04-11-21 - Introduction to Molecular Biology 4 Flashcards
Learning outcomes
- Explain the principles of the genetic (triplet) code and identify START and STOP codons.
- Outline the process of RNA-protein translation.
- List types of mutation and their consequences.
- Define the role of Transfer RNAs and how they are ““charged”” with specific amino acids.
- Give examples of post-translational modifications of proteins
- Explain the processes by which proteins transported within and out of the cell
What must happen after transcription occurs?
What is the nuclear envelope?
Where are nuclear pores found?
What are they made from?
How many are there per cell?
What do they allow the movement of?
What is the structure of the nuclear pore like?
What does it need to do before substances can pass through?
What does this process require?
- Mrna must be transported to the cytoplasm from the nucleus after transcription occurs
- The nuclear envelope that surrounds the nucleus is a double lipid bilayer
- Nuclear pores are found embedded within the nuclear envelope
- Nuclear pores are complex structures made from around 30 different proteins
- There are around 2000 nuclear pores per cell
- Small molecules can diffuse in and out of the nucleus, but larger molecules, such as Mrna must use nuclear pores
- Nuclear pores have a disordered structure that forms a plug
- Substances must be recognised, then the plug will reorganise to allow substances through
- This process requires energy
What does mrna need to travel through nuclear pores?
How can cells detect incorrect splicing?
What does it do with this mrna?
What is exchanged when Mrna moves out into the cytoplasm?
- Mrna has a cap-binding protein, which is recognised by the pore, which then opens and facilitates movement out of the nucleus
- There are EJC (exon junction proteins) at the site of splicing on the mRNA
- If these are not in the correct position, the cell can prevent this Mrna from moving into the cytoplasm
- When Mrna moves into the cytoplasm, the cap-binding protein is exchanged for an initiation factor for protein synthesis, which can initiate translation
How many bases are codons?
What do codons do?
What does the term degenerate mean?
Why is genetic code described as degenerate?
Where is the most common variation on codons?
- There are 3 bases per codon
- Codons code for amino acids
- Degenerate means an entity performs the same function as a structurally different entity
- Genetic code can be described as degenerate as, sometimes, multiple codons code for the same amino acid
- The most common variation in codons is found on the 3rd base
What is a point mutation?
What are the 3 effects of point mutations?
• A point mutation is when a single base is changed in a base sequence
• Effects of point mutations:
1) Silent mutation – The altered codon corresponds to the same amino acid
2) Missense (substitution) mutation – altered codon corresponds to a different amino acid
3) Nonsense mutation (insertion and deletion) – altered codon corresponds to a stop codon, leading to early termination of translation
Why are specific starting points for reading genetic code very important?
What are insertion and deletion mutations?
What do these mutations cause?
What can this lead to?
What are other names for these mutations?
- If the genetic code is read in 3s from a different a starting point, this will lead to a massive change in amino acid sequence, and will potentially code for an earlier stop codon
- Insertions and deletions mutations are the insertion and deletion of one or more bases in the base sequence in mrna
- The insertion and deletion of bases causes a reading frame shift
- This can result in different amino acids being coded for, and potentially the coding of an earlier stop codon, both of which can have serious consequences for the protein produced
- These mutations are also known as nonsense or frameshift mutations
What can substitution mutations also be known as?
What is a substitution mutation?
What can this cause in a protein?
Where else can these mutations also affect?
- Substitution mutations can also be known as a missense mutation
- A substitution mutation results in a base in the mrna being swapped out with another base
- This may result in a different amino acid being coded for, which will affect the way the polypeptide is folded
- It can also result in a stop codon being coded for, which will lead to a non-functional protein being formed
- Missense mutations in non-coding areas (introns) can also have significant effects
What is a silent mutation?
How is this made possible?
- A silent mutation is a mutation that results in the same amino acid being coded for
- This is made possible by the degenerate nature of genetic code
What is the start codon?
What is the code for start codon?
What precedes the start codon?
How can this be useful when trying to find the start codon?
How does the machinery in translation read?
- The start codon is the signal that determines where the reading frame begins during translation
- The code for the start codon is the first AUG, which codes for methionine
- The start codon is preceded by methylated guanine at the 5’ end of mrna, a non-coding region, then a kozac consensus sequence, which is directly before the first AUG
- An educated guess can be made as to where the initiation codon is by looking to see if it is preceded by a kozac consensus sequence
- The machinery during translation reads along in units of 3 bases, one after the other with no gaps
What is the stop codon for?
What is the code for the 3 stop codons?
What follows the stop codon?
What do these provide for the Mrna?
- The stop codon marks the end of translation
- UAA, UAG, UGA are all codes for the stop codon
- The stop codon is followed by the 3’ non-coding region and the poly A tail
- These provide stability to the Mrna
What does the structure of Trna look like?
What is at the 3’ end of Trna?
What is opposite to this?
How does trna add amino acids to the polypeptide?
How many codons are there?
How many types of Trna are there?
- The structure of Trna looks like a clover lead
- At the 3’ end of Trna there is an amino acid
- Opposite to this, there is an anti-codon
- The anti-codon loop of a trna base-pairs with the codon of an mrna
- This aligns 2 amino acids together, allowing a peptide bond to form
- There are 64 different codons
- There are between 40 and 60 types of trna in most cells
What is the function of aminoacyl-tRNA synthetases?
How many types are there?
Why is this?
What are the 2 stages in the process of checking amino acids?
• Aminoacyl-tRNA synthetases check to see the correct amino acid is added to the trna
• There are 20 different types of aminoacyl-trna synthetases
• Each of the 20 only recognises 1 amino acid, all of the codons that code for that amino acid, and all of its compatible trnas
1) Activation of amino acid by attachment to amino-acyl trna synthetases
2) Transfer of amino-acyl group to trna
What does the aminoacyl-trna synthetase check on the trna?
What does this interaction have to be and why?
What is this termed as?
What occurs at the other end of the molecule?
How does this reaction occur?
What do this this reaction require?
How is this reaction regulated?
• Aminoacyl trna synthetase raps round the trna and reads the anti-codon loop to check if this is the right trna to add that specific amino acid
• This reaction must be flexible, as the aminoacyl trna synthetase must be able to recognise more than 1 trna, as multiple codons can code for the same amino acid
• This flexibility is termed as a wobble
• At the other end of the molecule, the trna is in the activation site, where the amino acid is added to the trna
• This reaction requires energy
• The amino acid is esterified to the 3’-OH of the terminal adenosine of trna at the carboxyl terminal, which leaves the amino terminal free
• As the trna leaves the activation site, it passes through the editing site, where the amino acid can be checked and replaces if it is not the right amino acid or trna
What do the 2 subunits of the ribosome consist of?
What rrna do they contain?
What function do they have?
What are the secondary and tertiary structures of trna like?
What process occurs on ribosomes?
Where can they be found?
What are the binding sites for Mrna and trna like?
- The ribosome consists of a large unit made from 50 proteins. It contains 23S Rrna (large) and it primarily has a catalytic function
- The small subunit is made from 30 proteins. It contains 18S Rrna (small) and iits primary function is binding trnas
- Rrnas have significant secondary and tertiary structure
- The process of translation occurs on ribosomes
- They can be found free or attached to the ER
- Mrna has one binding site
• There are 3 binding sites for trna:
1) E-site – exit site
2) P site - Peptidyl-trna site
3) A site - Aminoacyl trna site
What are the 3 phases of translation?
1) Initiation
2) Elongation
3) Termination
What are the 4 steps that occur during the initiation phase of translation?
1) The small subunit of the ribosome has been pre-charged with the initiating trna associated with the start codon (AUG)
2) The small subunit scans along the mrna for the Kozak consensus and first AUG
3) Once identified, the large subunit of the ribosome comes to bind
4) Now the system is ready to start
What are the 5 steps that occur during the elongation phase of translation?
1) After the AUG trna, trna charged with amino acids come and bind their anti-codon loop to the mrna in the P-site and A-site of the ribosomes
2) The free amino group of trna in the P-site attacks the carboxyl group attached to the amino acid, which results in the synthesis of a peptide bond between adjacent amino acids
3) Translocation of the large subunit, and then the small subunit of the ribosome occurs as the ribosome moves along the mrna strand
4) This allows the trna from the P-site, who’s amino acid is now part of the polypeptide, to move into the E-site (exit site) and be ejected from the ribosome
5) This process occurs until the polypeptide is complete
When does termination of translation occur?
What occurs in the final trna?
What is needed for the polypeptide to be released?
What does the ribosome do after termination?
What end does polypeptide synthesis begin?
Where does it end?
- Termination of translation occurs when we reach the stop codon
- In the final trna, there is a hydrolysis reaction that separates the amino acid from the trna, resulting in the formation of the carboxyl end of the polypeptide
- Release factors are required to release the polypeptide
- After termination, the ribosome dissociates and can be reused
- Polypeptide synthesis starts at the N terminus and terminates at the C terminus
How is the process of translation made more efficient?
What does this form?
What does stability of mrna influence?
How is this controlled?
What is an example of this?
- Translation is made mor efficient by the use of multiple ribosomes that move along the mrna strand at the same time
- This forms structures known as polysomes
- The stability of mrna influences how much protein is produced, and how much will be used
- There ae control mechanisms that influence the stability of mrna
- Casein (in milk) has increase stability in the presence of the hormone prolactin, which aids in production of milk during pregnancy
What do antibiotics target?
What do antibiotics exploit?
Why do they do this?
What are examples of this?
- Anti-biotics target different stages of protein synthesis in bacteria
- Antibiotics exploit the differences in bacteria and eukaryotes in order to provide treatment that affects the bacterial cells, but not host cells
What is an example of translocation processes that occur co-translationally?
What else can these signal sequences be for?
What can multiple signal sequences result in?
What might occur to the signal polypeptide?
What occurs in a mutated localisation signal in a T-antigen?
- An example of this are proteins moved into the ER
- While the polypeptide chain is being produced, it can have an ER signal on it
- Signal recognition particles (SRPs) then aid to direct the polypeptide across the ER membrane and into the ER once it has been synthesised
- These signal sequences can also be for other organelles, such as the mitochondrion or nucleus
- Multiple signal sequences can cause the protein to shuttle between two sites, e.g transcription actors, which may be in the nucleus or cytoplasm
- The signal polypeptide may be cleaved
- In a mutated localisation signal in T-antigens, the T-antigen ends up in the cytoplasm instead of the nucleus
What else do signals on the polypeptide dictate?
What are example of 2 signal sequences for this?
What is an example of this process?
What are the 2 types of sugars that can be added?
Where does addition begin and end for these sugars?
- Signals on the polypeptide also dictate post-translational modification
- These sequences may be:
1) Asparagine – X – Serine (Asn – X – Ser)
2) Asparagine – X – Threonine (Asn – X – Thr)
- Sugars can be added to the polypeptide as it is synthesised
- Sugars that can be added:
1) End link sugars – go through asparagine, or arginine – addition starts in ER and ends in the ER
2) O link sugars – serine, threonine, tyrosine – addition occurs in the Golgi
How can PTM be harmful?
How is this shown in dementia?
What contributes to degree severity?
- Too much and too little modification can be harmful
- Tau (name of protein) hyperphosphorylation is associated with neurofibrillary tangles in dementia
- The number of tangles is proportional to the severity of the disease
What is the purpose of protein folding?
How are protein folding, protein modifications and disease linked?
Where can this be seen?
- The purpose of protein folding is to fine the most electrostatically stable conformation of the protein
- Defects in protein folding and modification are part of the effects of disease
- This can be seen in the transmembrane receptor of cystic fibrosis
What are the 6 effects mutations can have on protein formation and function?
Where can these all be seen?
1) No transcription
2) Protein incorrectly process – results in protein not translocating to the correct part of the cell
3) Inappropriate regulation of protein production – can cause disease
4) Inappropriate function e.g channels being too narrow or allowing the wrong substances through
5) Reduced transcript number
6) Unstable protein
