Humboldt State University ® Department of Chemistry

Richard A. Paselk

VUB Biology

Fall 2001

Lecture Notes:: 24 September

© R. Paselk 2001


Nucleic Acids and Nucleic Acid Structure 

Two major types of nucleic acids, DNA and RNA. (overhead, MvH 4.2)

In each case we see a polymer made by linking nucleotides via phosphodiester bonds. Biologically these bonds are synthesized by the attack of an alcohol residue from ribose on the a-phosphate to release a diphosphate residue, which is subsequently hydrolyed to phosphate (helps to drive synthesis to completion):


DNA DeoxyriboNucleic Acid: (overheads)

RNA RiboNucleic Acid:


Functions of Nucleic Acids

DNA: DNA is largely used for information storage. As such it is a very stable molecule with very precise replication and precision.

RNA: RNA is mostly an adaptor molecule, used to translate between information in DNA and protein machinery/structure. Three kinds of RNA:



Proteins are polymers of amino acids

Can be fibrous or globular

3D Structure of Proteins

In order to understand and categorize their organization, protein structure has been divided into four hierarchical levels and a couple of sublevels:



Enzymes are the heart of Biochemistry

Enzymes generally have a cleft for active site, generally <5%of surface: look like pac man. Need large structure to maintain shape etc. with many weak bonds.

Models for Enzyme Specificity:

Types of specificity:




The important aldoses (Figure 8.1, p 197) [overhead 9.4 P] include the five carbon aldopentose, ribose:

which commonly occurs in the cyclic furanose form.

The six carbon aldohexoses, glucose, mannose, and galactose: {Models of glucose, linear and ring forms, may be viewed by clicking on the buttons at this site.} These aldohexoses commonly occur in the six-membered "pyranose" ring form (glucopyranose below):

The six carbon ketohexose, fructose, is the other important hexose: (A model of fructose, in the ring form, may be viewed by clicking on the buttons at this site.}

Fructose commonly occurs in a cyclic five-membered ring form.



Can link sugars via acetal bonds, known as glycosidic bonds.

There are four common disaccharides [overhead 9.24, P]:

The first three are reducing sugars, that is they have "free" aldehyde groups, whereas fructose has both carbonyl groups tied up in the relatively stable glycosidic bond. Maltose and fructose are joined in a-glycosidic bonds. In general the a-glycosidic bond is easily cleaved (it is less stable chemically and organisms have enzymes to cleave it) whereas the b-glycosidic bond is very difficult to break down.

Thus for cellobiose, and more importantly, cellulose which is also linked by b-bonds, essentially only bacteria can digest this bond.

Animals also can't digest (possible exception of snails). You may ask, What about Cows and things? Well they use bacteria. Cows for instance are basically walking fermentation tanks. Cool biological examples: Desert Iguana consume feces to maintain culture; Rabbits eat and reprocess first pass feces (soft) to take advantage of fermentation; Multiple stomachs in Ruminants; Ultimate symbiosis in some termites: protozoans in gut have bacteria in gut, and use spirochetes as "cilia" (rowers).

Sucrose, Sucrase (Invertase), and the magic of liquid filled chocolate covered cherries.




Can have both homo- and heteropolysaccharides. We will focus on homopolysaccharides as most central, but will mention some heteropolysaccharides to illustrate their functions. Homopolysaccharides have a single type of residue. Most common contain glucose. Used for energy (food) storage (starches and glycogen) and structure (cellulose).

Starch (energy storage in plants). Two kinds

Glycogen: animal starch. Just like amylopectin, but more highly branched (every 8-12 residues). This allows more free ends for more rapid breakdown­important in animals.



Cellulose: b-1,4 linkages, thus resistant to breakdown (including acid hydrolysis) as want for structure (don't want to digest self). Multiple, extended strands come together as fibrils held together with H-bonds (Fig 5.7, p 63; 5.8, p 64), laid down in cell wall in criss-cross pattern, glued together with polyalcohols (lignin).

Chitin: Serves similar role to cellulose, but in animals (crustaceans and insects), fungi, and some algae. Homopolymer of N-acetyl-D-glucosamine. Like cellulose , it has b-1,4 linkages, and is thus resistant to breakdown. (p 65)

Among the heteropolysaccharides are the glycans such as Hyaluronic acid, an alternating polysaccharide of D-glucuronic acid and N-acetyl-D-glucosamine; MW to 5,000,000 which serves as a lubricant in joints and is a component of the vitreous humor. Again we see b-1,4 linkages.



Types of Lipids: (overhead 11.1, P)

Lipid Properties: An important consideration for lipids of all sorts is their fluidity. Thus membranes must be fluid enough to allow the diffusion of proteins, transport processes etc. but not so fluid as to weaken the membranes structure. For storage want fat to be fluid enough to flow to fill out body shape at normal operating temperatures. A number of strategies are used by organisms to adjust lipid fluidity:


Lipid Bilayers

Detergents & Micelles: Polar heads of detergents and soaps (such as long chain fatty acids) tend to associate with polar solvents such as water, while non-polar "tails" are excluded by water and are forced to associate with themselves making globules known as micelles.

Lipid Bilayer: Figure 5.13, p 67 [overhead 11-12, V&V; 12-11]:

The lipid bilayer forms the core for the lipid bilayer membrane as seen in the Fluid Mosaic Model of biological membranes which we will look at later in cells.

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Last modified 24 September 2001
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