IB Biology - 7.2 Transcription & Gene Expression

3 main sections of a gene

Promoter, Coding Sequence, Terminator

What is the promoter sequence of a gene?

-The non-coding sequence of a gene responsible for the initiation of transcription
-Found at the beginning of the gene (before the gene's coding sequence)
-A binding site for RNA polymerase (the enzyme responsible for transcription)

How do some proteins regulate gene expression?

- Transcriptional activity is regulated by proteins that mediate binding of RNA polymerase to the promoter
- RNA polymerase cannot initiate transcription without forming a complex with transcription factors and hence their levels regulate gene expression
- Their presence changes across tissues and may be influenced by chemical signals (e.g. hormones)

Name 2 groups of regulatory proteins that bind to DNA sequences and therefore affect gene expression

1. Activator proteins - bind to enhancer sites and increase the rate of transcription (by mediating complex formation)

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

Where do regulatory proteins bind?

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

What else impacts gene expression?

The environment of a cell and of an organism

What is the environmental impact on genes?

- Changes in the external or internal environment can result in changes to gene expression patterns
- Chemical signals within the cell can trigger changes in levels of regulatory proteins or transcription factors in response to stimuli

Give an example of an organism changing their gene expression in response to environmental changes

Siamese Cats
- Cats have a 'C' gene that codes for the production of the enzyme tyrosinase - this starts the production of a pigment
- A mutant allele allows normal pigment production only at temperatures below body temperature (on ears, feet, tail)
- At higher temperatures, the protein product is inactive so the pigment isn't produced

Eukaryotic DNA is wrapped around... What do these have that affect DNA?

Histones - they have protruding tails that determine how tightly DNA is packaged

What charge do histone tails typically have? What does this allow them to do?

Positive - this allows them to bind tightly to negatively charged DNA (inhibiting transcription)

What are the two ways these tails can be modified?

1. Adding an acetyl group to the tail (acetylation) - neutralises positive charge - less tightly coiled - higher levels of transcription

2. Adding a methyl group to the tail (methylation) - can either tighten coiling (inhibiting transcription) or loosen coiling (promoting transcription)

Direct methylation of DNA can... How?

- affect the expression of gene patterns
- it decreases gene expression by preventing the binding of transcription factors

DNA methylation patterns...

- may change over the course of a lifetime
- may be affected by environmental factors within cells (e.g. diet, pathogen exposure, etc.)
- are passed onto the daughter cell in cell division
- are mainly erased when a sperm cell and an egg cell meet (about 1% of the epigenome remains)

Types of Chromatin

heterochromatin and euchromatin

heterochromatin

Condensed DNA - supercoiled and not accessible for transcription

euchromatin

When the DNA is loosely packed and therefore accessible to the transcription machinery - open chromatin. E.g. when histones are acetylated

What are epigenetic tags?

Chemical modifications of chromatin that affect gene expression and thus impact the visible characteristics of an individual

What is an epigenome?

The sum of all the epigenetic tags in an organism

So name 2 ways a gene could be silenced?

- Repressor proteins could bind to silencer sequences and decrease the rate of transcription (by preventing the binding of RNA polymerase)

- methylation of histone - DNA would wrap tighter around histone - inhibiting transcription

What 2 strands does a gene consist of?

2 polynucleotide strands (antisense and sense strands)

What is the anti-sense strand?

is the strand that is used when transcribing RNA, Its sequence is complementary to the RNA sequence - template strand

sense strand

is the strand that is not transcribed into RNA (coding strand) - the 'DNA version' of the RNA sequence (identical apart from it will have Ts instead of Us)

Transcribe this DNA sequence to mRNA (antisense strand)
ATTCCGG

UAAGGCC

What is transcription?

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

mRNA (messenger RNA)

a single-stranded RNA molecule that encodes the information to make a protein - small enough to exit the nuclear pores

Give an overview of the process of transcription

1. INITIATION-
RNA polymerase binds to the promoter and causes the unwinding and separating of the DNA strands (by breaking hydrogen bonds between complementary base pairs)

2. ELONGATION-
RNA polymerase moves along the coding sequence in a 5' to 3' direction - adding RNA nucleotides using complementary base pairing - they're added onto the 3' end of the growing mRNA strand (U binds with A instead of T). RNA polymerase forms covalent bonds between the RNA nucleotides

3. TERMINATION-
Occurs when RNA polymerase reaches the terminator sequence. The DNA molecule and the new mRNA molecule will dissociate from the enzyme.

What does pre-mRNA contain?

introns (non-coding sequences, INTruding) and exons (coding sequences, EXpressing)

What are the 3 post-transcriptional events that must occur to form mature mRNA (in eukaryotes only)?

capping, polyadenylation, splicing

capping

- the addition of a methyl group to the 5'-end of the transcribed RNA
- this is called a cap
- it protects the mRNA

Polyadenylation

- the addition of a poly-A tail to the 3' end of a newly synthesized mRNA molecule
- the tail is made up of a long chain of adenine nucleotides
- it improves the stability of the mRNA

splicing

- introns are removed and exons are fused together to form a continuous sequence of mature mRNA
- this is done because of snRNPs which attach to either side of the intron and form a spliceosome to cut them out

what does splicing the mRNA allow the organism to do?

increase the number of different proteins it can produce

How to code different proteins from one gene?

- alternative splicing
- exons can be selectively removed to form different polypeptides from the same gene