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week 8 > intro to molecular biology 4 > Flashcards

intro to molecular biology 4 Flashcards

1
Q

where is mRNA translated into proteins?

A

cytoplasm

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2
Q

describe the process of mRNA being exported out of the nucleus

A
  • an energy-dependent process
  • 5’ binding cap is recognized and the mRNA interacts with export machinery and is tagged for export
  • travels out of the nuclear pore
  • the 5’ binding cap is exchanged with initiation factor for protein synthesis
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3
Q

why are DNA sequences read as a triplet (codon) to code for an amino acid

A

4 bases need to be able to code for 20 different amino acids. 1 base for 1 a.a. is not sufficient, 2 bases for 1 a.a. can only code for 16 a.a.
so 3 bases for one a.a. can code for 64 so its more than enough

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4
Q

what does ‘triplet code is degenerate mean’?

A

it means that there can be more than one triplet code for an amino acid (eg. valine)

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5
Q

Describe nonsense/frameshift mutation

A
  • caused by deletion or insertion resulting in a frameshift of the reading frame
  • this can cause the amino acid to be truncated (cut short) due to a high possibility of an early stop codon
  • not capable of making a proper functional protein
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6
Q

Describe missense/point mutation

A
  • caused by a single point substitution of a base

- may have severe consequences on protein structure and function but a protein can still be made

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7
Q

Describe silent mutation

A

-a change in a base at a single point but because of degenerate nature of genetic code, the amino acid is not changed even though the sequence in the codon was changed (eg. valine - its 3rd base can be any as it still codes for val)

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8
Q

what is the difference between polymorphism and mutation

A

Polymorphism : Minor change in DNA sequence that is
present in >1% of the population, can be viewed as natural variation
Mutation : change in DNA sequence that is present in
< 1% of population, can cause disease

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9
Q

What is the most common start codon for animals? what does the start codon do?

A

AUG, codes for Methionine

  • it is the initiation codon and defines the beginning of the open reading frame
  • right after the 5’ non-coding region
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10
Q

What are the three stop codons and what do they do?

A
  1. UAA
  2. UAG
  3. AGA
    defines the end of the open reading frame and is before the 3’ non-coding region
    - special stop tRNA bind to this to terminate translation
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11
Q

what is the role of tRNA in translation

A
  • ‘adaptor’ between the codon and a
    specific amino acid
  • has a 3’ amino acid binding site (CCA 3’ end) and a cloverleaf shaped structure
  • at the other end it has an anticodon loop which basepairs with the codon/triplets of the mRNA
  • brings the amino acids close together to allow them to form peptide bonds
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12
Q

how does the right amino acid get added to the right

tRNA? Describe how the tRNA gets charged with the amino acid.

A

an enzyme aminoacyl-tRNA synthetases is used to charge the tRNA with amino acid
- there are 20 different aminoacyl-tRNA synthetases (for the 20 diff amino acids) and each enzyme regonises ONLY ONE amino acid and ALL the compatible tRNAs.

  • the reaction is a 2 step reaction that ends with the amino acid being activated
    1. interaction between protein and anti-codon loop of tRNA allows the tRNA to be recognized

‘Wobble’ - the flexibility of the enzyme allowing it to identify all the different variations of the compatible tRNA

  1. at activation site of protein, the tRNA receives the amino acid on its acceptor stem(site on tRNA where a.a. is added on)
  2. protein shifts and rotates over so that editing site of protein can now check if the tRNA was charged with the right amino acid
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13
Q

describe the eukaryotic ribosome vs the prokaryotic ribosome. how is their difference exploited in antibiotics?

A

Eukaryotes
small subunit: 40S
large subunit : 60S
entire ribosome = 80S

Prokaryotes
small subunit: 30S
large subunit : 50S
entire ribosome = 70S

as they are different, antibiotics targeted at one will not affect the other

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14
Q

what are the specialized functions of the large and small subunit of the ribosome?

A
  1. Large subunit
    - has one 23S rRNA
    - has 50 proteins
    - functions mainly Catalytic
  2. Small subunit
    - has one 18S rRNA
    - 30 proteins
    - functions mainly binding RNA (tRNA and mRNA)
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15
Q

explain the 3 steps of translation

A
  1. INITIATION
    - the 5’ cap structure of the mRNA is recognized by the
    cap-binding protein complex which then recruits ribosomes.
    - small ribosomal subunit bound to initiator tRNA and initiation factors scans the mRNA along the non-coding region to find Kozak consensus sequence and initiation codon is found.
    - once AUG is found, initiation factors dissociate and large ribosomal subunit can bind
  2. ELONGATION
    - correct charged tRNA enters the A-site
    - the amino acid at correct charged tRNA at P-site has a high energy bond with tRNA so it is not very favorable and the carboxyl group of this a.a. attacks the amine group of the a.a. in the A-site thus forming a peptide bond between the amino acids
    - large ribosomal subunit translocated by one codon
    - small ribosomal subunit translocated by one codon
    - the deacylated tRNA previously at P site now in E site exits the complex and a new, charged, tRNA binds
  3. TERMINATION
    - the termination codon is encountered at the end of
    the open reading frame
    -stop codon recruits special tRNA which is bound to release factors which cause a hydrolysis reaction o that the bond between the protein and the (last)
    tRNA is broken to release the finished protein
    - the whole complex disassociates
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16
Q

what are the 3 binding sites for tRNA on the ribosome

A
  1. A-site : aminoacyl site
  2. P-site : peptidyl site
  3. E-site : exit site
17
Q

how do you regulate how much protein is generated from mRNA?

A

By altering the stability of the mRNA, stabilizing it keeps it in functional in the cytoplasm longer so it can produce even more proteins

18
Q

What is a polysome

A

a cluster of ribosomes held together by a strand of messenger RNA which each is translating

  • basically translation can happen at the same time on the same mRNA
19
Q

What happens after translation?

A
  1. protein folding
  2. translocation to the relevant part of the cell
  3. post-translational modification
20
Q

what proteins help with protein folding

A

chaperone proteins

21
Q

how does translocation of the protein to other structures occur co-translationally

A
  1. first few sequences of amino acids embedded in the growing protein chain could be an ER signal sequence (it wants to go into ER)
  2. the signal-recognition particle (SRP) can recognise signal sequence and bind and deliver the whole translation processes and machinery to the ER.
  3. at the ER, there are SRP receptor in membrane which allows SRP to bind and deliver the complex to the translocation channel.
  4. SRP displaced and recycled which amino acid translated into ER lumen
22
Q

what are some of the signal sequences in protein?

A
  1. Nucleus
  2. Endoplasmic reticulum
  3. Mitochondrion
    - proteins may display sequence that shows that they want to shuttle between two sites
    - after being translocated, signal peptide may be cleaved
23
Q

what signals affect the post-translational modification

A

signals on the growing peptide chain such as :
Asn-X-Ser
Asn-X-Thr

can affect post-translational modifications

24
Q

Give an example of why too much modification can be bad

A 
too much and too little cna be bad
example: 
Tau needs to be phophorylated
- however, hyperphosphorylation is associated with neurofibrillar tangles in
dementia
25
Q

give an example where defects in protein folding cause disease

A

cystic fibrosis
-defects in cystic fibrosis protein folding causes protein to not be able to be at the right surface of cells and are instead stuck in the ER thus patients have cystic fibrosis

26
Q

list 5 different effects mutations can have on the whole transcription, translation process and protein function

A 
I No transcription
II Protein incorrectly processed
III Inappropriately regulated
IV Inappropriate function
V Reduced transcript number
VI Unstable protein

week 8 (4 decks)

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