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Cell Biology (BIOL 2520) > Transcription + Translation > Flashcards

Transcription + Translation Flashcards

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1
Q

What is transcription?

A

Process in which RNA polymerase uses one strand of DNA as a template to synthesize a complimentary RNA sequence.

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2
Q

What are two basic differences between RNA and DNA?

A
  1. RNA = Ribose (OH), DNA = Deoxyribose (H)
  2. RNA = A,G,C,U ; DNA = A,G,C,T
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3
Q

What are the 5 steps of gene expression?

A
  1. Transcription: RNA polymerase II transcribes RNA from DNA template (pre-mRNA)
  2. Processing: pre-mRNA is capped, spliced and polyadenylated to make a finalized mRNA
  3. Transportation out of nucleus
  4. Translation: mRNA complexes with ribosome and information is translated into an ordered polymer of amino acids.
  5. Protein folding and modification
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4
Q

What is the difference between a coding strand and a template strand?

A

Coding: identical to mRNA (with U and T swapped)

Template: Strand that base pairs with mRNA

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5
Q

What are RNA polymerases?

A

Multi-subunit enzymes that catalyze formation of the phosphodiester bonds, linking nucleotides and forming the RNA’s sugar-phosphate backbone.

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6
Q

How is RNA transcript transcribed?

A

RNA Polymerase unwinds double helix to reveal next section on template strand. It moves along DNA bringing together ribonucleotides into a chain from the 5’ to 3’ direction

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7
Q

How is RNA Polymerase different from DNA polymerase?

A

RNA polymerase uses ribonucleoside triphosphates as substrates and catalyzes linkage of ribonucleotides, not deoxyribonucleotides. RNA Polymerase can start a chain without a primer and do not accurately proofread their work as they are not permanent storage of genetic information.

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8
Q

What are noncoding RNA’s? What are 3 examples?

A

RNA molecule that is the final product for the gene and DOES NOT code for a protein. They serve as regulatory, structural and enzymatic molecules. (e.g. ribosomal RNA, transfer RNA, micro RNA)

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9
Q

What do siRNAs, lncRNAs do?

A

Small interfering RNA: protect from viruses and proliferate transposable elements

Long noncoding RNA: act as scaffolds to organize proteins

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10
Q

What is a promoter?

A

DNA sequence UPSTREAM of starting point that initiates gene transcription, includes sequences recognized by RNA polymerase and accessory proteins.

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11
Q

What does RNA polymerase I, II, and III transcribe?

A

I: most rRNA genes

II: All protein-coding genes, microRNA genes, genes for noncoding RNAs

III: tRNA genes, 5S rRNA genes, genes for small RNAs

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12
Q

What are general transcription factors?

A

Proteins that assemble on the promoters of eukaryotic genes near the start site of transcription to pull apart the DNA and load RNA polymerase in the correct position.

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13
Q

How do general transcription factors assemble at the promoter?

A
  1. TBP subunit of TFIID binds to TATA box 30 bases upstream from start site and cause a dramatic local distortion on the DNA
  2. Distorted DNA allows TFIIB and TFIIA to attach and help RNA polymerase attach to TFIIF
  3. TFIIH uses ATP and opens double helix, exposes template strand, phosphorylates RNA pol I to release its attachment to the factors and begin transcription
  4. If TFIID remains attached to the promoter, more RNA polymerase II enzymes can bind, allowing multiple rounds of transcription
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14
Q

How does RNA capping work?

A

5’ end of RNA transcript (synthesized first) is given a methylated guanine nucleotide

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15
Q

How does polyadenylation work?

A

mRNA is trimmed by enzyme at specific sequence and finished off by adding a series of repeated adenine nucleotides to the trimmed end.

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16
Q

What is the purpose of polyadenylation and capping?

A

To increase stability, protect from nucleases, facilitate export from nucleus to cytosol, and mark the mRNA as mRNA.

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17
Q

What is the difference between an intron and an exon?

A

Intron: long, noncoding sequences that intervene protein sequence and spliced from mRNA

Exon: short coding sequences that are spliced into a complete chain.

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18
Q

How does RNA splicing work?

A

End of the intron is covalently bound to OH group of the ribose of the adenine nucleotide to form a lariat structure, allowing the two exons to join together. Intron is released and degraded in the nucleus.

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19
Q

What are small nuclear RNAs?

A

sRNAs are RNA molecules that contain the nucleotides that participate in RNA splicing. When packaged with additional proteins it forms small nuclear ribonucleoprotines.

20
Q

What are small nuclear ribonucleoproteins?

A

snRNPs are ribozymes that recognize splice-site sequences and form the active site responsible for catalyzing the splicing.

21
Q

What is the spliceosome?

A

Large assembly of RNA and protein molecules that carries out RNA splicing in the nucleus. Its core is made of snRNPs.

22
Q

What is alternative splicing?

A

Production of different mRNAs by splicing the same RNA sequence in different ways.

23
Q

How is mRNA exported from the nucleus?

A

Specialized set of RNA-binding proteins recognize different parts of a mature mRNA molecule as “Export Ready” and are sent out of the nuclear envelope.

24
Q

What is the difference between prokaryotic and eukaryotic transcription?

A
  1. Prokaryotes transcribe and translate in the same compartment simultaneously.
  2. 5’ and 3’ end of mRNA remain unmodified (no G cap or poly A tail) and directly produced by RNA polymerase
  3. Does not undergo splicing
25
Q

what are the basic properties of a mature mRNA?

A
  1. Code for specific polypeptide
  2. Found in cytoplasm
  3. Attached to ribosomes when translated
  4. Coding region is translated into polypeptide
  5. Non-coding segments at 5’ and 3’
  6. Eukaryotic mRNAs have modifications at 5’ guanosine cap and 3’ poly-A-tail
26
Q

What is genetic code?

A

Set of rules by which the nucleotide sequence is translated into the amino acid sequence through an intermediary mRNA molecule

27
Q

What is a codon?

A

Sequence of three nucleotides in mRNA that corresponds to a specific amino acid or serves as a start or stop signal.

28
Q

What is a reading frame? What direction is read?

A

One of the three possible ways in which a set of successive nucleotide triplets can be translated into protein. 5’ to 3’ is read.

29
Q

What are tRNAs?

A

Transfer RNAs (73-93 nucleotides) are molecules folded from a cloverleaf structure to an L shape that is covalently attached to AA and have an anticodon to base pair with the codons on the mRNA.

30
Q
A
31
Q

What is the wobble hypothesis?

A

Base pairing between the first two positions of a codon and an anticodon must be exact while the third isnt as strict. This allows multiple codons to code for the same amino acid and minimizes mistakes and mutations.

32
Q

What are aminoacyl-tRNA synthases?

A

Enzymes that uses ATP to covalently couple its designated amino acid to the appropriate set of tRNA molecules by recognition of anticodon.

33
Q

What are ribosomes structure and function?

A

Structure: complex of ribosomal proteins and ribosomal RNAs (rRNAs) that make up a small subunit and a large subunit

Function: bind to mRNA, capture and position appropriate tRNA molecules, and catalyze the covalent linkage of amino acids to form a polypeptide chain in the 5’-3’ direction.

34
Q

What is the difference between the small and large ribosomal subunits?

A

Small: matches tRNA to codon of mRNA

Large: catalyzes formation of peptide bonds that covalently link the amino acids together

35
Q

In what direction do ribosomes read mRNA?

A

5’-3’ direction

36
Q

What are translation initiation factors?

A

Proteins that promote the proper association of ribosomes with mRNA and is required for the initiation of protein synthesis.

37
Q

What are the stages of translation?

A

Initiation, Elongation, Termination

37
Q

What is peptidyl transferase?

A

Catalytic site in large subunit that orients two reactants and increase the likelihood of a productive reaction.

38
Q

What happens in initiation?

A
  1. Initiator tRNA carries methionine to the P site in small subunit with translation initiation factors bound.
  2. Small subunit-Methionine complex binds to the 5’ end of mRNA.
  3. They move along 5’-3’ in search of mRNA’s AUG codon.
  4. When latched on, initiation factors dissociate and the large ribosomal subunit assembles.
39
Q

What happens in elongation?

A
  1. After the large subunit assembles after binding of methionine, the next charged tRNA binds to the A site and a peptide bond is formed between them.
  2. The large subunit translocates, putting the tRNA in the E site which ejects it, and shifts the tRNA holding the chain to the P site.
  3. The small subunit translocates which allows a newly bound tRNA to bind to the A site.
40
Q

What happens in termination?

A
  1. The ribosome encounters a stop codon (UAA, UAG, UGA)
  2. Release factors bind to any stop codon that reaches the A site on the ribosome
  3. Binding alters the activity of peptidyl transferase, causing it to add a water molecule instead of an amino acid
  4. Addition of water frees carboxyl end of polypeptide chain from its attachment to a tRNA molecule and the protein chain, mRNA, large and small subunits dissociate.
41
Q

Why do proteins fold into the correct 3D shape and how do they do it?

A

Proteins must be modified and fold post translation in order for them to be fully functional.

They either spontaneously fold or fold with the assistance of chaperone proteins. Some are phosphorylated and glycosylated, while other bind or associate with small cofactors or other protein subunits.

42
Q

What are proteases

A

Enzyme complexes that degrade proteins by hydrolyzing peptide bonds between amino acids.

43
Q

Why must proteins be degraded?

A

Protein lifetime must be kept short and damaged/misfolded proteins must be recognized and removed.

44
Q

What is a proteasome?

A

Protein in protease complex that make up the central cylinder, which is the active site of a protease.

45
Q

What is the RNA/Protein conundrum? Its solution?

A

DNA encodes info to make proteins, but DNA and RNA replication requires proteins. As one cannot exist without the other, which happened first?

ANSWER: Life began as RNA which may be enzymatic as a ribozyme. The protein that synthesizes other proteins, the ribosome, happens to be a ribozyme.

Cell Biology (BIOL 2520) (10 decks)

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