Nucleic Acids - 7.2 Transcription (HL (+ some SL)) Flashcards
Transcription = basic understandings
- one of the two main stages in protein synthesis
- involves making a copy (mRNA) of a section of DNA (a section of DNA unwinds inside the nucleus)
- THYMINE is replaced with URACIL in the mRNA molecule
- the mRNA molecule moves (from the nucleus) to the ribosomes where protein synthesis takes place
Transcription is the process by which a DNA sequence (gene) is copied into a complementary RNA sequence by RNA polymerase
- Free nucleotides exist in the cell as nucleoside triphosphates (NTPs), which line up opposite their complementary base partner
- RNA polymerase covalently binds the NTPs together in a reaction that involves the release of the two additional phosphates
- The 5’-phosphate is linked to the 3’-end of the growing mRNA strand, hence transcription occurs in a 5’ → 3’ direction
Many RNA polymerase enzymes can transcribe a DNA sequence sequentially, producing a large number of transcripts
In eukaryotes, post-transcriptional modification of the RNA sequence is necessary to form mature mRNA
7.2 - transcription and gene expression = UNDERSTANDINGS
- Transcription occurs in a 5’ to 3’ direction
- Nucleosomes help to regulate transcription in eukaryotes
(DNA is wrapped around histone proteins forming nucleosomes - the ends of histone proteins can be modified. When histone proteins are methylated the transcription of genes can be promoted or inhibited)
- Eukaryotic cells modify mRNA after transcription
(The presence of a nuclear membrane in eukaryotic cells means that transcription and translation occur in different locations. mRNA can be extensively modified (post-translation modification) before it leaves the nucleus (eg. introns can be removed from mRNA before translation occurs)
- Splicing of mRNA increases the number of different proteins an organism can occur
(Some genes code for multiple proteins - these genes have a number of (and alternative introns) introns that cant be spliced (cut) out of the mRNA = different proteins being formed)
- Gene expression is regulated by proteins that bind to specific base sequences in DNA
Nucleosomes in transcription
Nucleosomes help to regulate transcription in eukaryotes
(DNA is wrapped around histone proteins forming nucleosomes - the ends of histone proteins can be modified. When histone proteins are methylated the transcription of genes can be promoted or inhibited)
Eukaryotic and mRNA after transcription
Eukaryotic cells modify mRNA after transcription
(The presence of a nuclear membrane in eukaryotic cells means that transcription and translation occur in different locations. mRNA can be extensively modified (post-translation modification) before it leaves the nucleus (eg. introns can be removed from mRNA before translation occours
___
One side of the DNA acts as a template on which the complementary molecule of mRNA is made - this process is catalysed by the enzyme RNA polymerase (transcriptase) and only occurs in the 5’ to 3’ direction. RNA polymerase adds the 5’ end of the free RNA nucleotide tot he 3’ end of the growing mRNA molecule
IMPORTANT NOTE - exons and introns
only the EXONS (coding regions) of the DNA are KEPT –> INTRONS (non-coding are edited/cut out)
why introns are cut out (taken from google)
they actually have to be removed in order for the mRNA to encode a protein with the right sequence. If the spliceosome fails to remove an intron, an mRNA with extra “junk” in it will be made, and a wrong protein will get produced during translation.
Promoters
= a sequence of DNA that is located near a gene
= binding site of RNA polymerase (the enzyme that catalyses the formation of the covalent bond between nucleotides during the synthesis of RNA)
(the promoter is not transcribed by is an example of non-coding DNA having a function
(basic) outline the process of transcription
- A section of DNA is unwound (inside the nucleus) and unzips - codes for a polypeptide
- copy of the section (= transcription section) is made and called mRNA (one side of the DNA acts as the template)
= Processed by the catalyst RNA polymerase (transcriptase) and only occurs in 5’ to 3’ direction
Controlling gene expression in prokaryotes - THE OPERON THEORY
worked out by F. jacobs and J. Monod on E.coli bacteria (a prokaryote) = THE LAC OPERON MODEL
(they put forward a hypothesis to explain why E.coli produced an enzyme galactosidase which breaks down lactose only when lactose is present)
LAC OPERON MODEL / THE OPERON THEORY - steps (4)
- One section of DNA that codes for the enzyme is called the STRUCTURAL GENE
- situated close to this is another section of DNA called the (OPERATOR GENE) (this activates the structural gene when the enzyme is needed
- the operator gene is controlled by the (REGULATOR GENE) situated further down the DNA chain - produces a REPRESSOR SUBSTANCE which turns the operator gene off ( = no enzyme is made = GENE REPRESSION)
- When the enzyme is needed, the repressor substance is inhibited = operator gene can now turn on the structural gene and the enzyme is made = GENE INDUCTION
(it has been found that lactose itself can inactivate the repressor by combining with it)
why is it important for cells to be able to control the production of certain enzymes?
control what is being produced = don’t make things we don’t use (+ wasting energy, space, resources)
role of the promoter in the Lac Operon
= the promoter is used by the RNA polymerase to express the genes which synthesised lactase (BINDING POINT FOR RNA POLYMERASE)
(when lactose is added to the E.coli environment discuss) what happens to start transcription of the lactose-utilization genes and why this is a benefit for cell such as E.coli
Lactose binds with the repressor - causing it to release from the operator and thus allowing the RNA polymerase to bind to the promoter and transcription can occur - it is a benefit as it stops the process from making unnecessary mRNA (process of DNA having mRNA taken from it)
Epigenetics - basic breakdown
(scientifically not well understood)
understandings:
the environment of a cell and of an organism has an impact on gene expression
Epigenetics = is the study of environmental factors can turn genes on and off and affect how cells read genes
(differences in ‘traits’ that occur from the environment - there are ways that DNA can be changed after it has been replicated)
The two types of epigenetics
- DNA methylation
- Histone modification
DNA methylation - Epigenetics (mechanisms)
It is a process which methyl groups (-CH3) are added to the bases C and A in DNA - methylation modifies the function of the DNA (typically acting to suppress gene transcription - eg. preventing a cell from reverting to a stem cell or converting into a different cell type)
Histone modification - Epigenetics (mechanisms)
DNA is wrapped around histones so alterations in the histone can affect the activity of DNA - Methylation of histones can promote or inhibit transcription
Modification of Histone Tails
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) neutralises 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
Epigenetics research areas
- cancer
- developmental abnormalities (due to exposure to chemicals)
- trans-generational stress
- cardiovascular disease
- diabetes
transcription vs translation
transcription:
- make RNA copies of individual genes
- produce mRNA, tRNA, rRNA, non-coding RNA
- 5’ cap adds to 3’ poly
- in the nucleus
- uses genes as templates to produce several functional form of RNA
translation:
- synthesis proteins that are used for cellular functions
- protein synthesis from mRNA template
- 2nd step of gene expressions
- rRNA = assembly plans, tRNA = translator for proteins
- produce proteins
- in the cytoplasm
why is epigenetics important in cell specialisation
essential to controlling the heritable cellular memory of gene expression during development - research eg. cancer, developmental abnormalities due to exposure to chemicals….
Skill: analysis of changes in the DNA methylation patterns
“during development the pattern of DNA methylation in the genome changes as a result of a dynamic process involving both de novo DNA methylation and demthylation - as a consequence, differentiated cells develop a stable and unique DNA methylation pattern that regulates tissue-specific gene transcription”
DNA methylation varies throughout a lifetime and can be affected by the enviornmal, age and lifestyle choices analysis of methylation patterns in a healthy cell and a cancerous cell can help identify disease marker genes. If we can identify cancer related genes then early diagnosis of the disease is more likely
Outline two examples of trans generational epigenetics
Environmental impact:
Feast vs Famine
- in sweden males who had lived through good harvests had sons and grandsons with a higher rate of diabetes and heart disease while males who lived through poor harvests had sons and grandsons who lived on average 32 years longer
(DNA methylation controls transcription so the phenotypic (overvable characteristics = methylation patterns are different in healthy and diseased cells) expression of disease)
Promoter - section of a gene
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)
gene =
A gene is a sequence of DNA which is transcribed into RNA and contains three main parts
Coding Sequence - section of a gene
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
Terminator - section of a gene
RNA polymerase will continue to transcribe the DNA until it reaches a terminator sequence
The mechanism for transcriptional termination differs between prokaryotes and eukaryotes
Antisense vs Sense
A gene (DNA) consists of two polynucleotide strands, but only one is transcribed into RNA
The antisense strand is the strand that is transcribed into RNA
Its sequence is complementary to the RNA sequence and will be the “DNA version” of the tRNA anticodon sequence
The antisense strand is also referred to as the template strand
The sense strand is the strand that is not transcribed into RNA
Its sequence will be the “DNA version” of the RNA sequence (i.e. identical except for T instead of U)
The sense strand is also referred to as the coding strand (because it is a DNA copy of the RNA sequence)
Either of the 2 polynucleotide strands may contain a gene, and hence the determination of sense and antisense is gene specific
Overview of Transcription
The process of transcription can be divided into three main steps: initiation, elongation and termination
initiation - transcription
RNA polymerase binds to the promoter and causes the unwinding and separating of the DNA strands
Elongation - transcription
occurs as the RNA polymerase moves along the coding sequence, synthesising RNA in a 5’ → 3’ direction
termination - transcription
When RNA polymerase reaches the terminator, both the enzyme and nascent RNA strand detach and the DNA rewinds
Messenger RNA
Understanding:
• Eukaryotic cells modify mRNA after transcription
In eukaryotes, there are three post-transcriptional events that must occur in order to form mature messenger RNA
1. Capping
2. Polyadenylation
3. Splicing
+ Post-Transcriptional Modifications
post-transcriptional events to mature messenger RNA:
1. 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 exonucleases
It also allows the transcript to be recognised by the cell’s translational machinery (e.g. nuclear export proteins and ribosome)
post-transcriptional events to mature messenger RNA:
2. 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
post-transcriptional events to mature messenger RNA:
3. 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
Gene expression (straight from bioninja)
Transcriptional activity is regulated by two groups of proteins that mediate binding of RNA polymerase to the promoter
Transcription factors form a complex with RNA polymerase at the promoter
RNA polymerase cannot initiate transcription without these factors and hence their levels regulate gene expression
Regulatory proteins bind to DNA sequences outside of the promoter and interact with the transcription factors
Activator proteins bind to enhancer sites and increase the rate of transcription (by mediating complex formation)
Repressor proteins bind to silencer sequences and decrease the rate of transcription (by preventing complex formation)
The presence of certain transcription factors or regulatory proteins may be tissue-specific
Additionally, chemical signals (e.g. hormones) can moderate protein levels and hence mediate a change in gene expression
Control Elements
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
Understanding:
• The environment of a cell and of an organism has an impact on gene expression
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
This allows gene expression to change in response to alterations in intracellular and extracellular conditions
There are a number of examples of organisms changing their gene expression patterns in response to environmental changes:
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)
Types of Chromatin - Epigenetics
When DNA is supercoiled and not accessible for transcription, it exists as condensed heterochromatin
When the DNA is loosely packed and therefore accessible to the transcription machinery, it exists as 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
