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Biology MCAT > DNA Packaging and Organization > Flashcards

DNA Packaging and Organization Flashcards

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1
Q

What does proliferate mean?

A

To grow or multiply by rapidly producing new tissue, parts, or cells. Increase or spread at a rapid rate.

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2
Q

How many base pairs are in one diploid cell?

A

6 billion

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3
Q

How many linear chromosomes are in the human genome?

A

23 base pairs so 46 total chromosomes

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4
Q

How many of the 46 total chromosomes are autosomes?

A
  1. 22 are inherited maternally and 22 are inherited paternally.
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5
Q

How many of the 46 total chromosomes are sex chromosomes?

A
  1. 1 from mom 1 from dad. These determine the sex of the individual.
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6
Q

How is DNA organized in the most granular level?

A

Into nucleosomes.

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7
Q

What are nucleosomes?

A

They are microscopic structures that consist of about 200 base pairs of DNA twice wrapped around a spool of eight histone proteins, plus an H1 histone linker protein.

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8
Q

How are nucleosomes connected? And what does a series of nucleosomes look like?

A

They are connected to each other by Linker DNA and a series of nucleosomes look like beads on a string when examined by electron microscopy.

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9
Q

What is the very first level of organization for DNA packaging?

A

Nucleosome

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10
Q

What are chromatin fibers?

A

They are a chain of nucleosomes that are further condensed and packaged. Each fiber is about 30 nm in diameter.

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11
Q

What is the most condensed form of DNA organization?

A

The highly condensed chromosome.

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12
Q

What are heterochromatin?

A

Tightly packages, and tightly coiled, dense form of chromatin. This is what we see during cell division.

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13
Q

What are euchromatin?

A

They are chromatin with a loose, spaghetti-like configuration. They are hard to see under light microscopy. They also allow DNA to be readily replicated and transcribed.

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14
Q

Why is DNA negatively charged?

A

Because of its phosphate backbone.

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15
Q

Why are histones positively charged?

A

Because of the lysine on their histone tails.

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16
Q

How is the natural interaction between histones and DNA regulated?

A

By enzymes that add or remove acetyl groups from the positively charged lysine on the histone tail.

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17
Q

What is acetylation and how does that affect the interaction between DNA and histones?

A

It is the addition of an acetyl group. It reduces the interactions between histones and DNA because it promotes a looser confirmation in form of euchromatin to allow transcription for a set of genes.

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18
Q

What is deacetylation and how does that affect the interaction between DNA and histones?

A

It is the removal of an acetyl group. It tightens the interactions between histones and DNA which forms the tightly coiled heterochromatin.

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19
Q

What enzyme catalyzes deacetylation?

A

Deacetylase enzyme

20
Q

When in the cell cycle is most euchromatin found?

A

In the synthesis (S) phase.

21
Q

What is tubulin?

A

A fibrous protein that enables cell to undergo mitosis.

22
Q

What percentage of the human genome is non-coding (junk) DNA? How much is actual genes (single copy genes)?

A

Non-coding - 98.8%

Actual Genes - 1.2%

23
Q

How many single copy, protein encoding genes are in 3 billion base pairs? What does this mean?

A

20,000. This means that these genes are quite versatile because they allow us to produce about 2 million unique proteins thanks to modifying processes like alternative splicing of mRNA and other post-transcriptional and post-translational modifications.

24
Q

What is the 98.8% of “junk” DNA composed of?

A 
This DNA does not contain genes that encode proteins.
Transposons - 44%
Introns and Regulatory Sequences - 24 %
Unique non-coding DNA - 15%
Repetitive DNA - 15%
25
Q

Describe repetitive DNA

A

It is usually composed of short repeats and has a higher mutation rate.

26
Q

What are two examples of repetitive DNA?

A

Variable Number Tandem Repeats (VNTR) - repeats of a short DNA sequence usually about 10-100 base pairs in length.

Short Tandem Repeats (STR) - each repeat is even shorter so about 2-6 nucleotides per repeat

27
Q

What are polymorphisms?

A

Genetic differences (variation)

28
Q

What is a single nucleotide polymorphism (snip)?

A

They are stretches of DNA in the genome that may differ in just one nucleotide at a specific location between different people. It can be used as a sort of biological marker.

29
Q

How does a base pair difference qualify as a snip?

A

The single nucleotide present at that specific position must be found in at least 1% of the population.

30
Q

What are transposons (transposable elements)?

A

They are mobile genetic elements, sometimes called “jumping genes” because they are sequences that have the means to jump to other parts of the genome.

31
Q

What are the two major classes of transposons?

A

Class I Transposons (COPY and paste)

Class II Transposons (CUT and paste)

32
Q

Explain how Class I Transposons work

A

First transcribed into RNA and they encode a reverse transcriptase enzyme that then uses that RNA template to synthesize a DNA copy of the transposon sequence. It can inset itself wherever it pleases in the genome.

33
Q

Class I Transposons

A

It encodes a transposase enzyme that splices the transposon sequence out of DNA and allows it to put down roots elsewhere.

34
Q

Can transposons be harmful?

A

Yes, they can disrupt gene function in deleterious ways when they insert themselves inside the 1.2% of the genomes which is composed of actual gene sequences.

35
Q

Can transposons be beneficial?

A

Yes, because they are though to increase genetic diversity and accelerate evolution.

36
Q

Where is repetitive DNA found on centromeres?

A

They contain blocks of repetitive DNA sequences that are rich in G-C base pairs and tightly packaged as heterochromatin. This helps maintain structural integrity of this region of the chromosomes.

37
Q

What are telomeres?

A

They are repetitive sequences of non-coding DNA, made up of the repeat TTAGGG. These repeats cap the end of chromosomes which makes our cells less worried about faithfully replicating the very ends of chromosomes.

38
Q

Why are telomeres so important?

A

Because the end part of a DNA sequence is very difficult to replicate.

39
Q

What is the lagging strand usually left with?

A

A short single-stranded overhang.

40
Q

What happens after every round of replication?

A

With each round, the telomeric ends keep shortening and this becomes a problem after many rounds. This is why shortening telomeres is thought to contribute to cell aging and limit the number of cell divisions a cell is capable of.

41
Q

Which type of cells found a workaround to the telomere problem? What do they all have in common?

A

Germ cells, stem cells, and cancer cells. These cells all express an enzyme called telomerase, that is capable of extending telomeres. Therefore, these cells are unlikely to run the risk of telomeric shortening cutting into actual genetic sequences.

42
Q

What is Telomerase?

A

It is an RNA-dependent DNA polymerase that binds a RNA sequence complementary to the telomere repeat. Using this RNA molecule as a template to synthesize and extend telomere DNA. Then DNA molemerase fills in the complementary strand.

43
Q

Why might limits to cell division not be such a bad idea/

A

Because of cancer cells.

44
Q

What are electrostatic interactions?

A

Positive and negative interactions.

45
Q

Is the centromeric DNA sequence itself highly conserved?

A

No.

Biology MCAT (6 decks)

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