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MOL BIO Exam #1- Lo > Lec 02- DNA Chromosomes and Genomes 2 > Flashcards

Lec 02- DNA Chromosomes and Genomes 2 Flashcards

1
Q

What is epigenetics?

A

a form of inheritance that is superimposed on the genetic inheritance based on DNA

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2
Q

What are 3 examples of epigenetics?

A
  • DNA methylation
  • Chromatin structure
  • Histone modification
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3
Q

What are the 3 challenges to the idea that histones are thought to just be involved in packaging of DNA?

A
  • Mammalian chromatin contains equal mass of histones and non-histone proteins
  • Histones are highly conserved
  • Heterochromatin silences the genes it packages without regard to sequence and is directly inherited by daughter cells
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4
Q

What does heterochromatin do?

A
  • silences the genes it packages without regard to sequence

- is directly inherited by daughter cells

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5
Q

What suggests that histones have other functions besides purely structural?

A

other proteins bind to histones

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6
Q

How many amino acid differences are there between mammals and peas?

A

only 2 amino acid differences on H4

any change = deleterious

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7
Q

Heterochromatin characteristics

A
  • chromatin that is very condensed
  • stains darkly throughout the cell cycle (even in interphase)
  • late replicating
  • genetically inactive
  • very few genes
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8
Q

The genes that are present on heterochromatin are resistant to ________

A

gene expression

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9
Q

Where is heterochromatin highly concentrated?

A

at centromeres and telomeres

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10
Q

What is position effect?

A

activity of a gene depends on position on the chromosome

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11
Q

What happens if a gene’s position is relocated near heterochromatin?

A
  • it will be silenced

- zone of inactivation spreads a different distance in different cells

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12
Q

What is euchromatin?

A

all the rest of chromatin that is less condensed than heterochromatin

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13
Q

What kind of modifications are the amino acid side chains of histones subject to?

A

covalent modifications

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14
Q

Where do covalent modifications of histones occur?

A

histone core and tail

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15
Q

Acetylation of lysine characteristics

A
  • loosens chromatin structure
  • added by histone acetyl transferases (HATs)
  • removed by histone deacetylase complexes (HDACs)
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16
Q

Characteristics of Mono, Di, and Tri-methylation of lysines

A
  • Added by methyl transferases

- Removed by histone demethylases

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17
Q

What covalent modifications occur with histones?

A
  • Acetylation of lysine
  • Mono, di-, tri-methylation of lysine
  • Phosphorylation of serine
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18
Q

What does the recruitment of the histone covalent modification enzymes depend on?

A

gene regulatory proteins

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19
Q

Are histone modifications reversible?

A

yes, but can persist long after regulatory proteins have disappeared

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20
Q

What determines how/when/if gene expression takes place?

A

the types of proteins the modified DNA attracts

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21
Q

Varient histone proteins exist for each core histone except which?

A

H4

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22
Q

Varient histone proteins are present in ___________ amounts than core histones and are __________.

A

much smaller amounts

less well-conserved

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23
Q

When are major histones synthesized?

A

during S-phase

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24
Q

What are major histones assembled into?

A

nucleosomes on daughter DNA helices just behind the replication fork

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25
Q

When are variant histones synthesized?

A

during interphase

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26
Q

What are variant histones inserted into?

A

already-formed chromatin

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27
Q

What do varient histones require?

A

histone exchange process catalyzed by chromatin remodeling complex

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28
Q

Histone code characteristics

A
  • has specific meaning for cell

- determines how/when DNA is packaged in nucleosome

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29
Q

How is the histone code read?

A

by the code reader complex

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30
Q

What does the code reader complex involve?

A

joint recognition of histone tail and covalent modifications

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31
Q

Histone code can ________ as the cell needs change

A

change

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32
Q

What happens after modifying enzyme marks one or few neighboring nucleosomes?

A

chain reaction can ensue

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33
Q

What enzymes spread the mark over the chromosome?

A

the code reader-writer enzyme

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34
Q

What do the code reader-writer complexes also contain?

A

an ATP-dependent chromatin remodeling protein

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35
Q

All the chromatin remodeling complexes work together to _________

A

either condense or decondense long stretches of chromatin as the reader moves along

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36
Q

What 2 mechanisms halt the spread of chromatin modifications?

A
  • physical barriers

- enzymatic barriers

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37
Q

What does the HS4 region on the chromatin do?

A

-protects the b-globin locus from silencing

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38
Q

What cluster does the HS4 rein on chromatin contain?

A

cluster of histone acetylase binding sites

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39
Q

What does the centromeric heterochromtin contain which makes it special?

A
  • centromere-specific H3 histone
  • CENP-A
  • other proteins that pack the nucleosomes into dense arrangements to form kinectochore
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40
Q

What kind of structure is required for attachment of the mitotic spindle to the heterochromatin?

A

dense arrangements of nucelosomes

41
Q

What kind of DNA sequences do centromere sequences in humans consist of?

A

alpha satellite DNA

42
Q

What is alpha satellite DNA?

A

short repetitive DNA sequences

43
Q

Centromeric heterochromatin is defined by assembly of proteins, not ____________

A

DNA sequence

44
Q

Where are alpha satellites found?

A

at non-centromeric positions in the genome

45
Q

Where can new centromeres (neocentromeres) form?

A

spontaneously on fragmented chromosomes

-some of which lack alpha satellite DNA

46
Q

How is centromeric chromatin organized?

A
  • 2 alternating types of chromatin

- CENP-A binds the kinectochore

47
Q

What are the 2 alternating types of chromatin?

A
  • nucleosomes with CENP-A (centromere-specific histone H3) on outside fold
  • nucleosomes with normal H3 that is dimethylated at lysine 4 on inside fold
48
Q

What does de novo centromere formation require?

A

requires a “seeding” event on alpha satellite DNA

49
Q

What are directly inherited by the daughter strands at the replication fork?

A

H3-H4 tetramers

50
Q

What happens once the de novo centromere is formed?

A

it is directly inherited in each round of replication

51
Q

What are the largest known chromosomes?

A

lampbrush chromosomes from amphibian oocytes

52
Q

How are the lampbrush chromosomes from amphibian oocytes structured?

A

series of large chromatin loops emanating from a linear chromosome axis

53
Q

Each chromosome occupies _________

A

its own area in the nucelus

54
Q

With what does heterochromatin preferentially associate?

A

the nuclear lamina

55
Q

Where are gene-rich regions dispersed?

A

throughout the chromosome

56
Q

Chromatin structure and location changes during ______________

A

gene expression

57
Q

When do you see “chromosome puffs”?

A

during decondensation of chromatin during gene transcription

58
Q

Where do actively transcribed genes extend?

A

extend out of its area on an extended chromosome loop

59
Q

How are different activities localized in the nucleus?

A
  • nucleus interior = very heterogeneous
  • different neighborhoods have effects on gene expression
  • biochemical environments have high local concentrations of enzymes and molecules for specific processes
60
Q

What are 2 processes that distinct biochemical environments have high local concentrations and enzymes for?

A
  • DNA repair “foci”

- RNA synthesis

61
Q

Characteristics of mitotic chromosomes

A
  • highly condensed

- final level in chromosome packaging

62
Q

Two daughter DNA molecules replicated in interphase are separately folded to produce ____________

A

2 sister chromatids

63
Q

What holds chromatids together

A

their centromeres

64
Q

What is the purpose of condensation?

A
  • Disengagement of sister chromatids to allow separation for cell division
  • Protection of fragile DNA molecule as separation occurs
65
Q

What proteins aid compaction?

A

condensins

66
Q

What are condensins?

A
  • use ATP hydrolysis
  • coil DNA molecules into chromatids
  • major structural component of the core of every Metaphase chromosome
67
Q

Cells that do not have condenses have ______________

A

abnormal condensation

68
Q

What are homologues?

A
  • genes that are similar in both sequence and function due to common ancestry
  • not the same as syntany
69
Q

Where do human homologues exist?

A
  • yeast
  • worms
  • fruit flies
  • bacteria
70
Q

What is the major clue to gene and protein function?

A

recognition of sequence similarity

71
Q

Gene sequences are more _____________ than genome structure

A

tightly conserved

-size of genome, number of genes, size of introns, and abundance of repetitive sequences can be quite different

72
Q

Number of genes only roughly correlated with ________ complexity of organism

A

phenotypic

73
Q

Where does phenotypic complexity arise from?

A

duplication and expansion of related gene families

74
Q

How do genomic changes occur?

A

as mistakes in DNA replication and repair

75
Q

How many nucleotide pairs is randomly changed in the germ line every million years?

A

1/1000 nucelotide pairs

rare occurrence

76
Q

What may also play a role in mistakes in DNA replication and repair?

A

movement of transposable elements

77
Q

What DNA changes can occur?

A
  • base pair substitiutions

- large scale rearrangements

78
Q

What are 4 large scale rearrangements?

A
  • duplications
  • deletions
  • inversions
  • translocations
79
Q

What does comparative genetics do?

A

reconstructs genome evolution by comparing genomes of contemporary organisms

80
Q

What are 2 reasons for sequence conversion?

A
  • not having much time for mutations to occur since lineages separated
  • purifying selection
81
Q

What does purifying selection mean?

A

elimination of mutations that interfere with important genetic functions

82
Q

Small size genome is due to small ________

A

introns

83
Q

Small size genomes lack _________

A

repetitive DNA

84
Q

Intron position of huntingtin gene is __________ compared to the human gene

A

conserved

85
Q

________% of human genome is conserved

A

5%

86
Q

Only ________% of the human genome codes for proteins

A

1.5%

87
Q

Little selective pressure is needed to maintain __________ genes

A

mutation-free

88
Q

What are pseudogenes?

A

duplicated gene that has become irreversibly inactivated by multiple mutations

89
Q

What is gene duplication and divergence?

A

both copies remain functional while diverging in sequence and pattern of expression

90
Q

What gave rise to “a” and “b” globin genes?

A

duplication and mutation

91
Q

What moved the “a” globin gene to a separate chromosome?

A

translocation

92
Q

What resulted in more specialized “b” globin molecules?

A

further duplication and mutation

93
Q

Human sequences vary ______% from one to another

A

0.1%

94
Q

Human and chimps differ _____%

A

1%

95
Q

Majority of human sequence variations are neither _______ or _______

A

harmful or beneficial

96
Q

What type of mutations can become fixed in a population?

A

neutral mutations

97
Q

What are SNPs?

A
  • single nucleotide polymophisms
  • points in the genome where one group has one molecule and another group has another
  • variation occurs at high rate (1%)
98
Q

What are CNVs?

A
  • copy number variants
  • presence of many duplications and deletions of large blocks of DNA
  • some blocks common, others rare

MOL BIO Exam #1- Lo (8 decks)

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