Systems Biology Flashcards
What makes up the eukaryotic chromosome?
A DNA strand with coding and non coding regions
What is gene expression?
Turning on a gene to produce RNA and proteins
What does it mean to turn on a gene?
That the gene is being expressed because the DNA is unwound and can bind the necessary transcription factors and can be translated later
What is protein expression?
The type and abundance of proteins in the cell
What is the most common type of RNA?
Noncoding RNA
What are cis-regulatory elements?
These are elements on the same chromosome as the coding gene and help transcription occur
Do all the cells in an organism have the same genome?
Yes, basically 99.5% of the genome is the same
What is the central dogma of biology?
The process of going from the gene to flesh and blood
What is epigenetics?
The process of altering chromatin structure to turn genes on or off
What is heterochromatin?
When the DNA is tightly wound
What is euchromatin?
When the DNA is loosely wound
What are histones?
These are proteins that DNA is wrapped around
What are nucleosomes?
This is a set of 8 histones that are wound with DNA
What is chromatin?
A region of DNA with its corresponding proteins
What is a chromosome?
A condensed structure of DNA
What is involved in post-transcriptional regulation?
- Splicing
- 5’ Cap
- 3’ Poly A tail
What is splicing?
The process of using the spliceosome to remove the introns this makes the mature mRNA and can also help generate different types of proteins
What is the 5’ Cap?
This is a sequence that is added to the 5’ tail to ensure that the mRNA is not degraded
What is the poly A tail?
A tail of A’s that are added to the 3’end to ensure that the RNA is translated
Are there areas where there is less RNA expression and high protein production?
Yes, where the RNA is not degraded and is stabalized
Why do different alleles generate different phenotypes?
The slight variation in the gene sequence leads to altered amino acid sequences generating different proteins
What is differential regulation?
Turning on certain genes and leaving others off
What is common between relatives and family members?
Common alleles and gene regulation which leads to similar protein expression and phenotype
What is transdifferentiation?
Being able to change one tissue type into another
What can transdifferentiation allow us to do?
Alter the gene expression of a cell type to get another cell and there would be no fear of transplant rejection if you were to reprogram the cell from the same organism
What does an organisms’ phenotype depend on?
Cell number, type, and function
How does the outside of the cell communicate with the inside of the cell?
Through a signal transduction pathway with a cascade of events
What is genome sequencing?
Establishing the order of the genes and the nucleotide base pairs on a strand of DNA
What can genome sequencing allow us to do?
- Crime and investigation
- Understand phenotypes
- Prognosis of diseases
What do you need to understand how life works?
You need to identify all the parts of the macromolecules in the cell or organism as well as their function and determine how they interact with one another
What are system structures?
Identifying the components
What are system dynamics?
How it changes with time or if it stays constant
What are system controls?
Are the movements random how does it stop and start
What is a systems design?
In what ways can this system be improved
What is systems biology?
Exploring the components of an organism and how they all work together
What is the systems biology approach?
To analyze all the components and their interactions at once
What is a reductionist approach?
Analyzing all the components separately
What are nodes?
These are proteins or genes
What are the edges?
These are the binding and regulatory interactions
What is the difference between the protein-protein interaction compared to the gene regulatory interaction?
Protein interactions have no directionality which means that in the diagram blue can interact with red and red can interact with blue but gene regulation is one way from the RNA it makes the proteins you can’t go from protein to RNA
What is connectivity?
The number of interactions between the nodes
What does high connectivity mean?
It’s an essential gene that is involved in many different pathways
What are macromolecules?
Proteins, RNA , lipids, metabolites, genes
How do these different interactions give rise to a phenotype?
The signals pass into the cell through a cascade and lead to activation of a gene
What parameters of mRNA/proteins change in the cell?
- Abundance (synthesis/degradation)
- Interactions (complex components)
- Activity (enzymes)
What are perturbations?
Genetic mutations or changes from the environment
What is a negative feedback loop?
Controls the amount of product made eventually turns it off
What is a positive feedback loop?
It promotes the production of the product eventually turns it on
What is redundancy?
If something breaks down is there a backup
What are the structural stability elements?
DNA repair, checkpoints, and chaperones
What is modularity?
Sub networks are physically or functionally insulated to prevent component failure
How can you determine gene function?
- Perturb gene function
- Measure mRNA
- Measure protein abundance
- Predict protein structure
What is reverse genetics?
Deleting every gene and study the phenotype
What is genetic interaction mapping?
Creating double mutant combination and assays to determine lethality
What is transcriptomics?
Determine the abundance of all RNA molecules
What is proteomics?
Determine abundance and interactions of all proteins
What is metabolomics?
Determine abundance of metabolites
