Lecture 16 (Gene expression - transcription)

Question 1

The Central Dogma of Molecular Biology

Answer 1

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

Question 2

Gene expression

Answer 2

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)

Question 3

Gene

Answer 3

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

Question 4

A gene (DNA) may contain sequences …

Answer 4

Responsible for the regulation of the synthesis of RNA

That produces the RNA

Responsible for further processing of the RNA

Question 5

Transcription

Answer 5

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.

Question 6

mRNA

Answer 6

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)

Question 7

RNA polymerase

Answer 7

RNA polymerase is an enzyme that is responsible for copying a DNA sequence into an RNA sequence, during the process of transcription.

Question 8

Which DNA strand is transcribed?

Answer 8

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

Question 9

mRNA is transcribed from the

Answer 9

template strand

Question 10

Outline of transcription

Answer 10

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)

Question 11

Initiation of transcription

Answer 11

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.

Question 12

Elongation of transcription

Answer 12

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

Question 13

Which part(s) of a “gene” sequence is transcribed and translated?

Answer 13

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)

Question 14

Anatomy of eukaryotic genes

Answer 14

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

Question 15

Intron

Answer 15

Non-coding regions of a RNA transcript or the DNA encoding it

Question 16

Introns and exons

Answer 16

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.

Question 17

Coding sequence

Answer 17

Portion of a gene’s DNA that is translated into a protein

Question 18

Promoter

Answer 18

DNA segment recognised by RNA polymerase to initiate transcription

The sequence of the promoter region does not become RNA

Question 19

5’ UTR and 3’ UTR (UnTranslated Region)

Answer 19

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

Question 20

5’G cap

Answer 20

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.

Question 21

Poly-A tail

Answer 21

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

Question 22

Splicing (pre-mRNA processing)

Answer 22

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

Question 23

Summary of eukaryotic gene structure elements

Answer 23

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

Question 24

Cellular location of eukaryotic transcription

Answer 24

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

Question 25

Gene regulation

Answer 25

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.

Question 26

Gene structure element where transcription starts

Answer 26

promoter region

Question 27

During transcription, RNA polymerase creates a …

Answer 27

Single stranded RNA molecule from a double stranded DNA helix

Question 28

What direction does RNA polymerase move?

Answer 28

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.

Question 29

Coding region of a gene

Answer 29

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.

Question 30

Mutations to non-coding regions of DNA

Answer 30

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.