AP Biology 2005-2006: October 2005

Chapter 3-The Chemistry of Organic Molecules

3.1 Organic Molecules

the most common elements in living things are carbon, hydrogen, nitrogen, and oxygen, which constitute about 95% of body weight
sameness and diversity of life are dependent upon carbon
organic molecules-molecules created by the bonding of hydrogen, oxygen, nitrogen, and other atoms to carbon
organic molecules always contain carbon and hydrogen, have covalent bonds, may be quite large with many atoms, and are usually associated with living organisms
organic molecules characterize structure and function of living things
inorganic molecules-nonliving matter
inorganic molecules usually contain positive and negative ions, have ionic bonding, always contain a small number of atoms, and are often associated with nonliving matter
living things are highly organized and are all composed of: carbohydrates, proteins, lipids, and nucleic acids
carbon has 4 electrons in its outer shell, so it can bond with as many as four other atoms; if the bonds are covalent, they are even stronger
carbon usually bonds with hydrogen, oxygen, nitrogen, or another carbon atom

as carbon can bond with itself, carbon chains of various lengths and shapes results
carbon can also share two pairs of electrons with another atom, giving a double covalent bond

carbon-to-carbon bonds can result in ring compounds of biological significance

functional groups-clusters of certain atoms that always behave in a certain way that can be attached to the carbon chain

hydroxyl
carboxyl
ketone
aldehyde
amino
sulfhydryl
phosphate

hydrophobic-not attracted to water
molecules composed of only carbon and hydrogen are hydrophobic
hydrophilic-attracted to water
polar molecules that are able to interact with other polar molecules are hydrophilic
since cells are 70-90% water, the ability to interact with and be soluble in water profoundly affects the function of organic molecules in cells
organic molecules containing carboxyl groups (--COOH) are both polar and acidic, the tend to ionize and release hydrogen ions in solution --COOH → --COO^- + H⁺
functional groups determine the polarity of organic molecules and also the types of reactions it will undergo
isomers-molecules with identical molecular formulas but are different molecules because the atoms in each are arranged differently
four classes of organic compounds in living things are lipids, proteins, carbohydrates, and nucleic acids
polymers-huge chains of unit molecules (polysaccharides, polypeptides, nucleic acids)
monomers-unit molecules (monosaccharides/single sugars, amino acids, nucleotides)
polymers can be so large that they are called macromolecules
monomers bond through condensation synthesis
condensation synthesis-a hydroxyl (--OH) is moved from one monomer and a hydrogen (--H) is removed from another, water is given off (condensation) and a bond is made (synthesis).
condensation synthesis cannot take place unless the proper enzyme is present and the monomers are in activated energy rich form
polymers are broken down by hydrolysis
hydrolysis-the reverse of condensation synthesis, water is added, an --OH group from water attaches to one monomer and an --H from water attaches to the other monomer, so water is used to break the bond
hydrocarbon chains are hydrophobic. When it has an attached ionized functional group such as carboxyl (--COOH), then that end of the molecule is hydrophilic.
polar molecules (with +/- charges) are hydrophilic... that's why they're attracted to water molecules. Nonpolar molecules are hydrophobic... that's why they're repelled by water (incapable of being dissolved in water).

3.2 Carbohydrates

carbohydrates-molecules that bear many hydroxyl groups (CH₂O)

monosaccharides (one sugar), disaccharides (two sugars bonded together), polysaccharides (starches like cellulose and glycogen)

sugars and some polysaccharides serve as energy storage compounds
cellulose is the most abundant organic compound on Earth because it supports plant cell walls
carbohydrates attached to cell wall surfaces are specific to the individual and antigenic to certain other individuals
monosaccharides-simple sugars with a carbon backbone of three to seven carbon atoms
hexoses-the best known sugars with 6 carbons

glucose-6 carbon sugar in the blood of animals
fructose-6 carbon sugar found in fruits
these two are isomers of each other: they both have C₆H₁₂O₆, but differ in structure

structural differences cause molecules to vary in shape, which is very important in determining how molecules interact with one another
pentoses-5 carbon sugars

ribose-found in RNA
deoxyribose-found in DNA

disaccharide-containts two monosaccharides joined by condensation

lactose-disaccharide that contains galactose and glucose and is found in milk
maltose-disaccharide composed of two glucose molecules found in the digestive tract as a result of starch digestion

sucrose-disaccharide that contains glucose and fructose; sugar is transported within the body of a plant in the form of sucrose, table sugar

disaccharides dissolve in water
polysaccharides-long polymers of monosaccharides formed by condensation synthesis
the most common polysaccharides in living things are starch, glycogen, and cellulose, which are chains of glucose molecules.. also chitin (modified glucose molecule)
glycogen-characterized by many branches/side chains of glucose
starch-fewer branches than glycogen
branching allows the breakdown of starch and glycogen to proceed at several points simultaneously; once glucose is released, it is used directly as an energy source
the orientation of the bond in starch and glycogen allows these polymers to form compact spirals, making polymers suitable as storage compounds
plants stoor sugar as starch within the cell, as roots, and as seeds
during seed germination, starch is brokwn down into maltose and then glucose which provides energy for growth
animal cells store extra carbohydrates as glycogen (muscles and liver join glucose molecules), between meals the liver releases glucose to keep the blood concentration of glucose near the normal 0.1% which moves from the blood into cells to participate in cellular metabolism
cellulose-glucose molecules that are joined together differently than in starch and glycogen, the polymers are straight and fibrous, long and unbranched, held together by hydrogen bonding within microfibrils which in turn make up a cellulose fibril
cellulose fibrils lie parallel in layers, which lie in angles, making plant cell walls stronger

cotton fibers are almost pure cellulose
wood contains a high percentage of cellulose

most animals digest little cellulose because digestive enzymes are unable to break the linkage, but it helps the body maintain regularity of elimination
cattle and sheep have a special stomach chamber, the rumen, where bacteria live that can digest cellulose
chitin-a polymer of glucose found in the exoskeletons of crabs and related animals like lobsters and insects

each glucose unit has an amino group attached to it
suture thread

3.3 Lipids

lipids-fats, insoluble in water because they lack polar groups, most familiar are found in fats and oils
fats are utilized for insulation and energy reserves
phospholipids and steroids (can serve as hormones) are components of the plasma membrane
fats and oils contain fatty acids and glycerol
fatty acid-a long hydrocarbon chain with a carboxyl acid group at one end

most contain 16-18 carbon atoms per molecule

because the carboxyl group is polar, fatty acids are soluble in water
saturated fatty acids-no double bonds between carbon atoms
unsaturated fatty acids-double bonds in the carbon chain wherever the number of hydrogens is less than two per carbon atom
glycerol-compound with three hydroxyl (--OH) groups, soluble in water
when a fat is formed, the acid portions of fatty acids react with these hydroxyl groups, resulting in water molecules

condensation synthesis reaction, fat can be hydrolyzed to its components

triglycerides-some fats and oils; there are three fatty acids per glycerol molecule, they lack polar groups and do not mix with water
triglycerides containing fatty acids with unsaturated bonds melt at an even lower temperature than those containing faty acids with saturated bonds
double bonds makes a kink that prevents close packingin general, fats are solid at room temperature and of animal origin and oils are liquid at room temperature and of plant origin
nearly all animals use fat in preference to glycogen for long-term energy storage
waxes-long chain fatty acids bonded with long-chain alcohol
waxes are solid at normal temperatures because they have a high melting point, hydrophobic, waterproof, resistant to degradation

cuticle
skin, fur maintenance, ear wax
honey comb

phospholipids-constructed like neutral fats except with a phosphate group or a grouping containing phosphate and nitrogen in place of a third fatty acid
the phosphate group becomes the polar head, while the hydrocarbon chains become the nonpolar tails
the plasma membrane which surrounds cells is a phospholipid bilayer in which the polar heads face outward into a watery mdeium and the tails face each other because they are water repelling
steroids-lipids that have an entirely different structure than that of fats, as they have a backbone of four fused carbon rings, each differing primarily by the types of functional groups attached to the rings
cholesterol is a component of animal cells plasma membranes and the precursor of several other steroids, such as estrogen and testosterone

3.4 Proteins

protein-composed of one or more polypeptides (polymers of amino acids)
proteins perform many functions

support: keratin, which makes up hair and nails; collagen, lends support to ligaments and tendons; skin
enzymes: bring reactants together and speed chemical reactions in cells, specific for one particular type of reaction and can function at body temperature
transport: channel proteins in the plasma membrane allow substances to enter and exit cells, carrier proteins transport molecules into and out of the cell or in the blood of animals (e.g. hemoglobin, which transports oxygen)
defense: antibodies are proteins that combine with antigens/foreign substances to prevent antigens from destroying cells and upsetiting homeostasis
hormones: regulatory proteins that serve as intercellular messengers that influence the metabolism of cells, insulin regulates the content of glucose in blood and in cells (e.g. the presence of growth hormone determines the height of an individual)
motion: contractile proteins actin and myosin allow parts of cells to move and cause muscles to contract, which accounts for the movement of animals from place to place

vertebrate cells function differently according to the type of protein they contain

muscle cells contain actin and myosin
red blood cells contain hemoglobin
support cells contain collagen, etc.

amino acid-a carbon atom bonded to one hydrogen atom and in addition three groups of atoms (amino group --NH2, acidic group --COOH, and R remainder of the molecule)
amino acids differ according to their R group
there are 20 different amino acids commonly found in cells because there are 20 different R groups
peptide bond-the resulting covalent bond between two amino acids joined by a condensation reaction between the carboxyl group of one and the amino group of another
the atoms associated with the peptide bond share the electrons unevenly because oxygen is more electronegative than nitrogen, so the hydrogen attached has a slightly positive charge while the oxygen has a slightly negative charge; this polarity means that hydrogen bonding is possible between the --CO of one amino acid and the --NH of another amino acid in a polypeptide
peptide-two ore more amino acids bonded together
polypeptide-chain of many amino acids joined by peptide bonds
a protein can have up to four levels of structure
fibrous proteins have to specific tertiary structure and many proteins have no quaternary sutrcture
the primary structure of a protein is the sequence of the amino acids joined by peptide bonds
when amino acids join together a polypeptide results, the primary structure is a polypeptide with its own particular sequence of amino acids
1953, Frederick Sanger determined the amino acid sequence of the hormone insulin by first breaking insulin into fragments and then determining the amino acid sequence of the fragments before determining the sequences of the fragments themselves
the secondary structure of a protein occurs when segments of a polypeptide coil or fold in a particular way
Linus Pauling and Robert Corey concluded that the coiling was an α helix and the pleated sheet was called a β sheet in the late 1930s
hydrogen bonding holds the secondary structure in place

for the α helix, hydrogen bonding between every fourth amino acid accounts for the spiral shape of the helix
for the β sheet, the polypeptide turns back upon itself and hydrogen bonding occurs between extended lengths of the polypeptide

in keratin, α helices are covalently bonded to one another by disulfide linkages (--S--S--) between two cysteine amino acids. When you get a perm, the hair is rolled and a reducing agent is used to break the present disulfide bonds, which become two --SH groups instead. When the agent is removed, newly formed disulfide bonds make the hair curly
tertiary structure is a folding and twisting that results in the final 3-D shape of a polypeptide
hydrogen bonds, ionic bonds, and covalent bonds all contribute to the tertiary structure of a polypeptide
strong disulfide linkages help maintain the tertiary shape
hydrophobic reactions are when hydrophobic R groups don't bond with other R groups and instead collect in a common region where they are not exposed to water, and though they aren't bonds they are very important in creating and stabilizing the tertiary structure
some proteins have a quaternary structure because they consist of more than one polypeptide, such as hemoglobin
temperature and pH can bring about a change in polypeptide shape

the addition of acid to milk causes curdling
heating causes egg white, which consists mainly of a protein called albumin, to congeal/coagulate

denatured-a protein that has lost its normal configuration
denaturation occurs because the normal bonding patterns between parts of a molecule have been disturbed
each type of enzyme is specific to the reaction it speeds
when an enzyme is denatured it can no longer bring the substrates, which are the reactants, together for the reaction to occur
enzymes work best at body temperature and each one also has an optimal pH at which the rate of the reaction is highest, at which it has its normal shape
a change in pH can change the polarity of R groups and disrupt the normal interactions that maintain the normal shape of the enzyme
if the conditions which caused denaturation were not too severe, and these are removed, some proteins regain the normal shape and biological activity

3.5 Nucleic Acids

nucleic acids-polymers of nucleotides with very specific functions in cells
DNA (deoxyribonucleic acid)-genetic material that stores information regarding its own replication and the order in which amino acids are to be joined to make a protein
RNA (ribonucleic acid)-another type of nucleic acid, important in the process of protein synthesis

mRNA is an intermediary

ATP (adenosine triphosphate)-a nucleotide that supplies energy for synthetic reactions and for various other energy-requiring processes in cells
nucleotide-complex of three types of molecules: phosphate (phosphoric acid), a pentose sugar, and a nitrogen-containing base

in DNA the pentose sugar is deoxyribose
in RNA the pentose sugar is ribose

the base of a nucleotide can be a pyrimidine with a single ring or a purine with a double ring

in DNA the bases are cytosine and thymine
in RNA the bases are uracil and cytosine
in both DNA and RNA the purine bases are adenosine or guanine, they are called bases because their presence raises pH

nucleotides join in a definite sequence when DNA and RNA form by condensation synthesis
polynucleotide-a linear molecule called a strand in which the backbone is made up of a series of sugar-phosphate-sugar-phosphate olecules
since the nucleotides occur in a definite order, so do the bases, which project to one side of the backbone
RNA is single stranded
DNA is double stranded in the shape of a double helix
the two strands are held together by hydrogen bonds between pryimidine and pruine bases
complementary base pairing

thymine is always paired with adenine

guanine is always paired with cytosine

ATP-a nucleotide in which adenosine is composed of adenine and ribose
ATP is a high-energy molecule because the last phosphate bonds are unstable and easily broken
in cells the terminal phosphate bond is hydrolyzed to give the molecule ADP (adenosine diphosphate) and a molecule of inorganic phosphate
the energy released by ATP breakdown is coupeld to energy requiring processes in the cell

synthesis of macromolecules (carbohydrates and proteins)
muscle contraction
conduction of nerve impulses

ATP is sometimes called the energy bond, symbolized by a wavy line, ebcause it releases energy when the last phosphate bonds are hydrolyzed, but the products of hydrolysis are more stable than ATP (ADP and inorganic phosphate)
the entire molecule releases energy, not just the bond

AP Biology 2005-2006

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