1. The Structure and Function of Macromolecules
Chapter 3
The Structure and Function of Macromolecules

2. The Molecules of Life Overview:
Another level in the hierarchy of biological organization is reached when small organic molecules are joined together
Atom ---> molecule --- compound

3. Macromolecules Are large molecules composed of smaller molecules
Are complex in their structures

4. Macromolecules Most macromolecules are polymers, built from monomers
Four classes of life’s organic molecules are polymers
Carbohydrates
Proteins
Nucleic acids
Lipids

5. A polymer
Is a long molecule consisting of many similar building blocks called monomers
Specific monomers make up a macromolecule
E.g. amino acids are the monomers for proteins

6. The Synthesis and Breakdown of Polymers
Monomers form larger molecules by condensation reactions called dehydration synthesis
Dehydration reaction in the synthesis of a polymer HO H 1 2 3 4
H2O
Short polymer
Unlinked monomer
Longer polymer
Dehydration removes a water molecule, forming a new bond

7. The Synthesis and Breakdown of Polymers
Polymers can disassemble by
Hydrolysis (addition of water molecules)
Hydrolysis of a polymer HO 1 2 3 H 4
H2O
Hydrolysis adds a water molecule, breaking a bond

8. 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
Enzymes facilitate their synthesis

9. Carbohydrates Serve as fuel (4 calories/g) and building material
Include both sugars and their polymers (starch, cellulose, etc.)

10. Sugars Monosaccharides Are the simplest sugars Can be used for fuel
Can be converted into other organic molecules
Can be combined into polymer of CH2O
Have a carbonyl group (aldoses and ketoses) and all other C’s have a hydroxyl group

11. Examples of monosaccharides
Triose sugars (C3H6O3)
Pentose sugars (C5H10O5)
Hexose sugars (C6H12O6)
H C OH
H C OH
HO C H
H C OH
C O
HO C H H C O
Aldoses
Glyceraldehyde
Ribose
Glucose
Galactose
Dihydroxyacetone
Ribulose
Ketoses
Fructose

12. Though often drawn as linear skeletons, in aqueous solutions,
Monosaccharides
May be linear
Can form rings
The numbering starts to the
right of the oxygen! H
H C OH
HO C H
H C O C 1 2 3 4 5 6 OH 4C
6CH2OH 5C
H OH
2 C 1C
3 C 2C
1 C
CH2OH HO
Though often drawn as linear skeletons, in aqueous solutions,
most sugars form rings

13. Disaccharides
Consist of two monosaccharides
Are joined by a glycosidic linkage (covalent bond formed between two monosaccharides by dehydration synthesis)

14. Dehydration reaction in the synthesis of maltose
Dehydration reaction in the synthesis of maltose. The bonding of 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. Joining the glucose monomers in a different way would result in a different disaccharide.
Dehydration reaction in the synthesis of sucrose. Sucrose is a disaccharide formed from glucose and fructose. Notice that fructose, though a hexose like glucose, forms a five-sided ring.
(a)
(b) H HO
H OH OH O
CH2OH
H2O 1 2 4
1– 4 glycosidic linkage
1–2 glycosidic linkage
Glucose
Fructose
Maltose
Sucrose

15. Polysaccharides Polysaccharides
Are polymers of sugars (few hundred to 1000’s monosaccharides!)
Serve many roles in organisms
The structure and function of polysaccharides are determined by its sugar monomers and by the positions of its glycosidic linkages

16. Storage Polysaccharides
Chloroplast
Starch
Amylose
Amylopectin
1 μm
Starch: a plant polysaccharide
Starch
Is a polymer consisting entirely of glucose monomers
Is the major storage form of glucose in plants

17. Storage Polysaccharides
It is a heteropolysaccharide:
Amylose with 1,4 linkages is unbranched and helical (20-30%)
Amylopectin has 1,4 and 1,6 linkages with branching (70-80%)

18. Storage Polysaccharides
Glycogen
Consists of glucose monomers
Made of only one molecule
Is the major storage form of glucose in animals
Like amylopectin, but more extensively branched

19. Structural Polysaccharides
Cellulose
Is a polymer of glucose
Is the most abundant organic compound!
Formed from  glucose, which has a slightly different ring structure than  glucose; when monomers join, every other monomer is upside down with respect to its neighbors (picture coming on next slide!)

20. Has different glycosidic linkages than starch
(c) Cellulose: 1– 4 linkage of β glucose monomers H O
CH2OH OH HO 4 C 1
(a) α and β glucose ring structures
(b) Starch: 1– 4 linkage of α glucose monomers
α glucose
β glucose
Polymers with  glucose are helical
Polymers with  glucose are straight

21. 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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22. Is a major component of the tough walls that enclose plant cells
Cell walls
Cellulose microfibrils
in a plant cell wall ∩
Microfibril
CH2OH OH O
Glucose monomer
Parallel cellulose molecules are
held together by hydrogen
bonds between hydroxyl
groups attached to carbon
atoms 3 and 6.
About 80 cellulose
molecules associate
to form a microfibril, the
main architectural unit
of the plant cell wall.
A cellulose molecule
is an unbranched
glucose polymer.
Cellulose
molecules

23. Cellulose is difficult to digest
Most organisms lack enzymes to hydrolize the  linkages
Cows have microbes in their stomachs to facilitate this process

24. Chitin, another important structural polysaccharide
Is found in the exoskeleton of arthropods and cell walls of fungi
Can be used as surgical thread
(a) The structure of the
chitin monomer. O
CH2OH OH H NH C
CH3
(b) Chitin forms the exoskeleton
of arthropods. This cicada
is molting, shedding its old
exoskeleton and emerging
in adult form.
(c) Chitin is used to make a
strong and flexible surgical
thread that decomposes after
the wound or incision heals.

25. Lipids Lipids are a diverse group of hydrophobic molecules Lipids
Are the one class of large biological molecules that do not consist of polymers
Share the common trait of being hydrophobic; composed mostly of hydrocarbons, which are nonpolar

26. Fats
Fats are constructed from two types of smaller molecules: glycerol and fatty acids
Function: Energy storage (9 calories/g)
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
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

27. Fatty acid (palmitic acid)
Fig. 5-11
Fatty acid
(palmitic acid)
Glycerol
(a) Dehydration reaction in the synthesis of a fat
Ester linkage (bond between a hydroxyl and carboxyl group)
Figure 5.11 The synthesis and structure of a fat, or triacylglycerol
(b) Fat molecule (triacylglycerol)

28. Unsaturated fatty acids have one or more double bonds
The fatty acids can be the same or there can be two or three different kinds
Fatty acids vary in length (number of carbons) and in the number and locations of double bonds
Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds
Unsaturated fatty acids have one or more double bonds
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

29. Saturated fat and fatty acid
Saturated fatty acids
Have the maximum number of hydrogen atoms possible
Have no double bonds; their flexibility allows them to pack tightly
Solid at room temperature
Saturated fat and fatty acid
Stearic acid

30. Unsaturated fat and fatty acid
Unsaturated fatty acids
Have one or more double bonds
Liquid at room temperature
Unsaturated fat and fatty acid
Oleic acid

31. Trans Fats Uncommon in nature
Formed by hydrogenating unsaturated fats (make peanut butter, margarine, cool whip, etc)
Contribute to atherosclerosis

32. Phospholipids Have only two fatty acids
Have a phosphate group instead of a third fatty acid

33. Phospholipid structure
Consists of a hydrophilic “head” (phosphate group is charged)and hydrophobic “tails”
CH2 O P CH C
Phosphate
Glycerol
(a) Structural formula
(b) Space-filling model
Fatty acids
(c) Phospholipid
symbol
Hydrophobic tails
Hydrophilic
head
Hydrophobic
tails –
Hydrophilic head
Choline +
N(CH3)3

34. The structure of phospholipids
Results in a bilayer arrangement found in cell membranes
Hydrophilic
head
WATER
Hydrophobic
tail

35. Steroids
Steroids
Are lipids characterized by a carbon skeleton consisting of four fused rings

36. One steroid, cholesterol
Is found in cell membranes
Is a precursor for some hormones; some steroids are hormones
High levels in blood can contribute to atherosclerosis HO
CH3
H3C

37. Proteins
Proteins have many structures, resulting in a wide range of functions
Account for more than ½ of the dry mass of most cells
Proteins do most of the work in cells and act as enzymes
Proteins are made of monomers called amino acids

39. Enzymes
Are a type of protein that acts as a catalyst, speeding up chemical reactions
Substrate
(sucrose)
Enzyme
(sucrase)
Glucose OH
H O
H2O
Fructose
3 Substrate is converted
to products.
1 Active site is available for
a molecule of substrate, the
reactant on which the enzyme acts.
Substrate binds to
enzyme. 2
4 Products are released.

40. Polypeptides Polypeptides A protein
Are polymers (chains) of amino acids
A protein
Consists of one or more polypeptides

41. Amino acids
Are organic molecules possessing both carboxyl and amino groups
Differ in their properties due to differing side chains, called R groups

42. Twenty Amino Acids 20 different amino acids make up proteins O O– H
H3N+ C
CH3 CH
CH2 NH
H2C
H2N
Nonpolar
Glycine (Gly)
Alanine (Ala)
Valine (Val)
Leucine (Leu)
Isoleucine (Ile)
Methionine (Met)
Phenylalanine (Phe)
Tryptophan (Trp)
Proline (Pro)
H3C S
20 different amino acids make up proteins

43. Polar Electrically charged Serine (Ser) Threonine (Thr) Cysteine (Cys)OH
CH2 C H
H3N+ O
CH3 CH SH
NH2
Polar
Electrically
charged –O
NH3+
NH2+
NH+ NH
Serine (Ser)
Threonine (Thr)
Cysteine
(Cys)
Tyrosine
(Tyr)
Asparagine
(Asn)
Glutamine
(Gln)
Acidic
Basic
Aspartic acid
(Asp)
Glutamic acid
(Glu)
Lysine (Lys)
Arginine (Arg)
Histidine (His)

44. Amino Acid Polymers
Amino acids
Are linked by peptide bonds

45. Protein Conformation and Function
A protein’s specific conformation (shape) determines how it functions

46. Four Levels of Protein Structure
Primary structure
Is the unique sequence of amino acids in a polypeptide –
Amino acid subunits
+H3N Amino end o
Carboxyl end c
Gly
Pro
Thr
Glu
Seu
Lys
Cys
Leu
Met
Val
Asp
Ala
Arg
Ser
lle
Phe
His
Asn
Tyr
Trp
Lle

47. Secondary structure
Is the folding or coiling resulting from hydrogen bonds between repeating constituents of the polypeptide backbone (not the R groups)
Includes the  helix and the  pleated sheet O C
α helix
Amino acid subunits N H R H

48. Is the overall three-dimensional shape of a polypeptide
Tertiary structure
Is the overall three-dimensional shape of a polypeptide
Results from interactions between R groups
CH2 CH
O H O C HO
NH3+ -O S
CH3
H3C
Hydrophobic interactions and van der Waals interactions
Polypeptide backbone
Hyrdogen bond
Ionic bond
Disulfide bridge

49. Quaternary structure
Is the overall protein structure that results from the aggregation of two or more polypeptide subunits
Polypeptide chain
Collagen
β Chains
α Chains
Hemoglobin
Iron
Heme

50. Review of Protein Structure
+H3N
Amino end
Amino acid
subunits
α helix

51. Sickle-Cell Disease: A Simple Change in Primary Structure
Results from a single amino acid substitution in the protein hemoglobin

52. . . . Primary structure Secondary and tertiary structures
Quaternary structure
Function
Red blood cell shape
Hemoglobin A
Molecules do not associate with one another, each carries oxygen.
Normal cells are full of individual hemoglobin molecules, each carrying oxygen α β
10 μm
Hemoglobin S
Molecules interact with one another to crystallize into a fiber, capacity to carry oxygen is greatly reduced.
β subunit 1 2 3 4 5 6 7
Normal hemoglobin
Sickle-cell hemoglobin
. . .
Exposed hydrophobic region
Val
Thr
His
Leu
Pro
Glul
Glu
Fibers of abnormal hemoglobin deform cell into sickle shape.

53. What Determines Protein Conformation?
Protein conformation depends on the physical and chemical conditions of the protein’s environment
Temperature, pH, etc. affect protein structure

54. Denaturation is when a protein unravels and loses its native conformation (shape)
Renaturation
Denatured protein
Normal protein

55. The Protein-Folding Problem
Most proteins
Probably go through several intermediate states on their way to a stable conformation
Denaturated proteins no longer work in their unfolded condition
Proteins may be denaturated by extreme changes in pH or temperature

56. Chaperonins
Are protein molecules that assist in the proper folding of other proteins
Keeps the protein separated from other molecules in the cytoplasm while folding
Hollow cylinder
Cap
Chaperonin (fully assembled)
Steps of Chaperonin Action: An unfolded poly- peptide enters the cylinder from one end.
The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide.
The cap comes off, and the properly folded protein is released.
Correctly folded protein
Polypeptide 2 1 3

57. Misfolding of Proteins
Is a serious problem
Alzheimer’s and Parkinson’s diseases are associated with accumulation of misfolded proteins

58. Nucleic Acids Nucleic acids store and transmit hereditary information
Genes
Are the units of inheritance
Program the amino acid sequence of polypeptides
Are made of nucleotide sequences on DNA

59. Nucleic Acids Made of nucleotide monomers
There are two types of nucleic acids
Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)

60. Deoxyribonucleic Acid
DNA
Stores information for the synthesis of specific proteins
Found in the nucleus of cells
Comprised of two strands
Sugar is deoxyribose
Bases are A,T,C,G

61. Ribonucleic Acid
RNA
Helps convert the information contained in DNA into functional gene products, like proteins
Is single stranded and does not stay in the nucleus
Has ribose sugar and U replaces T
3 types: mRNA, rRNA, tRNA

62. Synthesis of mRNA in the nucleus
DNA Functions
Directs RNA synthesis (transcription)
Directs protein synthesis through RNA (translation) 1 2 3
Synthesis of mRNA in the nucleus
Movement of
mRNA into cytoplasm
via nuclear pore
Synthesis
of protein
NUCLEUS
CYTOPLASM
DNA
mRNA
Ribosome
Amino acids
Polypeptide

63. The Structure of Nucleic Acids
5’ end
5’C
3’ end OH O
Nucleic acids
Exist as polymers called polynucleotides
Polynucleotide,
or nucleic acid

64. Each polynucleotide Consists of monomers called nucleotides
Sugar + phosphate + nitrogen base
Nitrogenous
base
Nucleoside O O− −O P
CH2
5’C
3’C
Phosphate
group
Pentose
sugar
(b) Nucleotide

65. Nucleotide Monomers Nucleotide monomers
Are made up of nucleosides (sugar + base) and phosphate groups CH
Uracil (in RNA) U
Ribose (in RNA)
Nitrogenous bases Pyrimidines C N O H
NH2 HN
CH3
Cytosine
Thymine (in DNA) T HC NH
Adenine A
Guanine G
Purines
HOCH2 OH
Pentose sugars
Deoxyribose (in DNA) 4’ 5” 3’ 2’ 1’
(c) Nucleoside components

66. A,T,C,G The nitrogenous bases in DNA
Form hydrogen bonds in a complementary fashion (A with T only, and C with G only)

67. Nitrogen bases A and G are purines C,T and U are pyrimidines
Have two rings
C,T and U are pyrimidines
Have one ring

68. Nucleotide Monomers
A-T forms double bond
C-G forms triple bond

69. Nucleotide Polymers 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

70. DNA Strands are antiparallel
LE 10-5b
DNA Strands are antiparallel
5’ end terminates in P group
3’ end terminates in sugar
5 end
3 end P HO 5¢ 4¢ 2¢ 3¢ A T 3¢ 1¢ 1¢ 2¢ 4¢ 5¢ P P P C G P P G C P P T A OH P
3 end
5 end

71. The DNA double helix Consists of two antiparallel nucleotide strands
3’ end
Sugar-phosphate backbone
Base pair (joined by hydrogen bonding)
Old strands
Nucleotide about to be added to a new strand A
5’ end
New strands

72. Chargaff’s Rule
In DNA, there is always equality in quantity between the bases A and T and between the bases C and G
If a sample of DNA is found to contain 20% T, what is the approximate % of the other three nucleotides in the sample?

73. DNA and Proteins as Tape Measures of Evolution
Molecular comparisons
Help biologists sort out the evolutionary connections among species

74. Which species are most closely related?

75. 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