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BIOS 222 with Kay and Wherpa > Chapter 5 The Structure of DNA > Flashcards

Chapter 5 The Structure of DNA Flashcards

1
Q

What are the bases in DNA?

A

ATCG

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2
Q

How are nucleotides connected across the double helix?

A

Hydrogen bonds

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3
Q

What is the structure of the nucleotide?

A

A base covalently bonded to the sugar phosphate backbone.

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4
Q

How is the sugar phosphate backbone held together to form polynucleotide chains?

A

Covalent bonds called phosphodiester bonds. These bonds link a DNA sugar to a phosphate group to another sugar to another phosphate group and so on. The bases link to the DNA sugar covalently.

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5
Q

How many polynucleotide chains make-up DNA?

A

2, held together by base pairs covalently linked

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6
Q

in Griffith’s experiment, hat were the two stains of bacteria used?

A

A smooth strain and a rough strain. The rough strain was non-virulent because antibodies were able to attach to its surface. The smooth strain was virulent because antibodies were not able to attach to it surface.

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7
Q

In Griffith’s experiment, which mice died?

A

Mice injected with smooth strain and heat killed smooth along with living rough strain lived.

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8
Q

Describe Avery, MacLeod and McCarty’s experiment?

A

He fractionalized the S-stain bacterial cells into RNA, protein, DNA, lipids and carbohydrates. He then added each fractionalized component to R-strain bacteria. The only fraction that caused transformation was the DNA.

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9
Q

Describe the Hershey Chase experiment?

A

Viruses are made of protein and DNA. Each was labelled with a radioactive protein. 32Phosporous for the DNA and 35Sulfur of the protein. The labelled viruses were then added to e. coli. After incubation the resulting soup was blended and centrifuged. The heavy bacteria formed a pellet. Whatever radioactive label was in this pellet would be the molecule of heredity. It was DNA. The radioactively labelled 32P was passed on to the dexter generation of bacteriaphages.

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10
Q

What is Chagraff’s rule?

A

The number of A=T and the number of C=G

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11
Q

How many hydrogen bonds form between A and T?

A

2

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12
Q

How many hydrogen bonds form between G and C?

A

3

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13
Q

What does anti-parelle mean?

A

oriented in the opposite direction

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14
Q

Where are phosphodiester bonds formed?

A

Between the 3’ Hydroxyl (-OH) of the sugar and the the 5’ of the phosphate

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15
Q

What are purines?

A

A and G. They have a two ring base

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16
Q

What are pyrimidines?

A

T and C. They are less bulky have and have single ring bases.

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17
Q

How does the width of the alpha helix stay consistent?

A

The purine and the pyrimidines always pair with their opposite.

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18
Q

What does each protein coding gene make?

A

An RNA molecule

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19
Q

What are chromosomes?

A

A long threadlike structure composed of DNA and proteins that carries he genetic information of an organism. it is only visible when it prepares to divide.

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20
Q

How to prokaryotes carry DNA?

A

in a single circular molecule, it is called a chromosome, but its structure is entirely different from eukaryotic chromosomes

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21
Q

What does each chromosome consist of?

A

One enormously long strand of DNA that is folded and packed into compact chromatin structure.

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22
Q

When are chromosomes post compact?

A

In the middle of nuclear division

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23
Q

What are homologous chromosomes?

A

The pair of inherited maternal and paternal chromosomes

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24
Q

Male/female genetic difference?

A

Both male and female get an x-chomsome from their mother. But, males get and y from their father in addition to an x from their mother

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25
Q

What is a karyotype?

A

An ordered display of the of the full set of human chromosomes.

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26
Q

What is FISH?

A

Fluorescent In Situ Hybridization. Used fluorescent probes to detect DNA sequences. Often used to used in human genetics to analyze the chromosomal content of cells and to detect mutational changes in chromosomes. It can detect the deletion of a gene.

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27
Q

What does FISH do?

A

It detects the location of a gene on a intact chromosome

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28
Q

What dies In Situ mean?

A

It is Latin for “In place”

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29
Q

How does it work?

A
  1. ) Cell arrested in metaphase
  2. ) Treated to make them swell
  3. ) They are then fixed on to the surface of a slide. This also fixes the chromosomes to the surface of a slide
  4. ) Chromosomal DNA is denatured into single stands
  5. ) DNA probes are flooded on to the slide. The DNA probes are small pieces of single stranded DNA with a complementary sequence to the gene of interest.
  6. ) They hybridize with the gene of interest (They DNA probes are either fluorescently labelled or fluorescent labels are attached to them).
  7. ) They are then viewed under a fluorescent microscope and the location of the gene of interest is revealed.
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30
Q

How does it work?

A
  1. ) Cell arrested in metaphase with colchicine
  2. ) Treated to make them swell
  3. ) They are then fixed on to the surface of a slide. This also fixes the chromosomes to the surface of a slide
  4. ) Chromosomal DNA is denatured into single stands
  5. ) DNA probes are flooded on to the slide. The DNA probes are small pieces of single stranded DNA with a complementary sequence to the gene of interest.
  6. ) They hybridize with the gene of interest (They DNA probes are either fluorescently labelled or fluorescent labels are attached to them).
  7. ) They are then viewed under a fluorescent microscope and the location of the gene of interest is revealed.
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31
Q

What does DNA hybridization work?

A

The DNA of one organism is labeled, then mixed with the unlabeled DNA to be compared against. The mixture is incubated to allow DNA strands to dissociate and renewal forming hybrid double-stranded DNA. Hybridized sequences with a high degree of similarity will bind more firmly, and require more energy to separate them: i.e. they separate when heated at a higher temperature than dissimilar sequences, a process known as “DNA melting”.

To assess the melting profile of the hybridized DNA, the double-stranded DNA is bound to a column and the mixture is heated in small steps. At each step, the column is washed; sequences that melt become single-stranded and wash off the column. The temperatures at which labeled DNA comes off the column reflects the amount of similarity between sequences (and the self-hybridization sample serves as a control). These results are combined to determine the degree of genetic similarity between organisms.

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32
Q

What happens in metaphase in cells?

A

When centrosomes line up the sister at the center of the center of the cell right before they are to be pulled apart in cell division.

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33
Q

What happens in metaphase in cells?

A

When centrosomes line up the sister at the center of the center of the cell right before they are to be pulled apart in cell division.

34
Q

Which part of DNA is charged?

A

The phosphate group on the sugar phosphate backbone

35
Q

How does DNA end?

A

With a 3’sugar or a 5’phosphate group.

36
Q

How much DNA is in the average human cell? How long is the nucleus?

A

2 meters

5-8 um

37
Q

What are the four levels of DNA packaging?

A
  1. ) Double helix
  2. ) Nucleosome
  3. ) Chomatin fiber
  4. ) DNA looping
  5. ) Chromosome
38
Q

What are nucleosomes?

A

Consists of DNA and histone proteins. It is the second level of DNA packaging. Sometimes referred to as bears on a string. DNA wraps around it 1.67 times.

39
Q

What are histone proteins?

A

They are a major class of proteins that are bound to DNA to form the nucleosome.

40
Q

What are the classes of histone proteins? How are they classified?

A

H1, H2A, H2B, H3, H4

They are classified by the ratio of the lysine: arginine amino acid present in the protein

41
Q

How many histone proteins per nucleosome core?
What is the function of the nucleosome core?
Which histone make up the nucleosome core?

A

8 histone proteins form the positively charged core around which the negatively charged DNA easily winds.
The nucleosome core is made of H2A:H2B pairs (dimers) and two H3:H4 pairs

42
Q

What is the linker histone? What does it do?

A

H1. It connects each core together

43
Q

Why are histone cores positive?

A

Because of the lysine and arginine present.

44
Q

What is a chromatin fiber?

A

The 30nm chromatin fiber is made of nucleosomes connected by the H1 protein. It is the third level of DNA packaging.

45
Q

What is DNA looping?

A

The forth level of DNA structure. The 30 nm fiber are packaged in to a looping structure that insists of thicker fibers.

46
Q

How many base pairs are in each DNA loop?

A

50,000-100,000 pairs

47
Q

What are chromosomes?

A

Chromatin is packed into chromosomes with contain long strings of gene.

48
Q

What are the two states that chromosomes exist in?

A

Interphase chromosomes, which are less condensed long threats of DNA because they are so spread out they cannot be seen

Metaphase chromosomes, which are more condenses because of this condensation they can be seen.

49
Q

What is the centromere?

A

structure that bind to the mitotic spindle during mitosis and allows for separation. No DNA sequence has been identified for them

50
Q

What is the kinetochore?

A

region where centromere associated proteins bind

51
Q

What is a karyotype?

A

It is an ordered set of the full set of an organism’s chromosomes. 23 homologous pairs expect for the the sex chromosome in men.

52
Q

What is a telomere?

A

End of the chromosomes that contains repetitive sequences that allow for chromosomal replication

53
Q

What states do chromatin exist in?

A

Euchromatin: A less condensed DNA structure
Heterochromatin: A more condenses DNA structure

54
Q

What does euchromatin do?

A

It allows packaged DNA to be accessible to other proteins

55
Q

Describe heterochromatin?

A

Because it is condenses the genes on heterochromatin are not expressed, therefro it contains few genes.

It is found mainly in centromere sand telomeres

56
Q

What control the entry and exit of large molecules from the nucleus?

A

Nuclear pore complex (NPC)

Small molecules can enter the nucleus without regulation, but large macromolecules such as RNA and proteins requires association with improtin to ender the nucleus and exportin to exit.

The number of NPC vary with the cell size and activity
roughly 200 in yeast
2000-5000 in a proliferating human cell

57
Q

What the structure of NPC that extends in the nucleoplasm?

A

It is a basket like structure called the nuclear base

58
Q

Does the passing of large molecules require energy?

A

Yes, it requires GTP. Anything under 40 kDa and pass by diffusion.

59
Q

How are cells bound for the nucleus identified?

A

They have an amino acid tag on the exposed surface of the protein. Generally it is positively charges and made of lysine and arginines. This is called the Nuclear localization signal (NLS).

The residues are not necessarily in a row. Sometimes they are together, sometimes they are separated.

60
Q

What does it mean that NLS tags are necessary and sufficient?

A

That it removed there is nothing else that will sent the macromolecule to the nucleus and if transferred to another cell that doesn’t become in the nucleus it will be sent there anyway

61
Q

Describe the structure of the nuclear pore?

A

cytosolic fibrils extend in the the cytosol, a nuclear basket extends in the the nucleus. It is a complex structure of 30 proteins. It is implanted in the nucleus’ double membrane structure. There are gel like fibers at its center, which interact with the phenylalanine on importune beta subunit and those many interactions move it through the pore.

62
Q

How does the NLS get the the cargo into the cell?

A

It is recognized by a nuclear import receptor, which directs the newly synthesize protein into a nuclear pore by interacting with the tentacle like fibril that extend from the of the pore. After it is captured, it moves through the gel-like meshwork of nuclear fibrils until entry into the nuclear pore triggers cargo release.

63
Q

What is RAN GTP?

A

It is in the nucleus. It binds to importin’s beta subunit causing it to discharge its cargo. It then powers the importin out of the cell.

64
Q

What is importin?

A

It is the nuclear import receptor that brings macromolecules into the nucleus. The alpha part grips the cargo and the beta part has amino acids (phenylalanine) that interact with the gel-like meshwork and guide it through the nuclear pore

65
Q

How can a macromolecule with an NLS be prevented from entering the cell?

A

1.) Phosphorylation (adding of a negative charge) to residues adjacent to the NLS can prevent it from binding to importin
2.) Conformational changes to the macromolecule with the NLS can prevent it from going towards the nucleus.
3.) Changes in protein protein interaction hiding the NLS
For example, if the NLS is covered it cannot bind to importin.
4.) Changes in calcium concentration lead to conformation changes exposing or hiding an NLS.

66
Q

How is androgen regulated?

A

When a hormone is passed through the membrane, it binds to its receptor and exposes the NLS. The hormone bound receptor then enters the nucleus and then encourages transcription to RNA of of genetic code for male proteins.

67
Q

What is RAN?

A

a small GTPase. It binds GTP and GDP. Changes shape depending on which it is bound to.

68
Q

Describe the structure of importin?

A

Importing alpha–cargo recognition (detects the NLS)

Importin beta–pore recognition

69
Q

What is the nuclear export signal (NES)?

A

A short sequence of the 5-6 hydrophobic residues on a protein that target it for export from the cell nucleus to the cytoplasm.

It is recognized by and bound by exportin

70
Q

Describe the process by which exportin leaves the cell?

A

In the nucleus exporting bind the cargo and RanGTP and diffuses through the cytoplasm. Once in the cytoplasm, cleaving the RanGTP to RanGDP releases the cargo.

71
Q

What is the zone of inactivation?

A

restrcition of expression of genes placed near heterochromatin

72
Q

What is position effect?

A

The activity of a gene depends on relative location to heterchromatin

73
Q

What is a karyotype?

A

An individual chromosome composition

74
Q

How are the condensation state of DNA created?

A

Through histone modification because histone control the packaging and modification of DNA

75
Q

What is on the tail of each histone protein?

A

An N-tail. The amino acids on the tail can be covalently modified to the effect the condensation of the DNA

76
Q

Name two common type of histone modification?

A

Acetylation and methylation

77
Q

What does acetylation do?

A

It removes a positive charge from the histone and loosens chromatin structure

78
Q

What does methylation do?

A

It tighten chromatin structure and prevent acetylation

79
Q

Discuss ranGTP and ran GDP concentration in the cell?

A

GTP is 10x concentration in the nucleus. GDP is 10x concentration cytoplasm
This is controlled by proteins on either side the regulate the making to the structure.

80
Q

Is ranGTP necessary to bind cargo for nuclear export?

A

YES!

81
Q

How does HIV use nuclear export?

A

The Rev protein somehow coopts the importin/exportin system to favor the replication and transport out the cell code to build more virus

82
Q

Why are some human diseases caused by a defect in the NLS or NES?

A

Many cancers occur because of mutation in the NLS. Moreover, the cell may have the right protein, but if it doesn’t get to its target (the nucleus) it cannot fulfill its function.

BIOS 222 with Kay and Wherpa (12 decks)

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