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Chapter 5
The Structure and Function of
Macromolecules
PowerPoint Lectures for
Biology, Seventh Edition
Neil Campbell and Jane Reece
Lectures by Chris Romero
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
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
Figure 5.1
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Concept 5.1: Most macromolecules are polymers, built from
monomers
Three of the classes of life’s organic
molecules are polymers




Carbohydrates
Proteins
Nucleic acids
A polymer

Is a long molecule consisting of many similar
building blocks called monomers
3
The Synthesis and Breakdown of Polymers
• Monomers form larger molecules by condensation
reactions called dehydration synthesis
• These are sometimes called condensation rxns because
a molecule of water is liberated when a bond is formed.
HO
1
3
2
H
Unlinked monomer
Short polymer
Dehydration removes a water
molecule, forming a new bond
HO
Figure 5.2A
1
2
H
HO
3
H2O
4
H
Longer polymer
(a) Dehydration reaction in the synthesis of a polymer
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Polymers
• Polymers can disassemble by
– Hydrolysis (water cleavage)
HO
1
2
3
4
Hydrolysis adds a water
molecule, breaking a bond
HO
1
2
3
H
Figure 5.2B (b) Hydrolysis of a polymer
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H
H2O
HO
H
The Diversity of Polymers
• Each class of polymer
– Is formed from a specific set of monomers
1
2
3
H
HO
• 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
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Concept 5.2: Carbohydrates serve as fuel and building
material
• Carbohydrates
– Include both sugars and their polymers
(starches)
– Most carbohydrates have the empirical formula
(CH20)n.
– Carbohydrates are composed of covalently
bonded atoms of carbon, hydrogen, and
oxygen.
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Sugars
• Monosaccharides
–
The basic unit of a carbohydrate is called a
monosaccharide or simple sugar.
–
Can be used for fuel; The principle source of energy for
organisms is glucose, C6H12O6 . Glucose is the form of
sugar generally transported in the human body (“blood
sugar”).
–
Monosaccharides can be burned (oxidized) to yield carbon
dioxide, water, and energy.
–
Can be converted into other organic molecules
–
Can be combined into polymers
–
Structurally a sugar consists of a carbon backbone of three
or more carbon atoms with either an aldehyde or ketone
carbonyl group on one carbon, and hydroxyl groups on
each of the other carbons.
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Monosaccharides
– May be linear
– Can form rings (when aqueous)
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• Examples of monosaccharides
Triose sugars Pentose sugars
(C3H6O3)
(C5H10O5)
H
O
H
Aldoses
C
O
H
C
H
O
C
C
OH
H
C
OH
H
C
OH
H
C
OH
H
C
OH
HO
C
H
C
OH
H
H
C
OH
H
H
Ribose
H
H
C
H
C
OH
H
HO
C
H
C
OH
HO
C
H
H
C
OH
H
C
OH
H
C
OH
H
C
OH
H
H
Glucose
Galactose
H
C OH
H
C
O
H
C OH
H
C OH
C
O
O
C OH
H
C OH
HO
H
H
C OH
H
C OH
Dihydroxyacetone
H
C OH
H
C OH
H
H
C OH
H
Ribulose
Figure 5.3
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O
C
H
Glyceraldehyde
Ketoses
Hexose sugars
(C6H12O6)
C H
H
Fructose
A side note: Isomers
These are compounds that have
the same molecular formula but
different three dimensional
structures and hence different
physical and/or chemical
properties. There are 3 types of
isomers:
•a. Structural Isomers: These differ in the arrangement of atoms. For example, glucose and
fructose both have the formula C6H12O6 but have different bonding arrangements.
•b. Geometric Isomers: These have the same covalent partnership but different spatial
arrangements because of the orientation of groups around a double bond, which does not
permit free rotation around it. The orientations of the constituent groups are spatially fixed
around the double bond. Such arrangements around a double bond are called cis-isomers
when the named constituents are oriented on the same side of the double bond, and transisomers when the constituents are oriented across from each other.
•c. Stereoisomers (Enantiomers): These are molecules that are mirror images of each
other. The result is a pair of compounds that are mirror images, right handed and left
handed isomers.
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ISOMERS
– Structural
– Geometric
– Enantiomers (stereoisomers)
(a) Structural isomers
(b) Geometric isomers
H H H H H
H C C C C C H
H H H H H
X
C C
H
(c) Enantiomers
H
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H
X
C
H
C H
C H
H
C C H
H H
C C
X
H
CO2H
CH3
Figure 4.7 A-C
H
H
H
H C
H
X
H
CO2H
NH2NH2
C
CH3
H
Enantiomers (stereoisomers)
• Are important in the pharmaceutical industry
Figure 4.8
L-Dopa
D-Dopa
(effective against
Parkinson’s disease)
(biologically
inactive)
(levo, dextro)
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Another side note… Drawing organic moleculesSometimes the drawings showing
monosaccharides are simplified to show
only the most important parts of the
molecules. The same sequence of
events diagrammed above could be
shown as:
Here the hydrogens that complete each molecule
are simply 'understood' to be present, and are not
included in the diagrams.
The diagrams can be still further
simplified by showing only the
carbons and the carbonyl group
[or the oxygen that is built into
the ring].
Sometimes even the carbons are not labeled,
but are assumed to be present at every
'bend or end' of the ring. Simple hexagon
diagrams such as those below can serve
as highly simplified models of the glucose
molecule.
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Polymers of Monosaccharides
• Disaccharides are formed by joining two
monosaccharides together. The two
monosaccharides are linked by a reaction
called a dehydration synthesis or
condensation reaction.
• Are joined by a glycosidic linkage
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Examples of disaccharides
(a) 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.
CH2OH
CH2OH
H
O
H
OH H
OH
HO
H
H
H
HO
O
H
OH
H
OH
H
CH2OH
H
OHOH
H
O
H
OH H
CH2OH
H
1–4
1 glycosidic
linkage
HO
4
O
H
H
OH H
OH
O
H
OH
H
H
OH
OH
H2O
Glucose
Glucose
CH2OH
H
(b) Dehydration reaction
in the synthesis of
HO
sucrose. Sucrose is
a disaccharide formed
from glucose and fructose.
Notice that fructose,
though a hexose like
glucose, forms a
five-sided ring.
O
H
OH
H
H
CH2OH
H
OH
HO
CH2OH
O
H
H
H
HO
CH2OH
OH
OH
Maltose
H
O
H
OH
H
1–2
glycosidic
1
linkage
H
Fructose
Figure 5.5
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2
H
H
CH2OH
OH H
OH
Sucrose
H
HO
O
HO
H2O
Glucose
CH2OH
O
Polysaccharides
Condensation reaction/dehydration synthesis: the joining of two
smaller organic compounds resulting in the formation of a larger
organic molecule and the release of a water molecule. The
condensation reaction, a synthesis reaction, is important because
it is the reaction that puts together polymers from monomer units.
Synthesis reactions require energy to complete.
Hydrolytic cleavage (hydrolysis): With the addition of water, the
splitting of a large organic molecule into two smaller organic
molecules. Hydrolysis reactions liberate energy. Hydrolytic
cleavage, or hydrolysis, is the opposite of a dehydration or
condensation reaction. For example, in the human digestive
system, sucrose (disaccharide) is split into glucose and fructose
(two monosaccharides).
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Polysaccharides
• Polysaccharides: are polymers of sugars
– Serve many roles in organisms
– Three examples of polysaccharides are starch,
glycogen, and cellulose.
A polysaccharide consists of three or more (usually
hundreds of) monosaccharides, joined together by
condensation reactions.
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Two different types of starches
• Starch
Chloroplast
Starch
– Is a polymer consisting
entirely of glucose
monomers
– Starch is the storage
polysaccharide in plants
and is an important
reservoir for energy.
– There are two common
types of (plant) starch:
1 m
Amylose
Amylopectin
Figure 5.6 (a) Starch: a plant polysaccharide
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Starches
1) Amylose: the simplest starch, consisting of unbranched chains of
hundreds of glucose molecules. Note: the [alpha] 1,4 glycosidic bond,
(the glucose units are connected to the first and fourth carbons)
2) Amylopectin: large molecule consisting of short glucose chains with
other glucose chains branching off of the main chain.
•
Note: the glucose units are linked by both [alpha] 1,4 AND [alpha] 1,6
bonds!
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“animal” starch
• Glycogen
– Consists of linked, highly branched, glucose monomers
– Is the major storage form of glucose in animals
Mitochondria
Giycogen
granules
0.5 m
Glycogen
Figure 5.6 (b) Glycogen: an animal polysaccharide
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Glycogen
•
Glycogen is the main energy storage polysaccharide in animals
•
Glycogen is composed of branching glucose chains, with more
branches than amylopectin.
•
It is found in the liver and muscles and acts as the temporary storage
form of glucose. The liver removes the excess glucose from the
bloodstream, converts the glucose monomers to glycogen via
condensation reactions, and stores it as glycogen.
•
When vertebrates need glucose for energy, glycogen is converted by
hydrolysis back to glucose.
•
In glycogen, or animal starch, the glucose units are again joined by [alpha] 1,4
linkages to produce long chains, but side chains are linked to the main chain
by [alpha] 1,6 linkages
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Structural Polysaccharides
– Cellulose is a structural polysaccharide and is the
major building material made by plants.
– It is the most abundant organic material on earth.
– Cellulose is made up of long, straight glucose
molecules. Cellulose is called a structural
polysaccharide because it gives the plant cell its
shape, is not soluble, and is very strong.
– Cellulose is flexible when the plant cell is young. As
the cell grows, the cellulose becomes thicker and more
rigid.
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Cellulose
•Cellulose is indigestible to humans because the
linkages are 1-4 beta linkages, and our enzymes
can only break down 1-4 alpha linkages because
the shapes are different.
•Cellulose is the so-called "fiber" in our diets.
•Some bacteria, protists, fungi, and lichens can
break down cellulose. For example, bacteria and
protists found in the stomachs of termites and
grazing animals break down the cellulose in the
grass and wood to provide the animal with glucose
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Cellulose
– Is a major component of the tough walls that
enclose plant cells
Cell walls
Cellulose microfibrils
in a plant cell wall
Microfibril
About 80 cellulose
molecules associate
to form a microfibril, the
main architectural unit
of the plant cell wall.
0.5 m
Plant cells
Parallel cellulose molecules are
held together by hydrogen
bonds between hydroxyl
groups attached to carbon
atoms 3 and 6.
Figure 5.8
OH CH2OH
OH
CH2OH
O O
O O
OH
OH
OH
OH
O
O O
O O
O CH OH
OH
CH2OH
2
H
CH2OH
OH CH2OH
OH
O O
O O
OH
OH
OH
OH
O
O O
O O
O CH OH
OH CH2OH
2
H
CH2OH
OH
OH CH2OH
O O
O O
OH
OH
OH O
O OH
O O
O
O CH OH
OH CH2OH
2
H
 Glucose
monomer
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Cellulose
molecules
A cellulose molecule
is an unbranched 
glucose polymer.
Cellulose is difficult to digest
– Cows have microbes in their stomachs to
facilitate this process
Figure 5.9
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Other structural polysaccharides
•
Chitin, another important structural polysaccharide
–
Is found in the exoskeleton of arthropods
–
Chitin is very soft but is combined with CaCO3 (calcium carbonate or
limestone) to become hard. Most animals cannot digest chitin
–
Can beCHused
as surgical thread
2
OH
H H O OH
OH H
OH
H
H NH
C O
C
H3
(b) Chitin forms the exoskeleton (c) Chitin is used to make a
(a) The structure of the
of arthropods. This cicada
strong and flexible surgical
chitin monomer.
is molting, shedding its old
thread that decomposes after
exoskeleton and emerging
the wound or incision heals.
Figure 5.10 A–C
in adult form.
Pectin and carrageenan: These are extracted from algae. Pectin and
carrageenan are put into food items such as jellies, jams, yogurt, icecream ,
and milkshakes to give them a jelly-like or creamy consistency.
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LIPIDS
• Concept 5.3: Lipids are a diverse group of
hydrophobic molecules
– Are the one class of large biological molecules that do
not consist of polymers
– Lipids are a diverse group of molecules defined by
their solubility rather than by their structures (Share the
common trait of being hydrophobic)
– Lipids dissolve in nonpolar solvents such as
chloroform, ether, and benzene.
– There are 5 classes of lipids: triglycerides,
phospholipids, glycolipids, steroids, and waxes.
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Triglycerides: Fats and Oils
• Fat: a lipid that is solid at room temperature.
Oil: a lipid that is a liquid at room temperature.
• Glycerol:
Fatty acids usually have an even
number of carbons, differ in the
length of the carbon chain, and
may contain double covalent
bonds.
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Triglycerides: Fats and oils
• A triglyceride is composed of one glycerol molecule and
three fatty acid molecules.
• The synthesis of a triglyceride occurs when a glycerol
molecule joins with three (of the seventy different) fatty
acids.
Fat molecule (triacylglycerol)
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Saturated fatty acids
– Have the maximum number of hydrogen atoms
possible
– Have no double bonds
Animal fats are
usually saturated
fats and solidify at
room temperature.
Stearic acid
Figure 5.12 (a) Saturated fat and fatty acid
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Unsaturated fatty acids
– Have one or more double bonds between carbons
• This structure means that
they have fewer hydrogens
than the saturated fats; these
are called unsaturated fats.
• Unsaturated fats can be
found in plants (olive oil,
peanut oil, corn oil) more
commonly than animals
Figure 5.12
• Usually liquids at room
temperature.
Oleic acid
• We can't make unsaturated
fats, so we need to eat small
amounts of unsaturated fats.
• Polyunsaturated fats have
more than one double bond.
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(b) Unsaturated fat and fatty acid
cis double bond
causes bending
Functions of Fats
• Triglycerides (fats and oils) are a concentrated
source of energy.
• When the fat is combined with oxygen, the fats
release a large amount of energy, more than
twice as much per gram as carbohydrates.
• Seeds store triglycerides, animals store energy as
fat for lean seasons or migration or insulation,
humans store fat under the skin and around
internal organs.
• Fat serves for insulation and flotation.
• Storage fat serves as padding in your fingers and
your bottom.
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PHOSPHOLIPIDS:
Important components of cell membranes
•
Have only two fatty acids
•
Have a phosphate group instead of a third
fatty acid (attached to the glycerol)
•
Consists of a hydrophilic “head” and hydrophobic “tails”
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Importance of phospholipids
• The structure of phospholipids
– Results in a bilayer arrangement found in cell
membranes
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Other Biologically Important Groups of Lipids
Glycolipids: The third carbon in the glycerol molecule
isn't bound to a phosphate group. Instead, it is bonded
to a short carbohydrate chain (1-15
monosaccharides).
The carbohydrate head is hydrophilic; thus glycolipids
behave in the same way as phospholipids. They are
also important components of the cell membrane.
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Other Biologically Important Groups of Lipids
Waxes:
Waxes are similar in structure to triglycerides, but
instead of glycerol there is a long chain alcohol.
Because of their hydrophobic quality, waxes are
found in many living things that need to conserve
water.
Insects have waxy cuticles, plants have wax on their
leaves, fruit skins and petals have wax as an outer
covering.
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Steroids
Steroids are not really that structurally similar to fatty acids or
lipids.
Since they are hydrophobic, however, they are called lipids.
All steroids have four linked carbon rings. Steroids have a
tail and many have an -OH group.
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Steroids
• Lanolin- Commercially refined from sheep's wool. Humans
have a small amount of lanolin in the hair and skin; lanolin helps
give these structures flexibility.
• Cholesterol- A major constituents of the cell membrane. When
bombarded with ultraviolet light, it rearranged into vitamin D.
When modified slightly, it makes sex hormones.
H3C
CH3
CH3
Figure 5.15
HO
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CH3
CH3
Steroids
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Proteins
• Concept 5.4: Proteins can be folded into many shapes,
resulting in a wide range of functions
• Proteins have many roles inside the cell
• Proteins are large, complex organic molecules that
are made of smaller monomer units, amino acids.
• Proteins are naturally occurring biological
molecules that are composed of amino acid
monomers linked together through dehydration
(condensation) reactions.
• Amino Acids are the building blocks (monomers)
of proteins.
• There are 20 different amino acids.
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An overview of protein functions
Table 5.1
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Basic Structure of an Amino Acid
Each amino acid has a carbon with four different groups attached.
(1) Amine group, NH2 , (basic, can accept H+ and thus have a
positive charge).
(2) Carboxyl group, -COOH, acidic, can donate H+ and thus have a
negative charge (-COO-)
(3) Hydrogen
(4) R group: (“variable” group) The R group is the portion of the
amino acids that is different in each amino acid. In the amino
acid glycine, the R group is replaced with an H atom.
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20 different amino acids make up proteins
CH3
CH3
H
H3N+
C
CH3
O
H3N+
C
H
Glycine (Gly)
O–
C
H3N+
C
H
Alanine (Ala)
O–
CH
CH3
CH3
O
C
CH2
CH2
O
H3N+
C
H
Valine (Val)
CH3
CH3
O–
C
O
H3N+
C
H
Leucine (Leu)
H3C
O–
CH
C
O
C
O–
H
Isoleucine (Ile)
Nonpolar
CH3
CH2
S
NH
CH2
CH2
H3N+
C
H
CH2
O
H3N+
C
O–
Methionine (Met)
C
H
H3 N+
C
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C
O–
Phenylalanine (Phe)
Figure 5.17
CH2
O
H
O
H2C
CH2
H2N
C
O
C
O–
H
C
O–
Tryptophan (Trp)
Proline (Pro)
R Groups
The R group of the amino acid determines the
physical and chemical properties of the
protein.
R groups can be nonpolar, polar, acidic, or basic.
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OH
OH
Polar
CH2
H3N+
C
CH
O
H3N+
C
O–
H
Serine (Ser)
C
CH2
O
H3N+
C
O–
H
C
CH2
O
C
H
O–
H3N+
C
O
H3N+
C
O–
H
Electrically
charged
H3N+
CH2
C
H3N+
O–
C
NH3+
O
C
CH2
C
CH2
CH2
CH2
CH2
CH2
CH2
O
CH2
C
O–
H
H3N+
C
O
CH2
C
H
O–
H3N+
C
H
O–
H
Glutamic acid
(Glu)
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NH+
C
O–
Lysine (Lys)
NH2+
H3N+
CH2
O
CH2
H3N+
C
H
Aspartic acid
(Asp)
O
C
Glutamine
(Gln)
NH2
C
C
C
Basic
O–
O
O
Asparagine
(Asn)
Acidic
–O
CH2
CH2
H
Tyrosine
(Tyr)
Cysteine
(Cys)
Threonine (Thr)
C
NH2 O
C
SH
CH3
OH
NH2 O
NH
CH2
O
C
C
O–
H
O
C
O–
Arginine (Arg)
Histidine (His)
R Groups
They can also be the site of the addition of prosthetic
groups, inorganic groups (vitamins, minerals) that are
essential for the functioning of the protein.
These prosthetic groups often determine the protein's
function, as in hemoglobin.
Minerals in our diets are often
essential parts of prosthetic
groups; for example, iron (Fe2+)
in our diet is essential for the
synthesis of the heme group the
prosthetic group in hemoglobin.
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Biological Sources and Utilization of Amino Acids
How do the cells in the body obtain amino acids?
Many foods contain proteins; the proteins are
broken down into small pieces called
peptides.
Peptides are small (about 30 amino acids long)
and are carried in the blood vessels.
When a cell is actively making proteins,
peptides are taken into the cell, broken
down, and the constituent amino acids are
reconfigured into a protein.
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Amino Acid Polymers
• Amino acids
– Are linked by peptide bonds
Peptide
bond
OH
CH2
SH
CH2
H
N
H
OH
CH2
H
C C
H
N C C OH H N C
H O
H O
H
(a)
C OH
O DESMOSOMES
H2O
OH
DESMOSOMES
DESMOSOMES
SH
OH
Peptide
CH2 bond CH2
CH2
H
H N C C
H O
Figure 5.18
(b)
Amino end
(N-terminus)
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H
H
N C C
H O
N C C OH
H O
Carboxyl end
(C-terminus)
Side
chains
Backbone
Determining the Amino Acid Sequence of a Polypeptide
• Proteins have a three dimensional configuration
which is determined by the amino acid
sequence.
• The amino acid sequences of polypeptides
– Were first determined using chemical means
– Can now be determined by automated
machines
http://en.wikipedia.org/wiki/Frederick_Sanger
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Protein Conformation and Function
• Proteins can be stringy or globular. The conformation
of the protein is its three dimensional shape.
• The function of the protein is determined by its
conformation. A protein may have four different levels
of structure that determine its conformation.
• A protein’s specific conformation:
– Determines how it functions. This is especially
important in ENZYMES (which are all proteins)
and HORMONES (many are proteins) that have to
FIT specifically with a target cell receptor or with a
substrate.
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Two models of protein conformation
Groove
(a) A ribbon model
Groove
Figure 5.19
(b) A space-filling model
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Four Levels of Protein Structure
• Primary structure
–
Is the unique sequence of amino
acids in a polypeptide
–
The protein is defined by the amino
acid sequence.
–
Each protein has a different primary
structure.
Gly ProThr Gly
Thr
+H N
3
Amino
end
Val
Leu
Asp
AlaVal Arg Gly
Ser
Pro
Ala
Glu Lle
–
Changing the amino acid sequence
can change the protein shape and
function.
Amino acid
subunits
Gly
Glu
Cys LysSeu
LeuPro
Met
Val
Lys
Leu Ala
Gly
Asp
Thr
Lys
Ser
Lys Trp Tyr
lle
Ser
ProPhe
His Glu
Ala Thr PheVal
Asn
His
Ala
Glu
Val
Asp
Tyr
Arg
Ser
Arg
Gly Pro
Thr Ser
Tyr
Thr
lle
Ala
Ala
Leu
Leu
Ser
Pro
SerTyr
Thr
Ala
Val
Val
LysGlu
Thr
AsnPro
Figure 5.20
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c
o
o–
Carboxyl end
Secondary structure
• Is the folding or coiling of the polypeptide into a
repeating configuration
– Includes the  helix and the  pleated sheet
 pleated sheet
O H H
C C N
Amino acid
subunits
C N
H
R
R
O H H
C C N
C C N
O H H
R
R
O H H
C C N
C C N
OH H
R
R
R
O
R
C
H
H
R
O C
O C
N H
N H
N H
O C
O C
H C R H C R
H C R H C
R
N H O C
N H
O C
O C
H
C
O
N H
N
C
C
H
R
H
R
N
C
C
H
H
 helix
Figure 5.20
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O H H
C C N
C C N
OH H
R
O
C
H
H
H C N HC
C N HC N
C
N
H
H
C
O
C
C
O
R
R
O
R
O
C
H
H
NH C N
C
H
O C
R
C C
O
R
R
H
C
N HC N
H
O C
Tertiary structure
Is the overall three-dimensional shape of a polypeptide
–
Results from interactions between amino acids and R groups
–
There are two types of three dimensional shapes: fibrous and globular. Some fibrous proteins are keratin
and collagen. Globular proteins are more numerous. An example of a globular protein is hemoglobin. The
bends and loops of the amino acid chain are caused by the R groups of the amino acids reacting with R
groups of other amino acids on the same polypeptide.
–
The nonpolar (hydrophobic) R groups will tend to group together away from the surface of the polypeptide
since water is the usual medium surrounding these molecules. Hydrogen bonds can form between polar R
groups. Two sulfhydryl groups can form a disulfide bridge. Charged R groups can repel or attract each other.
These bends and twists cause the polypeptide to have a three dimensional shape.
Hyrdogen
bond
CH22
CH
O
H
O
CH
H3C
CH3
H3C
CH3
CH
Hydrophobic
interactions and
van der Waals
interactions
Polypeptide
backbone
HO C
CH2
CH2 S S CH2
Disulfide bridge
O
CH2 NH3+ -O C CH2
Ionic bond
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Quaternary structure
•
A protein consisting of two or more
polypeptide chains has a quaternary
structure.
•
The quaternary structure is formed by
polypeptide chains interacting with other
polypeptide chains.
•
These interactions are of the same types
that are responsible for tertiary structure,
namely hydrogen bonds, disulfide bridges,
electrostatic attractions and hydrophobic
forces (London or dispersion forces).
Polypeptide
chain
Collagen
 Chains
Iron
Heme
 Chains
Hemoglobin
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The four levels of protein structure
Most proteins probably go through several
intermediate states on their way to a stable
conformation
+H
3N
Amino end
Amino acid
subunits
helix
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Chaperonins
– Are protein molecules that assist in the proper
folding of other proteins
Polypeptide
Cap
Correctly
folded
protein
Hollow
cylinder
Chaperonin
(fully assembled)
Figure 5.23
Steps of Chaperonin
Action:
1 An unfolded polypeptide enters the
cylinder from one end.
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2 The cap attaches, causing
3 The cap comes
the cylinder to change shape in off, and the properly
such a way that it creates a
folded protein is
hydrophilic environment for the released.
folding of the polypeptide.
Sickle-Cell Disease: A Simple Change in
Primary Structure
• Sickle-cell disease
– Results from a single amino acid substitution in
the protein hemoglobin
– Caused by an inherited defect in the gene that
codes for the hemoglobin AA sequence
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Hemoglobin structure and sickle-cell disease
Primary
structure
Normal hemoglobin
Val
His Leu Thr
1 2 3 4 5 6 7
Secondary
and tertiary
structures
Red blood
cell shape
Val
His
Leu Thr


Molecules do
not associate
with one
another, each
carries oxygen.


Quaternary
structure
Figure 5.21
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Val Glu
...




10 m
Red blood
cell shape
Exposed
hydrophobic
region
 subunit
Function
10 m
Normal cells are
full of individual
hemoglobin
molecules, each
carrying oxygen
Pro
structure 1 2 3 4 5 6 7
Secondary
 subunit and tertiary
structures
Quaternary Hemoglobin A
structure
Function
Pro Glul Glu
Sickle-cell hemoglobin
. . . Primary
Hemoglobin S
Molecules
interact with
one another to
crystallize into a
fiber, capacity to
carry oxygen is
greatly reduced.
Fibers of abnormal
hemoglobin
deform cell into
sickle shape.
What Determines Protein Conformation?
–
•
Often depends on the physical and chemical conditions of the protein’s environment
Denaturation
–
Is when a protein unravels and loses its native conformation
–
If pH, salt concentration, temperature, or other environmental aspects are altered, the protein may unravel and
lose its shape.
–
A protein that denatures is biologically inactive.
–
Chemicals can disrupt hydrogen bonds, ionic bonds, or disulfide bridges, and change the structure of proteins.
–
Excessive heat will also cause the protein to denature.
Denaturation
Normal protein
Figure 5.22
Denatured protein
Renaturation
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Determine a protein’s three-dimensional structure
• X-ray crystallography
Can be used to
determine the
shape of
molecules
X-ray
diffraction
pattern
Photographic film
Diffracted X-rays
X-ray
X-ray
beam
source
Crystal Nucleic acid Protein
Figure 5.24
(a) X-ray diffraction pattern
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(b) 3D computer model
Enzymes
– Are a type of protein that acts as a catalyst,
speeding up chemical reactions
1 Active site is available for
a molecule of substrate, the
reactant on which the enzyme acts.
Substrate
(sucrose)
2 Substrate binds to
enzyme.
Glucose
OH
Enzyme
(sucrase)
H2O
Fructose
H O
4 Products are released.
Figure 5.16
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3 Substrate is converted
to products.
Chemical Reactions
• The activation energy, EA
– Is the initial amount of energy needed to start a
chemical reaction
– Is often supplied in the form of heat from the
surroundings in a system
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The effect of enzymes on reaction rate
• An enzyme catalyzes reactions
Free energy
– By lowering the EA barrier
Course of
reaction
without
enzyme
EA
without
enzyme
EA with
enzyme
is lower
Reactants
Course of
reaction
with enzyme
∆G is unaffected
by enzyme
Products
Figure 8.15
Progress of the reaction
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Substrate Specificity of Enzymes
• The substrate (A)
– Is the reactant an enzyme acts on
• The enzyme
– Binds to its substrate, forming an enzymesubstrate complex (C)
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• The active site
– Is the region on the enzyme where the
substrate binds
• Their shape
(conformation)
makes each
enzyme substratespecific
• “Lock-and-key” fit
enables reaction
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• The active site can
lower an EA barrier by
– Orienting substrates
correctly
– Straining substrate
bonds
– Providing a favorable
microenvironment
– Covalently bonding to
the substrate
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Effects of Local Conditions on Enzyme Activity
• The activity of an enzyme
– Is affected by general environmental factors
• temperature
• pH
• salinity
• enzyme concentration
• substrate concentration
• presence of any inhibitors or activators.
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• Denaturation is a process in which proteins or
nucleic acids lose their tertiary structure and
secondary structure by application of some
external stress or compound, such as a strong
acid or base, a concentrated inorganic salt, an
organic solvent (e.g., alcohol or chloroform), or
heat.
• If proteins in a living cell are denatured, this
results in disruption of cell activity and possibly
cell death.
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Effects of Temperature and pH
• Each enzyme
– Has an optimal temperature in which it can
function
Optimal temperature for
enzyme of thermophilic
(heat-tolerant)
bacteria
Rate of
reaction
Optimal temperature for
typical human enzyme
0
20
40
80
Temperature (Cº)
(a) Optimal temperature for two enzymes
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100
Optimal pH for two enzymes
Optimal pH for trypsin
(intestinal enzyme)
Rate of
reaction
Optimal pH for
pepsin
(stomach enzyme)
0
1
2
3
4
5
6
7
8
9
– Each enzyme has an optimal pH in which it
can function
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Cofactors & Coenzymes
• Cofactors
– Are nonprotein enzyme helpers
– Most often minerals (metal ions)
– Zn 2+, Mg2+
• Coenzymes
– Are organic cofactors
– Usually vitamins
– B2, B6, B12, etc
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Enzymes Regulate reactions
• Concept 8.5: Regulation of enzyme activity
helps control metabolism
• A cell’s metabolic pathways
– Must be tightly regulated
Enzyme 1
A
Enzyme 2
D
C
B
Reaction 1
Enzyme 3
Reaction 2
Starting
molecule
Reaction 3
Product
Biochemical pathway
Feedback inhibition of a biochemical pathway
Enzyme action and the hydrolysis of sucrose
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Allosteric Activation and Inhibition
• Many enzymes are allosterically regulated
• Allosteric regulation
– Is the term used to describe any case in which a
protein’s function at one site is affected by binding
of a regulatory molecule at another site
– Enzymes can be “turned on” or “turned off” this way
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Enzyme Inhibitors
• Competitive inhibitors
– Bind to the active site of an enzyme, competing with
the substrate
A substrate can
bind normally to the
active site of an
enzyme.
Substrate
Active site
Enzyme
(a) Normal binding
A competitive
inhibitor mimics the
substrate, competing
for the active site.
Figure 8.19(b) Competitive inhibition
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Competitive
inhibitor
Noncompetitive inhibitors
• Noncompetitive inhibitors
– Bind to another part of an enzyme, changing
the function
A noncompetitive
inhibitor binds to the
enzyme away from
the active site, altering
the conformation of
the enzyme so that its
active site no longer
functions.
Noncompetitive inhibitor
(c) Noncompetitive inhibition
Figure 8.19
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Feedback inhibition
• In feedback
inhibition
Active site
available
– The end
product of a
metabolic
pathway shuts
down the
pathway
Initial substrate
(threonine)
Threonine
in active site
Enzyme 1
(threonine
deaminase)
Isoleucine
used up by
cell
Intermediate A
Feedback
inhibition
Active site of
enzyme 1 no
longer binds
threonine;
pathway is
switched off
Enzyme 2
Intermediate B
Enzyme 3
Intermediate C
Isoleucine
binds to
allosteric
site
Enzyme 4
Intermediate D
Enzyme 5
Figure 8.21
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End product
(isoleucine)
Nucleic Acids
Concept 5.5: Nucleic acids store and
transmit hereditary information
Are made of nucleotide monomers
Genes
Are the units of inheritance
Program the amino acid sequence of
polypeptides
Each amino acid is coded by a nucleotide
triplet
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Nucleic acids are the largest organic molecule made by organisms.
• There are two types of nucleic acids
–
Deoxyribonucleic acid (DNA)
–
Ribonucleic acid (RNA)
• Structure: Nucleotides are the basic units of both DNA
and RNA and can exist as free molecules. A
nucleotide is made up of three parts:
–
Pentose sugar: deoxyribose or ribose.
–
Phosphate: in free nucleotides, they occurs as a group of
three phosphates bonded to the sugar.
–
Nitrogenous base: there are two types of nitrogenous
bases. They are called bases because of the amine groups
which are basic.
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The 4 Nitrogenous Bases
•
Pyrimidines: single ring
compounds. The two
pyrimidines in DNA are
cytosine and thymine. In
RNA thymine is replaced by
uracil.
•
Purines: double ring bases.
The two purines are adenine
and guanine.
•
The sequence of bases
along a nucleotide polymer
is unique for each gene
•
The nitrogenous bases in
DNA form hydrogen bonds in
a complementary fashion (A
with T only, and C with G
only)
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The Structure of Nucleic Acids
• Nucleic acids
– Exist as polymers called polynucleotides
5’ end
5’C
O
3’C
Nucleoside
O
Nitrogenous
base
(a) Polynucleotide,
or nucleic acid
O
O

O
P O
5’C
CH2
O

5’C
O
Phosphate
group
O
3’C
OH
3’ end
Figure 5.26
Figure 5.26
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(b) Nucleotide
3’C
Pentose
sugar
Roles of Nucleic Acids
• DNA
– Stores information for the synthesis of specific proteins
– The pentose sugar in DNA, deoxyribose, has one
fewer oxygen atoms than ribose, the sugar in RNA.
– DNA contains an organism's genetic information.
Basically, DNA encodes the instructions for amino acid
sequences of proteins.
• RNA
– carries the encoded DNA information to the ribosomes
(m)
– carries the amino acids to the ribosomes (t)
– is a major constituent of ribosomes (r)
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The DNA Double Helix
• Cellular DNA molecules
– Have two
polynucleotides that
spiral around an
imaginary axis
5’ end
Sugar-phosphate
backbone
Base pair (joined by
hydrogen bonding)
Old strands
– Form a double helix
– Consists of two
antiparallel nucleotide
strands
3’ end
Figure 5.27
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3’ end
5’ end
A 3’ end
Nucleotide
about to be
added to a
new strand
5’ end
New
strands
3’ end
DNA and Proteins as Tape Measures of Evolution
• Molecular comparisons
– Help biologists sort out the evolutionary
connections among species
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