AP Biology CMR @ SOHI ‘98 B.Rife page 1 /6
I. Unit 1: The Molecules of Cells - Chapter 3
3.1 Life’s Diversity Is Based On The Properties Of Carbon
Organic chemicals contain at least one carbon atom.
Because there are 4 electrons in the outer shell of carbon, carbon has a strong tendency to fill the shell to 8 by covalently bonding to other atoms, particularly hydrogen, oxygen, and nitrogen.
Methane and other compounds composed of only carbon and hydrogen are called hydrocarbons.
The way bonding occurs among atoms in molecules determines an overall shape.
Isomers are molecules with the same numbers of each atom but with different structural arrangements of the atoms.
3.2 Functional Groups Help Determine The Properties Of Organic Compounds
Functional group - is an assemblage of atoms that form the chemically reactive part of an organic molecule.
These functional groups are generally attached to a carbon backbone (skeleton) of different macromolecules, and they exhibit consistent chemical properties. They behave almost as if they were individual atoms.
All of these functional groups are polar. Therefore, most of the molecules they are found on are polar.
(see table 3.2)
The polarity tends to make compounds containing these groups hydrophilic (water loving) and therefore soluble in water.
Nonpolar molecules tend to be hydrophobic and insoluble
3.3 Cells Make A Huge Number Of Large Molecules From A Small Set Of Small Molecules
Monomer - the fundamental molecular unit.
Polymer - a macromolecule made by linking many of the same kind of fundamental unit (monomers).
MonomerPolymer (Macromolecule)
monosaccharides polysaccharides
glycerol (fatty acids) lipids
amino acids proteins
nucleotides nucleic Acids (DNA, RNA)
Dehydration synthesis (Condensation) - molecules synthesized by loss of a water molecule between reacting monomers; the most common way organic polymers are synthesized.
Hydrolysis - literally, “breaking apart with water”; the most common war organic polymers are degraded.
Life’s chemical reactions occur in particular intracellular and extracellular environments and in controlled ways.
Chapter 4 will discuss the cellular framework on which and in which molecular reactions occur
3.4 Monosaccharides Are The Simplest Carbohydrates
Carbohydrates usually contain carbon and the components of water - hydrogen and oxygen in a 1:2:1 ratio with the general formula (CH2O)n.
Simple sugars are monosaccharides (one sugar) with a carbon backbone that has from three to seven carbon atoms
The hexose sugars: glucose is nearly always used as an immediate energy source in all cells.
fructose is frequently found in fruits
galactose occurs in milk
In solution, many monosaccharides form ring-shaped molecules.
3.5 Cells Link Single Sugars To Form Disaccharides
Cells construct a disaccharide, or double sugar, from two monosaccharides by dehydration synthesis.
Maltose = glucose + glucose
Sucrose = glucose + fructose
3.6 “How Sweet It Is”
Bacteria living in the mouth convert sugars to acids, which eat away tooth enamel.
3.7 Polysaccharides Are Long Chains Of Sugar Units
Using glucose as the monomer, different organisms build several different polymers: plant starch, animal starch (glycogen), and cellulose
Polysaccharides are polymers of a few hundred to a few thousand monosaccharides linked together by dehydration synthesis.
Plant starch has one kind of bond between monomers and is a long relatively unbranched, coiled polymer.
Plant starch is used for long-term energy storage only in plants.
Animals can hydrolyze this polymer to obtain glucose.
Glycogen has the same kind of bond between monomers, but it has relatively more side branches.
Glycogen also is used for long-term energy storage only in animals.
Animals can hydrolyze this polymer to obtain glucose.
Cellulose has a different kind of bond between monomers, forming linear polymers that are cross-linked with other linear chains.
Cellulose is the principal structural molecule in the cell walls of plants and algae.
Animals cannot hydrolyze this polymer to obtain glucose (only certain bacteria, protozoans, and fungi can).
Chitin, found in the exoskeleton of crabs and related animals like lobsters and insects, is also a polymer of glucose (the glucose is modified because there is an amino group attached to each molecule.
3.8 Lipids include Fats, Which Are Mostly Energy-Storage Molecules
In lipids, carbon and hydrogen predominate; there is very little oxygen.
General molecular formula: (CH2)n
Diverse types of lipids have different roles, but all are more or less hydrophobic.
Fats are polymers of fatty acids and glycerol, formed by dehydration synthesis reactions.
Triglyceride is “a fat” consisting of three fatty acids connected to a glycerol molecule.
Saturated fats have no or few double bonds between carbons (the carbons are “saturated” with hydrogen atoms). The molecular backbones are flexible and tend to ball up into tight globules.
Saturated fats like butter and lard are solid at room temperature.
Unsaturated fats include many double bonds between carbons. This causes the molecules to be less flexible and they do not pack into solid globules.
Unsaturated fats like olive oil and corn are liquid at room temperature.
By hydrogenating unsaturated oils, the double bonds are removed and the molecules become more solid at room temperature.
These structurally modified fats are as detrimental as their naturally saturated counterparts in leading to atherosclerotic plaques.
3.9 Phospholipids, Waxes, And Steroids Are Lipids With A Variety Of Functions
Phospholipids contain a phosphate group and this accounts for their name and are a major component of cell membranes.
Phospholipids have nonpolar tails and a polarized head and typically arrange themselves in a double layer in the presence of water.
Waxes are effective hydrophobic coatings formed by many organisms (insects, plants, humans) to ward off water. They consist of a fatty acid linked to an alcohol.
Steroids are lipids with backbones bent into rings.
Cholesterol is an important steroid formed by animals.
Among other things, cholesterol functions in the digestion of fats and as starting material for the synthesis of female and male sex hormones.
3.10 Anabolic Steroids Make Big Bodies And Big Problems
The use of anabolic steroids is linked to a number of medical problems.
3.11 Proteins Are Essential To The Structures And Activities Of Life
The general roles played by proteins include:
1. Structural (hair, cell cytoskeleton)
2. Contractile (as part of muscle and other motile cells, produce movement)
3. Storage (sources of amino acids, such as egg white)
4. Defense (antibodies, membrane proteins)
5. Transport (hemoglobin, membrane proteins)
6. Signaling (hormones, membrane proteins)
7. Catalyst (enzymes, both free and membane-bounded)
Enzymes are organic catalysts that speed up chemical reactions within cells.
Enzymes make “warm chemistry” possible.
3.12 Proteins Are Made From Just 20 Kinds Of Amino Acids
Amino acids are the monomers that undergo condensation to form proteins.
Amino acids are characterized by each having an alpha (“central”) carbon atom covalently bonded to one hydrogen, one amino group, one carboxyl group, and one other chemical group (symbolized by R)
Amino acids differ in the nature of the R group, which ranges in complexity from a single hydrogen to complicated ring compounds.
3.13 Amino Acids Can Be Linked By Peptide Bonds
Using amino acids as monomers, organisms build polymers by dehydration synthesis, forming peptide bonds between each former monomer.
A peptide is two or more amino acids joined together, and a polypeptide is many amino acids joined to form a long chain of amino acids.
Protein peptide bonds can be broken down by hydrolysis, to release free amino acids.
3.14 A Protein’s Specific Shape Determines Its Function
Long polypeptide chains include numerous and various amino acids.
The final structure of a protein, and thus its potential role, depend on the way these long, linear molecules fold up.
Each collection of amino acids folds in a different way under natural conditions.
Unnatural conditions, such as changes in heat, pH, salinity, and so on, can cause proteins to unravel (denaturation)
3.15 A Protein’s Primary Structure Is Its Amino Acid Sequence
Prealbumin is found in blood and is important in the transport of a thyroid hormone and vitamin A
The primary structure of a protein is the sequence of the amino acids joined together by peptide bonds.
Three-letter abbreviations represent amino acids; each amino acid is in a precise order in the chain. In prealbumin, there are four chains, each with 127 amino acids.
3.16 Secondary Structure Is Polypeptide Coiling Or Folding Produced By Hydrogen Bonding
The secondary structure of a protein comes about when the polypeptide chain takes a particular orientation in space.
Hydrogen bonds occur between -NH and -C=O groups of amino acids in sequence along each polypeptide chain.
Depending on where the groups are relative to one another, the secondary structure takes the shape of a coil (alpha helix) or a pleated sheet.
The R groups do not play a role in secondary structure.
3.17 Tertiary Structure Is The Overall Shape Of A Polypeptide
Tertiary structure results from the bonding (hydrogen and ionic) between certain R groups along the coils and pleats.
In prealbumin, the tertiary shape is essentially globular.
3.18 Quaternary Structure Is The Relationship Among Multiple Polypeptides Of A Protein
Many (but not all) proteins consist of more than one primary chain.
Prealbumin consists of four chains,each identical. Other proteins might have all chains different or be additionally complexed with other atoms or molecules.
Within the protein, these separate chains are arranged to give a fourth level of structure termed the quaternary structure. Quaternary bonding is largely by hydrogen bonds.
3.19 Talking About Science: Linus Pauling Has Contributed To Our Understanding Of The Chemistry Of Life
Pauling’s accomplishments are:
First describing the coiled and pleated-sheet secondary protein structures
First describing the structure of hemoglobin and the abnormal form in sickle-cell anemia.
Biological processes of aging and Vitamin C preventing colds (antioxidant)
3.20 Nucleic Acids Are Polymers Of Nucleotides
Every nucleotide is a molecular complex of three types of unit molecules: phosphoric acid (phosphate), a pentose sugar, and a nitrogen base.
Nucleotides have metabolic functions in cells.
ATP (adenosine triphosphate) is a nucleotide used in cells to supply energy for synthetic reactions and various other energy-requiring processes.
Nucleic acids are huge polymers of nucleotides with very specific functions in cells.
DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are nucleic acids, polymers of nucleotides. DNA makes up the genes and along with RNA controls protein synthesis within the cell.
DNA nitrogen bases: double ring purines: adenine (A) & guanine (G)
single ring pyrimidines: thymine (T) & cytosine (C)
RNA nitrogen bases: double ring purines: adenine (A) & guanine (G)
single ring pyrimidines: uracil (U) & cytosine (C)
Hydrogen bonding between nitrogenous bases causes the final structure of the nucleic acid.
In DNA, two linear chains are held together in a double helix.
In RNA, one linear chain may be wrapped around itself in places, forming an RNA or tRNA molecule.