 6 7 3 4 5 6 721
Normal hemoglob n Sickle cell hemoglobin. . .. . . Exposed
hydrophobic region
Val ThrHis Leu Pro Glul Glu Val His Leu Thr Pro Val Glu
structures
Quaternary structure
Hemoglobin Aα
β
βα
β
βα
ystructures
Quaternary structure Hemoglobin S
Function Molecules donot associate
ith n
β α βFunction
Molecules interact with one another tocrystallize into a fiber capacity
Red bloodcell shape
with oneanother, eachcarries oxygen.Normal cells arefull of individual
10 μm 10 μm
Red blood
fiber, capacity to carry oxygen is greatly reduced.
Fibers of abnormalhemoglobin d f ll
cell shape full of individualhemoglobinmolecules, eachcarrying oxygen
cell shape
Figure 5.21
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deform cell into sickle shape.
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What Determines Protein What Determines Protein Conformation?
• Protein conformation Depends pon the physical and chemical conditions of the protein’s penvironment
• Temperature, pH, etc. affect Temperature, pH, etc. affect protein structure
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•Denaturation is when a protein •Denaturation is when a protein unravels and loses its native conformation(shape) Denaturation(shape)
Renaturation
Denatured proteinNormal protein
Figure 5.22
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g
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The Protein-Folding ProblemThe Protein-Folding Problem• Most proteinsMost proteins
– Probably go through several intermediate states on their way to a intermediate states on their way to a stable conformation
– Denaturated proteins no longer work Denaturated proteins no longer work in their unfolded condition
– Proteins may be denaturated by y yextreme changes in pH or temperature
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• Chaperonins– Are protein molecules that assist in the
proper folding of other proteins
Cap
CorrectlyfoldedproteinPolypeptide
Hollowl dcylinder
St f Ch i The cap attaches causing The cap comesChaperonin(fully assembled)
Steps of ChaperoninAction:
An unfolded poly-peptide enters the cylinder from one
The cap attaches, causing the cylinder to change shape insuch a way that it creates a hydrophilic environment for
The cap comesoff, and the properlyfolded protein is released.
2
1
3
Fi 5 23
54
y f mend.
y pthe folding of the polypeptide. Figure 5.23
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• X-ray crystallographyX ray crystallography– Is used to determine a protein’s three-
dimensional structure X raydimensional structure X-raydiffraction pattern
Photographic filmDiffracted X-
raysraysX-raysource
X-raybeam
Crystal Nucleic acid Protein
55(a) X-ray diffraction pattern(b) 3D computer model
Figure 5.24
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Nucleic AcidsNucleic Acids
Nucleic acids store and transmit • Nucleic acids store and transmit hereditary informationG• 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 AcidsThe Roles of Nucleic Acids• There are two types of nucleic acidsThere are two types of nucleic acids
– Deoxyribonucleic acid (DNA)– Ribonucleic acid (RNA)– Ribonucleic acid (RNA)
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Deoxyribonucleic AcidDeoxyribonucleic Acid• DNADNA
– Stores information for the synthesis of specific proteinsof specific proteins
– Found in the nucleus of cells
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DNA FunctionsDNA Functions– Directs RNA synthesis (transcription)– Directs protein synthesis through RNA Directs protein synthesis through RNA
(translation)1 S nth sis f
DNA
1 Synthesis ofmRNA in the nucleus
NUCLEUS
mRNA
2 Movement of
NUCLEUSCYTOPLASM
mRNA
Rib
3
mRNA into cytoplasm via nuclear pore
Synthesisof protein
Ribosome
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p
AminoacidsPolypeptideFigure 5.25
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The Structure of Nucleic The Structure of Nucleic Acids
5’ end
• Nucleic acids– Exist as polymers called
5 end
5’C
3’C
O
Exist as polymers called polynucleotides
3 C
O
O
3’C
5’C O
60(a) Polynucleotide,
or nucleic acid
3 C3’ end
OH
Figure 5.26
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• Each polynucleotideE p y u– Consists of monomers called nucleotides– Sugar + phosphate + nitrogen baseSugar + phosphate + nitrogen base
Nucleoside
Nitrogenousbase
O 5’C
O
O−
−O P CH2
3’CPhosphate
O
3’CPhosphategroup Pentose
sugar
(b) NucleotideFigure 5.26
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Nucleotide MonomersM m
• Nucleotide monomers• Nucleotide monomers– Are made up of
nucleosides (sugar + CHCH
Nitrogenous basesPyrimidines
CN
NCO
NH2
CHCH
OC
N CHHN C
O
C CH3
N
HNC
CO
O
CHCHnucleosides (sugar +
base) and phosphate groups
Uracil (in RNA)U
OH
O NH
NH
O
CytosineC
Thymine (in DNA)T
NH2 OPurines
Uracil (in RNA)U
groupsN
HCN C
C N
C
CHN
2
NHC
NHH
C C
N
NHC NH2
AdenineA
GuanineG
OHOCH2
HH H
OH
H
OHOCH2
HH H
OH
H
Pentose sugars
OHOH
4’
5”
3’OH H
2’
1’
5”
4’
3’ 2’
1’
62(c) Nucleoside componentsFigure 5.26
Ribose (in RNA)Deoxyribose (in DNA) Ribose (in RNA)OHOHOH H
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Nucleotide PolymersNucleotide Polymers• Nucleotide polymersNucleotide polymers
– Are made up of nucleotides linked by the–OH group on the 3´ carbon of one the OH group on the 3 carbon of one nucleotide and the phosphate on the 5´carbon on the next
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GeneGene• The sequence of bases along a The sequence of bases along a
nucleotide polymer– Is unique for each gene– Is unique for each gene
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The DNA Double HelixThe DNA Double Helix• Cellular DNA moleculesCellular DNA molecules
– Have two polynucleotides that spiral around an imaginary axisan imaginary axis
– Form a double helix
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• The DNA double helix• The DNA double helix– Consists of two antiparallel nucleotide
strandsstrands3’ end
Sugar-phosphatebackbone
5’ end
Base pair (joined byhydrogen bonding)Old strands
Nucleotideb t t b about to be
added to a new strand
A 3’ end
3’ end New
5’ end
663’ end
3 end
5’ end
strands
Figure 5.27
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A T C GA,T,C,G• The nitrogenous bases in DNAThe nitrogenous bases in DNA
– Form hydrogen bonds in a complementary fashion (A with T only and C with G only)fashion (A with T only, and C with G only)
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DNA and Proteins as Tape DNA and Proteins as Tape Measures of Evolution
• Molecular comparisons Molecular comparisons – Help biologists sort out the
evolutionary connections among evolutionary connections among species
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The Theme of Emergent Properties The Theme of Emergent Properties in the Chemistry of Life: A Review
• Higher levels of organizationR lt i th f – Result in the emergence of new properties
O i ti• Organization– Is the key to the chemistry of
liflife
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