7.2 Transcription Flashcards
What is a gene?
A gene is a sequence of DNA which is transcribed into RNA and contains three main parts:
What is a promoter?
The non-coding sequence responsible for the initiation of transcription
Where is the core promoted located?
he core promoter is typically located immediately upstream of the gene’s coding sequence
What is the function of the promoter?
The promoter functions as a binding site for RNA polymerase (the enzyme responsible for transcription)
What mediates the binding of RNA polymerase?
The binding of RNA polymerase to the promoter is mediated and controlled by an array of transcription factors in eukaryotes
Where do transcription factors bind?
These transcription factors bind to either proximal control elements (near the promoter) or distal control elements (at a distance)
What happens once RNA polymerase has bound to the promoter?
After RNA polymerase has bound to the promoter, it causes the DNA strands to unwind and separate
What is the coding sequence?
The region of DNA that is transcribed by RNA polymerase is called the coding sequence
When will RNA polymerase finish transcription?
RNA polymerase will continue to transcribe the DNA until it reaches a terminator sequence
Is the mechanism for transcriptional termination in eukaryotes and prokaryotes the same?
NO
The mechanism for transcriptional termination differs between prokaryotes and eukaryotes
What is the antisense strand?
The antisense strand is the strand that is transcribed into RNA
What is the antisense strand’s sequence relation to the transcribed strand?
Its sequence is complementary to the RNA sequence and will be the “DNA version” of the tRNA anticodon sequence
What is another name for the antisense strand?
The antisense strand is also referred to as the template strand
What is the sense strand?
The sense strand is the strand that is not transcribed into RNA
What is the sense strand’s sequence relation to the transcribed strand?
Its sequence will be the “DNA version” of the RNA sequence (i.e. identical except for T instead of U)
What is another name for the sense strand?
The sense strand is also referred to as the coding strand (because it is a DNA copy of the RNA sequence)
Is a specific strand always anti/sense?
NO
Either of the 2 polynucleotide strands may contain a gene, and hence the determination of sense and antisense is gene-specific
What is transcription?
Transcription is the process by which a DNA sequence (gene) is copied into a complementary RNA sequence by RNA polymerase
- What is the first step of transcription?
Free nucleotides exist in the cell as nucleoside triphosphates (NTPs), which line up opposite their complementary base partner
- How are the NTP’s joined? transcription
RNA polymerase covalently binds the NTPs together in a reaction that involves the release of the two additional phosphates
- In what direction does transcription occur?
The 5’-phosphate is linked to the 3’-end of the growing mRNA strand, hence transcription occurs in a 5’ → 3’ direction
What are the 3 main steps of transcription?
The process of transcription can be divided into three main steps: initiation, elongation and termination
What occurs during initiation?
In initiation, RNA polymerase binds to the promoter and causes the unwinding and separating of the DNA strands
What occurs during elongation?
Elongation occurs as the RNA polymerase moves along the coding sequence, synthesising RNA in a 5’ → 3’ direction
What occurs during termination?
When RNA polymerase reaches the terminator, both the enzyme and nascent RNA strand detach and the DNA rewinds
Can only 1 gene transcript be generated at a time?
Many RNA polymerase enzymes can transcribe a DNA sequence sequentially, producing a large number of transcripts
What must be done in eukaryotes after transcription?
In eukaryotes, post-transcriptional modification of the RNA sequence is necessary to form mature mRNA
What 3 post-transcriptional events must occur?
capping
polyadenylation
splicing
What does capping involve?
Capping involves the addition of a methyl group to the 5’-end of the transcribed RNA
What is the role of the methyl cap?
The methylated cap provides protection against degradation by exonucleases
It also allows the transcript to be recognised by the cell’s translational machinery (e.g. nuclear export proteins and ribosome)
What does polyadenylation involve?
Polyadenylation describes the addition of a long chain of adenine nucleotides (a poly-A tail) to the 3’-end of the transcript
What is the purpose of the poly a tail?
The poly-A tail improves the stability of the RNA transcript and facilitates its export from the nucleus
What is the purpose of splicing?
Within eukaryotic genes are non-coding sequences called introns, which must be removed prior to forming mature mRNA
What is done once the introns have been removed? splicing
The coding regions are called exons and these are fused together when introns are removed to form a continuous sequence
What is the difference between introns and exons?
Introns are intruding sequences whereas exons are expressing sequences
What is alternative splicing?
Splicing can also result in the removal of exons – a process known as alternative splicing
What is the purpose of alternative splicing?
The selective removal of specific exons will result in the formation of different polypeptides from a single gene sequence
Give an example of when alternative splicing is used?
For example, a particular protein may be membrane-bound or cytosolic depending on the presence of an anchoring motif
What regulates transcriptional activity?
Transcriptional activity is regulated by two groups of proteins that mediate binding of RNA polymerase to the promoter
What are the two groups of proteins that regulate transcriptional activity?
transcription factors and regulatory proteins
How do transcription factors and RNA polymerase interact?
Transcription factors form a complex with RNA polymerase at the promoter
How do transcription factors regulate gene expression?
RNA polymerase cannot initiate transcription without these factors and hence their levels regulate gene expression
What is the role of regulatory proteins?
Regulatory proteins bind to DNA sequences outside of the promoter and interact with the transcription factors
What are the 2 types of regulatory proteins?
activator and repressor proteins
What is the role of activator proteins?
Activator proteins bind to enhancer sites and increase the rate of transcription (by mediating complex formation)
What is the role of repressor proteins?
Repressor proteins bind to silencer sequences and decrease the rate of transcription (by preventing complex formation)
Is the presence of transcription factors and regulatory proteins the same in every cell?
The presence of certain transcription factors or regulatory proteins may be tissue-specific
What may also affect transcriptional activity?
Additionally, chemical signals (e.g. hormones) can moderate protein levels and hence mediate a change in gene expression
What are control elements?
The DNA sequences that regulatory proteins bind to are called control elements
Where are control elements located?
Some control elements are located close to the promoter (proximal elements) while others are more distant (distal elements)
Where do regulatory proteins usually bind, in relation to control elements?
Regulatory proteins typically bind to distal control elements, whereas transcription factors usually bind to proximal elements
How many control elements do genes have?
Most genes have multiple control elements and hence gene expression is a tightly controlled and coordinated process
What can cause changes in the internal or external environment cause?
Changes in the external or internal environment can result in changes to gene expression patterns
How may the external/internal environment affect gene expression?
Chemical signals within the cell can trigger changes in levels of regulatory proteins or transcription factors in response to stimuli
How do chemical signals affect gene expression?
This allows gene expression to change in response to alterations in intracellular and extracellular conditions
How do hydrangeas change their gene expression in response to environmental changes?
Hydrangeas change colour depending on the pH of the soil (acidic soil = blue flower ; alkaline soil = pink flower)
How do Himalayan rabbits change their gene expression in response to environmental changes?
The Himalayan rabbit produces a different fur pigment depending on the temperature (>35ºC = white fur ; <30ºC = black fur)
How do humans change their gene expression in response to environmental changes?
Humans produce different amounts of melanin (skin pigment) depending on light exposure
How do fish change their gene expression in response to environmental changes?
certain species of fish, reptile and amphibian can even change gender in response to social cues (e.g. mate availability)
What do the histone tails determine?
These histone proteins have protruding tails that determine how tightly the DNA is packaged
How do histone tails typically associate with DNA?
Typically the histone tails have a positive charge and hence associate tightly with the negatively charged DNA
In what two ways can the histone tails be modified?
acetylation and methylation
How does acetylation affect the DNA?
Adding an acetyl group to the tail (acetylation) neutralises the charge, making DNA less tightly coiled and increasing transcription
How does methylation affect the DNA?
Adding a methyl group to the tail (methylation) maintains the positive charge, making DNA more coiled and reducing transcription
What is heterochromatin?
When DNA is supercoiled and not accessible for transcription, it exists as condensed heterochromatin
What is euchromatin?
When the DNA is loosely packed and therefore accessible to the transcription machinery, it exists as euchromatin
Will all cels have the same amount of eu and heterochromatin?
NO
Different cell types will have varying segments of DNA packaged as heterochromatin and euchromatin
Is this packaging permanent?
Some segments of DNA may be permanently supercoiled, while other segments may change over the life cycle of the cell
How can DIRECT methylation of DNA affect gene expression patterns?
Increased methylation of DNA decreases gene expression (by preventing the binding of transcription factors)
Which genes exhibit more DNA methylation?
Consequently, genes that are not transcribed tend to exhibit more DNA methylation than genes that are actively transcribed
What is epigenetics?
Epigenetics is the study of changes in phenotype as a result of variations in gene expression levels
What does epigenetic analysis show?
Epigenetic analysis shows that DNA methylation patterns may change over the course of a lifetime
What can influence epigenetic changes?
It is influenced by heritability but is not genetically pre-determined (identical twins may have different DNA methylation patterns)
Will the same cell types have the same methylation?
NO
Different cell types in the same organism may have markedly different DNA methylation patterns
What environmental factors may influence DNA methylation?
Environmental factors (e.g. diet, pathogen exposure, etc.) may influence the level of DNA methylation within cells
