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Micro Midterm 2
| Question | Answer |
|---|---|
| Why is the major groove of DNA important? | The major groove is important because it provides accessible binding sites for proteins to read DNA sequences. |
| What does the enzyme gyrase do to DNA? | Gyrase introduces negative supercoils into DNA to relieve tension during replication and transcription. Reduces pos supercoiling ahead of replication fork. |
| What is a gene? | A gene is a segment of DNA that encodes a functional product, typically a protein or RNA molecule. |
| What is the difference between a chromosome and a plasmid? | A chromosome is an essential genetic element required for survival, while a plasmid is a non-essential, extra-chromosomal DNA element. |
| How do we tell if a genetic element is a chromosome or a plasmid? | We determine this by whether the cell can survive without it—chromosomes are essential, plasmids are not. |
| What is the difference between the enzymatic functions of DNA polymerase I and III? | DNA polymerase III synthesizes most of the new DNA strand, while DNA polymerase I removes RNA primers and fills in gaps. |
| What are the important characteristics of DNA polymerases? (Most importantly which direction do they synthesize the new DNA?) | DNA polymerases synthesize DNA in the 5' to 3' direction, require a primer, and have proofreading ability. |
| What are the functions of helicase, SSB, primase, and ligase in DNA replication? | Helicase unwinds DNA, SSB prevents reannealing, primase synthesizes RNA primers, and ligase seals DNA fragments together. |
| What is the difference between the lagging and leading strands in DNA replication? | The leading strand is synthesized continuously toward the replication fork, while the lagging strand is synthesized discontinuously away from it. |
| What is the difference between RNA polymerase holoenzyme and core enzyme? | The holoenzyme includes the core enzyme plus the sigma subunit, while the core enzyme lacks sigma and cannot initiate transcription properly. |
| Why is sigma subunit important for RNA polymerase? | The sigma subunit helps RNA polymerase recognize and bind to specific promoter sequences. |
| What determines how often transcription will start at a promoter? | The strength of the promoter sequence determines how often transcription will start. |
| What does rho protein do in transcription? | Rho protein is a termination factor that causes RNA polymerase to dissociate from DNA. |
| How can the structure of the mRNA produced by RNA polymerase cause transcription termination? | Formation of a stem-loop (hairpin) structure in the mRNA can cause the polymerase to pause and dissociate, terminating transcription. |
| What types of transcripts are processed in bacteria and why? | In bacteria, rRNA and tRNA transcripts are processed by cleavage and modification to produce functional molecules. |
| What are the characteristics of a polycistronic mRNA? | A polycistronic mRNA encodes multiple proteins from several genes transcribed together as one transcript. |
| Do all protein coding genes in a mRNA require a ribosome binding site for translation? | Yes, all protein-coding genes in a polycistronic mRNA require their own ribosome binding site (Shine-Dalgarno sequence). |
| How does the mRNA codon match up to the tRNA anticodon? | Via ARS |
| What does an aminoacyl tRNA synthetase do? | ARS enzyme recognizes different parts of the tRNA and adds the correct amino acid acceptor to acceptor stem. The reaction requires ATP and releases AMP plus pyrophosphate |
| How does an aminoacyl tRNA synthetase "know" which amino acid to attach to which tRNA? | by recognizing a combination of specific features unique to each pair: the shape of the tRNA molecule and the chemical properties of the amino acid |
| How many aminoacyl tRNA synthetases are there in a cell? | There are 20 aminoacyl tRNA synthetases, one for each amino acid. |
| What is a reading frame? | A reading frame is the way nucleotide triplets are grouped into codons during translation |
| What is an open reading frame (orf)? | An open reading frame (ORF) is a stretch of DNA/RNA between a start codon and a stop codon that potentially encodes a protein. |
| How many potential reading frames are in a DNA sequence? | There are six potential reading frames in a DNA sequence (three on each strand). |
| How does a ribosome "know" where to start translation on a mRNA? | The ribosome recognizes the Shine-Dalgarno sequence (ribosome binding site) upstream of the start codon on the mRNA. |
| What is the function of the 16S rRNA in the ribosome? | The 16S rRNA in the small subunit binds to the Shine-Dalgarno sequence to position the ribosome correctly. |
| What amino acid is always the first one in bacterial translation? | N-formylmethionine (fMet) is always the first amino acid in bacterial translation. |
| What are the E, P, and A sites in a ribosome? | The E site holds the empty tRNA before exit, the P site holds the tRNA with the growing peptide chain, and the A site receives the incoming aminoacyl-tRNA. |
| How do the E, P, and A sites work during addition of a new amino acid to the growing polypeptide? | The new aminoacyl-tRNA enters the A site, the peptide bond forms, then tRNAs shift from A to P to E sites as the ribosome moves. |
| What is the function of the 23S rRNA in the ribosome? | The 23S rRNA in the large subunit catalyzes peptide bond formation (peptidyl transferase activity). |
| What energy molecule is utilized in translation? | GTP is the energy molecule utilized in translation. |
| Do transcription and translation occur at the same time in bacteria? | As mRNA is being transcribed from DNA, ribosomes can attach to the nascent mRNA strand and begin translating it into protein |
| What is an operator? | a DNA sequence that acts as a binding site for repressor proteins to regulate gene expression. It is a key component of an operon, a cluster of genes in prokaryotes that are transcribed together |
| What is a promoter and how does it relate positionally on the DNA to the operator? | A promoter is where RNA polymerase binds to initiate transcription; it is typically located upstream of the operator. |
| Why do transcription regulatory proteins often bind to inverted sequences in the DNA? | Inverted sequences allow regulatory proteins to bind as dimers with symmetrical binding domains, increasing specificity and affinity. |
| A common signature of bacterial regulatory proteins is the helix-turn-helix structure. How does this protein interact with DNA? | The helix-turn-helix structure inserts one alpha helix into the major groove of DNA to read the sequence. |
| What enzyme makes the signal molecule? | Adenylyl cyclase makes cAMP. |
| What are the two parts for a two component regulation system? | The two parts are a sensor kinase (histidine kinase) and a response regulator. |
| What does each protein do in a two component regulatory system? | The sensor kinase detects environmental signals and phosphorylates itself, then transfers the phosphate to the response regulator, which then affects gene expression. |
| What role does phosphate play in two component regulatory systems? | Phosphate is transferred from the sensor kinase to the response regulator to activate or deactivate it. |
| How can small RNAs (sRNA) control degradation of a mRNA? | Small RNAs can recruit RNases to degrade specific mRNAs or protect mRNAs from degradation. |
| Define a riboswitch. | A riboswitch is an mRNA regulatory element that changes conformation when bound by a small molecule, affecting transcription or translation. |
| How does attenuation control transcription? | causing premature termination of a nascent RNA transcript when the amino acid it codes for is abundant. |
| What is homologous recombination? | process where genetic material is exchanged between two similar strands of DNA to repair double-strand breaks, shuffle genetic information for reproduction |
| What protein is the most important for the homologous recombination process? | RecA protein is the most important for homologous recombination. |
| What is a heteroduplex in recombination? | A heteroduplex is a DNA double helix formed from strands of two different DNA molecules during recombination. |
| What two different types of molecules can result from recombination? | Recombination can produce recombinant molecules (with exchanged segments) or patch/splice molecules. |
| In natural transformation does the DNA enter the cell as double or single strands? | In natural transformation, DNA enters as single strands after one strand is degraded outside the cell. |
| What is a prophage? | A prophage is phage DNA that is integrated into the bacterial chromosome. |
| What is a lysogen? | A lysogen is a bacterial cell carrying integrated prophage DNA. |
| What is the difference between generalized and specialized transduction? | Generalized transduction transfers any bacterial DNA randomly, while specialized transduction transfers only specific genes near the prophage integration site. |
| What is oriT? | OriT is the origin of transfer, the site where DNA transfer begins during conjugation. |
| Explain the rolling circle model for conjugative replication. | In rolling circle replication, one strand is nicked at oriT, the 3' end is extended while the 5' end is displaced and transferred to the recipient cell. |
| Does conjugative DNA enter the recipient cell in double strand or single strand form? | Conjugative DNA enters the recipient cell as a single strand. |
| Which end (3' or 5') of the DNA enters the recipient cell first during conjugation? | The 5' end of the DNA enters the recipient cell first during conjugation. |
| What is an HFR strain? | An Hfr strain is a bacterial strain with the F plasmid integrated into the chromosome. |
| What is a transposable element? | A transposable element is a DNA sequence that can move from one location to another in the genome. |
| What does the transposase enzyme do? | Transposase catalyzes the movement of the transposable element by cutting and rejoining DNA. |
| What is the difference between an Insertion Sequence and a Composite Transposon? | An Insertion Sequence contains only genes for transposition, while a Composite Transposon contains additional genes (like antibiotic resistance) between two insertion sequences. |
| What is the importance of the inverted repeats at the ends of the transposable element? | They act as binding sites for the transposase enzyme, which recognizes and cleaves the element from its original location before reinserting it elsewhere in the genome. |
| What is the difference between conservative and replicative transposition? | Conservative transposition moves the element without replication (cut and paste), while replicative transposition copies the element to a new location (copy and paste). |
Created by:
smurtab