Lecture 2
The genetic code & Enzymes:
Organic Catalysts
Translation of RNA
code into protein
The code consists of at least three bases, according
to astronomer George Gamow. To code for the 20
essential amino acids a genetic code must consist of at
least a 3-base set (triplet) of the 4 bases.
If one considers the possibilities of arranging four
things 3 at a time (4X4X4), we get 64 possible code
words, or codons (a 3-base sequence on the mRNA that
codes for either a specific amino acid or a control
word).
Translation of RNA code into
protein
The genetic code was broken by Marshall
Nirenberg and Heinrich Matthaei, a decade
after Watson and Crick's work.
Nirenberg discovered that RNA,
regardless of its source organism, could
initiate protein synthesis when combined
with contents of broken E. coli cells.
By adding poly-U to each of 20 test-tubes
(each tube having a different "tagged"
amino acid) Nirenberg and Matthaei were
able to determine that the codon UUU (the
only one in poly-U) coded for the amino acid
phenylalanine.
Steps in breaking the genetic code: the deciphering of a poly-U mRNA. Image from Purves et al., Life: The
Science of Biology, 4th Edition
Translation of RNA code into
protein
Likewise, an artificial mRNA consisting of alternating A and C bases would
code for alternating amino acids histidine and threonine. Gradually, a
complete listing of the genetic code codons was developed.
Deciphering the code: poly CA. Image from Purves et al., Life: The Science of Biology, 4th Edition
Translation of RNA code into
protein
The genetic code consists of 61 amino-acid coding codons and
three termination codons, which stop the process of translation.
The genetic code is thus redundant (degenerate in the sense of
having multiple states amounting to the same thing), with, for
example, glycine coded for by GGU, GGC, GGA, and GGG codons.
If a codon is mutated, say from GGU to CGU, is the same amino
acid specified?
Translation of RNA code into
protein
The genetic code. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates
(www.sinauer.com) and WH Freeman (www.whfreeman.com).
Protein synthesis
Prokaryotic gene regulation differs from eukaryotic regulation, but since
prokaryotes are much easier to work with, we focus on prokaryotes at this
point
Promoters are sequences of DNA that are the start signals for the
transcription of mRNA. Terminators are the stop signals. mRNA molecules
are long (500- 10,000 nucleotides).
Ribosomes are the organelle (in all cells) where proteins are synthesized.
They consist of two-thirds rRNA and one-third protein. Ribosomes consist
of a small (in E. coli , 30S) and larger (50S) subunits. The length of rRNA
differs in each. The 30S unit has 16S rRNA and 21 different proteins. The
50S subunit consists of 5S and 23S rRNA and 34 different proteins. The
smaller subunit has a binding site for the mRNA. The larger subunit has
two binding sites for tRNA.
Subunits of a ribosome. Image
from Purves et al., Life: The
Science of Biology, 4th Edition,
by Sinauer Associates
(www.sinauer.com) and WH
Freeman
(www.whfreeman.com).
Protein synthesis
Transfer RNA (tRNA) is basically cloverleaf-shaped. tRNA
carries the proper amino acid to the ribosome when the codons call
for them. At the top of the large loop are three bases, the anticodon,
which is the complement of the codon.
There are 61 different tRNAs, each having a different binding
site for the amino acid and a different anticodon. For the codon
UUU, the complementary anticodon is AAA. Amino acid linkage
to the proper tRNA is controlled by the aminoacyl-
tRNA synthetases. Energy for binding the amino acid to tRNA
comes from ATP conversion to adenosine monophosphate (AMP).
Protein synthesis
Protein synthesis
Translation is the process of converting the mRNA codon sequences into
an amino acid sequence. The initiator codon (AUG) codes for the amino
acid N-formylmethionine (f-Met). No transcription occurs without the
AUG codon. f-Met is always the first amino acid in a polypeptide chain,
although frequently it is removed after translation. The intitator
tRNA/mRNA/small ribosomal unit is called the initiation complex. The
larger subunit attaches to the initiation complex. After the initiation phase
the message gets longer during the elongation phase.
Translation image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates
(www.sinauer.com) and WH Freeman (www.whfreeman.com).
Protein synthesis
New tRNAs bring their amino acids to the open binding site on the
ribosome/mRNA complex, forming a peptide bond between the amino acids.
The complex then shifts along the mRNA to the next triplet, opening the A
site. The new tRNA enters at the A site.
When the codon in the A site is a termination codon, a releasing factor binds
to the site, stopping translation and releasing the ribosomal complex and mRNA.
Protein synthesis
Often many ribosomes will read the same message, a structure
known as a polysome forms. In this way a cell may rapidly
make many proteins.
Many ribosomes translating the same message, a polysome. Image from Purves et al., Life: The Science of Biology,
4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com).
Enzymes: Organic Catalysts
The Labors
Enzymes allow many chemical reactions to occur within the
homeostasis constraints of a living system.
Enzymes function as organic catalysts. A catalyst is a chemical
involved in, but not changed by, a chemical reaction.
Many enzymes function by lowering the activation energy of
reactions.
By bringing the reactants closer together, chemical bonds may be
weakened and reactions will proceed faster than without the catalyst.
Enzymes: Organic Catalysts
The use of enzymes can lower the activation energy of a reaction (Ea). Image from
Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates
(www.sinauer.com) and WH Freeman (www.whfreeman.com).
Enzymes: Organic Catalysts
Enzymes can act rapidly, as in the case of carbonic anhydrase (enzymes
typically end in the -ase suffix), which causes the chemicals to react 107
times faster than without the enzyme present.
Carbonic anhydrase speeds up the transfer of carbon dioxide from cells
to the blood. There are over 2000 known enzymes, each of which is
involved with one specific chemical reaction.
Enzymes are substrate specific. The enzyme peptidase (which breaks
peptide bonds in proteins) will not work on starch (which is broken down
by human-produced amylase in the mouth).
Enzymes: Organic Catalysts
Enzymes are proteins. The functioning of the enzyme is determined by
the shape of the protein.
The arrangement of molecules on the enzyme produces an area known
as the active site within which the specific substrate(s) will "fit".
It recognizes, confines and orients the substrate in a particular direction.
Space filling model of an enzyme working on glucose. Note the shape change in the enzyme (indicated
by the red arrows) after glucose has fit into the binding or active site. Image from Purves et al., Life:
The Science of Biology, 4th Edition.
Enzymes
Enzymes
Enzymes
Enzymes
Enzymes
Enzymes
Enzymes
Enzymes
Enzymes
Enzymes
Enzymes
Enzymes
Enzymes
Enzymes
Enzymes
Enzymes
Enzymes: Organic Catalysts
Plot of enzyme activity as a function of pH for several enzymes. Note that each
enzyme has a range of pH at which it is active as well as an optimal pH at which
it is most active. Image from Purves et al., Life: The Science of Biology, 4th
Edition.
Enzymes: Organic Catalysts
Negative feedback and a metabolic pathway. The production of the end product (G) in sufficient
quantity to fill the square feedback slot in the enzyme will turn off this pathway between step C and
D. Image from Purves et al., Life: The Science of Biology, 4th Edition.
Enzymes: Organic Catalysts
Specific case of succinate dehydrogenase and its natural substrate (succinate) and competitors (oxalate et
al.). Images from Purves et al., Life: The Science of Biology, 4th Edition,
Thank You