Cell Bio Exam 2 study guide

What is the mismatch repair system?

System that corrects errors made by DNA polymerase during DNA replication.

How does the mismatch repair system correct errors?

By replacing incorrect bases with correct ones.

What is a replication error?

An incorrect base insertion during DNA replication.

What is the order of events for mismatch repair?

1. Recognition of DNA damage

2. Identification of newly synthesized strand - existing nick in the sugar-phosphate backbone

3. removal of a segment of the new strand - endonuclease activity by repair proteins

4. filling the gap - by repair DNA polymerase

5. sealing the strand - by DNA ligase

What can prolonged exposure to ultraviolet light cause?

Damage to DNA and formation of thymine dimers.

What are thymine dimers? What can replication of thymine dimers cause?

Covalent links between two thymine bases on the same DNA strand.

Replication can stall DNA replication machinery.

How do repair proteins recognize thymine dimers?

As a distortion in the DNA backbone.

What is nonhomologous end joining?

A form of DNA repair used for double-strand breaks.

What is the result of nonhomologous end joining?

Loss of information at the site of repair.

How does nonhomologous end joining repair double-strand breaks?

By rejoining the broken ends of DNA.

What 3 things can nonhomologous end joining cause?

Loss of nucleotides, translocation of DNA fragments, and disruption of gene expression.

What is homologous recombination?

A mechanism for repairing double-strand breaks in DNA.

What happens during homologous recombination?

Double-strand breaks are repaired using a homologous DNA molecule as a template.

What is DNA replication machinery?

The cellular machinery responsible for copying DNA.

What is the proofreading ability of DNA replication machinery?

Ability to correct mistakes made during DNA replication.

What is the most common dimer formed by UV light exposure?

Thymine dimer.

What can thymine dimers cause?

Stalling of DNA replication machinery.

What is the purpose of DNA ligase?

To seal the repaired DNA strand.

What is an endonuclease?

An enzyme that cleaves DNA at internal sites.

What is the role of the backup copy of DNA in homologous recombination?

Used as a template to fix double strand DNA breaks.

What is required for homologous recombination to occur?

Long stretch of DNA with sequence similarity, nucleases, and 3' DNA strand overhangs.

How is RNA different from DNA?

Single stranded, contains uracil instead of thymine.

What are the bases present in RNA?

Uracil, Adenine, Guanine, and Cytosine.

What are the bases present in DNA?

adenine, guanine, cytosine, thymine

What is the difference in sugar between RNA and DNA?

RNA contains ribose sugar, DNA contains deoxyribose sugar.

How is transcription by RNA polymerase similar to DNA replication by DNA polymerase?

Both occur in the 5' to 3' direction.

What does RNA polymerase catalyze?

Linkage of ribonucleotides.

What does DNA polymerase catalyze?

Linkage of deoxyribonucleotides.

What can RNA polymerase do that DNA polymerase cannot?

Unwind DNA and catalyze phosphodiester bonds between nucleotides

What is the role of helicase in DNA replication?

Unwinds the DNA strands for DNA polymerase.

Can RNA polymerase make a new RNA molecule without a primer?

Yes.

Does DNA polymerase require a primer?

Yes.

Does RNA polymerase proofread its work?

No.

Does DNA polymerase proofread its work?

Yes.

Can genes be transcribed by RNA polymerase with different efficiencies or rates?

Yes.

Can an RNA polymerase begin synthesizing from a gene before a previously bound RNA polymerase has completed synthesis of that gene?

Yes.

What is the difference between ribose sugar and deoxyribose sugar?

Ribose sugar has an additional hydroxyl group.

Where would a new ribonucleotide be attached on a growing RNA strand by RNA polymerase?

To the ribose sugar.

What is the role of transcriptional regulators in eukaryotic gene expression?

Influence transcription by binding to regulatory sequences.

How do eukaryotic genes differ from prokaryotic genes in terms of response to signals?

Eukaryotic genes can respond to a greater variety of signals.

What is combinatorial control in eukaryotic gene expression?

Integration of signals by different transcriptional regulators.

What is the function of sigma factor in bacteria RNA polymerase?

Recognizes promoter sites in DNA.

How does bacteria RNA polymerase differ from eukaryotic RNA polymerase in terms of initiation of transcription?

Bacteria RNA polymerase can initiate transcription on its own, while eukaryotic RNA polymerase requires general transcription factors.

What is the role of TFIIH in eukaryotic transcription?

Phosphorylates the C-terminal tail of RNA polymerase II.

What is the function of the TATA box in eukaryotic gene expression?

Bound by TBP of TFIID and located at the promoter region.

What modifications occur to eukaryotic mRNA before export from the nucleus?

Addition of 7' methyl guanosine, polyadenylation of 3' end, removal of introns by spliceosome, and dissociation of RNA polymerase.

What are introns and exons?

Introns are non-coding regions of DNA that are removed during RNA processing, while exons are coding regions that are expressed in the final RNA molecule.

What is the function of the spliceosome?

The spliceosome function is responsible for removing introns from eukaryotic genes during RNA processing.

What are small nuclear RNAs (snRNAs)?

snRNAs are RNA molecules that are part of the spliceosome and catalyze the removal of introns from eukaryotic genes.

How do snRNAs bind to intron-exon boundaries?

snRNAs bind to specific sequences at the intron-exon boundaries through complementary base pairing.

What is the purpose of splicing?

Splicing allows for the production of different proteins from the same eukaryotic gene through alternative splicing.

What is the genetic code?

The genetic code is the set of rules that determines how the nucleotide sequence of a gene is translated into the amino acid sequence of a protein.

How many codons encode for amino acids?

There are 61 codons that encode for the 20 amino acids.

How many stop codons are there?

There are three stop codons that signal the end of protein synthesis.

Why is the genetic code considered redundant?

The genetic code is redundant because multiple codons can encode for the same amino acid.

Which amino acids are encoded by a single codon?

Methionine and tryptophan are the only amino acids that are encoded by a single codon.

What are ribosomes composed of?

Ribosomes are composed of rRNA and proteins.

Where are ribosomes synthesized?

Ribosomes are synthesized, in part, in the nucleolus within the nucleus.

What is the function of rRNA within the ribosome?

rRNA within the ribosome has peptidyl transferase activity and catalyzes the formation of peptide bonds.

How many tRNAs can a ribosome bind at a time?

A ribosome can bind multiple tRNAs at a time.

How do eukaryotic ribosomes find the translation start site?

Eukaryotic ribosomes scan the 5' end of the mRNA in search of the start codon.

What is the difference between eukaryotic and prokaryotic mRNA translation?

In eukaryotes, a single mRNA is translated into a single protein, while in prokaryotes, a single mRNA can be translated into several proteins.

What is unique about prokaryotic mRNA?

Prokaryotic mRNA is not polyadenylated at the 3' end and does not contain a 5' cap.

Can a ribosome bind to an RNA in prokaryotes?

Yes, ribosomes can bind to an RNA in prokaryotes.

What is gene expression?

Mechanism for transcribing and translating genes.

What is the role of RNA polymerase II?

Transcribes genes that encode for mRNA and proteins.

What is the function of the proteasome?

Degrades damaged or unneeded proteins.

How does the proteasome recognize proteins for degradation?

By the attachment of ubiquitin chains.

What is the role of the 19S particle in the proteasome?

The role is that this recognizes ubiquitin and unfolds proteins for degradation.

What is the central cylinder of the proteasome?

Contains proteases that break down proteins.

What is the wobble position in tRNA?

Third position that can tolerate a mismatch in base pairing.

How do tRNAs with multiple codon base pairing work?

Accurate base pairing required at first two positions.

What is the role of transcription regulators?

Bind to DNA to regulate gene transcription.

How do transcription regulators bind to DNA?

Form hydrogen bonds, ionic bonds, and hydrophobic interactions.

Where do transcription regulators bind on the DNA helix?

In the major groove.

Does the binding of transcription regulators disrupt the DNA helix?

No, it does not disrupt the hydrogen bonds holding the helix together.

What is the role of RNA polymerase during translation?

Starts translation before transcription is complete.

What determines the functionality and identity of a cell?

Expressed RNAs and proteins.

What type of genes does RNA polymerase II transcribe?

Genes that encode for mRNA and proteins.

What types of proteins are targeted by the proteasome?

Damaged, misfolded, or unneeded proteins.

What is the main function of the proteasome?

Degrade proteins.

What is the function of the 19S particle in the proteasome?

Recognize ubiquitin and unfold proteins for degradation.

What is the function of tRNA?

Carry amino acids to the ribosome during translation.

What are operons?

Clusters of genes transcribed as a single RNA.

Where are operons commonly found?

In bacteria, not as common in eukaryotes.

What controls operons?

Operators and promoters.

What is the function of an operator?

To bind a repressor.

What is the function of a promoter?

To initiate transcription.

What is the structure of mRNA in an operon?

Polycistronic (single mRNA for multiple genes).

Why are genes with related functions clustered together in an operon?

To allow coordinated regulation of their transcription.

What is an operator in an operon?

A base sequence to which a repressor binds.

What is the tryptophan operator?

The base sequence bound by the tryptophan repressor.

When does the tryptophan repressor bind to the tryptophan operator?

When the repressor is bound to tryptophan.

How is the lactose operon regulated?

By the CAP activator, lactose repressor, and presence of lactose and glucose.

When will the Lac operon not be transcribed?

When lactose is not present.

When will the Lac operon produce RNA?

When lactose is present and glucose is absent.

Does the lactose repressor bind to the operator when lactose is present?

No.

How are eukaryotic genes regulated?

By proximal control elements, enhancers, and silencers.

What is the role of transcriptional regulators in eukaryotic gene regulation?

They bind to enhancers and silencers and influence transcription

How do transcriptional regulators impact transcription at the core promoter?

By forming loops in the intervening DNA and binding to Mediator.