Objectives: Know what a polymer is.  Differentiate among the 4 kinds of macromolecules: carbohydrates, lipids, proteins, and nucleic acids.  Know the basic properties of carbohydrates and lipids and what organisms use them for.  Know the basic properties of amino acids, and proteins, and what organisms use proteins for.  Know the 4 levels of protein structure: primary, secondary, tertiary and quaternary structure.  Know the basic properties of nucleic acids, and what organisms use them for.  Readings: Text: 37-47  Web resources: Cell Chemistry Proteins Folding: What are protein structures like?

Contents: Polymers: An overview Carbohydates - sugars/starches (monosaccharides, disaccharides, and polysaccharides) Lipids -  fats, phospholipids, steroids  Proteins - amino acids The 20 amino acids in proteins Protein structure: conformation Genes: regions of DNA Nucleic Acids - genes, DNA, RNA, nucleotide bases  (pyrimidines, purines)  Summary Key terms

1. Carbon is a flexible atom (can make different kinds of carbon backbones, etc.) because of tetravalence. 
2. Functional groups give organic compounds their distinctive properties. The groups that we examined made organic compounds more polar. 

Macromolecules (polymers) are distinctly biological in nature. They usually do not exist unless an organism makes them. Comprised of monomers, or relatively simple molecules, the resulting complex molecules - macromolecules -  are the "Godzilla" of the chemical world. There are relatively few kinds of monomers, but seemingly limitless polymers.  In polymer synthesis, monomers are connected together by condensation or dehydration reactions. For example, two monomers are bonded covalently and a water molecule is made. This process requires energy.  In the reverse process - hydrolysis - polymers are broken into monomers by adding water.

• Carbohydrates
• Sugars 
• Starches (animal starch/glycogen and plant starch/cellulose)
• Lipids 
• Fatty acids
• Phospholipids
• Steroid hormones (estrogen, testosterone). 
• Cholesterol, Triglycerides
• Proteins/Nitrogen-containing molecules  (e.g. enzymes, muscle protein, collagen skin protein)
• Amino acids - the building blocks of proteins. 
• Peptides (small proteins)
• Nucleic acids

Monosaccharides, like glucose and fructose, are the simplest kind of sugars - maybe that's why they are called simple sugars. The molecular formula is n(CH₂). For example, glucose is C₆H₁₂O₆. A sugar with 6 carbons, like glucose, is called a hexose; a sugar with 3 carbons is called a triose. What you call a sugar with 5 sugars? (hint) 

Each carbon has a hydroxyl group except 1, which has a carbonyl group. (7 Functional Groups) 

Disaccharides consist of 2 simple sugars bonded together. They are joined by a glycosidic linkage.  Monosaccharides and disaccharides are "small change." Plants and animals can move these forms of energy around easily.

When many monosaccharide and disaccharide "cars" are bonded end-to-end by glycosidic bonds the resulting train is called a polysaccharide, for "many sugars."  Organisms use many kinds of polysaccharides to store energy and to build structures (structural polysaccharides). 
Starches 
Starch is a specific kind of polysaccharide in which the component "cars" are glucose. The angle of the 1-4 glycosidic bond makes starch a helical structure (the secondary structure). Starches function as reserve nutrient sources, because sugar molecules can be cleaved off the starch and used for fuel. An unbranched chain of starch is called amylose, while branched chains are called amylopectins. 

Plants use starch as "money in the bank"- as an energy source. They store starch in special storage sites in cells called plastids. Potatoes are mostly starch. 

Glycogen is a highly branched polysaccharide that humans use as for carbohydrate storage ("money in the bank"). 

Cellulose,  used in making plant cell walls, is the most abundant organic compound on earth. Like glycogen, cellulose is composed of glucose cars. The glucose, however, is of a different isomer, thus the secondary structure is different. Bonds in cellulose are very hard to break. 

Chitin is another structural polysaccharide used by insects and other hard-shelled animals to build their exoskeleton. 

Lipids
Lipids, which include fats and the fatty acids, are non-polar macromolecules. They are composed of fatty acids and have lots of C-H bonds. Lipids are insoluable in water, i.e. hydrophobic. Serving a diverse number of uses, they are: fats, phospholipids, and steroids. 
 

Fats consist of a chains of a glycerol (a 3-carbon alcohol) linked to three fatty acids. They are like stocks-- long term energy storage.  Fatty acid is the "choo choo car" of lipid trains. Fatty acids have a functional group linked to a long carbon backbone.  Fatty acids generally vary in the number and location of double bonds-- giving them their distinctive properties.

If there are double bonds, the fats are unsaturated. Unsaturated fats are liquid at room temperature. Example: cooking oil. 

If there are no double bonds, the fats are saturated. Saturated fats are olid at room temperature. Example: margarine. Animals make mainly saturated fats. Plants make mainly unsaturated fats. However, they can be hydrogenated to make them saturated. 
 
 

Phospholipids are important in cell membranes. They consist of a hydrophilic head, and two hydrophobic fatty acid tails.  Steroids (sterols) are lipids with four (4) interconnected rings and a functional group. These are precursors of hormones and serve a variety of purposes.

Phospholipids

Activity: 3D

Proteins
Proteins compose over 50% of cell weight. The "choo choo cars" of proteins are amino acids. Amino acids combine to form small chains of amino acids called peptides, or even longer chains called polypeptides or proteins. ⁽¹⁾

Amino acid structure 
The properties of the R group give the amino acids their distinctive properties -- polar, non-polar, acidic, basic. They can be hydrophobic/water-insoluable (example: leucine) or hydrophilic/water-soluable (examples: serine, cysteine) 

How are proteins made? Amino acids are bonded together with a peptide bond, which is the product of dehydration synthesis  -- polypeptide chain. A properly folded polypeptide chain is a protein. 

The primary structure - the sequence of amino acids -  is the most important determinant of conformation, i.e. the protein's shape. The primary structure also determines the other levels of protein structure and function.  Secondary structure- the coils and folds of amino acids caused by hydrogen bonding of amino acids.  Alpha helix caused by H bonds between every 4th amino acid.  Beta pleated sheets-- polypeptide chain is folded back and forth or parallel chains are H bonded together.  The tertiary structure is the larger 3 dimensional shape caused by R group interactions. The tertiary structure causes proteins to be globular in nature and biologically active.  Quaternary structure. Some proteins are made of different subunits (chains) that interact to form a multi-chained protein. Tertiary structure Environmental factors - such as high temperature, high salts, high or low pH, and physical shaking - can cause protein denaturation, i.e. the disruption of tertiary and quaternary structure. This causes a protein to lose it's function.    Activity: 3E, 3F Quaternary structure Question: What determines protein primary structure?  Answer: Genes. Genes are regions of DNA, (deoxyribonucleic acid). There are thousands of genes in a DNA molecule. DNA codes for RNA (ribonucleic acid), which in turn gets translated into proteins: In other words, DNA provides the "programming code"  or "blueprint" to construct protein.  DNA and RNA are nucleic acids.  DNA is copied over and over again and gets passed from generation to generation.  DNA is to organisms as software code is to computer hardware. One may think of protein as the software program that interacts with the user.

Nucleotide bases are the "choo choo" cars of nucleic acids. 

Nucleic bases are made of a pentose sugar (either ribose for RNA or deoxyribose for DNA), bonded to a phosphate group, and also bonded to a nitrogenase base. 

The bases are classified as two types: pyrimidines and purines. 

• Pyrimidines have a 6-membered ring: cytosine (C) and thymine (T) (or instead of thymine RNA has uracil (U)). 
• Purines have a 6-membered ring fused to a 5-membered ring: adenine (A) and guanine (G). 

DNA exists naturally as a double-stranded molecule in the shape of a double helix. On opposite stands T hydrogen bonds with A, and C hydrogen bonds with G. Therefore in any organism's DNA, there are as many Ts as As, and as many Cs as Gs. 

Summary:

1. Protein monomers are called amino acids.
2. There are 20 different amino acids.
3. The primary structure (sequence of amino acids) is important in defining a protein's function (and other levels of structure).
4. Tertiary structure can be lost by denaturation.
5. Nucleic acid (DNA and RNA) monomers are nucleotides.
6. DNA is double stranded and codes for proteins.