Basic organic chemistry of important
macromolecules
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Structure
1.
2.
3.
4.
5.
6.
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What are the organic molecules?
Polymer Principles
Carbohydrates – Fuel and Building Material.
Lipids – Diverse Hydrophobic Molecules.
Proteins – The Molecular Tools of the Cell
Nucleic Acids – Informational Polymers
1. Organic molecules
Organic molecules are those that:
1) formed by the actions of living things; and/or
2) have a carbon backbone.
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Carbon has four electrons in outer shell, and can bond with
up to four other atoms (usually H, O, N, or another C).
Since carbon can make covalent bonds with another carbon
atom, carbon chains and rings that serve as the backbones
of organic molecules are possible.
Chemical bonds store energy.
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The C-C covalent bond has 83.1 Kcal (kilocalories) per
mole, while the C=C double covalent bond has 147
Kcal/mole.
Energy is in two forms: kinetic, or energy in use/motion; and
potential, or energy at rest or in storage.
Chemical bonds are potential energy, until they are
converted into another form of energy, kinetic energy
(according to the two laws of thermodynamics).
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1. Organic molecules
•
•
Methane (CH4) is an example of this.
If we remove the H from one of the methane units below,
and begin linking them up, while removing other H units,
we begin to form an organic molecule.
(NOTE: Not all methane is organically derived, methane is a
major component of the atmosphere of Jupiter, which we
think is devoid of life).
When two methanes are combined, the resultant molecule is
Ethane, which has a chemical formula C2H6.
Molecules made up of H and C are known as hydrocarbons.
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The shapes of three simple organic molecules.
Whenever a carbon atom has four single bonds, the bonds angle
toward the corners of an imaginary tetrahedron.
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The shapes of three simple organic molecules.
When two carbons are joined by a double bond, all bonds around
those atoms are in the same plane.
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Variations in carbon skeletons
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Hydrocarbons
Three types of isomers
Compounds with the same
molecular formula but different
structures.
Isomers are a source of
diversity in organic molecules.
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The pharmacological importance of
enantiomers.
L-dopa is a drug used to
treat Parkinson's disease,
a disorder of the central
nervous system.
The drug's enantiomer,
the mirror-image
molecule designated ddopa, has no effect on
patients.
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Functional groups in organic molecules.
Small groups of atoms that are frequently bonded to the
carbon skeleton of organic molecules.
Have specific chemical and physical properties.
Are the regions of organic molecules which are
commonly chemically reactive.
Behave consistently from one organic molecule to
another.
Depending upon their number and arrangement,
determine unique chemical properties of organic
molecules in which they occur.
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Functional groups in organic molecules.
Hydroxyl group:
Polar water
soluble.
Carbonyl group:
Polar water
soluble;
Found in sugars.
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Functional groups in organic molecules.
Carboxyl group:
Polar, water
soluble;
Donates protons,
has acidic
properties
Amino group:
Polar, water
soluble;
Act as weak base,
The unshared pair of electrons on the N can accept a
proton, giving the amino group a +1 charge.
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Functional groups in organic molecules.
Phosphate group:
dissociated form
of phosphoric acid
(H3PO4);
negatively
charged and has
acid properties;
polar, water
soluble.
Important in cellular energy storage and transfer.
Sulfhydryl group:
stabilizes the protein structure;
organic compounds with this group are called thiols.
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2. Polymer principles
A polymer is a long molecule consisting of many identical
or similar parts linked by covalent bonds.
The repeating units are called monomers.
Macromolecules: large organic molecules formed from
smaller building block molecules.
Four major classes:
1. Carbohydrates
2. Proteins
3. Lipids
4. Nucleic acids
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Polymer principles
Monomers are connected by a reaction in which two
molecules are covalently linked to each other through loss
of a water molecule: so called condensation (dehydration)
reaction.
Polymers are disassembled to monomers by hydrolysis:
bonds between monomers are broken by the addition of
water.
Digestion is one form of hydrolysis.
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Condensation reaction
Formation of a peptide bond between two amino acids by the
condensation (dehydration) of the amino end of one amino
acid and the acid end of the other amino acid.
The reverse reaction - hydrolysis
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3. Carbohydrates
Carbohydrates – are organic molecules made of sugar and
their polymers.
They have the general formula [CH2O]n where n is a number
between 3 and 6.
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3. Carbohydrates
Carbohydrates function in short-term energy storage (such
as sugar);
as intermediate-term energy storage (starch for plants and
glycogen for animals);
and as structural components in cells (cellulose in the cell
walls of plants and many protists),
and chitin in the exoskeleton of insects and other
arthropods.
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Carbohydrates
Sugars are structurally the simplest carbohydrates.
They are the structural unit which makes up the other types
of carbohydrates.
Monosaccharides are single (mono=one) sugars.
Important monosaccharides include ribose (C5H10O5),
glucose (C6H12O6), and fructose (same formula but different
structure than glucose).
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The structure and classification of some
monosaccharides
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The structure and classification of some
monosaccharides
Depending on the location of the carbonyl group (pink),
sugars may be
aldoses (aldehyde sugars) or
ketoses (ketone sugars).
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The structure and classification of some
monosaccharides
According to the length of their carbon skeletons:
Triose
Pentose
Hexose
A third point of variation is in the spatial arrangement around
asymmetric carbons (compare, for example, the gray
portions of glucose and galactose).
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Linear and ring forms of glucose.
(a) Chemical equilibrium between the linear and ring
structures greatly favors the formation of rings.
To form the glucose ring, carbon 1 bonds to the oxygen
attached to carbon 5.
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Linear and ring forms of glucose.
(b) In this abbreviated ring formula, the carbons in the ring
are omitted.
The ring's thicker edge indicates that you are looking at the
ring edge-on; the components attached to the ring lie above
or below the plane of the ring.
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Carbohydrates
In aqueous solution, glucose tends to have two structures, a
and b, with an intermediate straight-chain form.
The a form and b form differ in the location of one -OH
group. Glucose is a common hexose in plants.
The products of photosynthesis are assembled to make a
glucose. Energy from sunlight is converted into the C-C
covalent bond energy.
One mole of glucose yields 673 Kcal of energy.
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Disaccharides
are formed when two
monosaccharides are
chemically bonded
together.
Sucrose, a common Formation of a disaccharide (top) by condensation
plant disaccharide is
composed of the
monosaccharides
glucose and fructose.
Lactose (milk sugar)
composed of glucose
and the
monosaccharide
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galactose.
Polysaccharides are large molecules composed
of individual monosaccharide units.
They can be broadly divided to storage (starch) and
structural (cellulose).
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Polysaccharides
Starch is a common plant polysaccharide, which is made up
of many glucoses (in a polypeptide these are referred to as
glucans).
There are two forms of starch, amylose (unbranched) and
amylopectin (branched).
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Glycogen is an animal storage product that accumulates in
the vertebrate liver and muscle cells.
It is more extensively branched.
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Structural polysaccharide – cellulose.
Cellulose is a polysaccharide which forms the fibrous part
in plant cell walls.
Cellulose is indigestible, and thus forms an important,
easily obtained part of dietary fiber.
As compared to starch and glycogen, which are each made
up of mixtures of a and b glucoses, cellulose (and the
animal structural polysaccharide chitin) are made up of
only b glucoses.
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Cellulose
The three-dimensional structure of the structural
polysaccharides is constrained into straight microfibrils by
the uniform nature of the glucoses.
It resists the actions of enzymes (such as amylase) that
breakdown storage polysaccharides (such a starch).
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Cellulose Fibers from Print Paper (SEM x1,080).
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Starch and cellulose
structures compared.
(a) Glucose forms
two
interconvertible
ring structures,
designated alpha
and beta.
These two forms
differ in the
placement of the
hydroxyl group
attached to the
number 1 carbon.
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Starch and cellulose
structures compared.
(b) The a ring form is
the monomer for starch.
(c) Cellulose consists of
glucose monomers in
the b configuration.
The angles of the bonds
that link the rings make
every other glucose
monomer "upside
down."
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4. Lipids
Lipids are compounds which grouped together because of
following features:
-little or no affinity for water;
-they are not real polymers;
-they consist of mostly hydrocarbons.
They are involved mainly with long-term energy storage.
Lipids are composed of three fatty acids (usually) covalently
bonded to a 3-carbon glycerol.
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Lipids
Diverse group of organic compounds that are insoluble in
water, but will dissolve in nonpolar solvents (chloform,
benzene).
The fatty acids are composed of CH2 units, and are
hydrophobic/not water soluble.
The three most important families of lipids are:
-fats;
-phospholipids (the major building block in cell
membranes);
-steroids ("messengers" (hormones) that play roles in
communications within and between cells)
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Fat
A fat is constructed from two kinds of smaller molecules:
glycerol and fatty acids.
Glycerol is an alcohol with three carbons, each bearing a
hydroxyl group.
A fatty acid has a long carbon sceleton with the “head”
consisting of a carboxyl group at the end.
Long non-polar hydrocarbon “tail” is the reason fats are
hydrophobic.
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The synthesis and structure of a fat, or
triacylglycerol.
The molecular building blocks
of a fat are one molecule
of glycerol and three
molecules of fatty acids.
(a) One water molecule is
removed for each fatty
acid joined to the
glycerol.
(b) The result is a fat.
The attached fatty acids
may be similar or
different.
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The synthesis and structure of a fat, or
triacylglycerol.
Fats are insoluble in water (hydrophobic because of the
many nonpolar C-H bonds).
Fatty acid composition is the source of variation among fat
molecules
Fatty acids in a fat may be the same or different
Fatty acids may vary in length
Fatty acids may vary in the number and location of carbonto-carbon double bonds.
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Saturated (top and middle) and unsaturated
(bottom) fatty acids.
Fatty acids can be
saturated (meaning
they have as many
hydrogens bonded
to their carbons as
possible) or
unsaturated (with
one or more double
bonds connecting
their carbons,
hence fewer
hydrogens).
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Difference in energy storage: plants
versus animals
Animals convert excess sugars (beyond their glycogen
storage capacities) into fats.
Most plants store excess sugars as starch, although some
seeds and fruits have energy stored as oils (e.g. corn oil,
peanut oil, palm oil, canola oil, and sunflower oil).
Fats yield 9.3 Kcal/gm, while carbohydrates yield 3.79
Kcal/gm.
Fats store six times as much energy as glycogen.
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Difference in energy storage: plants
versus animals
Most animal fats are saturated (lard, butter) and are solid at
r.t.
In contrast, the fats of plants and fish are generally
unsaturated – liquid at r.t.
The reason: the kinks where the double bonds are located
prevent the molecules from packing together closely
enough to solidify at r.t.
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Diet attempt
Diets are attempts to reduce the amount of fats present in
specialized cells known as adipose cells that accumulate in
certain areas of the human body.
By restricting the intakes of carbohydrates and fats, the
body is forced to draw on its own stores to makeup the
energy debt.
The body responds to this by lowering its metabolic rate,
often resulting in a drop of "energy level.“
Successful diets usually involve three things:
-decreasing the amounts of carbohydrates and fats;
-exercise;
-and behavior modification.
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Phospholipids
Phospholipids are similar to fats but have only two fatty acids attached to
glycerol.
Phospholipids are modified so that a phosphate group (PO4-) replaces
one of the three fatty acids normally found on a lipid making a polar
"head" and two nonpolar "tails".
Additional variable group
Phosphate
Glycerole
Fatty acids
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Space-filling model (left) and chain model
(right).
Two structures of phospholipids in water
(a) A micelle, in cross
section.
(b) A cross section of a
phospholipid bilayer
between two aqueous
compartments.
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Two structures of phospholipids in water
Such bilayers are the
main fabric of biological
membranes.
The hydrophilic heads
(spheres) of the
phospholipids are in
contact with water,
whereas the hydrophobic
tails are in contact with
each other and remote
from water.
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Function
Phospholipids are important structural components of cell
membranes.
At the surface of a cell, phospholipids are arranged in a bilayer.
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Steroids:
are lipids characterised by a carbon skeleton
consisting of four fused rings.
Cholesterol is a common component of animal cell
membrane, a precursor of other steroids.
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Negative features
Excess cholesterol in the blood has been linked to
atherosclerosis, hardening of the arteries.
Recent studies suggest a link between arterial plaque
deposits of cholesterol, antibodies to the pneumoniacausing form of Chlamydia, and heart attacks.
The plaque increases blood pressure, much the way
blockages in plumbing cause burst pipes in old houses.
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Proteins
Proteins are very important in biological systems as:
-structural support,
-storage,
-transport of other substances,
-signaling,
-movement and
-defense against foreign susbstances.
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Proteins
The building block of any protein is the amino acid, which has an
amino end (NH2) and a carboxyl end (COOH).
R-group is the variable component of
each amino acid.
Alanine and Valine, for example, are
both non-polar amino acids, but they
differ, as do all amino acids, by the
composition of their R-groups.
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Proteins
All living things (and even viruses) use various combinations
of the same twenty amino acids. A very powerful bit of
evidence for the phylogenetic connection of all living things.
Polymers of amino acids are called polypeptides.
A protein consists of one or more folded and coiled
polypeptides.
Control functions of proteins are carried out by enzymes and
hormones.
Enzymes are chemicals that act as organic catalysts.
Structural proteins function in the cell membrane, muscle
tissue, etc.
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Nonpolar
These amino acids all have nonpolar side chains (R
groups), highlighted in white.
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Charged
amino acids.
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Uncharged
amino acids.
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Peptide
Amino acids are linked together by joining the amino end of
one molecule to the carboxyl end of another.
Removal of water allows formation of a type of covalent bond
known as a peptide bond.
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Four levels of protein structure
Primary structure is a unique amino acid sequence
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Four levels of protein structure
The secondary structure is the tendency of the polypeptide
to coil (a-helix) or pleat (pleated sheet) due to H-bonding
between R-groups.
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Four levels of protein structure
The tertiary structure is controlled by bonding (or in some
cases repulsion) between R-groups.
Types of bonding that contribute to tertiary structure:
-hydrophobic interaction;
-disulfide bridges (between cysteines);
-hydrogen bond;
-ionic bond.
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Four levels of protein structure
Many proteins, such as hemoglobin, are formed from one or
more polypeptides. Such structure is termed quaternary
structure.
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Four levels
of protein
structure
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Four levels of protein structure
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Structural proteins
Structural proteins, such as collagen, have regular repeated
primary structures.
Like the structural carbohydrates, the components determine
the final shape and ultimately function.
Collagens have a variety of functions in living things, such as
the tendons, hide, and corneas of a cow.
Keratin is another structural protein. It is found in fingernails,
feathers, hair, and rhinoceros horns.
Microtubules, important in cell division and structures of
flagella and cilia (among other things), are composed of
globular structural proteins.
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Denaturation and renaturation of a protein
High temperatures or various chemical treatments will
denature a protein, causing it to lose its conformation and
hence its ability to function.
If the denatured protein remains dissolved, it can often
renature when the chemical and physical aspects of its
environment are restored to normal.
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The protein-folding problem
Knowing the primary structure is not enough for predicting
rules of protein folding.
Discovery of chaperone proteins – molecules assisting the
folding of other proteins – helps scientists to understand
protein folding.
If this was achieved, design of the proteins that will carry
out specific tasks would have been possible.
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Nucleic Acids and the Genetic code
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DNA -->RNA -->
protein:
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Nucleic acids are molecules that:
1) contain the information prescribing amino acid
sequence in proteins (DNA) and
2) serve in the several cellular structures that
choose, and then link into the correct order the
amino acids of a protein chain (RNA).
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The structures of nucleotides and polynucleotides.
(a) Nucleotides, the
monomers of nucleic
acids, are themselves
composed of three
smaller molecular
building blocks:
a nitrogenous base
(either a purine or a
pyrimidine),
a pentose sugar,
(either deoxyribose or
ribose),
and a phosphate
group.
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The structures of nucleotides and polynucleotides.
(b) In polynucleotides,
each nucleotide
monomer has its
phosphate group
bonded to the sugar
of the next nucleotide.
The polymer has a
regular sugarphosphate backbone
with variable
appendages,
the four kinds of
nitrogenous bases.
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Deoxyribonucleic acid (DNA)
Cellular library that contains all the information
required to build the cells and the tissues of an
organism.
Genetic information is arranged in genes, hereditary
units controlling specific traits of an organisms.
In the process of transcription, the information
stored in DNA is copied into ribonucleic acid (RNA).
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DNA
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DNA
As illustrated here with symbolic shapes for the
bases,
adenine (A) can pair only with thymine (T),
and guanine (G) can pair only with cytosine (C).
As a cell prepares to divide,
the two strands of the double helix separate,
and each serves as a template for the precise
ordering of nucleotides into new complementary
strands.
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Ribonucleic acid (RNA)
Ribonucleic acid has three distinct roles in protein
synthesis:
- messenger RNA (mRNA) carries the instructions
from DNA that specify the correct order of amino
acids during protein synthesis;
-
transfer RNA (tRNA) with the aid of ribosomal
RNA (rRNA) interprets information from mRNA
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RNA
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Structure of nucleic acids
Similarities:
- in the primary structure both are linear polymers
(multiple chemical units) composed of monomers
(single chemical units), called nucleotides;
-
both consist of only four different nucleotides;
-
nucleotides have a common structure – a phosphate
group linked by a phosphoester bond to a pentose
that is linked to an organic base
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Structure of nucleic acids
Differences:
-
the pentose in RNA is ribose, in DNA is deoxyribose;
-
in one of the four organic bases – thymine (T) in
DNA and uracil (U) in RNA.
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Secondary and tertiary structure of RNA
A. Secondary structure
Doublehelical
stem region
Stem-loop
Hairpin
B. Tertiary structure
5’
5’
Folding
3’
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3’
Pseudoknot
Reading
• CH.4 58-67
• CH.5 68-91
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