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Intro Molecular Biology > Midterm 1 > Flashcards

Midterm 1 Flashcards

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1
Q

Chromosomes

A

Long double-stranded DNA molecules

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2
Q

What is the purpose of DNA packaging?

A

Increases organization, thus no messes

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3
Q

What is the structure of bacteria chromosomes?

A

Single, circular DNA

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4
Q

Chromatin

A

DNA and protein

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5
Q

Homologous chromosomes

A

The maternal and paternal chromosomes of a pair

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6
Q

What technique does chromosome painting use?

A

DNA hybridization

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7
Q

How does chromosome painting work?

A

Different colours of fluorescent dye are applied to the chromosome which can form base pairs (hybridize) to certain ones

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8
Q

What is the traditional way of staining?

A

Dyes that bind to certain DNA sequences, such as those with A-T vs G-C, producing different bands

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9
Q

Karyotype

A

A display of the full set of 46 chromosomes with homologous one numbered and arranged in pair

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10
Q

Gene

A

Segment of DNA that contains instructions to make a functional protein or RNA molecule

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11
Q

What do the RNA molecules produce?

A

A protein or can be the final product itself

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12
Q

Genome

A

The total genetic information carried by all the chromosomes in a cell or organism

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13
Q

What genomes are very compact?

A

Bacteria

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14
Q

What additional DNA do eukaryotes have?

A

Junk DNA that doesn’t code (intron)

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15
Q

What is the purpose of junk DNA?

A

Evolution of species or for activity of the genes

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16
Q

Does junk DNA differ between organisms?

A

No, it’s highly conserved

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17
Q

What is the relationship between gene number and total genome size?

A

There isn’t a relationship just that it’s roughly correlated with species complexity

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18
Q

What makes up the cell cycle?

A

Interphase and mitosis

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19
Q

Interphase

A

Where chromosomes are duplicated and the cell grows

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20
Q

Mitosis

A

The chromosomes are distributed to two daughter nuclei

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21
Q

How do the chromosomes appear during interphase?

A

Long, thin threads that can’t be seen under a microscope

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22
Q

Replication origin

A

Where DNA replication begins based on a sequence

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23
Q

How many replication origins are in a eukaryote?

A

Multiple that occur bidirectionally

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24
Q

What is the structure of a telomere?

A

Repeated nucleotide sequences

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25
Q

What is the purpose of a telomere?

A

Prevent DNA from being broken during cellular division (at the ends) and aids in replication of chromosome ends

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26
Q

How do chromosomes appear in mitosis?

A

Condensed and can be viewed under a microscope

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27
Q

What are the basic points in mitosis?

A
  1. Chromosomes condense
  2. Nuclear envelope breaks down
  3. Mitotic spindles attach to sister chromatids
  4. They pull apart to opposite sides
  5. Nuclear envelope reforms and two separate cells are formed (split)
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28
Q

What three DNA sequence elements are important?

A
  1. Telomere
  2. Replication origin
  3. Centromere
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29
Q

What is the purpose of a centromere?

A

Attaches the duplicated chromosomes to a mitotic spindle, thus allowing segregation of the two and holds the chromosomes compact

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30
Q

How do chromosomes exist within the interphase nucleus?

A

Occupy a particular region either on the nuclear envelope or in the nuclear lamina

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31
Q

What is the purpose of the nuclear lamina?

A

The protein meshwork that supports the envelope

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32
Q

What exists within the nucleolus?

A

Parts of the different chromosomes that carry genes to encode for ribosomal RNA

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33
Q

What is the purpose of heterochromatin?

A

Contain noncoding DNA and few genes where dense chromosomes exist

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34
Q

What is the purpose of histones?

A

Packing chromatins

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35
Q

What is the structure of a nucleosome?

A

Core particle with wrapped DNA, linker DNA, and H1

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36
Q

How is the core particle revealed?

A

Nuclease which cut down the phosphodiester bond between nucleotides

37
Q

What histones form a core particle?

A

The histone octamer has two molecules of each: H2A, H2B, H3, and H4

38
Q

What does the formation of multiple nucleosomes lead to?

A

Chromatin thread

39
Q

What is the structure of each histone in the octamer?

A

Long, unstructured N-terminal amino acid tail

40
Q

How do the histone octamer differ between species?

A

Don’t as they are highly conserved due to their vital role in controlling eukaryotic chromosome structure

41
Q

What does the packaging of multiple nucleosomes depend on?

A

H1, as it pulls the adjacents ones into a repeating array (condensed)

42
Q

What is the structure of histone 1?

A

Globular region with a pair of long tails are its C-terminal and N-terminal ends

43
Q

What is the purpose of the long C-terminal tail?

A

Required for H1 to bind to chromatin

44
Q

How are chromatin fibers folded?

A

Into a series of loops

45
Q

DNA repair

A

Correct temporary DNA damage

46
Q

What happens if there is a malfunction in a repair protein?

A

Malfunctions in some repair proteins result in an infective inherited gene that can’t repair damaged DNA
ex. one of UV radiation

47
Q

How do depurination and deamination take place?

A

Both spontaneous loss reactions

48
Q

What is not broken in depurination and deamination?

A

Phosphodiester backbone

49
Q

What is depurination?

A

The loss of a purine base (A and G) by removing a purine base from the nucelotide

50
Q

What does depurination result in?

A

Lesions to the DNA (similar to missing teeth)

51
Q

What is deamination?

A

The loss of an amino group from a cytosine in DNA to produce the base uracil

52
Q

How can chemical changes in DNA occur?

A
  1. Depurination
  2. Deamination
  3. Chemically reactive by-products of cell metabolism that react with bases to alter their properties
53
Q

Thymine dimer

A

The covalent linkage between two adjacent pyrimidine bases caused by UV radiation

54
Q

What happens if deamination is left uncorrected?

A

Substitution of one base and therefore the replicate machinery will insert an adenine (uracil)

55
Q

What happens if depurination is left uncorrected?

A

Loss of a nucleotide pair and therefore the replication machinery skips it, resulting in a daughter DNA molecule having a deletion.

56
Q

What do thymine dimers cause to replication machinery?

A

Stall it at the site of damage

57
Q

What do repair mechanisms depend on?

A

The double-helical DNA, specifically at least one strand that is not altered

58
Q

Explain the steps of repair mechanisms.

A
  1. Damaged DNA recognized by enzymes and nuclease cleave the covalent bonds around the damaged section to leave a gap (unique)
  2. A repair DNA polymerase binds to the 3’ hydroxyl end of the cut DNA strand and fills in the gap with a complementary sequence to the undamaged strand
  3. The nick in the backbone is sealed by DNA ligase
59
Q

What is a mismatch repair?

A

Fixes the copying errors of a replication machinery where there is a mispaired nucleotide.

60
Q

How inaccurate in the replication machine (DNA replication with proofreading)?

A

Makes one mistake in 10^7 nucleotides copied

61
Q

How does the mismatch repair system work?

A
  1. Proteins recognize the mismatch
  2. Remove a portion of the strand with the error (nucleases)
  3. Resynthesize the missing DNA
62
Q

What happens if a mismatch is left uncorrected by the replication machinery?

A

Permanent mutation in the next round of DNA replication

63
Q

How does the mismatch system decided which strand to remove the portion from?

A

In bacteria the newly synthesized DNA is less methylated, plus other strategies

64
Q

What does mismatch repair play a huge role in?

A

Preventing cancer

65
Q

How does mismatch nucleotides result in cancer?

A

Predisposition is caused by inherited mutations in genes that encode mismatch repair gene (both copies damaged = more likely to develop mutations and become cancerous).

66
Q

What are double stranded breaks caused by?

A

Radiation or mishaps at the replication fork

67
Q

Why are double stranded breaks dangerous?

A

Fragmentation of chromosomes and loss of genes

68
Q

Why are double stranded breaks difficult to repair?

A

The broken pieces separate so there is no copy to reconstruct missing information

69
Q

Nonhomologous end joining

A

Where the broken ends are rapidly glued back together before the DNA fragments and drifts apart

70
Q

Explain the steps of nonhomologous end joining

A
  1. Break cleaned by nuclease that chews back broken ends to produce flushed ones
  2. Flushed ends stitched together by DNA ligase
71
Q

What is the problem with nonhomologous end joining?

A

Nucleotides are lost at the site of repair, thus disrupting the activity of the gene

72
Q

Why use homologous recombination?

A

Restore the original DNA sequence at the site of the break; no loss of genetic information.

73
Q

When does homologous recombination occur?

A

When there is a double stranded break in a daughter DNA strand, but before the daughter DNA strands are separated, so that the undamaged strand can be used as the template. MUST have identical sequences around the damage.

74
Q

Explain the steps of homologous recombination.

A
  1. Nuclease chews the 5’ ends of the two broken strands at the break
  2. Enzymes enter the 3’ ends of the unbroken DNA and search for a complementary sequence through base pairing
  3. Invading strand elongated by repair DNA polymerase
  4. Additional DNA synthesis at the 3’ ends of the strands of the broken double helix
  5. DNA ligation
75
Q

What is homologous recombination used in?

A

Exchange of genetic information during the formation of the germ cells; meiosis.

76
Q

How can mutations be deadly? Give example.

A

A single nucleotide change in a vital position can alter protein function to poor or none at all
ex. single nucleotide in hemoglobin gene = sickle cell anemia which produces sickle red blood cells leading to blocking small vessels, thus organ failure

77
Q

Why must reproductive cells be protected against mutation?

A

A mutation in a germ cell will be passed onto all the cells in the body that develop from it and those germ cells responsible for the next generation as well.

78
Q

Why must somatic cells be protected from mutation?

A

Mutations in somatic cells lead to variations where some can grow uncontrabbly = cnacer

79
Q

Explain cancer in terms of mutations.

A

The gradual accumulation of random mutations in a somatic cell.

80
Q

Give an example of DNA mutations were preserved.

A

Those that have no effect on the fitness of the organism. For instance, humans and chimps have DNA sequences that are at least 98% identical.

81
Q

Mutation

A

The permanent change to a DNA nucleotide sequence

82
Q

Replisome

A

The complex replication machine that contains different proteins with specific functions for DNA replication

83
Q

How inaccurate is DNA replication with mismatch repair?

A

1 in 10^9 nucleotides

84
Q

How inaccurate is DNA replication (without proofreading or the mismatch repair)?

A

1 in 10^5 nucleotides

85
Q

What can the inaccuracy of the mismatch repair lead to (in terms of biological disorders)?

A

Mutations can lead to heritable changes which make someone more susceptible to a gene
ex. BRCA1/2
- therefore if already have one functional copy = more likely to get disorder (loss of heterozygosity)

86
Q

When does nonhomologous end joining occur? Why?

A

G1 since the chromosomes are farther apart from one another, thus there would be more differences in their sequences

87
Q

When does homologous recombination occur? Why?

A

S and G2 because chromosomes are closer to each other/duplicated, so similar sequences (templates).

88
Q

What is the difference between endonuclease and exonuclease?

A

Endonuclease can cleave bonds internal in a phosphodiester bond (thus removing multiple) while exonuclease cleave at the end of bonds, to remove singular nucleotides

Intro Molecular Biology (5 decks)

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