L2 - Structure and Properties of RNA Flashcards
Describe the relationship between DNA, genes and the genome
The DNA encodes gene and the genes are the protein coding regions of the genome
What role do ‘junk’ genes hold?
- Not directly involved as genes in protein coding but act as regulators for the expression of those genes
- Important for stability and expression, as well as regulation of individual regions on individual chromosomes
What is a gene coding for?
A protein
What intermediate is used to express genetic information from genes to form a protein?
RNA
What slight structural difference is there between DNA and RNA? Why does this make a difference
- 2-deoxyribose has a hydrogen on the 2’ carbon
- Ribose has a hydroxyl group on the 2’ carbon
Why does the hydroxyl group on the 2’ carbon in ribose in RNA affect its stability?
Makes RNA more prone to degradation because the phosphodiester bond formed between subsequent nucleotides is less stable than it is in DNA
What nitrogenous bases are in RNA?
Adenine
Guanine
Cytosine
Uracil (no thymine)
How does uracil differ to thymine? Why does this make a difference?
Uracil has a hydrogen
Thymine has a methyl group
Uracil is demethylated so is less stable
What is thymine more resistant to than uracil? How does this make a difference?
- More resistant to photochemical mutation
- Enables DNA to be more resistant to mutagens, maintaining the fidelity of DNA
- RNA is therefore more prone to degradation
What direction is RNA read in?
5’ to 3’ direction
What are the main properties of RNA?
- RNA is single stranded
- RNA had uracil instead of thymine
- RNA has ribose not 2-deoxyribose
- Sequence comes from DNA
- RNA carries genetic information
- Shorter than DNA
- Can form hairpin structures
What is the main functional difference between a gene and RNA?
A gene codes
RNA expresses the protein
Describe the structure of a single strand of RNA
- Starts at the 5’ end and moves into the stem
- Loops into a hairpin
- Back along the stem to the 3’ end
- The stem has complementary base pairing between bases to aid stability and allow the RNA to remain in the nucleus for long enough - less vulnerable to degradation
How many loops does tRNA have?
- 3 conserved loops
- 1 small variable loop - dependent on the type of tRNA
What do all tRNA molecules have in common?
An acceptor stem which has the amino acid that is being coded for by the anticodon, which is read from the RNA
How many domains does mRNA have? What do the domain sizes depend on?
- 4 domains (still single stranded)
- Size is dependent on the length of the transcript that has come form the gene
Define transcription
The synthesis of RNA under the direction of DNA - uses DNA as a template
Define translation
The actual synthesis of a protein, which occurs under the direction of mRNA
What determines all visible phenotypes?
Result of actions of enzymes, which are proteins that catalyse and regulate all bodily functions
What would a change that affects proteins effect?
Would potentially affect the expression of phenotypes
Give an overview of the process of transcription
1) The DNA double helix is opened up by helicase, to allow access for transcriptional machinery to the coding region
2) 2 SSBP keep the conformation open
3) RNA polymerase reads the code to make complementary mRNA using the other strand in the 3’-5’ direction as a template
4) pre-mRNA is formed first, which forms a transcript of the whole of the coding region from a gene through translation
5) RNA processing happens which forms mature mRNA from pre-mRNA by removing introns, and splicing together exons.
6) Mature mRNA is transported out of the nucleus via nuclear pores into the cytoplasm to the ribosomes on the RER for translation. This produces a polypeptide chain
Where does transcription occur?
In the nucleus
Where else can the process of transcription and translation take place?
In a mitochondrion - mitochondrial DNA and expression remain with that mitochondrion
What are the 4 types of RNA? What are their functions?
- mRNA: protein coding genes, which encodes the amino acid sequence of a polypeptide
- tRNA: brings/ transports amino acids to ribosomes during translation
- rRNA: Formed in the nucleolus, and will be transported out of the nuclear pores to the nucleus to make ribosomal subunits for translation of mRNA
- snRNA: With proteins, forms complexes that are used in RNA processing in eukaryotes (not in prokaryotes)
What effect do mutations infidelity and replication have towards RNA genes?
High possibility of a mutation which has a detrimental effect on key fundamental genes in a eukaryotic cell. Without the processing on the RNA, proteins cannot be formed, so there in no expression of the phenotype by RNA
What does a protein coding gene consist of?
A promoter at the 5’ end followed by the coding sequence for the protein and then an terminator at the 3’ end
What makes up a promoter region of a protein coding gene?
- Variable in sequence
- Some regions of the promoter are highly conserved to allow transcription factors and DNA polymerase to bind and start transcription
What is the function of a promoter?
Is the transcriptional start site for RNA polymerase. A base-pair sequence that specifies where to begin
What is the function of the termination region of a protein coding gene?
A base pair sequence which that ends mRNA transcription and stops RNA polymerase
Combined, what do the promoter and termination region determine?
The length of the transcripts
There are various types of promoters, but what do they all have in common?
All perform the same function - place where transcriptional machinery starts on a gene
Why does the coding region of a gene vary?
Specific for a polypeptide chain specified by a gene, because the coding sequence of a gene is different for every protein.
Are all mutations detrimental?
No, mutations can be detrimental or advantageous. This is dependent on the mutation and the function of the resulting protein. This allows adaptations.
What direction does RNA polymerase move in, along coding region of the gene?
5’ to 3’ direction
How does RNA polymerase produce pre-mRNA?
- RNA polymerase will recognise the promoter, which signifies the transcriptional start site.
- The polymerase moves in a 5’ to 3’ direction
- RNA polymerase moves along the DNA template to form pre-mRNA
- RNA polymerase is released and the DNA double helix reforms automatically. The process of reforming happens as soon as the RNA polymerase has transcribed a region
- The terminator disengages the polymerase, ready to start again
How long will RNA polymerase continue?
RNA polymerase will continue until the need for mRNA is met for a particular protein
Which DNA strand acts as a template for transcription?
The DNA strand in the 3’ to 5’ direction to allow RNA polymerase to move in the 5’ to 3’ direction
Draw the complementary DNA strand and subsequent RNA strand for the following coding strand DNA sequence:
5’ ACTCAATGCG 3’
- Red is the RNA strand
How is the coding strand different and similar to the template strand?
- The coding strand is different because it isn’t used as a template
How is the coding strand identical to mRNA?
Identical in sequence to mRNA except for thymine instead of uracil
What is the relationship between the sequence of prokaryotic protein coding gene and that of the translated mRNA?
The sequence of prokaryotic protein coding gene is collinear with translated mRNA
How does the process of transcription differ in prokaryotes to eukaryotes?
In prokaryote there is no additional RNA processing, therefore pre-mRNA is not formed unlike in eukaryotes
What is the pre-RNA coding sequence made up of?
Exons and introns
What are introns? What are exons?
Introns do not code for the protein. These must be removed
Exons are the protein coding part
What does pre-mRNA undergo?
Pre-mRNA must be post-translationally modified to increase stability to be used in translation
What modification occurs at the 5’ end of pre-mRNA?
At the 5’ end, there is the addition of a cap of modified guanosine triphosphate (GTP)
What is the function of adding a cap to the 5’ end of pre-mRNA?
The five prime cap is used as a recognition signal for ribosomes to bind to mRNA. This is to increase the integrity and prevent loss of fidelity to the coding region
What modification occurs at the 3’ end of pre-mRNA?
A poly(A) tail is added, which is made up of adenine
What is the function of adding a tail to the 3’ end of pre-mRNA?
This aids stability and allows mRNA to remain in the nucleus and cytoplasm for longer
What sequence is located after the GTP cap and before the poly(A) cap on pre-mRNA?
A leader sequence after the GTP cap and a trailer sequence before the poly(A) cap
What is the function of the leader and trailer sequences on pre-mRNA?
These protect the coding part of transcripts and are untranslated regions
What process occurs to remove introns from the pre-mRNA?
Pre-mRNA undergoes RNA processing in the nucleus to remove introns and splice exons together into translatable mRNA
What are snRNPs?
Small nuclear ribonucleoprotein particles
These are complexes of snRNA and proteins
Describe the process in which introns are removed
-snRNPs come in and bind to either end of the intron
- This loops out the intron
- Two more snRNPs come in and stabilise the looped out section and form a complex called the spliceosome
- The whole intron is excised and exons are spliced together
- This creates a transcript which is shorter than the coding DNA sequence
- Resulting mRNA may exit the nucleus and be translated in the cytoplasm
How many exons and introns are there for a protein coding gene?
There are a different number of exons and introns for each protein coding gene
These are not highly conserved from one protein to another
What is associated with mRNA to transport out of the nucleus into the cytoplasm?
Export signals
What will the ribosome detect on the mRNA to allow for translation?
The ribosome will detect the GTP cap on mRNA allowing the transport and translation of a particular protein
Where is rRNA formed?
rRNA his formed in the nucleolus which is transported out via nuclear pores to the nucleus to make ribosome or sub units for translation
