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Molecular Biology > Chromatin and Chromosomes > Flashcards

Chromatin and Chromosomes Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

Nucleoid

A

is an irregularly shaped region, occupying 1/3 of a prokaryotic cell, where its genetic material is localized

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2
Q

Lysozyme

A

is an enzyme able to lyse the bond between peptidoglycans in the bacterial wall and can be found in human epithelial secretions

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3
Q

lysozyme is more effective on what kind of bacteria

A

gram +

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4
Q

what’s the difference between gram + and gram- bacteria

A

Gram + has a much thicker peptidoglycan layer than gram -. Gram - also has an external membrane on top of the peptidoglycan

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5
Q

how do we isolate the nucleoid?

A

~Treat the E.coli cells with lysozyme
~induce osmotic shock
~low speed centrifugation

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6
Q

what kind of genes does Plasmidic DNA code for

A

for non-essential traits, that could contribute to an evolutionary advantage.
~it has 1000’s of bases
~circular DNA

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7
Q

what kind of genes does Genomic DNA code for

A

essential informations, house-keeping genes
~has 1000000’s of bases
~circular DNA

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8
Q

vector

A

piece of DNA which can replicated autonomously and can accept a piece of DNA from another source

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9
Q

why do plasmids make good vectors?

A

~They are small and easy to manipulate
~There are many within a cell and so many copies are available.
~They always contain a site of origin of replication and almost always contain a gene giving resistance to a specific antibiotic - which allows for selection in lab situations.
~Can contain a marker which allows for selection and have a poly linker or MCS

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10
Q

Bacterial conjugation

A

method by which bacteria exchange info, through a sex pillus

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11
Q

how is DNA organized in a bacterial cell?

A

it is supercoiled and attached to a protein core

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12
Q

what effect does DNase have on bacterial DNA

A

it creates small nicks in the super coils

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13
Q

each loop in a E.coli genome corresponds to a

A

structural domain

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14
Q

why is bacterial DNA organized in domains?

A

because the E.coli cell cannot contain a completely relaxed chromosome and only relaxed DNA can be transcribed

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15
Q

Chromatin

A

was coined by alexander flemming in 1882

it is stained by the Feulgen reagent (red)

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16
Q

what is chromatin made of?

A

~DNA
~Histones
~Non histonic proteins (neutral/acidic)
~RNA

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17
Q

costitutive heterochromatin

A

always in compact form, is usually repetitive DNA

18
Q

facultative heterochromatin

A

is present depending on cell type

19
Q

how long is the human genome

A

2m

20
Q

the nucleus diameter is

A

5-10 micrometers

21
Q

chromosome length is

A

1.6-8.2 cm

22
Q

how to study proteins associated with DNA

A

~treat with DNase
~use salts to break interaction between histones and bases of DNA
~use polyacrylamide gel to separate the proteins
~treat with SDS - makes the proteins negatively charged
~heat and use betamercaptoethanol to denature (it breaks disulfide bridges)

23
Q

electron dense beads on the beads in a string structure are made of?

A

DNA and histone proteins

24
Q

the beads on a string structure is

A

a left handed solenoid supercoiling

25
Q

beads are

A

histone octamer around which 1.65 left handed turns of DNA are wrapped.

26
Q

string is

A

linker DNA ranging from 8bp to 114 bp

27
Q

nucleosome

A

is a core of 8 histone proteins and linker DNA wrapped around it

28
Q

the tails of a protein are called the - terminal

A

N terminal

29
Q

histones are

A

small polypeptides
~positively charged
~enriched in basic aa: Arg/Lys
~pL=9~10

30
Q

which histone has a more conserved sequence? H4 or H1

A

H1

31
Q

the minor groove faces away/towards the histone?

A

towards. Note that there are mostly AT pairs here

32
Q

What is the 2nd level of condensation?

A

the beads on a string structure coils into a 30nm diameter helical structure
~this is not present along the whole chromosome

33
Q

explain the solenoid model of condensed chromatin

A

the DNA does not cross the superhelix longitudinal axis, the linker DNA is less accessable

34
Q

explain the zig-zag model of condensed chromatin

A

the linker DNA is longer and more accessible

35
Q

what is the 3rd level of condensation

A

loops of 300nm fibers and nuclear scaffold

36
Q

what is the 4 level of condensation

A

the loops form rosettes (6 loops per flower) which then form coils made of 30 rosettes

37
Q

each chromatid is made of - coils

A

10

38
Q

what modification of histone tails are possible?

A

acetylation, methylation, ubiquitination, sumolyation and phosphorylation.

39
Q

acetylation

A

Usually occurs on lysine. The specific enzyme is Histone Acetyl Tranferases (HAT) they acetylate lysine. The reverse is done by Histone Deacetylase (HDAC)
Acetylation changes the properties of lysine (which are basic residues and so have a positive charge) by removing the positive charge. This change in charge makes it more difficult for the histone to interact with DNA, and so it favours the opening of the chromatin structure.

40
Q

Explain methylation

A

Lysine can also be methylated. HOWEVER, it cannot be both acetylated and methylated. they are competing reactions and are mutually exclusive. It is possible for lysine to be di and tri- methylated also. Methylation does not remove the positive charge and so does not favor the opening of the chromatin.

41
Q

Ubiquitination

A

It is a type of acylation which uses a small polypeptide of 7-8 amino acids called ubiquitin. It also acts on lysine.
It occurs through a slightly complex reaction. It requires 3 different enzymes; E1 (which is ubiquitinated through ATP hydrolysis) the ubiquitin is transferred to E2 which uses E3 (an enzyme which can recognise both the target molecule and the E2 enzyme carrying the ubiquitin

42
Q

phosphorylation

A

May either activate or inactive a protein. It requires an alcohol group to be present in the protein. This is present in serine, threonine and tyrosine. A phosphate group is added, requiring ATP and catalysed by kinases. Phosphatases reverse the reaction

Molecular Biology (19 decks)

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