Lesson

Protein synthesis:
Transcription and
1.1 Translation
DNA has the code of instruction for the expression of inherited traits. A
certain inherited trait cannot be expressed if the right protein is not made. The
direction in which genetic information flows is from the DNA to RNA to proteins.
This idea was first proposed by Francis Crick in 1958 which he called the Central
Dogma of Molecular Genetics, which can be represented in a diagram as follows:

Based on the central dogma, a given gene is transcribed to produce a

messenger RNA (mRNA) complementary to one of the DNA strands, and that
transfer RNA (tRNA) molecules translate the sequence of bases in the mRNA
into the appropriate sequence of amino acids to form specific protein.

Protein synthesis is a term that means making protein. The recipe for
protein synthesis uses ingredients like mRNA, tRNA, and amino acids as well as a
special piece of equipment called a ribosome. In this lesson, we'll talk about how
your cells use the ingredients of protein synthesis to build new proteins inside of
ribosomes.

There are two steps of protein synthesis: transcription and translation.

If you transcribe something it means you write it down. So, in this step, the
DNA’s genetic information, or secret code gets written onto a strand of RNA. RNA is
a copy, or a transcription, of DNA. See, the DNA is very important, since it holds the
information needed for making new cells and maintaining life, so it never leaves the
nucleus. The RNA is the one that goes out into the cytoplasm to do work throughout
the cell. It's also super important because without RNA our bodies would not be able
to make proteins, which make up about 20% of our bodies.

The process of making a copy of RNA from the DNA is called transcription.
This is important to making proteins! The DNA, which is a double helix, is
transcribed or copied, into a single helix--the RNA. The RNA then takes on one of
these three forms:

Ribosomal RNA, or rRNA, helps make up the ribosome. Forms the structural
component of the ribosome which serves as the site for attachment of mRNA and
tRNA and the site for protein synthesis. The ribosome is the protein factory of the
cell.

Messenger RNA, or mRNA, carries the blueprint copied from the cell's
original DNA. It's like a piece of mail sent to the ribosomes, providing instructions
on how to build proteins. It serves as the basis to determine the amino acid sequence
during protein synthesis

Transfer RNA, or tRNA, is also part of the way a cell builds proteins--it does
the heavy lifting. Think of tRNA like a dump truck that brings the amino acid (the
raw material for making proteins) to the ribosome. It translates the nucleotide
sequence in mRNA into protein amino acid sequence because it has an anticodon
that complements with the codon of mRNA

RNA can base-pair with a single-stranded DNA, and this pairing obeys the
same hydrogen-bonding rules as in DNA, except the adenine pairs with uracil (U)
instead of thymine. RNA can also base-pair with itself.

Genetic information is stored in the DNA contained in the nucleus. How does
the genetic information get out from the nucleus and reach the cytoplasm,
particularly the ribosome, which is the workbench of protein synthesis?
 According to the messenger hypothesis developed by Crick and his colleagues,
RNA molecule forms as a complimentary copy of one DNA strand of a particular
gene. During transcription the information contained in the DNA is exactly copied
by the messenger
RNA, or mRNA. This
mRNA, then travels from
the nucleus to the
ribosome in the
cytoplasm, where it
serves as a template
for the synthesis of
proteins.

Steps of Transcription: (see the diagram below to visualize the processes or steps)

1. Initiation - In the nucleus, RNA Polymerase recognizes the recognition sites or

initiation sites causing it to bind to a promoter (the start of a gene). The RNA
Polymerase then separates the DNA into single strands so the template strand
can be read in the 3’ to 5’ direction.

2. Elongation – Pre-mRNA nucleotides are quickly paired with their complementary

bases which correspond with the template strand of the DNA. The pre-mRNA
moves in the 5’ to 3’ direction while the template strand of DNA moves oppositely
 from the 3’ to 5’ direction. Pre-mRNA does not contain thymine, instead uracil
(U) is used as the complementary base for Adenine.

3. Termination – When the RNA polymerase reaches the terminator, it signals the
RNA polymerase to stop and release from the DNA. Once separated the two DNA
strands come back together and reform the double helix. The newly formed
premRNA molecule is then released.

Translation involves “decoding” a messenger RNA (mRNA) and using its

information to build a polypeptide, or chain of amino acids. For most purposes, a
polypeptide is basically just a protein.

In an mRNA, the instructions for building a polypeptide come in groups of

three nucleotides called codons. Here are some key features of codons to keep in
mind as we move forward:
• There are 61 different codons that encode only 20 amino acids
• Three “stop” codons mark the polypeptide as finished
• One codon, AUG, is a “start” signal to kick off translation (it also specifies the
amino acid methionine)

These relationships between mRNA codons and amino acids are known as the
genetic code. The genetic code chart may be used to determine the triplet code(s)
for each amino acid. It can be noticed that there are many more codons than there
are different amino acids in proteins. Combinations of the four available “letters”
(the bases) give 64 (43) different three-letter codons, yet only 61 codons encode only
20 amino acids. AUG, which a code for methionine, is also the start codon that
initiates translation. The three of the codons, (UAA, UAG, UGA) are stop codons, or
chain terminators; when the translation machinery reaches one of these codons,
translation stops, and the polypeptide is released from the translation complex.
 In translation, the codons of an mRNA are read in order (from the 5' end to
the 3' end) by molecules called transfer RNAs, or tRNAs. Each tRNA has an
anticodon found in one of the three loops of the cloverleaf-shaped tRNA.
Anticodon is a set of three nucleotides that binds to a matching mRNA codon
through base pairing. The other end of the tRNA carries the amino acid (simplest
form of protein) that's specified by the codon.
The chart above shows the Universal Genetic Code. Genetic information is
encoded in mRNA in three-letter units – codons – made up of the bases uracil (U),
cytosine (C), adenine (A), and guanine (G). To decode a codon, find its 1 st letter in
the left column, then read across the top of its second letter, then read down the
right column to its third letter. The place where the three letters intersect is the
amino acid the codon specifies. For example, codon GUU codes for valine (Val for
short) while AAA is for Lysine (Lys).
 Structure of Transfer RNA (tRNA)

Transfer RNAs bind to messenger RNAs inside of a protein-and-RNA structure

called the ribosome.
This organelle facilitates the specific coupling of tRNA anticodons with mRNA
codons during protein synthesis. A ribosome is composed of two subunits, the large
and the small subunits. These ribosomal subunits are constructed of proteins and
another type of RNA molecule called ribosomal RNA (rRNA). These subunits are
made in the nucleolus and are exported to the cytoplasm. The ribosome has a
binding site for mRNA and another three binding sites for tRNA. These are the P site
(peptidyl-tRNA site) that holds the tRNA carrying the growing polypeptide chain; the
A site (aminoacyl-tRNA site) that holds the tRNA carrying the next amino acid to be
added to the chain; and lastly the E site (exit site) that releases tRNA that has
unloaded amino acid. As tRNAs enter slots in the ribosome and bind to codons, their
amino acids are linked to the growing polypeptide chain in a chemical reaction. The
end result is a polypeptide whose amino acid sequence mirrors the sequence of
codons in the mRNA.
Let’s have a closer look at the different steps of translation.

1. Initiation
In order for translation to start, we need a few key ingredients. These include:
• A ribosome (which comes in two pieces, large and small)
• An mRNA with instructions for the protein we'll build
• An "initiator" or tRNA carrying the first amino acid in the protein, which is
almost always methionine (Met)

Together, they form the initiation complex, the molecular setup needed to start
making a new protein. The tRNA carrying methionine attaches to the small ribosomal
subunit. Together, they bind to the 5' end of the mRNA by recognizing the 5' GTP
cap (added during processing in the nucleus). Then, they "walk" along the mRNA in
the 3' direction, stopping when they reach the start codon (often, but not always, the
first AUG).

2. Elongation
 Elongation is when the polypeptide chain gets longer. Our first,
methioninecarrying tRNA starts out in the middle slot of the ribosome, called the P
site. Next to it, a fresh codon is exposed in another slot, called the A site. The A site
will be the "landing site" for the next tRNA, one whose anticodon is a perfect
(complementary) match for the exposed codon.
Once the matching tRNA has landed in the A site, it's time for the action: that is,
the formation of the peptide bond that connects one amino acid to another. This
step transfers the methionine from the first tRNA onto the amino acid of the second
tRNA in the A site.
Once the peptide bond is formed, the mRNA is pulled onward through the
ribosome by exactly one codon. This shift allows the first, empty tRNA to drift out
via the E ("exit") site. It also exposes a new codon in the A site, so the whole cycle
can repeat. And repeat it does...from a few times up to a mind-boggling 30,000 times!
The protein titin, is made of 30, 000 amino acids and includes 320 protein domains
and therefore is known as the largest human protein.

3. Termination
Translation ends in a process called termination. Termination happens when a
stop codon in the mRNA (UAA, UAG, or UGA) enters the A site.
Stop codons are recognized by proteins called release factors, which fit neatly into
the P site (though they aren't tRNAs). Release factors mess with the enzyme that
normally forms peptide bonds: they make it add a water molecule to the last amino
acid of the chain. This reaction separates the chain from the tRNA, and the newly
made protein is released.
This free polypeptide chain begins to coil and fold spontaneously, forming a
functional protein of specific conformation to express the trait controlled by a certain
gene.

STEPS OF TRANSLATION