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BIOC0005 > Translation and Protein synthesis > Flashcards

Translation and Protein synthesis Flashcards

1
Q

What is transcription?

A

When gene base sequence converted into the complementary base sequence of RNA.

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2
Q

What is translation?

A

When the mRNA base sequence if converted into a sequence of amino acids in a polypeptide chain.

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3
Q

What is the transcriptome?

A

All the mRNAs present in the cell… 100,000… larger that the number of annotated genes due to splicing and modification.

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4
Q

What is the proteome?

A

The proteins present in a cell… 400,000… even more proteins because can be modified.

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5
Q

What are the main phases of protein synthesis?

A

Initiation, Elongation and termination.

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6
Q

What are the different component involved in coordinating protein synthesis?

A

DNA (genes), mRNA, tRNA, miRNA, ribosomes, translation factors, amino acids, ATP/ GTP and various regulatory proteins.

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7
Q

What is the function of mRNA, tRNA and rRNA?

A

mRNA- carries the genetic information.

tRNA- carries the amino acid and deciphers the code.

rRNA- catalyses the peptide bond formation.

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8
Q

How many codons can be generated from the four nucleotides in mRNA, and how many of these codons correspond to individual amino acids?

A

64 codons generated…
61 correspond to individual amino acids, and 3 are stop codons (UAA, UGA and UAG).
AUG is the start codon.

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9
Q

What is meant by the genetic code is degenerate?

A

I.e. most amino acids except methionine and tryptophan can be coded fro by ore than one codon.

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10
Q

What feature of mRNA makes it easy to spot?

A

The 3’ poly(A) tail and the 5’ and 3’ UTR regions.

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11
Q

What enhances mRNA stability?

A

The poly(A) tail and the 5’ 7-methyl guanosine cap.

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12
Q

Describe the structure of tRNA.

A
  • 74-95 bases long.
  • There are about 30-40 different tRNAs in prokaryotes, and 100 in eukaryotes.
  • Have four stems, bonded to another by Watson Crick pairing.
  • After synthesis and processing of tRNA… a CCA sequence is added to the 3’ acceptor stem… either on the 2’ or 3’ OH of the terminal adenosine in the corresponding tRNA.
  • Have an anticodon loop… responsible for specificity of the aminoacyl-tRNA.
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13
Q

What joins the CCA sequence to the acceptor stem ?

A

High energy ester bonds… by aminoacyl tRNA synthetase/ transferase…
Energy of this bond drives the formation of the peptide bonds linking adjacent amino acids in a growing polypeptide chain.

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14
Q

What is aminoacyl tRNA transferase?

A

An enzyme that catalyses the aminoacylation reaction by covalently linking (with an ester bond) an amino acid to its cognate tRNA in the first step of protein translation.

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15
Q

What bond links an amino acid with its cognate tRNA?

A

Ester bond.

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16
Q

What features of the tRNA acceptor arm determines the interaction?

A

The acceptor stem and the acceptor end.

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17
Q

What is crucial for the specific recognition of the correct tRNA?

A

The discriminator base.

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18
Q

What is the purpose of the editing site in the aminoacyl tRNA synthetase?

A

It ensures the right amino acid has been loaded, and can cleave incorrectly paired aminoacyl-tRNA molecules.

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19
Q

What are ribosomes and what rate do they function at?

A

These are protein-synthesizing machines, which are capable to elongate a polypeptide chain at 3-5 amino acids per second.

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20
Q

What is the ribosome composed of?

A

Both RNA and proteins.

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21
Q

What subunits make up an 80S ribosome complex, and what binds to each?

A

60S (binds tRNA) and 40S (binds mRNA) subunits.

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22
Q

What are the functions of the E, P and A sites on the large subunit?

A

E- Exit site… the tRNA released from ribosome from here when no longer needed.

P- Interacts with the tRNA that is carrying the growing polypeptide chain. ie. Polypeptide… P.

A- Interacts with the tRNA carrying the next amino acid in sequence. I.e. the Aminoacyl tRNA… A…

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23
Q

Why it necessary to recognise the specific start codon?

A

Because there may be many AUG codons in the sequence… ned to determine which one is the start codon.

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24
Q

What is the start sequence in prokaryotes?

A
  • The Shine-Dalgarno sequence i.e. where the ribosome will bind…
  • 5’-GGAGG-3’
  • Located around 8 bases before the AUG start codon.
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25
Q

What is the start sequence in eukaryotes?

A
  • The Kozak sequence… around the AUG binding site not before it…
  • 5’-CCACCAUGG-3’
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26
Q

What is a polysome?

A

A cluster of ribosomes held together by a strand of mRNA which they are translating.

27
Q

What can be deduced from the purification of polysomes?

A

Can see which mRNA is engaged in translation… by purifying and sequencing them… can see the transcriptional profile in cells at a particular time, in response to a certain stimuli.

28
Q

What determines a protein’s half life?

A

Degradation… if not needed, then will be degraded and amino acids recycled.

29
Q

Why is degradation important?

A

Ensures efficiency of the cells.

30
Q

What fate paths can a newly translated protein follow?

A

Translocation, post-translational modification, activation and degradation.

31
Q

Name 9 forms of post-translational modifications.

A

Phosphorylation, glycosylation, ubiquitination, SUMOylation, disulfide bond, acetylation, lipidation, methylation, hydroxylation.

32
Q

What is the purpose of post-translational modifications in cells?

A

Creation of docking sites in signaling complexes, activation/ inhibition of enzymatic activities, modification of subcellular localisation and targeting for degradation.

33
Q

What is protein phosphorylation?

A

A post-translational modification of proteins in which an amino acid residue is phosphorylated by a protein kinase, by the addition of a covalently bound phosphate.

34
Q

What is usually the source of the phosphates used in phosphorylation?

A

The gamma phosphate of ATP.

35
Q

What can be the effects of phosphorylation on a protein?

A

Involves the introduction of a charged and hydrophilic group in the side chain of amino acids… Can alter the structural conformation of a protein, causing it to become activated, deactivated or modified in function.

36
Q

What enzymes are involved in phosphorylation and dephosphorylation?

A

Protein kinases… phosphorylation.

Protein phosphatases… dephosphorylation.

37
Q

What are the most commonly phppshorylatie amino acid residues in eukaryotes, and in prokaryotes?

A

EUK: Serine, threonine and tyrosine.

PROK: Histidine.

Phosphorylated by the relative kinase i.e. serine kinase etc.

38
Q

Transcription factors are often phosphorylated as a result of a phosphorylation pathway, what does this result in?

A

Usually transcription factors are folded, and once phosphorylated, they will unfold, and bind another molecule i.e. coactivator, initiating the process of transcription.

39
Q

What is acetylation?

A

The process whereby acetyl group are transferred (usually from acetyl CoA) to the lysine residues within the N-terminal tail protruding from the histone core of the nucleosome, as part of gene regulation.

40
Q

Which enzymes are involved in acetylation and deacetylation?

A

Acetylation- histone acetyltransferase

Deacetylation- histone deacetylase.

41
Q

How do acetyl groups interact with histones?

A

Acetylation removes the positive charge on the histones, and so decreases the strength of interaction of the N-termini of the histones, with the negatively charged phosphate groups of DNA.

42
Q

How does acetylation affect gene transcription?

A

Therefore, the chromatin is transformed from a condensed structure into a more relaxed structure, associated with greater levels of gene transcription.
Transcription factors recognise acetylated histones, bind to them and initiate transcription.

43
Q

What is heterochromatin and euchromatin?

A

Heterochromatin- more condensed, tightly packed DNA.

Euchromatin- more relaxed, open DNA.

44
Q

What processes can bring about condensation of DNA?

A

Deacetylation and methylation.

45
Q

What processes can bring about relaxation of DNA ?

A

Acetylation and demethylation.

46
Q

What is a bromodomain?

A

A 110 amino acid protein domain that recognises acetylated lysine residues on the N-terminal tails of histones. Transduces the signal carried by acetylated lysine residues and translating it into various normal or abnormal phenotypes.
Can bind acetylated histones.

47
Q

What is a chromodomain?

A

A structural domain of about 40-50 amino acid residues. Commonly found in proteins involved in the remodelling and manipulation of chromatin and repressors of trasncription.
Highly conserved domain in plants and animals.
Chromodomain-containing proteins can also bind methylated histones.

48
Q

What is methylation?

A

The process whereby methyl groups are transferred to amino acids of histone proteins that make up nucleosomes, which the DNA double helix wraps around to form chromosomes.

49
Q

How does methylation affect the histones and DNA?

A

Methylation doesn’t change the charge… so the histone domain is still compact.
Methylation can wind DNA tighter at the histones, to halt transcription of a gene.
Depending on the amino acids methylated in the histnes… can influence the effect of methylation.

50
Q

What enzyme catalyses the methylation reaction?

A

Histone methyltrasnferase.

51
Q

What is methylation generally associated with?

A

Silencing of gene expression.

52
Q

What is ubiquitin?

A

A 8kDa, highly stable, 76 amino acid protein.

It can be conjugated to lysine residues on a target protein.

53
Q

What enzyme catalyses the conjugation of ubiquitin to lysine residues?

A

Ubiquitin ligase.

54
Q

What is the role of ubiquitination?

A

Acts as a key regulatory steps that guide protein degradation through regulation of proteasome activity.

55
Q

Outline the process of ubiquitination.

A

Involved the attachment of ubiquitin to lysine residues of target proteins via the action of ubiquitin ligase, and can result in protein mono-ubiquitination or polyubiquitination.

This process involves a set of enzymes i.e. E1, E2 and E3.

56
Q

What is the function of the proteins E1, E2 and E3?

A

E1- Activating enzyme… activates UB1s in the presence of ATP.

E2- Conjugative enzyme.

E3- Ligase.

57
Q

In what ways may a protein be ubiquitinated?

A

Monoubiquitylation, multi-monoubiquitylation, homogenous ubiquitin chain, mixed ubiwuting chain, branched ubiquitin chain and unanchored ubiquitin chain.

58
Q

Why can ubiquitin moderate a variety of functions?

A

Because has the ability to be linked to proteins as a monomer, or as one, or more substrate lysines, or as a polymer, by sequential addition of further Ubs to each other through Ub lysines.

59
Q

Name two examples that involved Ub.

A

USP2a-mediated ubiquitination.

Proteasome-mediated degradation of STAT1.

60
Q

What is CoAlation?

A

The covalent attachment of CoA to cysteine thiols.

This is a reversible post-translational modification induced in mammalian cells and tissues by oxidising agents and metabolic stress.

A redox regulated protein modification by coenzyme A in mammalian cells.

61
Q

What instigates CoAlation?

A

Oxidising agents and metabolic stress.

62
Q

Compare the use of CoA in normal cells vs cells under stress.

A

Normal cells:
- Use CoA mainly through thioester derivatives… generates many things needed for growth i.e. nutrients.

Cell under stress:
-CoA is an obligatory cofactor in all branches of life. Involved in major metabolic pathways and regulating gene expression.

63
Q

Why is a CoAlation response important when a cell is under oxidative stress?

A

Because when a reactive oxygen species is produced in cells, they are highly reactive and will damage proteins through oxidation… the oxygen radical can form toxic products.

BIOC0005 (9 decks)

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