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
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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)