Topic 7.2 Transcription and Gene Expression

Question 1

Sections of a gene - promoter

Answer 1

• The non-coding sequence responsible for the initiation of transcription
• The core promoter is typically located immediately upstream of the gene’s coding sequence
• The promoter functions as a binding site for RNA polymerase (the enzyme responsible for transcription)
• The binding of RNA polymerase to the promoter is mediated and controlled by an array of transcription factors in eukaryotes
• These transcription factors bind to either proximal control elements (near the promoter) or distal control elements (at a distance)

Question 2

Sections of a gene - Coding Sequence

Answer 2

• After RNA polymerase has bound to the promoter, it causes the DNA strands to unwind and separate
• The region of DNA that is transcribed by RNA polymerase is called the coding sequence

Question 3

Sections of a gene - Terminator

Answer 3

• RNA polymerase will continue to transcribe the DNA until it reaches a terminator sequence
• The mechanism for transcriptional termination differs between prokaryotes and eukaryotes

Question 4

Antisense

Answer 4

• The antisense strand is the strand that is transcribed into RNA
  a. Its sequence is complementary to the RNA sequence and will be the “DNA version” of the tRNA anticodon sequence
  b. The antisense strand is also referred to as the template strand

Question 5

Sense

Answer 5

• The sense strand is the strand that is not transcribed into RNA
  a. Its sequence will be the “DNA version” of the RNA sequence (i.e. identical except for T instead of U)
  b. The sense strand is also referred to as the coding strand (because it is a DNA copy of the RNA sequence)

Question 6

Transcription (HL)

Answer 6

the process by which a DNA sequence (gene) is copied into a complementary RNA sequence by RNA polymerase

Question 7

Three main steps of transcription

Answer 7

Initiation, elongation and termination

1. In initiation, RNA polymerase binds to the promoter and causes the unwinding and separating of the DNA strands
2. Elongation occurs as the RNA polymerase moves along the coding sequence, synthesizing RNA in a 5’ → 3’ direction
3. When RNA polymerase reaches the terminator, both the enzyme and nascent RNA strand detach and the DNA rewinds

Question 8

Post-transcriptional modification in eukaryotes

Answer 8

modification of the RNA sequence is necessary to form mature mRNA

Question 9

Three eukaryotic post-transcription events that must occur

Answer 9

Capping

• Capping involves the addition of a methyl group to the 5’-end of the transcribed RNA
• The methylated cap provides protection against degradation by exonuclease
• It also allows the transcript to be recognized by the cell’s translational machinery (e.g. nuclear export proteins and ribosome)

Polyadenylation

• Polyadenylation describes the addition of a long chain of adenine nucleotides (a poly-A tail) to the 3’-end of the transcript
• The poly-A tail improves the stability of the RNA transcript and facilitates its export from the nucleus

Splicing

• Within eukaryotic genes are non-coding sequences called introns, which must be removed prior to forming mature mRNA
• The coding regions are called exons and these are fused together when introns are removed to form a continuous sequence
• Introns are intruding sequences whereas exons are expressing sequences
• The process by which introns are removed is called splicing

Question 10

Alternative splicing

Answer 10

The selective removal of specific exons will result in the formation of different polypeptides from a single gene sequence

Question 11

Transcriptional activity is regulated by…

Answer 11

two groups of proteins that mediate binding of RNA polymerase to the promoter

Question 12

Transcription factors

Answer 12

form a complex with RNA polymerase at the promoter

Question 13

Regulatory proteins

Answer 13

bind to DNA sequences outside of the promoter and interact with the transcription factors

Question 14

Activator proteins

Answer 14

bind to enhancer sites and increase the rate of transcription (by mediating complex formation)

Question 15

Repressor proteins

Answer 15

bind to silencer sequences and decrease the rate of transcription (by preventing complex formation)

Question 16

Chemical signals

Answer 16

can moderate protein levels and hence mediate a change in gene expression

Question 17

Control elements

Answer 17

The DNA sequences that regulatory proteins bind to are called control elements

• Some control elements are located close to the promoter (proximal elements) while others are more distant (distal elements)
• Regulatory proteins typically bind to distal control elements, whereas transcription factors usually bind to proximal elements
• Most genes have multiple control elements and hence gene expression is a tightly controlled and coordinated process

Question 18

Changes in the external or internal environment

Answer 18

can result in changes to gene expression

• Chemical signals within the cell can trigger changes in levels of regulatory proteins or transcription factors in response to stimuli
• This allows gene expression to change in response to alterations in intracellular and extracellular conditions

Question 19

Examples of organisms changing their gene expression due to environment changes

Answer 19

• Hydrangeas change colour depending on the pH of the soil (acidic soil = blue flower ; alkaline soil = pink flower)
• The Himalayan rabbit produces a different fur pigment depending on the temperature (>35ºC = white fur ; <30ºC = black fur)
• Humans produce different amounts of melanin (skin pigment) depending on light exposure
• Certain species of fish, reptile and amphibian can even change gender in response to social cues (e.g. mate availability)

Question 20

Modification of Histone Tails

Answer 20

Typically the histone tails have a positive charge and hence associate tightly with the negatively charged DNA

• Adding an acetyl group to the tail (acetylation) neutralizes the charge, making DNA less tightly coiled and increasing transcription
• Adding a methyl group to the tail (methylation) maintains the positive charge, making DNA more coiled and reducing transcription

Question 21

When DNA is supercoiled and not accessible for transcription, it exists as condensed?

Answer 21

HETEROCHROMATIN

Question 22

When the DNA is loosely packed and therefore accessible to the transcription machinery, it exists as?

Answer 22

EUCHROMATIN

• Different cell types will have varying segments of DNA packaged as heterochromatin and euchromatin
• Some segments of DNA may be permanently supercoiled, while other segments may change over the life cycle of the cell

Question 23

Increased gene methylation decreases…

Answer 23

gene expression.

Consequently, genes that are not transcribed tend to exhibit more DNA methylation than genes that are actively transcribed

Question 24

Epigenetics

Answer 24

the study of changes in phenotype as a result of variations in gene expression levels

Question 25

Epigenetic analysis

Answer 25

• Epigenetic analysis shows that DNA methylation patterns may change over the course of a lifetime
• It is influenced by heritability but is not genetically pre-determined (identical twins may have different DNA methylation patterns)
• Different cell types in the same organism may have markedly different DNA methylation patterns
• Environmental factors (e.g. diet, pathogen exposure, etc.) may influence the level of DNA methylation within cells