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SF:Biochemistry > Transcription & Translation > Flashcards

Transcription & Translation Flashcards

1
Q

Describe the three steps of transcription.

A

The three steps of transcription are initiation, elongation, and termination.

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2
Q

Define the initiation step of transcription.

A

The initiation step involves identifying the portion of DNA to be transcribed, regulated by a promoter, and forming a transcription initiation complex with transcription factors and RNA Polymerase.

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3
Q

How does the elongation step of transcription occur?

A

During elongation, RNA Polymerase unzips the DNA double strands to form a transcription bubble, reading one strand as a template to create a complementary RNA strand in the 5’ → 3’ direction.

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4
Q

What is the role of the template strand in transcription?

A

The template strand is the DNA strand that is read by RNA Polymerase to synthesize the complementary RNA transcript.

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5
Q

What is the non-template strand in transcription?

A

The non-template strand, also known as the coding or sense strand, is the DNA strand that is not read by RNA Polymerase during transcription.

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6
Q

Explain the termination step of transcription.

A

The termination step occurs when RNA Polymerase reaches a termination sequence, causing it to detach from the DNA and end the RNA transcript.

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7
Q

How does alpha amanatin affect transcription?

A

Alpha amanatin is a poison that inhibits RNA Polymerase II and III, leading to liver failure, but does not affect RNA Polymerase I.

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8
Q

What is a key difference between RNA and DNA synthesis?

A

Making RNA is slower and less accurate than making DNA.

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9
Q

What is the significance of mutations in pre-mRNA splicing?

A

30% of mutations arise from mistakes in pre-mRNA splicing, which can lead to conditions like Thalassemia, causing facial changes and liver enlargement.

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10
Q

How is mRNA processed in eukaryotes?

A

In eukaryotes, mRNA is processed by adding a 5’ cap, a poly-A tail, and undergoing splicing.

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11
Q

Describe the processing of mRNA in prokaryotes.

A

In prokaryotes, mRNA is not processed; translation can begin while the mRNA is still being transcribed due to the lack of a nucleus.

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12
Q

What is the function of the 5’ cap on mRNA?

A

The 5’ cap, a modified guanine nucleotide, protects the mRNA from degradation and assists the ribosome in attaching to the mRNA for protein synthesis.

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13
Q

What is the poly-A tail and its purpose?

A

The poly-A tail is a sequence of 100-200 adenine nucleotides added to the 3’ end of mRNA, enhancing transcript stability and aiding in its export from the nucleus.

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14
Q

What condition is associated with mutations in RNA Polymerase I?

A

Treacher Collins Syndrome is associated with mutations in RNA Polymerase I, leading to craniofacial deformities.

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15
Q

How is the lac operon relevant to transcription?

A

The lac operon is used as a model to understand transcription, although it is not crucial for understanding the process itself.

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16
Q

Describe the process of splicing in mRNA.

A

Splicing in mRNA involves the removal of introns and, in some cases, the removal of certain exons during alternate splicing.

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17
Q

Define a ribozyme.

A

A ribozyme is an enzyme made of RNA that catalyzes specific biochemical reactions, including RNA splicing in gene expression.

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18
Q

How do small nuclear RNAs (snRNAs) and small nuclear ribonucleoproteins (snRNPs) function in splicing?

A

Small nuclear RNAs (snRNAs) combine with proteins to form small nuclear ribonucleoproteins (snRNPs), which assist in the splicing process.

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19
Q

What is the role of a spliceosome in mRNA processing?

A

A spliceosome, formed by snRNPs and other proteins, performs splicing by removing introns and joining the ends of remaining exons.

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20
Q

Explain the significance of introns in gene expression.

A

Introns are non-coding sequences that allow for alternative splicing, leading to a greater variety of mRNA sequences and ultimately a wider range of proteins.

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21
Q

How do bacteria differ from eukaryotes regarding introns and splicing?

A

Bacteria do not have introns and therefore lack the machinery necessary for splicing.

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22
Q

What is the consequence of changes in nucleotides at splice sites?

A

Changes in nucleotides at splice sites can prevent splicing from occurring.

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23
Q

Identify the role of RNA polymerase II in mRNA synthesis.

A

RNA polymerase II is responsible for synthesizing mRNA, which constitutes a small fraction of the total RNA in the body.

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24
Q

What genetic condition is associated with problems in the spliceosome?

A

Spinal Muscular Atrophy (SMA) is associated with the deletion of the SMN1 gene due to issues with the spliceosome.

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25
Q

Describe the function of mRNA in translation.

A

mRNA serves as the template RNA transcript, with its sequence read in codons that correspond to amino acids or stop signals during polypeptide elongation.

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26
Q

What is the role of tRNA in the translation process?

A

tRNA carries the anticodon for binding to mRNA codons and transfers specific amino acids to the elongating polypeptide.

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27
Q

Explain the process of charging a tRNA.

A

Charging a tRNA involves aminoacyl tRNA synthetases (aaRS) reading the genetic code and attaching the correct amino acid to the tRNA.

28
Q

What is the function of rRNA in translation?

A

rRNA is a component of ribosomal subunits that provides active sites for translation, facilitating the process of protein synthesis.

29
Q

Describe the structure of ribosomes.

A

Ribosomes consist of two subunits: a large subunit and a small subunit. The large subunit is responsible for the peptidyl transfer reaction, while the small subunit recognizes mRNA and binds to the Shine-Dalgarno sequence (Kozak sequence in eukaryotes). Both subunits are essential for translation and come together to form three active sites: E site, P site, and A site, which accommodate tRNA molecules.

30
Q

Define the ribosome structure in eukaryotes and prokaryotes.

A

Eukaryotic ribosomes have a 60S and a 40S subunit, forming an 80S ribosome. Prokaryotic ribosomes consist of a 50S and a 30S subunit, resulting in a 70S ribosome. The naming does not reflect the sum of the subunits.

31
Q

How does the A (aminoacyl) site function in ribosomes?

A

The A site provides space for a new tRNA with an attached amino acid and corresponding anticodon to match the next codon in the mRNA sequence. The start codon is matched to its tRNA at the P site during initiation.

32
Q

Describe the role of the P (peptidyl) site in ribosomes.

A

The P site holds a tRNA with an amino acid adjacent to another tRNA in the A site. The ribosome’s rRNA catalyzes the transfer of the amino acid from the P site tRNA to the A site tRNA, forming a peptide bond, while the ribosome moves along the mRNA.

33
Q

What happens at the E (exit) site of the ribosome?

A

The E site is where a tRNA, having released its amino acid, dissociates from the ribosome and mRNA, exiting the ribosome.

34
Q

How do initiation co-factors assist in translation?

A

Initiation co-factors help assemble the 5’ end of the mRNA, the ribosomal subunits, and the correct tRNA into the P site, with GTP mediating the process.

35
Q

Describe the function of the Shine-Dalgarno sequence.

A

The Shine-Dalgarno sequence is located just before start codons and helps to identify the start codon for the ribosome during translation.

36
Q

Explain the elongation step in translation.

A

During the elongation step, translocation occurs, which is the movement of the ribosome from the A site to the P site, allowing for the addition of new amino acids to the growing polypeptide chain.

37
Q

Describe how termination co-factors function in protein synthesis.

A

Termination co-factors bind to the ribosome when a stop codon appears in the A site, signaling the end of polypeptide synthesis. This leads to the release of the completed polypeptide and the disassembly of the ribosome into its subunits.

38
Q

Explain the peptidyl transferase reaction.

A

The peptidyl transferase reaction occurs spontaneously as tRNAs bring amino acids close together, allowing them to react and form a peptide bond without the need for an enzyme.

39
Q

Define what a ribozyme is in the context of the ribosome.

A

A ribozyme is a type of RNA that acts as a catalyst in biochemical reactions, specifically in the ribosome where no proteins are present near the reaction site.

40
Q

How is protein synthesis directionally organized?

A

Protein synthesis starts at the N terminus and finishes at the C terminus, with the amino group of a new amino acid attacking the carboxyl group of the growing chain.

41
Q

Outline the Central Dogma of molecular biology.

A

The Central Dogma describes the flow of genetic information as DNA → mRNA → Protein, involving transcription of DNA into mRNA and translation of mRNA into proteins.

42
Q

What is the significance of the revised Central Dogma?

A

The revised Central Dogma expands on the original concept by including additional processes such as reverse transcription and the role of various types of RNA in gene expression.

43
Q

How many possible codons can be formed from RNA nucleotides?

A

There are 64 possible codon combinations, derived from three positions filled by one of four nucleotides (adenine, cytosine, guanine, uracil).

44
Q

Explain the relationship between codons and anticodons.

A

Codons are sequences of three RNA nucleotides that are read by anticodons, which are part of tRNA molecules that base pair with codons to deliver the correct amino acid during protein synthesis.

45
Q

Define the concept of the degenerate code in genetics.

A

The degenerate code refers to the redundancy in the genetic code, where multiple codon combinations can encode for the same amino acid, despite there being only 20 amino acids and 64 codons.

46
Q

What is wobble pairing in the context of codons and anticodons?

A

Wobble pairing refers to the flexibility in the third position of a codon, allowing different codons to encode the same amino acid due to loose bonding between the codon and anticodon.

47
Q

Define a missense mutation.

A

A missense mutation results in the translation of a different amino acid due to a change in the nucleotide in the codon.

48
Q

Describe the effect of a nonsense mutation.

A

A nonsense mutation results in the translation of a premature stop codon, truncating the translated protein.

49
Q

How does a nonsense codon function in translation?

A

A nonsense codon does not have a matching tRNA; instead, release factors terminate the polypeptide sequence.

50
Q

What is the role of the initiation codon in protein synthesis?

A

The initiation codon, AUG, encodes for methionine and signals the start of translation.

51
Q

List the termination codons and their significance.

A

UAA, UAG, and UGA are stop codons that terminate translation and do not code for amino acids.

52
Q

Define mRNA and its function.

A

mRNA is a temporary set of instructions for protein production.

53
Q

Describe the role of free-floating ribosomes in translation.

A

Free-floating ribosomes exist in the cytosol and produce proteins that function within the cytosol.

54
Q

What distinguishes Rough ER ribosomes from free-floating ribosomes?

A

Rough ER ribosomes are attached to the endoplasmic reticulum and produce proteins destined for transport to organelles or the cell membrane.

55
Q

Where do post-translational modifications occur?

A

Post-translational modifications occur in the endoplasmic reticulum (ER) and Golgi apparatus.

56
Q

What types of modifications can occur post-translation?

A

Post-translational modifications may include phosphorylation, formation of disulfide bonds, glycosylation, and ubiquitination.

57
Q

Explain the process of phosphorylation in post-translational modifications.

A

Phosphorylation involves the addition of a negatively charged phosphoryl group to certain amino acid residues, such as serine, threonine, and tyrosine.

58
Q

What is glycosylation in the context of protein modification?

A

Glycosylation is the linkage of short carbohydrate polymers to the protein during post-translational modifications.

59
Q

How does ubiquitination affect proteins?

A

Ubiquitination attaches a protein known as ubiquitin to mark the protein for degradation in the proteasome.

60
Q

What is the significance of Diptheria Toxin in translation?

A

Diptheria Toxin is important as it inhibits translation by binding to specific sites on the ribosome.

61
Q

Describe the origin and toxicity of Ricin.

A

Ricin is derived from castor beans and is extremely deadly, functioning by cleaving adenine on ribosomes.

62
Q

How does Actinomycin D affect RNA polymerase activity?

A

Actinomycin D intercalates into DNA, widening the minor groove and thinning the major groove, which may increase RNA polymerase access to some genes but ultimately inhibits RNA polymerase from binding to DNA, thus inhibiting mRNA production and protein synthesis.

63
Q

Define the role of RNA polymerase II in cellular function.

A

RNA polymerase II is responsible for the production of mRNA, which is essential for synthesizing new proteins.

64
Q

What happens to a hiker who consumes a death cap mushroom containing a toxin that attacks RNA polymerase II?

A

The hiker will lose the ability to produce new mRNA transcripts, leading to a failure in producing new proteins, although symptoms may not appear immediately.

65
Q

Explain why spliceosomes cannot be purified from bacteria.

A

Spliceosomes are only present in eukaryotes because only eukaryotic genes contain introns that need to be spliced out.

66
Q

How does puromycin inhibit translation?

A

Puromycin acts as a tRNA analogue that cannot be properly transferred from the A to the P site of the ribosome, blocking translation by acting as a peptide-chain terminator.

SF:Biochemistry (14 decks)

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