FOM 5.1.1 Flashcards

1
Q

What class of human genomic DNA will have the least amount of UV-induced damage after a day at the beach? Why?

A

Exons b/c it makes up the smallest portion of DNA.

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2
Q

What is the clinical presentation of facioscapulohumeral muscular dystrophy (FSHD)?

A

Progressive, asymmetric weakness of upper extremities. (Scapular winging)

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3
Q

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?

A

Heterochromatin. Loss of repeats can lead to decreased recognition by methylation machinery, which could lead to increased expression of nearby genes.

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4
Q

What are LINEs? What is their common function?

A

Long Interspersed Nuclear Elements. They are transposons that move around via RNA intermediates (retrotransposons)

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5
Q

SINEs are also know as ____

A

Alu repeats

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6
Q

What is different about SINEs compared to LINEs?

A

They’re shorter and inactive, but movement can be facilitated by nearby transposons.

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7
Q

What process converts an RNA transcript of LINE back into DNA?

A

Reverse transcription, which leads to re-integration

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8
Q

In study of overall survival, they analyzed methylation status compared to life expectancy. Did high or low methylation lead to increased survival?

A

High methylation led to increased survival (lower odds of dying)

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9
Q

When analyzing tumor stages, as the diseases progresses through the staging what are the corresponding methylation rates of LINE-1 and SINEs?

A

LINE-1 methylation decreased as stages increase. SINE (Alu) methylation was unchanged.

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10
Q

In familial hypercholesterolinemia (FH), what is elevated in the serum due to mutations in the receptor gene? Where is this deposited in the body?

A

LDL cholesterol. This gives rise to frequent tendon xanthomas along w/ accelerated atherosclerosis.

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11
Q

Look at the sequence in the picture. What is a possible outcome of cross over recombination?

A

See attached. This is because of the similarity of the Alu repeats found in the introns of the protein

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12
Q

How might we be able to activate histone acetylation? What would be the net effect?

A

Inhibit histone deacetylase (HDAT). The net effect would be opening up the DNA allowing for increased gene expression

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13
Q

What is genetic mosaicism? What are two potential origins of this condition?

A

The presence of multiple genomes. Two possibilities: mutation early in embryo development or fusion of multiple zygotes.

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14
Q

What does chromatin structure affect?

A

Gene expression

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15
Q

How much of the genome is repetitive sequences?

A

~1/2 (transposons, HERVs)

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16
Q

What is the most common form of the DNA Double Helix?

A

“B” double helix

17
Q

How many BPs are in the human genome? Coding genes?

A

3.2X10^9 bp, 20,296 coding genes

18
Q

Euchromatin vs. Heterochromation.

A

Eu: light staining, gene rich, actively expressed, referred to as “open” Hetero: dark staining, much is repetitive, gene free, highly compact

19
Q

What is the difference b/t constitutive and facultative?

A

Constitutive: repeats, telomeres, centromeres Facultative: developmentally silenced genes

20
Q

Where is DNA most readily methylated, accounts for ~70% of methylation?

A

5’-CpG pairs methylated on carbon-5

21
Q

Is DNA methylation more or less reversible than histone methylation?

A

DNA methylation is less reversible (long-term modification). Can be done but it’s cumbersome.

22
Q

What is the higher order of chromatin organization?

A
23
Q

What are the components of the histone octamer? What is the linker histone?

A

2 of H2A, H2B, H3, H4 Linker: Histone H1

24
Q

What are two AA’s highly present in histones?

A

Lysine and Arginine, highly basic

25
Q

What are the effects of acetylation and methylation on histones?

A

Acetylation (Lys): looser, pro-txn Methylation (Lys or Arg): depends

26
Q

How are histone modifications different than DNA modifications?

A

More dynamic

27
Q

What is epigenetics?

A

Classically refers to info in DNA not based on sequence but still inherited. Examples: histone modifications, DNA methylation, and microRNA

28
Q

What is the difference b/t interspersed repeats and tandem repeats?

A

Interspersed: spread out on same or different chromosome Tandem: repeats occur next to eachother

29
Q

What are the 4 main types of repeats?

A

LINEs, SINEs, HERVs (Human Endogenous Retroviruses), DNA Transposon Fossils

30
Q

Name the 3 types of Tandem repeats and location.

A

Satellite DNA (centromere), Minisatellite DNA (telomere), Microsatellite DNA (DNA fingerprint)

31
Q

How many nucleotides per turn in most common form of DNA double helix?

A

10

32
Q

Where does acetylation occur on histone proteins?

A

N-terminus