Lecture 16 (Gene expression - transcription) Flashcards
The Central Dogma of Molecular Biology
The central dogma of molecular biology describes the two-step process, transcription and translation, by which the information in genes flows into proteins: DNA → RNA → protein.
Fancy way of saying how information flows in a cell
Gene expression
The process by which information from a gene is used in synthesis of a functional gene product: protein or non-coding RNA (an RNA molecule that will NOT give rise to a protein and has some other function)
Gene
A defined region (sequence) of DNA that produces a type of RNA molecules that has some function
Fundamental unit of inheritance
Codes for a protein
A gene (DNA) may contain sequences …
Responsible for the regulation of the synthesis of RNA
That produces the RNA
Responsible for further processing of the RNA
Transcription
DNA-dependent RNA synthesis
Catalysed by the enzyme RNA polymerase
RNA polymerase synthesises mRNA by catalysing the formation of phosphodiester bonds between ribonucleotides
RNA polymerase selects the correct nucleotides to incorporate into mRNA based on the sequence of the DNA which is being transcribed
Double stranded DNA helix is used as information to create a single stranded RNA.
mRNA
Carries the message that orders for a particular protein from the nucleus (where the DNA master copy is) to the cytoplasm (where proteins are synthesised)
RNA polymerase
RNA polymerase is an enzyme that is responsible for copying a DNA sequence into an RNA sequence, during the process of transcription.
Which DNA strand is transcribed?
DNA has two strands which are complimentary in sequence. One strand is known as the coding strand (5’ to 3’ direction), the other is the template strand (3’ to 5’ strand) (a.k.a the non-coding strand). Coding strand is the strand that contains the information and this makes sense as you have to read strands in the 5’ to 3’ direction for them to make sense . Only one strand in DNA contains the information and the other strand is essentially a mirror image. The RNA transcript is going to be antiparallel to the template strand
mRNA is transcribed from the
template strand
Outline of transcription
Initiation (RNA polymerase binds to the double stranded DNA and once it has bound it, it will start to pull the 2 DNA strands apart), elongation (then as the RNA polymerase moves along, complimentary nucleotides are inserted against the template strand to make a copy of the coding strand), termination (this then stops at a particular signal)
Initiation of transcription
Gene may contain sequences responsible for the regulation of the synthesis of RNA
1 - Transcription factors bind to the TATA box and other regions of the promoter (the promoter region is a particular region before the coding sequence and the coding sequence is the part that will give you the protein) (the TATA box is a very A and T rich region. This is important because there are only two hydrogen bonds between them therefore it is easier to split apart 2 DNA strands and also this A and T rich region is recognised by other proteins known as transcription factors which are essential and are essentially guiding the RNA polymerase to the gene)
2- RNA polymerase II binds, forming a transcriptional initiation complex together with the transcription factors
3- The two DNA strands seperate and RNA polymerase II starts mRNA synthesis without the need of a primer ( RNA polymerase makes its own primer as it has an internal 3’ hydroxyl group that it can use to start from scratch
Summary (very simplified) - An enzyme called RNA polymerase, binds to the DNA at a region called the promotor regions, breaking the hydrogen bonds between bases/unzips the two strands.
Elongation of transcription
Gene may contain sequences that produce the RNA
RNA polymerase II uses the template strand, which runs in the 3’ to 5’ direction, as a template, and inserts complementary RNA nucleotides in the 5’ to 3’ direction
Which part(s) of a “gene” sequence is transcribed and translated?
Gene is used in transcription in the nucleus to create mRNA and the mRNA is used in translation in the cytoplasm to create a protein (it is used as a set of instructions to make a protein)
Anatomy of eukaryotic genes
DNA goes through transcription to get to mRNA goes through translation to get to protein. There are specific features that are involved in these processes
Intron
Non-coding regions of a RNA transcript or the DNA encoding it
Introns and exons
Introns and exons are nucleotide sequences within a gene. Introns are removed by RNA splicing as RNA matures, meaning that they are not expressed in the final messenger RNA (mRNA) product, while exons go on to be covalently bonded to one another in order to create mature mRNA.
Coding sequence
Portion of a gene’s DNA that is translated into a protein
Promoter
DNA segment recognised by RNA polymerase to initiate transcription
The sequence of the promoter region does not become RNA
5’ UTR and 3’ UTR (UnTranslated Region)
Contain regulatory elements that influence on gene expression at the transcriptional and/or transitional level (e.g. by influencing on mRNA stability, translation efficiency or localisation)
Transcribed but (usually) not translated
5’ UTR means that its at the 5’ end
UTRs have an important role in deciding when transcription is going to happen (regulatory role) and they also decide when translation is going to happen
5’G cap
Prevents mRNA degradation, regulates translation (by providing a ribosome, recognition and binding site), regulation of nuclear export, promote intron excision
To the 5’ end, a specifically modified nucleotide with a G base is added. This protects the 5’ end.
Poly-A tail
Prevents mRNA degradation, regulates translation and nuclear export
3’ end is protected by a long chain of As (about 200), once it is added it protects the end
Helps with transport through the nuclear pore for translation
mRNA needs protection as lots of things in the cell each single stranded molecules
Splicing (pre-mRNA processing)
The coding sequence of eukaryotic genes is not one continuous sequence that will give rise to the protein, it is a disruptive sequence
RNA splicing, in molecular biology, is a form of RNA processing in which a newly made precursor messenger RNA (pre-mRNA) transcript is transformed into a mature messenger RNA (mRNA). During splicing, introns (Non-coding regions) are removed and exons (Coding Regions) are joined together.
After an RNA molecule has been transcribed, but prior to its departure from the nucleus to be translated, the RNA is processed and the introns are removed by splicing.
mRNA will initially contain intronic sequences however no protein can be made with intronic sequences. Splicing gives rise to one continuous coding sequence
Summary of eukaryotic gene structure elements
Contains non-coding DNA regions upstream and downstream of the coding sequences as well as pithing the coding sequence
These non-coding DNA regions can be transcribed but not translated
These non-coding DNA elements are involved in regulating gene expression
Changes (mutations) in these non-coding gene sequences may ‘disrupt’ normal gene expression
Cellular location of eukaryotic transcription
Transcription occurs in the nucleus and translation occurs in the cytoplasm. Transcription and translation are not coupled (mRNA is transported into the cytoplasm)
Transcription and translation in cytoplasm. Transcription and translation are coupled
Gene regulation
Gene regulation is how a cell controls which genes, out of the many genes in its genome, are “turned on” (expressed). Thanks to gene regulation, each cell type in your body has a different set of active genes – despite the fact that almost all the cells of your body contain the exact same DNA. These different patterns of gene expression cause your various cell types to have different sets of proteins, making each cell type uniquely specialized to do its job.
Gene structure element where transcription starts
promoter region
During transcription, RNA polymerase creates a …
Single stranded RNA molecule from a double stranded DNA helix
What direction does RNA polymerase move?
RNA polymerase synthesizes an RNA transcript complementary to the DNA template strand in the 5’ to 3’ direction. It moves forward along the template strand in the 3’ to 5’ direction, opening the DNA double helix as it goes.
Coding region of a gene
The coding region of a gene is the part of the gene that will be eventually transcribed and translated into protein, i.e., the sum total of its exons.
Mutations to non-coding regions of DNA
These mutations include changes in single DNA building blocks (point mutations), insertions, deletions, duplications, and translocations. Noncoding DNA mutations can be inherited from a parent or acquired during a person’s life
Non-coding DNA sequences are components of an organism’s DNA that do not encode protein sequences. Some non-coding DNA is transcribed into functional non-coding RNA molecules (e.g. transfer RNA, ribosomal RNA, and regulatory RNAs). Other functions of non-coding DNA include the transcriptional and translational regulation of protein-coding sequences, scaffold attachment regions, origins of DNA replication, centromeres and telomeres.
