BIO 2200 Exam 3 Flashcards
What is gene expression?
transcription of gene into mRNA followed by translation of mRNA into protein
Why is regulation important?
It helps conserve energy and resources by making sure the right genes are turned on or turned off
What are the two major levels of regulation in the cell?
One controls the activity of preexisting enzymes, while the other controls the amount if an enzyme
What is the main site of protein binding on DNA?
the major groove; inverted repeat sequences are frequently binding sites for regulatory proteins
What are homodimeric proteins?
proteins composed of two identical polypeptides which interact with inverted repeats on DNA
Describe the helix-turn-helix domain of binding proteins.
First helix is the recognition helix and second helix is the stabilizing sequence. Examples are lac and tcp repressors of E. coli
Describe the zinc finger domain of protein.
A protein structure that binds to a zinc ion. Typically two or three zinc fingers on proteins that use them for DNA binding.
Describe the leucine zipper domain of protein.
Leucine residues are spaced every seven amino acids. It does not interact directly with DNA.
What are three outcomes of DNA-binding proteins?
DNA-binding proteins may catalyze a specific reaction on the DNA molecule (i.e., transcription by RNA polymerase). The binding event can block transcription (negative regulation) or activate transcription (positive regulation).
How is gene expression controlled in bacteria?
These systems are greatly influenced by environment in which the organism is growing. Presence or absence of specific small molecules can also control gene regulation. Interactions between small molecules and DNA-binding proteins result in control of transcription or translation.
What is negative control of transcription?
a regulatory mechanism that stops transcription
What is repression?
prevention of the synthesis of an enzyme in response to a signal; typically affects anabolic enzymes
What is induction?
production of an enzyme in response to a signal; typically affects catabolic enzymes
What is an inducer?
substance that induces enzyme synthesis; turns on expression
What is a corepressor?
substance that represses enzyme synthesis
What is an effector molecule?
collective term for inducers and repressors; can either turn on or off expression
What molecules do repressors bind to?
allosteric repressor protein, which becomes active and binds to regions of DNA near promoter called the operator
What is an operon?
cluster of genes arranged in a linear fashion whose expression is under control of a single operator (operator is located downstream of the promoter)
What is positive control of transcription?
regulator protein activates the binding of RNA polymerase to DNA
Give an example of positive control.
Maltose catabolism in E. coli;
Maltose activator protein cannot bind to DNA unless it first binds maltose
What is the site where activator proteins bind?
activator-binding site
What is a regulon?
Multiple operons controlled by the same regulatory protein are called a regulon; exist in both positive and negative control
What are global control systems?
regulate expression of many different genes simultaneously
What is catabolite repression?
example of global control; synthesis of unrelated catabolic enzymes is repressed if glucose is present in growth medium; lac operon is under control of catabolite repression; it ensures the “best” carbon and energy source is used first
What is diauxic growth?
two exponential growth phases; when glucose is available, the organisms uses that as energy, then stops, then breaks down lactose for energy
What is a key molecule in many metabolic control systems?
Cyclic AMP; it is a regulatory nucleotide
What happens during diauxic growth?
CRP is an activator protein; cAMP is an allosteric inducer for CRP; when glucose is present, there are low levels of cAMP, but when glucose is absent, there are high levels of cAMP; When cAMP is present, CRP is activated
What happens when lactose is absent during diauxic growth?
the lactose repressor is bound, even in the presence of cAMP, which blocks the RNA polymerase
What must happen in order to break down lactose?
you must have both absence of glucose and presence of lactose
What do Archaea use to control transcription?
Archaea use DNA-binding proteins to control transcription –> more closely resembles control by Bacteria than Eukarya.
What are the repressor proteins in Archaea?
NrpR is an example of an archaeal repressor protein from Methanococcus maripaludis –> Represses genes involved in nitrogen metabolism
What type of regulatory system do prokaryotes?
two-component regulatory system
What is signal transduction?
in prokaryotes, when external signal is detected by sensor and transmitted to regulatory machinery; most are two-component regulatory systems
Give an example of a modified two-component regulatory system.
Modified two-component system used in chemotaxis to sense temporal changes in attractants or repellents and regulate flagellar rotation.
What are the three main steps in chemotaxis?
1) Response to Signal: sensory proteins in cytoplasmic membrane sense attractants and repellents. Methyl-accepting chemotaxis proteins (MCPs) bind to attractant or repellent and initiate flagellar rotation.
2) Controlling Flagellar Rotation: controlled by CheY protein –> CheY results in counterclockwise rotation and runs and CheY-P results in clockwise rotation and tumbling.
3) Step 3: Adaptation: Feedback loop allows the system to reset itself to continue to sense the presence of a signal. This involves modification of MCPs
What does the Che protein do?
provides motility to flagella in the clockwise or counterclockwise rotation
What is quorum sensing and what does it do?
mechanism by which bacteria assess their population density; ensures sufficient number of cells are present before initiating a response that requires a certain cell density to have an effect (e.g., toxin production in pathogenic bacterium)
What do autoinducer molecules do? (3)
diffuses freely across the cell envelope,
reaches high concentrations inside cell only if many cells are near, and binds to specific activator protein and triggers transcription of specific genes
What was the first autoinducer discovered?
Acyl homoserine lactone
How was quorum sensing first discovered?
Quorum sensing was first discovered as mechanism regulating light production in bacteria including Aliivibrio fischeri.
What are two examples of quorum sensing?
P. aeruginosa switches from free living to growing as a biofilm; Virulence factors of Staphylococcus aureus
What is a stringent response? What is it triggered by?
global control mechanism triggered by amino acid starvation; triggered by (p)ppGpp
What happens during the stringent response?
Alarmones, produced by RelA, signal amino acid starvation –> rRNA and tRNA synthesis decreases –> amino acid synthesis increases
What is the heat shock response controlled by? What do heat shock proteins do?
largely controlled by alternative sigma factors; Heat shock proteins counteract damage of denatured proteins and help cell recover from temperature stress (very ancient proteins); Heat shock response also occurs in Archaea
What is endospore formation in bacillus triggered by?
Triggered by adverse external conditions (i.e., starvation or desiccation)
What is caulobacter differentiation? What is it controlled by?
when bacteria is in two different forms: Swarmer cells (dispersal role) and stalked cells (reproductive role); Controlled by three major regulatory proteins
What regulates mRNA? How is transcription of these enhanced?
Antisense RNA’s (small); transcription of antisense RNA is enhanced when its target genes need to be turned off
What are riboswitches? Where are they located? Where are they found? What type of control is riboswitch control analogous to?
RNA domains in an mRNA molecule that can bind small molecules to control translation of mRNA. Located at 5’ end of mRNA. Found in some bacteria, fungi, and plants. Riboswitch control is analogous to negative control.
What is attenuation? What was the first example?
Transcriptional control that functions by premature termination of mRNA synthesis. First example was the tryptophan operon in E. coli.
Where does translation-independent attenuation?
Gram-positive Bacteria, such as Bacillus
What is a virus?
genetic element that cannot replicate independently of a living (host) cell
What is the study of viruses called?
virology
What is a virion (virus particle)? What is it made of?
extracellular form of a virus; exists outside host and facilitates transmission from one host cell to another; contains nucleic acid genome surrounded by a protein coat and, in some cases, other layers of material
What are two characteristics of viral genomes?
either DNA or RNA genome; some circular, but most linear
How can viruses be classified?
on the basis of the hosts they infect (bacterial viruses; arc heal viruses, animal viruses, plant viruses, etc)
What is the size of viruses?
most are smaller than prokaryotic cells (0.02 to 0.3 micrometers)
What is a capsid? What is it composed of?
the protein shell that surrounds the genome of a virus particle; composed of a number of protein molecules arranged in a precise and highly repetitive pattern around the nucleic acid
What is a capsomere?
subunit of the capsid; smallest morphological unit visible with an electron microscope
What is a nucleocapsid?
complete complex of nucleic acid and protein packaged in the virion
What is an enveloped virus?
virus that contains additional layers around the nucleocapsid; envelope makes initial contact with the host cell
What is helical symmetry of viruses? What are the length and width determined by?
rod-shaped viruses (e.g. tobacco mosiac virus); length of virus determined by length of nucleic acid; width of virus determined by size and packaging of protein subunits
What is icosahedral symmetry?
spherical viruses (e.g. human papillomavirus); most efficient arrangement of subunits in a closed shell
What is a complex virus?
virions composed of several parts, each with separate shapes and symmetries; bacterial viruses contain complicated structures (icosahedral heads and helical tails)
What does the lysozyme do?
makes hole in cell wall and lyses bacterial cell