7.2 Transcription and gene expression Flashcards
What is a gene?
A sequence of DNA which is transcribed into RNA
What are the three parts of a gene?
Promoter
Coding sequence
Terminator
What is the promoter?
The non coding sequence responsible for the initiation of transcription
Where is the promoter typically located?
Immediately upstream of the genes coding sequence
What does the promoter function as?
A binding site for RNA polymerase
What controls and mediates the binding of RNA polymerase to the promoter?
An array of transcription factors in eukaryotes
What do the transcription factors bind to?
Proximal or distal control elements
What is the coding sequence?
The region of DNA that is transcribed by RNA polymerase
What happens after RNA polymerase has bound to the promoter?
It causes the DNA strands to unwind and separate
What does the mechanism for transcriptional termination differ between?
Prokaryotes and eukaryotes
What stops RNA polymerase transcribing the DNA?
The terminator (sequence)
How many strands does a gene have?
Two
How many strands are transcribed into RNA?
One
What is the antisense strand?
The strand that is transcribed into RNA
What is the sense strand?
The strand that is not transcribed into RNA
What is the sequence of the antisense strand complimentary to?
The RNA sequence
When will the antisense strand be the DNA version?
During the tRNA anticodon sequence
What is the antisense strand referred to as?
The template strand
When will the sense strand be the DNA verion?
In the RNA sequence
What else is sense strand referred to as?
The coding strand
Why is the determination of sense and antisense gene specific?
Either of the 2 polynucleotide strands may contain a gene
What is transcription?
The process where a DNA sequence is copied into a complementary RNA sequence by RNA polymerase
How do free nucleotides exist in cells as?
Nucleoside triphosphates
How do nucleoside triphosphates line up?
Opposite their complementary base partner
What type of bond does RNA polymerase use to bing NTPs together?
Covalent
What is released when RNA polymerase binds NTPs together?
Two additional phosphates
What direction does transcription occur in?
5’ - 3’ direction
Why does transcription occur in a 5’ - 3’ direction?
The 5’ phosphate is linked to the 3’ end of the growing mRNA strand
What are the three stages of transcription?
Inititation
Elongation
Termination
What happens in initiation?
RNA polymerase binds to the promoter and causes the unwinding and separating of the DNA strands
What happens in elongation?
The RNA polymerase moves along the coding sequence in a 5’ - 3’ direction
What happens in ternination?
The RNA polymerase reaches the terminator and both the enzyme and nascent RNA strand detach and the DNA rewinds
Why can a large number of transcripts be produced?
Many RNA polymerase enzymes can transcribe a DNA sequence sequentially
In eukaryotes what is necessary to form mature mRNA?
Post transcriptional modification of the RNA sequence
In eukaryotes what are the three post transcriptional events that must happen for mature mRNA?
Capping
Polyadenylation
Splicing
What is capping?
The addition of a methyl group to the 5’ end of the transcribed RNA
What does the methylated cap provide in capping?
Protection against degradation by exonucleases
What does capping allow the transcript to do?
Be recognised by the cells translational machinery
What is polydenylation?
The addition of a long chain of adenine nucleotides to the 3’ end of the transcript
What is the long chain of adenine nucleotides also known as?
poly-A-tail
What does the poly-A-tail improve?
The stability of the RNA transcript and facilitates its export form the nucleus
What is splicing?
The process by which introns are removed
In eukaryotic genes what must be removed prior to forming mature mRNA?
Introns
What are introns?
Intruding Non-coding sequences
What are the coding regions called?
Exons
What happens to exons when introns are removed?
They are fused together to form a continuous sequence
In splicing are introns or exons being kept?
Exons are being kept
What is alternative splicing?
When splicing can also result in the removal of exons
What does the selective removal of specific exons result in?
The formation of different polypeptides from a single gene sequence
What is transcriptional activity regulated by?
Two groups of proteins
What do transcription factors form?
A complex with RNA polymerase at the promoter
What do levels of transcriptional factors regulate?
Gene expression
Why do transcriptional factor levels regulate gene expression?
As RNA polymerase cannot initiate transcription without them
What do regulatory proteins bind to?
DNA sequences
Where do regulatory proteins bind to DNA sequences?
Outside the promoter
What do regulatory proteins interact with?
The transcription factors
What do activator proteins bind to?
Enhancer sites
How do activator proteins affect the rate of transcription?
Increase it by mediating complex formation
What do repressor proteins bind to?
Silencer sequences
How do repressor proteins affect the rate of transcription?
Decrease it by preventing complex formation
In gene expression what may be tissue specific?
The presence of certain transcription factors or regulatory proteins
How can chemical signals mediate a change in gene expression?
By moderating protein levels
What are control elements?
The DNA sequences that regulatory proteins bind to
Where are control elements located?
proximal or distal to the promoter
What are the two types of control elements?
Distal control elements
Proximal control elements
What typically binds to distal control elements?
Regulatory proteins
What typically binds to proximal control elements?
Transcription factors
Why is gene expression a tightly controlled and coordinated process?
As most genes have multiple control elements
What can cause changes to gene expression patterns?
Changes in the external or internal environment
What can chemical signals within the cell trigger?
Changes in levels of regulatory proteins or transcription factors in response to stimuli
What does chemical signals allow in gene expression?
To change in response to change to intracellular and extracellular conditions
How can humans change their gene expression patterns in response to environmental changes?
Producing different amounts of melanin depending on light exposure
How can hydrangeas change their gene expression patterns in response to environmental changes?
Can change colour depending on the pH of the soil
How can himalayan rabbits change their gene expression patterns in response to environmental changes?
By producing a different fur pigment depending on the temperature
What is eukaryotic DNA wrapped around?
Histone proteins
Why is eukaryotic DNA wrapped around histone proteins?
To form compact nucleosomes
What determines how tightly packaged DNA is?
The histone proteins have protruding tails
Why do histone tails associate tightly with DNA?
As histones have a positive charge and DNA has a negative charge
How does adding an acetyl group to the tail affect the charge?
It neutralises it
How does adding an acetyl group to the tail affect transcription?
It increases transcription as it makes DNA less tightly coiled
How does adding a methyl group to the tail affect the charge?
It maintains the positive charge
How does adding a methyl group to the tail affect transcription?
Reduces it as it makes DNA more coiled
What is acetylation?
Adding an acetyl group to the tail
What is methylation?
Adding a methyl group to the tail
What is condensed heterochromatin?
When DNA is supercoiled and not accessible for transcription
What is euchromatin?
When DNA is loosely packed and accessible for transcription
Are segments of DNA always supercoiled?
Sometimes but it can change over the life cycle of the cell
What can direct methylation of DNA also affect?
Gene expression patterns
How does increased methylation of DNA affect gene expression?
Decreases it by preventing the binding of transcription factors
What types of genes exhibit more DNA methylation?
Genes that are not transcribed
What is epigenetics?
The study of changes in phenotype as a result of variations in gene expression
What does epigenetic analysis show about DNA methylation?
The patterns may change over the course of a lifetime
What influences DNA methylation patterns?
Heritability but it is not genetically pre-determined
and environmental factors
Can different cell types in the same organism have different DNA methylation patterns?
Yes
