Lecture 9. The
Flow of genetic information
I. Importance- To understand how information
from genes can direct metabolism etc, we need to fully
Understand how
genes influence the phenotype
II. The genetic code: how
precise groupings of the 4 nucleotides specify 20 amino Acids
A. In the genetic code, a
triplet codon represents each amino acid
B. Mapping studies confirmed
that a gene’s nucleotide sequence is colinear with a
polypeptide’s amino acid sequence
C. Genetic analysis revealed
that nonoverlapping codons
are set in a reading frame
A codon
is composed of three nucleotides, and the designated starting point for each
gene
establishes the reading frame for these
triplets
Most amino acids are
specified by more than one codon, which makes the
genetic code a
“degenerate”
code
D. Cracking the code:
biochemical manipulations revealed which codons
represent which
amino acids
1. The discovery of
messenger RNAs, molecules for transporting genetic
information
2. Synthetic mRNAs and in
vitro translational systems made it possible to discover which
codons designate which amino acids
3. The 5’-to-3’ direction in
mRNA corresponds to the N-terminal-to-C- terminal direction in
a polypeptide
4. Nonsense codons cause termination of a polypeptide chain
E. The genetic code: a
summary
F. Using genetics to verify
the code
G. The genetic code is
almost, but not quite, universal
Yanofsky’s expt.
In eukaryotes, mRNA
processing after transcription produces a mature messenger RNA
1. Adding a methylated cap at the 5’ end and a poly-A tail at the 3’
end
2. RNA splicing removes
sequences known as introns from the primary
transcript
3. Alternative splicing
often produces different mRNAs from the same primary transcript
IV. Translation: base-pairing
between mRNA and tRNAs
directs assembly of a polypeptide on the
ribosome
A. Transfer RNAs mediate the translation of mRNA codons
to amino acids
1. tRNA structure: A compact “L” carrying an anticodon at one end and an amino acid at the
other
2. Base-pairing between an
mRNA codon and a tRNA anticodon directs incorporation of an
amino acid into a growing
polypeptide
3. Wobble: Some tRNAs can recognize more than one codon
B. Ribosomes
are the sites of polypeptide synthesi
1. Ribosomes
are complex structures composed of RNA and protein
2. Different parts of the
ribosome have different functions
C. The mechanism of
translation; there are some significant differences in translation between
prokaryotes and eukaryotes
D. Processing after
translation can change a polypeptide’s structure
V. Mutations and gene
expression
Essential Concepts
Gene expression is the process by which
cells convert the
sequence of a transcript, and then
decode the RNA sequence to the amino acid sequence of a
polypeptide.
The nearly universal genetic
code consists of 64 codons composed
of 3 nucleotides apiece. 61 of
these codons
specify amino acids, while 3 UAA,
codons that do not specify an amino acid.
a. The code is degenerate:
More than one codon specifies every amino acid except
methionine and
tryptophan.
b. AUG in the context of a
ribosome binding site is the initiation codon; it
establishes a reading
frame that determines the grouping
of nucleotides into triplet codons.
c. The code is nonoverlapping. Within a reading frame, the first
three nucleotides constitute one
codon, the next three, the second codon, and so
forth.
Gene expression based on the
genetic code produces the colinearity of
a gene’s nucleotide
sequence and a protein’s sequence of
amino acids.
Transcription is the first stage of gene
expression. During transcription, RNA polymerase
synthesizes a single stranded mRNA
transcript from a
a. RNA polymerase initiates
transcription by binding to the promoter sequence of the
unwinding the double helix to expose
bases for pairing.
b. RNA polymerase extends
the mRNA in the 5’-to-3’ direction by catalyzing formation of
phosphodiester bonds between successively aligned nucleotides.
c. Terminator sequences
in the RNA cause RNA polymerase to dissociate from the
d. In prokaryotes, the
primary transcript is the mRNA that guides polypeptide synthesis.
In eukaryotes, RNA processing
after transcription produces a mature mRNA that travels from the
nucleus to the cytoplasm to direct
polypeptide synthesis.
a. RNA processing adds a methylated cap to the 5’ end and a poly-A tail to the 3’
end of the
eukaryotic mRNA.
b. The spliceosome
removes introns from the primary transcript and
precisely splices together the
remaining exons.
Alternative splicing makes it possible to produce different mRNAs from
the
same primary transcript.
Translation is the stage of gene
expression when the cell synthesizes proteins according to
instructions in the mRNA.
a. tRNAs
carry amino acids to the translation machinery. Aminoacyl
tRNA synthetases connect
amino acids to their
corresponding tRNAs. Each tRNA
molecule has an anticodon
complementary to the mRNA codon specifying the amino acid it carries. Because of
wobble,
some tRNA
anticodons recognize more than one mRNA codon.
b. Translation occurs on
complex molecular machines called ribosomes. Ribosomes have two
binding sites for tRNAs ð P and A, and an enzyme known as peptidyl
transferase that catalyzes
formation of a peptide bond between
amino acids carried by the tRNAs at these two sites.
c. Initiation: To start
translation, part of the ribosome binds to a ribosome binding site on
the
mRNA, which includes the AUG
initiation codon. Special initiating tRNAs with codons
complementary to AUG carry the amino acid
f-met in prokaryotes or met in eukaryotes to the
ribosomal P site. This amino acid
will become the N-terminus of the growing polypeptide.
d. Elongation: When the
carboxyl group of the amino acid connected to a tRNA
at the ribosome’s
P site becomes attached
through a peptide bond to the amino acid carried by the tRNA
at the A
site, the ribosome travels three
nucleotides toward the 3’ end of the mRNA. This movement
exposes the next codon and allows the next round of amino acid addition.
This mechanism of
translation dictates that the 5’-3’
direction in the mRNA corresponds to the N-terminus-to-Cterminus
direction in the polypeptide under
construction.
e. Termination: When the
ribosome encounters in-frame nonsense codons, it ends
translation by
releasing the mRNA and disconnecting
the complete polypeptide from the tRNA.
Processing after translation
may alter a
polypeptide by adding or removing chemical constituents
to or from particular amino
acids, or by cleaving the polypeptide into smaller molecules.
Mutations affect gene
expression in several ways.
a. Mutations in a gene may
modify the message encoded in a sequence of nucleotides. Silent
mutations usually change the third
letter of a codon and have no effect on polypeptide
production.
Missense mutations change the codon for one amino acid to the codon
for another amino acid and
thereby direct incorporation of a
different amino acid. Nonsense mutations change a codon
for an
amino acid to a stop codon, causing synthesis of a truncated polypeptide.
Frameshift mutations change the reading frame of
a gene, altering the identity of amino acids
downstream of the mutation.
b. Mutations outside of
coding sequences that alter signals required for transcription, mRNA
splicing, or translation, will also
disrupt gene expression.
c. Mutations in genes
encoding molecules of the gene expression machinery are often lethal.
Exceptions arise when
another gene supplies a molecule with a similar function. Among these
exceptions are mutations in tRNA genes that suppress mutations in polypeptide-encoding
genes.
VI. Conclusions
A gene is all the
includes the promoter sequences that govern where
transcription begins and ends and those sequences
dictating where
translation starts and stops. Genes also contain the introns
which need to be spliced out.
Terms/Concepts to
Know:
Genetic code, gene-protein colinearity, wobble,
intron, exon, intragenic suppressor, frameshift,
nonsense,
missense,
degenerate code, transcription, splicing, translation, tRNA,
mRNA, anticodon, important
experiments
Know: Figs in chapter 8:
3-11, 14, 16, 18, 21, 24, Table 1