BIO151 Exam 2 Study Guide: Translation and Gene Regulation

What is the difference between transcription and translation in prokaryotic cells?

Both transcription and translation occur simultaneously in the cytoplasm.

Where do transcription and translation occur in eukaryotic cells?

Transcription occurs in the nucleus, while translation occurs in the cytoplasm.

What modifications must occur to eukaryotic mRNAs before translation?

Eukaryotic mRNAs must undergo capping (5' cap addition), polyadenylation (poly-A tail addition), and splicing (removal of introns). These modifications protect mRNA and facilitate its export from the nucleus.

Define exon and intron.

Exons are coding regions of a gene that are retained in the mature mRNA, while introns are non-coding regions that are removed during RNA splicing.

Can one gene encode multiple proteins?

Yes, one gene can encode multiple proteins through alternative splicing, where different combinations of exons are joined together.

What biological macromolecules make up the spliceosome?

The spliceosome is composed of small nuclear RNAs (snRNAs) and proteins.

What is RNA splicing?

RNA splicing is the process of removing introns from pre-mRNA and joining exons together to form mature mRNA.

What are the rules regarding splicing?

Exons cannot be chopped out, introns must be removed, and the order of exons generally cannot be changed.

What advantages does splicing provide to organisms?

Splicing allows for the production of multiple protein variants from a single gene, increasing protein diversity and adaptability.

How do RNAs exit the nucleus in eukaryotes?

RNAs exit the nucleus through nuclear pores after being processed and exported.

What is a codon and how many nucleotides does it contain?

A codon is a sequence of three nucleotides that corresponds to a specific amino acid.

Are codons overlapping or non-overlapping?

Codons are non-overlapping.

What is the significance of the reading frame in translation?

The reading frame determines how the sequence of nucleotides is divided into codons for translation.

How many reading frames are there in a single stranded nucleic acid?

There are three possible reading frames in a single stranded nucleic acid.

What determines the reading frame used for translation?

The starting point of translation (the start codon) determines the reading frame.

What does UTR stand for?

UTR stands for Untranslated Region.

How many types of RNA are required for the process of translation?

Three types of RNA are required: mRNA, tRNA, and rRNA.

Why are tRNAs referred to as 'adaptor' molecules?

tRNAs are called adaptor molecules because they connect specific amino acids to their corresponding codons on the mRNA.

What is the relationship between an mRNA codon and a tRNA anticodon?

The tRNA anticodon is complementary to the mRNA codon, allowing for accurate translation.

What is the impact of a mutation in the anticodon of a tRNA molecule?

If a mutation occurs in the anticodon but the tRNA is charged with the original amino acid, it may lead to incorrect pairing with the mRNA codon, potentially resulting in a faulty protein.

What do aminoacyl-tRNA synthetases do?

Aminoacyl-tRNA synthetases catalyze the formation of a covalent bond between an amino acid and its corresponding tRNA.

What is the significance of the first and last amino acids in a newly translated polypeptide?

The first amino acid is typically methionine, while the last amino acid varies depending on the stop codon.

What do aminoacyl-tRNA synthetases catalyze the formation of?

A covalent bond between an amino acid and its corresponding tRNA.

Where does the energy for the bond formation by aminoacyl-tRNA synthetases come from?

The energy comes from the hydrolysis of ATP.

What is meant by the term 'third base wobble'?

It refers to the flexibility in base pairing at the third position of a codon, allowing for some tRNAs to recognize multiple codons.

How does the third base wobble relate to the number of amino acids and codons?

There are 20 amino acids but 64 different codons, allowing for redundancy in the genetic code.

How can two species encode identical proteins with different DNA sequences?

Through variations in the DNA sequence that do not affect the protein's amino acid sequence, often due to synonymous mutations.

If two species have proteins that differ by a single amino acid, how can you determine possible mutations?

By using a codon table to identify nucleotide changes that could lead to the different amino acid.

What is a ribosome?

A ribonucleoprotein complex that synthesizes proteins by translating mRNA.

Where are ribosomes found in prokaryotic and eukaryotic cells?

In prokaryotic cells, ribosomes float freely in the cytoplasm; in eukaryotic cells, they are found in the cytoplasm and attached to the endoplasmic reticulum.

What are the three sites in the ribosome and their functions?

The A site (aminoacyl site) holds the tRNA with the next amino acid, the P site (peptidyl site) holds the tRNA with the growing peptide chain, and the E site (exit site) is where tRNAs exit the ribosome.

In what order does the mRNA codon pass through the ribosomal sites?

The mRNA codon passes through the A site first, then the P site, and finally the E site.

Which end of the mRNA gets loaded into the ribosome first?

The 5' end of the mRNA.

What codon, anti-codon, and tRNA are required to begin translation?

The start codon (AUG), the anti-codon (UAC), and the initiator tRNA (methionine tRNA) are required.

In which ribosomal site does translation initiation occur?

Translation initiation occurs in the P site.

How is translation initiated?

By the binding of the initiator tRNA to the start codon on the mRNA in the ribosome.

How is translation terminated?

Translation is terminated when a stop codon is reached, leading to the release of the polypeptide chain.

What type of bond formation does the ribosome catalyze?

The ribosome catalyzes peptide bond formation.

Is there a tRNA that associates with a stop codon?

No, there is no tRNA for stop codons.

What is a release factor?

A protein that recognizes stop codons and promotes the release of the newly synthesized polypeptide from the ribosome.

What is differential gene expression?

The process by which cells with identical DNA can express different genes, leading to different cell types.

At what points in gene expression can regulation occur?

Regulation can occur during transcription, RNA processing, translation, and post-translational modifications.

What are cis-acting and trans-acting factors?

Cis-acting factors are DNA elements that regulate gene expression, while trans-acting factors are proteins that bind to these elements.

What is an operon?

A cluster of genes under the control of a single promoter, common in prokaryotes, allowing coordinated expression.

What is the Shine-Dalgarno sequence?

A ribosomal binding site in bacterial mRNA that is essential for the initiation of translation.

How many promoters, start codons, stop codons, and Shine-Dalgarno sequences are needed for an operon encoding five different proteins?

One promoter, five start codons, five stop codons, and five Shine-Dalgarno sequences.

What are activators and repressors?

Activators enhance gene expression, while repressors inhibit it; both are types of trans-acting factors.

What are enhancers and silencers?

Enhancers increase transcription levels, while silencers decrease them; both are cis-acting elements.

Can cis-acting factors alone regulate transcription?

No, they typically require trans-acting factors to function.

What are cis-regulatory modules?

DNA sequences that regulate the expression of nearby genes, acting as 'genetic switches'.

What is the mediator complex?

A multi-protein complex that facilitates communication between transcription factors and RNA polymerase, crucial for transcription initiation.

What are the functions of genes like Pitx1 in an organism?

Genes often have multiple functions, and regulatory mutations are typically less harmful than coding mutations.

Why do mutations in coding or regulatory sequences of transcription factors have broad effects?

Mutations in these sequences can significantly alter gene expression and protein function, leading to widespread effects on the organism.

How does chromatin structure impact gene expression?

Chromatin structure influences the accessibility of DNA for transcription; tightly packed chromatin (heterochromatin) is less accessible than loosely packed chromatin (euchromatin).

Is chromatin structure more important for gene expression regulation in eukaryotes or prokaryotes?

Chromatin structure is more important for gene expression regulation in eukaryotes.

Define euchromatin and heterochromatin.

Euchromatin is loosely packed chromatin that is actively involved in transcription, while heterochromatin is tightly packed and generally inactive in transcription.

What effect does methylation of histone tails have on chromatin structure and gene expression?

Methylation of histone tails typically leads to a more compact chromatin structure, resulting in reduced gene expression.

What effect does acetylation of histone tails have on chromatin structure and gene expression?

Acetylation of histone tails generally results in a more relaxed chromatin structure, promoting increased gene expression.

What is an epigenetic change, and how does it differ from mutation?

An epigenetic change refers to modifications that affect gene expression without altering the DNA sequence, while a mutation involves a change in the DNA sequence itself.

Define mutation.

A mutation is a change in the DNA sequence that can affect gene function and expression.

Where do most mutations come from?

Most mutations arise from errors during DNA replication, environmental factors, or spontaneous chemical changes.

How can mutations in different regions of a eukaryotic gene impact protein function?

Mutations in coding regions can alter protein sequence, while mutations in regulatory regions can affect gene expression levels.

What are the potential impacts of a point mutation in the coding region of a gene?

A point mutation can lead to changes in the amino acid sequence, potentially altering protein structure and function.

How can you describe the impact of a mutation on DNA and the encoded protein?

Using correct terminology, you can describe the mutation type (e.g., substitution, deletion) and its effects on the protein (e.g., missense, nonsense).

Which mutation types generally have the most severe consequences for the organism?

Frameshift mutations and large deletions/insertions often have the most severe consequences, depending on the affected gene and its function.

Why do deletion and insertion mutations often cause major changes in protein sequence?

They can shift the reading frame of the gene, altering all downstream amino acids.

Would a 1 base deletion or a 3 base deletion be more likely to cause a dramatic change in protein sequence?

A 1 base deletion is more likely to cause a dramatic change due to frameshift effects.

In sexually reproducing organisms, in which cell types must a mutation occur to be inherited by offspring?

A mutation must occur in germ cells (sperm or eggs) to be inherited.

Are mutations always inherited from parent cell to daughter cell during mitosis?

Not always; some mutations may not be passed on if they occur in non-dividing cells or are repaired.

What is the cell cycle?

The cell cycle is the series of phases that a cell goes through to grow and divide.

What are the phases of the cell cycle?

The phases include G1, S (synthesis), G2, and M (mitosis).

At what phase does the cell enter the cell cycle from G0?

The cell enters the cell cycle from G0 during the G1 phase.

At what phase could the cell exit the cell cycle to G0?

The cell can exit to G0 from the G1 phase.

What phases of the cell cycle are considered interphase?

Interphase includes G1, S, and G2 phases.

When does DNA replication occur?

DNA replication occurs during the S phase of interphase.

When does cell division occur?

Cell division occurs during the M phase.

How does the length of the gap phases impact the size of daughter cells?

Longer gap phases allow for more growth, resulting in larger daughter cells.

What does the cell do during the G phases?

During the G phases, the cell grows, synthesizes proteins, and prepares for DNA replication.

How does the DNA content of the cell change through the cell cycle?

DNA content doubles during the S phase and remains constant until the next S phase.

What types of proteins are involved in the regulation of the cell cycle?

Cyclins and cyclin-dependent kinases (Cdks) are key regulatory proteins.

How are cyclins and cyclin-dependent kinases related?

Cyclins activate Cdks, which then regulate the cell cycle progression.

When are specific cyclins present in the cell?

Specific cyclins are present at different phases of the cell cycle, corresponding to the phase they regulate.

When are specific Cdks present in the cell, and when are they active?

Cdks are present throughout the cell cycle but are only active when bound to their corresponding cyclins.

What do Cdks do in terms of cell cycle regulation?

Cdks phosphorylate target proteins to drive the cell cycle forward.

Why does phosphorylation of a protein often alter its activity?

Phosphorylation can induce conformational changes that affect the protein's function.

What is a cell cycle checkpoint? What is checked at each checkpoint?

Checkpoints are regulatory points that assess cell readiness to proceed; they check for DNA damage, proper chromosome alignment, and cell size.

What is retinoblastoma protein, and what is its role?

Retinoblastoma protein regulates the cell cycle by inhibiting progression from G1 to S phase.

What is p53, and what is its role?

p53 is a tumor suppressor protein that responds to DNA damage and can induce cell cycle arrest or apoptosis.

Why do mutations in retinoblastoma protein and p53 often lead to cancer?

Mutations in these proteins disrupt cell cycle regulation, leading to uncontrolled cell division.

What do eukaryotic chromosomes look like during G1 phase? What do they look like during G2 phase?

During G1, chromosomes are unreplicated and exist as chromatin; during G2, they are duplicated and consist of sister chromatids.

How do sister chromatids stay attached after synthesis?

Sister chromatids are held together by cohesin proteins.

What does it mean that chromosomes condense at the beginning of M phase?

Condensation refers to the tightening and shortening of chromatin into distinct chromosomes, triggered by specific proteins.

What kinds of cells undergo mitosis?

Somatic cells undergo mitosis for growth and repair.

What are the stages of M phase, and what events occur in each?

The stages include prophase (chromosomes condense), metaphase (chromosomes align), anaphase (sister chromatids separate), and telophase (nuclear envelope reforms).

Define cytoskeleton. What does the cytoskeleton do for the cell?

The cytoskeleton is a network of protein filaments that provides structural support, facilitates cell movement, and aids in intracellular transport.

Why are microtubules important in cell division?

Microtubules form the mitotic spindle, which is essential for separating sister chromatids during cell division.

What are the effects of drugs that prevent polymerization and depolymerization of microtubules on cell division?

Drugs that prevent polymerization halt cell division during metaphase by stopping the formation of the mitotic spindle, while drugs that prevent depolymerization halt division by preventing the separation of chromosomes.

What is the centrosome and its relationship to the spindle?

The centrosome is an organelle that serves as the main microtubule organizing center and is crucial for the formation of the spindle apparatus during mitosis.

What is the difference between the centrosome and the centromere?

The centrosome is the microtubule organizing center, while the centromere is the region of a chromosome where the two sister chromatids are joined and where the kinetochore forms.

What is the kinetochore, its location in mitosis, and its function?

The kinetochore is a protein structure on the centromere of a chromosome that attaches to microtubules and facilitates the movement of chromosomes during mitosis.