BioPhysics 101 Biology section #2 Sept. 30 2003

Today’s topics:

•Dogmas

•Operons

•Cis and Trans

•Haplotypes

Transcription

For a given gene, only one strand of the DNA serves as the template for transcription.  An example is shown below.   The bottom (blue) strand in this example is the template strand, which is also called the minus (-) strand,or the sense strand. It is this strand that serves as a template for the mRNA synthesis. The enzyme RNA polymerase synthesizes an mRNA in the 5' to 3' direction complementary to this template strand. The opposite DNA strand (red) is called the coding strand, the non-template strand, the plus (+) strand, or the anti-sense strand. 

The easiest way to find the corresponding mRNA sequence (shown in green below) is to read the coding, non-template, plus (+), or anti-sense strand directly in the 5' to 3' direction substituting U for T. 

PLUS (anti-sense) STRAND: 5' T G A C C T T C G A A C G G G A T G G A A A G G 3'

MINUS (sense) STRAND: 3' A C T G G A A G C T T G C C C T A C C T T T C C 5‘

mRNA STRAND: 5' U G A C C U U C G A A C G G G A U G G A A A G G 3'

Plus strand, Minus strand, Sense Strand, Anti-sense strand.

Prokaryotic cell

Eukaryotic cell

Tree of life

Characteristic Euacteria Archaea Eukarya

nuclear envelope absent absent present

membrane-enclosed organelles

absent absent present

peptidoglycan in cell wall present absent absent

membrane lipids unbranched hydrocarbonssome branched hydrocarbons

unbranched hydrocarbons

RNA polymerase one kind several kinds several kinds

initiator amino acid for start of protein synthesis

formyl-methionine methionine methionine

introns absentpresent in some

genespresent

antibiotic sensitivitygrowth inhibited by streptomycin

and chloramphenicolnot inhibited by these antibiotics

not inhibited by these antibiotics

A comparison of the three domains of life.

The central dogma

At what stage do prokaryotes and eukaryotes differ?

Eukaryote central dogma

Operons: DNA segment = protein sequence + control circuitry

RNA polymerase transcription

Prokaryotic vs Eukaryotic RNA PolII

Transcription initiation: get bent

Prokaryotic Transcription initiation

Eukaryotic transcription initiation

Eukaryotic pre-initiation

Eukaryotic mRNA packaging.

What is this?

mRNA nuclear export

Nuclear pore

lacZ: Beta-galactosidase

The E. coli Lactose operon

Lactose transporter: lacY

V-class proton pumps

P-class pumps

F-class proton pumps

Cell membrane receptors for hormones,

neurotransmitters, odors, and light.

The potassium channel

Cis/Trans effect testing for markers in the E. coli lac operon using a plasmid.

Cis/Trans testing in haploid organisms

Genotypes vs. HaplotypesConsider a diploid organism, such as a mouse (two copies of each gene per cell).

Consider two mouse markers MA, and MB, that are biallelic (two known alleles for each). Represent the alleles as A, a, B, and b.

For a mouse cell with the genotype AaBb, there are two possible haplotypes:

Haplotype (AB, ab) Haplotype (Ab, aB)

*Haplotypes ignore the (maternal, paternal) chromosome labels

If one or more of the markers was cis acting:

The haplotype (AB, ab) would result in the phenotype L.

The haplotype (Ab, aB) would result in the phenotype l.

Cis vs. Trans

Using our mouse example, suppose the linked markers MA, and MB , both influence a phenotype controlling hair length. Furthermore, assume that the wild type alleles A and B are dominant:

•The genotypes AAbb, aaBB and aabb would all result in the phenotype l.

•The genotype AABB would result in the phenotype L.

•The genotype AaBb would result in the phenotype L if both markers were dominant and trans acting.

Cis and Trans are terms that express a relationship between two linked markers that influence a given phenot The genotypes AAbb, aaBB and aabb would all result in the phenotype l. ype.