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Gene Function
19 Jan, 2005
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
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
RNA Nucleotides
Transcription
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 Mg2+
energy from NTP substrates
• Termination
– at 3’ end of gene
– terminator loop (prokaryote) or processing enzyme
5’UTR
coding region
3’UTR
Promoters
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 nonproteinencoding genes have
self-splicing introns.
Processing Overview
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
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)
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
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
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
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)
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
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
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
normal phenotype
– A/a, (a+/a) heterozygous
– a/a, homozygous recessive
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
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.