Macromolecules
Macromolecules:
• Large molecules – greater than 100,000 daltons
• Polymers – consist of many identical or similar
building blocks
• Building blocks = monomers with molecular
weight 500 daltons.
• Belong to 1 of 4 classes: carbohydrates, lipids,
proteins, nucleic acids.
• All classes of polymers assembled in same
fundamental way
Macromolecules:Carbohydrates
Example: Subunit, function and example
1. Starch: alpha glucose; energy storage in
plants; found in grains, potatoes, corn
2. Glycogen: alpha glucose; energy storage in
animals; liver and muscle
3. Cellulose: beta glucose; structural carb.
Found in cell walls; paper, wood
4. Chitin: modified beta glucose; structural
support, arthropod exoskeleton
Storage Carbohydrates
Macromolecules:Lipids
Example; subunit, function, example
1. Fats; glycerol and 3 fatty acids, energy
storage; butter, lard, seeds
2. Phospholipids; glycerol and 2 fatty acids and a
phosphate group; cell membranes, lecithin.
3. Steroids; 4 fused carbon rings, hormones;
estrogen, testosterone
4. Prostaglandins; ring structure and 2 fatty acids;
cause muscle contractions in labor and
delivery.
Macromolecules: Proteins
General types; subunit; function; example
1. Globular; 20 amino acids; catalysis,
transport; hemoglobin, myoglobin,
protease
2. Structural; 20 amino acids; support;
keratin (hair/nails), collagen (connective
tissue).
Macromolecules:Nucleic Acids
Types; subunits; function; examples
1. Deoxyribose Nucleic Acid (DNA); 4
nucleotides Adenine,
Thymine,Cytosine,Guanine; encode
genes, chromosomes.
2. Ribonucleic Acid (RNA); 4 nucleotides
Adenine, Uracil, Cytosine, Guanine;
needed for gene expression; messenger
RNA, ribosomal RNA, transfer RNA
Polymers
General Principles:
1.
All Living Organisms have the same kind of
monomeric subunits.
2. All macromolecules are assembled the same
fundamental way:
A. Form covalent bonds between 2 subunit molecules
B. An –OH group is removed from 1 subunit and
C. A -H atom is removed from the other
Monomer to a polymer requires energy; process is called
dehydration synthesis or condensation; anabolic
chemical reaction.
General Principles continued
3. All macromolecules are disassembled
into constituent subunits the same way:
A. Molecule of water is added
Polymer changed to monomer with a
release of energy. Name of reaction:
Hydrolysis; catabolic reaction.
Carbohydrates
1.
Most abundant molecules on earth: e.g. cellulose
which is a product of photosynthesis in plants and in
algae.
2.
“Hydrates of Carbon” e.g. glucose
C6H12O6 = C6 (H2O)6
3.
C-H bonds yield energy when broken so ideal for
energy storage.
4.
Simplest are simple sugars: single sugars = fuel
a) Monosaccharides: as little as 3 carbon atoms to as
many as 7 atoms; 6 common. 3 = triose; 5 = pentose;
6= hexose. Either ketone or aldehyde.
Monosaccharides: Simple Sugars
Sugar in water
In water solutions: glucose and most other
sugars form rings (#1 Carbon bonds to O
of #5 Carbon); major nutrient of cells.
e.g. glucose, fructose, galactose (fuel),
ribose, deoxyribose (nucleic acids).
Glucose: Linear and Ring forms
Disaccharides: 2 monosaccharides
joined by glycosidic linkage
Disaccharides are used for transport:
e.g.
Glucose + glucose = maltose
Glucose + galactose = lactose
Glucose + fructose = sucrose
Dissacharide Formation
Storage Polysaccharides
2. Storage in animals: glycogen
Glucose monomers: highly branched;
largely insoluble in water; greater chain
length and more branched than starch.
3. Structural Polysaccharides
a) Cellulose: most abundant organic compound
on earth; major component of cell wall.
Found in plants; confers rigidity and strength.
Most animals cannot digest because of B
glucose. Animals that can digest cellulose
contain bacteria or protists that break B
glycosidic linkage. E.g. termites and ruminants.
Cellulose microfibrils
Chitin: exoskeleton of arthropods;
modified cellulose (amino sugar)
Lipids
1. Contain even more C-H bonds than
carbohydrates.
2. C-H bonds are non-polar and cannot
form hydrogen bonds with water.
3. Hydrophobically excluded by water
molecules – so they cluster together;
insoluble and can be deposited at
specific locations within the organisms.
(Neutral) Fat: Structure
Made up of 2 kinds of
subunits:
a) glycerol (backbone of a
fat molecule); 3 carbon
alcohol.
b) b) Fatty acids: long
hydrocarbon chains
ending in a carboxyl
group.
O
CH3-(CH2)n-C
OH
Generalized formula for a
fatty acid: memorize!
Fatty Acids
• Fatty acids are also called triglycerides or
triacylglycerol.
Consider: saturated (no double bonds)
and unsaturated fatty acids (presence of
double bonds).
Saturated and Unsaturated Fatty
Acids
Fats as storage molecules
•
•
•
•
•
More energy/gram
Insoluble in water
Take up less space
Excellent for long term storage
Also used for insulation and buoyancy
Phospholipids
Composed of glycerol, 2 fatty acids and a
phosphate group.
Polar head and Nonpolar tails.
Major lipid in lipid bilayer of plasma
membrane.
In water, phospholipids self-assemble into
micelle. Hydrophilic head on outside.
Hydrophobic tail on inside.
Phospholipids
Phospholipid organization
Steroid: 4 fused rings e.g.
Cholesterol
• Glycerol + fatty acid – water = glyceride
• Glyceride + water = Glycerol + fatty acid
1.
1.
2.
3.
4.
Types Of Proteins
Class = Enzymes; Function= metabolism
e.g. amylase, a digestive enzyme (Globular)
polymerases, produce nucleic acids
Class = Globins; Transport through body
e.g. hemoglobin carries oxygen in blood
myoglobin carries oxygen in muscle
(Globular)
Class = Structural support: (fibers)
e.g. Keratin (hair, nails), collagen (cartilage),
fibrin (blood clots). (Fibrous)
Class = Hormones; regulation of body function
e.g. Insulin (controls blood glucose levels);
oxytocin (stimulates uterine contractions) Glob.
More types of proteins
5. Movement; Muscle proteins; e.g. actin and
myosin for contraction of muscle fibers.
(Fibrous).
6. Storage: Ion binding; e.g. ferritin which stores
iron especially in spleen; casein which stores
ions in milk. (Globular)
7. Defense: Immunoglobins and toxin; e.g.
antibodies which mark foreign proteins for
elimination and snake venom which blocks
nerve function.(Globular)
Structure: polymers made up of 20
amino acids
Amino acid: molecule with an amino group
and a carboxyl group; R = atom or atoms
which make up the variable group.
Specific to each of the 20 amino acids.
H
N
H
R
C
H
O
C
OH
memorize
Chemical classes of amino acids
based on R
a) Non-polar: R = -CH3; folded into interior of
protein by hydrophobic exclusion. Perfect for
the outside of proteins that have to fit in a
membrane (membrane channels and pumps).
b) Polar uncharged: R groups with O; hydrophilic.
Perfect for outside of enzymes; or to line
tunnels for polar/ionic molecules placed in
membranes.
c) Polar charged (Ionizable): R groups contain
acids or bases. Hydrophilic.
Nonpolar amino acids
Polar Amino Acids
Peptide Bond
Bond between amino
acids formed from
dehydration synthesis
or condensation
reaction. Called
peptide bond.
• Note repetitive
polypeptide backbone
N-C-C-N-C-C-N
• Amino acid + amino acid – water =
dipeptide
• Dipeptide + amino acid – water =
polypeptide
• Polypeptide + water = dipeptide + amino
acid
Lysozyme: Ribbon and Space filled
models
Protein Structure
• 1st elucidated was myoglobin (Linus
Pauling), 2nd was hemoglobin
• Primary structure: unique sequence of
amino acids determined by inherited
information: DNA
RNA
Protein
Primary Structure of Lysozyme,
129 amino acid sequence
Red Blood Cells: Normal and
Sickled hemoglobin; valine
replaces glutamic acid at #6
Secondary Structure
• Refers to the local conformation of some part of
the polypeptide.
• Result of hydrogen bonds
• Get folding
• Two very stable secondary structures occur
widely in proteins:
1. The alpha helix (coil) 2. beta pleated sheet.
Bonds between 2 chains linking the amino acids
in one chain to those in the other in the same
protein.
Secondary Structures of Proteins
Secondary Structure
• Definition: The folding of the amino acid chain
by hydrogen bonding into these characteristic
coils and pleats is called a protein’s secondary
structure.
• Supersecondary structure: Motifs. Beta Alpha
Beta motif creates a fold or crease.
Beta Barrel: a beta sheet folded around to form a
tube.
Alpha turn Alpha; many proteins uses it to bind
to the DNA double helix.
Tertiary Structure:
• Final folded shape of a protein which positions
the various motifs and folds nonpolar side
groups into the interior. Nonpolar groups fit
together snugly, leaving no holes. Small
changes in amino acids can greatly change the
3-D nature of a protein.
• A protein is driven into its tertiary structure by
hydrophobic interactions with water.
• Also important are strong covalent bonds called
disulfide bridge which form when 2 cysteine
monomers are brought close together by the
folding of the protein (use sulfhydryl groups).
Tertiary Structure of a Protein
Quarternary Structure
• A protein’s subunit arrangement (not all
proteins have a quarternary structure).
Occurs when 2 or more polypeptide chains
form a functional protein.
• E.g. hemoglobin is a protein composed of
two alpha-chain subunits and two betachain subunits. Quarternary structure can
bind prosthetic groups such as iron.
• This kind of protein is a conjugated protein
Quarternary Structure of Protein
with Prosthetic Group (hb)
Factors affecting protein structure
a) Physical and chemical conditions such as pH,
salt concentration, temperature. Can cause
the unraveling of protein: denaturation (think
egg white cooked). Protein’s loss of its 3-D
structure.
b) Presence of chaperone proteins; normal cells
contain more than 17 different kinds of proteins
that act as molecular chaperones…they seem
to rescue proteins that are misfolded.
Summary of Protein Structure
Protein Denaturation: Loss of 3-D
structures
Chaperonin: Chaperone proteins to
assure proper folding of proteins
Nucleic Acids
1. Function: to store and transmit
hereditary information.
2. Types: DNA – deoxyribonucleic acid;
hereditary material
RNA – ribonucleic acid; reads the
cell’s DNA-encoded information and
directs the synthesis of proteins
Nucleotide components of DNA
and RNA
Structure of DNA
Long polymers of repeating subunits called nucleotides
Nucleotides: a) a five-carbon sugar (pentose) either
deoxyribose or ribose (memorize the ring structure of
ribose).
b) a phosphate group
c) an organic nitrogen-containing base (nitrogenous
base); 2 families of bases: pyrimidine (6-membered ring)
and purine (6-member ring fused to 5-member ring).
DNA: Cytosine, Thymine (pyrimidines); Adenine and
Guanine (purines)
RNA: thymine is replaced by Uracil
Bond: phosphodiester covalent bond between the
phosphate of one nucleotide and the sugar of the next
monomer. (Formed through dehydration-synthesis and
removal of a water).
Backbone of polymer: sugar-phosphate-sugar-phosphate
DNA Molecule
• Double helix (Watson and Crick, 1953). 2
chains of nucleotides with sugar and
phosphate on the outside (hydrophilic) and
nitrogenous bases on the inside
(hydrophobic).
• Precise pairing of bases such that A = T
and C = G. Chains held together with
hydrogen bonds. Each strand is the
template of the other strand.
• Strands run anti-parallel to one another.
DNA Double Helix
Watson and Crick
Rosalind Franklin
Chitin Monomer: modified B
glucose
Cellulose digestion as the result of
gut bacteria in rumen
1. Be able to identify:
2. List 3 examples of
• Compound
Example
Monosaccharide
• Glucose, Galactose, Fructose
Disaccharide
• Maltose, Sucrose, lactose
Polysaccharide
• Starch, Cellulose, glycogen
3. Functions of Carbs in
Animals
• Glucose = carried by blood to transport
energy to cells throughout body.
• Lactose = sugar in milk, provides energy
to young mammals until weaned
• Glycogen= short-term energy storage in
liver and in muscles.
3. Functions of carbs in plants
• Fructose = used to make fruit sweettasting, attracting animals to disperse
seeds in fruit.
• Sucrose = Plants transport energy to cells
throughout plant in phloem. (From sugar
source to sugar sink.)
• Cellulose = Basic structural unit of the
plant cell wall: used to make strong fibers.
4. Functions of Lipids
1. Energy Storage – fat in humans, oils in
plants
2. Building membranes – phospholipids and
cholesterol form membrane structure
3. Heat insulation – layer of fat under the
skin reduces heat losses
4. Buoyancy – lipids less dense than water
so help animals float
5. Compare the use of carbohydrates and
lipids in energy storage
Carbohydrates
Lipids
• More easily digested
• More energy per
providing rapid
gram
energy release
• Lighter storage
• Water soluble so easy
method for same
to transport and store
amount of energy.
• Insoluble in water.
6. Outline the role of condensation and hydrolysis
in the relationships between:
•
•
Condensation Reactions
– 2 Amino Acids  Dipeptide +
Water
– Many amino acids 
Polypeptide + Water
– Monosaccharides  Di or
Polysaccharides +
Water
– Fatty acids + Glycerol 
Glycerides + water
Hydrolysis Reactions
– Polypeptides + Water 
Dipeptides or AAs
– Polysaccharides + Water 
Di or monosaccharides
- Glycerides + water  Fatty
acids + Glycerol
7. Structure of proteins
Primary Structure: sequence
of amino acids
Quarternary Structure
8. Fibrous vs. Globular proteins
•
•
•
•
•
•
•
•
•
Shape: fibrous = long, narrow
globular = rounded
Solubility in water: fibrous = insoluble
globular = soluble
Function: fibrous = structural
globular = enzymes, transport,
defense
Examples: fibrous = collagen, keratin, myosin
globular = catalase, hemoglobin, insulin
9. Significance of Non polar and
polar amino acids
Polar and Non-polar amino
acids in proteins
• Outside membranes
• 1. Polar aa on surface:
water soluble
• 2. Nonpolar aa on inside:
stabilize structure.
• 3. Superoxide
dismutase: directs
substrate to active site.
• 4. Lipase: active site is
non-polar/ outside is polar
• Inside membranes
• 1. Polar aa when in
contact with water
(cytoplasm + extracellular
matrix) to create channel
for hydrophilic
substances.
• 2. Non-polar aa cause
proteins to remain
embedded in
membranes.
10. State 4 Functions of
proteins with example of each
•
•
•
•
•
•
Enzymes
Structural
Transport
Movement
Hormones
Defense
11. 12. Outline DNA nucleotide
structure (RNA?)
Nucleotides: a) a five-carbon sugar
(pentose) either deoxyribose or ribose
(memorize the ring structure of ribose).
b) a phosphate group
c) an organic nitrogen-containing base
(nitrogenous base); 2 families of bases:
pyrimidine (6-membered ring) and purine
(6-member ring fused to 5-member ring).
DNA: Cytosine, Thymine (pyrimidines);
Adenine and Guanine (purines)
RNA: thymine is replaced by Uracil
13. Outline how DNA nucleotides are linked
together by covalent bonds
Bond: phosphodiester covalent bond
between the phosphate of one nucleotide
and the sugar of the next monomer.
(Formed through dehydration-synthesis
and removal of a water).
Backbone of polymer: sugar-phosphatesugar-phosphate
14. Explain how a DNA double helix is formed
using complementary base pairing and hydrogen
bonds. 15. Draw and label.
• Precise pairing of
bases such that A = T
and C = G. Chains
held together with
hydrogen bonds.
Each strand is the
template of the other
strand.
• 2 H bonds between A
and T; 3 between C
and G
15. Draw and label
• Include these labels:
1. Phosphate group
2. Deoxyribose sugar
3. Nitrogenous base
4. Purine, Pyrimidine
5. Adenine, Thymine, Guanine, Cytosine
6. H bond
7. Nucleotide
8. Phosphodiester Bond
9. Antiparallel strands
10. 3’ end; 5’ end
7.6.1 Characteristics of
Metabolic Pathways
• Sequence of chemical reactions
• Could be chains: eg.
• Glycolysis; synthesis of amino acids;
synthesis of DNA
• Could be cycles where substrate
continually regenerated by the cycle: eg.
• Krebs and Calvin
7.6.2 Models of EnzymeSubstrate Specificity
Lock and Key
Fit between the shape and
chemistry of its active site
and the shape of the
substrate described as
lock (enzyme) and key
(substrate).
Implies rigidity. Shape is
not flexible.
Each enzyme only binds to
one substrate.
• Induced Fit: more like a
handshake. Active site is
rigid; as substrate enters
the active site, it is
induced to change shape
by the substrate. Result:
active site fits even more
snugly around the
substrate. An enzyme
might bind >1 substrate.
Accounts for the broad
specificity of some
enzymes.
Advantage of Induced Fit:
• Induced fit brings chemical groups of the
active site into positions that enhance their
ability to work on the substrate and
catalyze the chemical reactions.
7.6.3 Explain how enzymes
catalyze chemical reactions
7.6.4. Types of Inhibitors with
Examples
• Chemicals other than intended reactant
bonded to the active site or changing the
shape of the active site.
• Two general types: Competitive and
Noncompetitive
Competitive vs. Non-competitive
inhibition
Eg. Competitive Inhibitors
• An inhibiting molecule structurally similar
to the substrate molecule binds to the
active site, preventing substrate binding.
Eg. Inhibition of folic acid synthesis in
bacteria by the sulfonamide (antibiotic)
Prontosil. E.g. Carbon monoxide binds to
the active site of hemoglobin and is a
competitive inhibitor that binds irreversibly.
• See page 86 in new textbook
• See page 70 in review guide
Competitive Inhibitor
• Always give 1) Inhibitor 2) Enzyme it
inhibits
• Malonate inhibits Succinate
dehydrogenase which should bind
succinate and turn it into fumarate in
Krebs Cycle
• Antibiotic, Prontosil (sulfur drug), inhibits
Folic Acid synthesis enzyme
(dihydropteroate synthetase) in bacteria.
Usually binds to PABA
Non-competitive Inhibitor
• Always give Inhibitor and what it interferes with
• E.g. Opioids (morphine) are inhibitors of the
enzyme nitric oxide synthase which should bind
arginine.
• Nitric oxide is a signalling molecule.
• E.g. Eg. Metal ions disrupting disulfide bridges in
many enzymes including cytochrome oxidase
(enzyme in electron transport chain). Hg2+, Ag+,
Cu2+ bind to –SH groups, breaking –S-Slinkages; changes shape of the active site.
7.6.5 Explain the control of
Metabolic pathways.
7.6.5 Explain the control of
metabolic pathways.
• E.g. End-product inhibition. Name the enzyme, the endproduct that turns it off.
• Phosphofructokinase turned off by ATP; one of the first
enzymes active in glycoslysis.
• Binding site: On-off switch
• Allosteric site
• Advantage:
• Do not accumulate unneeded intermediates.
• An example of:
• Negative feedback
E.g. Threonine to isoleucine
• Isoleucine turns off the enzyme threonine
dehydratase which catalyzes the first
chemical reaction in the conversion of
threonine to isoleucine.