Chapter 3 – The molecules of life
Organic Molecules – Carbon-based molecules
Carbon is unparalleled in it’s ability to form large. Complex, diverse molecules necessary for life
Organic compounds – compounds that contain carbon – organic chemistry.
Carbon has a versatile ability to bond w/ many types of elements – due to the fatc that C has 4
electrons in it’s outmost shell. Carbon completes its outer shell by sharing electrons with other atoms in
4 covalent bonds.
A carbon atom can also bond with other carbon atoms creating an endless diversity of carbon
skeletons (FIG 3.2, p37).
The carbon atoms of other organic molecules can bond with other elements most commonly O,
H, and N.
The simplest organic compounds are hydrocarbons which contain only carbon and Hydrogen.
The simplest hydrocarbon is methane = 1 C 4 H. Methane is just 1 example of many hydrocarbons
produced by prokaryotes in swamps, sewage systems, and digestive tracts.
Hydrocarbons are also important fuels – ancient hydrocarbons in the earth.
Hydrocarbons are alos fuel sources for living organisms (fat).
The unique properties of various hydrocarbons are due to functional groups (FIG 3.5, P38).
Functional groups for Biology - hydroxyl (OH), carbonyl (C=O), amino (H-N-H), carboxyl
Functional groups give an organic compound it’s reactive properties.
Macromolecules – BIG biological molecules are made from the uniting of smaller organic ones.
Monomer + Monomer = Polymer – made possible by dehydration reactions facilitated by cells.
These polymers are broken down through hydration reactions i.e., hydrolysis.
4 Macromolecules – Carbs, Lipids, Proteins, Nucleic Acids
Carbohydrates – primary source of energy for animals – in plants for energy reserves and
structural parts. There are >30 different carbohydrates in 3 main groups mono-di-poly
Carbohydrates are polymers made up of simple sugars monomers –– monosaccharides.
Monosaccharide – single sugar
Glucose and Fructose – isomers (Fig 3.8 p39). Same molecular formula but different
arrangement of functional groups – in biological systems, shape is important.
Fructose taste sweeter than glucose – shape is everything to receptors.
Sugars are linear in shape but form ring structures in solution.
Monosaccharides are the main energy for cellular work.
Monosaccharides also provide cells w/ carbon skeletons used as raw material for constructing
other kinds of organic molecules.
Disaccharide - double sugar
Formed by a dehydration reaction (FIG 3.10 p40).
e.g., maltose = 1 glucose + 1 glucose – found in germinating seeds and used for making beer,
malt whiskey, malted milk shakes, and malted milk ball candy
lactose = 1 glucose + 1 galactose – milk sugar
lactase breaks down lactose – lactose intolerance
sucrose = 1 glucose + 1 fructose = table sugar – common in plants
cane sugar, beets,
SO FAR We have talked about the “sugars” = mono & di- saccharides. They are important sources of
fuels for cellular work HOWEVER, they represent empty calories – you do not get any nutrition from
them. The only carbs that provide nutrition are Polysaccarides. A healthy diet also includes proteins,
fats, vitamins, minerals.
Polysaccharides – complex carbohydrates – long chains of sugars.
Polysaccharide – Polymer monosaccharide = monomer
Starch – glucose monomers strung together (FIG 3.13, p41) – plants store starch
as a reserve to be broken down into the fuel (sugar – monosaccharide) when the cells of the
plant needs it. E.G., potatoes & grains are sources of starch – the digestive tract breaks the
starch down into sugars for fuel through hydrolysis.
Glycogen – similar to starch only more extensively branched. Animals store
glycogen in the liver – when an excess of sugars are ingested but not use for immediate fuel,
they are linked together and stored as granules in our liver. When our body later needs
immediate fuel, the glycogen granules are broken down into the monosaccharides and released
into the bloodstream. This is what happens when you “carb-load”
Cellulose – The most abundant organic compound on earth. A highly branched
network of glucose monomers. Similar to starch and glycogen but the glucose
monomers are linked in a different orientation which cannot be broken down by most
animals’ digestive tracts.
Used as a structural component of plant cell walls – wood.
Since cellulose remains unchanged in the digestive tract, it passes out
unchanged = roughage – dietary fiber.
Grazing animals & wood-eating insects have specialized prokaryotes
(bacteria) that release enzymes capable of breaking down the cellulose.
Ruminants – cattle, bison, deer, goats, sheep,
MANY OTHER TYPES OF CARBS EXIST INCLUDING:
Arabinose, deoxyribose, ribose, ribulose, xylose, fructose, galactose, glucose, mannose,
sedoheptulose, cellobiose, gentiobiose, lactose, maltose, melibiose, sucrose,
gentianose, melezitose, raffinose, stachyose, araban, xylan, cellulose, glycogen, lichenin,
starch, inulin, pectic acid, pectin, protopectin, chitin.
Lipids – in contrast to carbs, lipids are hydrophobic. - Fats & Lipid Steroids
Fats – molecules of triglycerides
Triglyceride = glycerol + 3 fatty acids via dehydration reaction (FIG 3.15, p43).
Fatty acids are long chains of hydrocarbons – LOTS OF ENERGY -2X that of an
equivalent weight of carbohydrates. These long packets of energy are stored as
fuel reserves in adipose tissue (fat cells). In addition to energy, fat acts as an
insulator for vital organs & insulation for the biody as a whole from the outside
Saturated Vs. unsaturated
Most animal fats, lard & butter, have high proportion of saturated fat – linear
shape allows for them to stack easier and are hence solid at room temperature.
Since they stack so easy, they clog pipes easily = atherosclerosis.
Reduce blood flow – heart attack & stroke
Plant (corn, peanut, & canola) & fish fats (cod liver oil) have a high proportion
of unsaturated fat. The bent shape make s them less likely to solidify and they
remain liquid at room temperature.
Tropical plants are an exception – Cocoa butter
Hydrogenation – sometime the manufacturer of a product needs to ensure that
product solidifies so he adds hydrogen – hydrogenation. This converts much of
the unsaturated fat to trans fat; a version of unsaturated fat that can change
shape to behave like saturated fat. NEW REGULATIONS in 2006.
Omega-3 fats are healthy – nuts, fish, and plants. Help w/ cardiovascular,
arthritis, and inflammatory bowel diseases.
Lipid Steroids – The carbon skeleton of a steroid is bent to form 4 fused rings (FIG3.17)
Cholesterol - a key component of cell walls; highly insoluble in water / blood.
Also runs w/ lipoproteins which have protein exteriors and lipid-cholesterol
Cholesterol serves as a a base (raw material) for the formation of testosterone
and estrogen – sex hormones.
Anabolic steroids – synthetic testosterone
Phospholipids – A key component of cellular membranes
2 regions – hydrophobic tail = 2 fatty acids + hydrophilic head = glycerol,
choline, phosphate group.
Proteins – the most elaborate of life’s molecules – body has > 10,000 different kinds
Antibodies, contractile proteins, enzymes, hormones, structural, storage, transport, toxins
Proteins are polymers of amino acid monomers (20 amino acids).
Amino acids = Amino group + Carboxyl group + side group; amino acids vary according to the
side groups i.e, side groups give amino acids their characteristics.
Amino acids are joined by dehydration reactions forming peptide bonds.
A protein usually contains more than 100 amino acids linked together by peptide bonds forming
a chain – polypeptide.
A polypertide is similar to a string of beads where each bead is an amino acid.
This string of beads is a ploypeptide – simple protein –primary structure.
Proteins are very complex molecules
1o structure – a beaded string polypeptide
2 strcuture – the beaded string winds back on itself either as a helix or pleated sheet
3 structure – the helix or pleated sheet winds on itself = an autonomous unit
4 structure – several poypeptide chains are put together = complete protein
The size, shape, and complecity of the complete protein depends on its purpose – the function
of a protein is shape-specific
Denature – to break the complete protein into polypeptide due to temp, pH, salinity, organic
How are proteins mdae – DNA – blueprints for the manufacturing of proteins. DNA is made up
of genes – genes are the independent books encoding the instructions for proteins.
Remember, a proteins shape and function depends on its arrangement of monomers (amino
acids) – 20 amino acids in various combinations = limitless possible combinations.
500,000-1million words in the English language – based on 26 letters
Nucleic Acids – Information storage molecules – life’s computer (1) DNA (2) RNA
Monomers – nucleotides
Nucleotide- Phosphate group + sugar + nitrogenous base (ie, Phosphate-sugar backbone + N
base) (FIG 3.26, p49)
DNA – Adenine, Guanine, thymine, cytosine
RNA – A, G, Uracil, C
DNA = blueprint RNA = Xerox copy of blueprint Protein = product from blueprint (FIG 3.25, p49)
A’s bond w/ T’s C’s bond w/ G’s = Double Helix (FIG3.28, p50)
Proteins and DNA as evolutionary tape measures
Genes (on DNA) and their products (proteins) are historical documents
They are precise measure of time since divergence
Testable hypotheses are the heart of science – DNA analyses and protein adds a tool to our ability to run
experiments and test hypotheses.
Pick a protein or a gene and look at its structure – it is a highly accurate reflection of the
organism’s ancient past. Those species closely related will have similar proteins and DNA sequences;
those distantly related will have less and less in common (FIG 3.30, p51).
Most of the time old school biologists were either correct or somewhere in the ball park as DNA
and protein analyses have confirmed. However, occasionally previous ideas and assumptions are
completely debunked.= paradigm shift.
DNA and protein analyses have completely revolutionized science
We can now find answers to questions that where unthinkable in the recent past.
We are rapidly discovering the origins of everything including disease – medical advances.
This is why we respect Darwin so much – he had the insight to answer questions based on his
own intuition, observation, and busy mind. We now can confirm what Darwin said.