Download DNA Replication, Transcript

Unit 9 Notes: Transcription and
Translation
IB Biology
Protein synthesis Introduction
• Protein synthesis includes two reactions,
transcription and translation.
• The following table compares DNA and RNA
DNA
RNA
Contains a 5-carbon sugar
Contains a 5-carbon sugar
5-carbon sugar is deoxyribose
5-carbon sugar is ribose
Each nucleotide has one of four
nitrogenous bases
Each nucleotide has one of four
nitrogenous bases
The nitrogenous bases are cytosine,
guanine, adenine, and thymine
The nitrogenous bases are cytosine,
guanine, adenine, and uracil
Double-stranded molecule
Single-stranded molecule
Transcription produces RNA molecules
• The sections of DNA that code for
polypeptides are called genes.
• Genes are specific sequences of nitrogenous
bases found in specific locations in a DNA
molecule.
• Molecules of DNA are found within the
nucleus, proteins are synthesized outside the
nucleus in the cytoplasm.
Transcription produces RNA molecules
• There has to be an intermediate molecule
which carries the message of the DNA to the
cytoplasm, where the enzymes, ribosomes,
and amino acids are found.
• The intermediate molecule is called
messenger RNA or mRNA.
Transcription produces RNA molecules
• Transcription process:
– The process of transcription begins when an area
of DNA of one gene becomes unzipped. This
process is very similar to the unzipping process in
DNA replication. In this case only the area of the
DNA where a gene is found is unzipped.
– The two complementary strands of DNA are now
single-stranded in the area of the gene.
Transcription produces RNA molecules
– RNA is a single stranded molecule which means
that only one of the two strands of the DNA will
be used as a template to create the mRNA
molecule. The enzyme RNA polymerase is used as
the catalyst for this process.
– As RNA polymerase moves along the strand of
DNA acting as the template, RNA nucleotides float
into place by complementary base pairing.
– Base pairing is the same as DNA replication with
the exception that adenine pairs with uracil.
Transcription produces RNA molecules
• The following pertains to transcription:
– Only one of the two strands of DNA is copied, the
other strand is not used.
– mRNA is always single stranded and shorter than
the DNA that is copied from as it is a
complementary copy of only one gene.
The central dogma
• The idea that information passes from genes
on DNA to an RNA copy, the RNA copy then
directs the production of proteins at the
ribosome by controlling the sequence of
amino acids is called the central dogma.
• The central dogma can be summarized as
follows:
• DNA → RNA → Proteins
Transcription: DNA → RNA
• Transcription has some similarities to replication.
• First, the double helix must be opened to expose the
base sequence of the nucleotides. Helicase unzips the
DNA in replication, however in transcription RNA
polymerase separates the two DNA strands.
• The RNA polymerase also allows polymerization of RNA
nucleotides as base-pairing occurs along the DNA
template.
• The RNA polymerase must first combine with a region
of the DNA strand called a promoter. RNA polymerase
only allows assembly in the 5’ to 3’ direction.
Transcription: DNA → RNA
• Which strand of DNA is copied:
– One strand is complementary to the other, so
there would be a difference in the code of the
strands.
– The genetic code is made up of codons which are
three nucleotide triplets.
– The codons are specific for certain amino acids.
Therefore, complementary strands mean different
codons, different amino acids, and different
proteins.
Transcription: DNA → RNA
• The DNA strand that carries the genetic code is called
the sense strand (or coding strand). The other strand is
called the antisense strand (or the template strand).
• The sense strand has the same sequence as the newly
transcribed RNA except thymine is in the place of uracil
in the DNA strand.
• The antisense strand is the strand that is copied during
transcription.
• The promoter region for a particular gene determines
which DNA strand is the antisense strand. For any
particular gene, the promoter is always on the same
DNA strand.
Transcription: DNA → RNA
• The promoter region is a short sequence of
bases that is not transcribed.
• Once RNA polymerase has attached to the
promoter region for a particular gene
transcription begins.
• The DNA opens and a transcription bubble
occurs. This bubble contains the antisense
DNA strand, the RNA polymerase, and the
growing RNA transcript.
Transcription: DNA → RNA
• The terminator
– The sections of DNA involved in transcription are:
promoter → transcription unit → terminator. The
transcription bubble moves from the DNA
promoter region towards the terminator.
– The terminator is a sequence of nucleotides that,
when transcribed, causes the RNA polymerase to
detach from the DNA, which stops transcription.
Transcription: DNA → RNA
• The transcript carries the code of the DNA and
is referred to as messenger RNA (mRNA).
• In eukaryotes, transcription continues beyond
the terminator for a significant number of
nucleotides until it is eventually released from
the DNA molecule.
Transcription: DNA → RNA
• Nucleoside triphosphates (NTP’s) containing
three phosphates and the 5-carbon sugar, ribose
are paired with the appropriate exposed bases of
the antisense strand.
• Polymerization of the mRNA strand occurs with
the catalytic help of RNA polymerase and the
energy provided from the release of two
phosphates from NTP.
• This portion of the transcription process is
referred to as elongation.
Transcription: DNA → RNA
• Post-transcription processing
– Eukaryotic DNA contains large stretches of noncoding DNA, which is different from prokaryotic
DNA.
– The large stretches of non-coding DNA are called
introns.
– In order to make the mRNA strand functional in
eukaryotes, the introns must be removed.
– Prokaryotic mRNA does not require processing
because no introns are present.
The genetic code is written in triplets
• Polypeptides are composed of amino acids
covalently bonded together in a specific
sequence.
• The message written into the mRNA molecule is
the message that determines the order of the
amino acids.
• Every three bases of RNA codes for one of the 20
amino acids.
• Any set of three bases is called a triplet, in an
RNA molecule the triplets are called codons.
Translation results in the production of
a polypeptide
• There are three types of RNA molecules.
– mRNA (messenger RNA) – each mRNA is a
complementary copy of DNA that codes for a
single polypeptide.
– tRNA (transfer RNA) – each type of tRNA transfers
one of the 20 amino acids to the ribosome for
polypeptide formation.
– rRNA (ribosomal RNA) – each ribosome is
composed of rRNA and ribosomal protein.
Translation results in the production of
a polypeptide
• Each tRNA molecule contains an anticodon that
determines which of the 20 amino acids will be
transferred to mRNA.
• Translation process:
– The mRNA will locate a ribosome and align with it so
that the first two codon triplets are within the
boundaries of the ribosome.
– A specific tRNA molecule then floats in – its tRNA
anticodon must be complementary to the first codon
triplet of the mRNA molecule, thus the first amino
acid is brought in.
Translation results in the production of
a polypeptide
• While the first tRNA ‘sits’ in the ribosome holding the
amino acid, a second tRNA floats in and brings a
second amino acid.
• The second tRNA matches its three anticodon bases
with the second codon triplet of the mRNA.
• An enzyme now catalyzes a condensation reaction
between the two amino acids and the resulting
covalent bond between them is called a peptide bond.
• The next step in the translation process involves the
breaking of the bond between the first tRNA molecule
and the amino acid that is transferred in.
Translation results in the production of
a polypeptide
• The bond is no longer needed as the second tRNA
is currently bonded to its own amino acid which
is covalently bonded to the first amino acid.
• The first tRNA floats away into the cytoplasm to
bond with another amino acid of the same type.
• The ribosome that has only one tRNA in it now
moves one codon triplet down the mRNA
molecule, which puts the second tRNA in the
ribosome position that the first originally
occupied and creates room for a third tRNA to
float in with its amino acid.
Translation results in the production of
a polypeptide
• This process repeats itself as another peptide
bond forms, the ribosome moves down the
mRNA by another triplet each time until the last
codon triplet is reached.
• The final codon triplet will be a triplet that does
not act as a code for an amino acid, it signals a
‘stop’ to the translation process.
• The entire polypeptide breaks away from the final
tRNA molecule and becomes a free floating
polypeptide in the cytoplasm.
The one gene/one polypeptide
hypothesis
• In the early 1940s, experimental work was performed
which led to the hypothesis that every one gene of DNa
produced one enzyme. Which was soon amended to
include all proteins.
• It was later discovered that many proteins are actually
composed of more than one polypeptide and it was
proposed that each polypeptide required a separate gene.
• Researchers in the last few years have discovered that at
least some genes are not that straightforward. One gene
may lead to a single mRNA molecule, but the mRNA
molecule may then be modified in many different ways,
which may result in the production of a different
polypeptide.
Ribosomes
• Translation occurs within a ribosome.
• Ribosomes can be seen with an electron
microscope, each consists of a large subunit and a
small subunit.
• The subunits are composed of ribosomal RNA
(rRNA) molecules and many distinct proteins.
• rRNA proteins are generally small and are
associated with the core of the RNA subunits.
Roughly two-thirds of the ribosome mass is rRNA.
Ribosomes
• The molecules of the ribosomes are constructed
in the nucleolus of eukaryotic cells and exit the
nucleus through the membrane pores.
• Prokaryotic ribosomes are smaller than
eukaryotic ribosomes. They are also molecularly
different than eukaryotic ribosomes.
• Decoding of a strand of mRNA to produce a
polypeptide occurs in the space between the two
subunits.
Ribosomes
• In this area, there are binding sites for mRNA and
three sites for binding tRNA, as shown below:
Site
Function
A site
Holds the tRNA carrying the next amino acid
to be added to the polypeptide chain
P site
Holds the tRNA carrying the growing
polypeptide chain
Site from which tRNA that has lost its amino
acid is discharged
E site
Ribosomes
• Polypeptide chains are assembled in the cavity
between the two subunits.
• This area is generally free of proteins, so binding
of mRNA and tRNA is carried out by rRNA.
• tRNA moves sequentially through the three
binding sites: from the A site, to the P site, and
finally to the E site.
• The growing polypeptide chain exits the
ribosome through a tunnel in the large subunit
core.
Translation: RNA → protein
• The translation process involves the following
phases:
– Initiation
– Elongation
– Translocation
– Termination
Translation: RNA → protein
• Codons carry the genetic code from DNA to
the ribosomes by mRNA.
• There are 64 possible codons, three codons
have no complementary tRNA anticodon
(these are stop codons).
• There is a start codon (AUG) that signals the
beginning of a polypeptide chain.
• This codon also encodes the amino acid
methionine.
Translation: RNA → protein
• The Initiation Phase
– The start codon (AUG) is on the 5’ end of all
mRNAs.
– Each codon, other than the three stop codons,
attach to a particular tRNA. The tRNA has a 5’ end
and a 3’ end like all other nucleic acid strands.
– The 3’ end of the tRNA is free and has the base
sequence CCA. This is the site of amino acid
attachment.
Translation: RNA → protein
• Because there are complementary bases in a
single stranded tRNA, hydrogen bonds form in
four areas. This causes the tRNA to fold and take
on a three dimensional structure.
• If the molecule is flattened, it has the twodimensional appearance of a clover leaf.
• One of the loops of the clover leaf contains an
exposed anticodon. This anticodon is unique to
each type of tRNA. It is the anticodon that pairs
with a specific codon of mRNA.
Translation: RNA → protein
• Each of the 20 amino acids binds to the
appropriate tRNA due to the action of an enzyme,
each of the 20 amino acids has its own enzyme.
• The active site of each enzyme allows it to only fit
between a specific amino acid and the specific
tRNA. The actual attachment of the amino acid
and tRNA requires energy that is supplied by ATP.
• At this point the structure is called an activated
amino acid, and the tRNA may now deliver the
amino acid to a ribosome to produce the
polypeptide chain.
Translation: RNA → protein
• So, the first step in initiation of translation is
when an activated amino acid – methionine
attached to a tRNA with the anticodon UAC –
combines with an mRNA strand and a small
ribosomal subunit.
• The small subunit moves down the mRNA
until it contacts the start codon (AUG). This
contact starts the translation process.
Translation: RNA → protein
• Hydrogen bonds form between the initiator tRNA
and the start codon.
• Next, a large ribosomal subunit combines with
these parts to form the translation initiation
complex.
• Joining the initiation complex are proteins called
initiation factors that require energy from
guanosine triphosphate (GTP) for attachment.
GTP is an energy-rich compound very similar to
ATP.
Translation: RNA → protein
• The elongation phase
– Once initiation is complete elongation occurs.
– This phase involves tRNAs bringing amino acids to the
mRNA-ribosomal complex in the order specified by
the codons of mRNA.
– Proteins called elongation factors assist in binding to
the tRNAs to the exposed mRNA codons at the A site.
The initiator tRNA then moves the the P site.
– The ribosomes catalyze the formation of peptide
bonds between adjacent amino acids
Translation: RNA → protein
• The translocation phase
– The translocation phase actually happens during
the elongation phase.
– Translocation involves the movement of tRNAs
from one site of the mRNA to another.
– First, a tRNA binds with the A site. Its amino acid
is then added to the growing polypeptide chain by
a peptide bond.
Translation: RNA → protein
• This causes the polypeptide chain to be attached
to the tRNA at the A site.
• The tRNA then moves to the P site. It transfers its
polypeptide chain to the new tRNA that moves
into the now exposed A site.
• The now empty tRNA is transferred to the E site
where it is released. This process occurs in the 5’
to 3’ direction.
• Therefore, the ribosomal complex is moving
along the mRNA toward the 3’ end.
Translation: RNA → protein
• The termination phase
– The termination phase begins when one of the
three stop codons appears at the open A site.
– A protein called a release factor then fills the A
site. The release factor does not carry an amino
acid.
– It catalyzes hydrolysis of the bond linking the tRNA
in the P site with the polypeptide chain.
Translation: RNA → protein
• This frees the polypeptide, releasing it from the
ribosome.
• The ribosome then separates from the mRNA and splits
into its two subunits.
• The termination phase completes the process of
translation.
• Proteins synthesized in this manner have several
different destinations.
• If they are produced by free ribosomes, the proteins
are primarily used by the cell, if they are produced by
ribosomes bound to the ER, they are primarily secreted
or used in lysosomes.
Proteins
• Protein functions and structures
– The following are just a few proteins and their
functions:
Protein
Function
Hemoglobin
Protein containing iron that transports oxygen from the lungs to all
parts of the body in vertebrates
Actin and myosin
Proteins that interact to bring about muscle movement
(contraction) in animals
Insulin
A hormone secreted by the pancreas that aids in maintaining blood
glucose level in vertebrates
Immunoglobulins
Group of proteins that act as antibodies to fight bacteria and
viruses
Digestive enzyme that catalyzes the hydrolysis of starch
Amylase
Proteins
• There are proteins that perform structural
tasks, that store amino acids, and some that
have receptor functions so cells can respond
to stimuli.
• There are four levels of organization in protein
structure (primary, secondary, tertiary, and
quaternary):
Proteins
• Primary organization:
– The primary level of protein structure is the
unique sequence of amino acids held together by
peptide bonds in each protein.
– There are 20 amino acids and they can be
arranged in any order.
– The order or sequence in which the amino acids
are arranged is determined by the nucleotide base
sequence in the DNA of the organism.
Proteins
• Every organism has its own DNA, so every
organism has its own unique proteins.
• The primary structure is simply the amino acid
chain attached by peptide bonds.
• Polypeptide chains may include hundreds of
amino acids.
Proteins
• Changing one amino acid in a chain may
completely alter the structure and function of
the protein.
• For example, sickle cell disease is caused by
just one amino acid change in the normal
hemoglobin protein of red blood cells. The
result is that red blood cells are unable to
carry oxygen.
Proteins
• Secondary organization:
– Hydrogen bonds form between the oxygen from
the carboxyl group of on amino acid and the
hydrogen from the amino group of another
– Secondary structure does not involve the side
chains, or R groups of amino acids. The two most
common configurations of secondary structure
are the α-helix and the β-pleated sheet.
– Both have regular repeating patterns.
Proteins
• Tertiary organization:
– The polypeptide chain bends and folds over itself
because of interactions among R groups and the
peptide backbone, which results in a definite
three-dimensional conformation.
– Interactions that cause tertiary organization
include:
• Covalent bonds between sulfur atoms to create
disulfide bonds – these are often called bridges
because they are strong.
Proteins
• Hydrogen bonds between polar side chains.
• Van der Waals interactions among
hydrophobic side chains of the amino acids. –
these interactions are strong because many
hydrophobic side chains are forced inwards
when the hydrophilic side chains interact with
water toward the outside of the molecule.
• Ionic bonds between positively and negatively
charged side chains.
Proteins
• Tertiary structure is extremely important
in determining the specificity of proteins
such as enzymes.
Proteins
• Quaternary organization:
– Quaternary structure is unique in that it involves
multiple polypeptide chains which combine to
form a single structure.
– Not all proteins have quaternary structure.
– All the bonds mentioned in the previous three
levels of organization are involved in this level.
Proteins
• Some proteins with quaternary structure
include prosthetic or non-polypeptide groups,
these are called conjugated proteins.
• Hemoglobin is an example of a conjugated
protein, because it contains four polypeptide
chains, each of which contains a heme group
(non-polypeptide). Heme contains iron which
binds to oxygen.
Proteins
• Fibrous and globular protein
– Fibrous proteins are composed of many
polypeptide chains in a long narrow shape, they
are usually insoluble in water.
• One example is collagen, which is important in the
structure of connective tissue of humans.
• Actin is another example, which is important in human
muscle contraction.
Proteins
• Globular proteins are more three-dimensional
in shape and are mostly soluble in water.
– Hemoglobin is one type of globular protein.
– The hormone insulin is another globular protein,
which regulates blood glucose levels in humans.
Proteins
• Polar and non-polar amino acids
– Amino acids are often grouped according to the
properties of their R groups.
– Amino acids with non-polar side chains are
hydrophobic. Non-polar amino acids are found in
regions of proteins that are linked to the
hydrophobic are of the cell membrane.
Proteins
• Polar amino acids have hydrophilic
properties, and are found in regions of
proteins that are exposed to water.
• Membrane proteins include polar amino
acids toward the interior and exterior of
the membrane, these amino acids create
hydrophilic channels through which polar
substances can move.
Proteins
• Polar and non-polar amino acids are
important in determining the specificity of an
enzyme.
• Each enzyme has an active site, in which only
a specific substrate can bind.
• Combination is possible through ‘fitting’ which
involves the general shapes and the polarity of
the substrate and the amino acids at the
active site.