Exam 4 GRQs

Point:

A change in a single nucleotide in the DNA sequence.

What is a coactivator?

A coactivator is a protein that helps to activate transcription. Coactivators can interact with transcription factors to increase their ability to activate transcription

Describe the mechanism of nucleotide excision repair.

A damage recognition protein binds to the damaged DNA. An endonuclease cleaves the DNA on either side of the damage. A DNA helicase unwinds the DNA around the damage. An exonuclease removes the damaged nucleotides. A DNA polymerase fills in the gap. A DNA ligase seals the DNA strand.

What is a double stranded break?

A double stranded break (DSB) is a break in both strands of DNA. DSBs can be caused by a variety of factors, including ionizing radiation, chemicals, and errors during DNA replication.

What is the term for a gene that can be turned down or off by a corepressor or inhibitor?

A gene that can be turned down or off by a corepressor or inhibitor is called a repressible gene.

What is the term for a gene that can be turned on or turned up by an inducer?

A gene that can be turned on or turned up by an inducer is called an inducible gene.

What is a merozygote?

A merozygote is a cell that contains a mixture of genetic material from two different strains of bacteria.

What is a mutation?

A mutation is a change in the DNA sequence of an organism. Mutations can be caused by a variety of factors, including environmental exposure, radiation, and errors during DNA replication.

What is a beneficial mutation?

A mutation that gives an organism a selective advantage. This means that the organism with the mutation is more likely to survive and reproduce than organisms that do not have the mutation.

Neutral:

A mutation that has no effect on the phenotype of the organism

Insertion/Deletion:

A mutation that involves the addition or deletion of one or more nucleotides in the DNA sequence.

Transversion:

A point mutation in which a purine is replaced by a pyrimidine or a pyrimidine is replaced by a purine.

Transition:

A point mutation in which a purine is replaced by another purine or a pyrimidine is replaced by another pyrimidine

Missense:

A point mutation that changes the amino acid sequence of the protein that is encoded by the gene.

Nonsense:

A point mutation that creates a premature stop codon, which results in the production of a truncated protein

Silent:

A point mutation that does not change the amino acid sequence of the protein that is encoded by the gene.

What is a polycistronic mRNA?

A polycistronic mRNA is an mRNA molecule that encodes multiple genes. Polycistronic mRNAs are typically found in prokaryotes, such as bacteria.

Repressor:

A repressor is a protein that binds to DNA and prevents transcription from occurring.

What type of transcription factor will bind to a silencer?

A repressor is a type of transcription factor that will bind to a silencer. Silencers are located upstream of the core promoter and can repress transcription from many different promoters

What is a transcription factor?

A transcription factor is a protein that binds to DNA and regulates the transcription of genes. Transcription factors can either activate or repress transcription.

Activator:

An activator is a protein that binds to DNA and promotes transcription from occurring.

What is an inducer and how do inducers work?

An inducer is a small effector molecule that binds to a repressor and prevents it from binding to DNA. This allows transcription to occur.

Frameshift:

An insertion/deletion mutation that changes the reading frame of the DNA sequence. This can result in the production of a truncated protein or a protein with a completely different amino acid sequence.

What is an operon

An operon is a group of genes that are transcribed together into a single mRNA molecule. Operons are often regulated by a single regulatory protein.

What types of DNA damage does base excision repair fix?

Base excision repair (BER) fixes a variety of DNA damage, including deamination, oxidation, and alkylation

Define combinatorial control.

Combinatorial control is the process by which multiple regulatory transcription factors interact with each other to regulate transcription. This type of control is very common in eukaryotic cells.

Which sugar does E. coli prefer to use, glucose or lactose?

E. coli prefers to use glucose over lactose. This is because glucose is a more efficient source of energy

What causes enzyme adaptation?

Enzyme adaptation is the process by which cells change the activity of enzymes in response to changes in the environment. This can be caused by changes in the levels of small effector molecules, or by changes in the structure of the enzyme itself.

What are the 4 levels where eukaryotic genes are commonly regulated?

Epigenetic Transcriptional Post-transcriptional Translational

What is error prone replication?

Error prone replication is a type of DNA replication that is more likely to introduce errors into the DNA. Error prone replication is often used in cells that are under stress, such as cells that are dividing rapidly or cells that have been exposed to DNA damage.

T/F Regulatory elements have to be within 200 bases of the core promoter.

False. Regulatory elements can be located anywhere in the genome, but they are most commonly found within 200 bases of the core promoter.

Define feedback inhibition.

Feedback inhibition is a type of post translational regulation in which the product of a gene inhibits the activity of the enzyme that produced it. This is a way for the cell to regulate the amount of a particular product that is produced.

What is gene regulation?

Gene regulation is the process by which cells control the expression of genes. This means that cells can control whether or not a gene is turned on or off, and how much of the gene product is produced.

Contrast general transcription factors and regulatory transcription factors.

General transcription factors are proteins that are essential for transcription to occur. They bind to the core promoter of a gene and help to recruit RNA polymerase, the enzyme that actually transcribes the gene. Regulatory transcription factors are proteins that bind to DNA sequences that are located upstream of the core promoter. These sequences are called regulatory elements. Regulatory transcription factors can either activate or repress transcription, depending on the sequence they bind to

Describe what would happen to the lac operon in the presence of both glucose and lactose.

In the presence of both glucose and lactose, the lac operon will be turned off. This is because glucose is a more efficient source of energy than lactose, so the bacteria will prefer to use glucose

What can cause a double stranded break?

Ionizing radiation Chemicals Errors during DNA replication

What is a mediator?

Mediator is a large protein complex that helps to coordinate the activities of transcription factors and other proteins that are involved in transcription. Mediator is essential for transcription to occur.

How do mismatch repair systems tell the newly synthesized strand from parent strand?

Mismatch repair systems use a process called 'strand discrimination' to tell the newly synthesized strand from the parent strand. Strand discrimination is based on the fact that the newly synthesized strand is more likely to have mismatches than the parent strand.

Where, outside the coding sequence of a gene, could a mutation have an impact gene expression?

Mutations can have an impact on gene expression outside of the coding sequence in a number of ways. For example, mutations in regulatory regions can alter the expression of a gene, and mutations in introns can affect the splicing of the RNA transcript.

Which method of double strand break repair may result in mutation?

NHEJ is the method of double strand break repair that may result in mutation. This is because NHEJ does not require a homologous DNA molecule as a template, so it can introduce errors into the DNA.

Negative control:

Negative control is a type of gene regulation in which a repressor protein binds to DNA and prevents transcription from occurring.

Do all mutations harm the organism? Explain.

Not all mutations harm the organism. Some mutations have no effect, while others can be beneficial or even necessary for evolution. For example, the mutation that gave humans the ability to digest lactose is a beneficial mutation.

What type of DNA damage does nucleotide excision repair fix?

Nucleotide excision repair (NER) fixes bulky DNA lesions, such as thymine dimers.

How do operons relate to polycistronic mRNA?

Operons are often associated with polycistronic mRNAs. This is because the genes in an operon are often involved in the same biochemical pathway. For example, the lac operon encodes the genes that are required for the metabolism of lactose.

Positive control:

Positive control is a type of gene regulation in which an activator protein binds to DNA and promotes transcription from occurring.

What are the functions of promoters and terminators in operons?

Promoters are sequences of DNA that RNA polymerase binds to in order to initiate transcription. Terminators are sequences of DNA that RNA polymerase binds to in order to terminate transcription.

The binding of other proteins:

Regulatory transcription factor proteins can be activated or inhibited by the binding of other proteins. For example, the binding of a coactivator protein can activate a transcription factor, while the binding of a repressor protein can inhibit a transcription factor.

What do regulatory transcription factors bind to?

Regulatory transcription factors bind to specific DNA sequences that are located upstream of the core promoter of a gene. These sequences are called regulatory elements

Describe two methods of translational regulation.

Repression: This is the process of preventing the translation of an mRNA. This can be done by binding a protein to the mRNA and preventing the ribosome from binding to the mRNA. In attenuation: This is the process of causing premature termination of translation. This can be done by a sequence of DNA within the mRNA that causes the ribosome to prematurely terminate translation.

How do small effector molecules play a role in transcriptional regulation?

Small effector molecules are molecules that can bind to proteins and change their activity. These molecules can play a role in transcriptional regulation by binding to repressors or activators and changing their ability to bind to DNA.

Compare spontaneous and induced mutations.

Spontaneous mutations are mutations that occur naturally, without any exposure to environmental factors. They are caused by errors during DNA replication or by chemical reactions that damage DNA. Induced mutations are mutations that are caused by exposure to environmental factors such as radiation or chemicals. These mutagens can damage DNA, leading to mutations.

What is the name of the DNA sequence that a transcription factor that is an activator will bind to?

The DNA sequence that a transcription factor that is an activator will bind to is called an enhancer. Enhancers are located upstream of the core promoter and can activate transcription from many different promoters.

How does the attenuator impact the trp operon?

The attenuator is a sequence of DNA that is located within the trp operon. The attenuator can affect the translation of the trp operon by causing premature termination of transcription. When the level of tryptophan in the cell is high, the attenuator is active and causes premature termination of transcription. This prevents the cell from producing too much tryptophan. When the level of tryptophan in the cell is low, the attenuator is inactive and transcription of the trp operon can continue.

We've learned the regulatory transcription factor proteins play roles in modulating the transcription levels of genes. How are the regulatory transcription factor proteins themselves modulated?

The binding of other proteins The phosphorylation of specific amino acids The presence of small molecules

Describe the process of nonhomologous end joining (NHEJ).

The ends of the DNA molecule are trimmed. The ends of the DNA molecule are joined together. The DNA is repaired by DNA ligase.

How does the expression level of constitutive genes change over time?

The expression level of constitutive genes can change over time in response to changes in the environment. For example, if a bacterium is exposed to a nutrient that it needs, it may increase the expression of genes that are involved in the uptake and metabolism of that nutrient.

Is the lac repressor a cis or trans acting factor?

The lac repressor is a cis acting factor. This means that it must be bound to the operator site in order to prevent transcription from occurring. This means that it must be present in the DNA in order to prevent transcription from occurring.

What is the lac repressor? What gene encodes the lac repressor?

The lac repressor is a protein that binds to the operator site of the lac operon and prevents transcription from occurring. The lac repressor is encoded by the lacI gene.

What does the lac repressor on its own do?

The lac repressor on its own binds to the operator site of the lac operon and prevents transcription from occurring.

What is the difference between a mutation in a somatic cell vs. one in a germ cell?

The main difference between a mutation in a somatic cell and a mutation in a germ cell is that mutations in somatic cells are only passed on to the cells that are descended from the mutated cell. Mutations in germ cells, on the other hand, can be passed onto offspring.

What kind of mutation does the mismatch repair system fix?

The mismatch repair system fixes mismatches that occur during DNA replication. Mismatch repair is a very important DNA repair system because it helps to maintain the accuracy of the genome.

Describe the mechanism of mismatch repair, include the names of the proteins that are used in prokaryotes and their roles in the process.

The mismatch repair system in prokaryotes is made up of three proteins: MutS, MutL, and MutH. MutS binds to mismatches, MutL binds to MutS, and MutH cleaves the DNA strand at the site of the mismatch. The DNA is then repaired by DNA polymerase and DNA ligase.

How many new mutations are likely present in your DNA that are not in your parents?

The number of new mutations that are likely present in your DNA that are not in your parents depends on a number of factors, including your age, your exposure to environmental mutagens, and your genetic makeup. However, it is estimated that each person has about 100 to 1,000 new mutations in their DNA that are not in their parents

The phosphorylation of specific amino acids:

The phosphorylation of specific amino acids in a transcription factor can also activate or inhibit the protein. For example, the phosphorylation of a serine residue in a transcription factor can activate the protein, while the phosphorylation of a threonine residue can inhibit the protein.

How does the position of a gene impact its expression?

The position of a gene can impact its expression in a number of ways. For example, genes that are closer to the transcription start site are more likely to be transcribed than genes that are further away. Additionally, genes that are located in regulatory regions are more likely to be affected by mutations that alter the expression of the gene.

The presence of small molecules:

The presence of small molecules, such as hormones, can also modulate the activity of transcription factor proteins. For example, the binding of a hormone to a receptor protein can activate a transcription factor, which in turn can increase the transcription of genes that are involved in the response to that hormone.

How does the regulation of the lac operon allow the bacteria to respond to environmental change?

The regulation of the lac operon allows the bacteria to respond to environmental change by allowing the bacteria to only produce the enzymes that are needed to metabolize lactose when lactose is present in the environment

One of the core tenants of biology is "Structure fits function." Explain how the structure of regulatory transcription factors fit their function.

The structure of regulatory transcription factors fits their function in a number of ways. First, the DNA-binding domain of a transcription factor binds to a specific DNA sequence. This specificity is determined by the amino acid sequence of the DNA-binding domain. Second, the transactivation domain of a transcription factor activates transcription. The transactivation domain is usually located in a separate region of the protein from the DNA-binding domain.

What is the function of a transactivation domain?

The transactivation domain is a region of a transcription factor protein that activates transcription. The transactivation domain interacts with other proteins that are involved in transcription, such as RNA polymerase and coactivators.

What is the function of the trp operon?

The trp operon encodes the genes that are required for the synthesis of the amino acid tryptophan.

How does the trp repressor regulate transcription of the trp operon?

The trp repressor is a protein that binds to the operator site of the trp operon and prevents transcription from occurring. When the level of tryptophan in the cell is low, the trp repressor is inactive and transcription of the trp operon can occur. When the level of tryptophan in the cell is high, the trp repressor is active and transcription of the trp operon is prevented.

Describe the process of homologous recombination repair (HRR)?

The two DNA molecules are aligned. The DNA is cleaved at the site of the break. The DNA is exchanged between the two molecules. The DNA is repaired by DNA polymerase and DNA ligase.

Define wild type and mutant alleles.

The wild type allele is the most common allele in a population, and it is the allele that is considered to be "normal." The mutant allele is any other allele that is different from the wild type allele.

How many different genes could lead to the condition xeroderma pigmentosum?

There are at least 7 different genes that could lead to the condition xeroderma pigmentosum. These genes are involved in different steps of nucleotide excision repair.

Why would a bacterium want to change the expression level of a gene?

There are many reasons why a bacterium might want to change the expression level of a gene. For example, a bacterium might want to increase the expression of a gene if it needs to produce more of a particular protein. Or, a bacterium might want to decrease the expression of a gene if it is producing too much of a particular protein.

What are two methods through which double stranded breaks can be repaired?

There are two main methods through which double stranded breaks can be repaired: homologous recombination repair (HRR) and nonhomologous end joining (NHEJ).

Base analogues:

These are molecules that are similar to the natural bases in DNA. However, they can mispair with other bases during DNA replication, leading to mutations.

Intercalating agents:

These are molecules that can insert themselves between the base pairs of DNA. This can cause the DNA to become distorted, leading to mutations.

Base excision and nucleotide excision repair:

These two types of repair systems repair DNA damage by removing the damaged base and replacing it with the correct base

Oxidative DNA damage:

This type of mutation occurs when DNA is damaged by free radicals. Free radicals are unstable molecules that can damage DNA by reacting with the bases. This can lead to mutations.

Base modification:

This type of mutation occurs when a base is chemically modified. This can be caused by exposure to chemicals such as nitrous acid or alkylating agents.

Depurination:

This type of mutation occurs when a purine base (adenine or guanine) is lost from DNA. This can happen due to chemical reactions that break the bonds between the base and the sugar-phosphate backbone of DNA.

Deamination:

This type of mutation occurs when a pyrimidine base (cytosine or thymine) is deaminated. This means that the amino group (-NH2) is removed from the base, leaving a keto group (-C=O). This can change the base's chemical properties, making it more likely to mispair with another base during DNA replication.

Tautomeric shift:

This type of mutation occurs when a pyrimidine base undergoes a chemical change that causes it to exist in two different forms. These forms are called tautomers. If the wrong tautomer is incorporated into DNA during replication, it can lead to a mutation.

Ionizing radiation:

This type of radiation can damage DNA by breaking the bonds between the base and the sugar-phosphate backbone of DNA

Non-ionizing radiation:

This type of radiation can damage DNA by causing the bases to become unstable. This can lead to mutations

Direct repair:

This type of repair system repairs DNA damage by directly reversing the damage. For example, if a base is deaminated, this type of repair system can replace the deaminated base with the correct base.

Nonhomologous end joining:

This type of repair system repairs DNA damage by joining the ends of the DNA molecule together.

Homologous recombination:

This type of repair system repairs DNA damage by using a homologous DNA molecule as a template to repair the damaged DNA.

Mismatch repair:

This type of repair system repairs mismatches that occur during DNA replication.

What mechanism of repair can fix thymine dimers?

Thymine dimers can be fixed by nucleotide excision repair (NER). NER is a DNA repair mechanism that removes damaged nucleotides from DNA.

Prokaryotic cells regulate their genes to respond to changes in the environment. Why do eukaryotic cells regulate their genes?

To respond to changes in the environment, just like prokaryotic cells. To differentiate into different cell types. To repair damaged DNA. To control the expression of genes that are involved in diseases.

At what points can gene regulation occur?

Transcription: This is the process by which DNA is copied into RNA. Gene regulation can occur at the level of transcription by controlling whether or not a gene is transcribed into RNA. Translation: This is the process by which RNA is translated into protein. Gene regulation can occur at the level of translation by controlling how much of a gene product is produced. Post-translational modification: This is the process by which proteins are modified after they are translated. Gene regulation can occur at the level of post-translational modification by controlling how a gene product is modified.

What is the difference between translational and post translational regulation?

Translational regulation is the regulation of gene expression at the level of translation. This means that the regulation occurs after transcription has occurred and the mRNA has been produced. Post translational regulation is the regulation of gene expression after translation has occurred and the protein has been produced.

How can a trinucleotide repeat cause a mutation?

Trinucleotide repeats are sequences of three nucleotides that are repeated multiple times in DNA. These repeats can be unstable, and they can expand or contract over time. If a trinucleotide repeat expands, it can lead to a mutation. For example, if a trinucleotide repeat that normally repeats 10 times expands to 11 times, this can change the amino acid sequence of the protein that is encoded by the gene.

T/F Regulatory elements need to be upstream of the core promoter.

True. Regulatory elements need to be upstream of the core promoter in order to regulate transcription.

What is up regulation? Down regulation?

Upregulation is the process of increasing the transcription of a gene. Downregulation is the process of decreasing the transcription of a gene.

What happens to the lac repressor when allolactose is added to the cell?

When allolactose is added to the cell, it binds to the lac repressor and changes its shape. This change in shape prevents the lac repressor from binding to the operator site, which allows transcription to occur.

Describe in detail how the presence of lactose impacts the lac operon.

When lactose is present in the environment, it binds to the lac repressor and changes its shape. This change in shape prevents the lac repressor from binding to the operator site, which allows transcription to occur. Transcription of the lac operon results in the production of the enzymes that are needed to metabolize lactose.

Compare intragenic and intergenic suppressors.

are mutations that occur within the same gene as the original mutation. These mutations can suppress the effects of the original mutation, making the organism more functional.