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Biochem K > mol. bio. chapter 35 => DNA and chromosome structure etc. > Flashcards

mol. bio. chapter 35 => DNA and chromosome structure etc. Flashcards

1
Q

What does chromatins consist of?

A

A long dsDNA molecule, Histones(basic proteins) of nearly eaqual mass and small amounts of larger acidic non-histone proteins (include enzymes needed for replication, translation, RNA processing&transport and DNA repair). + small amount of RNA.

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2
Q

What is a nucleosome?

A

An octamer structure with 1,75 turns of dna around it as well as one more histone which acts as a stabilizing agent and interacts with the DNA most.

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3
Q

What does the octamer consist of?

A

4 core histones 2x H2A and 2x H2B+(H3&H4)x2

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4
Q

When does octamer formation occur?

A

Under Physiological pH.

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5
Q

Where can the amino terminals of the histones be found?

And why?

A

The amino-terminal ends extend outside the octamer as the have to be available for posttranslational modifications such as acetylation etc.

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6
Q

How is the octamer formed?

A

-Initially the H3&H4 form a tetramer containing two molecules of each.
the H3H4 tetramer can confer nucleosome properties on the DNA thus has a central role in nucleosome formation.
-The H2A&H2B forms a Dimer which the joins the tetramer and stabilizes the primary particle and strongly binds to another half turn of DNA which before was bound only loosely to the primary tetramer particle.

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7
Q

Which part of the histone is hydrophobic and which is basic?

A

2/3ds of the histones carboxyl ends are hydrophobic and 1/3d of the amino is quite basic.

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8
Q

Which are the six types of covalent modifications which the core histones are subjects to?

A
  • Acetylation
  • Phosphorylation
  • Methylation
  • ADP-ribosylation
  • Monoubiquitilation
  • Sumoylation
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9
Q

What is the acetylation oh histones associated with?

A
  • Acetylation of the H3,H4 histones are associated with the activation or inactivation of gene transcription.
  • Acetylation of the ore histones is associated with chromosomal assembly during replication cycle.
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10
Q

What is Phosphorylation associated with in histones?

A

-Phosphorylation of H1 is associated with the condensation of chromosomes during cell cycle.

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11
Q

What is methylation oh the histones associated with?

A

Repression of gene expression.

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12
Q

ADP-Ribosylation of Histones is associated with…?

A

DNA-repair.

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13
Q

Monoubiquitilation of histones is associated with….?

A

Gene activation, gene repression and heterochromatic gene silencing.

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14
Q

Sumoylation

A

(SUMO =Small ubiquitin-related modifier)

Associated with transcription repression.

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15
Q

What are linkers?

A

the DNA parts of roughly 30 bp that separate the core particles.

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16
Q

What are Histone Chaperones?

What is their function?

A

A group of proteins that exhibit high affinity for histone binding.

  • They aid in assembly of nucleosomes which is mediated by one of several nuclear chromatin assembly factors which they help.
  • The Chaperones release the Histones as the nucleosome is assembled.
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17
Q

What is Phasing?

What does it depend on?

A

The non-random distribution of DNA to histones.
=> Some histones appear to favor certain DNA regions.
=> Phasing isn’t fully understood but is thought to depend on:
-Relative Physical flexibility of certain nucleotide sequences to accommodate regions of kinking within the Supercoils.

-The presence of DNA bound factors which limit the sites of nucleosome deposition.

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18
Q

Which are the two higher orders of structure of the chromatin compction?

A
  • The 10 nm fibril.

- The 30nm chromatin fiber.

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19
Q

Which structure is referred to as beans on a string?

A

The 10nm fibril structure/order.

-It consists nucleosomes arranged with their edges separated by linkers.

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20
Q

How is the 30nm fibers formed?

A

The 10nm fibrils are further supercoiled into 30nm fibers with 6-7 nucleosomes per turn.
The 30nm fibers seem to be stabilized by the H1 histones.

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21
Q

How is a mitotic chromosome formed?

A

The 30nm fiber structure must be further condensed or compacted in length another 100-fold.

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22
Q

How compact is an Interphase chromosome.

A

After having compacted the 30nm fibers 100 fold to get a mitotic chromosome, the structure must be further organized into 30k-100k bp loops or domains which are anchored in a supporting matrix in the nucleus .

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23
Q

How is the DNA within the domains of a chromosome ordered?

A

Probably not randomly, however we don’t know. It is suggested however that they are organized or grouped after genetic functions. each group containing both coding and non-coding regions of the cognate gene/genes.

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24
Q

What kind of chromatin is transcriptionally inactive?

A

Heterochromatin.

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25
Q

What kind of chromatin is transcriptionally active?

A

Euchromatin.

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26
Q

How do our cells differentiate into all different tissues if they contain the same genetic material?

A

It’s explained by differential expression of the common genetic information through activation and inactivation of genes in chromatin.

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27
Q

How doest the Euchromatin differ from heterochromatin property wise?

A
  • The Euch. which are (potentially- and) transcriptionally seem to have their structures altered
  • They contain sensitive sites of about 100k bp which are more sensitive to digestion of nucleases such as DNase I.
  • Those regions lack the presence Methyldeoxycytosine MeC, modified nucleotides which are believed to protect the DNA from nucleophilic attack.
  • Histones in those regions have ofter undergone, or can be Posttranslationally modified by the six covalent modifications mentioned previously.

Mention them!

-Conatain Hypersensitive sites (within the sensitive sites?).

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28
Q

What are Hypersensitive sites?

What do they result from?

Where are they located?

A
  • Shorter regions of about 100-300 bp’s in length and have another 10 fold greater sensitivity to digestion by DNase (than the sensitive sites).
  • They probably result from structural conformations that favor the enzyme accessibility.
  • They’re usually located right upstream from the active gene and are free from nucleosomal structures due to the binding of non-histone regulatory transcriptional factors instead.
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29
Q

What leads to the formation of Hy

A

-Non-histone regulatory proteins involved in both transcription regulation and those involved in accessibility to the template strand.

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30
Q

What are the characteristics of the Heterochromatin?

A
  • More densely packed since inactive.
  • Stains more using an electron microscope
  • More rich in Mec
  • Histones in these regions have a lower level of “activating” covalent modifications and higher level of repressive PTM’s instead.
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31
Q

Which are the two types of heterochromatin?

How do they differ from each other?

A

-Constitutive Heterochromatin; Heterochromatin that is condensed at all times. Found near chromosomal centromeres and chromosomal ends (Telomers)
=> are always inactive

-Facultative Heterochromatin; Is at times condensed and at times uncondensed, actively transcribed and thus appears like Euchromatin.
Eg. the second Xchromosome during gametogenisis.

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32
Q

What is the structure of the chromosome in Metaphase?

A

two sisterchromatids connected by a centromere.

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33
Q

What forms the kinetochore complex and where are they found?

A

Found in the centromere.
is a complex consisting of nucleotides which consist of a
h3 variant protein called CENP-A and other specific centromere biding proteins.
-Provides anchor for the mitotic spindle, thus in essential for the segregation of chomosomes during mitosis.

34
Q

What does the Centromere consist of?

A

its an adenine-thymine rich region containing repeated DNA sequences (highly repetative sequences)
=> 10’6 bp’s
bound by…

35
Q

What are telomeres?

A

Found at the ends of the chromosomes. Consisnts of highly repetitive TG- sequences.
- 5’- TTAGGG-3’

36
Q

Which enzyme is responsible for synthesis and length maintenance of the telomere?

A

Telomerase.

37
Q

What is the function of Telomerases.

A

They’re enzymes responsible for the maintenance of the length of the telomeres and their synthesis.
It’s a multisubunit RNA-template containing complex which is related to reverse-transcriptases.

38
Q

characteristics of chromosomes in metaphase?
vs
Chromosomes in interphase?

A

interphase chromosomes are less densely packed but still almost completely inactive.
-Chromosomes in Metaphase on the other hand are well condensed, another 8000 fold.

39
Q

What is the function of Lamins?

A

Lamins are proteins that constitute integral components of the inner nuclear membrane within the nucleus.
-They are likely responsible for anchoring the proximal portions of the looped domains (which the 30nm fibers are folded into) through interaction with them.

40
Q

What is the packing ratio of a naked double helical DNA?

A

ca 1,0

41
Q

What is the packing ratio of a 10nm fibril nucleosome?

A

7-10

42
Q

What is the packing ratio of a 30nm chromatin fiber of superhelical nucleosomes?

A

60-40

43
Q

What is the packing ratio of condensed metaphase chromosome loops?

A

8000

44
Q

What is hnRNA?

A

mRNA precursor, before processing and splicing, consisting of both exons and introns.

45
Q

What are introns?

A

Non-coding intervening sequences of RNA which separate the coding sequences in a gene. they have to be removed.

46
Q

What is the function of introns?

A

Not clear, however they’re thought to serve as “spacers” which allows different splicing, thus production of different, but closely related proteins from a single gene.
-They may also serve to separate functional domains (exons) in a form that permits gene rearrangement by recombination to occur more rapidly
=> May allow more rapid evolution of bio. functions.

47
Q

What can be found within the introns at times?

A

Sometimes other coding or noncoding RNA’s can be found within the intonic DNA of certain genes.

48
Q

how is an mRNA formed from the precursor?

A

Introns are removed in processing of mRNA and the exons are spliced together.
Other posttranscriptional modifications also +Capping.

49
Q

How much of the human genome is exons?

A

ca 1%

50
Q

Where are small RNA’s transcribed from and what are their function?

A

They’re transcribed from one of the repeat families and modulate transcription either directly or indirectly:

  • Directly: by interacting with the transcription machinery
  • Indirectly: by affecting the activity of the chromatin tamplate.
51
Q

What classes can the human DNA be divided into?

A

-Non-repetative, or Unique sequence DNA. More than half of the encoded is unique.
This class includes the single copy genes that code for a protein.
-Repetative:Is at least 30% of human genome.
Can be further classified as :
-Moderately repetitive
-Highly repetitive.

52
Q

What is Highly repetitive DNA?

A
  • Consists of 50-500 bp (length) which are repeated many times.
  • They’re often clustered in the centromeres and telomeres of the chromosomes where their sequences are repeated 1-10 million times/haploid cell.
  • The majority of these are transcriptionally inactive and some play a structural role in chromosomes.
53
Q

Define Moderately repetitive DNA sequences.

A

They’re defined as being present in less than 10’6 copies/haploid cell.
-They’re not clustered but interspersed with unique sequences.
-They are transcribed by Pol II and contain Caps that cant be distinguished from those of mRNA (eg.miRNA).
-They’re further classified as:
*Long interspersed repeat sequences(LINE’s) :6k-7k Bp long. => there’s 20-50k copies of LINE’s per genome
*Short interspersed repeat sequences (SINE’s)3-7 hundrad bp long. =>there are 100k copies of SINE’s per genome.
=> Sines may be capable of jumping into and outof various sites within the genome.
Both of these are Retroposons.

54
Q

Define Retroposons

A

They are sequences that are able to move from one location to another through an RNA intermediate by the action of reverse transcriptase (which transcribes RNA into DNA)

55
Q

What is the ALU family?

A

A SINE family that accounts for 10% of the human genome.

  • They’re transcribed as integral components of mRNA precursors (hnRNA), or as discrete RNA molecules
  • 4,5s RNA and 7s RNA are included in this group.
56
Q

What is the function of Alu B1 and B2?

A

They regulate mRNA production at levels of transcription and mRNA splicing.

57
Q

What are Microsatellite repeat sequences?

How can they be detected?

A

it’s a category of repeat sequences which can be both interspersed and grouped.
-They’re most commonly found as dinucleotide repeats
(AC)
(TG)
-The number of these repeats may vary on the the chromosomes, thus providing heterozygosity.
-The numbers of copies are heritable traits.
-They’re easily detected with PCR (polymerase chain reaction) and therefore useful in mapping since most links are associated with one or more satellite markers.

58
Q

Explain the microsatellite instability phenomenon?

A

Trinucleotide sequences that increase in number and causes disease.
eg. (CGC)n repeat sequences is associated with fragile X syndrome.

59
Q

What is microsatellinte polymorphism?

A

Dont have a fucking clue, look up!!

60
Q

Where are the polypeptide chains in mitochondria encoded from?

A

The majority, 54 out of 67 are encoded from nuclear genes (eukaryotic DNA genes) and the rest (13) are encoded from mitochondrial DNA.

61
Q

Why can only females transmit diseases which come from a defect in mitochondrial DNA?

A
  • Because all mitochondria are contributed by the ovum during zygote formation.
  • Unless its deletion in oogenesisand, thus not inherited from the mother.
    eg. myopathies, neurologic disorders and some forms of diabetes.
62
Q

Describe the structure of mitochondrial DNA and what does it transcribe?

A

Its circular and composed of chains, or strands that are classified as either H-eavy or L-ight.
=> has ca 2-10 copies of small circular copies of about 16k bp of ds DNA.

  • Mitochodrial DNA encodes for mt- specific rRNA and tRNA.
  • codes for 22mt tRNA’s
  • Encodes for:
  • large (16s) mt rRNA
  • Small (12s) mt rRNA
  • Encodes for 13 proteins that play key role of the respiratory chain.
  • 7 subunits of NADH (complex I)
  • cytochrome b of complex III
  • 3 subunits of the cytochrome oxidase (complex IV)
  • 2 subunits of ATP-synthase.
63
Q

how does the mt DNA differ from nuclear DNA?

A
  • It’s circular like bacteria
  • has a higher mutation rate (5-10 times higher).
  • has different codons:
    • the nuclear DNA stop codon “UGA” is read as Tpr in mitochondria.
    • and the AGA&AGG, which in nuclear DNA codes for Arg, are stop codons in mitochondria.
  • Contains very few untranslated sequences.
64
Q

What is DNA recombination?

A

The exchange of genetic information between similar homologous chromosomes.
-Occurs primarily during meiosis and homologous metaphase chromosomes are required for this crossing over process.

65
Q

what does crossing over, or recombination usually result in?

A

in a reciprocal exchange in genetic informaition between homologous chromosomes.
However sometimes the alignment isnt exact =unequal exchange.
can be either deletion or insertion, or duplication.

66
Q

Explain the terms Deletion, insertion/duplication regarding recombination.

A

Deletion: occurs as a result of unequal exchange of genetic material resulting in a chromosome that has recieved LESS genetic material
Insertion, or duplication: is when a chromosome has recieved MORE genetic material.

67
Q

Give an example of an unequal recombination. Which results from deletion and which from insertion?

A

The region that has the gene which encodes for hemoglobin may be crossed over unequally and produce:
Delta-Beta Lepore, which is a result of deletion and Delta-anti Lepore, which gets more genetic material and is a result of duplcation.

68
Q

What is chromosomal integration?

A

When some bacteriophages are recombined with the DNA of a bacterial host cell, where they incorporate their DNA in a linear fashion.
This is also a form of recombination.

69
Q

Explain how a bacteriophage incorporates its DNA into a host.

A
  • The site of integration is chosen through two mechanisms:
  • through crossing over.
  • through site specific integration

-The genetic material of the bacterial virus is linearized.

The circular backbone of the bacteriophage is broken down to resemble the DNA of the host, as is the DNA of the host for incorporation and then it releases its appropriate ends with the proper polarity.

70
Q

What is site specific integration of bacterial viruses?

A

Some bacteriophages can produce proteins which enable integration through binding to the (host) bacterial DNA without it being a homologous site.

71
Q

When does the bacterial viruses integrate their genome through crossing over recombination?

A

If bacteriophage genome contains a genetic material sequence which is homologous to a DNA sequence of the host DNA, crossing over occurs in the same fashion as homologous chromosomes recombine during meiosis.

72
Q

Is integration of animal viruses to animal genome site specific?

A

Generally not, however it does have site preferences.

73
Q

What is the structure of processed genes and where are they believed to come from?

A

Processed genes consists of DNA sequences nearly identical to those of RNA for appropriate gene product.

  • They consist of a 5’ nontranslated region Without intron representation and a 3’poly A-tail.
  • This shows that it must have been a result from reverse transcriptase action and incorporation of a mRNA from which introns had been removed and A-tails adde already.
  • Processed genes have short terminal repeats.
74
Q

What are jumping genes?

A

Some small DNA elements (non-viral) in eukaryotic cells that are capable of transposing themselves in and out of host genome in ways that affect the neighboring DNA sequences, thus they affect evolution.
-The Alu family is a great example of that.

75
Q

Define Pseudogenes.

A

They’re Processed genes that have been randomly altered through evolution and therefore contains certain nonsense codons which take away their ability to encode for any functional proteins.

76
Q

Which are the 3 mechanisms which can affect rapid changes in genetic material?

A
  • Crossing over/recombination.
  • Transposition (Jumping genes/processed genes?)
  • Gene conversion.
77
Q

What is gene conversion?

A

When homologous or non homologous chromosomes that normally (occasionally) come together to eliminate any mismatched sequences between them accidentally “fixate” one variant or another throughout a family of repeated sequences and thereby homogenize it.

Förklara/ fråga om

78
Q

Define sister chromatid exchange.

A

Crossing over between sisterchromatids which contain identical genetic information. This type of exchange has no genetic consequences as long as the crossing over is equal.

79
Q

imuunoglobin gene rearrangement?

A

kolla upp på sida 380

80
Q

When do the human cell contain a tetraploid content of DNA?

A

After they have progressed through S phase.

Biochem K (10 decks)

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