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CHAPTER 5:
THE STRUCTURE & FUNCTION OF
LARGE BIOLOGICAL MOLECULES
Overview: The Molecules of Life
• All living things are made up of four classes of
large biological molecules: carbohydrates,
lipids, proteins, and nucleic acids
• Within cells, small organic molecules are joined
together to form larger molecules
• Macromolecules are large molecules
composed of thousands of covalently
connected atoms
• Molecular structure and function are
inseparable
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Monomers
•Small organic
•Used for building
blocks of polymers
•Connects with
condensation reaction
(dehydration synthesis)
Polymers
Macromolecules
•Long molecules of
•Giant molecules
monomers
•2 or more polymers
•With many identical or bonded together
similar blocks linked by
covalent bonds
ie. amino acid  peptide  polypeptide  protein
smaller
larger
Lipids do not have monomers and polymers
Dehydration Synthesis
(Condensation Reaction)
Hydrolysis
Make polymers
Breakdown polymers
Monomers  Polymers
Polymers  Monomers
A + B  AB
AB  A + B
+
+ H2O
+ H2O
+
• Enzymes are macromolecules that speed up
these processes
Fig. 5-2
HO
1
2
3
H
Short polymer
HO
Unlinked monomer
Dehydration removes a water
molecule, forming a new bond
HO
2
1
H
3
H2O
4
H
Longer polymer
(a) Dehydration reaction in the synthesis of a polymer
HO
1
2
3
4
Hydrolysis adds a water
molecule, breaking a bond
HO
1
2
3
(b) Hydrolysis of a polymer
H
H
H2O
HO
H
I. Carbohydrates
• Fuel (short-term energy) and building material
(structure)
• Include simple sugars (fructose) and polymers (starch)
• Ratio of 1 carbon: 2 hydrogen: 1 oxygen or CH2O
• monosaccharide  disaccharide  polysaccharide
• Monosaccharides = monomers (eg. glucose, ribose)
• Polysaccharides:
 Storage (plants-starch, animals-glycogen)
 Structure (plant-cellulose, arthropod-chitin)
Differ in
position &
orientation of
glycosidic
linkage
• The structure and
classification of some
monosaccharides
• Monosaccharides are
classified by
•
The location of the
carbonyl group (C=O)
• Aldose (end) or Ketose
(middle)
•
The number of carbons
in the carbon skeleton
Linear and ring forms of glucose
Monosaccharide + monosaccharide = disaccharide
Covalent bond = glycosidic linkage
Carbohydrate synthesis
Cellulose vs. Starch (storage polysaccharides)
Two Forms of Glucose:  glucose &  glucose
Cellulose vs. Starch (storage polysaccharides
• Starch =  glucose monomers
• Cellulose =  glucose monomers
• Storage polysaccharides of plants (starch) and animals (glycogen)
Starch is stored in chloroplasts; Glycogen stored in liver and
muscle cells
•
Structural polysaccharides: cellulose (cell wall of plants)
& chitin (exoskeleton of arthropods and cell walls of
fungi)
• 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
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Sample FRQ- Short Response
Acidic Mammalian Chitinase (AMCase) activity
(nmol/ml/hour) of subject at different pH values
(Paoletti et al.2007)
•Predict and explain where in the human body AMCase is most
likely to be found.
•Identify what types of food an individual that lacks properly
functioning AMCase would have difficulty digesting.
•Pose an evolutionary explanation for the AMCase secretions in
humans.
Lipids are a diverse group of hydrophobic
molecules
• Lipids are the one class of large biological
molecules that do not form polymers
• The unifying feature of lipids is having little or
no affinity for water
• Lipids are hydrophobic because they consist
mostly of hydrocarbons, which form nonpolar
covalent bonds
• The most biologically important lipids are fats,
phospholipids, and steroids
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
II. Lipids
A.Fats (triglyceride): store energy
– Glycerol + 3 Fatty Acids (joined by ester linkage)
– saturated, unsaturated, polyunsaturated
B.Steroids: cholesterol and hormones
C.Phospholipids: lipid bilayer of cell membrane
– hydrophilic head, hydrophobic tails
Hydrophilic head
Hydrophobic tail
Saturated
Unsaturated
Polyunsaturated
“saturated” with H
Have some C=C, result in kinks
In animals
In plants
Solid at room temp.
Liquid at room temp.
Eg. butter, lard
Eg. corn oil, olive oil
• A diet rich in saturated fats may contribute to
cardiovascular disease through plaque deposits
• Hydrogenation is the process of converting
unsaturated fats to saturated fats by adding
hydrogen
• Hydrogenating vegetable oils also creates
unsaturated fats with trans double bonds
• These trans fats may contribute more than
saturated fats to cardiovascular disease
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• The major function of fats is energy storage
• Humans and other mammals store their fat in
adipose cells
• Adipose tissue also cushions vital organs and
insulates the body
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
• Steroids are lipids characterized by a carbon
skeleton consisting of four fused rings
• Cholesterol, an important steroid, is a component
in animal cell membranes
Cholesterol, a steroid
The structure of a phospholipid
Hydrophobic/hydrophilic interactions make a
phospholipid bilayer
III. Proteins
• “Proteios” = first or primary
• 50% dry weight of cells
• Contains: C, H, O, N, S
Myoglobin protein
Protein Functions (+ examples)
• Enzymes (lactase)
• Defense (antibodies)
• Storage (milk protein = casein)
• Transport (hemoglobin)
• Hormones (insulin)
• Receptors
• Movement (motor proteins)
• Structure (keratin)
Overview of protein functions
Overview of protein functions
• 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
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 5-16
Substrate
(sucrose)
Glucose
OH
Fructose
HO
Enzyme
(sucrase)
H2O
Four Levels of Protein Structure
• Primary
– Amino acid (AA) sequence
– 20 different AA’s
– peptide bonds link AA’s
Amino Acid
• R group = side chains
• Properties:
• hydrophobic
• hydrophilic
• ionic (acids &
bases)
• “amino” : -NH2
• “acid” : -COOH
• Amino acids are linked
by peptide bonds
• A polypeptide is a
polymer of amino acids
• Polypeptides range in
length from a few to
more than a thousand
monomers
• Each polypeptide has a
unique linear sequence
of amino acids
Four Levels of Protein Structure (continued)
2.Secondary
– Gains 3-D shape (folds, coils) by H-bonding
– Alpha (α) helix, Beta (β) pleated sheet
Four Levels of Protein Structure (continued)
3.Tertiary
– Bonding between side chains (R groups) of amino
acids
– H bonds, ionic bonds, disulfide bridges, van der
Waals interactions
Four Levels of Protein Structure (continued)
4.Quaternary
– 2+ polypeptides bond together
– R groups of polypeptide chains held together with H bonds,
ionic bonds, disulfide bridges, van der Waals interactions
amino acids  polypeptides  protein
Chaperonins assist in proper folding of
proteins
• Protein structure and function are sensitive
to chemical and physical conditions
• Unfolds or denatures if pH and temperature
are not optimal
change in structure = change in function
IV. Nucleic Acids
Function: store hereditary info
DNA
RNA
• Double-stranded helix
• N-bases: A, G, C,
Thymine
• Stores hereditary info
• Longer/larger
• Sugar: deoxyribose
• Single-stranded
• N-bases: A, G, C,
Uracil
• Carry info from DNA to
ribosomes
• tRNA, rRNA, mRNA,
RNAi
• Sugar: ribose
Fig. 5-26-3
DNA
Information
flow in a
cell:
DNA 
RNA 
protein
1 Synthesis of
mRNA in the
nucleus
mRNA
NUCLEUS
CYTOPLASM
mRNA
2 Movement of
mRNA into cytoplasm
via nuclear pore
Ribosome
3 Synthesis
of protein
Polypeptide
Amino
acids
Nucleotides: monomer of DNA/RNA
Nucleotide = Sugar + Phosphate + Nitrogen Base
Polynucleotide or nucleic acid = Polymer
Nucleotide
phosphate
Nitrogen
base
5-C sugar
Purines
A–T
G–C
Pyrimidines
•Adenine
•Guanine
•Cytosine
•Thymine (DNA)
•Uracil (RNA)
•Double ring
•Single ring
Nucleotide Polymers
• Nucleotide polymers are linked together to build
a polynucleotide
• Adjacent nucleotides are joined by covalent
phosphodiester bonds that form between the
–OH group on the 3 carbon of one nucleotide
and the phosphate on the 5 carbon on the next
– These links create a backbone of sugarphosphate units with nitrogenous bases as
appendages
• The sequence of bases along a DNA or mRNA
polymer is unique for each gene
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
The DNA Double Helix
• A DNA molecule has two polynucleotides spiraling
around an imaginary axis, forming a double helix
• In the DNA double helix, the two backbones run in
opposite 5 → 3 directions from each other, an
arrangement referred to as antiparallel
• One DNA molecule includes many genes
• The nitrogenous bases in DNA pair up and form
hydrogen bonds: adenine (A) always with thymine
(T), and guanine (G) always with cytosine (C)
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 5-28
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
5' end
New
strands
5' end
3' end
5' end
3' end
Fig. 5-UN9
You should now be able to:
1. List, describe, explain the formation of, and give
examples of the four major classes of molecules
2. Distinguish between mono, di, and polysaccharides
3. Distinguish between saturated and unsaturated fats
and between cis and trans fat molecules
4. Describe the four levels of protein structure and
explain how the function of a protein can be affected
by a small change
5. Distinguish between the following pairs: pyrimidine
and purine, nucleotide and nucleoside, ribose and
deoxyribose, the 5 end and 3 end of a nucleotide
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings