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Protein Synthesis
(Sections 5.1 to 5.4)
 Inherited instructions stored in DNA direct the production of
A Brief History
 Gregor Mendel = factors are responsible for inherited traits
How genes control metabolism?
1. One gene – one enzyme
 Archibald Garrod (1909) = hypothesis states “one gene
 Cells synthesize and degrade organic compounds via
metabolic pathways, with each sequential step catalyzed
by a specific enzyme (figure 2, p. 234)
 Beadle and Tatem experiment (3o years later) were able
to demonstrate this experimentally
i. Neurospora (bread mold) - can survive with minimal
nutrients, however some mutants were not able to
survive why?
ii. Looked at metabolic pathway for the synthesis of
arginine- they distinguished mutants by which
substance needed to be added to the medium in
order for the mold to grow
enzyme A
enzyme B
enzyme C
arginine enzyme D arginine
iii. Conclusion: each mutant lacked a different
functional enzyme, thus blocked at different parts
of the metabolic pathway (see fig. 2, p. 235)
2. One gene – one polypeptide
 Today, we understand that genes code for proteins, and not
all proteins are enzymes. Also, some proteins consist of
more that one polypeptide, each peptide coded by a different
gene (Vernon Ingram) see p. 235
The Central Dogma
The central dogma of molecular biology (Francis Crick,1958)
 The central dogma of molecular biology deals with the
detailed residue-by-residue transfer of sequential
 It states that information cannot be transferred back from
protein to either protein or nucleic acid. DNA  RNA  protein
 DNA cannot leave the nucleus (keeps it from being damaged)
An Overview of Protein Synthesis
 RNA links the genetic code stored in DNA to the production
of Proteins – RNA copies the code in DNA (transcription)
and translates the message into a polypeptide chain
 DNA structure vs RNA structure:
double-stranded, RNA single-stranded
has thymine, RNA has uracil
has Deoxyribose sugar, RNA has ribose sugar
is the genetic code, RNA interprets the code
The Flow of genetic information:
 The linear sequence of nucleotides in DNA ultimately
determines the linear sequence of amino acid in a protein.
RNA processing
Protein Synthesis occurs in Two Stages:
1. Transcription = the synthesis of messenger RNA (mRNA)
using DNA as a template
 Resulting mRNA strand carries this transcript
(small strand) to the protein-synthesizing
2. Translation = synthesis of a polypeptide, which occurs
under the direction of mRNA
 Linear sequence of bases in mRNA is translated
into the linear sequence of amino acids
 Translation occurs at protein-synthesizing
machinery, which consists of ribosomes,
ribosomal RNA (rRNA), and proteins that facilitate
the addition of amino acids to form polypeptide
NOTE: ****Prokaryotes and eukaryotes differ in how protein
synthesis is organized within their cells.
 In Prokaryotes – happens in rapid successions (no nucleus)
 In Eukaryotes – mRNA is modified prior to leaving the
Ribonucleic Acid - RNA
 There are three major classes of RNA:
o Messenger RNA (mRNA) – hold code
o Transfer RNA (tRNA) – help in carrying amino acids
to ribosomal complex
o Ribosomal RNA (rRNA) – structural component of
ribosomal complext
Transcription – In General
 Flow of information from gene to protein is based on a
triplet code (p. 240)
o Recall, there are only 4 different types of nucleotide,
but there are 20 different amino acids. How can we
code for all these amino aicds?
o RNA is read 3 nucleotide bases at a time = a codon
Ex. AUG = methionine – start codon / UUA, UAG, UGA = stop
o The ability to extract the intended message depends
on how the code is read
o The reading frame dictate that this is done 3 bases at
a time with no overlap ex. THE RED DOG
 Genes are first transcribed into mRNA:
o For each gene, only one of the two DNA strands
(template strand) is transcribed
o The strand that is not transcribed is called the parent
o Which strand serves as the template stand varies for
each gene
 mRNA stand is complimentary to DNA template strand
o Recall, uracil (U) in RNA is used in place of thymine
(T)  ie. U pairs with A
Translation – In General
 Linear sequence of codons in mRNA is translated into linear
sequence of amino acids in polypeptide
o Each mRNA codon specifies which amino acid is
incorporated next into growing polypeptide
o Thus, the number of nucleotides is 3 times > a.a.
Cracking the Genetic Code
The first codon was deciphered in 1961 by Nirenberg of the
 61 of 64 triplets code for amino acids
 AUG is the start signal for translation and codes for
 UAA, UAG, UGA code only for signal termination = stop
 There can be two or more codons for each amino acid (ex. UUU,
UUC both code for phenylalanine)
 Codons only code for one amino acid (ex. UUU only codes for
 The correct ordering (called the reading frame) and
grouping of nucleotides is important in the molecular
language of cells. A change in the reading frame leads to a
change in the peptide sequence!  mutation
Proteins Synthesis – The Specifics!
A. Transcription = synthesis of mRNA
transcription of mRNA is catalyzed by RNA polymerase
(separates DNA and builds mRNA in 5’ to 3’ direction)
specific DNA nucleotide sequences mark where
transcription of a gene begins (initiation) and ends
The nucleotide sequence that is transcribed into mRNA
by RNA polymerase is called a transcription unit.
1. Binding of RNA polymerase =
RNA poly. Binds to specific DNA region called the
promoter region  marks initiation
In eukaryotes, the promoter region is approx. 100
nucleotides long and consists of:
i. Promoter region
ii. Binding site – where DNA binding
proteins attach
DNA binding proteins (aka transcription factors) =
bind to TATA box just upstream to initiation site
TATA Box = short repeating nucleotide sequence (~25)
upstream to promoter region (initiation site)
RNA polymerase recognizes transcription factors and
binds to promoter region.
2. Elongation of RNA Strand =
RNA polymerase continues to unwind DNA and add
RNA nucleotides in 5’ to 3’ direction
mRNA strand grows about 30-60 nucleotides/second
several molecules of RNA polymerase can
simultaneously transcribe the same gene!
3. Termination of Transcription =
transcription continues until RNA polymerase
transcribes a terminator sequence
in eukaryotes the most common terminator sequence is
4. Modification of RNA Transcript – Eukaryotes only!
Primary transcript = general term for initial RNA
strand transcribed from DNA
Pre-mRNA = primary transcript that will be processed
to functional mRNA
Transcript can be processed in two ways:
a. alteration of both the 3’ and 5’ ends
- 5’ CAP = guanosine triphosphate is added
(protects the mRNA strand from degradation,
helps in initiation of translation
- 3’ END = poly A tail (protects mRNA from
degredation, facilitates attachment to ribosomal
complex, assists in export of nucleus)
b. removal of intervening sequences
- coding regions (exons) are interrupted by non
coding regions (introns)
- during processing introns are removed by
splicosomes, and exons are joined (RNA splicing)
are removed before mRNA leaves the nucleus
- small nuclear ribonucleoproteins (SnRNPs) play a
key role in RNA splicing
Why have introns?
 Intron DNA sequences may control gene activity
 The splicing process may help regulate the export of mRNA
 Introns may allow a single genet to direct the synthesis of
different proteins (i.e if the same RNA transcript is processed
B. Translation = synthesis of peptide, coordinated by mRNA
We Need:
amino acids
 are made up of two subunits (60% rRNA and 40% protein)
that hold the mRNA in place in order for translation to
 Each ribosome has three biding sites:
 P site = holds tRNA carrying growing peptide
 A site = holds tRNA carrying next amino acid
 E site = where tRNA exits from
Transfer RNA, tRNA:
 RNA strand (~80 bp) transcribed from DNA in nucleus
 3D shape held together by H-bonds
 can be used repeatedly during translation
 proteins are synthesized according to the sequence of codons,
tRNA helps in translation of RNA code to a.a sequence. How?
 tRNA aligns the appropriate amino acid by:
- transfers amino acid from cytoplasm to ribosomal
- each tRNA strand has an amino acid attachment
site at one end and a anticodon at the opposite
- Anticodon is complimentary to the RNA codon for
that amino acid
- The attaching of the a.a. to its tRNA is catalyzed
by a specific aminoacyl-tRNA synthetase
(required ATP)  each amino acid has its own
Building a polypeptide – Occurs in Thee Stages
1. Initiation of Translation
 Small (40) subunit of ribosome binds to mRNA strand (5’ cap
of mRNA helps binding)
 Initiator Met-tRNA (start anticodon) finds AUG (start codon)
downstream on mRNA and binds to it, large subunit then
binds to initiator tRNA forming initiation complex (small
ribosome unit, mRNA and met-tRNA)
 Large ribosomal subunit (60) attached to small one; initiator
tRNA fits into P-site of ribosome  vacant A site is ready for
next amino acid
2. Elongation
 Codon recognition: mRNA codon in A site of ribosome forms
H-Bonds with anticodon of entering tRNA carrying the next
amino acid
 Peptide bond formation: a peptide bond is formed between
growing polypeptide in P-site and new amino acid in A-site
by peptidyl transferase  polypeptide is transferred to Asite
 Translocation (ribosome moves forward one codon): the tRNA
that was in the P-site is released (E-site). The tRNA in the Asite is translocated to the P-site (taking growing peptide with
it)  this repeats along the length of mRNA …..
3. Termination
 Occurs when a stop codon is reached (UGA,UAG, or UAA)
 Stop codons do not code for any amino acid
 Reaching stop sequence causes a release factor or bind to
the A-site of the ribosome and facilitates the release of the
 Small and large ribosomal units separate
 Polypeptide is now ready for further processing and folding!
 A protein’s sequence (primary structure) determines how the
peptide will coil and fold into its 3D shape
 Some proteins undergo post-translational modifications
before they become fully functional (ie chemical
modifications, or chain length modifications)
Multiple Roles of RNA in the cell
 RNA has many other critical roles in the cell:
1. information carrier = mRNA carries genetic info form
DNA to ribosomes
2. adaptor molecule = tRNA translate info from mRNA
into protein SRP RNA directs the translation complex to
3. catalysts and structural molecule – rRNA plays
structural and enzymatic role in ribosomes; snRNA
catalyzses RNA splicing
4. viral genomes – some viruses use RNA as genetic
Control Mechanisms
(Section 5,5)
Not all of our 42,000 genes are needed at all times, so
transcription factors turn genes on and off as required
Note: some housekeeping genes are always being transcribed
since cells need these at all times.
In eukaryotes, there are 4 levels of gene control (expression):
translational, and
iv) posttranslational.
See table 1.p 255  know them!
Operons = are clusters of genes under the control of one
promoter and one operator  ex lac operon, trp operon
Lac operon
Form of control only used in bacteria
In bacteria such as E.coli found in the digestive
system of mamals, β-galactosidase is the enzyme
responsible for breaking down lactose (enzyme is not
always required)
β-galactosidase is part of an operon
lacl protein binds to operon blocking transcription
in the presence of lactose a repressor protein (lacl
protein) normally bound to operon leaves and binds
to lactose  transcription of the lac operon no longer
blocked (no enzymes are made)  see fig. 2 p. 256
Why? When there is no milk, no enzyme is needed
The trp Operon
Works in the opposite manner to the lac operon
tryptophan is an amino acid used by bacteria to produce
proteins, when available in its environment bacteria stop
producing tryptophan and absorb it from its environment
operon acitivity is inhibited when the concentration of
tryptophan in the environment increases  tryptophan
binds to operator region of operon  see fig. 3, p. 257