1 Part 1 is it to jog your memory DNA is very nearly the universal - PDF document

Topic 2: A primer on the structure and function of genes Additional graphic from: http://www.accessexcellence.org http://www.eportalit.com/igx/igx.html 1

Part 1 is it to jog your memory DNA is very nearly the universal genetic material • All hereditary information is encoded in nucleic acids • Nucleic acids are a polymer made of nucleotide monomers OH H DNA: RNA: other viruses some viruses all other life on earth 2

RNA compared with DNA Base pairing and Chargaff’s rule DNA: A = T and G ≡ C RNA: A = U and G ≡ C Base pairing explains Chargaff’s rules for double stranded DNA • %A = %T and %C = %G • The ratio %G+C : %A+T varies among organisms C% G% C+G% Strand A 5% 30% 35% Strand B 30% 5% 35% Strand asymmetric Strand symmetric 3

Mammalian mitochondrial genome is highly strand symmetric H-strand nucleotide composition G rich (C poor) strand: Heavy (H) strand C rich (G poor) strand: Light (L) strand Distance from origin of replication 3’ end DNA is anti-parallel 5’ end Note: an important convention is to write out DNA in the 5’ to 3’ direction! 5’ – A T T C A G T A A – 3’ is NOT the same as 3’ – A T T C A G T A A – 5’ 5’ end 3’ end 4

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Transcription : In the nucleus Translation : In the cytoplasm 6

Part 2: What is the definition of a gene? GENE: the genetic element which is transmitted from parent to offspring during the process of reproduction that influences hereditary traits. • Beadle and Tatum (1941): one gene, one-enzyme hypothesis • one-gene, one-polypeptide hypothesis GENE: is the segment of DNA involved in producing a polypeptide chain; it includes regions preceding and following the codon region (leader and trailer) as well as intervening sequences (introns) between individual coding segments (exons). [Note this is also the definition of a cistron.] The traditional definitions imply that functional and structural diversity arises via local changes in the DNA sequence Important motivation for private backing of human genome sequencing 7

Human Genome Project (HGP)and the definition of a gene Genome Number of genes Human ~30,000 Mouse ~30,000 Fruit fly ~13,000 Nematode ~19,000 HGP: • many genes encode more than one protein • much functional divergence between humans, chimpanzee, and mice due to changes in gene regulation (Clark et al. 2003) •We should reconsider our definition of a gene if we want to define it according to its function • genome-function relationship is more complex than we (some) had thought What is a gene? 1. a unit of inheritance 2. a location on a chromosome 3. a sequence of base pairs 4. a transcriptional unit 5. a determinant of phenotype They are all correct. Types of genes: 1. Protein-coding genes 2. Regulatory signal genes 3. RNA encoding genes 8

A note about the definition of a gene: In some population genetics books, alternate forms of genetic variation at a locus are called genes; i.e., allele = gene. In this course allele ≠ gene 1. Protein coding genes . This type easily fits the modern definitions, in that they transcribe a messenger RNA (mRNA) that is used as a template for making a polypeptide. These genes are sometimes called structural genes. We can see the problems with defining a gene as a segment of DNA involved in producing a polypeptide chain, as this differs among eukaryotes, prokaryotes and virus’s. 9

Prokaryotic protein-coding genes are colinear with the polypeptide Promoter for regulatory gene Regulatory gene Structural genes DNA P i i P lac Operator Z Y a Promoter for lac operon z = Structural gene for β - galactosidase y = Structural gene for β - galactoside permease a = Structural gene for β - galactoside transacetylase Promoter: A region of DNA extending 150-300 bp upstream from the transcription start site that contains binding sites for RNA polymerase and a number of proteins that regulate the rate of transcription of the adjacent gene. Operator: a region of DNA that indicates the starting point for reading the coding sequences of bacterial structure genes and controls the expression of those genes via interaction with a repressor. OPERON: several protein coding genes that are regulated and expressed as a single unit. Eukaryotic protein-coding genes differ substantially from prokaryotic ones Regulatory Signals RNA start Introns DNA Exon 1 Exon 2 Exon 3 Poly-A addition site +2400 -220 10

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2. Regulatory signal genes. These are elements or motifs of DNA that are not transcribed, and serve as signals to regulate the processing of the DNA molecule. The prominent types of such genes are: • Replicator signals : These signal the initiation or termination of DNA replication. • Telomeres : These are repeats of specific DNA sequences found at the ends of eukaryotic chromosomes. • Segregator signals : These determine the specific sites at which the segregation machinery of the cell attaches to the chromosomes for the process of mitosis and meiosis. • Recombination signals : The sequence element that provides a recognition site for a recombination enzyme. Regulator signals in prokaryotes Promoter for regulatory gene Regulatory gene Structural genes DNA P i i P lac Operator Z Y a Promoter for lac operon z = Structural gene for β - galactosidase y = Structural gene for β - galactoside permease a = Structural gene for β - galactoside transacetylase Promoter: A region of DNA extending 150-300 bp upstream from the transcription start site that contains binding sites for RNA polymerase and a number of proteins that regulate the rate of transcription of the adjacent gene. Operator: a region of DNA that indicates the starting point for reading the coding sequences of bacterial structure genes and controls the expression of those genes via interaction with a repressor. 12

Eukaryotic DNA is packaged into a structure called chromatin Structure of chromatin can place regulatory signal genes that are dispersed in the primary DNA polymer in close proximity in 3D space . Regulator signals in Eukaryotes 1. Regulatory elements in primary DNA 2. Txn factor finds it’s cognate regulatory site 3. Txn factor recruits co-activators 4. co-activators open up the chromatin 5. Open chromatin allows the binding of basal txn factors 6. RNA polymerase binds to complex 7. RNA polymeraseinduced strand seperation and begins to transcribe DNA to RNA 13

3. RNA encoding genes. In contrast to mRNA of protein coding genes, the final product of the RNA gene is only transcribed RNA. RNA molecules specified by such genes fold into complex structures that USUALLY associate with proteins to form a sort of “chemical machine”. i. Transfer RNA (tRNA) ii. Ribosoaml RNA (rRNA) iii. Small nuclear RNA (snRNA) iv. Others: (snaRNA, microRNA, gRNA) 14

Ribosomal RNA (rRNA) gene Transfer RNA (tRNA) gene 15

Two sources for combinatorial evolution: 1. Mix and match exons for alternate splice products 2. Mix and match regulatory elements for different patterns of gene expression 16

Example of combinatory possibilities: Let’s take a look at a familiar example. Say you have a deck of 52 cards and are about to play a game a poker. You wonder how many different 5 card hands are possible. notation C(n,r) n = 52 things taken r = 5 at a time C(n,r) = n! / (n-r)!r! C(52,5) = 52! / 47! × 5! C(52,5) = 2,298,960 Now take 50 genes, each with two alternative splice products. We have (50 × 2) = 100 products. How many different possibilities if we express 10 genes at one time. C(n,r) = n! / (n-r)!r! C(100,10) = 100! / 90! × 10! C(100,10) = 1.7 × 10 13 The evolutionary dynamics of regulatory genes, and in particular combinatorial evolution, warrants serious attention • mutation is an extremely slow process • combinatorial evolution change can be achieve much more quickly via the much faster process of recombination 17

Additional graphic from: http://www.accessexcellence.org http://www.eportalit.com/igx/igx.html 18