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Biology 202 > Lecture 8 - DNA Structure II > Flashcards

Lecture 8 - DNA Structure II Flashcards

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1
Q

Genome Info

A

Human genome has been completely sequenced
Contains about 20,000 protein coding genes
Average genome is about 25kB

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2
Q

Comparing genomes

A

Similarity between two human genomes is about 99.7% (SNP’s and copy number variation)
Single base pair differences between humans is called SNP’s, about 10 million SNP’s, can change alleles
SNP’s close to each other are more likely to be inherited together, more similar to parent than stranger

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3
Q

What is repeat DNA?

A

Repeated sequences are patterns of nucleic acids that occur in multiple copies throughout the genome. Repetitive DNA was first detected because of its rapid re-association kinetics (denatured and allowed to renature)

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4
Q

Does repeat or non repeat DNA come together faster?

A

Repeated DNA - the composition of each sequence is the same meaning in can come together faster

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5
Q

What is tandem repeated DNA?

A

When repeated units are right next to each other, known as SSR’s, usually less than 10bp’s, usually non-coding regions
Can give chromosome unique properties

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6
Q

What are the three types of repeat DNA?

A

Regular satellite (about 10^5-10^7 bp)
Minisatellite (about 10^2-10^5 bp)
Microsatellite (about 10^1-10^2 bp)

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7
Q

What do centromeres and telomeres do?

A

Centromeres - spindle firbres attatch to on sister chromatids
Telomeres - ends of linear chromosomes
Both full of tandem repeats

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8
Q

How does DNA fingerprinting work?

A

DNA + restriction enzymes (cuts fragments of DNA), transferred to gel, then to paper, probe, rinse, analyze inheritance
Microsatellite DNA is now done instead of Restriction Fragment Length Polymorphism (RFLP)

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9
Q

How is everyone’s tandem DNA different?

A

They are different sizes, it is very unlikely that two non related people have the same profile.

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10
Q

What are some repeat DNA diseases?

A

Huntington’s disease (>36 repeats, protein doesn’t function properly, it accumulates and causes death), Fragile X, and Myotonic Dystrophy

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11
Q

What is interspersed repeated DNA?

A

Repeat DNA is scattered throughout the genome

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12
Q

What are transposons?

A

A transposable element is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell’s genetic identity and genome size. Transposition often results in duplication of the same genetic material

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13
Q

What are LINE’s and SINE’s?

A

LINE - Long interspersed nuclear elements, contains genes required for their own mobilization
SINE - Short interspersed nuclear elements, does not contain genes required for their own mobilization

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14
Q

Describe bacterial chromosomes

A

Circular, nucleoid region, and negatively supercoiled

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15
Q

Describe bacterial plasmids

A

Pieces of DNA for specialized functions and replicate autonomously

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16
Q

What is chromatin?

A

Mixture of DNA and proteins, 10-3-0nm in diameter, these chromatin fibers condense into chromosomes

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17
Q

What is the difference between chromatin and chromosomes?

A

chromatin consists of the unraveled condensed structure of DNA for the purpose of packaging into the nucleus whereas chromosome consists of the highest condensed structure of the DNA double helix for the proper separation of the genetic material

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18
Q

What are histones and what do they do?

A

Most abundant protein in chromatin, DNA binds to them through ionic bonding, it helps condense it into chromatin

19
Q

What are the 5 highly conserved histone proteins?

A

H1, H2A, H2B, H3, and H4

20
Q

What is a nucleosome?

A

Chromatins repeating structural unit “beads on a string”, 10nm diameter

21
Q

What is the relationship between histones and nucleosomes?

A

Each nucleosome contains a histone protein core (8 histones), made of dimers of H2A, H2B, H3, and H4, the base pairs of DNA wrap around and gets smaller

22
Q

What is the first step in DNA packaging?

A

Nucleosome formation (DNA wraps around histone complex)

23
Q

What is the second step in DNA packaging?

A

The linker DNA binds the H1 histone, nucleosomes undergo further packaging, diameter increases from 10nm to 30nm

24
Q

What alters levels of gene expression? Provide 2 examples

A

Chromatin remodeling. Acetylation - looser packing, methylation - tighter packing

25
Q

What is the last step in DNA packaging?

A

Fiber is packed in a zig-zag structure then looped domains, then looped domains attach to an insoluble protein network (chromosome scaffold proteins)

26
Q

What are the different levels of increasing diameters?

A

2nm, 10nm, 30nm, 300nm

27
Q

What is heterochromatin?

A

Regions of DNA that are not actively transcribed may be further compacted, results in low accessibility. Some cells have other cells that are not necessary for their function so its stored as this

28
Q

What is euchromatin?

A

DNA that is being actively transcribed is more loosely packed

29
Q

What are some activities that occur in the nucleus?

A

Chromosome storage, transcription activity, and ribosome synthesis. Bound by the nuclear envelope (double membrane)

30
Q

On a diagram of a cell, what do the different colors indicate?

A

Different colors mean differences in thickness - how densely everything is packed

31
Q

Describe the nuclear structure

A

Nuclear membranes are separated by the perinuclear space, the outer membrane is continuous with the endomembrane system and studded in places with ribosomes, also have proteins, contains nuclear pores that allow passage in and out of the cell

32
Q

Do nuclear pores go through both layers of the membrane?

A

Yes, anything that leaves or enters the cell has to go through a pore

33
Q

Describe the nuclear pore complex

A

Multisubunit protein complex and the center of the pore is filled with a large transporter protein

34
Q

What passes through the pores?

A

out - ribosomes/rRNA, mRNA, tRNA, regulatory RNA
in - proteins/histones and enzymes
Mostly based on size, small will slip through and big need to be carried (nuclear import/export)

35
Q

What are the functions of the nuclear localization signal and importin?

A

Proteins that are synthesized in the cytoplasm and function in the nucleus have this signal, needs this signal to enter the nucleus if its too big
Importin (protein) in the cytoplasm recognizes the NLS and binds to the protein, complex then moves into the nuclear pore

36
Q

What happens in the nucleus during nuclear import?

A

RAN is activated by RCC1 (GEF), RAN-GTP binds to importin, cargo is released, RAN-GTP-importin complex is transported out of the nucleus through pores, then GTP is hydrolyzed (RAN-GAP), importin is released, RAN taken back to nucleus by NTF2

37
Q

What are the two functions of RAN?

A

Release cargo and get importin out of the nucleus

38
Q

What is the nuclear export signal and associated protein on adapter proteins that bind to RNA cargo?

A

NES and exportin proteins (bind RAN-GTP)

39
Q

What is the function of the nucleoskeleton?

A

Helps maintain the shape of the nucleus and provide a skeleton for chromatin fibers

40
Q

What is the function of nuclear lamins?

A

Localize to inner surface of inner membrane (intermediate filaments)

41
Q

What does the term “chromosome territory” refer to?

A

The chromatin of each chromosome has its own discrete location

42
Q

What is the function of the nuncleolus? What are fibrils and granules?

A 
Ribosomal subunits are assembled, the more proteins = more ribosomes = bigger
Contains fibrils (DNA being transcribed into RNA) and Granules (rRNA being packaged with proteins)
43
Q

What is the nucleus organizer region (NOR)?

A

Stretch of DNA containing many copies of rRNA genes (bit of chromosome is “dipping in” to the nucleolus)

44
Q

What are some other nuclear structures?

A

Cajal bodies, gemini of cajal bodies, speckles, PML bodies

Biology 202 (4 decks)

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