FOM 5.1.1 Flashcards
What class of human genomic DNA will have the least amount of UV-induced damage after a day at the beach? Why?
Exons b/c it makes up the smallest portion of DNA.
What is the clinical presentation of facioscapulohumeral muscular dystrophy (FSHD)?
Progressive, asymmetric weakness of upper extremities. (Scapular winging)
Unaffected people have 100 repeats near the end of a telomere, whereas people with FSHD have 1-10 repeats. What’s the most common chromatin status of repeats? Losing repeats can lead to what?
Heterochromatin. Loss of repeats can lead to decreased recognition by methylation machinery, which could lead to increased expression of nearby genes.
What are LINEs? What is their common function?
Long Interspersed Nuclear Elements. They are transposons that move around via RNA intermediates (retrotransposons)
SINEs are also know as ____
Alu repeats
What is different about SINEs compared to LINEs?
They’re shorter and inactive, but movement can be facilitated by nearby transposons.
What process converts an RNA transcript of LINE back into DNA?
Reverse transcription, which leads to re-integration
In study of overall survival, they analyzed methylation status compared to life expectancy. Did high or low methylation lead to increased survival?
High methylation led to increased survival (lower odds of dying)
When analyzing tumor stages, as the diseases progresses through the staging what are the corresponding methylation rates of LINE-1 and SINEs?
LINE-1 methylation decreased as stages increase. SINE (Alu) methylation was unchanged.
In familial hypercholesterolinemia (FH), what is elevated in the serum due to mutations in the receptor gene? Where is this deposited in the body?
LDL cholesterol. This gives rise to frequent tendon xanthomas along w/ accelerated atherosclerosis.
Look at the sequence in the picture. What is a possible outcome of cross over recombination?
See attached. This is because of the similarity of the Alu repeats found in the introns of the protein
How might we be able to activate histone acetylation? What would be the net effect?
Inhibit histone deacetylase (HDAT). The net effect would be opening up the DNA allowing for increased gene expression
What is genetic mosaicism? What are two potential origins of this condition?
The presence of multiple genomes. Two possibilities: mutation early in embryo development or fusion of multiple zygotes.
What does chromatin structure affect?
Gene expression
How much of the genome is repetitive sequences?
~1/2 (transposons, HERVs)
What is the most common form of the DNA Double Helix?
“B” double helix
How many BPs are in the human genome? Coding genes?
3.2X10^9 bp, 20,296 coding genes
Euchromatin vs. Heterochromation.
Eu: light staining, gene rich, actively expressed, referred to as “open” Hetero: dark staining, much is repetitive, gene free, highly compact
What is the difference b/t constitutive and facultative?
Constitutive: repeats, telomeres, centromeres Facultative: developmentally silenced genes
Where is DNA most readily methylated, accounts for ~70% of methylation?
5’-CpG pairs methylated on carbon-5
Is DNA methylation more or less reversible than histone methylation?
DNA methylation is less reversible (long-term modification). Can be done but it’s cumbersome.
What is the higher order of chromatin organization?
What are the components of the histone octamer? What is the linker histone?
2 of H2A, H2B, H3, H4 Linker: Histone H1
What are two AA’s highly present in histones?
Lysine and Arginine, highly basic
What are the effects of acetylation and methylation on histones?
Acetylation (Lys): looser, pro-txn Methylation (Lys or Arg): depends
How are histone modifications different than DNA modifications?
More dynamic
What is epigenetics?
Classically refers to info in DNA not based on sequence but still inherited. Examples: histone modifications, DNA methylation, and microRNA
What is the difference b/t interspersed repeats and tandem repeats?
Interspersed: spread out on same or different chromosome Tandem: repeats occur next to eachother
What are the 4 main types of repeats?
LINEs, SINEs, HERVs (Human Endogenous Retroviruses), DNA Transposon Fossils
Name the 3 types of Tandem repeats and location.
Satellite DNA (centromere), Minisatellite DNA (telomere), Microsatellite DNA (DNA fingerprint)
How many nucleotides per turn in most common form of DNA double helix?
10
Where does acetylation occur on histone proteins?
N-terminus
