from a definition of the gene page 540 in text.."A gene's nucleotide sequence specifies a polypeptide or RNA and is subject to mutational alteration"
However, there are other definitions of a gene...see page 43 of workbook
We are now interested in the transcription and translation of the gene
Simplified transcription model (see Figure 11.1) ... TranscriptionModel.gif
We use transcription and translation of beta globin as a model ..ProteinSynthesis.GIF
RNA serves as the "machinery" for transcription; RNA is derived from transcription of RNA genes
So, we must consider protein coding genes (structural genes) and RNA genes.
Difference between DNA and RNA .. DnaRnaDifference.GIF
Types of RNA
1. mRNA; messenger RNA
2. tRNA; transfer RNA
3. rRNA; ribosomal RNA
4. snRNA; small nuclear RNA (used RNA processing)
Associated with each gene are transcription regulatory elements
Learning the difference between the words transcription and translation is important and easily confusing. Here is a quote from the 2 Nov 00 issue of Nature, page 26. It is a review of Evelyn Keller's book: The Century of the Gene.
"She claims, for example, that the idea of the gene as a unit of structure or function is outmoded because some bits of DNA do not produce proteins, but instead regulate genes,because some genes can be spliced or read in alternative ways, and because the products of some genes perform several functions. Although it is true that genes are often complex, the word gene is still a perfectly good working term for biologists, especially when defined as a piece of DNA that is translated into messenger RNA."
Continue with description of the gene and transcription
In our development there are several different hemoglobin molecules....HemoglobinPicture3a.gif
The genes for the various polypeptides are located on chromosomes 11 and 16 ...HemoglobinPicture4.gif
A detail of chromosome 11... HemoglobinPicture5.gif
Look at hemoglobin sheet (illustration #6)
(Access the hemoglobin sheet... betaglobin.pdf )
(Access the "official" beta like gene sequence ... http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&db=nucleotide&list_uids=455025&dopt=GenBank&term=HUMHBB&qty=1 )
sequence given is 5'...3' Why53given.GIF
exercise: Why53given2.GIF
Directionality within the gene from first base transcribed ..........UpDownStream.GIF
return exams
continue with transcription
Gene is divided into subunits: .. SynMRNA2.GIF
......as text..betaGlobinGene.GIF
First portion of Figure 6 ... HemoglobinPicture6.gif
Last portion of Figure 6 ... ../HemoglobinPicture6b.gif
term intron well defined
term exon has variable definitions
consensis definition (general agreement) :
"Part of a gene whose sequence is present in a mature mRNA after splicing."http://www.informatics.jax.org/mgihome/other/glossary.shtml#e
Other features:
In the 5' flank we find promoter sequences (boxed and underlined). From your text: "A specific regulatory nucleotide sequence in the DNA to which RNA polymerase binds for the iniation of transcription"
The signal for start translation in the mRNA, the first ATG
At the 3' end of the transcription unit: line 26, the dot indicates a cleavage of the primary transcript and site of attachment of adenines.
Enzymes for transcription in eukaryotes ...RNAPolymerases.gif
Transcription of mRNA
Post transcription modifications: guanine cap at 5' end, removal of introns, addition of adenines at 3' end of transcript
overview of gene processing .... ../SynMRNA.GIF ..
control elements may be cis or trans acting
Cis acting sequences - as promoter
"cis acting regulatory sequences control the activity of a gene only when it is part of the same DNA molecule or chromosome"
Trans acting factors - as TATA binding protein
"trans-acting factors (protein or maybe RNA) affect expression of all copies of a gene, whereas cis-acting factors (normally DNA sequences) regulate only the DNA molecule of which they are a part)"
quotations from: Strachan, T. and A. P. Read 1999. Human molecular genetics 2. 2nd ed. Wiley, New York.
Transcription initiation complex (as Figure 11.5b)
Complete complex ...Enhancer.GIF
from text: "In eukaryotes, a type of DNA sequence element having a strong, positive effect on transcription by RNA polymerase II"
location of enhancer sequences, for HS (hyper sensitive) sites see #5 on Hb sheet
Transcription termination
in prokaryotes hairpin turn in mRNA beyond stop translation codon; little information in eukaryotes.
two new words
nutrigenomics - "Nutrigenomics reserchers im to learn how nutrients interact with genes to lead to health or disease Nature 426:107 13 Nov 03
potogenes - "...DNA sequences with a potential for becoming new genes" Annual Review of Genetics 37:123 2003
Question of source of new genes:
"Most genomes show a high degree of redundancy, which can arise from single-gene duplications, duplications of short chromosomal segments or of entire chromosomes, or by duplication of the entire genome. All of these events are believed to play an important part in biological evolution. Two genes derived from a gene duplication are said to be paralogous. One of the paralogues is often subsequently deleted from the genome. Rarely, paralogues are preserved because they differentiate and become functionally specialized" ..... Langkj, A. R. B., P. F. Cliften, et al. (2003). "Yeast genome duplication was followed by asynchronous differentiation of duplicated genes." Nature 421(6925): 848-52.
paralogous genes: genes derived by duplication within a species, often same chromosome
Question of transcription in two directions
to read in both directions, depends on placement of promoters. ........./TranscriptionDir.GIF
For the histone genes....... ../HistoneGenesDrosoph.gif
Important item: alternative splicing, variable mRNAs from a single gene.
AlternativeSplicing.gif
Also, large genes with many introns.
dystrophin gene: gene 25000 kb long, mRNA is only 14 kb long, more than 80 introns removed in processing.
transcription of rRNA ........SynRRNA.GIF
(ribosomal chromosomes.......ribosomalideograms.gif)
transcription of tRNA .........SynTRNA.GIF
hemoglobin chromosomes
alpha like genes on chromosome 16..... GlobinIdeograms.gif
beta like genes on chromosome 11