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Molecular Biology - Jourdan > Lecture 2 > Flashcards

Lecture 2 Flashcards

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0
Q

What is the difference between genetic inheritance and epigenetic inheritance?

A

Genetic inheritance is a change in DNA sequence that gets passed on to progeny.
Epigenetic is a change in chromatin, not in DNA.
the chromatin can turn off a gene in DNA but once the gene is in a germ cell the chromatin is removed and the DNA is turned on.

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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 examples of epigenetic inheritance?

A

DNA methylation
Chromatin structure
Histone modification

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3
Q

What are three facts that challenge the view that histones are only involved in packaging of DNA?

A
  1. Mammalian chromatin contains equal mass of histone and non histone proteins
  2. Histones are highly conserved
  3. One form of chromatin silences the genes it packages without regard to sequence
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4
Q

What is heterochromatin?

A

Form of chromatin that silences the genes it packages without regard to sequence and is directly inherited by daughter cells

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5
Q

What are characteristics of heterochromatin?

A

Chromatin that is very condensed (stains darkly)
Last DNA to be replicated during cell cycle and is genetically inactive
Highly concentrated at centromeres and telomeres
Contains very few genes; those that are present are resistant to gene expression

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6
Q

What is the position effect?

A

Activity of a gene will be silenced if relocated near heterochromatin
Position effect variegation: breakage events that bring heterochromatin near active genes tends to silence them.
Zones of inactivation spreads a different distance in different cells

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7
Q

What is euchromatin?

A

Less condensed chromatin that can be transcribed

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8
Q

What separates heterochromatin from euchromatin?

A

A barrier that protect genes that need to be expressed

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9
Q

What covalent modifications occur to the core and tail of histones during acetylation?

A

Acetylation of lysines loosens chromatin structure. It is added by histone actyl transferases and is removed by histone deacetylase complexes

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10
Q

What histone modification occurs with methyl transferases and histone demethylases?

A

Mono, did and tri methylation of lysines. Added by methyl transferases and removed by demethylases

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11
Q

What histone modification occurs with the modification of serines?

A

Phosphorylation

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12
Q

What does the recruitment of histone modifying enzymes depend on?

A

Gene regulatory proteins

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13
Q

Are histone modifications permanent?

A

No, they are all reversible but can persist long after regulatory proteins have disappeared.

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14
Q

What are important consequences for the types of proteins the modified DNA attracts?

A

Determines how/when/if gene expression takes place

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15
Q

What are variant histone proteins?

A

Variants that exist for each of the core histones except for H4

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16
Q

How common are variant histone proteins?

A

Present in much smaller amounts than core histones

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17
Q

Are variant histone proteins conserved or non conserved?

A

They are less well conserved than core proteins

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18
Q

When are regular core histone proteins synthesized and where are they assembled into nucleosomes?

A

During S-phase and assembled into nucleosomes on daughter DNA helices just behind replication fork.
So when DNA is replicated more histones are needed so during S-phase, more are made.

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19
Q

When are most variant histones synthesized and inserted? What is required during this process?

A

Most are synthesized during interphase and inserted into already-formed chromatin. Requires histone exchange process catalyzed by chromatin remodeling complex
Not when DNA replication is not going on.

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20
Q

What is the purpose of variant histone CENP-A?

A

Centromere function and kinetochore assembly

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21
Q

What is the purpose of variant histone H2AX?

A

When DNA is damaged, it helps in DNA repair and recombination

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22
Q

What is the purpose of H2AZ?

A

Gene expression and chromosome segregation

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23
Q

What is the purpose of macroH2A?

A

Transcriptional repression and X-chromosome inactivation

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24
Q

What do the modifications that can occur on the histone tail result in?

A

There are thousands of combinations of modification (methylation, acetylation, etc.) may exist that cause further diversity to be created by variant histones
infinite combinations can occur.

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25
Q

What is the histone code?

A

Code has specific meaning for cell, determining how/when DNA is packaged in nucleosome

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26
Q

What is the code reader complex?

A

Combination of proteins that read the histone code. Protein modules binding to specific histone modifications on nucleosomes. Involves joint recognition of histone tail and covalent modifications.

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27
Q

If the cells need change what happens to the code?

A

Code can change as the cells need change

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28
Q

What can the code reader complex bring in?

A

Bring in other components in nucleus that can lead to gene expression, gene silencing, and other biological function

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29
Q

What can happen after modifying enzyme marks one or few neighboring nucleosomes?

A

Chain reaction can ensue. Code reader -writer enzymes spread the mark over chromsome

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30
Q

Along with the code reader-writer, what do complexes also contain? What do they do?

A

ATP-dependent chromatin remodeling protein. All work together to either condense or decondense long stretches of chromatin as reader moves along

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31
Q

What halts the spread of chromatin modifications?

A

Barrier sequences.
-Physical barriers
-Enzymatic barriers
HS4 region
-protects the beta globin locus from silencing
-contains a cluster of histone acetylase binding sites

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32
Q

What does centromeric heterochromatin contain?

A

Contains centromere-specific H3 histone, CENP-A, and other proteins that pack the nucleosomes into dense arrangements to form the kinetochore

33
Q

What is important about a kinetochore?

A

It is a structure that is required for attachment of mitotic spindle

34
Q

What do centromere sequences in humans consist of?

A

Short repetitive DNA sequences called alpha satellite DNA

35
Q

What are centromeric heterochromatin defined by?

A

Assembly of proteins, not DNA sequence

  • alpha satellites are found at non-centromeric position in the genome
  • New centromeres can form spontaneously on fragmented chromosomes, some of which lack alpha satellite DNA
36
Q

How is the centromeric chromatin organized?

A

2 alternating types of chromatin

  • nucleosomes with CENP-A on the outside fold
  • –CENP-A binds to kinetochore
  • Nucleosomes with normal H3 on the inside
37
Q

What is the theory of inheritance of chromatin structures?

A

De novo centromere formation requires a “seeding” event on alpha satellite DNA
H3-H4 tetramers are directly inherited by the daughter strands at the replication fork
Once formed, it is directly inherited in each round of replication

38
Q

What are Lampbrush chromosomes?

A

Chromosomes from amphibian oocytes that are the largest chromosomes known.
They can be visualized by light microscopy
A series of large chromatin loops emanating from a linear chromosome axis can be seen

39
Q

What are the loops of lampbrush chromosome?

A

Extended chromatin that can be transcribed. Chromatin along the axis is highly condensed

40
Q

What is the location of chromatin in the nucleus?

A

Each chromosome occupies its own area in the nucleus.
Heterochromatin (red) outline the nucleus (preferentially associates with the nuclear lamina)
Gene-rich regions that are transcribed are dispersed throughout

41
Q

What changes during gene expression in the nucleus?

A

Chromatin structure and location

42
Q

What are chromosome puffs?

A

Decondensation of chromatin during gene transcription

43
Q

What do actively transcribed genes do in the nucleus?

A

Extends out of its area on an extended chromosome loop

44
Q

Are the locations of chromatin random in the nucleus?

A

No. Now there is a map that can show where each chromosome is in the nucleus

45
Q

What are “neighborhoods” in a nucleus?

A

Neighborhoods are a heterogeneous mix of proteins, enzymes, and molecules for specific processes. Different “neighborhoods” have different effect on gene expression

Some can be for gene silencing, gene expression etc

46
Q

What do distinct biochemical environments have?

A

High local concentrations of enzymes and molecules for specific processes.

  • DNA repair “foci”
  • RNA synthesis
47
Q

What are mitotic chromosomes?

A

Highly condensed chromosomes that are in the final level in chromosome packaging

48
Q

What are sister chromatids?

A

Two daughter DNA molecules replicated in interphase that are separately folded. They are held together at their centromeres

49
Q

What do two sister chromatids form?

A

A chromosome

50
Q

What are the steps of folding to create a mitotic chromosome?

A
  1. DNA double helix + histones form “beads on a string” chromatin
  2. Chromatin fiber is zig zagged (theory) packed - nucleosomes
  3. Chromosome condense further and the net result:
    - Each DNA molecule has been packaged into a mitotic chromosome that is 10,000 fold shorter than its extended length
51
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

52
Q

What aids in compaction?

A

Proteins called condensins

53
Q

Who do condensins compact DNA?

A

-Use ATP hydrolysis to coil the DNA molecules into chromatids

54
Q

What is the major structural component of the core of every metaphase chromosome?

A

Condensins

55
Q

What is the exact mechanism of condensins?

A

Unknown

What is known: cells depleted of condensins have abnormal condensation

56
Q

What are homologues?

A

Genes that are similar in both sequence and function due to common ancestry

57
Q

Where do human homologues exist?

A

Yeast, worms, fruit flies, and bacteria

58
Q

What is the difference between homologues and syntany

A

Syntany- large blocks of genes are conserved in the same order on the chromosome between species
Homologues-not only similar in sequence but also function

59
Q

What is a major clue to gene and protein function?

A

Recognition of sequence similarity

60
Q

What is more tightly conserved? Gene sequences or genome structure? Why?

A

Gene sequences are more tightly conserved

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

61
Q

What do the number of genes roughly correlate with? Why

A

Number only roughly correlated with phenotypic complexity of organism.
Complexity arises from duplication and expansion of related gene families

62
Q

How do genomic changes occur?

A

Occur as mistakes in DNA replication and repair

63
Q

How often do genomic changes occur?

A

Rare occurrence: 1/1000 nucleotide pairs is randomly changed in the germ line every million years

64
Q

What also may play a role in genomic changes?

A

Movement of transposable elements

65
Q

What range of change can occur?

A

Base pair substitiution
Large scale rearrangements
-duplications, deletions, inversion, translocations

66
Q

How can genome evolution be reconstructed?

A

By comparing genomes of contemporary organisms

67
Q

What is the phylogenetic tree?

A

Shows differences between species and the last common ancestor

68
Q

What are reasons for sequence conservation?

A

Not having much time for mutations to occur since lineages separated

Purifying selection

69
Q

What is purifying selection?

A

Elimination of mutations that interfere with important genetic functions. Darwin’s effect

70
Q

What can cause genome size to vary considerably?

A

Small size due to small introns - lacks repetitive DNA

71
Q

How much of the human genome is conserved?

A

5% but only 1.5% code for proteins

72
Q

What is the reason that 5% of the human genome is conserved but only 1.5% codes for proteins?

A 
Must have an important function since it is highly conserved
Possibly:
-RNA molecules
-Regulatory regions
-Much is unknown
73
Q

What allows gene duplication?

A

Little selective pressure to maintain mutation-free

74
Q

What are pseudogenes?

A

Duplicated gene that has become irreversibly inactivated by multiple mutations

75
Q

What can cause duplication and divergence?

A

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

76
Q

What is an example of duplication and divergence of genes?

A

Globin gene family derives from common ancestral gene
Gave rise to beta and alpha genes
Translocation moved alpha to separate chromosome
Further duplication and mutation resulted in more specialized beta molecules

77
Q

How much do human sequences vary?

A

0.1% from one to another

78
Q

What do the variations in human sequences cause?

A

Majority of mutations are neither harmful or beneficial

Neutral mutations can become fixed in a population

79
Q

What are SNPs single nucleotide polyporphisms

A

Points in the genome where one group has one nucleotide and another group has another.
Variation occurs at a high rate (1% or more)

80
Q

What are CNVs-copy number variants?

A

Presence of many duplications and deletions of large blocks of DNA
Some blocks are common and others rare-significance of most are unknown

Molecular Biology - Jourdan (8 decks)

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