Unit 2 Review Flashcards
(18 cards)
Describe, from an evolutionary perspective, the importance of gene regulation and relate this to the different levels at which gene regulation may occur.
In an evolutionary perspective, gene regulation allows an organism to respond adaptively to changing environments
Different Levels:
1. Epigenetic regulation
- histone modification
- DNA methylation
2. Transcriptional Regulation
- regulatory protiens
3. Post-Transcriptional Regulation
- mRNA splicing
4. Translational Regulation
- control mRNA translation amount
5. Post-Translational Regulation
- protein modification- phosphorylation
Describe—using drawings and text—how multiple genes in bacteria can be controlled by the same promoter and regulatory region (e.g., an operon)
Drawing
Here’s how an operon works, step-by-step:
Promoter:
The operon begins with a promoter, a DNA sequence where RNA polymerase binds to start transcription. The promoter is the site where the transcription machinery initiates the process of transcribing the genes into mRNA.
Operator:
Close to the promoter is an operator, a DNA sequence that acts as a binding site for a repressor protein. The repressor can block the action of RNA polymerase, preventing transcription of the genes in the operon. If the repressor is bound to the operator, transcription does not occur.
Genes:
The operon contains multiple genes that are related in function. These genes are arranged in a linear sequence and are transcribed together into a single mRNA molecule. In bacteria, these genes often code for enzymes that work together in a metabolic pathway (e.g., enzymes for breaking down a sugar).
Regulatory Protein (Repressor/Activator):
A regulatory protein, often a repressor, can bind to the operator region and prevent transcription. However, environmental conditions or other signals can influence whether the repressor is active or not. For example, in the lac operon, when lactose is present, a repressor is inactivated, allowing transcription to proceed.
Transcription and Translation:
If the repressor is not bound to the operator, RNA polymerase can move past the promoter and operator, transcribing the genes into a single mRNA. This mRNA is then translated into proteins. Since all the genes are transcribed together, the proteins are made in equal amounts, allowing a coordinated response to environmental changes.
Example - The Lac Operon:
In the lac operon of E. coli, genes involved in lactose metabolism (like lacZ, lacY, and lacA) are controlled by a single promoter. The repressor binds to the operator when lactose is absent, preventing the expression of these genes. When lactose is present, it binds to the repressor, changing its shape and causing it to release from the operator, allowing the genes to be transcribed and the enzymes needed for lactose metabolism to be produced.
Describe—using drawings and text—how DNA binding proteins can regulate transcription initiation in bacteria
Drawing
Activator proteins: Bind upstream of the promoter to help RNA polymerase initiate transcription.
Repressor proteins: Bind to the operator to prevent RNA polymerase from binding to the promoter or initiating transcription.
Inducers and co-repressors: Regulate the activity of repressors and activators, providing a way for bacteria to adapt to environmental changes.
Differentiate between cis and trans regulatory elements.
Cis-regulatory elements: Located on the same DNA molecule as the gene they regulate (e.g., promoters, enhancers, silencers).
Trans-regulatory elements: Usually proteins or RNAs that are produced elsewhere in the genome and act on distant cis-regulatory elements (e.g., transcription factors, repressors, activators).
Describe—using drawings and text—how small molecules can influence the activity of a DNA binding protein (e.g., bind a change its shape)
Small molecules regulate DNA-binding proteins by inducing conformational changes that influence the protein’s ability to interact with DNA. This regulatory mechanism allows cells to quickly and efficiently respond to environmental signals, modulating gene expression without changing the underlying DNA sequence.
Describe the role of antisense RNA in regulation of gene expression
Antisense RNA regulates gene expression primarily by forming complementary base pairs with sense RNA (mRNA), which can lead to:
mRNA degradation,
Inhibition of translation, or
Disruption of RNA-RNA interactions that control other aspects of gene expression.
This regulation allows cells to control gene expression at the RNA level, adding an additional layer of flexibility and precision in gene control.
Describe gene regulation by riboswitches.
Riboswitches are RNA-based regulatory elements that control gene expression in response to small molecule binding. They function through transcriptional regulation by forming structures that cause transcription termination or through translational regulation by controlling access to the ribosome-binding site. Riboswitches provide a fast and energy-efficient way for cells to adapt to changing environments by modulating gene expression based on the availability of specific metabolites or other small molecules.
Explain what genomic equivalency is.
same genome different function across somatic cells
Describe how modifications to chromatin structure affect gene expression
Chromatin structure controls gene expression by regulating DNA accessibility.
Loosening chromatin (via acetylation or remodeling) → activates gene expression.
Tightening chromatin (via deacetylation, methylation) → represses gene expression.
These modifications allow eukaryotic cells to dynamically regulate genes during development, in response to signals, or across different cell types.
Discuss the differences between promoters (both core and regulatory) and enhancers.
Core promoters are essential for starting transcription and binding general transcription machinery.
Regulatory promoters nearby help fine-tune expression by binding specific transcription factors.
Enhancers are distal elements that boost gene expression, often in a cell-type-specific or signal-dependent way, by interacting with promoters through chromatin looping.
Where they occur: somatic vs germline mutation consequences
Somatic mutation- will not be inherited to offspring and often caused by environmental factors
Germline mutation- passed to offspring, inherited from parents
types of mutations: Base substitutions, insertions, deletions, expanding nucleotide repeats
Base Substitution: alterations of a single nucleotide
Two Types:
1. Transition: purine is replaced with different purine
2. Transversion: purine is replaced with pyrimidine
Insertions: adding one of more nucleotides
Deletions: removing one or more nucleotide pairs
Functional consequences:
Missense, Nonsense, Silent
negative, positive, neutral
loss-of-function mutation vs. gain-of-function mutation
Missense Mutation: a base substitution that results in a different amino acid in the protein
Silent Mutation: is a missense mutation that alters the amino acid sequence of a protein but does not change its function
Nonsense Mutation: changes a sense codon to a nonsense codon- terminates translation
Neutral Mutation: is a missense mutation that alters amino acid sequence of a protein but does not significantly change its function
Loss-of-Function: cause the complete or partial absence of normal protein function
Gain-of-Function: causes the appearance of a new trait or causes expression at an inappropriate time
Causes:
Spontaneous Replication errors: on your own pick one and explain molecularly
Spontaneous Chemical changes
Chemically Induced Mutations: on your own pick one and explain molecularly
Radiation alpha, beta, gamma, x-ray and UV light.
Transposable elements
Spontaneous Replication Errors: Tautomeric shift- if base exists in rare tautomer then bases can pair with other uncommon bases
Spontaneous Chemical Changes: Depurination- loss of purine base from nucleotide- can change C to U
Chemically Induced Mutations: Alkylation- add alkyl group (CH3) is added to guanine and can then allow it to pair to thymine
Radiation-Induced Mutations: Effect of UV- UV can induce mutations can cause pyrimidine dimers to form and cause thymine-thymine bonds which make it hard to replicate DNA
Repair: be able to describe how 1 repair mechanism from C18 works we will go over Nucleotide-excision repair
NER works by detecting and removing damage to the DNA helix and replacing it with the correct nucleotide sequence.
