The Nature of a GENE;Component Parts

Susquehanna MAGNET School for Medicine and Health Sciences

October 7, 2013Professor Michael Chorney

Learning ObjectivesExplain the nature of codons and the information inherent intheir base composition

Explain what is meant by degeneracy

Describe the nature of a gene, its component parts andhallmarks

Discuss the nature of exons, and what is meant by an openreading frame; in addition, define the what is meant byexon splicing

DNA Scale, the numbers, Review

We have a lot of DNA in each gamete (3.1647 x 109 basepairs); cf a bacterium which contains about 4.6 million basepairs

200 phonebooks the size of Manhattan’s (1,000 pages) would be required to tally the information; if you read the bases nonstop, it would take 9.5 years to complete

The fertilized ovum contains twice a much DNA as each gamete, or (6.4 x109 basepairs); half maternal, half paternal*

• The body contains 10-100 trillion cells=1014

• A cell contains 12 picograms of DNA= 12x10-12=6x109 basepairs (G, A, T, C) • The body contains 1014 cells x 12x10-12 g=1,200 g of DNA=0.25% wt=6.4x1022 basepairs

*

DNA Scale, the numbers.2, Review

The DNA in each somatic cell is arranged into chromosomes, i.e., linear strands of DNA of varying lengths

The DNA is condensed by proteins of opposite charge, called histones, which provides a means for regulating base (information) access by other proteins

Condensed DNA, during mitosis, can be easily stained, revealing the chromosomes’ size and banding variation (reflected in the variation of A/T and C/G content)

Giemsa-stained metaphase spread of human chromosomes fromone cell, the most condensed form of DNA within the cell, seen atMITOSIS

Vocabulary

metacentricsub-metacentricacro(telo)centriccentromerep armq armbandingheterochromatineuchromatintelomeresautosome

Cytogenetics

Each chromosome is a linear strand ofhelical ds-DNA with capped ends calledtelomeres

Figure 6-2 Molecular Biology of the Cell (© Garland Science 2008)

Information flow

Sense strand

Anti-sensestrand

A GENE

Like copying the lead-ing strand

TRANSCRIPT

Figure 6-21 Molecular Biology of the Cell (© Garland Science 2008)

Figure 6-4 Molecular Biology of the Cell (© Garland Science 2008)

RNA polymerasereplaces U for T (why?) inRNA and ribose forthe deoxy sugar

Deaminated C=U

Only a small amount (percentage) of human DNA contains information that is ostensibly converted into proteins: these sequences are associated with genes. The proteins coded for by genes do biochemical work and regulate cell division, generate energy, respond to the environment, provide immunity to invasive DNA sequences (infection), etc.

DNA, the Puzzle, Review

What (and where) is this information we keep hearing so much about?

It resides in the bases; particular triplet base combinations which comprise the exons and provide information called codons

You should have been exposed to the list of codonslast week in the case study, next slide

There are 64 codons that equate to the twenty aminoacids (a.a’s), with multiple codons existing for most of the a.a.’s, called degeneracy. Three of the codonsare called termination codons, more later

For starters,

Figure 6-50 Molecular Biology of the Cell (© Garland Science 2008)

CODONS, what do you notice?

Figure 4-7 Molecular Biology of the Cell (© Garland Science 2008)

The question for molecular biologists:

What distinguishesa gene (1-2% of DNA)from the remainingDNA (98%)?

This has posed a problem for some time; now that this isbecoming solved, thequestion becomes, what does the ‘gene’do?

Can you see, ata quick glance, agene in the sequence at theleft?

The yellow highlightedbases signify thebeta globin gene!!!

Genes are subject to the following:

1. They must be recognized by a polymerase, thatis, an RNA polymerase that will guide gene copyingcalled TRANSCRIPTION—compare DNA polymerase

2. The collective DNA sequence that summons forthRNA polymerase is called a PROMOTER

3. The information copied into RNA immediately adjacent to the promoter must be readable (CODING SEQUENCE); i.e. no stop codons untilthe naturally determined end of translation

4. There has to be a place after the coding sequencethat signals the end of transcription, different than theend of translation

The eukaryotic gene’s general features and processing characteristics

exon exon exon exon5’ 3’

The gene is controlled by a promoter (p) which is not simple – there are generalized transcription factors and more gene-specific ones that may reside outside of the promoter proper, within the gene, within the 3’ end of the geneor even far 5’ and/or 3’ of the gene itself –they open the DNA and expose sites

p

The gene is structured in ‘staccato,’ with coding sequence (exons) interrupted bynoncoding intervening sequences, called introns; the first exon begins with the ATG met codon, the last exon ends with one of three translational terimantion codons (TAA, TAG, TGA)

Termination of transcription occurs in the 3’ untranslated region (3’UTR) whichpossesses termination signals and an RNA domain which drives 3’ processing, the AATAAA polyadenylation signal

3’UTR

AATAAA

ATG STOP

Exon-intron borders possess sequences which aid in splicing, AG/GT……A……AG/G along with small, nuclear RNAs forming the spliceosome

AGGT A AGG AGGT A AGG AGGT A AGG

5’UTR exon1 exon 2 exon 3 exon 4 3’UTR

exon exon exon exon5’p

3’UTR

AATAAA

AUG STOP

AGGT A AGG AGGT A AGG AGGT A AGG

[CG]

Maintaining DNA euchromatic also rests upon factors that bind to C’s and G’s, whichprotect the CpG ‘islands’ from cytosine methylases best known for their role inimprinting

CpG Islands: under-represented nucleotides found at the 5’ end of eukaryotic genes

CH3ase

…..WlsjeutlsjimsatouttutyecmdsisladksltkaldThedayforeeeuslkeiandseveeubhismomand ttugosocunntewherebudtedandtueislsiecnTisnggotallsixeooaltaxlekqzztiellforthebigbadsumrrrrrrrrrrrrteidas………

Let’s try a poor analogy, constrained by the Englishlanguage and a dearth of three-letter words, but Here goes….

Find the three letter (codon)-containing ‘exons’ that make a kind of a sensible phrase (names included)-This is comparable to an open reading frame

Answer: jimsatoutthedayforhismomandbudtedandgotallsixforthebigbadsum……….

WordDNA

jim sat out the day for his mom and bud tedand got all six for the big bad sum……….

…..WlsjeutlsjimsatouttutyecmdsisladksltkaldThedayforeeeuslkeiandseveeubhismomand ttugosocunntewherebudtedandtueislsiecnTisnggotallsixeooaltaxlekqzztiellforthebigbadsumrrrrrrrrrrrrteidas………

What happens if I delete the s?

Jim sat out the day for him oma ndb udt edandg ota lls ixf ort heb igb ads um……….

FRAMESHIFT—the OPEN READING FRAMEIS GONE

Figure 6-51 Molecular Biology of the Cell (© Garland Science 2008)

RNA

Figure 4-76 Molecular Biology of the Cell (© Garland Science 2008)

CODINGSEQUENCEIS CONSERVEDSEQUENCEACROSSSPECIES

LEPTINGENEALIGNMENT

Figure 4-78 Molecular Biology of the Cell (© Garland Science 2008)

THERE IS GREATER EVOLUTIONARY PRESSURETO CONSERVE CODING SEQUENCE (EXONS) THANINTRON SEQUENCES

Humans have approximately 23,000 genes (down from the 80-140k prediction

Genes are dispersed along the chromosomes in what appears to be a random fashion, although many gene clusters exist which seem to aid coordinate expression: globin, histone, immunoglobulin, MHC, etc.

Some chromosomes are more rich in genes than others, although chromosome size roughly correlates with gene number

A gene’s location is termed its locus as we have touched upon

DNA, the puzzle.2

Genes vary in size, from beginning to end

And in their number of exons, whose tally following splicing must = an open reading frame, or ORF

The average protein is 45Kd (110 for the mw of an average amino acid); the average size of a spliced gene (mRNA) is 1.5 kb, therefore, the amount of coding sequence in the human genome is 0.14%

Exons’ size varies, but average about 200 basepairs (based on myKnowledge of the Ig superfamily members); their translated sequences often equate to ‘domains,’ units of primary amino acid sequence that perform function

http://www.cshlp.org/ghg5_all/section/gene.shtm BIG GENESl