biol 3301 exam 3 study guide

What are the four characteristics of genetic material?

Must contain information, be transmissible from parents to offspring, be replicable, and capable of variation.

What did Griffith's experiment demonstrate?

The transforming principle that allowed R bacteria to become type S, indicating DNA's role in heredity.

What was the conclusion of Avery, MacLeod, and McCarty's experiment?

DNA is the transforming principle, as the sample without DNA did not transform R bacteria.

What did the Hershey-Chase experiment determine?

DNA is the genetic material for the T2 phage, as only the radiolabeled DNA entered the bacterial cells.

What are the components of a nucleotide?

A phosphate group, a pentose sugar (deoxyribose in DNA, ribose in RNA), and a nitrogenous base.

What are the two types of nitrogenous bases?

Purines (Adenine and Guanine) and Pyrimidines (Thymine, Cytosine, and Uracil in RNA).

What type of bonds link nucleotides in DNA?

Ester bonds link nucleotides, and phosphodiester linkages connect the 5' carbon of one nucleotide to the 3' carbon of another.

Describe the structure of DNA.

DNA consists of two strands forming a double helix, with an antiparallel orientation and a right-handed twist.

What stabilizes the DNA double helix?

Hydrogen bonds between complementary bases stabilize the double helix structure.

What are the major and minor grooves in DNA?

The major groove is wider and allows protein binding, while the minor groove is narrower and serves as a binding site for smaller molecules.

What are the key features of RNA?

RNA contains ribose, uses uracil instead of thymine, and is typically single-stranded.

What is the semiconservative model of DNA replication?

Each new DNA molecule consists of one parent strand and one newly synthesized daughter strand.

What is the role of helicase in DNA replication?

Helicase separates the two DNA strands by breaking hydrogen bonds.

What is the function of DNA polymerase III?

DNA polymerase III synthesizes the daughter strand of DNA in the 5' to 3' direction.

What are Okazaki fragments?

Short DNA fragments synthesized on the lagging strand during DNA replication.

What is the role of DNA ligase?

DNA ligase catalyzes the formation of ester bonds to connect DNA backbones and join Okazaki fragments.

What is the origin of replication in bacteria?

The origin of replication in bacteria is called oriC, which contains DnaA boxes and AT-rich regions.

What is the problem at the end of eukaryotic chromosomes?

DNA polymerase cannot initiate synthesis on an unprimed strand, leading to the shortening of chromosomes.

What is the function of telomerase?

Telomerase extends telomeres, which are repetitive nucleotide sequences at the ends of chromosomes.

What is a gene?

A gene is a segment of DNA that contains the instructions for making a specific protein or RNA molecule.

What is the role of proteins in transcription?

Proteins must recognize and act on DNA for transcription to occur.

What are regulatory sequences in DNA?

DNA sites for the binding of regulatory proteins that influence transcription.

What is a promoter in transcription?

The site for RNA polymerase binding, marking the beginning of transcription.

What is a terminator in transcription?

The site that signals the end of transcription.

What is the template strand in DNA transcription?

The DNA strand being transcribed, with the RNA transcript being complementary to it.

What is the coding/sense/nontemplate strand?

The DNA strand not being transcribed during RNA synthesis.

What is a transcription factor?

Proteins that recognize the promoter and regulatory sequences to facilitate transcription.

What are the stages of transcription in bacteria?

Initiation, elongation, and termination.

What is the function of the RNA polymerase holoenzyme?

It catalyzes RNA synthesis and consists of the core enzyme and sigma factor.

What is the difference between rho-dependent and rho-independent transcriptional termination?

Rho-dependent requires the rho protein to separate RNA from DNA, while rho-independent relies on a stem loop structure and a uracil-rich sequence.

What are the three types of RNA polymerase in eukaryotes?

RNA pol I (transcribes rRNA), RNA pol II (transcribes mRNA and some snRNA), and RNA pol III (transcribes tRNA and 5s rRNA).

What is the core promoter in eukaryotic transcription?

A short sequence that includes the TATA box and transcriptional start point, producing basal transcription.

What are enhancers and silencers in gene transcription?

Enhancers stimulate transcription, while silencers inhibit transcription.

What are cis-acting and trans-acting factors?

Cis-acting factors are DNA sequences affecting a gene, while trans-acting factors are regulatory proteins that bind to these sequences.

What are introns and exons?

Introns are intervening sequences removed during RNA processing, while exons are coding sequences that are spliced together.

What is the function of the spliceosome?

It removes introns and covalently links exons in pre-mRNA.

What is Group I self-splicing?

A process where RNA acts as its own ribozyme to splice itself without enzymes.

What is Group II self-splicing?

Similar to Group I, but involves a 2' OH group in adenosine to initiate the splicing process.

What is pre-mRNA?

The initial RNA transcript that undergoes processing to become mature mRNA.

What is the significance of the consensus sequence in promoter regions?

It is the most common sequence that results in a high level of transcription.

What is the role of transcription factors in eukaryotic transcription?

They bind to regulatory elements and influence the rate of transcription.

What is the start codon in the genetic code?

AUG, which codes for methionine.

What are the stop codons in the genetic code?

UAA, UAG, and UGA.

What does it mean that the genetic code is degenerate?

More than one codon can specify the same amino acid.

What is the significance of the third base in a codon?

It is variable and can wobble, allowing for some mismatches.

How is the genetic code described in terms of universality?

It is nearly universal across different organisms.

What is the relationship between mRNA, codons, and protein products?

mRNA is composed of 3 nucleotides that form codons, which dictate the protein product.

What is the directionality of polypeptides in relation to mRNA?

Polypeptide directionality is parallel to the 5' to 3' orientation of mRNA.

What is the N-terminal end of a polypeptide?

The first amino acid with an exposed amino group.

What is the C-terminal end of a polypeptide?

The last amino acid with an exposed carboxyl group.

What are the general characteristics of amino acids?

Amino acids can be hydrophobic or hydrophilic, with various subcategories.

What are the four levels of protein structure?

Primary, secondary, tertiary, and quaternary.

What did Nirenberg contribute to the understanding of the genetic code?

He created a translation system to show that codon sequences dictate amino acid sequences.

What is the purpose of aminoacyl tRNA synthetase?

It attaches amino acids to their corresponding tRNAs.

What is the wobble hypothesis?

It states that the first two positions of a codon pair strictly, while the third can wobble.

What is the E site in the bacterial ribosome?

The exit site where the completed polypeptide exits.

What is the role of the A site in the bacterial ribosome?

The aminoacyl site where new tRNAs enter.

What is the P site in the bacterial ribosome?

The peptidyl site where the polypeptide chain is elongated.

What are the three stages of translation?

Initiation, elongation, and termination.

What is the function of the lac operon?

It regulates the metabolism of lactose in bacteria.

What is the role of the lac repressor protein?

It binds to the operator site to inhibit transcription of the lac operon.

What is an inducer in the context of gene regulation?

A small effector molecule that increases transcription by binding to activators.

What is the function of cAMP in the regulation of the lac operon?

cAMP binds to CAP and increases transcription when glucose levels are low.

What are transcription factors?

Proteins that influence RNA polymerase's ability to transcribe a gene.

What is the difference between general and regulatory transcription factors?

General factors are required for basal transcription, while regulatory factors control the rate of transcription.

What are enhancers in gene regulation?

DNA sequences that activators bind to, increasing transcription rates.

What is the role of silencers in gene regulation?

DNA sequences that repressors bind to, decreasing transcription rates.

What is combinatorial control in eukaryotic gene regulation?

Regulation by multiple activators and repressors affecting transcription.

What is the histone code?

A pattern of histone modifications that provide binding sites for proteins affecting transcription.

What is the significance of chromatin remodeling?

It alters chromatin structure to make DNA more or less accessible for transcription.

What are glucocorticoid response elements (GRE)?

Enhancers located near genes that can be activated by steroid hormones.

What is feedback inhibition in gene regulation?

A mechanism where the product of a metabolic pathway inhibits an enzyme involved in its synthesis.