Test 2 Material

What is the main difference between core RNA polymerase and RNA polymerase holoenzyme in E coli?

The core RNA polymerase does not contain the sigma factor; which is essential for promoter recognition and initiation during transcription.

Why does transcription differ between prokaryotes and eukaryotes?

Transcription differs significantly between prokaryotes and eukaryotes primarily because of the structural difference in their cells, where prokaryotes lack a nucleus, meaning transcription and translation occur simultaneously in the cytoplasm, while in eukaryotes, transcription happens within the nucleus, spatially separating it from translation and requiring additional regulatory mechanisms to control gene expression; this results in a more complex transcription process in eukaryotes compared to prokaryotes. 

What are two methods of transcription termination in prokaryotes?

Intrinsic termination and Rho-dependent termination.

What is intrinsic termination?

A mechanism of transcription termination in prokaryotes that relies on the formation of a hairpin structure in the RNA followed by a stretch of uracils, causing RNA polymerase to dissociate from the DNA.

What is Rho-dependent termination?

A mechanism of transcription termination in prokaryotes that involves the Rho protein and a rut site in the RNA, which helps the Rho protein to bind and facilitate the release of RNA polymerase from the DNA.

Three types of ribonucleic acid?

mRNA, tRNA, rRNA

mRNA

A type of ribonucleic acid that carries genetic information from DNA to the cytoplasm.

tRNA

A type of ribonucleic acid that helps translate the genetic code by bringing amino acids to the ribosome during protein synthesis.

rRNA

A type of ribonucleic acid that reads the order of amino acids and linking them together to form proteins in the ribosome.

Transcription

The process by which genetic information from DNA is copied into mRNA, allowing for the synthesis of proteins.

Translation

The process of decoding mRNA into a polypeptide chain, where tRNA brings specific amino acids to the ribosome according to the mRNA sequence.

Tetranucleotide hypothesis

A theory suggesting that DNA is composed of repeating units of four nucleotides, which was later proven incorrect.

B-DNA

The most common form of DNA in cells, characterized by a right-handed helical structure and a major and minor groove.

A-DNA

A rarer and shorter form of DNA in cells, characterized by a right-handed helical structure that is more compact than B-DNA.

Z-DNA

A left-handed helical form of DNA that is less common.

DNA is double stranded while RNA is single stranded.

True

DNA contains ribose sugar while DNA contains sugar deoxyribose

False; RNA contains ribose sugar while DNA contains deoxyribose sugar.

DNA uses thymine while RNA uses uracil

True

What do DNA and RNA have in common?

Both have a sugar phosphate backbone and nucleotide bases.

List the steps in bacterial transcription.

The steps in bacterial transcription include initiation, elongation, and termination.

What happens during initiation in bacterial transcription?

During initiation, RNA polymerase binds to the promoter region of the DNA, unwinding the DNA strands to begin RNA synthesis.

What happens during elongation in bacterial transcription?

During elongation, the RNA molecule is extended by adding RNA nucleotides complementary to the DNA template strand.

What happens during termination in bacterial transcription?

During termination, RNA polymerase reaches a termination signal in the DNA sequence, causing the newly synthesized RNA molecule to be released and the RNA polymerase to detach from the DNA.

What is the difference between transcription in eukaryotes and archaea?

Transcription in eukaryotes involves three RNA polymerases and extensive post-transcriptional modifications, while archaea primarily use a single RNA polymerase similar to eukaryotic RNA polymerase II, with fewer modifications.

What is the function of polymerase I?

It transcribes rRNA genes

What happens after transcription in eukaryotes?

After transcription, the pre-mRNA undergoes capping, polyadenylation, and splicing to become mature and stable mRNA before being transported to the cytoplasm for translation.

What is capping?

Capping is the addition of a modified guanine nucleotide to the 5' end of pre-mRNA. This modification protects the mRNA from degradation and assists in ribosome binding during translation.

What is spilcing?

Splicing is the process of removing introns from pre-mRNA and joining exons together to form a continuous coding sequence. Splicing is essential for generating functional mRNA that can be translated into proteins.

What is polyadenylation?

Polyadenylation is the addition of a poly(A) tail, consisting of a sequence of adenine nucleotides, to the 3' end of pre-mRNA, which enhances stability and facilitates transport.

List three different techniques used for analyzing DNA.

Common techniques include PCR, gel electrophoresis, and DNA sequencing.

Describe the structure of DNA.

DNA is a double helix composed of two strands of nucleotides, held together by hydrogen bonds between complementary bases (adenine pairs with thymine, and guanine pairs with cytosine).

Each nucleotide is made up of what?

a sugar, phosphate group, and a nitrogenous base.

List the four nitrogenous bases in DNA.

Adenine, thymine, guanine, and cytosine.

How do DNA strands run?

DNA strands run antiparallel to each other, meaning one strand runs in the 5' to 3' direction while the other runs in the 3' to 5' direction.

In a nucleotide, the phosphate group is attached to the ____ of the sugar molecule and the base is attached to the ____.

5’ carbon and 1’ carbon

DNA is always replicated in which direction?

5' to 3' direction

Adenine and thymine are held together by how many hydrogen bonds?

Two hydrogen bonds

Cytosine and guanine are held together by how many hydrogen bonds?

Three hydrogen bonds

Describe how DNA replicates.

DNA replicates “semi-conservatively”, meaning each of new DNA strands consist of one strand of the original DNA and one newly synthesized strand.

What is the function of DNA helicase?

DNA helicase unwinds the double helix by breaking hydrogen bonds between the base pairs, allowing for replication.

What is the function of topisomerase?

Topoisomerase relieves the strain of unwinding DNA by cutting, twisting, and rejoining the strands, preventing supercoiling during replication.

What is the function of primase?

Primase synthesizes short RNA primers that provide a starting point for DNA polymerase during DNA replication.

What is the function of DNA polymerase?

DNA polymerase synthesizes new DNA strands by adding nucleotides complementary to the template strand, playing a crucial role in DNA replication.

What is the function of DNA ligase?

DNA ligase joins Okazaki fragments on the lagging strand during DNA replication by forming phosphodiester bonds, ensuring the continuity of the DNA molecule.

What is the leading strand?

The leading strand is the DNA strand that is synthesized continuously in the same direction (5’ to 3’) as the replication fork during DNA replication, allowing for efficient and rapid elongation.

What is the lagging strand?

The lagging strand is the DNA strand that is synthesized discontinuously in short segments called Okazaki fragments, moving away from the replication fork during DNA replication, which requires additional processing to connect the fragments.

What are Okazaki fragments?

Short DNA segments synthesized on the lagging strand during DNA replication, which are later joined by DNA ligase.

What is telomerase?

An enzyme that adds repetitive nucleotide sequences to the ends of chromosomes, known as telomeres, helping to maintain chromosome stability and prevent degradation.

What are telomeres?

Repetitive nucleotide sequences at the ends of chromosomes that protect them from deterioration.

The enzyme telomerase is most abundant in which type of cells? Why?

Telomerase is most abundant in egg cells because these cells undergo extensive division and require the maintenance of telomere length to ensure genetic stability and longevity.

What are the two categories of nucleotides?

Pyrimidines and purines

What are purines?

Purines are a category of nucleotides characterized by a double-ring structure, including adenine and guanine, which are essential components of DNA and RNA.

What are pyrimidines?

Pyrimidines are a category of nucleotides characterized by a single-ring structure, including cytosine, thymine, and uracil, which play crucial roles in the synthesis of DNA and RNA.

What are promotors?

Regions of DNA that initiate transcription by RNA polymerase.

What are enhancers?

Enhancers are regulatory DNA sequences that increase the likelihood of transcription of specific genes by binding transcription factors, often located far from the promoter.

What is the function of polymerase II?

It transcribes mRNA

What is the function of polymerase III?

It transcribes tRNA