Protein Synthesis
3.5, 7.3, 7.4
Remember Gregor Mendel?

Mendel’s experiments with garden peas
led to the foundations of genetics

Hypothesized that characteristics such as
height, shape and colour of the seed,
colour of flowers, etc were inherited
factors.
Today we call those factors GENES
(A gene is a sequence of nucleotides in
DNA that performs a specific function.)
 Genes direct production of PROTEINS
 Proteins:
- antibodies
- hormones
- enzymes that drive cellular processes
- determine physical characteristics
- manifest genetic disorders


Nt -> amino acids -> proteins
One gene- one polypeptide
A single gene codes for one polypeptide
(protein)
 Some proteins consist of more than one
polypeptide chain (ex: hemoglobin)
 Each chain is controlled by a different
gene.

p235

P 236
Overview of Protein Synthesis
DNA contains the blueprints for making
proteins.
 The sequence of nucleotides must be read
by a ribosome to determine the sequence
of amino acids to make the protein.
 DNA is found in the nucleus but protein
synthesis takes place in the cytoplasm

Problems:
DNA can’t leave the nucleus
 Could be damaged if it did which would
lead to the death of the cell (possibly the
organism)
 Inefficient if DNA was read by ribosomes
because then only 1 protein from a single
strand could be created at a time.


A mechanism has evolved for protein
synthesis that prevents DNA from having
to leave the cell.
TRANSCRIPTION
TRANSLATION
nucleus
OVERVIEW
1. TRANSCRIPTION – DNA is transcribed into
mRNA in the nucleus
2. mRNA exits the nucleus and enters the
cytoplasm
3. TRANSLATION – mRNA is “read” by ribosomes
to make the polypeptide chain
4. Polypeptide chain is released and folds into a
protein. mRNA strand can be used again.
DNA vs RNA





Deoxyribonucleic acid
Pentose sugar:
deoxyribose (1 less O)
Double stranded
N bases: A,C,G, T
(no uracil!)
A–T
In nucleus





Ribonucleic acid
Pentose sugar: ribose
Single stranded
N bases: A,C,G and
URACIL (U) (no
thymine!)
A–U
In nucleus and in
cytoplasm
RNA

1)
2)
3)
There are 3 types of RNA
mRNA: messenger RNA – an RNA
version of a gene
tRNA: transfer RNA – brings the
appropriate amino acid to the ribosome
rRNA: ribosomal RNA – structural
component of ribosomes (involved in
assembly of polypeptide)
The Genetic Code
The building blocks of proteins are amino
acids.
 There are 20 amino acids
 A sequence of 3 nucleotides called a
CODON code for different amino acids.
 There are 64 different codons (43 = 64)
 Therefore, there may be more than one
codon for a given amino acid.

Ser
Ser
Ser
Ser
p43
The first codon is the “start codon”
 It signals the start of protein synthesis.
 In almost all polypeptides, AUG is the start
codon. AUG also codes for methionine.
 (GUG and UUG are sometimes act as
start codons)
 There are 3 “stop codons”: UAA, UAG,
UGA
 These do not code for amino acids but
stop synthesis.


Homework: Read 5.1 and 5.2
5.1 p236:
Q: 5
5.2 page 241:
Q’s: 1,3-5,8,10-13
Transcription
Transcription

The process of making an mRNA strand
from the DNA gene sequence

3 steps: initiation, elongation, termination
INITIATION

The enzyme RNA polymerase attaches to
the DNA double helix at the promoter
region.

PROMOTER REGION: A sequence of
DNA “upstream” from the gene that
contains a lot of A-T base pairs. (easier to
break apart than G-C)
Initiation con’t

RNA polymerase unwinds and separates
the helix exposing the template strand.

Since RNA polymerase only binds at the
promoter region, it allows only the gene to
be transcribed.
Rich in A-T
Coding strand
ELONGATION

Once the helix is open, RNA polymerase
starts building a single stranded mRNA in
the 5’-3’ direction using RNA nucleotides
and complimentary base pairing rules.

Only one strand of DNA is used. This is
the template strand.
Elongation con’t….
The other DNA strand is the coding strand
 This strand is identical to the mRNA strand
except that it has thymine instead of uracil.
 Note: the promoter region does not get
transcribed.
 As the DNA is transcribed, it is rewound
into its helix

Termination
The mRNA strand is synthesized until
RNA polymerase reaches the terminator
sequence at the end of the gene.
 The mRNA strand will detach from the
DNA template.
 This mRNA strand is called the primary
transcript

Post-transcription

After transcription, the mRNA primary
transcript must go to the cytoplasm to be
translated.

In eukaryotes, before it leaves the nucleus
it needs a “cap” and a “tail” to protect it
and prevent it from being broken down.
5’ CAP

A 5’ cap is added to mRNA.

This is a modified guanine nucleoside
triphosphate.

The cap protects the mRNA from digestion
from enzymes when it enters the
cytoplasm
Poly-A tail

A sequence of ~ 200 adenine
ribonucleosides is added to the 3’ end to
protect the mRNA from breaking down

This is called a poly-A tail

The tail is added with the help of the
enzyme poly-A polymerase
Exons and Introns

In eukaryotic DNA, a gene consists of
introns and exons

EXONS: coding regions – they code for
the specific protein

INTRONS: noncoding – “filler DNA” that
does not code for proteins.
Introns and Exons con’t…

Before mRNA goes into the cytoplasm, the
introns must be removed from the mRNA

Proteins called spliceosomes cut the
introns out and join the remaining exons
together.
mRNA transcript

Once the cap and tail have been added,
and the introns removed, the mRNA is
called an mRNA transcript

It can now go to the cytoplasm for
translation

Unlike in DNA replication, there is no
enzyme to “spell check” the mRNA.

But errors are not too detrimental since
multiple mRNA transcripts are made for
each gene so sufficient amounts of protein
will be produced by the correct copies.
TRANSLATION
Remember…..

Protein synthesis = the making of a protein
chain (polypeptide)

A protein chain is made of several amino
acids bonded together.

The order of the amino acids in a protein is
important to the overall shape of the
protein. Therefore, it is important that the
correct amino acids be placed in the
correct sequence.
Step # 1: Transcription:

a template strand of DNA is used to create
an mRNA strand
Template strand
(antisense strand)
3’ CCT TAG GTA GGT ATT 5’
5’ GGA ATG CAT CCA TAA 3’
Coding strand
(sense strand)
5’ GGA AUG CAU CCA UAA 3’
mRNA transcript
Remember, the primary mRNA transcript
will have introns that need to be removed.
Also a cap and a tail will be added before
the mRNA can leave the nucleus.
Step #2: Translation:

Following the sequence determine by the
mRNA strand, tRNA brings amino acids to
the ribosome in the correct order to create
the polypeptide.
How does an amino acid bond
to the tRNA?

tRNA (transfer RNA) – a clover shaped
molecule made of RNA nucleotides.
This 3’ end is the acceptor
stem. This is where the amino
acid will bind. Only one type of
amino acid will bind to any
given tRNA.
This is the anticodon. The
anticodon is the codon that
determines which amino
acid will bind to the tRNA
strand at the acceptor stem.
The anticodon is
complimentary to the codon
on the mRNA strand that
codes for the amino acid. Ex:
the codon for methionine is
AUG, so if this tRNA wanted
to carry methionine, its
anticodon would be UAC.

For the amino acid to bind at the acceptor
stem, the process is catalyzed by a tRNAactivating enzyme.

There are 20 different amino acids, and so
20 different tRNA activating enzymes.

The amino acid reacts with the adenine of
the CCA codon at the acceptor stem to
form a covalent bond through a
condensation reaction.
How many different tRNA
molecules are there?

How many different tRNA molecules are
there? There are 64 different codons,
however, 3 of those codons are stop
codons and do not code for an amino acid,
and so tRNAs do not exist for these.
Therefore, there are 61 different tRNA
molecules.
How many tRNA activating
enzymes are there?

1 for every amino acid, so 20
What are ribosomes?
Ribosomes are the organelle where
translation takes place.
 They are extremely small, but abundant.
 Ribosomes hold the mRNA strand in place
and are where the tRNA bind to the
mRNA, bringing with it the appropriate
amino acid.
 Ribsosomes are made or ribosomal RNA
(rRNA) and proteins

Ribosomes
Ribosomes consist of 2 subunits:
 The “small subunit” is made of 1 rRNA
molecules (and proteins)

 This

is where mRNA binds
The “large subunit”: is made of 2 rRNA
molecules
 This
is where the tRNA binds
 Has the A, P, and E sites

When the ribosomes are not translating,
the subunits are separated. They only
come together for translation.

Occasionally, several ribosomes may be
attached to a single mRNA strand, with
each ribosome constructing a polypeptide
chain. In This way, several polypeptides
can be made simultaneously.
A, P, E sites of Ribosome
A = “attachment” site: this is where tRNA
enters the ribosome and attaches to the
mRNA strand
 P = “peptidyl” site: where peptide bonds
formed
 E = “exit” site: where the tRNA detaches
from the ribosome and the mRNA strand

Translation
Occurs in the 5’ – 3’ direction of mRNA
 Divided into 3 stages: initiation, elongation
, termination

INITIATION

the ribosome attaches to mRNA

The start codon on the mRNA is AUG. So
the 1sttRNA required will have the
anticodon UAC and the amino acid
methionine attached to it.
Initiation

The tRNA will bind to the base of the P
site on the small subunit of the ribosome.
This is catalyzed with the help of the
enzyme ATPase.

The rRNA of the small subunit will attach
to a binding site on the mRNA.
Initiation

The small subunit slides along the mRNA
until the P site reaches the start codon
(AUG).

Then the larger subunit, containing the
binding sites for the tRNA, join the
complex.
ELONGATION

building of the protein strand

with the 1sttRNA (carrying met) in the P
site, the next tRNA can bind to the A site.
(All tRNA bind to the ribosome with the
help of ATPase)
Elongation

The amino acid methionine of the 1st
tRNA will detach from the tRNA and form
a peptide bond with the amino acid
attached to the 2nd tRNA which is in the A
site. This is catalyzed by the enzyme
peptidyltransferase.
Elongation

The ribosome moves down the mRNA
chain toward the 3’end.

Now the 1st tRNA no longer has its amino
acid and it is now in the E site and can be
released from the ribosome.
TERMINATION

release from the ribosome complex
The stop codon will be near the 3’ end of
the mRNA strand
 When a stop codon is in the A site, there is
no tRNA available and this is a signal to
end protein synthesis.

Termination
A “protein release factor” will come to
release the last tRNA from the last amino
acid.
 The polypeptide can now be released from
the ribosome.
 The ribosome will disassociate into the
small and large subunits again and can be
used again and again. The tRNAs and the
mRNA can also be used again.

Animations

http://highered.mcgrawhill.com/sites/0072437316/student_view0/
chapter15/animations.html#

http://www.youtube.com/watch?v=NJxobg
kPEAo&feature=email

http://www.youtube.com/watch?v=B6O6u
Rb1D38&list=PL1AD35ADA1E93EB6F
Ribosome Distribution

If the protein being synthesized is to be
used inside the cell by the cell, the mRNA
will use ribosomes scattered throughout
the cytoplasm.

If the protein being synthesized is to be
exported out of the cell or used by
lysosomes, the mRNA will use ribosomes
attached to the endoplasmic reticulum.
They will then go to a Golgi complex to be
packaged into vesicles (have a membrane
place around it).