week 6 Flashcards
promoter
is located at the start of the gene (recognition/binding site for RNAP/Oreinets polymerase)
coding region
- produces codon AUG and ends with stop codon
leader sequence
- in DNA transcribed into mRNA but not amino acids (folding)
- gives rise to SD (helps facilitate translation)
operon
- found predominantly in bacteria and archeal genes, encoding proteins involved in related processes are transcribed by a single promoter (not common in euk - monocistronic)
mono= start codon, coding region ,and stop codon - transcription can yield mRNA consisting of a leader, coding region, spacer, and a second coding region (polycistronic)
What are the two kinds of regulation mechanisms in bacteria?
- constitutive genes - housekeeping genes) - constant supply needed (central metabolic pathway ) - always on
= give off basal expression - expression is regulated - some enzymes are only needed during specific conditions/environments.
What are regulatory proteins that control transcription initiation? what structure is involved?
- initiation = when sigma subunit position RNAP at a promoter
- Transcription factors - regulatory proteins that bind at promoter
- helix-turn-helix motif, which allows them to interact with the grooves of the DNA, similar to a “cowboy on a horse.” This interaction can alter the DNA’s topology or flip regions to either promote or inhibit transcription
What protein is used by negative control? positive control?
- repressor protein - The protein binds to the operators to block RNAP binding (lac)
- activator protein -The protein binds upstream of the promoter and encourages RNAP binding
what are the enzymes that repress and induce enzyme synthesis?
- inducer- small effector molecule that stimulates gene expression, inducible genes- encode inducible enzymes - required only when their substrates are available (lac)
- co-repressor- small effector molecule, irrepressible genes - genes for enzyme involved in biosynthetic pathways - generally present unless the end PDT is available
How does the lac repressor regulate transcription in the presence and absence of lactose?
- absence: the lac repressor binds to the operator and creates DNA loops to prevent RNAP and sigma factors from accessing the promoter, inhibiting transcription. (negative control - repressor prevents gene expression )
- lactose is present, lactose permease brings lactose into the cell, and β-galactosidase converts lactose to allolactose, which will bind to the repressor, preventing the repressor form from binding to the operator = allowing transcription from happening (induces the expression of the operon)
what are the three genes for lactose uptake and metabolism?
- lacZ - encodes for an enzyme that cleaves disaccharides to release two monomers for consumption
- B-galactosidase - hydrolyzes lactose into galactose and glucose
- Lac repressor (lacL) binds the operator and inhibits transcription when no lactose
What is repressible control? How does the presence of tryptophan regulate transcription in the trp operon? operon function when?
- Turns transcription OFF by the presence of specific molecules
- In the trp operon, tryptophan acts as a co-repressor (when present), meaning that when tryptophan is abundant, it binds to the repressor protein, enabling it to bind to the operator and block transcription.
- When tryptophan levels are low, the repressor is inactive, allowing transcription of the genes responsible for synthesizing tryptophan to occur.
- open only functions in the absence of trp
How can the transcription elongation step be regulated? example
- attenuation: Is the termination of transcription within the leader region
- happens through a stem-loop structure in the leader RNA depending on the level of trp (high trp means that there is one and stops transcription)
What is used to regulate transcription elongation?
- riboswitch - It is a specialized form of transcription attenuation that is found in bacteria and archaea.
- Folding of the RNA leader sequence determines if transcription will occur or terminate and is a response to the effector molecule binding to teh RNA
What is used to regulate translation?
- RNA thermometers are RNA secondary structures located in the leader sequence of mRNA that regulate translation in a temperature-dependent manner.
- The RNA thermometer folds into a structure to prevent access of the ribosome to the Shine-Dalgarno (SD) sequence within the mRNA at lower temperatures.
What is the global regulatory system? how do they help bacteria adapt to changing conditions? regulon?
- are regulatory networks that can simultaneously affect many genes, operons, and pathways, allowing bacteria to adapt to changing environmental conditions.
- regulon genes or operons controlled by a common global regulatory protein
what are the four types of regulations that global regulatory systems use?
Two-component signal transduction systems
Phophorelays system
Sigma factors
Second messengers
What is the two-component system? Sensor kinase?
- Direct line for a bacterial system
- a sensor kinase (e.g., EnvZ) spans the plasma membrane, so a part of it is exposed to the external environment, and the other part is in the cytoplasm, detecting environmental changes such as osmolarity.
- The sensor kinase phosphorylates itself and then transfers the phosphate to a response regulator in the cytoplasm.
- The response regulator undergoes a conformational change, which triggers transcriptional changes, allowing the bacteria to respond to the detected environmental signal.
what are alternate sigma factors? What do these help with?
- these change the expression of many genes, directing RNAP to specific subsets of bacteria promoters.
- These help bacteria control which genes should be turned on or off in response to different conditions
- differ in consensus binding sites and protein subunits
What are second messengers? What cellular process can be affected? example?
- Small molecules respond to a signal outside the cell. (Receptors and signals that are relayed into the cell and impact gene expression through transduction can change form. )
- Allows for the cell cycle progression, biofilm formation, virulent gene expression, etc
- catabolite repression, cap, stringent response
Catabolite repression? Diauxic growth (2 parts)?
- Catabolite repression is a global regulatory mechanism and regulates transcription by both activators and repressors
- Diauxic growth refers to the biphasic growth pattern in which a cell preferentially uses glucose as its carbon source first.
1. Biphasic growth pattern - preferential use of one carbon source over another (glucose first)
2. Once glucose is exhausted, there is a lag phase - where now lactose is being used ( after the preferred substrate is used, growth will resume using the second carbon source)
what is anotehr name for CAP?
- cAMP
- when bound, stimulates transcription
- glucose levels are regulated by it : High =no cAMP, low= no inactivation = cAMP
What are the four scenarios of lactose and glucose interaction that regulate lac operon transcription?
- Lactose but no glucose: Allolactose binds to the inactive repressor, and transcription occurs with high cAMP levels activating CAP.
- Lactose + glucose: The repressor is inactive due to allolactose, but low cAMP results in inactive CAP, and transcription does not occur.
- Neither lactose nor glucose: The repressor remains active, and transcription is repressed.
- Glucose but no lactose: The repressor binds to the operator, CAP is inactive due to low cAMP, and no transcription occurs.
what is a stringent response?
- Amino acid starvation - decreases the production of tRNA and rRNA in cells while increasing the transcription of amino acid genes.
- Protein RelA produces pppGpp when an uncharged tRNA enters the ribosome.
what do cyclic dinucleotides act as? two classes? in high concentrations, what happens?
- act as key signaling molecules in bacteria by binding to effector molecules in the cytoplasm.
- Two classes of enzymes control their synthesis and degradation. These molecules regulate essential cellular processes, such as transitioning from a motile (swimming) state to a sessile (stationary) state.
- In higher concentrations, cyclic dinucleotides trigger the production of polysaccharides, leading to the formation of biofilms.
What is chemotaxis? porcess?
- Movement in response to chemical stimulus
- MCP/ methyl-accepting chemotaxis protein = chemoreceptors in the membrane will bend to environmental chemicals, initiating phosphorelay towards cheY, which governs flagella rotation
what is quorum sensing?
- Cell-to-cell communication
What is the role of the restriction-modification system in bacteria? Restriction endonucleases?
- used to restrict the growth of viruses.
- it is encoded in the bacterial genome and expressed at low levels.
- which recognizes specific DNA sequences in foreign viral DNA and cuts them, preventing viral replication and growth.
What is used to respond to viral infections? process?
- adaptive immunity
- Adaptation stage - occurs upon infection by a virus
- If the cell survives, it adds pieces of the viral genome to its Casper array
- Expression stage - CRISPR region transcribed to yield a precursor RNA (Cas protein processes this into mature CRISPR RNAs (crRNAs) )
- Interface stage - during viral infection, the cas-crRNAs block VIRAL DNA/mRNA
How does DNA replication in eukaryotes compare to archaea?
- E: bacterial replisomes work bidirectionally until a circular chromosome is replicated. Large chromosomes and chromosomes are wound around histones in nucleosomes.
- Multiple origins of replication
- A: they are more similar to bacteria in size and circularity (some are polyploid), sometimes single-origin but usually 2-4, and involve origin-binding proteins and origin-recognition complex.
What is the hay flick limit? What problem do telomeres try to solve?
- In EUK, telomeres have a finite life span and after each round of replication shortens the chromosome
- they’re DNA complexes at the end of the chromosome to protect DNA from degradation (only found in euk)
What are the two features in how telomerase replicates telomeric DNA of euk chromosomes?
- there is an internal template that has complementary base pairs to the g-tails and is used as the template for DNA synthesis
- Reverse transcriptase activity
- 3’ OH serves as a primer for DNA synthesis
- Lengthening creates enough room for an RNA primer on the lagging strand end.
- This maintains the length of the chromosome end.
How is transcription in bacteria different from that in eukaryotes?
- in bacteria, they use a single RNAp; bacterial genes with related functions are organized into operons and controlled by one promoter, and Polycistronic
- in eukaryotes:
- Transcription occurs in the nucleus (RNA products must move to the cytoplasm)
- each protein-coding gene has its promoter (monocistronic transcripts)
- Eukaryotic genes are split into regions
- Exons -sequences that code for part of the polypeptide
- introns- noncoding regions
- Primary or pre-mRNA with both introns and exons
Introns are spliced out to make mature mRNA
What are the three major RNAPs of eukaryotes?
1 catalyzes rRNA Synthesis
2 catalysizes mRNA synthesis
3 synthesis tRNA molecules
- very similar elemenst in B A E
What are the two regions in eukaryotic promoters? what do e AND a share?
- Core promoter - minimal region needed for transcription ( Regulatory region)
- TATA box - Present in housekeeping genes and Absent of regulated genes
- EUK and A promoters share sequences
What has to happen to the mRNA in eukaryotes that is not seen in the other two domains?
- Initial transcripts must be modified befores they are ready to be translated
- 5’ cap - stabilizes and facilitates translation, facilitate splicing
- 3’ poly A-tail - aids recognition, prevents degradation, signal for transport
what is a splicesome and its two products?
- Splicosome - ribozyme that removes introns from pre-mRNA - made of proteins and RNA
- Two products
Mature mRNA that goes to the ribosomes
Lariat - exercised RNA molecule
What is alternative splicing?
- Different patterns of exons remain after pre-mRNA splicing
- Allows for a single gene to code for more than one protein-coding capacity of the genome is expanded
This is not available in bacteria or archaea.
what are the similarities that archea have with bacteria and eukaryotes in terms of transcription initiation?
- Eukaryotic-like RNAP in bacterial-environment
- Similarities with bacteria
=Occurs in nucleoid
= mRNA is polycistronic
=Introns are rare, removed by different processes than eukaryotes
Use single RNA polymerase - Similarities with eukaryotes
RNA pol resembles RNA pol 2
Accessory factors needed like TATA
What are chaperones and transcription factors?
- chaperons - help deliver or fold proteins
- TF: gauges environmental signals and respond to It by gene expression
how is folding done in eukaryotes?
- chaperons are used to fold proteins properly or refold them after denaturing
Often designed as heat shock proteins
Folding is co-translational or posttranslational
how are proteins localized and secreted in eukaryotes?
- Vesicular transport - is used to move proteins directly across a membrane
- Direct translocation is used to place proteins into ER, mitochondria, and chloroplasts
- Sec system - protein translocation system (homologous for sec proteins in all three domains)
- Tat system 0 twin argin residues ( function in chloroplast and mitochondria)
what are some characteristics of archeal translation initiation ?
- Transcription and translation are coupled
- Some archaeal mRNA have SD sequences; some are polycistronic
- Initiation is similar to bacteria but uses a eukaryotic-style initiator, met-tRNA
- More initiation factors are used in bacteria, some identical to eukaryotes, others unique to archa
What is maturation in archaea? How does localization happen in archaea?
- Folding of archeal proteins is accomplished with chaperons
- Sec and tat protein translocation system is identified
what effect does activate genes for expression have in eukaryotes?
- Activating genes for expression requires changing chromatin structure to become accessible to transcription factors
What does the regulation of gene expression in an archea look like?
- similar to b and e
- 2 component regulatory system rare
- TF causes positive and negative gene regulation
- histone DNA complex carry in size
- no post-translational modifications
