Molecular Biology  Lecture 5

 

Macromolecular Interactions and the Structure of Complex Aggregates

 

 

Macromolecules interact with each other:

 

DNA with proteins

DNA with RNA

Proteins with lipids

Polysaccharides with proteins and lipids

 

The E. coli chromosome:  (also called the nucleoid)

What does it look like?

Supercoiled, circular molecule, about 1300 um long (See fig 5-2 and 5-1)

The nucleoid has: DNA, protein, and some RNA

 

The nature of the scaffold (or core) structure is still mysterious.

The DNA is organized into a number of highly supercoiled loops which are attached to the scaffold (Fig 5-3)

 

Eucaryotic Chromosomes are shown in Fig 5-4

In eukaryotes the genomic DNA is bound to basic proteins called histones.  (Basic proteins are high in lysine and arginine.  Why would these amino acids make the proteins basic?)

 

See the table of histones in  Table 5-1.  These proteins are highly conserved through evolution.

 

The basic histones are attracted electrostatically to the negatively-charged DNA molecules.  An attraction that can be overcome with high salt solutions (0.5 M NaCl).

 

Note the Òstructural hierarchyÓ of nucleic acid packing in eukaryotes: Figure 5-6

 

Look at Figures 5-7 and 5-8 to see how this is studied:  Treatment of eukaryotic genomic DNA with pancreatic DNAse I followed by treatment with 0.5 M NaCl causes the formation of 200 bp long DNA fragments and free hisones

 

Also look at Fig 5-10 to get a sense of how much DNA is present in a eukaryotic chromosome. Also note the protein scaffold.  (Compare this with the E.coli chromosome in fig 5-2).

 

Besides histones, what other proteins bind to DNA??

o      Polymerases

o      Regulatory proteins

o      Nucleases

 

Many of these proteins bind to specific sequences.  These binding sequences are often called ÒmotifsÓ because of a pattern that can often be discerned.

 

o      The DNA binding site is often an area of two-fold symmetry

o      The DNA binding protein is often a dimmer

 

Biological Membranes Ð Basic properties and functions:

  1. Separation Ð inside cell from outside; also partition intracellular compartments
  2. Selective permeability Ð possesses molecular pumps, channels, pores, gates
  3. Transmit signals and electrical impulses
  4. Anchor to the cytoskeleton

 

Look at the bilayer in Fig. 5-14

Also look at the phospholipid molecule in fig 5-15

 

Membrane proteins exist as:

Integral membrane proteins

Peripheral membrane proteins

 

Look at figures 5-16 and 5-17