Single-letter code: M D L Y

The Genetic CodeHow the genetic code was deduced is quite an interesting but horribly complicated story of prokaryotic genetics. Ill just give you the Cliff notes version:Francis Crick and Sidney Brenner figured out that:The genetic code maps codons of 3 bases into one amino acid.AUA->IleGAU->AspAGA->ArgmRNA-> Amino Acid

The Genetic CodeCrick and Brenner figured out that:The DNA code is read sequentially from a fixed position in the gene

The mechanism and machinery for translating a proteinThree components:

mRNA, rRNA, tRNA and protein synthesisIn translation, the language of nucleic acids is translated into a newlanguage, that of proteinsmRNA provides the code, in linear digital form, for making a proteintRNA provides an adaptor that links the code in a polynucleotide chainto amino acids that make up the polypeptide chain rRNA and ribosomes provide the decoder. Ribosomes bring togethermRNA and tRNA, and catalyze the translation of an mRNA into apolypeptide chain. Ribosomes are the site of protein synthesis. Ribosomes create peptide bonds between amino acids to create proteins

tRNA is the adapter.Complementary to the CodonAmino acid is matched to the Anti-codon.

Two views of the adaptor molecule,transfer RNA (tRNA), which guidesamino acids to the mRNA-ribosomecomplexThe anticodon of the tRNA aligns with the codon in mRNA throughcomplementary base pairing53

Translation occurs 5 to 3Translation is performed with the help of the Ribosome.Is tRNA orientationwith mRNA correctas drawn?

RNA is the major component of the Ribosome.About 2/3 of the Ribosome is RNA by mass. These RNA molecules are called rRNA and they play a central role in the translation of mRNA into polypeptides.

Ribosomal RNAs (rRNAs) form complex2o and 3o structures that are essential for their functionWhat does this rRNAmolecule look like in three dimensions?

3-D model of 16s rRNA molecule as it folds in the ribosomeand overlaid withits protein subunits

Behold, the large subunit containing the 23s + 5s rRNAsProteins are blue, RNAs are redand white

Translation - Initiation

Translation - Elongation

Translation - ElongationAminoacyl tRNA

Translation - Elongation

Translation - Elongation

Translation - Elongation

Translation - TerminationSTOP

Translation - TerminationSTOP

Translation normallyoccurs on polyribosomes,or polysomesThis allows for amplificationof the signal from DNA andRNA, i.e.,One gene copy

Hundreds of mRNAs

Thousands of proteins

Translation: the movie

How many bases are required to make a genetic code toserve 20 different amino acids?# of 2-base combos = 42 = 16# of 3-base combos = 43 = 64Not enough!Too many!What is the solution?Evolve a code that is redundant!How?Degeneracy at the third codon positionLets look at the Genetic Code

Transfer RNA (tRNA) andthe genetic code

Many different base modificationsoccur in tRNAWhy are these modifications necessary?

Transfer RNA (tRNA) andthe genetic codeLegitimateG-U bpWobble bp

Inosine can pair legitimatelywith three other bases, when inosineis in the wobble position, i.e., thefirst, or 5 base of the anticodon How many chemical changes arerequired to convert guanine to Inosine?How many chemical changes arerequired to convert adenine to Inosine?

Is there a logic to the Genetic Code? 8 codon families where the third codon position is fully degenerate, i.e, any of the four bases has the same meaning: (4-fold degeneracy)

AC__ ThrGC__AlaCU__Leu

UC__SerGG__GlyGU__Val

CC__ProCG__Arg

Thus, for these 8 amino acids, substituting one base foranother at the 3rd position is a SYNONYMOUS change

Is there a logic to the Genetic Code? 7 codon pairs where meaning is the same whichever pyrimidine occurs at 3rd position: (2-fold degeneracy)

UAUTyrUGUCys AGUSerAAUAsnUACUGC AGCAAC

UUUPheCAUHis GAUAspUUCCAC GAC5 codon pairs where purines in the 3rd position are interchangeable:(2-fold degeneracy)

AGAArgGAAGluCAAGlnUUALeuAGGGAGCAGUUG

AAALysAAGTherefore, half of 3rd position substitutions will be SYNONYMOUSand half will be NON-SYNONYMOUS

This accounts for 17 amino acids:

- Trp (UGG) and Met (AUG) are specified by unique codons (non-degenerate codons)

- Whats left?Isoleucine (Ile)

-- How is Ile specified? (This is one of todays homework questions)

The logic of the Genetic Code8 families with 4-fold degeneracy = 32 codons12 families with 2-fold degeneracy = 24 codons+ 3 STOP codons (UAA, UGA, UAG)= a 64 total codons

Point mutations

Point mutations can affect protein structure and function

Type of point mutations:- substitutions (missense and nonsense mutations)- insertions and deletions (frameshift mutations)

Frame Shift MutationsWhat happens when you get insertions or deletions of bases in the DNA sequence?Usually you end up with a mess.THE BIG FAT CAT ATE THE RAT AND GOT ILLDeletion of one baseTHE IGF ATC ATA TET HER ATA NDG OTI LLAnd its all pops and buzzes.Usually frame shift mutations result in premature stop codons.

What is wrong with the mouse on the right?Relationship between genes and proteinsExample of a monogenic, or single-gene disorder

Alkaptonuria, aka Black Urine disease, in humansSymptoms:

urine and ear wax turns black as ink shortly after exposure to airochronosis: musculoskeletal effects, including progressive degenerative arthritis of the large joints, esp. hip and shoulder- signs of ochronosis: -black deposits in the sclerae (white of eye)-blue colored auricles (ear lobes)

What is the gene defect, or molecular genetic basis, in alkaptonuria?

four point mutations occur in the human HGO gene - Blastp comparison of HGO gene from human and fungusAre any of the sites in these proteins functionally constrained?

RGVRYRVTLPDGPVRGYICELYQGHYQLPELGPIGSNGLANARDFQAPVAAFDDEEGPTE 247

RG+R+ + + + RGYI E+Y H++LP+LGPIG+NGLAN RDF P+A ++D + P

RGMRFSIDVFE-ETRGYILEVYGVHFELPDLGPIGANGLANPRDFLIPIAWYEDRQVPGG 242

T196fs (frameshift)

P230S (missense)

YRLYSKFNNHLFSARQDHTPFDIVAWHGNYYPYKYDLGRFNTMGSVSFDHPDPSIYTVLT 307

Y + +K+ LF+A+QD +PF++VAWHGNY PYKY+L F + SV+FDHDPSI+ TVLT

YTVINKYQGKLFAAKQDVSPFNVVAWHGNYTPYKYNLKNFMVINSVAFDHADPSIFTVLT 302

(missense) V300G

GPSDHVGTAIADFVIFPPRWLVAEKTFRPPWYHRNTMSEFMGLITGNYDAKTGGGFQPAG 367

S G AIADFVIFPPRW VA+KTFRPP+YHRN MSEFMGLI G+Y+AK GGF P G

AKSVRPGVAIADFVIFPPRWGVADKTFRPPYYHRNCMSEFMGLIRGHYEAKQ-GGFLPGG 361

R321X (nonsense)

Molecular basis of AlkaptonuriaMutations: Proline230Serine and Valine300Glycine account for most cases of the disorder

Haplotypes:each of these two mutant alleles constitutes a haplotype, i.e., one haploid type. Progeny inherit one haplotype from each parent.

Categorize three different types of point mutations ATA TAC GTA CAT ile tyr val his GAAglu AAA GAA TGG GTT lys glu trp val TGCcys TCG CCA TGG CCA ser pro trp proTAGX (stop)123Chemicaltype:Informationaltype:Functionaltype:TransversionTransversionTransitionMissenseMissenseNonsenseDeleteriousNon-synonymousNondegenerate siteDeleteriousNon-synonymousNondegenerate siteDeleteriousNon-synonymousNondegenerate site

Categorize three more types of point mutations ATA TAC GTA CAT ile tyr val his GTCval AAA GAA TGT GTT lys glu cys val cys TCG CCA TGG CCA ser pro trp pro A456Chemicaltype:Informationaltype:Functionaltype:TransversionTransitionIndel (insertion)MissenseMissenseFrameshiftNeutral (silent)Synonymous(4-fold degenerate site)NeutralSynonymous(2-fold degenerate site)DeleteriousNon-synonymousTGC TCG CAC ATG GCC A ser his met gly Is a 4-fold degenerate site ever functionally constrained?

Where can you get more information about the basic conceptsembedded within the Central Dogma of Molecular Biology?Here is a great site, full of simple, clear, and animated (!) tutorials:http://www.dnaftb.org/dnaftb/Chapters 15-28 in this series provides an excellent review of the first group of lectures in Bioinformatics:http://www.dnaftb.org/dnaftb/15/concept/

Homework #5 : due Monday, Feb. 12Express fractions as a %

Ribosomes are large ribonucleoprotein (RNP)complexesThey are complex affairs, composed of an array ofRNA + proteins