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Malika Biochem MCAT > Chapter 7 > Flashcards

Chapter 7 Flashcards

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1
Q

During the processes of replication, transcription, and translation, DNA and RNA is synthesized in what direction?

A

5’ to 3’

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2
Q

What is the purpose of mRNA?

A

It is the only RNA that specifies an amino acid sequence which encodes into a protein.

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3
Q

mRNA is transcribed from DNA utilizing what protein?

A

RNA polymerase

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4
Q

Where do post-transcriptional modifications occur in the cell?

A

In the nucleus

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5
Q

Which DNA strand does RNA polymerase use to transcribe DNA into mRNA?

A

mRNA is transcribed from the DNA template strand

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6
Q

If you are a given the DNA coding strand, how would you write the corresponding mRNA sequence?

A

You would write the mRNA strand exactly the way it is except change the thymine bases to uracil bases.

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7
Q

How would you write the mRNA sequence if you were given the DNA template strand?

A

You would take the complementary bases of the strand, and then change the thymine bases to uracil bases.

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8
Q

What is the function of tRNA?

A

Found in the cytoplasm, its main function is to bind the specific codon in the mRNA and transfer the corresponding amino acid it to a growing polypeptide chain in the ribosome. The tRNA contains the anti-codon on one end.

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9
Q

What is the function of rRNA?

A

It combines with proteins to make ribosomes that are essential for translation. (Acts as the polymer of which ribosomes are constructed).

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10
Q

What is the role of small nuclear RNA (snRNA)?

A

In eukaryotes snRNA is found in the nucleus and plays a role in post-transcriptional processing more specifically splicing. It is part of the spliceosome.

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11
Q

What is the function of micro RNA (miRNA)?

A

Found in plant and animal cells, it also plays a role in post-transcriptional processing of mRNA and silencing translation by binding the mRNA in complementary and noncomplementary sequences.

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12
Q

What is the origin and function of small interfering RNA (siRNA)?

A

They are derived from highly repetitive double stranded sequences like centromeres and transposable elements.
They are involved in regulating gene expression (specifically heterochromatin formation) by recruiting histone modification enzymes such as histone methylases.

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13
Q

What is the 1eukaryotic start codon?

A

AUG

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14
Q

What are the 3 eukaryotic stop codons?

A

UAA, UGA, UAG

(You are annoying, You go away, You are gone)

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15
Q

What is the wobble position for a codon?

A

It is the third nucleotide in a codon which is variable meaning that it can be U, G, A, or C and it wouldn’t change the actual amino acid.

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16
Q

What are point mutations?

A

It is where one of the nucleotides in a codon is substituted for another.

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17
Q

What is a frameshift mutation?

A

It is when a number of nucleotides are either inserted or deleted, shifting the reading frame of the sequence and resulting in amino acid changes.

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18
Q

What is the silent mutation?

A

It is when one nucleotide is substituted for another, but this doesn’t change the amino acid sequence. It can also be a mutation within an intron, which also doesn’t change the amino acid sequence.

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19
Q

What is a missense mutation?

A

It is when one nucleotide is substituted for another, causing a change in the amino acid sequence.

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20
Q

What is a nonsense mutation?

A

It is when one nucleotide is substituted for another nucleotide, which changes the codon to a premature stop codon.

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21
Q

Which eukaryotic RNA polymerase is involved in transcription of mRNA?

A

RNA polymerase II

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22
Q

What is the function of RNA polymerase I?

A

It is located in the nucleolus and transcribes rRNA genes.

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23
Q

What is the function of RNA polymerase III?

A

It is located in the nucleus, and synthesizes tRNA and the 5S protein in the rRNA.

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24
Q

Explain the process of eukaryotic transcription.

A
  1. RNA polymerase II recognizes, and binds to the promoter region, known as the TATA box with the help of transcription factors.
  2. RNA polymerase initiates MRNA synthesis, downstream of the promoter region at the +1 site (about 20 basepairs downstream)
  3. when the first 8 to 10 nucleotides have been synthesized, the sigma subunit from the polymerase enzyme dissociates.
  4. As RNA polymerase moves on, the DNA double helix behind it reforms and ahead of the enzyme the DNA is unwound more.
  5. Transcription comes to a stop when RNA polymerase reaches a stop codon.
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25
Q

What is the name of mRNA before it undergoes post-transcriptional modifications?

A

Heterogenous nuclear RNA (hnRNA) or pre-mRNA

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26
Q

What is the spliceosome made of?

A

It is made of snRNA and small nuclear ribonucleoproteins (SNRPs)

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27
Q

How does alternative splicing regulate gene expression?

A

By splicing in different regions, the assembly of exons in different orders contributes to different protein being made from a limited amount of genes.

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28
Q

What regions are spliced?

A

Introns

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29
Q

True or false:
Mature mRNA still contains untranslated regions (UTRs) at the 5’ and 3’ end.

A

True; these untranslated regions are important because they are where the ribosome binds to initiate translation.

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30
Q

When is the 5’ cap added to the pre-mRNA?
Before transcription
During transcription
After transcription

A

During transcription

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31
Q

What is the function of the 5’ cap?

A

It functions as the ribosome binding site as well as protects mRNA from degradation in the cytoplasm.

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32
Q

What is the function of the 3’ poly A tail?

A

Composed of adenine bases, it functions as an initial barrier against rapid degradation. In other words, the longer the tail, the longer duration the mRNA survives in the cytoplasm.

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33
Q

Where does translation occur in the cell?

A

It can occur in the cytoplasm on a free-floating ribosome, in ribosomes bound to the rough ER, and in the mitochondria.

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34
Q

What subunits is a eukaryotic ribosome made of?

A

It is made of a 60S and 40S subunit that forms a whole 80S ribosome.

35
Q

What subunits is a prokaryotic ribosome made of?

A

It is made of a 50S subunit and 30S subunit, which makes a whole 70S ribosome.

36
Q

What are the names for the three binding sites for tRNA in the ribosome?

A

A (aminoacyl)
P (peptidyl)
E (exit)

37
Q

What is an example of a co-translational modification?

A

Acetylation of the methionine amino acid in the peptide chain during the process of translation.

38
Q

Define the post translational modification: proteolysis

A

It involves cleaving longer inactive polypeptides called zymogens into a smaller active form.

39
Q

What are the names of the proteins that assist in protein folding?

A

Chaperones

40
Q

What are examples of post-translational molecular additions to peptide chains?

A

Phosphorylation, carboxylation, glycosylation, prenylation, ubiquitination

41
Q

What is the purpose of the carboxylation post translational modification?

A

It adds a carboxylic acid group that serves as a calcium binding site.

42
Q

What is the purpose of the ubiquitination postranslational modification?

A

It adds a ubiquitin proteins to the peptide chain, marking it for eventual degradation in the cell.

43
Q

What is the purpose of the prenylation post-translational modification?

A

It adds lipid groups to the peptide, allowing it to travel to the plasma membrane.

44
Q

What is the purpose of glycosylation?

A

The addition of sugar groups to proteins can occur as the protein chain travels through the ER or Golgi apparatus. These additions contribute to protein diversity (for example different blood groups) and protein localization.

45
Q

In eukaryotes at the start of translation, the small ribosomal subunit binds to what region of the mRNA?

A

The ribosome binds to the 5’ cap

46
Q

In prokaryotes the small ribosomal unit binds to what region of the mRNA at the start of translation?

A

It binds to the Shine-Dalgarno sequence.

47
Q

Explain the initiation step of translation.

A

1.The small ribosomal unit binds to either the 5’ cap or the Shine-Dalgarno sequence (depending on whether it’s a prokaryote or eukaryote).
2. Small subunit moves along mRNA until it reaches the start codon. A charged initiator tRNA binds to the AUG start codon on the mRNA.
3. Then, the large ribosomal subunit binds to the small subunit with the help of initiation factors.

48
Q

Explain the elongation step of translation.

A
  1. A new tRNA carrying an amino acid enters the A site and lines up its anti-codon with the codon of the mRNA.
  2. Then, a peptide bond forms between the two amino acids in the P and A site which requires peptidyl transferase and GTP.
  3. Then the tRNA in the P site releases its amino acid and lets the tRNA in the A site hold the dipeptide.
  4. The ribosome moves forward, leading each tRNA move up a slot, causing the empty uncharged tRNA that was in the P site to move to the E site and exit the ribosome.
  5. The cycle repeats for each codon.
49
Q

Explain the termination step of translation.

A

If any of the three stop codons from the mRNA moves into the A site, a release factor protein binds to the stop codon (instead of a tRNA) which causes an H2O molecule to be added to the polypeptide chain, allowing it to be released.
Finally, the ribosomes subunits dissociate.

50
Q

What are the purpose of signal sequences in eukaryotes?

A

Signal sequences direct proteins to a specific location in the cell, such as the nucleus, lysosome, cell membrane, and even the ER, where the process of translation is continued.
A signal sequence for a protein that will either be secreted outside or locate in the plasma membrane, moves the protein to the rough ER to finish translation. Then, it is moved to its final destination (outside/plasma membrane).

51
Q

What is an operon structure?

A

It is a system where there are a cluster of genes that are regulated under a single promoter. These genes are transcribed as a single mRNA and the system is very common in prokaryotes.

52
Q

How does the Jacob-Monod model describe an operon system?

A

It says an operon system has several components: regulator gene region, promoter region, operator region, and structural gene.

53
Q

What is the function of the regulator gene in an operon system?

A

The regulator gene is the furthest region upstream, and it codes for a protein known as the repressor.

54
Q

What is the function of the promoter site in the operating system?

A

The promoter site is responsible for the binding of RNA polymerase and transcription factors which allows for transcription to begin.

55
Q

What is the revolutionary role of Introns?

A

Introns play a role in regulating gene expression. For example, there are enhancers found within introns which increase the rate of gene expression.

56
Q

What is the operator site in an operon system?

A

It is downstream of the promoter region, it’s a non-transcribable region of DNA that is capable of binding a repressor protein.

57
Q

What are the role of structural genes in an operon system?

A

These are the genes that code for the proteins of interest.

58
Q

Describe the inducible operon system in a few words.

A

It is a system that is normally off, but can be made to turn on if an inducer binds.

59
Q

Describe a repressible operon system in a few words.

A

It is a system that is always on, but can be made to turn off when a repressor binds.

60
Q

What is an inducible operon system?

A

It is when a repressor is always bound tightly to the operator site, blocking transcription from occurring, unless an inducer binds to the repressor causing the inducer-repressor complex to unbind and gene transcription to occur.

61
Q

True or false:
A repressor bound to the operator site is a mechanism of negative control of gene expression.

A

True

62
Q

What is a repressible operon system?

A

It is a system where there is no repressor bound to the operator site, allowing for constant production of a protein. The repressor is always inactive, unless a corepresser binds to it and as a complex they bind to the operator site to stop transcription.

63
Q

What is an advantage of the inducible operon system?

A

It allows for precise control of gene expression, that is proteins products are only produced when they are needed.

64
Q

What is an example of positive control of gene expression in prokaryotes?

A

Positive control is when binding of a molecule increases gene transcription. An example is binding of a transcriptional activator called CAP to the promoter region, which increases transcription of the lactase gene.

65
Q

What are the two categories of transcription factors?

A

Transcription activators and transcription repressors

66
Q

True or false:
Transcription factors only bind to promoter regions.

A

False. transcription factors can also bind to enhancer regions in the DNA.

67
Q

Transcription factors have two domains. What are they?

A

A DNA binding domain, which binds to a specific part of the promoter region or a sequence of DNA that only binds specific TFs. An activation domain which allows for binding of other transcription factors and regulatory proteins such as RNA polymerase and histone acetylases.

68
Q

How does acetylation affect the gene expression?

A

Acetylation increases the rate of gene expression. Histone acetylases acetylate lysine residues in the histone proteins which increases the space between histone proteins. this promotes a euchromatin structure.

69
Q

How does DNA methylation affect gene transcription?

A

DNA methylates add methyl groups to C and G nucleotides to silence gene expression. Gene expression is silenced because methylated DNA recruits methyl CpG binding proteins which act as repressors.

70
Q

What are enhancer sequences?

A

They are regions of DNA that increase the level of transcription of targeted genes. They bind transcription factors that form a protein bridge, causing the DNA to bend and link the transcription factors from the enhancer sequence to RNA polymerase at the promoter sequence.

71
Q

Where are enhancer sequences located in the DNA sequence?

A

Enhancers sequences can be located within an intron or non-coding region of the DNA. They can also be located within the coding region of a gene, downstream of a gene, or thousands of nucleotides away..

72
Q

What are silencers sequences?

A

They are sequences of DNA that reduce transcription of a target gene by binding repressor proteins. They can be located upstream or downstream of the target gene.

73
Q

Can a gene duplicate be located on the same chromosome?

A

Yes, genes can be duplicated in series on the same chromosome, yielding many copies in a row of the same genetic information. Genes can also exist in parallel on the same chromosome.

74
Q

Lac Operon System in Prokaryotes

A

Lactose is a promoter and glucose is an inhibitor. The lac operon is an inducible system, so it always has a repressor bound to the operator site stopping transcription. In the presence of lactose (and absence of glucose), the lactose binds to the repressor protein causing the repressor complex to unbind from the operator site. Now transcription can occur.
Since glucose is absent, it doesn’t cause second hand inhibition and transcription will occur.

75
Q

Which strand of DNA is complementary to the pre-mRNA transcript?

A

The template DNA strand.

76
Q

Which strand of DNA is identical to the pre-mRNA transcript?

A

The DNA coding strand (non-template strand).
1. If given the mRNA strand, the coding strand is written identical to the mRNA 5’ to 3’ EXCEPT all the U’s are replaced w/ T’s.

77
Q

What is the role of glucose in the Lac Operon system?

A

Glucose acts as an inhibitor, so even if the inducer, lactose, is present the system won’t be turned on because glucose binds to the operator site and inhibits transcription.

78
Q

What are several post-transcriptional modifications?

A

Alternative splicing, addition of 5’ cap, and addition of poly-A tail

79
Q

Why is the genetic code considered unambiguous?

A

The code is unambiguous, because when given a specific codon, there is no ambiguity about which amino acid it will code for. An individual codon represents only one specific amino acid.

80
Q

Why is the genetic code considered degenerative?

A

It is degenerative because for one amino acid, there are several codons which could have been used. 1 amino acid = several codons

81
Q

Two-hit/multiple hit hypothesis of cancer

A

Theory which says multiple mutations must accumulate before a cell becomes cancerous.
(Ex: If a proto-oncogene becomes mutated, the cell might not become cancerous because of the non-mutated tumor suppressor gene. If the tumor suppressor gene also mutates, then the cell becomes cancerous).

82
Q

True or false:
Mutations in somatic cells and germline cells will be passed on to the next generation of offspring.

A

False, only mutations in germline cells are passed on to offspring.

83
Q

In what direction does RNA polymerase read the template strand? In what direction does it synthesize? What about DNA Polymerase

A

Reads in the 3’ to 5’ direction.
It synthesizes mRNA 5’ to 3’.
DNA Polymerase does the same.

84
Q

Explain polycistronic genes/mRNA.

A

mRNA which has multiple translation sites within the gene which can produce multiple different protein products.
ONLY prokaryotes have this ability.

Malika Biochem MCAT (11 decks)

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