CHAPTER 5
STRUCTURE AND FUNCTION OF MACROMOLECULES
WHAT IS A MACROMOLECULE?
MACROMOLECULE- a molecule weighing over 100,000 daltons
- most macromolecules are polymers
POLYMER- a long molecule consisting of many similar or identical building blocks linked by covalent
bonds
- much like a train consisting of a chain of cars
MONOMERS- the repeating units that make up polymers
- the macromolecules differ in their monomers, but the chemical reactions that make and break polymers
are the same
- monomers are connected when 2 molecules are covalently bonded to each other through the loss of a
water molecule> CONDENSATION REACTION
- this is specifically called a DEHYDRATION REACTION because the molecule lost is water
- when the bond forms, each monomer contributes part of the water molecule that is lost
* one monomer provides a hydroxyl group (-OH) and the other provides a hydrogen (-H)
- to build polymers, this reaction repeats over and over
Polymers are broken down into monomers by HYDROLYSIS, the reverse of dehydration
- bonds between monomers are broken by the addition of water molecules
* a hydrogen attaches to one monomer, a hydroxyl attaches to another monomer
MANY POLYMERS ARE MADE FROM FEW MONOMERS
Complex polymers are constructed from only 40-50 common monomers
- can be compared to constructing thousands of words from only 26 letters
- arrangement is the key
- most biological polymers are much longer than the longest word
CARBOHYDRATES
CARBOHYDRATES- include both sugars and their polymers
- sugars, the smallest carbohydrates, serve as fuel and carbon sources
MONOSACCHARIDES- “single sugars”
- molecular formulas that are some multiple of CH2O
Ex: Glucose C6H12O6
CLASSIFYING MONOSACCHARIDES
Carbonyl group (C=O) is trademark of a sugar
- depending on the location of the carbonyl group, a sugar is either an aldose or a ketose
* ALDOSE- carbonyl on end
* KETOSE- carbonyl in middle
(most names for sugars end in ose)
Another factor in classifying monosaccharides is the size of the carbon skeleton
* TRIOSE- 3 carbon sugar
* PENTOSE- 5 carbon sugar
* HEXOSE- 6 carbon sugar
- although it is easier to represent sugars in a linear form, they usually form rings
DISACCHARIDES
DISACCHARIDE- consists of 2 monosaccharides joined by a glycosidic linkage
GLYCOSIDIC LINKAGE- a covalent bond formed between 2 monosaccharides by a dehydration reaction
Ex: glucose + glucose > maltose
- maltose (malt sugar) is an ingredient used in brewing beer
Glucose + fructose > sucrose (table sugar)
- plants transport carbohydrates in the form of sucrose
Glucose + galactose > lactose (milk sugar)
POLYSACCHARIDES
POLYSACCHARIDES- polymers with a few hundred to a few thousand monosaccharides joined by
glycosidic linkages
* some serve as storage material
* some serve as building materials for structures that protect
STORAGE POLYSACCHARIDES
STARCH- storage polysaccharide of plants
- made up entirely of glucose molecules
- glucose joined by 1-4 linkages (number 1 carbon to number 4 carbon)
- the molecules are helical (spiral shaped)
Forms of starch
1. Amylose- simplest form, unbranched
2. Amylopectin- more complex, is branched
By making starch, plants can store up glucose, a major cellular fuel
- the sugar can later be withdrawn by hydrolysis, which breaks the bonds between the glucose monomers
GLYCOGEN- animal storage polysaccharide
- similar to amylopectin, but has more branches
- stored mainly in liver and muscle cells
- hydrolysis in these cells releases glucose when it is needed
- in animals, glycogen can not be stored for long> replenish
STRUCTURAL POLYSACCHARIDES
CELLULOSE- major component of cell walls of plants
- similar in structure to starch, but glucose has different forms
* α (alpha)
* β (beta)
- in starch, all glucose monomers are in the α form
- in cellulose, the glucose monomers are in the β form, making every other glucose upside down with
respect to the others
These forms of glucose give starch and cellulose different shapes
* starch is helical
* cellulose is straight (never branched)
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* in cell walls, parallel cellulose molecules are grouped into units called microfibrils- strong building
materials for plants
DIGESTING CELLULOSE
Enzymes that digest starch by hydrolyzing its α linkages are unable to hydrolyze the β linkages of
cellulose
- humans cannot digest cellulose, but it is still important for a healthy diet
- called “dietary fiber”- stimulates lining of digestive system to produce mucus
Some organisms have microbes that can digest cellulose, breaking it down into glucose
- cows can get nourishment from grass
- termites are able to make a meal out of wood
Figure 5.8 The arrangement of cellulose in plant cell walls
CHITIN
CHITIN- carbohydrate used by insects to build their exoskeletons- hard protective covering
- similar in structure to cellulose, but glucose monomers have a nitrogen containing group attached
- chitin is also used to make a strong surgical thread that decomposes after the wound heals
Figure 5.9 Chitin, a structural polysaccharide: exoskeleton and surgical thread
LIPIDS
Lipids are the one class of macromolecules that do not include polymers
- they are grouped together because they share little or no affinity for water
- this hydrophobic behavior is based on structure
- lipids are made up mostly of hydrocarbons
- include waxes, fats, phospholipids, and steroids
FATS
FAT- constructed from 2 kinds of smaller molecules: glycerol and fatty acids
- although fats are not polymers, they are still assembled from smaller molecules by dehydration
reactions
GLYCEROL- alcohol with 3 carbons, each with a hydroxyl group
FATTY ACID- long carbon skeleton
- at one end is a carboxyl group; attached to the carboxyl group is a long hydrocarbon chain
To make a fat, 3 fatty acids each join to glycerol by an ESTER LINKAGE- a bond between a hydroxyl group
and a carboxyl group
- resulting molecule is a TRIGLYCERIDE
SATURATED FATTY ACID- no double bonds between the carbon atoms; as many hydrogen atoms as
possible are bonded to the carbon skeleton
UNSATURATED FATTY ACID- has one or more double bonds; has a kink in its tail wherever the double
bond is
Figure 5.10 The synthesis and structure of a fat, or triacylglycerol
Saturated fats usually come from animals
- solid at room temperature
- Ex: lard and butter
Unsaturated fats usually come from plants and fish
- liquid at room temperature
- oils
- kinks prevent molecules from packing closely enough to be solid
Figure 5.11 Examples of saturated and unsaturated fats and fatty acids
FATS DO HAVE A PURPOSE!
- major function is energy storage
- a gram of fat stores twice as much energy as a gram of polysaccharide
- humans need to have a compact reservoir of fuel- stored in fat
PHOSPHOLIPIDS
PHOSPHOLIPIDS- similar to fats, but have only 2 fatty acid tails rather than 3
Figure 5.12 The structure of a phospholipid
Phospholipids have a strange behavior towards water:
- the tails (made up of hydrocarbons) are hydrophobic and stay away from water
- the head (made up of the phosphate group) is hydrophilic and likes water
If phospholipids are added to water, they clump and try to shield their hydrophobic tails
- they form a cluster called a MICELLE- a droplet with phosphate heads on the outside, and hydrocarbon
tails on the inside
- on the surface of a cell, phospholipids are arranged in a bilayer- heads on the outside, tails on the inside
Figure 5.13 Two structures formed by self-assembly of phospholipids in aqueous environments
STEROIDS
STEROIDS- lipids having carbon skeletons consisting of 4 fused rings
- the different steroids differ in the functional groups attached to the carbons
Ex: CHOLESTEROL- a component of animal cell membranes
- many hormones are produced from cholesterol- some is crucial
Figure 5.14 Cholesterol, a steroid
PROTEINS
IMPORTANCE OF PROTEINS
Proteins make up more than 50% of the dry weight of most cells
Proteins are used for:
-Structural support
-Storage
-Transport of other substances
-Signaling from one part of an organism to another
-Movement
-Defense
Proteins are all polymers constructed from the same set of 20 amino acids
-Polymers of amino acids are called POLYPEPTIDES
PROTEIN- consists of one or more polypeptides folded and coiled into specific structures
AMINO ACIDS
AMINO ACIDS- organic molecules possessing both carboxyl and amino groups
GENERAL FORMULA
http://www2.glos.ac.uk/gdn/origins/images/amino.gif
-At the center of the amino acid is an asymmetric carbon atom called the alpha (α) carbon
-Its four different partners are an amino group, a carboxyl group, a hydrogen atom, and a variable group
symbolized by R
-The R group, also called the side chain, differs with each amino acid
-Again, there are 20 amino acids in all used to build proteins
Physical and chemical properties of the side chains determines the characteristics of an amino acid
-One group has amino acids with nonpolar side chains and are hydrophobic
-One group has amino acids with polar side chains and are hydrophilic
-One group has amino acids with charged side groups and are ionic
Figure 5.15 The 20 amino acids of proteins: nonpolar
Figure 5.15 The 20 amino acids of proteins: polar and electrically charged
POLYPEPTIDES
HOW DO AMINO ACIDS LINK TOGETHER TO FORM POLYMERS?
PEPTIDE BOND- covalent bond formed when the carboxyl group of one amino acid is adjacent to the
amino group of another amino acid
Repeated over and over, this forms a polypeptide
-At one end of the polypeptide is a free amino group, and at the other end is a free carboxyl group
Animation of Peptide Bond Formation
PROTEIN CONFORMATION
The term polypeptide does not mean the same thing as protein
-A functional protein is one or more polypeptide chains twisted, folded, and coiled into a unique molecule
-The amino acid sequence determines the
3-D structure of a protein
-Conformation also determines how a protein works
4 LEVELS OF PROTEIN STRUCTURE
When a cell makes a polypeptide, the chain generally folds to assume the functional shape of that protein
-This folding is caused by the formation of several types of bonds between parts of the chain
-The four levels of protein structure are primary, secondary, tertiary, and quaternary
PRIMARY STRUCTURE
PRIMARY STRUCTURE- the unique sequence of amino acid
- The primary structure is like the order of letters in a very long word
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Even a slight change in primary structure can affect a protein’s ability to function
Ex: substitution of one amino acid for another in the primary structure of hemoglobin, the protein that
carries oxygen in red blood cells, causes sickle-cell disease
- Can clog blood vessels
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SECONDARY STRUCTURE
SECONDARY STRUCTURE- coils and folds in polypeptide chain
-Result of hydrogen bonding at regular intervals along the polypeptide backbone
-Only atoms of the backbone are involved, not the side chains
-The bonds are between the hydrogen attached to the nitrogen atom and the oxygen of a nearby peptide
bond
2 TYPES OF SECONDARY STRUCTURE
1.α helix- coil held together by hydrogen bonding between every fourth amino acid
2.β pleated sheet- 2 or more regions of the polypeptide chain lie parallel to each other
-Hydrogen bonds between the parts of the backbone in the parallel regions hold the structure together
Figure 5.20 The secondary structure of a protein
TERTIARY STRUCTURE
TERTIARY STRUCTURE- results from interactions between the side chains (R groups) of various amino
acids
WHAT CAUSES THIS STRUCTURE?
1. HYDROPHOBIC INTERACTION- as the polypeptide folds, amino acids with hydrophobic side chains
clump together near the core of the protein, away from water
2. HYDROGEN BONDS between polar side chains and IONIC BONDS between positive and negatively
charged side chains
3. DISULFIDE BRIDGES- strong covalent bonds that form when amino acids with sulfhydryl groups (-SH)
on their side chains are brought close together by the folding of the protein
- sulfur of one bonds to sulfur of another
(-S-S-)
Figure 5.22 Examples of interactions contributing to the tertiary structure of a protein
QUATERNARY STRUCTURE
QUATERNARY STRUCTURE- overall protein structure that results from combining 2 or more
polypeptides
Ex: COLLAGEN- fibrous protein that has helical subunits coiled into a larger helix
- similar to a rope, gives the fibers great strength
Ex: HEMOGLOBIN- oxygen-binding protein of red blood cells
- consists of 2 kinds of polypeptide chains, 2 of each kind per hemoglobin molecule
- each chain has a nonpolypeptide component called HEMME, with an iron atom that binds oxygen
Figure 5.23 The quaternary structure of proteins
Figure 5.24 Review: the four levels of protein structure
WHAT DETERMINES PROTEIN CONFORMATION?
1. the interactions responsible for secondary and tertiary structure: hydrogen bonds, hydrophobic
interactions, ionic bonds, disulfide bridges
2. ALSO physical and chemical conditions of the protein’s environment
- pH, salt concentration, temperature
If any of these conditions are changed or ALTERED, a protein may unravel and lose its native
configuration>> DENATURATION
- this makes the protein inactive
Figure 5.25 Denaturation and renaturation of a protein
DENATURATION AGENTS
PROTEINS MAY BECOME DENATURED IF:
- they are transferred from an aqueous environment to an organic solvent (such as ether or chloroform)protein will turn inside out
- they are exposed to chemicals that disrupt hydrogen bonds, ionic bonds, and disulfide bridges
- they are exposed to excessive heat
Ex: Whites of eggs become opaque during cooking because denatured proteins are insoluble and solidify
-when a protein in a test tube solution has been denatured, it often returns to its functional shape if
denaturing agent is removed
Protein Structure
THE SEQUENCE OF AMINO ACIDS DETERMINES PROTEIN CONFIGURATION
NUCLEIC ACIDS
WHAT DETERMINES THE AMINO ACID SEQUENCE OF POLYPEPTIDES?
GENE- unit of inheritance consisting of DNA
2 types of NUCLEIC ACIDS:
1. deoxyribonucleic acid (DNA)
2. ribonucleic acid (RNA)
DNA
- DNA is the genetic material that organisms inherit from their parents
- a molecule of DNA usually consists of hundreds or thousands of genes
- though DNA contains the instructions for all cell activities, it is not directly involved in running the
operations of the cell
- proteins are required to run cell programs
RNA
- each gene in a DNA molecule directs the synthesis of a type of RNA called messenger RNA (mRNA)
- the mRNA then directs the building of proteins
DNA > RNA > protein
- sites of protein synthesis are in structures called ribosomes, found in the cytoplasm of the cell
- DNA, however, always stays in the nucleus
- mRNA takes the genetic instructions for building proteins from the nucleus to the cytoplasm
Figure 5.28 DNA RNA  protein: a diagrammatic overview of information flow in a cell
NUCLEIC ACIDS ARE POLYMERS OF NUCLEOTIDES
NUCLEOTIDE- made up of 3 parts:
1. nitrogen base
2. a pentose (5 carbon sugar)
3. a phosphate group
There are 2 families of nitrogen bases:
1. pyrimidines- 6 member rings of carbon and nitrogen atoms
The pyrimidines are:
Cytosine (C)
Thymine (T)
Uracil (U)
2. purines- larger, with the six-membered ring fused to a five-membered ring
The purines are:
Adenine (A)
Guanine (G)
Adenine, guanine, and cytosine are found in both DNA and RNA
- Thymine is found only in DNA
- Uracil is found only in RNA
The pentose connected to the nitrogen base in RNA is RIBOSE, and in DNA is DEOXYRIBOSE
- the only difference is that deoxyribose does not have an oxygen on its number 2 carbon
A NUCLEOSIDE is a nitrogen base and a sugar
- to make a complete nucleotide, a phosphate group is attached to the number 5 carbon of the sugar
In a nucleic acid polymer or POLYNUCLEOTIDE nucleotides are joined by covalent bonds
- these are called PHOSPHODIESTER LINKAGES- between the phosphate of one nucleotide and the sugar
of another
- this makes up a backbone of repeating patterns of sugar-phosphate units
Figure 5.29 The components of nucleic acids
- the nitrogen bases stick out along this backbone
Sequences of bases along a DNA polymer is unique for each gene
- the sequence of bases in a gene specifies the amino acid sequence that makes up proteins
INHERITANCE IS BASED ON REPLICATION OF DNA
DNA molecules have 2 polynucleotides that spiral around an imaginary axis to form a DOUBLE HELIX
- James Watson and Francis Crick
- the 2 sugar-phosphate backbones are on the outside of the helix, and the nitrogenous bases are paired
on the inside
- the strands are held together by hydrogen bonds between the paired bases and by van der Waals
interactions between the stacked bases
- Adenine (A) only pairs with thymine (T), and guanine (G) only pairs with cytosine (C)
- by reading the sequence of one strand, you would know the sequence of the other> the strands are
COMPLEMENTARY
- this is what makes the copying of genes for inheritance possible
Figure 5.x3 James Watson and Francis Crick
In preparation for cell division, each of the strands of DNA serves as a template for a new strand
- the result is 2 exact copies of the original DNA molecule which are then distributed to the daughter cells
Figure 5.30 The DNA double helix and its replication