Download Basic organic chemistry of important macromolecules (Lecture 11-12)

Basic organic chemistry of important macromolecules
(Lecture 11-12)
1.What are the organic molecules?
2.Polymer Principles
3.Carbohydrates – Fuel and Building Material.
4.Lipids – Diverse Hydrophobic Molecules.
5.Proteins – The Molecular Tools of the Cell
6.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.
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.
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).
•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.
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.
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.
When two carbons are joined by a double bond, all bonds around those atoms are in the
same plane.
(Notice, for example, that ethane is a flat molecule; its atoms all lie in the same plane.)
Three types of isomers
Compounds with the same molecular formula but different structures.
Isomers are a source of diversity in organic molecules.
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 d-dopa, has no effect on
patients.
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.
Carbohydrates, proteins and nucleic acids are chainlike molecules called polymers.
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.
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.
Polymers are disassembled to monomers by hydrolysis:
bonds between monomers are broken by the addition of water.
Digestion is one form of hydrolysis.
3. Carbohydrates
Carbohydrates have the general formula [CH2O]n where n is a number between 3 and 6.
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.
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).
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).
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).
The α form and β 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.
This energy is released in living organisms in such a way that not enough heat is
generated at once to incinerate the organisms.
One mole of glucose yields 673 Kcal of energy. (A calorie is the amount of heat needed
to raise one gram of water one degree C. A Kcal has 1000 times as much energy as a cal.)
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.
(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.
Disaccharides are formed when two monosaccharides are chemically bonded together.
Sucrose, a common plant disaccharide is composed of the monosaccharides glucose and
fructose.
Lactose (milk sugar) composed of glucose and the monosaccharide galactose.
Polysaccharides are large molecules composed of individual monosaccharide units.
They can be broadly divided to storage (starch) and structural (cellulose).
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).
Glycogen is an animal storage product that accumulates in the vertebrate liver and muscle
cells. It is more extensively branched.
.
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 α and β
glucoses, cellulose (and the animal structural polysaccharide chitin) are made up of only
β glucoses.
Cellulose
The three-dimensional structure of the structural polysaccharides is thus constrained into
straight microfibrils by the uniform nature of the glucoses, which resist the actions of
enzymes (such as amylase) that breakdown storage polysaccharides (such a starch).
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.
(b) The a ring form is the monomer for starch.
(c) Cellulose consists of glucose monomers in the beta configuration. The angles
of the bonds that link the rings make every other glucose monomer "upside
down."
4.
Lipids
Lipids are compounds which grouped together because of following features:
-little or no affinity for water;
-they are not polymers;
-they consist of mostly hydrocarbons.
They are involved mainly in long-term energy storage.
Lipids are composed of three fatty acids (usually) covalently bonded to a 3-carbon
glycerol.
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)
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 nonpolar hydrocarbon “tail” is the reason fats are hydrophobic.
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.
Although the fat shown here has three identical fatty acid units, other fats have two or
even three different kinds of fatty acids.
Saturated and unsaturated 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).
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.
Most animal fats are saturated (lard, butter) and are solid at r.t.
In contrast, the fats of plants and fishes 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.
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.
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".
Two structures of phospholipids in water
(a) A micelle, in cross section.
(b) A cross section of a phospholipid bilayer between two aqueous compartments.
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.
Function
Phospholipids are important structural components of cell membranes. At the surface of a
cell, phospholipids are arranged in a bilayer.
Waxes are an important structural component for many organisms, such as the cuticle,
a waxy layer covering the leaves and stems of many land plants;
and protective coverings on skin and fur of animals.
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.
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 pneumonia-causing form of Chlamydia, and heart attacks.
The plaque increases blood pressure, much the way blockages in plumbing cause burst
pipes in old houses.
6. Proteins
Proteins are very important in biological systems as:
structural support, storage, transport of other substances, signaling, movement and
defense against foreign susbstances.
The building block of any protein is the amino acid, which has an amino end (NH2) and
a carboxyl end (COOH) and R-group.
R-group is the variable component of each amino acid. Alanine and Valine, for example,
are both nonpolar amino acids, but they differ, as do all amino acids, by the composition
of their R-groups.
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.
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.
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.
Four levels of protein structure
Primary structure is a unique amino acid sequence
The secondary structure is the tendency of the polypeptide to coil (a-helix) or pleat
(pleated sheet) due to H-bonding between R-groups.
The tertiary structure is controlled by bonding (or in some cases repulsion) between Rgroups.
Types of bonding that contribute to tertiary structure:
-hydrophobic interaction;
-disulfide bridges (between cysteines);
-hydrogen bond;
-ionic bond.
Many proteins, such as hemoglobin, are formed from one or more polypeptides. Such
structure is termed quaternary structure.
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.
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.
What determines protein conformation?
It a lot dependents on chemical and physical conditions of the protein’s environment.
The loss of native conformation in unfriendly environment is called denaturation,
biological inactivation.
Move from aquatic to organic (chloroform) environment forces the protein to turn inside
out (hydrophobic regions change place with its hydrophilic portions).
Other denaturation agents are: hydrogen, ionic bonds and disulfide bridges disrupting
agents; excessive heat.
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.
Nucleic Acids and the Genetic code
DNA -->RNA --> protein:
In a eukaryotic cell, DNA in the nucleus programs protein production in the cytoplasm by
dictating the synthesis of messenger RNA (mRNA), which travels to the cytoplasm and
binds to ribosomes.
As a ribosome moves along the mRNA, the genetic message is translated into a
polypeptide of specific amino acid sequence.
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).
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.
RNA has ribose as its sugar, and DNA has deoxyribose.
Also, RNA has uracil, and DNA has thymine.
(b) In polynucleotides, each nucleotide monomer has its phosphate group bonded to the
sugar of the next nucleotide.
The polymer has a regular sugar-phosphate backbone with variable appendages,
the four kinds of nitrogenous bases.
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
organisms.
In the process of transcription, the information stored in DNA is copied into ribonucleic
acid (RNA).
The DNA molecule is usually double-stranded, with the sugar-phosphate backbone of
the polynucleotides (abbreviated here by blue ribbons) on the outside of the helix.
In the interior are pairs of nitrogenous bases, holding the two strands together by
hydrogen bonds.
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.
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
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
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.
Reading
CAMPBELL ET AL. BIOLOGY. Ch. 4 (58-67) Ch. 5 (68-91)