Lesson 5 - Transcription, Translation and DNA Repair

DNA Polymerase I is an ____________________, and DNA Polymerase III is an ____________________.

Exonuclease, exonuclease

True or false? DNA Ligase, which is also involved in linking Okazaki Fragments, can also proofread the DNA.

False

What is the function of small nucleolar RNA (snoRNA) versus small nuclear RNA (snRNA)?

snoRNA guides covalent modifications of rRNA, tRNA, and small nuclear RNA through methylation and pseudouridylation. snRNA processes pre-mRNA in the nucleus aide in the regulation of RNA polymerase and transcription factors and help maintain telomeres.

What specific structure binds to the codon? Does anything else bind to this structure?

tRNA has an anti-codon that binds to the codon. The corresponding amino acid is also bound to the tRNA. For every amino acid, there is one tRNA.

There are only three steps to Nucleotide Excision Repair. What are they?

(1) Endonuclease removes pyrimidine dimer and surrounding nucleotides (2) DNA Polymerase will fill in the gap with the proper nucleotides (3) DNA Ligase will repair the backbone by connecting the new nucleotides to the old nucleotides

What would be the mRNA strand from the template strand:3'-TACTAG-5'? (A) 5'-AUGAUC-3' (B) 5'-ATGATC-3' (C) 5'-GAUCAU-3' (D) 5'-GACTAT-3'

(A) 5'-AUGAUC-3'

Which of the following is NOT a possible name for the site where the Glycosylase Enzyme has removed the affected base? (A) Anucleotidic site (B) Apurinic site (C) Apyrimidinic site (D) Abasic site

(A) Anucleotidic site Once the base has been removed, that site lacking a base can be called an Apurinic/Apyrimidic Site (AP Site) or an Abasic Site.

After post-transcriptional modifications are complete, where will the mature mRNA go next? (A) Cytosol (B) Golgi (C) Nucleolus (D) Lysosome

(A) Cytosol

Which DNA Polymerase is responsible for removing the RNA Primer during replication? (A) DNA Polymerase I (B) DNA Polymerase II (C) DNA Polymerase III (D) DNA Polymerase IV

(A) DNA Polymerase I

DNA replication is: (A) Fast and precise (B) Fast but not precise (C) Slow and precise (D) Slow but not precise

(A) Fast and precise

In Prokaryotes, where does the small Ribosomal Subunit first bind for translation? (A) Shine-Dalgarno Sequence (B) TATA box (C) TATAAT (D) Inititator sequence

(A) Shine-Dalgarno Sequence The Shine Dalgarno-sequence is in the 5' untranslated region of the RNA, and is where the small Ribosomal Subunit first binds.

The spliceosome splices introns through: (A) Two sequential transesterification reactions followed by a ligation reaction. (B) Two sequential ligation reactions followed by a transesterification reaction. (C) One transesterification reaction followed by two sequential ligation reactions. (D) One ligation reaction followed by a two sequential transesterification reactions.

(A) Two sequential transesterification reactions followed by a ligation reaction.

Which of the following is the proper term for any compound that can cause mutations? (A) Cancerous (B) Mutagen (C) Carcinogen (D) None of the above

(B) Mutagen This differs from a Carcinogen, which would aid in the process of tumor development in general.

What enzyme is responsible for constructing mRNA using DNA as a template? (A) DNA Polymerase (B) RNA Polymerase (C) DNA Transcriptase (D) RNA Transcriptase

(B) RNA Polymerase

Introns are removed via a process known as __________________. (A) Dicing (B) Splicing (C) Cutting (D) Crossing

(B) Splicing

Which of the following nitrogenous bases is NOT found in mRNA? (A) A (B) T (C) C (D) G

(B) T

Typically ncRNA plays a role in which two processes? (A) Synthesis and Replication (B) Translation and Transcription (C) Translation and Replication (D) Replication and Transcription

(B) Translation and Transcription Typically ncRNA plays a role in translation and transcription.

What is the spliceosome composed of? (A) snRNA and snoRNA (B) snRNA and snRNP (C) snoRNA and snRNP (D) snRNA and miRNA

(B) snRNA and snRNP A spliceosome is a complex protein composed of small nuclear RNA (snRNA) and small nuclear ribonucleic proteins (snRNP) and it is responsible for post-transcriptional splicing of introns in mRNA.

Since DNA Ligase does not have Proofreading capabilities, which of the following is most likely to have mutations? (A) Beginning of a strand (B) Leading Strand (C) Lagging Strand (D) End of a strand

(C) Since DNA Ligase does not have Proofreading capabilities, the lagging strand is most likely to have mutations.

miRNA may silence gene expression through which of the following methods? I. Blocking translation II. mRNA modification III. mRNA degradation (A) I Only (B) I and II Only (C) I and III Only (D) I, II, and III

(C) I and III Only miRNA may silence gene expression through blocking translation or mRNA degradation. miRNA will not modify mRNA sequences.

What are the primary components of a ribosome? I. tRNA II. rRNA III. Proteins

(C) II and III Only A ribosome is composed of proteins and ribosomal RNA (rRNA).

The t-RNA with the anticodon of UAC will initially bind at which site within the ribosome? (A) A-site (B) E-site (C) P-site (D) S-site

(C) P-site UAC is the anticodon for AUG, which is the start codon. This tRNA molecule carries methionine into the P site to start the translation process.

After replication is completed, there is a thymine base-paired with a guanine. What will fix this issue? (A) The DNA Polymerase III Proofreading Mechanism (B) The Base Excision Repair Mechanism (C) The Mismatch Repair Mechanism (D) The Nucleotide Excision Repair Mechanism

(C) The Mismatch Repair Mechanism The mismatch repair mechanism happens after DNA replication. Through this mechanism, mismatches in the DNA sequence missed by the DNA polymerases during replication

Which of the following is the umbrella term for "functional RNA that does not get translated into a protein"? (A) miRNA (B) snoRNA (C) ncRNA (D) siRNA

(C) ncRNA

Which organelle might be considered a potential producer of endogeneous agents? (A) Golgi Apparatus (B) Cytosol (C) Cell Membrane (D) Mitochondria

(D) Mitochondria

Which repair mechanism is responsible for fixing Pyrimidine Dimers? (A) The DNA Polymerase III Proofreading Mechanism (B) The Base Excision Repair Mechanism (C) The Mismatch Repair Mechanism (D) The Nucleotide Excision Repair Mechanism

(D) The Nucleotide Excision Repair Mechanism

Which of the following is not a modification made to pre-mRNA before it becomes mature mRNA? (A) The addition of 5' cap (B) The addition of the poly-A tail (C) The splicing of introns (D) The removal of telomeric mRNA

(D) The removal of telomeric mRNA

You look into a microscope and see a pyrimidine dimer in DNA. What has the DNA likely been exposed to? (A) X-rays (B) Visible Light (C) Infrared Light (D) Ultraviolet Light

(D) Ultraviolet Light You can conclude that the DNA has been exposed to UV rays because UV rays cause the formation of pyrimidine dimers.

RNA Polymerase reads the template strand in the _______ direction, and RNA is generated in the ________ direction.

3' to 5' 5' to 3'

Eukaryotes contain a 5' cap and a poly-A tail to protect their mRNA. Compare the composition of these two structures.

5' cap is methylated guanosine triphosphate poly A tail is a tail with 100-250 adenine repeats

Ribosomes read the mRNA template from the ___ end to the ___ end.

5' end to the 3' end

What is a pyrimidine dimer?

A pyrimidine dimer is a type of DNA damage in which two pyrimidine nucleotides (typically thymine) are stuck together.

What are the three sites on a ribosome? Explain them.

A site P site E site The P site is where the growing polypeptide chain is forming and attaches to the tRNA. The A site is where an incoming tRNA comes to bind to its corresponding codon with its amino acid attached. When the ribosome shifts to the right, the tRNA in the P site moves to the E site or "exit site" and the A site tRNA shifts on codon over, making room for a new tRNA to bind to the next codon with its amino acid.

What is the start codon for translation?

AUG (methionine)

What role does formylmethionine play in the human body?

Acts as an alarm clock and triggers immune response when a bacteria is detected.

What does Adenosine Deaminase Acting on RNA (ADAR) do?

Adenosine Deaminase Acting on RNA (ADAR) is an enzyme involved in RNA editing that converts adenosine residues into inosine via hydrolytic deamination.

What does Cytosine Deaminase Acting on RNA (CDAR) do?

An RNA editing enzyme called Cytosine Deaminase Acting on RNA (CDAR) converts cytosine residues into uridine via deamination.

What is the role of an antioxidant molecule in preventing DNA damage/mutation?

An antioxidant molecule helps protect DNA aganist the damaging effect of reactive oxygen species.

Compare senescence versus apoptosis

Apoptosis = cell death Senescence = cell goes into dormant state and ceases to divide

Why doesn't prokaryotic mRNA need the 5' cap and poly-A tail?

B/c transcription and translation both happen at the same time in the cytosol. It does not travel and therefore does not need extra protection the way eukaryotic cells do.

What is the difference between exonuclease activity and endonuclease activity?

Both involve removing an incorrect nucleotide. Exonuclease activity happens at the end of the strands while endonuclease activity occurs in the middle of the strands

What is the difference between DNA mutations and DNA damage? Think of an example of each.

DNA mutations change the order of the DNA sequence. An example would be a mutation from 5'-ATCG-3' to 5'-AACG-3'. DNA damage is the structural damage to DNA that leaves nucleotides in the correct order. An example of this is a pyrimidine dimer.

What is the difference between endogenous agents vs exogenous agents when talking about DNA damage?

Endogenous agents are internal factors, such as reactive oxygen species found within our own cells, that can cause DNA damage. Exogenous agents are external factors, such as UV rays, gamma rays and x-rays, that can cause DNA damage.

Which enzyme is involved in a nucleotide excision repair? An endonuclease or exonuclease?

Endonuclease b/c the nucleotide needs to be removed from the middle of the DNA strand.

During the process of transcription, the RNA goes through some extra steps such as adding a cap, adding a tail, and the splicing of introns. In which type of cell does this extra processing occur?

Eukaryotes

True or false? Tumor Suppression genes are often described as being a "Two-Hit Model", since the two alleles must be mutated in the same tissue.

False. Need to be mutated in the same cell not the same tissue

True or False? The Shine-Delgarno Sequence acts as a both a 5' cap and a start codon.

False. ribosome binds to shine delgarno sequence. then moves down to start codon AUG and starts translating

True or False? Prokaryotic mRNA does not contain any non-coding regions.

False. From the 5' to 3' end, prokaryotic mRNA contains non-coding mRNA, the Shine-Delgarno Sequence, non-coding mRNA, the start codon, coding mRNA, the stop codon, and then more non-coding mRNA.

True or false? After the ribosome releases the newly-formed proteins, another class of proteins called Chaperones help this protein be transported.

False. After the ribosome releases the newly-formed proteins, another class of proteins called Chaperones help this protein fold properly.

Which stage in the cell cycle is the mismatch repair mechanism active?

G2, after S phase where transcription occurs.

Which of the following may happen to a cell that has accumulated a lot of DNA damage and/or mutations? I. The cell enters a dormant state and cell does not divide anymore II. The cell dies. .III. The cell becomes a cancer cell due to unregulated cell division

I , II and III

Which of the following statements about Base Excision Repair are true? I. Base Excision Repair can detect non-helix distorting mutations II. Base Excision repair will remove the affected base using a Glycosylase Enzyme. III. An AP Endonuclease will then remove the damaged DNA sequence, so DNA polymerase and ligase can finish the repairs.

I II and III

Which of the following are mechanisms that may allow an RNA polymerase to know when to stop transcription? I. RNA polymerase recognizes a known sequence of DNA called a terminator that signals the RNA polymerase to stop transcription. II. mRNA forms a hairpin on itself that impairs the polymerase from moving forward. III. RNA Polymerase receives a signal from telomerase that the DNA template is ending, causing transcription to end.

I and II

Which enzyme(s) is/are responsible for proofreading? I. DNA Polymerase I II. DNA Polymerase II III. DNA Polymerase III

I and III

When DNA Repair processes fail, cancer is likely to follow. Which of the following would likely cause an increased risk of cancer? I. Breaking the DNA backbone II. Altering bases and base pairs III. Incorporating incorrect bases during replication

I, II and III

As the tRNA in the P-site shifts to the E-site, which of the following is true? I. The ribosome shifts towards the 5' end of the mRNA. II. The tRNA in the A-site shifts to the P-site. III. The amino acid from the A-site moves to bind to the polypeptide chain in the P-site.

II Only Why not III? B/c the polypeptide chain moves to bind to the amino acid on the tRNA in the A site

Which enzyme(s) is/are required in proofreading, mismatch repair, and nucleotide excision repair? I. Endonuclease II. DNA Polymerase III. DNA Ligase

II and III

Put the following steps of the Mismatch Repair Mechanism in order: I. DNA Ligase repairs the DNA backbone. II. Exonuclease removes the misplaced nucleotide. III. DNA Polymerase adds the correct nucleotide. IV. The mismatched DNA is marked with a cut.

IV - II - III - I

What is the difference between introns vs. exons in terms of expression?

Introns are not expressed while exons are expressed

Compare Missense, Nonsense and Frameshift Mutations

Missense mutation replaces one amino acid with another Nonsense mutation is when a premature stop codon is added frameshift mutation changes the number of nucleotides, this shifts the sequence after the change and changes all the codons

Transcription in the eukaryotic cell takes place in the ___________ while transcription in the prokaryotic cell takes place in the ___________.

Nucleus Cytosol

How does the mismatch repair mechanism distinguish between the parent strand and the newly synthesized strand that has the mistake on it in bacteria?

Parent strand will have more adenine nucleotides that are methylated.

What is the role of polyadenylate polymerase?

Polyadenylate polymerase is the enzyme responsible for catalyzing the construction of the poly-A tail

During translation in _____________ cells, the first amino acid in the polypeptide chain is formylmethionine. During translation in _________________ cells, the first amino acid in the polypeptide chain is methionine.

Prokaryotic, eukaryotic

__________________ are genes that, if one copy is mutated, then they can cause cancer. ____________ are genes that would need both copies to be mutated to promote cancer.

Proto-oncogenes Anti-oncogenes

What is pseudouridylation?

Pseudouridylation is the addition of an isomer of the nucleoside uridine by small nucleolar RNA (snoRNA).

What is RNA editing?

RNA editing is a post-transcriptional process that may entail the insertion, deletion, and base substitution of nucleotides. This process is quite rare!

What is the function of an micro RNA (miRNA)?

Regulate transcription and post transcription by base pairing with complementary sequences, resulting in gene silencing.

What is the function of the ribosome?

Ribosomes read an mRNA template to produce a polypeptide.

What site does the ribosome recognize and initially bind to in eukaryotic vs. prokaryotic cells?

The ribosome recognizes and binds to the 5' cap of eukaryotic mRNA. The ribosome recognizes and binds to the Shine-Delgarno Sequence of prokaryotic mRNA.

What is the function of the spliceosome?

The spliceosome is responsible for splicing introns out and ligating exons together in making mature mRNA.

What is the difference between the template strand and coding strand in the process of transcription?

The template strand is the strand of DNA that the RNA Polymerase reads as it generates mRNA. The coding strand is not read by RNA Polymerase. Its sequence resembles the newly synthesized strand of mRNA except that the coding strand contains Thymine instead of Uracil.

Because the genetic code is Degenerate and the third nucleotide could be changed and not alter the amino acid coded for, there are also Silent or Degenerate Mutations that do not affect the protein.

True

True or False? Proofreading takes place during replication.

True

True or false? Because Prokaryotes have circular chromosomes, they look like the Greek letter ϴ when being transcribed, and their replication is sometimes called Theta Replication.

True

True or false? The Coding Strand is also called the Sense Strand.

True

True or false? Many rRNA actually form Ribozymes, which are like enzymes that are not made out of proteins.

True Many rRNA actually form Ribozymes, which are like enzymes that are not made out of proteins.

True or false? Base Excision repair would notice if a Cytosine is Deaminated (forming a Uracil) and trigger that repair.

True. Base Excision repair would notice if a Cytosine is Deaminated (forming a Uracil) and trigger that repair.

True or False? The poly-A tail may assist in the termination of transcription.

True. The poly-A tail may assist in the termination of transcription.

How many stop codons are there? What are they?

UGA "U go away" UAA "U are away" UAG "U are gone"

Describe how UV Light and multiple Thymines on the same strand could require the Nucleotide Excision Repair mechanism to function.

UV light can excite the electrons of Thymines and cause neighboring Thymines to bond, forming a Thymine Dimer, distorting the double-helix and proper functions. The Nucleotide Excision Repair mechanism will recognize this error and replace the affected DNA section.