1. The Structure and Function of Large Biological Molecules
Chapter 5
The Structure and Function of Large Biological Molecules

2. Overview: The Molecules of Life
four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids.
small organic molecules are joined together to form larger molecules.
Macromolecules: large molecules of thousands of covalently connected atoms.
Molecular structure and function are inseparable.
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3. Why do scientists study the structures of macromolecules?
Figure 5.1

4. Macromolecules are polymers, built from monomers
Polymer: long chain-like molecule consisting of many similar building blocks, monomers.
Three of the four classes of life’s organic molecules are polymers:
Carbohydrates
Proteins
Nucleic acids
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5. The Synthesis and Breakdown of Polymers
condensation reaction (dehydration reaction): two monomers bond together through the loss of a water :
dehydration synthesis = build by removing HOH.
Enzymes: organic catalysts, speed up rxn
Polymers are disassembled to monomers by hydrolysis: breaking down by adding HOH.
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6. The synthesis and breakdown of polymers HO 1 2 3 H HO H Short polymer
Unlinked monomer
Dehydration removes a water
molecule, forming a new bond
H2O HO 1 2 3 4 H
Longer polymer
(a) Dehydration reaction in the synthesis of a polymer HO 1 2 3 4 H
Figure 5.2
Hydrolysis adds a water
molecule, breaking a bond
H2O HO 1 2 3 H HO H
(b) Hydrolysis of a polymer

7. Carbohydrates : fuel and building material
Carbohydrates: sugars
Monosaccharides: single sugars
CH2O
Glucose (C6H12O6): most common
Disaccharide: two monosaccharides by removing HOH to form a covalent bond.
glycosidic linkage.
dehydration synthesis
C6H12O6 + C6H12O6 = C12H22O11
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8. Linear and ring forms of glucose
Abbreviated
ring structure
Figure 5.4 Linear and ring forms of glucose

9. Examples of disaccharide synthesis
1–4
glycosidic
linkage
Glucose
Glucose
Maltose
(a) Dehydration reaction in the synthesis of maltose
1–2
glycosidic
linkage
Figure 5.5
Glucose
Fructose
Sucrose
(b) Dehydration reaction in the synthesis of sucrose

10. Polysaccharides Starch: plant storage; chloroplast
Polysaccharides: many sugars
storage and structural roles.
determined by their sugar monomers and the positions of the glycosidic linkages.
Starch: plant storage; chloroplast
Glycogen: animal storage; liver & muscles.
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11. Storage polysaccharides of plants and animals
Chloroplast
Starch
Mitochondria
Glycogen granules
0.5 µm
1 µm
Figure 5.6
Amylose
Glycogen
Amylopectin
(a) Starch: a plant polysaccharide
(b) Glycogen: an animal polysaccharide

12. Structural Polysaccharides
Cellulose: plant cell walls.
polymer of glucose, but the glycosidic linkages differ.
Polymers with  glucose are helical.
Polymers with  glucose are straight.
H atoms on one strand can bond with OH groups on other strands.
grouped into microfibrils, which form strong building materials for plants.
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13. cellulose in plant cell walls
The
arrangement of
cellulose in plant cell walls
Cell walls
Cellulose
microfibrils
in a plant
cell wall
Microfibril
10 µm
0.5 µm
Cellulose
molecules
Figure 5.8
Glucose
monomer

14. Some microbes use enzymes to digest cellulose.
Enzymes that digest starch by hydrolyzing  linkages can’t hydrolyze  linkages in cellulose.
Cellulose in human food passes through the digestive tract as insoluble fiber.
Some microbes use enzymes to digest cellulose.
Many herbivores, from cows to termites, have symbiotic relationships with these microbes.
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15. Chitin also provides structural support for the cell walls of fungi.
Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods.
Chitin also provides structural support for the cell walls of fungi.
polysaccharide with nitrogen ( N ) in each sugar monomer.
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16. Chitin = a structural polysaccharide
The structure
of the chitin
monomer.
(b)
Chitin forms the
exoskeleton of
arthropods.
(c)
Chitin is used to make
a strong and flexible
surgical thread.
Figure 5.10

17. Lipids do not form polymers.
Hydrophobic: little or no affinity for water.
nonpolar covalent bonds.
fats, phospholipids, and steroids
fats  energy storage
Adipose: fat cells, cushions vital organs, insulates the body
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18. Fats Glycerol: 3-C alcohol with a hydroxyl group
fatty acid : carboxyl group attached to a long hydrocarbon chain.
Saturated fatty acids: maximum number of hydrogen & no double bonds; single C bonds
Unsaturated fatty acids have one or more double bonds C = C
Triacylglycerol (triglyceride): 3 fatty acids joined to glycerol
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19. The Synthesis and Structure of a fat = triacylglycerol Fatty acid
(palmitic acid)
Glycerol
(a) Dehydration reaction in the synthesis of a fat
Ester linkage
Figure 5.11
(b) Fat molecule (Triglyceride)

20. Examples of Saturated and Unsaturated Fats and Fatty acids bending
Structural
formula of a
saturated fat
molecule
Stearic acid, a
saturated fatty
acid
(a) Saturated fat
Figure fats and fatty acids
Structural formula
of an unsaturated
fat molecule.
The chain bends
Oleic acid, an
unsaturated
fatty acid
cis double
bond causes
bending
(b) Unsaturated fat

21. unsaturated fatty acids
solid at room temperature.
animal fats.
unsaturated fatty acids
Oils
liquid at room temperature.
Plant and fish fats
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22. Phospholipids -- Cell Membranes
two fatty acids and a phosphate group are attached to glycerol.
Hydrophobic: fatty acid tails
Hydrophillic head: phosphate group
amphipathic: both hydrophillic and hydrophobic
added to water, self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior.
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23. The structure of a phospholipid amphipathic
Choline
Hydrophilic head
Phosphate
Glycerol
Fatty acids
Hydrophobic tails
Hydrophilic
head
Figure 5.13
Hydrophobic
tails
(a)
Structural formula
(b)
Space-filling model
(c)
Phospholipid symbol

24. Bilayer structure formed by self-assembly of phospholipids into a membrane in an aqueous environment
Hydrophilic
head
WATER
Figure 5.14
Hydrophobic
tail
WATER

25. Steroids = Lipids with 4 fused rings …
Cholesterol: in animal cell membranes.
high blood levels  cardiovascular disease.
For the Cell Biology Video Space Filling Model of Cholesterol, go to Animation and Video Files.
For the Cell Biology Video Stick Model of Cholesterol, go to Animation and Video Files.
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

26. Proteins more than 50% of the dry mass of most cells.
structural support, storage, transport, cellular communications, movement, defense against foreign substances, and organic catalysts (enzymes).
Enzymes: LARGE proteins; catalysts
Specific, shape-match to molecules
Used repeatedly
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27. The catalytic cycle of an enzyme
Substrate is the reactant
(sucrose)
Products
Glucose
Enzyme
(sucrase) OH
H2O
Figure 5.16 The catalytic cycle of an enzyme
Fructose H O

28. Proteins 20 amino acids (monomers)  Polypeptides (polymers)
AA linked by covalent peptide bond, C-N
sequence of amino acids determines a protein’s 3D three-dimensional structure & fxn
Amino acids: organic molecules with carboxyl and amino groups attached to a central carbon.
variable side chains, called R group
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29. The 20 amino acids of proteins Nonpolar Polar Electrically charged
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)
Trypotphan
(Trp or W)
Proline
(Pro or P)
Polar
Serine
(Ser or S)
Threonine
(Thr or T)
Cysteine
(Cys or C)
Tyrosine
(Tyr or Y)
Asparagine
(Asn or N)
Glutamine
(Gln or Q)
Figure 5.17
Electrically
charged
Acidic
Basic
Aspartic acid
(Asp or D)
Glutamic acid
(Glu or E)
Lysine
(Lys or K)
Arginine
(Arg or R)
Histidine
(His or H)

30. Making a polypeptide chain Side chains Backbone Peptide bond Peptide
Figure 5.18
Backbone
Amino end
(N-terminus)
Carboxyl end
(C-terminus)
(b)

31. A ribbon model of lysozyme A space-filling model of lysozyme
A protein folds into a specific Shape / Structure so it can perform its Function
Groove
Groove
Figure 5.19 Structure of a protein, the enzyme lysozyme
(a)
A ribbon model of lysozyme
(b)
A space-filling model of lysozyme

32. An antibody binding to a protein from a flu virus
Antibody protein
Protein from flu virus
Figure 5.20

33. Four Levels of Protein Structure -- becoming Functional Proteins:
Primary: amino acids sequence
Secondary: coils (alpha helix) and folds (beta sheets) with hydrogen bonds.
Tertiary: interactions among R groups.
H bonds, ionic bonds, hydrophobic interactions, van der Waals interactions, and disulfide bridges
Quaternary: multiple polypeptide chains.
Collagen: fibrous protein, 3 polypeptides coiled like a rope.
Hemoglobin: globular protein, 4 four polypeptides: two alpha and two beta chains each with an iron heme group.
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34. 4 Levels of protein structure
Primary
Structure
Secondary
Structure
Tertiary
Structure
Quaternary
Structure
 pleated sheet
+H3N
Amino end
Examples of
amino acid
subunits
 helix
Figure 5.21

35. Tertiary Structure Hydrophobic interactions and van der Waals
Polypeptide
backbone
Hydrogen
bond
Disulfide bridge
Figure 5.21 Levels of protein structure—tertiary and quaternary structures
Ionic bond
Tertiary Structure

36. Hemoglobin Quaternary structures Collagen Polypeptide  Chains chain
Iron
Figure 5.21 Levels of protein structure—tertiary and
Heme
 Chains
Hemoglobin
Collagen

37. A single amino acid substitution in a protein causes sickle-cell disease
Normal hemoglobin
Sickle-cell hemoglobin
Primary
structure
Primary
structure
Val
His
Leu
Thr
Pro
Glu
Glu
Val
His
Leu
Thr
Pro
Val
Glu 1 2 3 4 5 6 7 1 2 3 4 5 6 7
Exposed
hydrophobic
region
Secondary
and tertiary
structures
Secondary
and tertiary
structures
 subunit
 subunit    
Quaternary
structure
Normal
hemoglobin
(top view)
Quaternary
structure
Sickle-cell
hemoglobin    
Function
Molecules do
not associate
with one
another; each
carries oxygen.
Function
Molecules
interact with
one another and
crystallize into
a fiber; capacity
to carry oxygen
is greatly reduced.
Figure 5.22
10 µm
10 µm
Red blood
cell shape
Normal red blood
cells are full of
individual
hemoglobin
moledules, each
carrying oxygen.
Red blood
cell shape
Fibers of abnormal
hemoglobin deform
red blood cell into
sickle shape.

38. Environmental Factors Affect Protein Structure
Denaturation: shape change in protein is biologically inactive
pH, salt concentration, temperature
protein unravels and looses its shape.
Chaperonins: protein molecules that assist the proper folding of other proteins.
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39. Denaturation and renaturation of a protein
Figure 5.23
Normal protein
Denatured protein
Renaturation

40. Nucleic acids store and transmit hereditary information
Genes: sequences of DNA nucleotides.
Determines the amino acid sequence of polypeptides
Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)
DNA: directions for its own replication and the synthesis of messenger RNA (mRNA)  protein synthesis in ribosomes.
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41. Central Dogma: DNA → RNA → protein1
Synthesis of
mRNA in the
nucleus
mRNA
NUCLEUS
CYTOPLASM
mRNA 2
Movement of
mRNA into cytoplasm
via nuclear pore
Ribosome
Figure 5.26 3
Synthesis
of protein
Amino
acids
Polypeptide

42. The Structure of Nucleic Acids
Polynmer: Nucleic acids
monomers : nucleotides.
nitrogenous base
pentose sugar
phosphate group.
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43. (a) Polynucleotide, or nucleic acid (c) Nucleoside components: sugars
Components of nucleic acids
5 end
Nitrogenous bases
Pyrimidines
5C
3C
Nitrogenous
base
Cytosine (C)
Thymine (T, in DNA)
Uracil (U, in RNA)
Purines
Phosphate
group
Sugar
(pentose)
5C
Adenine (A)
Guanine (G)
3C
(b) Nucleotide
Sugars
3 end
Figure 5.27
(a) Polynucleotide, or nucleic acid
Deoxyribose (in DNA)
Ribose (in RNA)
(c) Nucleoside components: sugars

44. Nucleotide Monomers
Pyrimidines: C T (U) (cytosine, thymine, and uracil) have a single six-membered ring
Purines: A G (adenine and guanine) have a 6-membered ring fused to a 5-membered ring
Nucleotide = nucleoside + phosphate group. Nucleoside = nitrogenous base + sugar
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45. Nucleotide Polymers
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.
dehydration synthesis
phosphodiester bonds
backbone of sugar-phosphate units.
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46. The DNA Double Helix
Double helix: two polynucleotides spiraling around
antiparallel : two backbones run in opposite 5 → 3 directions
One DNA molecule includes many genes
The nitrogenous bases in DNA pair-up forming hydrogen bonds: A - T and C - G
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47. The DNA double helix and its Replication Semi-Conservative Replication
5' end
3' end
Sugar-phosphate
backbones
Base pair (joined by
hydrogen bonding)
Old strands
Nucleotide
about to be
added to a
new strand
3' end
Figure
5' end
New
strands
5' end
3' end
5' end
3' end

48. Nucleic Acid :
Chain of
Nucleotides

49. You should be able to draw and explain a review chart of organic molecules:

50. You should now be able to:
List and describe the four major classes of organic molecules.
Explain: monomers, polymers, dehydration synthesis with the type of covalent bond for each.
Distinguish between monosaccharides, disaccharides, and polysaccharides. Give examples of each.
Explain lipids in general. Distinguish between saturated and unsaturated fats. Describe phospholipids, amphipathic molecules.
Describe steroids
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51. You should now be able to:
6. Explain proteins, amino acids.
7. Explain the four levels of protein structure.
8. Explain DNA and RNA.
9. Distinguish between the following: pyrimidine and purine / nucleotide and nucleoside / ribose and deoxyribose / the 5 end and 3 end of a nucleotide
10. Apply the Base-Pair Rule: A-T(U) C-G
11. Explain: anti-parallel, double helix.
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