Chapter 3 – The molecules of life Organic Molecules – Carbon-based

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					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 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,

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
               (polypeptide chain)

               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.

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