The Genetic Code tRNAs charged with uncharged tRNAs an amino acid - - PowerPoint PPT Presentation

The Genetic Code

Polypeptide chain mRNA tRNA’s charged with an amino acid uncharged tRNA’s

Ribosome: note there are two sites for binding a charged tRNA (A-site and P-site) Steps in polypeptide elongation: 1. Prior to peptide bond formation: Peptidyl tRNA (bound to growing peptide chain) occupies the P-site. A charged tRNA occupies the A-site. 2. Peptide bond formation: Formation of bond is catalyzed by ribosome, and involves transfer of polypeptide from tRNA in the P-site to the tRNA in the A-site. This is stage shown above. 3. Translocation: Ribosome moves one codon down the mRNA. After this translocation the peptidyl tRNA will be in the P-site and the uncharged tRNA leaves the ribosomal complex. A P

A A A U U U

mRNA 5’ 3’

anticodon codon

Relationship between RNA and amino acid sequence: RNA polymer: 4 subunits / Polypeptide: 20 subunits

• 1:1 can’t work
• 2:1 provides 42 = 16 possibilities (still can’t work)
• 3:1 provides 43 = 64 possibilities (BINGO!)

“Universal” genetic code

UAG, UGA, UAA Stop AUG, GUG Start GUU, GUC, GUA, GUG Val AUU, AUC, AUA Ile UAU, UAC Tyr CAU, CAC His UGG Trp GGU, GGC, GGA, GGG Gly ACU, ACC, ACA, ACG Thr GAA, GAG Glu UCU, UCC, UCA, UCG, AGU,AGC Ser CAA, CAG Gln CCU, CCC, CCA, CCG Pro UGU, UGC Cys UUU, UUC Phe GAU, GAC Asp AUG Met AAU, AAC Asn AAA, AAG Lys CGU, CGC, CGA, CGG, AGA, AGG Arg UUA, UUG, CUU, CUC, CUA, CUG Leu GCU, GCC, GCA, GCG Ala

Redundancy of genetic code

Features of the Genetic code:

• The code is a triplet code.
• The code is comma free
• The code in non-overlapping
• The code is highly degenerate
• Wobble occurs in the anti-codon

Pairing for leucine tRNA between standard nucleotides

G G U G G C G G A

Wobble pairing for Glycine tRNA is associated with the non- standard nucleotide Inosine (I).

C U C C U U G A G G A G

Leu Leu

C C I

Gly

C C I

Gly

C C I

Gly Wobble: non Watson-Crick bases pairing between codon and anti-

• codon. Wobble accounts for the ability of a single tRNA to recognise

more than one codon. Wobble is predominantly a third codon positions effect, Some have suggested that the pattern of degeneracy

• f the genetic code is a adaptation to minimize errors arising from

“unintended” wobble at third positions. 5’ anticodon G C A U I 3’ codon U or C G U A or G A, U or C

Codon – anticodon paring in the genetic code

The genetic code determines how random changes to a protein-coding gene brought about by the process of mutation will impact the function of the encoded protein.

• 1. Degeneracy
• 2. Physiochemical similarity

Evolution of the genetic code: How old is the genetic code?

• The earth is 4.6 billion years old
• Youngest estimate of photosynthesis is 2.5 billion years ago

Window: 4.6 billion - 2.5 billion years ago

Photosynthesis evolved once in the cyanobacteria. It was later “stolen” by the eukaryotic ancestors of plants; in that it was probably acquired via the evolution of symbiosis between a eukaryotic cell and an cyanobacterium. Photosynthesis appears later in other lineages of eukaryotes as they “stole” it from each other. The cellular machinery for photosynthesis is highly derived and dependent upon a triplet genetic code. Hence the modern form of the code must have evolved prior to photosynthesis.

Banded iron formations indicate the existence of free O2

RNA World DNA evolves DNA & RNA World

Archaea Bacteria Eucarya

Genetic code evolves back here

“Tree of life” showing three “domains, as estimated from rRNA sequences. Note that the notion of a tree for the early divergences of life is

• controversial. I have also

specified a basal trichotomy, as the inferred position of the root also is controversial.

Archaea: prokaryotes with a plasma membrane of isoprene ester lipids. They have distinct acrhaebacterial-type riboosomes Bacteria: prokaryotes with a plasma membrane of fatty acid ester lipids. They have distinct Eubacterial--type ribosomes Eukarya: Cells with true nucleus. The plasma membrane consists of isoprene ester lipids. Ribosomes appear related to the acrhaebacterial-type. Posess double membrane bound

• rganelles derived from bacterial

endosymbionts

Eubacteria, and the genetic code are alder than 2.5 billion years, be we don’t know how much older. Evolution of the genetic code: How old is the genetic code?

Window: 3.9 billion - 2.5 billion years ago Evolution of the genetic code: How old is the genetic code? Conditions for pre-cellular life (RNA World, etc) were not present prior to 3.9 biollion years ago. The genetic code is ANCIENT! RNA world:

• Pre-life, organic world
• All RNA molecules
• RNA acts as first genetic molecule and as enzyme
• Controversial: RNA is unstable and known enzymatic activities are narrow

Evolution of the genetic code: How did it evolve?

• 1. “Frozen accident” hypothesis:
• Francic Crick (1968)
• Code evlved very early
• Most extreme version states that organization of the code was

an accidient of history [i.e., neutral], and it have remianed unchanges ever since [frozen]

• Less extreme verion lets natural selection play a role in
• ptimizing the original code, then it becomes frozen

Evolution of the genetic code: How did it evolve?

RNA

• A. Early stage:

direct interactions with “RNA handles”

• B. Later stage: use of a

template and other RNA molecules.

• C. Late stage: RNA

handles evolve into modern tRNAs RNA

Amino acid with multiple codons in RNA handle direct interaction among many RNA Handles Peptide synthesis via catalytic RNA? Perhaps an additional catalytic RNA (Ribozyme) is required here? The use of a template for some of the codons evolves. Modern tRNA structure evolves

One possible model for the evolution of tRNAs and the genetic code from a direct interaction between the involved amino acid and an “RNA handle” molecule.

• 2. Stereochemical compatibility hypothesis:

Note: current tRNAs require an enzyme to catalyze cobalent bond between amino acid and tRNA Modern tRNAs have only very weak affinity for cognate amino acid

Evolution of the genetic code: How did it evolve?

• 3. Co-evolution with biosynthesis pathways
• 4. Minimize impact of mutation

Adapted from Knight et al. (1999) TIBS 24:241-247

• 5. Genetic flexibility
• degeneracy at third positons
• physiochemical similarities

Evolution of the genetic code: Is the code frozen?

Evolution of the genetic code: Is the code nearly frozen because of cellular constraints?

AGGA UCCU archaeal tRNALys Un-natural amino acid Natural amino acid archaeal tRNALys

Natural triplet codon in E. coli Artificial quadruplet codon in E. coli

Andersen et al. PNAS (2004); and artificial quadruplet genetic code