Function And Dysfunction In Genomic Regulation Flashcards
What is the total volume of the cell that the nucleus takes up?
6%
What is the very basic explanation of the central dogma?
DNA is transcribed to RNA which is translated into proteins.
What enzyme do RNA viruses such as HIV use to incorporate their RNA into host DNA?
Reverse transcriptase
Describe the structure of DNA
DNA is double stranded and anti parallel, forming a double helix with a major groove and a minor groove.
The two sides of DNA are held together by what type of interaction?
Hydrogen bonds.
A double bonds to T
C triple bonds to G—this is a stronger bond.
Why are mitotic chromosomes condensed 500 times when compared to chromosomes in interphase?
This condensation prevents physical damage to the DNA while the chromosomes are separating.
To condense DNA, it is wrapped around what type of proteins, and how many hydrogen bonds are formed?
What is this DNA-protein structure called?
DNA wraps around histone octamers, forming 142 hydrogen bonds.
This structure is referred to as a nucleosome.
What amino acid residues are abundant in histone proteins?
Lysine (K) and Arginine (R)
Remember that the location sequence for proteins destined for the nucleus are also rich in K and R. This makes sense because histones need to be transported to the nucleus to make nucleosomes.
What residues in the histone are targets of post translational modifications?
Lysine is the most highly targeted residue.
What is the term for NON-HISTONE chromosomal proteins?
Transcriptions factors
euchromatin vs heterochromatin
Euchromatin is loosely packed, allowing the DNA to be more easily reached for transcription and translation. Genes of highly expressed proteins are euchromatin.
Heterochromatin is very condensed and stains darkly. This DNA is genetically inactive and found near centromeres and telomeres.
Describe the Position Effect
Activity of a gene depends on the relative position on the chromosome.
Who first published a paper asserting the double helical structure of DNA? Who actually did all the work to obtain this information?
Watson and Crick described this model in a paper in 1953.
Rosiland Franklin produced the images that led to this paper.
Who determined the genetic code, when?
Nuremberg, Khorana, and Holley in 1966.
The Human Genome Project, when and what was it?
What surprising but helpful information was discovered?
Started in the 90’s and ended in 2004.
A project to sequence the entire human genome.
Genes in human and mice are INCREDIBLY similar, therefore they are excellent lab models.
The majority of DNA is…..
Non coding/regulatory.
Only 1.5% is coding
What kind of testing can be done to help with personalized medicine?
CGH (Comparative Genome Hybridization) arrays.
Compare patient’s DNA against a reference DNA to determine Copy Number Variations (CNV)
RNAi is carried out by what molecule and how does it work?
miRNA—
MicroRNA folds back on itself (double stranded) via hydrogen bonds, and then is cleaved into small pieces via Dicer enzyme. These, now single stranded pieces are carried to target mRNA via protein complex. Once bound to the target mRNA, expression prevented by degrading the target, or by blocking transcription.
On average, how many alternative splicing products does a gene have?
Two.
There are only 26k genes that encode for ~100k proteins.
What base pairs do introns begin and end with?
[…GT] and [AG…]
What do Histone Deacetylase (HDAC) and Histone Acetyl Transferase (HAT) do and how does that relate to gene expression?
HDAC—takes acetyl off histone proteins. This allows the DNA to be more condensed, and therefor turning genes off.
HAT—puts acetyl on the histones. This makes the DNA less condensed and more easily accessible, turning the gene on.
What part of the nucleosome undergoes post translational modification most regularly?
What kind of modifications can occur?
Histone tails are the target of numerous PTMs.
They can be modified in many ways:
- Methylation
- Acetylation
- Phosphorylation
- Ubiquitination
- SUMOylation
- Citrullination
- ADP-ribosylation
DNA Methylation: what kind of enzyme preforms this action, and what does it do to DNA?
Methyl transferases add methyl groups to cytosine and adenine.
Methylation represses transcription when at a gene promoter.
What happens when CpG islands are hypermethylated?
Gene promoter CpG islands can be hypermethylated. This trascriptionally silences the gene.
This methylation can be inherited by daughter cells. (Epigenetics)
In what direction does DNA-dependent DNA polymerase synthesize new DNA?
DNA is made from 5’-3’
DNA that is being read, is read 3’-5’