DNA part 2 Flashcards
What are histones?
Eukaryotic DNA associated with proteins
Describe the function of histones
Package the DNA into globular structures called nucleosomes.
What does the association of histones with DNA contribute to?
Supercoiling. During condensation of chromosomes in the early stages of mitosis and meiosis the tails of histones in adjacent nucleosomes link up and pull the nucleosomes togther
What is transcription?
The process by which a gene is copied into a complementary RNA using DNA as template.
Where does transcription take place?
In eukaryotes it takes place in the nucleus during interphase
Describe the process of transcription.
- RNA polymerase binds to a sequence at the start of the gene called the promoter. In eukaryotes the binding of the RNA polymerase to the promoter is mediated and controlled by transcription factors
- RNA polymerase moves along the gene, separating the DNA strands and assembling an RNA molecule along one of the DNA strands.
- The template DNA strand which is used is the antisense strand
- RNA nucleotides are assembled based on complementary base pairing as in DNA replication, except that uracil and not thymine pairs with adenine.
- RNA polymerase links together the RNA nucleotides by making phosphodiester bonds between the 5’ end of the free RNA nucleotide and the 3’ end of the growing mRNA. So transcription occurs in a 5’ to 3’ end.
- Free nucleotides exist in cells as NTPs. RNA polymerase covalently binds the NTP in a reaction that involves the release of 2 phosphates.
- The RNA strand separates from the DNA strand as it is produced
- Transcription is terminated at the end of the gene and the DNA, RNA and RNA polymerase separate. The DNA rewinds.
Which strand is transcribed and which is not?
Transcribed- antisense strand
not transcribed- sense strand
What happens in post- transcriptional modifications in eukaryotes?
In eukaryotes the mRNA is modified after transcription and this happens in the nucleus before the mRNA exists through a nuclear pore.
What is the immediate product of transcription?
pre-mRNA
What are the coding sequences interrupted by?
Non-coding sequences called introns. The remaining coding parts of the mRNA are exons
Describe the post-transcriptional modifications
- Introns are removed from pre-mRNA in the nucleus
- Exons are spliced together to form the mature mRNA
- This process is called mRNA splicing
- Some genes have more exons and different combinations of them can be spliced together to produce different proteins. This is alternative splicing
What does alternative splicing cause?
A single gene codes for multiple proteins. This increases the total number of proteins an organism can produce from its gene.
What happens when post- transcriptional modification at the end?
addition of a 5’ cap usually before transcriptional has been completed and a poly- A tail is added at the 3’ end after the transcript has been made
What is the genetic code?
A triplet code: 3 bases in the mRNA code for one amino acid
What is a codon?
3 bases on the mRNA that code for one amino acid
What are most amino acids coded by?
Two or more codons- so the genetic code is called a degenerate
What is the start codon?
AUG for initiation of translation- this codes for the amino acid methionine
How many stop codons are there?
Three
Describe the genetic code
It is universal meaning that almost all organisms use the same genetic code- allowing for gene transfer between species to create genetically modified organisms which produce a polypeptide from a different species.
There are however minor variations in some organisms
What is translation?
The synthesis of polypeptides on ribosomes
In which stage does translation take place?
Interphase
What are the three components of translation?
mRNA
tRNA
ribosome
What is the role of complementary base pairing in translation?
The amino acid sequence of the synthesised polypeptide is determined by the base sequence of the mRNA according to the genetic code- 3 bases on mRNA, called a codon- code for one amino acid.
Each tRNA molecule has a special triplet of bases called an anticodon and carries a specific amino acid that corresponds to this anticodon.
Translation depends on complementary base pairing between codons on mRNA and anticodons on tRNA and hydrogen bonds are formed.
Describe the structure of tRNA.
- Double- stranded sections formed by base pairing and single- stranded loops
- A triplet of bases called the anticodon which is part of a loop of 7 unpaired bases
- There are two other loops
- The base sequence CCA at the 3’ end forms a site for attaching the amino acid.
What is the structure of a ribosome?
- consist of proteins and ribosomal RNA molecules
- have two subunits: one large and one small
- having a binding site for mRNA on the surface of the small subunit
- have three binding sites for tRNA molecules on the surface of the large subunit These are the E, P, A sites [2 tRNAs can be bound to the ribosome at a time]
Can be free ribosomes or bound to rER.
What are tRNA- activating enzymes?
Activate the tRNA by attaching an amino acid using ATP for energy
Describe tRNA - activating enzymes
- Each tRNA molecule has distinctive shape and chemical properties and is recognised by a specific tRNA- activating enzyme
- There are 20 different tRNA- activating enzymes. Each is specific to one of the 20 amino acids and the correct tRNA. The active site of the enzyme is specific to both the amino acid and tRNA. Each enzyme attaches one particular amino acid to all tRNA molecules that have an anticodon corresponding to that amino acid.
Describe the attachment of amino acid to the tRNA
- Energy from ATP is needed for the attachment of the amino acid
2, Once ATP and amino acid are attached to the active site, ATP is hydrolysed and a pair of phosphates is released. The remaining adenine monophosphate (AMP) bonds to the amino acid, raising its energy level and activating it - The correct tRNA binds to the active site and the activated amino acid is covalently attached to the CCA site at the 3’ end of the tRNA. AMP is released
- Activated tRNA is released.
- The energy from ATP is later used to link the amino acid to the growing polypeptide chain.
What are the three mechanisms of translation?
Initiation
Elongation
Termination
What happens in the initiation of translation?
- An mRNA binds to the small subunit of the ribosome at the mRNA binding site
- An initiator tRNA carrying the amino acid methionine binds to the start codon AUG by complementary base pairing
- The large ribosomal subunit binds
- The initiator tRNA is in the P site. Another tRNA with anticodon complementary to the next codon binds occupying the A site. A peptide bond is formed between amino acids help by the tRNAs in the P and A sites
What happens in the elongation of translation?
- Elongation occurs through a series of repeated steps
- The ribosome translocate 3 bases along the mRNA. This moves the tRNA in the P site to the E site, where it leaves the ribosome, and the tRNA carrying the growing polypeptide from the A site to the P site. This the A site becomes vacant.
- A tRNA with an anticodon complementary to the next codon binds to the A site, carrying the specific amino acid that corresponds to its anticodon.
- A peptide bond is formed between the amino acid at the A site and the polypeptide at the P site. The polypeptide is transferred to the tRNA in the A site
- The ribosome translocate again along the mRNA and the steps are repeated
- The translation of the mRNA is from 5’ end to the 3’ end
What happens in the termination of translation?
- The process continues along the mRNA in a 5’ to a 3’ direction until a stop codon is reached.
- Stop codons do not recruit a tRNA, but instead release factors binds to the A site, causing the release of the polypeptide
- The tRNA and mRNA molecules detach from the ribosome and the ribosome splits into large and small subunits
What do free ribosomes do?
Synthesise proteins for use primarily within the cell
What is synthesised in the ribosomes bound to the rough ER?
Proteins that are destined for use outside the cell or in lysosomes, plasma membrane, ER, Golgi apparatus
Where are all proteins synthesised?
Initially in the ribosomes free in the cytoplasm
What determines whether a ribosome remains free or become bound?
On depends on the presence of a signal sequence on the first part of the polypeptide being translated
Describe how a free ribosome becomes a bound ribosome
- As the signal sequence is created, it binds to a signal recognition particle(SRP). The SRP stops translation until it binds to a receptor on the surface of the ER. Then, translation is re-initiated and the polypeptide chain moves into the ER lumen as it is created via a transport channel.
- Once the polypeptide is completely synthesised within the ER, the signal sequence is cleaved and the SRP recycled
- A vesicle containing the protein then buds off the ER
- If there is no signal sequence, the ribosome remains free and continues translation in the cytoplasm
Describe the coupling of transcription and translation in prokaryotes
In prokaryotes there is no nuclear membrane and so translation can occur immediately after transcription. Translation can even begin before the mRNA has fully transcribed.
Describe the coupling of transcription and translation in eukaryotes
There is compartmentalization so transcription and translation are separated spatially and in time
What are polysomes?
Groups of ribosomes attached to a single mRNA molecule
What is the following structure?
polysome
Where do polysomes occur in prokaryotes and eukaryotes?
Prokaryotes- associated with one gene
Eukaryotes- occur in both the cytoplasm and next to the rER.
What does the presence of a polysome indicate?
That much protein of a type is needed so the mRNA is repeatedly translated
