Final Exam Flashcards
1
Q
function and components of lac operon system
A
- regulatory system in bacteria
- controls the expression of genes involved in lactose metabolism
Components:
1. Regulatory gene (laCl)
2. Promoter region
3. Structural genes (lacZ, lacY, lacA)
1
Q
Regulatory gene (laCl)
A
- encodes the lac repressor protein
- lac repressor binds to the operator region of the lac operon in the absence of lactose, preventing RNA polymerase from binding to the promoter and initiating transcription of the structural genes
- undergoes an allosteric change upon binding to lactose, causing it to release from the operator region and allow transcription of the structural genes when lactose is present
2
Q
promoter region (lac operon system)
A
- DNA sequence upstream of the lac operon that serves as the binding site for RNA polymerase
- RNA polymerase binds to the promoter and initiates transcription of the structural genes lacZ, lacY, and lacA in the presence of lactose and when the lac repressor is not bound to the operator
3
Q
Influence of Glucose and/or lactose on Gene expression (lac operon system)
A
- glucose is present and lactose is absent, the lac operon is typically repressed, even in the presence of lactose
- Glucose inhibits the production of cyclic AMP (cAMP), which is required for the activation of the lac operon
- lactose is present and glucose is absent, lactose acts as an inducer of the lac operon
- RNA polymerase can bind to the promoter, allowing transcription of the lacZ, lacY, and lacA gene
- both glucose and lactose are present, the lac operon is subject to both catabolite repression and induction. In this case, glucose repression takes precedence, and the lac operon remains repressed
4
Q
Leaky Scanning and impact on protein sequences
A
- leaky scanning is when ribosome may bypass 1st AUG start codon and initiate downstream at another AUG
- can occur if 1st AUG is followed by suboptimal Kozak sequence that weakens recognition by the ribosome
- can cause synthesis of shorter proteins, lacking amino acids
- can influence N-terminal sequence, altering stability and function
5
Q
Prokaryote translation intiation
A
- small ribosomal subunit bins to Shine-Dalgano sequence on mRNa that is located upstream of start codon
- initiation factors recruit initiator tRNA to start codon
- large ribosomal subunit joins complex and forms functional ribosome
6
Q
eukaryote translation initiation
A
- formation of PIC, consists of small ribosomal subunit, eukaryotic initiation factors (elFs), initiator tRNA and mRNA
- PIC binds to 5’ cap of mRNA via elFs and scans mRNA until finds start codon, triggers recruitment of large ribosomal subunit and formation of functional ribosome
7
Q
polysome formation in prokaryotes
A
- common and efficient
- ribosomes quickly bind to mRNA as it is being synthesized by RNA pol
8
Q
polysome formation in eukaryotes
A
- more dynamic and regulated
- mRNA undergoes processing before exported for translation
- regulatory elements can affect
- responsive to cellular and environmental cues
9
Q
How 2 diff proteins evolved to contain same domain
A
- due to domain shuffling
- genes undergo recombination events
- diff parts of genes get mixed which can lead to creation of new genes containing combos of domains from pre-existing genes
10
Q
protein domain
A
- structural and functional unit in protein molecule
- folds independently
- maintains specific 3D structure that usually performs a specific function
11
Q
protein domain relation to protein folding
A
- since they fold independently, they can facilitate folding of entire protein molecule
- folding of protein domain is facilitated by interactions between amino acids
12
Q
protein domain relation to functions
A
- each type of domain performs specific biochemical or structural role
- proteins often contain multiple domains that each contribute to diff aspects of overall function
13
Q
protein domain and relation to gene evolution
A
- evolution of genes often involves acquisition, duplication, deletion, or rearrangement of domains
- when existing domains combined in new way, can lead t0 proteins with new functions
- can also undergo mutation
14
Q
function of promoters
A
DNA sequences located upstream of genes that serve as binding sites for RNA polymerase, initiating the process of transcription
15
Q
weak promoters
A
have sequences that deviate from the consensus sequence, resulting in less efficient transcription initiation
16
Q
strong promoters
A
have sequences that closely match the consensus sequence recognized by RNA polymerase, leading to efficient transcription initiation
17
Q
repressors
A
- proteins that bind to specific DNA sequences called operators, blocking the binding of RNA polymerase and thereby preventing transcription of the associated genes
- They negatively regulate gene expression by inhibiting transcription initiation
18
Q
activators
A
- proteins that enhance the binding of RNA polymerase to the promoter region, facilitating transcription initiation.
- They positively regulate gene expression by promoting transcription
19
Q
operators
A
- short DNA sequences located adjacent to or overlapping with promoters
- serve as binding sites for repressor proteins.
- When a repressor protein binds to the operator, it physically obstructs RNA polymerase from binding to the promoter, leading to repression of gene expression.
20
Q
activator binding site
A
- DNA sequences located near the promoter region that serve as binding sites for activator proteins.
- When an activator protein binds to its binding site, it enhances the recruitment and activity of RNA polymerase at the promoter, thereby promoting gene expression
21
Q
ligands
A
- small molecules that bind to regulatory proteins, altering their conformation and activity
- can act as inducers or co-repressors, modulating the activity of regulatory proteins such as repressors or activators
22
Q
allosteric regulation
A
the regulation of a protein’s activity by the binding of an effector molecule to a site other than the active site
23
Q
differential gene expression
A
- refers to the phenomenon where different cells or tissues within an organism express distinct sets of genes, leading to diverse phenotypes and functions
- This regulation allows cells to respond to developmental cues, environmental stimuli, and metabolic demands by selectively activating or repressing specific genes
24
Q
genomic equivalence
A
refers to the concept that all cells within an organism contain the same genetic information or genome, regardless of their specialized functions or developmental stage
25
Q
evidence for differential gene expession
A
- Cell-Type-Specific Gene Expression: For example, neurons express genes encoding neurotransmitter receptors and ion channels, while muscle cells express genes encoding contractile proteins
- Developmental Regulation: During development, gene expression patterns change dynamically as cells differentiate into specialized cell types
- Environmental response: For instance, the expression of heat shock proteins increases in response to elevated temperatures, aiding in cellular stress response and survival
26
Q
evidence for genomic equivalence
A
- Somatic Cell Nuclear Transfer (cloning):demonstrate that the nucleus of a somatic cell, which has undergone differentiation and expresses tissue-specific genes, can be transferred into an enucleated egg cell. This results in the development of a whole organism with the same genetic material as the donor somatic cell
- Cellular reprogramming: Studies on induced pluripotent stem cells (iPSCs) have shown that differentiated somatic cells can be reprogrammed into a pluripotent state by overexpressing key transcription factors.
- Transcriptional profiling: Genome-wide transcriptional profiling studies have revealed that all cells within an organism share a common set of genes, known as the core transcriptome
27
Q
stem cells
A
- undifferentiated cells with the unique ability to self-renew and differentiate into specialized cell types.
- serve as the foundation for the development and maintenance of tissues and organs throughout an organism’s life
- can be classified based on their potency or differentiation potential, which determines their ability to differentiate into various cell types
28
Q
pluripotent stem cells
A
have the capacity to differentiate into cells of all three germ layers: ectoderm, endoderm, and mesoderm
29
Q
multipotent stem cells
A
can differentiate into a limited range of cell types within a particular tissue or lineage.
30
Q
unipotent stem cells
A
- can only differentiate into one specific cell type
- They are committed to a particular lineage and serve to replenish and maintain the tissue in which they reside
31
Q
commitment
A
refers to the irreversible commitment of a stem cell to a particular lineage or differentiation pathway
32
Q
differentiated cells
A
- are the end products of the differentiation process
- have lost the ability to self-renew and typically have a more limited differentiation potential compared to stem cells
- exhibit specialized functions and are often organized into tissues and organs to perform specific physiological roles
33
Q
differentiation
A
- process by which stem cells undergo specialization and become more specialized cell types with distinct functions and characteristics. - cells acquire specific morphological, biochemical, and functional features that enable them to perform specialized roles within tissues and organs
34
Q
Expressing a protein and amplification
A
- involves amplification at both transcriptional and translational levels
transcriptional amplification: increase number of mRNA transcripts synthesized from the gene
translational amplication: increases number of protein molecules syntehsized from each mRNA transcript
35
Q
reporter genes and gene regulation
A
- genes that encode easily detectable proteins or enzymes whose expression levels can be used as indicators of the activity of regulatory elements controlling the expression of another gene of interest
- are often fused to the promoter region or regulatory sequences of the gene of interest, creating a reporter construct
-activity of the regulatory elements can be assessed by measuring the expression level of the reporter gene
36
Q
deletion mapping and gene regulation
A
- systematically deleting or mutating specific regions of a gene or its regulatory sequences to identify functional elements and determine their roles in gene regulation
- effects of deletions on gene expression are assessed by comparing the expression levels of the wild-type gene with those of the deletion mutants
37
Q
how nucleosomes impact binding and contribute to gene regulation
A
- positioning and density of nucleosomes along the DNA influence the accessibility of specific DNA sequences
- can either block or facilitate the binding of DNA-binding proteins depending on their positioning relative to the target site
- Remodeling complexes can evict or reposition nucleosomes to expose DNA sequences that are otherwise inaccessible, allowing DNA-binding proteins to access their target sites and regulate gene expression
- Histone modifications can influence the recruitment and activity of DNA-binding proteins, including transcription factors, by modulating chromatin accessibility and the binding affinity of these proteins for their target sites
- positioning of nucleosomes relative to gene regulatory elements, such as promoters, enhancers, and silencers, can impact gene expression
38
Q
cis regulatory elements
A
- DNA sequences located adjacent to or within the gene they regulate. - They exert their regulatory effects in a localized manner
Examples of cis-regulatory elements include promoters, enhancers, silencers, and insulators
39
Q
trans regulatory elements
A
regulatory factors, such as transcription factors and RNA-binding proteins, that are encoded by genes located elsewhere in the genome
- They act in trans, meaning they can influence the expression of target genes located at different genomic
loci
- modulating gene expression by binding to specific cis-regulatory elements and regulating transcriptional activity
40
Q
co-regulatory networks
A
- Transcription factors can form complex regulatory networks by interacting with co-regulatory proteins, such as co-activators and co-repressors, to modulate gene expression.
- Co-regulatory proteins can enhance or inhibit the transcriptional activity of transcription factors by influencing chromatin structure, promoting protein-protein interactions, and facilitating the assembly of transcriptional complexes
41
Q
mechanisms to stably maintain gene expression patterns in a given cell or cell lineage
A
- epigenetic modifications
- Histone modifications can alter chromatin structure and accessibility, influencing gene expression patterns
- epigenetic marks are inherited by daughter cells - chromatin remodeling complexes
- can reposition, evict, or modify nucleosomes, influencing the accessibility of regulatory elements and the transcriptional activity of target genes
- ensuring the fidelity of chromatin structure and the transmission of epigenetic information to daughter cells - regulatory feedback loops
- can stabilize gene expression patterns by providing buffering mechanisms that counteract fluctuations in gene expression levels and maintain homeostasis
42
Q
how mechanisms of gene regulation could allow coordinated expression of groups of genes during development or in response to external stimuli
A
- non-coding RNAs : miRNAs can target multiple genes within the same pathway or functional module, leading to coordinated regulation of gene expression
- signaling pathways: can converge on transcription factors and co-regulators, leading to the coordinated regulation of target genes
- transcriptional networks: integrate signals from multiple pathways and coordinate the expression of genes involved in specific biological processes or responses
43
Q
transcriptional regulation
A
- involves controlling the initiation of transcription from DNA to RNA by RNA polymerase.
- Key regulatory elements involved in transcriptional regulation include promoters, enhancers, silencers, and transcription factors
- allows cells to control which genes are transcribed and at what levels, providing a rapid and reversible mechanism for modulating gene expression
44
Q
post-transcriptional regulation
A
- refers to the regulation of gene expression after mRNA synthesis, involving processes that affect mRNA stability, processing, and translation
- Key mechanisms of post-transcriptional regulation include alternative splicing, mRNA stability, mRNA localization, microRNA (miRNA) regulation, and translational control
- involves regulating the rate at which mRNA molecules are translated into proteins
45
Q
components of a eukaryotic gene
A
- enhancer/silencer
- promoter
- 5’ UTR
- Exon
- Intron
- 3’ UTR
- Start codon
- Stop codon
- transcriptional initiation and terminations site
