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Chapter 7

BIO206H5 Chapter Notes - Chapter 7: Regulatory Sequence, Alternative Splicing, Dna Replication

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George S Espie

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Chapter 7 – From DNA to Protein: How Cells Read the Genome
DNA information can be passed on unchanged from a cell to its descendants through the process of DNA
Even before the DNA code was broken, it was known that the information contained in genes somehow
directed the synthesis of proteins
oProteins are the principal constituents of cells and determine not only cell structure but also cell
The properties and function of a protein molecule are determined by the sequence of the 20 different
amino acid subunits it its polypeptide chain
The genetic instructions carried on DNA must therefore specify the amino acid sequences of proteins
When a particular protein is needed by the cell, the nucleotide sequence of the appropriate segment of a
DNA molecule is first copied into RNA – that segment of DNA is called a gene
The flow of genetic information in cells is from DNA to RNA to protein
oThe central dogma of molecular biology
Transcription and translation are the means by which cells read out, or express the instructions on their
Many identical copies can be made from the same gene, and each RNA molecule can direct the synthesis
of many identical protein molecules
oThis successive amplification enables cells to rapidly synthesize large amounts of protein
whenever necessary
Each gene can be transcribed and its RNA translated at different rates, providing the cell with a way to
make vast quantities of some proteins and tiny quantities of others
A cell can change (or regulate) the expression of each of its genes according to the needs of the moment
Portions of DNA Sequence Are Transcribed into RNA
The first step a cell takes in expression one of its many thousands of genes is to copy the nucleotide
sequence of that gene into RNA
oThe process is called transcription because the information, though copied into another
chemical form, is still written in essentially the same language – the language of nucleotides
Like DNA, RNA is a linear polymer made of four different nucleotide subunits, linked together by
phosphodiester bonds
It differs from DNA chemically in two respects…
oThe nucleotides in RNA are ribonucleotides they contain the sugar ribose rather than
oAlthough like DNA, RNA contains the bases adenine (A), guanine (G), and cytosine (C), it
contains uracil (U) instead of thymine (T)
DNA and RNA differ quite dramatically in overall structure
RNA is single stranded
oBecause an RNA chain is single-stranded, it can fold up into a variety of shapes, just as a
polypeptide chain folds up to form the final shape of a protein
The ability to fold into a complex three-dimensional shape allows RNA to carry out
various function in cells, in addition to conveying information between DNA and proteins
Whereas DNA function solely as an information store, some RNAs have structural, regulatory, or catalytic
Transcription Produces RNA That Is Complementary to One Strand of DNA
Transcription begins with the opening and unwinding of a small portion of the DNA double helix to expose
the bases on each DNA strand
One of the two strands of the DNA double helix then acts as a template for the synthesis of RNA
Ribonucleotides are added one by one and the nucleotide sequence is determined by complementary
base-pairing with the DNA template
When a good match is made, the incoming ribonucleotide is covalently linked to the growing RNA chain
by the enzyme RNA polymerase
The RNA chain produced by transcription the RNA transcript is therefore elongated one nucleotide
at a time and has a nucleotide sequence exactly complementary to the strand of DNA used as a template

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The RNA strand does not remain hydrogen-bonded to the DNA template strand
oJust behind the region where ribonucleotides are being added, the RNA chain is displaced and
the DNA double-helix reforms
RNA molecules are much shorter than DNA molecules because they are only copied from a limited
region of DNA
RNA polymerase catalyzes the formation of phosphodiester bonds that link the nucleotides together and
form the sugar-phosphate backbone of the RNA chain
RNA polymerase moves stepwise along the DNA, unwinding the DNA helix just ahead to expose a new
region of the template strand for complementary base-pairing
In this way, the growing RNA chain is extended by one nucleotide at a time in the 5’ to 3’ direction
The incoming ribonucleoside triphosphates (ATP, CTP, UTP, and GTP) provide the energy needed to
drive the reaction forward
Many RNA copies can be made from the same gene in a relatively short time
oThe synthesis of the next RNA is usually started before the first RNA has been completed
Unlike DNA polymerase, RNA polymerase…
oUses ribonucleoside for phosphates as substrates, so it catalyzes the linkage of ribonucleotides
oIt can start an RNA chain without a primer
oRNA polymerases make about one mistake for every 104 nucleotides copied into RNA
RNA is not used as the permanent storage form of genetic information in cells, so mistakes in RNA
transcripts have relatively minor consequences for a cell
Cells Produce Various Types of RNA
The vast majority of genes carried in a cell’s DNA specify the amino acid sequences of proteins
oThe RNA molecules encoded by these genes – which ultimately direct the synthesis of proteins –
are called messenger RNAs (mRNAs)
In eukaryotes, mRNA is monocistronic while in prokaryotes, mRNA can be polycistronic
The final product of other genes is the RNA itself, not a protein
oThese nonmessenger RNAs, like proteins, have various roles, serving as regulatory, structural,
and catalytic components of cells
Ribosomal RNAs (rRNAs) form the structural and catalytic core of the ribosomes, which translate mRNAs
into proteins
Transfer RNAs (tRNAs) act as adaptors that select specific amino acids and hold them in place on a
ribosomes for their incorporation into protein
microRNAs (miRNAs) serve as key regulators of eukaryotic gene expression
The term gene expression refers to the process by which the information encoded in a DNA sequence
is translated into a product that has some effect on a cell or organism
oIn cases where the final product of the gene is a protein, gene expression includes both
transcription and translation
Signals in DNA Tell RNA Polymerase Where to Start and Finish Transcription
To begin transcription, RNA polymerase must be able to recognize the start of a gene and bind firmly to
the DNA at this site
The way in which RNA polymerases recognize the transcription start site of a gene differs somewhat
between bacteria and eukaryotes
When an RNA polymerase collides randomly with a DNA molecule, the enzyme sticks weakly to the
double helix and then slides rapidly along its length
oRNA polymerase latches on tightly only after it has encountered a gene region called a promoter,
which contains a specific sequence of nucleotides that lies immediately upstream of the starting
point for RNA synthesis
Once bound tightly to the promoter, the RNA polymerase opens up the double helix immediately in from of
the promoter to expose the nucleotides on each strand of a short stretch of DNA
oOne of these two exposed strands then acts as a template for complementary base pairing with
incoming ribonucleoside triphosphates
Chain elongation then continues until the enzyme encounters a second signal in the DNA, the terminator,
where the polymerase halts and releases both the DNA template and the newly made RNA transcript

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This terminator sequence is contained within the gene and is transcribed into the 3’ end of the newly
made RNA
In bacteria, it is a subunit of RNA polymerase, the sigma (σ) factor that is primarily responsible for
recognizing the promoter sequence on the DNA
Each base presents unique features to the outside of the double helix, allowing the sigma factor to find
the promoter sequence without having to separate the entwined DNA strands
Every promoter has a certain polarity: it contains two different nucleotide sequences upstream of the
transcriptional start site that position the RNA polymerase, ensuring it binds to the promoter in only one
Because the polymerase can only synthesize RNA in the 5’ to 3direction, once the enzyme is bound it
must use the DNA strand oriented in the 3’ to 5’ direction as the template
With respect to the chromosome as a whole, the direction of transcription varies from gene to gene
oBut because each gene typically has only one promoter, the orientation of its promoter
determines in which direction that gene is transcribed and therefore which strand is the template
Initiation of Eukaryotic Gene Transcription Is a Complex Process
Eukaryotic cells have 3 types of RNA polymerases that are responsible for transcribing different types of
oRNA polymerase I – transcribe genes encoding transfer RNA, ribosomal RNA, and various other
RNAs that play structural and catalytic roles in a cell
oRNA polymerase II – transcribes the vast majority of eukaryotic genes, including all those that
encode proteins and miRNAs
oRNA polymerase III – transcribe genes encoding transfer RNA, ribosomal RNA, and various other
RNAs that play structural and catalytic roles in a cell
Eukaryotic RNA polymerases require the assistance of a large set of accessory proteins
oPrincipal among these are the general transcription factors, which must assemble at each
promoter along with the polymerase, before the polymerase can begin transcription
The mechanisms that control initiation are very elaborate
oIndividual genes are spread out along the DNA – this architecture allows a single gene to be
controlled by a large variety of regulatory DNA sequences scattered along the DNA
oAlso enable eukaryotes to engage in more complex forms of transcriptional regulation
Eukaryotic initiation must take into account the packing of DNA into nucleosomes and more compact
forms of chromatin structure
Eukaryotic RNA Polymerase Requires General Transcription Factors
Purified eukaryotic RNA polymerase II cannot initiate transcription on its own so it requires general
transcription factors
These accessory proteins assemble on the promoter, where they position the RNA polymerase and pull
apart the DNA double helix to expose the template strand, allowing the polymerase to begin transcription
The assembly process typically begins with the binding of the general transcription factor TFIID to a short
segment of DNA double helix composed primarily of T and A nucleotides; because of its composition, this
part of the promoter is known as the TATA box
Upon binding to DNA, TFIID causes a dramatic local distortion in the DNA double helix, which helps to
serve as a landmark for the subsequent assembly of other proteins at the promoter
One TFIID has bound to the TAT box, the other factors assemble, along with RNA polymerase II, to form a
complete transcription initiation complex
After RNA polymerase II has been positioned on the promoter, it must be released from the complex of
general transcription factors to begin its task (liberated by adding a phosphate group to its tail – initiated
by the general transcription factor TFIIH)
Once transcription has begun, most of the general transcription factors dissociate from the DNA and then
are available to initiate another round of transcription with a new RNA polymerase molecule
Eukaryotic mRNAs Are Processed in the Nucleus
Transcription takes place in the nucleus, but protein synthesis takes place on ribosomes in the cytoplasm
– mRNA must be transported out of the nucleus through small pores in the nuclear envelope
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