exam 2

Which experiment first showed bacterial transformation?

Griffith's experiment showed that harmless bacteria could become dangerous by taking in genetic material from dead bacteria

Who established DNA as the transforming material (responsible for changing harmless bacteria into dangerous bacteria)?

Avery, MacLeod, and McCarty.

What did Hershey-Chase show?

Showed DNA enters bacteria while the virus's protein coat stays outside (DNA, not protein, carries the genetic instructions needed to make new viruses)

DNA vs RNA sugar and base?

DNA: deoxyribose, thymine; RNA: ribose, uracil.

What does DNA gyrase (type II topoisomerases) do?

Introduces negative supercoils using ATP to control twisting and tangling of DNA

What does helicase do?

Unwinds the DNA double helix so DNA can be copied during replication

What does primase do?

Makes RNA primers (Short pieces of RNA that give DNA polymerase a starting point to copy DNA) so DNA polymerase (enzyme that builds new DNA by adding matching DNA nucleotides.) can begin.

DNA polymerase III works in which direction?

Synthesizes/Builds DNA 5′ to 3′.

Leading vs lagging strand?

Leading is built continuously; lagging makes Okazaki fragments (Short pieces of DNA made on the lagging strand that are later joined together; DNA ligase connects pieces to make one complete strand).

What removes and replaces RNA primers?

DNA polymerase I (and RNase H helps remove primers (Primers help START DNA replication, but they eventually get replaced with DNA)).

What seals any breaks between DNA fragments?

DNA ligase.

What does semiconservative replication mean?

Each daughter DNA has one old strand and one new strand.

What makes a secondary chromosome unlike a plasmid?

It contains at least one gene essential for viability (that the cell needs to survive).

What is metagenomics?

studying DNA from a whole microbial community, not just one organism

What is an operon?

a group of genes that work together to perform a related function

What is polycistronic mRNA?

One mRNA encoding (carrying instructions to make) multiple proteins

What does sigma factor do?

A protein that Guides bacterial RNA polymerase to a promoter (specific spot on DNA where RNA polymerase will start making RNA).

two specific spots that tell the RNA polymerase how far is the bacterial promoter

The −10 and −35 regions.

How does rho-independent (intrinsic) termination work?

RNA hairpin (forms when part of the RNA folds back and sticks to itself, creating a little loop) followed by Uracil-rich region, stopping transcript.

Rifamycin

An antibiotic that blocks bacterial RNA polymerase, preventing RNA production.

mRNA, tRNA, rRNA roles?

mRNA carries protein coding info from the DNA in the cell's nucleus out into the cytoplasm; tRNA delivers amino acids to the ribosomes; rRNA makes up the ribosomes and catalyzes protein synthesis

What is AUG?

Common translation start codon, coding methionine.

Which are the three stop codons?

UAA, UAG, UGA.

What does the Shine-Dalgarno sequence do?

Helps position bacterial ribosome at the start codon.

What amino acid starts bacterial translation?

N-formylmethionine (fMet).

What are A, P, and E ribosome sites?

A: incoming tRNA; P: growing chain; E: exit.

Which rRNA catalyzes peptide bonds in bacteria?

23S rRNA.

What attaches amino acids to tRNAs?

Aminoacyl-tRNA synthetases using ATP.

Transition vs transversion?

Transition: same base class; transversion: switching groups purine ↔ pyrimidine.

Silent vs missense vs nonsense mutation?

Same amino acid; changed amino acid; premature stop.

What is a frameshift mutation?

When DNA letters are added or removed, shifting how the genetic instructions are read in groups of three

Does every mutation affect the phenotype?

No; all affect genotype, many have no visible phenotype.

What does the Ames test detect?

A test that uses bacteria to determine whether a chemical causes DNA mutations.

What repairs UV-induced dimers?

Photolyase = Uses light to fix the damage; Excision repair = Cuts out and replaces the damaged DNA

What does MutS recognize?

DNA mismatches after replication.

What does SOS DNA repair trade away?

Accuracy; It allows DNA copying to continue, but increases the chance of mutations.

Conjugation vs transformation vs transduction?

One bacterium transfers DNA directly to another bacterium through cell-to-cell contact, often using a structure called a pilus. vs A bacterium takes in free DNA from its surroundings. vs A virus that infects bacteria (called a bacteriophage) accidentally carries bacterial DNA from one bacterium to another.

Generalized vs specialized transduction?

Any bacterial genes vs genes near prophage insertion.

What is an Hfr cell?

A bacterium that can transfer chromosome DNA because its F factor is attached to the chromosome

Orthologs vs paralogs?

Both are genes that share a common ancestor. Orthologs: Related genes found in different species because the species evolved from a common ancestor. vs genes related by duplication.

What is a pathogenicity island?

a group of genes that a bacterium acquired from another source, which helps it cause disease.

lac operon normally ON or OFF?

OFF; LacI repressor blocks transcription.

What induces lac operon?

Allolactose. Allolactose binds to the LacI repressor and makes it release the DNA. Now RNA polymerase can transcribe the lac genes.

What is needed for strong lac expression?

Lactose present and glucose low (cAMP-CRP active).

trp operon normally ON or OFF?

ON; tryptophan corepresses it when abundant. When the bacterium doesn't have enough tryptophan, it needs to make more, so the operon stays ON.

What does anti-sigma factor do?

Binds sigma and prevents transcription initiation.

What is a regulon?

Multiple operons controlled by one regulatory system.

When does trp attenuation stop transcription?

High tryptophan; terminator hairpin forms.

What is a riboswitch?

mRNA structure binding a metabolite to regulate expression.

What does (p)ppGpp do during starvation?

Triggers stringent response; reduces ribosome production. Because making proteins requires energy, and the bacterium needs to conserve energy to survive.

High c-di-GMP promotes what?

Biofilm (A community of bacteria sticking together on a surface, often surrounded by a protective coating.) formation and reduced motility. When c-di-GMP levels are high, bacteria tend to stick to surfaces and form biofilms instead of swimming around.

What is quorum sensing?

How bacteria communicate and detect when many other bacteria are nearby. When enough signals are present, the bacteria respond by turning certain genes ON or OFF together.

LuxI vs LuxR roles?

LuxI makes autoinducer (chemical signal); LuxR responds and activates genes.

What is phase variation?

When bacteria switch certain genes ON or OFF, and can switch them back later, often by DNA inversion.

What does an RNA thermometer sense?

Temperature via RNA folding and ribosome-binding access.

What is an intein?

A protein piece that cuts itself out and joins the remaining pieces.