1. Gene Function 19 Jan, 2005

3. Transfer of information DNA  RNA  polypeptide Complementary base pairing transfers information –during transcription to form RNA –during translation between codon and anticodon DNA binding proteins –recognize double- or single-stranded DNA –recognize specific nucleotide sequences –are coded by genes –have variety of important functions

4. RNA Transcription: copying nucleotide sequence of DNA into RNA –forms RNA transcript –DNA may be transcribed multiple times RNA –single-stranded polynucleotide –contains ribose sugar –contains the pyrimidine uracil (U) hydrogen bonds with A –5’ and 3’ ends critically important

5. RNA Nucleotides

6. Transcription

8. Transcription steps Initiation –at 5’ end of gene –binding of RNA polymerase to promoter –unwinding of DNA Elongation –addition of nucleotides to 3’ end –rules of base pairing –requires Mg 2+ –energy from NTP substrates Termination –at 3’ end of gene –terminator loop (prokaryote) or processing enzyme coding region 5’UTR3’UTR

9. Promoters

11. Eukaryote RNA processing 5’ end: capping –addition of 7-methylguanosine –linked by three phosphates 3’ end: poly(A) tail –addition of up to 200 adenine nucleotides –downstream of AAUAAA polyadenylation signal Intron removal by spliceosome –all introns have 5’GU and 3’AG recognition sequence (GU – AG rule) –snRNPs of spliceosome provide catalysis –intron excised as lariat, destroyed Some nonprotein- encoding genes have self-splicing introns.

15. Processing Overview

16. Protein structure Protein is polymer of amino acids (polypeptide) –each amino acid has R group conferring unique properties –amino acids connected by peptide bond –each polypeptide has amino end and carboxyl end Structures –primary: amino acid sequence –secondary: hydrogen bonding,  -helix and  -sheet –tertiary: folding of secondary structure –quaternary: two or more tertiary structures Shape and function determined by primary structure encoded by gene

20. Translation mRNA is translated by tRNA at ribosome nucleotide sequence is read three nucleotides at a time –each triplet is called a codon –each amino acid has one or more codons –64 possible codons (4  4  4) = genetic code used by all organisms with few exceptions Genetic code specifies 20 different amino acids (sometimes selenocysteine)

21. Codon translation tRNA –anticodon consists of 3 nucleotides base pairs with codon in antiparallel fashion –3’ acceptor end attaches amino acid attachment catalyzed by aminoacyl-tRNA synthetases one for each different tRNA Wobble hypothesis –permits third nucleotide of anticodon (5’ end) to hydrogen bond with alternative nucleotide –permits a tRNA to translate more than one codon

25. Translation at the ribosome Ribosome –large subunit –small subunit 3 ribosomal sites –A site (amino site), accepts incoming charged tRNA –P site (polypeptide site), peptide bond –E site (exit site), tRNA exits ribosome Amino terminus synthesized first, beginning near 5’ end of mRNA

28. Protein function Function determined by amino acid sequence Colinearity between DNA nucleotide sequence and amino acid sequence of protein Two broad types of protein –structural proteins –active proteins, including enzymes Proteins often have specialized domains

30. Malfunctioning alleles Mutation alters gene function by altering structure/function in product –wild-type: normal allele designated by plus (+) sign example: arg-3 + –mutation: change in nucleotide sequence sometimes designated by minus (–) sign Nutritional mutants –prototroph: wild-type, synthesizes nutrients –auxotroph: mutant, fails to make essential nutrient (e.g., amino acid)

32. Types of mutation Mutant site: area of nucleotide change Three types of mutation –substitution of different amino acid e.g., 5’GGA3’  5’GAA3’, gly  glu –premature stop codon e.g, 5’GGA3’  5’UGA3’, gly  stop –frameshift insertion or deletion of one or two nucleotides alters reading frame from point of change all downstream codons altered

33. Effect of mutation Often reduces or eliminates protein function –leaky mutation: reduced function –null mutation: no function –silent mutation: no change in function, though amino acid sequence may be changed Mutations in information transfer –mutations in exon-intron junction –mutations in promoter or regulatory sequences –mutations in UTRs

34. Dominance and recessiveness Recessive genes typically produce little or no product. One dose of wild-type gene produces sufficient product, resulting in dominant phenotype (haplo-sufficiency) Nomenclature –recessive genes, lower case italicized letter, e.g., a –dominant gene, upper case italicized letter, e.g., A Genotypes –A/A, (a + /a + ) homozygous dominant –A/a, (a + /a) heterozygous –a/a, homozygous recessive normal phenotype

36. Haplo-insufficiency Wild-type gene provides insufficient product to fulfill normal cell function –in this case, defective gene is dominant B+/B+, homozygous recessive B/B+, heterozygous B/B, homozygous dominant defective phenotype

39. Assignment: Concept map, solved problems 1 and 2, basic problems 2, 8 through 12, challenging problems 18, 21, 23-25 Continue with web-based NCBI tutorial sections from Introduction to Using BLAST to compare sequences.