Gene regulation and Protein synthesis Flashcards
True or false: RNA is a single chain
False- RNA is single stranded but not a single chain
What are the 3 main classes of RNA?
- Ribosomal RNA (rRNA) - combines with proteins to form ribosomes where protein synthesis takes place
- Transfer RNA (tRNA) - carries amino acids to be incorporated into the protein. Acts as adapters between nucleic acid code and amino acid code
- Messenger RNA (mRNA) - carries genetic information for protein synthesis
What kind of structures do RNA form?
RNA forms stem-loop structures
What are the base pairing rules in RNA?
Adenine pairs with uracil (replaces thymine) and cytosine pairs with guanine
What is the purpose of RNA polymerase?
RNA polymerase synthesises RNA by using one DNA strand as a template to copy the nucleotide sequence into RNA. Prokaryotic cells have one type of RNA polymerase where as eukaryotic cells have 3 types (Pol I, Pol II, Pol III). Pol II is used to synthesise all mRNA
Compared to eukaryotes, how does the location of transcription/translation/protein synthesis etc differ in prokaryotes
In eukaryotes, DNA replication, transcription/translation and processing all takes place in the nucleus then mRNA is transported to the cytoplasm for protein synthesis. However in prokaryotes, all these processes occur in the same place
Explain the steps of transcription
- RNA polymerase binding - detection of initiation sites (promotors) on DNA. This also requires transcription factors
- DNA chain separates and unwinds
- Transcription initiation - adding of the first nucleotide of the growing RNA
- Elongation - addition of more nucleotides to RNA chain
- Termination - release of the finished RNA and RNA polymerase dissociates and is recycled
Which strand is being read and which strand is not being transcribed/read?
The template strand is the one being read and the coding strand is not being read
What is a TATA box?
A TATA box is part of a promoter sequence. The TATA box is usually present about 25 nucleotides upstream of many genes transcribed by RNA polymerase II (Pol II)
What is the TBP (TATA box binding protein)?
This is the protein that recognises the TATA box. It is part of TFIID which is a general transcription factor and is required for all Pol II transcribed genes. It also induces kinks to DNA. TBP also provides a landing platform for further transcription factors and for RNA polymerase
What are transcription factors?
Transcription factors are proteins that control the rate of transcription
What is meant by “specific” transcription factors?
These are DNA binding proteins which contain 2 domains that can be physically separated:
1. DNA-binding domain
2. Transcriptional activation/depression domain
These transcription factors bind to specific DNA sequences called enhancers, which are in the vicinity of a promoter so they can regulate transcription positively or negatively
How can an activator protein on a strand of DNA be brought into contact with the transcription complex?
DNA can bend to bring these 2 things closer together
How does coordinated gene expression work?
This is in response to specific stimuli (e.g hormones, steroids)
- A stressor activates transcription of a regulatory protein through a specific sensitive transcription factor
- Binding of the regulatory protein to the stress response element (SRE) stimulates transcription of genes
- This produces different proteins participating in the stress response
How are the ends of mRNA processed?
- Splicing
- Addition of poly (A) tail
- Addition of a 5’ cap
During translation, what part of tRNA molecules binds with mRNA?
The anti-codons of tRNA molecules form base pairs with the codons of mRNA. This binds in triplets
What is the meaning of degenerate?
This means many amino acids have more than one codon (e.g there are 4 codons that code for serine)
What is the meaning of unambiguous?
This means that each codon codes for only one amino acid (e.g AUG = start codon)
True or False: Reading frames on RNA molecules can be different depending on where translation starts
True
Name 7 components that are required for translation
- tRNA molecules
- ATP + GTP for energy source
- Amino acids
- Specific sets of protein factors for different steps
- Ribosomes
- mRNA
- aminoacyl-tRNA synthetase (tRNA-ligase)
What is aminoacyl-tRNA synthetases?
This binds amino acids to their corresponding tRNA molecule. They are highly specific and ATP provides the energy for the formation of covalent bond
Where does translation occur?
Translation occurs in the ribosome
What does ribosomes contain?
Contain 4 different rRNA molecules and they also contain protein components. There are 2 different sub-units in ribosomes - one small and one large
How many tRNA binding sites do ribosomes have and what are they called?
Ribosomes have 3 tRNA binding sites:
- E = Exit
- P = peptidyl
- A = aminoacyl acceptor
Explain how the ribosome is a multi-step assembly line for protein synthesis
The first tRNA starts at the P site. The A site is where a donor tRNA molecule, which is carrying the appropriate amino acid, is positioned before that amino acid is incorporated into the protein. These then form a peptide bond to create a chain and everything moves along by one codon so that the A site is free to accept another tRNA molecule with a new amino acid so that this can repeat and the chain can continue to grow. This peptide bond formation is catalysed by peptidyl transferase. Once a polypeptide chain has formed it moves along to the E site where it will soon be exiting the ribosome. The polypeptide chain is finished when the A site encounters a STOP codon
What are the 3 steps called in translation?
- Initiation - the ribosome gets together with the mRNA and the first tRNA so translation can begin.
- Elongation - amino acids are brought to the ribosome by tRNAs and linked together to form a chain
- Termination - the finished polypeptide is released to go and do its job in the cell
Name 4 types of chromosomal mutations
- T - Translocations
- I - Inversions
- D - Duplications
- D - Deletions
Name 3 types of point mutations
- S - Substitution
- I - Insertion
- D - Deletion
What is meant by missense mutation?
Missense mutation is when a mutation results in a change in the amino acid so can alter the function of a protein
What is meant by nonsense mutation?
Nonsense mutation is when a mutation results in a new STOP codon so can shorten the chain, usually causing the protein to not work
What is meant by silent mutation?
Silent mutation is when there may have been a base change however this didn’t result in a change of amino acid so no effect on protein function
What is meant by frameshift mutation?
Frameshift mutation is when there is an insertion or deletion of bases which causes the reading frame to change so can effect all amino acids after the mutation
What 3 things may need to be done to a protein to completely finish it?
- Targeting - moving a protein to final destination. This depends on the specific amino acid sequence within the translated protein
- Modification - adding of further chemical groups or cleavage
- Degradation - unwanted or damaged proteins have to be removed
When does post-translational modification occur and name some examples of post-translational modifications?
Post-translational modification can occur at any time during the “life cycle” of a protein however, it most commonly occurs after translation has been completed. Examples of post-translational modifications include:
• Phosphorylation - addition of phosphate by kinase
• Proteolysis - cleaving polypeptide
• Glycosylation - Addition of carbohydrates
What is the difference between “free” and “bound” ribosomes?
“Free” ribosomes are in the cytosol and makes proteins for the cytosol, nucleus, mitochondria. These are translocated post-translationally
“Bound” ribosomes are on the RER and make proteins for the plasma membrane, ER, golgi apparatus, secretion. These are translocated co-translationally
What are 2 destinations of newly synthesised proteins?
- Go to the organelles or cytosol
2. Go to the rough endoplasmic reticulum
