D1.2 Protein synthesis Flashcards
D1.2.1—Transcription as the synthesis of RNA using a DNA template
Students should understand the roles of RNA polymerase in this process.
In transcription, one of the two strands of a DNA molecule is used as a template for synthesizing a molecule of RNA. The process is carried out by the enzyme RNA polymerase. There are some similarities between DNA replication and transcription, but whereas cells replicate entire DNA molecules, they only transcribe part of a DNA molecule usually just one gene.
RNA polymerase binds to a site on the DNA at the start of the gene and then moves along it, transcribing the gene in a series of stages.
5. The DNA strands pair up again and wind back into a
double helix.
RNA
RNA polymerase moves along the
polymerase
DNA molecule in this direction
sense strand
4. The assembled RNA strand separates from the template
DNA strand.
“- RNA
transcript
3. RNA polymerase links the RNA nucleotides together with covalent bonds between the pentose sugar of one nucleotide and the phosphate of the next, to form a continuous strand of RNA nucleotides.
1. RNA polymerase unwinds DNA and separates it into two single strands, exposing the bases.
Only about one turn of the DNA double helix is unwound
template
and split open at
strand
any time during the transcription of a gene.
2. RNA polymerase pairs up free
RNA nucleotides to DNA nucleotides on the template strand, by complementary base pairing, with the bases of the nucleotides linked by hydrogen bonds.
D1.2.2—Role of hydrogen bonding and complementary base pairing in transcription
Include the pairing of adenine (A) on the DNA template strand with uracil (U) on the RNA strand.
The same rules of complementary base pairing are
followed in transcription as in replication (except that
uracil pairs with a d e n i n e b e c a u s e RNA d o e s not
contain thymine).
base on DNA
template strand
base on
RNA strand
adenine
cytosine
guanine
thymine -
The bases in RNA and DNA pair up by hydrogen
bonding, which can easily be broken to separate the
RNA transcript from the DNA template strand. Hydrogen
bonds then form again between bases in the template
strand and the other DNA strand (called the sense
* uracil
* guanine
* cytosine
* adenine
strand). Logically, the sense strand and RNA transcript
must have the same base sequence (apart from the
A-T difference) because they both have a sequence
complementary to that of the template strand.
Strand:
sense
template A T C G A A G T G T C C
⼆ ⼀ ⼀ ⼀ ⼆ ⼀ ⼀ ⼆ ⼀
TA G C T T C A C A G G
RNA AUCGAAGUGUCC
D1.2.3—Stability of DNA templates
Single DNA strands can be used as a template for transcribing a base sequence, without the DNA base
sequence changing. In somatic cells that do not divide, such sequences must be conserved throughout
the life of a cell.
The components of DNA (phosphate, deoxyribose The stability of DNA ensures that the base sequence of
sugar and the four bases A, C, G and T) are all chemically a gene rarely changes during this process-the structure
stable. They are linked together in a strand of DNA by of DNA promotes continuity rather than change. A
strong covalent bonds. Alternating sugar and phosphate gene may be transcribed many times, especially the
groups form the strong backbone to which sequences of “housekeeping” genes needed to maintain cells; in
bases are attached. During transcription the DNA is split some cases, such as brain cells, this is throughout a
into single strands, with bases exposed, while a strand of person’s life.
RINA is a s s e m b l e d on the template strand.
D1.2.4—Transcription as a process required for the expression of genes
Limit to understanding that not all genes in a cell are expressed at any given time and that transcription,
being the first stage of gene expression, is a key stage at which expression of a gene can be switched on
and off.
The sequence of bases in a gene is a store of information.
A gene is expressed when the information it holds is used and an observable characteristic is generated within a cell or organism. At any specific time, some genes are being expressed in a cell, but most are not. This is because cells are specialized for particular functions and only develop the characteristics that they need.
The first stage in gene expression is transcription— production of an RNA copy of the base sequence of the sense strand by transcribing the template strand, Transcription of a gene can be switched on or off-this is a key stage in the control of gene expression. The flow chart shows this and subsequent stages in expression of a protein-coding gene—the commonest type.
polypeptide
structural polypeptides are the direct cause of observable characteristics
transcription— an RNA copy of the sense strand’s base
sequence is produced and moves to a ribosome
translation-the base sequence of an RNA transcript is translated into
the amino acid sequence of a polypeptide, by a ribosome
DNA
RNA
substrate
product
many polypeptides are enzymes that catalyse a reaction, with the product causing an observable characteristic
D1.2.5—Translation as the synthesis of polypeptides from mRNA
The base sequence of mRNA is translated into the amino acid sequence of a polypeptide
Translation is the synthesis of a polypeptide, with its amino
acid sequence determined by the base sequence of an
RNA molecule. The RNA molecule is transcribed from a
protein-coding gene and is called messenger RNA (mRNA).
Each base in the polypeptide is coded for by one codon on
the mRNA. A codon is a sequence of three bases.
G O U is translated into
o n e of the 6 4
different codons
alanine-one of the 20
different amino acids
D1.2.6—Roles of mRNA, ribosomes and tRNA in translation
Students should know that mRNA binds to the small subunit of the ribosome and that two tRNAs can bind
simultaneously to the large subunit.
Ribosomes are the site of translation. They have two subunits (large and small). On the small subunit there is a
binding site for mRNA. On the large subunit there are three binding sites for tRNA, with tRNAs attached to at least
two of these at all times during translation. The amino acid carried by the most recently arrived tRNA is linked to the
growing chain of amino acids held by the previous amino acid to arrive. The linkage is a peptide bond, made at a
catalytic site on the surface of the large subunit of the ribosome.
4. The amino acids carried by the tRNA
anticodon large subunit
of ribosome
molecules are bonded together by a
peptide linkage. A dipeptide is formed,
attached to the tRNA on the right. The
tRNA on the left detaches. The ribosome
2. Transfer RNA molecules
are present around the
ribosome in large numbers.
Each tRNA has a special
moves along the mRNA to the next codon.
Another tRNA carrying an amino acid
binds. A chain of three amino acids is
formed. These stages are repeated until a
triplet of bases called an
anticodon and carries the
amino acid corresponding
to this anticodon.
polypeptide is formed.
amino acid
direction of movement
of r i b o s o m e
1. Messenger RNA binds to a
site on the small subunit of the
ribosome. The mRNA contains a
series of codons consisting of three
bases, each of which codes for one
amino acid.
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small subunit of ribosome
3. There are three binding sites for tRNA molecules on the large subunit of
the ribosome but only two ever bind at once. A tRNA can only bind if it has
the anticodon that is complementary to the codon on the mRNA. The
bases on the codon and anticodon link together by forming hydrogen
bonds, following the same rules of complementary base pairing as in
replication and transcription.
D1.2.7—Complementary base pairing between tRNA and mRNA
Include the terms “codon” and “anticodon”.
Translation depends on a group of RNA molecules called transfer RNA (tRNA). Three bases at one end of a tRNA molecule bind to a codon on mRNA during translation, following the rules of complementary base pairing. The three bases are known as the anticodon.
At the other end of the tRNA molecule is a site for attaching an amino acid.
codon on mRNA
anticodon on tRNA|
complementary base pairing by formation of hydrogen bonds
Each type of tRNA has a distinctive three-dimensional shape (like a twisted clover leaf). This is recognized by an enzyme that links on the amino acid corresponding to the anticodon.
D1.2.8—Features of the genetic code
Students should understand the reasons for a triplet code. Students should use and understand the terms
“degeneracy” and “universality”.
Triplet
A codon, consisting of three bases, codes for one amino acid, so it is a triplet code. With two bases there would only be 16 codons (43)—not enough for the 20 amino acids. With three bases there are 64 different codons (43)—more than enough for the 20 amino acids in polypeptides.
Degeneracy
There are more codons than the minimum needed to code for the 20 amino acids. None of the 64 codons are unused and instead there are two or more codons for most amino acids. A code in which more than one symbol is used to represent the same thing is known as a degenerate code.
Universality
The 64 codons of the genetic code have the same meanings in the cells of all organisms, apart from a few minor variations. Universality of the genetic code is strong evidence for all life on Earth having evolved from the same original cells, with the minor coding differences accruing since this common origin.
D1.2.9—Using the genetic code expressed as a table of mRNA codons
Students should be able to deduce the sequence of amino acids coded by an mRNA strand
The elongation of polypeptides involves a repeated cycle of events.
A peptide bond is made between
the amino acid held by the A site
tRINA a n d the amino acid at the e n d
of the polypeptide held by the P site
tRNA. This transfers the polypeptide
to the A site tRNA. The catalyst for
peptide bond formation is ribosomal
RNA in the large subunit.
peptide bond
¡E sitellp
The ribosome moves three bases
on along the mRNA towards the 3’
end.
This m o v e s the tRNA in the P site
to the E site and moves the tRNA
carrying the growing polypeptide
from the A to the P site, so the A site
b e c o m e s vacant.
¡E site!
٨٠٠٨٦٨٨١١
N a٠ n i n n٠
A tRINA with an anticodon
The tRNA in the E site detaches and
exits, so this site b e c o m e s vacant.
complementary to the next codon
on the mRINA binds to the A site.
The tRNA at the P site is carrying
The A site is available for binding of
a tRNA charged with an amino acid.
Any tRNA may approach the site, but
the polypeptide so far assembled
and the E site is vacant.
unless it has an anticodon that is
complementary to the next
D1.2.10—Stepwise movement of the ribosome along mRNA and linkage of amino acids by peptide
bonding to the growing polypeptide chain
Focus on elongation of the polypeptide, rather than on initiation and termination.
The meaning of each codon in the genetic code is shown in the table. Three codons arestop signals that indicate
when the synthesis of the polypeptide is complete and translation should end. One codon represents both the start
signal and a specific amino acid (methionine).
The table can be used to deduce the sequence of
amino acids coded for
by an mRNA strand. For
example, the sequence
CACAGAUGGGUC would
be translated into histidine,
arginine, tryptophan, valine.
First base of codon
(5’ end)
Second base of codon on messenger RNA
U
Phenylalanine
Phenylalanine
Leucine
Leucine
G
Serine
lyrosine
Tyrosine STOP
Cysteine Cysteine
Serine
STOP
STOP
Tryptophan
Leucine
Leucine
Proline Proline
Histidine
Histidine
The table could also be used
to find possible codons for
Leucine
Proline
Glutamine
an amino acid. For example,
the amino acid glutamine is
coded for either by CAA or
CAG.
Isoleucine
Isoleucine
Isoleucine Methionine / START
Valine
Valine
Valine
Va l i n e
Asparagine Lysine
Serine
Lysine
Arginine
Alanine
Aspartic acid
Alanine Alanine
Aspartic acid
Glutamic acid
Glycine Glycine Glycine
Glutamic acid
Glycine
D1.2.11—Mutations that change protein structure
Include an example of a point mutation affecting protein structure
Protein structure can be changed by a mutation as small as a single base change (a point mutation) in the gene coding for the protein. A single base substitution changes one codon in mRNA transcribed from the gene. In most cases this will change one amino acid in the polypeptide translated from the mRNA. Even a single changed amino acid in a polypeptide can cause radical changes in protein structure, especially if the substitution is between hydrophilic and hydrophobic amino acids. In contrast, some base substitutions have no effect, either because they are same-sense mutations (changing a codon into another codon for the same amino acid), or because the amino acid is chemically similar to the original one and is in a non-critical part of the protein structure.
Example of a point mutation that affects protein structure: the sickle cell mutation
HBB is the gene that codes for the beta polypeptide of haemoglobin, which consists of 146 amino acids.
A base substitution mutation has changed adenine (A) to thymine (T) in the codon for the sixth amino acid.
This changed Hb* (the original allele of the gene) into Hb§ (the sickle cell allele) with major consequences.
part of HbA
glutamic acid
mutation
one base is changed in the transcribed mRNA…
valine
5
….SO tRNA with o different anticodon binds..
part of HbS
..bringing a different amino acid.
red blood cells
-with normal haemoglobin
Haemoglobin with valine (which is hydrophobic) instead of glutamic acid (which is hydrophilic) has an altered structure, and tends to link up into chains.
sickle cells due to chains of
haemoglobin
D1.2.12—Directionality of transcription and translation
Students should understand what is meant by 5’ to 3’ transcription and 5’ to 3’ translation.
Transcription
RNA polymerase adds the 5’ end of the free RNA
nucleotide to the 3’ end of the growing mRNA molecule,
so transcription occurs in a 5’ to 3’ direction.
direction of transcription
sense strand
수
31
DNA
5003-
5’ 5’ end of a nucleotide is the
phosphate
template
strand
Translation
The ribosome binds to mRNA near its 5’ end and moves
along it towards the 3’ end, translating each codon into an
amino acid on the elongating polypeptide, until it reaches
a stop codon, so translation occurs in a 5’ to 3’ direction.
) ›
5 ー
— 3’
→ >
direction of
translation
D1.2.13—Initiation of transcription at the promoter
Consider transcription factors that bind to the promoter as an example. However, students are not
required to name the transcription factors.
Adjacent to the start of every gene is a section of DNA
that is a promoter. It is where transcription of the gene is
initiated. The promoter is not itself transcribed and does
not code for an amino acid sequence.
RNA polymerase binds directly to the promoter in
prokaryotes and then starts transcribing. Repressor
proteins can bind to the promoter and prevent
transcription.
transcription
factors bind
The control of gene expression is more complicated
n eukaryotes. Proteins called transcription factors
first bind to the promoter or sites close to it, which
allows RNA polymerase to bind to the promoter.
Several transcription factors are required, some of
which may need to be activated by the binding of a
hormone or other chemical signal. As in prokaryotes,
repressor proteins can bind to the promoter,
preventing transcription. There is diversity in the
base sequences of promoters and the sites to which
transcription factors and repressor proteins bind. A cell
can therefore switch on some genes and cause them
to be transcribed, while other genes are not being
transcribed.
The promoter is “upstream” of the gene, so once
transcription has been initiated, RNA polymerase moves
TATA boX promoter
(part of the
(upstream
promoter) of the gene)
5’C
31
5’
RNA polymerase
binds to the
promoter
sense strand
731
v
template strand
13
5’
start point
more transcription
factors bind together
with RNA polymerase
direction of transcription
RNA
transcript
along the whole gene, assembling an RNA copy one
nucleotide at a time.
D1.2.14—Non-coding sequences in DNA do not code for polypeptides
Limit examples to regulators of gene expression, introns, telomeres and genes for rRNAs and tRNAs in
eukaryotes.
There are thousands of sequences of bases that code
for proteins in the DNA of a species. These coding
sequences are transcribed and translated when a cell
requires the protein that they code for.
There are also non-coding sequences. Some non-
coding sequences have important functions.
* Regulating gene expression-some base sequences
are sites where proteins can bind that either promote
or repress the transcription of an adjacent gene.
* Introns-in many eukaryote genes the coding
sequence is interrupted by one or more non-coding
sequences. These introns are removed from mRNA
before it is translated. Introns have numerous functions
associated with mRNA processing.
* Telomeres-these are repetitive base sequences at the
ends of chromosomes. When the DNA of a eukaryote
chromosome containing many genes
-shown as it appears in metaphase of mitosis
H D A D
telomere telomere
(not transcribed)
section of
c h r o m o s o m e
containing one gene
* promoter-not transcribed
transfer RNA not
translated
ribosomal RNA)
transcription
messenger
RNA
i n t r o n s
* (edited out)
exons (translated
DNA RNA
into a polypeptide)
chromosome is replicated, the end of the molecule
cannot be replicated, so a small section of the base
sequence is lost. The presence of the telomere prevents
parts of important genes at the ends of the chromosomes
from being lost each time DNA is replicated.
* Genes for tRNA and rRNA-transcription of these
genes produces the transfer RNA used during
translation and also the ribosomal RNA that forms
much of the structure of the ribosome.
D1.2.15—Post-transcriptional modification in eukaryotic cells
Include removal of introns and splicing together of exons to form mature mRNA and also the addition of 5’
caps and 3’ polyA tails to stabilize mRNA transcripts.
Eukaryotic cells modify mRNA after transcription. This happens before the mRNA exits the nucleus.
There are two main types of post-transcriptional modification: removal of nucleotides from within
the RNA transcript and addition of nucleotides to the ends of the transcript.
1. The RNA transcript is modified by adding extra
nucleotides to give each end of mRNA a special
s t r u c t u r e :
2. In many eukaryote genes the coding sequence is
interrupted by one or more non-coding sequences.
These introns are removed from mRNA before it
is translated. The remaining parts of the mRNA
Five-prime c a p - a modified nucleotide is added to the
5’ end of the RNA. This nucleotide has three phosphate
are exons. They are spliced together to form
mature mRNA.
groups instead of one, so it is similar to ATP. Its base is
guanine, with an extra methyl group added.
DNA inside
the nucleus
0 0 0
СН 3
Poly-A tail-between 100 and 200 adenine nucleotides
are added to the 3’ end of the RNA. Translation stops
before the ribosome reaches the poly-A tail.
بسسسسسا 5
5’ cap
poly-A tail
The 5’ cap and the poly-A tail both stabilize the ends
of the mRNA by protecting them from digestion by
nuclease enzymes.
48
5’ cap
introns are removed
and digested
mature mRNA exits
t h e n u c l e u s via a
transcription
poly-A tail
RNA
“ transcript
exons are spliced together
a mature mRNA
ribosomes translate
mRNA in the cytoplasm
nuclear por
