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Chapter 5
The Structure and Function of Macromolecules
• Overview: The Molecules of Life– Another level in the hierarchy of biological
organization is reached when small organic molecules are joined together
• Macromolecules– Are large molecules composed of smaller
molecules
– Are complex in their structures
• 4 main classes of macromolecules:
• carbohydrates
• lipids
• proteins
• nucleic acids
Most macromolecules are polymers, built from smaller molecules (repeating units)
• three of the classes of life’s organicmolecules are polymers
– Carbohydrates
– Proteins
– Nucleic acids
• A polymer– Is a long molecule consisting of many similar
building blocks called monomers
The Synthesis and Breakdown of Polymers
• Monomers form larger molecules by condensation reactions called dehydration(synthesis) reactions
(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
• Polymers can disassemble by hydrolysis
(b) Hydrolysis of a polymer
HO 1 2 3 H
HO H1 2 3 4
H2O
HHO
Hydrolysis adds a watermolecule, breaking a bond
The Diversity of Polymers
• Each class of polymer is formed from a specific set of monomers
• 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
Carbohydrates
• Elements: C, H, O
• General formula: CH2O (ex. C6H12O6)
• Include: – sugars and their polymers (ex. starches)
• Functions: – Energy (fuel & storage)
– Raw materials (for synthesis of other organic molecules)
– Structural materials
Sugars
• Most names end in “-ose”
• Classified by # of carbons:
– 6C = hexose (ex. Glucose)
– 5C = pentose (ex. deoxyribose & ribose)
– 3C = triose (ex. Glyceraldehyde
• Characteristic functional groups:– Hydroxyl (multiple)
– Carbonyl (one; in linear form only)
Sugars
• Aldehyde vs. Ketone sugars:– Depends on location of carbonyl group
– Sugars start out as linear molecules!
– If carbonyl located on C1 (at end) = aldehyde sugar = aldose (ex. Glucose)
– If carbonyl located on C2 = ketone sugar = ketose (ex. Fructose)
Sugars
• Linear vs. ring structure:– Equilibrium greatly favors ring
– 5C & 6C sugars form rings in aqueous solutions (i.e. in cells!)
– Carbons are numbered!
– Spatial arrangement of parts around asymmetric carbon becomes important
– Many isomers result from arrangement of hydroxyl groups (“down, down, up, down”)
– Glucose vs. galactose (1 asymmetric carbon)
Sugars
• Monosaccharides
– simplest sugars = monomers• Ex. Glucose, fructose, galactose
– can be:
• used directly for fuel
• converted into other organic molecules
• combined into polymers
• Examples of monosaccharides
Triose sugars(C3H6O3)
Pentose sugars(C5H10O5)
Hexose sugars(C6H12O6)
H C OH
H C OH
H C OH
H C OH
H C OH
H C OH
HO C H
H C OH
H C OH
H C OH
H C OH
HO C H
HO C H
H C OH
H C OH
H C OH
H C OH
H C OH
H C OH
H C OH
H C OH
H C OH
C OC O
H C OH
H C OH
H C OH
HO C H
H C OH
C O
H
H
H
H H H
H
H H H H
H
H H
C C C COOOO
Ald
oses
Glyceraldehyde
RiboseGlucose Galactose
Dihydroxyacetone
Ribulose
Ket
oses
Fructose
• Monosaccharides– May be linear or can form rings
H
H C OH
HO C H
H C OH
H C OH
H C
OC
H
1
2
3
4
5
6
H
OH
4C
6CH2OH 6CH2OH
5C
HOH
C
H OH
H2 C
1C
H
O
H
OH
4C
5C
3 C
H
HOH
OH
H2C
1 C
OH
H
CH2OH
H
H
OHHO
H
OH
OH
H5
3 2
4
Linear and ring forms: • Chemical equilibrium between linear & ring structures
greatly favors ring formation.• To form the glucose ring, carbon 1 bonds to the oxygen
attached to carbon 5.
OH 3
O H OO
6
1
• Disaccharides– Consist of two monosaccharides
– Are joined by a glycosidic linkage
• Examples of disaccharides Dehydration synthesis of maltose: glycosidic link joins carbon 1 of glucose to carbon 4 of another glucose
Dehydration synthesis of sucrose: glycosidic link joins carbon 1 of glucose to carbon 2 of fructose
(a)
(b)
H
HO
H
HOH H
OH
O H
OH
CH2OH
H
HO
H
HOH H
OH
O H
OH
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
Polysaccharides
• Are polymers of sugars
• Serve many roles in organisms
Storage Polysaccharides
• Starch– Is a polymer consisting
entirely of glucose monomers
– Is the major storage form of glucose in plants
Chloroplast Starch
Amylose Amylopectin
1 m
Starch: a plant polysaccharide
• Glycogen– Also consists of
glucose monomers
– Is the major storage form of glucose in animals
Mitochondria Giycogen granules
0.5 m
Glycogen: an animal polysaccharide
Glycogen
Structural Polysaccharides• Cellulose
– Is a also polymer of glucose
– Has different glycosidic linkages than starch
(c) Cellulose: 1– 4 linkage of glucose monomers
H O
O
CH2OH
HOH H
H
OH
OHH
H
HO
4
C
C
C
C
C
C
H
H
H
HO
OH
H
OH
OH
OH
H
O
CH2OH
HH
H
OH
OHH
H
HO4 OH
CH2OH
O
OH
OH
HO41
O
CH2OH
O
OH
OH
O
CH2OH
O
OH
OH
CH2OH
O
OH
OH
O O
CH2OH
O
OH
OH
HO 4O
1
OH
O
OH OHO
CH2OH
O
OH
O OH
O
OH
OH
(a) and glucose ring structures
(b) Starch: 1– 4 linkage of glucose monomers
1
glucose glucose
CH2OH
CH2OH
1 4 41 1
– Cellulose is a major component of the tough cell walls that enclose plant cells
Plant cells
0.5 m
Cell walls
Cellulose microfibrils in a plant cell wall Microfibril
CH2OH
CH2OH
OHOH
OO
OHOCH2OH
OO
OHO
CH2OH OH
OH OHO
O
CH2OHO
OOH
CH2OH
OO
OH
O
O
CH2OHOH
CH2OHOHOOH OH OH OH
O
OH OH
CH2OH
CH2OH
OHO
OH CH2OH
OO
OH CH2OH
OH
Glucose monomer
O
O
O
O
O
O
Parallel cellulose molecules areheld together by hydrogenbonds between hydroxyl
groups attached to carbonatoms 3 and 6.
About 80 cellulosemolecules associate
to form a microfibril, themain architectural unitof the plant cell wall.
A cellulose moleculeis an unbranched glucose polymer.
OH
OH
O
OOH
Cellulosemolecules
• Cellulose is difficult to digest– Cows have microbes in their stomachs to facilitate
this process
• Chitin, another important structuralpolysaccharide– arthropods (exoskeletons) & fungi (cell walls)– 2nd most abundant after cellulose; most organisms
can’t digest it (N-containing side group)– leathery in pure form; becomes hardened by CaCO3
(a) The structure of thechitin monomer.
O
CH2OH
OHHH OH
HNHCCH3
O
H
H
(b) Chitin forms the exoskeletonof arthropods. This cicada is molting, shedding its old exoskeleton and emergingin adult form.
(c) Chitin is used to make a strong and flexible surgicalthread that decomposes afterthe wound or incision heals.
OH
• A.K.A. fats or triglycerides• diverse group of hydrophobic molecules• are the one class of large biological molecules
that do not consist of polymers– Share the common trait of being hydrophobic
Lipids
Lipids • Are constructed from two types of smaller
molecules, a single glycerol and usually three fatty acids
(b) Fat molecule (triacylglycerol)
H HH H
HHH H
HH H H
HH
HHO
H O HC
C
C
H
H OH
OH
H
HH
HH
H H HH
H H H H HH
H
HCCCCC
CCCCC
CC
CCC C
Glycerol
Fatty acid(palmitic acid)
HH
H
H
H H HH
HH
HH
HH H H
HH H H
HHHHHHHHHHHHHHHH
H
HH H H H H H H H H H H H H H
H
HHHHHHHHHHHHHH
H H H H H H H H H H H H H H HH
HHHHHHHHHHHHHHH
HO
OO
O
OC
C
C C C C C C C C C C C C C C C C C
C
CCCCCCCCCCCCCCCC
C C C C C C C C C C C C C C CO
O
(a) Dehydration reaction in the synthesis of a fatEster linkage
• Fatty acids vary in:– length– number– locations of double bonds they contain
• Saturated fatty acids– Have the maximum number of hydrogen atoms
possible– Have no double bonds– Are solid at room temperatures. Why??
(a) Saturated fat and fatty acid
Stearic acid
• Unsaturated fatty acids– Have one or more double bonds (causes “kink”)– Are liquid at room temperatures. Why??
(b) Unsaturated fat and fatty acidcis double bondcauses bending
Oleic acid
• Phospholipids– Have only two fatty acids
– Have a phosphate group instead of a third fatty acid
• Phospholipid structure– Consists of a hydrophilic “head” and hydrophobic
“tails”
CH2
OPO OO
CH2CHCH2
OO
C O C O
Phosphate
Glycerol
(a) Structural formula (b) Space-filling model
Fatty acids
(c) Phospholipid symbol
Hydrophilichead
Hydrophobictails
–
CH2 Choline+N(CH3)3
• The structure of phospholipids– Results in a bilayer arrangement found in cell
membranes
Hydrophilichead
WATER
WATER
Hydrophobictail
• Steroids– Are lipids characterized by a carbon skeleton
consisting of 4 fused rings
• Cholesterol– steroid found in cell membranes
– precursor for some hormones
HO
CH3
CH3
H3C CH3
CH3
• have many structures, resulting in a wide range of functions– Have many roles inside the cell
Proteins
• An overview of protein functions
Animation: Structural ProteinsAnimation: Structural Proteins
Animation: Storage ProteinsAnimation: Storage Proteins
Animation: Transport ProteinsAnimation: Transport Proteins
Animation: Receptor ProteinsAnimation: Receptor Proteins
Animation: Contractile ProteinsAnimation: Contractile Proteins
Animation: Defensive ProteinsAnimation: Defensive Proteins
Animation: Hormonal ProteinsAnimation: Hormonal Proteins
Animation: Sensory ProteinsAnimation: Sensory Proteins
Animation: Gene Regulatory ProteinsAnimation: Gene Regulatory Proteins
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Polypeptides• Polypeptides are polymers of amino acids
• A protein consists of one or more polypeptides– All proteins are polypeptides, but not all
polypeptides are proteins
Amino Acid Monomers
• Amino acids are organic molecules possessing both carboxyl and amino groups– 20 different amino acids make up proteins
– properties differ based on different side chains called R groups
Fig. 5-UN1
Aminogroup
Carboxylgroup
carbon(asymmetric)
Nonpolar
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
Asparagine(Asn or N)
Glutamine(Gln or Q)
Serine(Ser or S)
Threonine(Thr or T)
Cysteine(Cys or C)
Tyrosine(Tyr or Y)
Acidic
Arginine(Arg or R)
Histidine(His or H)
Aspartic acid(Asp or D)
Glutamic acid(Glu or E)
Lysine(Lys or K)
Basic
Electricallycharged
Amino Acid Polymers• Amino acids are linked by peptide bonds
OH
DESMOSOMES
DESMOSOMESDESMOSOMES
OH
CH2
C
N
H
CH O
H OH OH
Peptidebond
OH
OH
OH
H H
HH
H
HH
H
H
H H
H
N
N N
N N
SHSide
chains
SH
OO
O O O
H2O
CH2 CH2
CH2 CH2 CH2
C C C C C C
C CC C
Peptidebond
Amino end(N-terminus)
Backbone
(a)
(b) Carboxyl end(C-terminus)
Protein Conformation and Function
• The amino acid sequence determines a protein’s specific conformation (shape)
• A protein’s shape determines how it functions
• The amino acid sequences of polypeptides– Were first determined using chemical means
– Can now be determined by automated machines
• Two models of protein conformation
(a) A ribbon model
(b) A space-filling model
Groove
Groove
• Shape determines function!– Example: enzymes act as catalysts (speed up
chemical reactions) by binding with specific molecules (substrates); the shape of the enzyme’s active site matches the shape of the substrate.
Substrate(sucrose)
Enzyme (sucrase)
Glucose
OH
H O
H2OFructose
2Active site
Four Levels of Protein Structure
• Primary structure– unique amino acid
sequence in a polypeptide
–
Amino acid subunits
+H3NAmino end
oCarboxyl end
oc
Gly ProThr GlyThr
Gly
GluSeuLysCysProLeu
MetVal
Lys
ValLeu
AspAla Val ArgGly
SerPro
Ala
Gly
lleSerProPheHis Glu His
Ala
GluValValPheThrAla
Asn
AspSer
Gly ProArg
ArgTyrThr
lleAla
Ala
Leu
LeuSer
ProTyrSerTyrSerThrThr
AlaVal
ValThrAsn ProLysGlu
ThrLys
SerTyrTrpLysAlaLeu
Glu Lle Asp
O C helix
pleated sheet
Amino acidsubunits NC
H
CO
C N
H
CO H
R
C NH
C
O H
CR
NHH
R CO
R
CH
NH
C
O HN
CO
R
CH
NH
H
CR
C
O
C
O
C
NH
H
R
CCO
NH
H
CR
C
O
NH
R
CH C
ONH H
CR
C
ONH
R
CH C
ONH H
CR
C
O
N H
H C RN H O
O C N
C
RC
H O
CHR
N HO C
RC
H
N H
O CH C R
N H
CC
N
R
H
O C
H C R
N H
O C
RC
H
H
CR
NH
CO
C
NH
R
CH C
ONH
C
• Secondary structure– folding or coiling of the polypeptide into a
repeating configuration
– includes the helix and the pleated sheet
H H
• Tertiary structure
– overall three-dimensional shape of a polypeptide
– Results from interactions between amino acids and R groups
CH2CH
OHOCHO
CH2
CH2 NH3+ C-O CH2
O
CH2SSCH2
CH
CH3
CH3
H3CH3C
Hydrophobic interactions and van der Waalsinteractions
Polypeptidebackbone
Hyrdogenbond
Ionic bond
CH2
Disulfide bridge
• Quaternary structure– overall protein structure that results from the
aggregation of two or more polypeptide subunits
Polypeptidechain
Collagen Chains
ChainsHemoglobin
IronHeme
• The four levels of protein structure
+H3NAmino end
Amino acidsubunits
helix
Let’s look at the animation!
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Sickle-Cell Disease: A Simple Change in Primary Structure
• Sickle-cell disease
– Results from a single amino acid substitution in the protein hemoglobin
• Hemoglobin structure and sickle-cell disease
Fibers of abnormalhemoglobin deform cell into sickle shape.
Primary structure
Secondaryand tertiarystructures
Quaternary structure
Function
Red bloodcell shape
Hemoglobin A
Molecules donot associatewith oneanother, eachcarries oxygen.Normal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen
10 m 10 m
Primary structure
Secondaryand tertiarystructures
Quaternary 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. . .. . . Exposed
hydrophobic region
Val ThrHis Leu Pro Glul Glu Val His Leu Thr Pro Val Glu
What Determines Protein Conformation?
• Protein conformation depends on the physical and chemical conditions of the protein’s environment
• Denaturation– when a protein unravels and loses its native
conformation
Denaturation
Renaturation
Denatured proteinNormal protein
The Protein-Folding Problem
• Most proteins– Probably go through several intermediate states on
their way to a stable conformation– Can sometimes get misfolded along the way
• Chaperonins– Are protein molecules that assist in the proper
folding of other proteins
Hollowcylinder
Cap
Chaperonin(fully assembled)
Steps of ChaperoninAction:
An unfolded poly-peptide enters the cylinder from one end.
The cap attaches, causing the cylinder to change shape insuch a way that it creates a hydrophilic environment for the folding of the polypeptide.
The cap comesoff, and the properlyfolded protein is released.
Correctlyfoldedprotein
Polypeptide
2
1
3
• X-ray crystallography– Is used to determine a protein’s three-
dimensional structureX-raydiffraction pattern
Photographic filmDiffracted X-rays
X-raysource
X-raybeam
Crystal Nucleic acid Protein
(a) X-ray diffraction pattern (b) 3D computer model
Nucleic acids
• store and transmit hereditary information
• make up genes (units of inheritance)– program the amino acid sequence of
polypeptides
• There are two types of nucleic acids– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)
• DNA– Stores information
for the synthesis of specific proteins
– Directs RNA synthesis
– Directs protein synthesis through RNA
1
2
3
Synthesis ofmRNA in the nucleus
Movement of mRNA into cytoplasm via nuclear pore
Synthesisof protein
NUCLEUSCYTOPLASM
DNA
mRNA
Ribosome
AminoacidsPolypeptide
mRNA
Structure of Nucleic Acids
• Nucleic acids exist as polymers called polynucleotides
(a) Polynucleotide, or nucleic acid
3’C
5’ end
5’C
3’C
5’C
3’ endOH
O
O
O
O
• Each polynucleotide consists of monomers called nucleotides
Nitrogenousbase
Nucleoside
O
O
O
O P CH2
5’C
3’CPhosphategroup Pentose
sugar
(b) Nucleotide
O
• Nucleotide monomers are made up of nucleosides and phosphate groups
(c) Nucleoside components
CHCH
Uracil (in RNA)U
Ribose (in RNA)
Nitrogenous basesPyrimidines
CN
NCO
H
NH2
CHCH
OC
NH
CHHN
CO
CCH3
N
HNC
C
HO
O
CytosineC
Thymine (in DNA)T
NHC
N C
C N
C
CHN
NH2 ON
HCNHH
C C
N
NHC NH2
AdenineA
GuanineG
Purines
OHOCH2
HH H
OH
H
OHOCH2
HH H
OH
H
Pentose sugars
Deoxyribose (in DNA) Ribose (in RNA)OHOH
CHCH
Uracil (in RNA)U
4’
5”
3’OH H
2’
1’
5”
4’
3’ 2’
1’
• 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
Nitrogenousbase
Nucleoside
O
O
O
O P CH2
5’C
3’CPhosphategroup Pentose
sugar
(b) Nucleotide
O
• The sequence of bases along a nucleotide polymer is unique for each gene
DNA Double Helix
• Cellular DNA molecules– Have two polynucleotides that spiral around an
imaginary axis
– Form a double helix
• The DNA double helix– Consists of two antiparallel nucleotide strands
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
• The nitrogenous bases in DNA– Form hydrogen bonds in a complementary fashion
(A with T only, and C with G only)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The Theme of Emergent Properties in the Chemistry of Life: A Review
• Higher levels of organization
– Result in the emergence of new properties
• Organization
– Is the key to the chemistry of life