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Biochem K > Molecular biology > Flashcards

Molecular biology Flashcards

1
Q

Explain chromosomal integration of bacterial viruses

A

Some bacteriophages can recombind with DNA of a bacterial host causing an incorporation of their own DNA into the genetic information of their host.
This is a form of recombination, where the backbone of the circular bacteriophage genome is broken tr resemble the DNA of its host——-) becomes linerized.
and joins the proper ends of the host (the end witch same polarity)

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2
Q

How is the site where the bacteriophage chooses to integrate itself into the host chosen?

A

2 mechanisms;
1) If the macrophage contains genetic material sequence which is Homologous to the DNA sequence of the Host, then Crossing over will occur. (same way as homologous chromosomes cross over).

2) SITE SPECIFIC: Some bacteriophages can produce proteins that are able to bind specific sites of bacterial chromosomes to a nonhomolougus site.

Integration of animal viruses that have been transcribed by reverse transcriptase, into human Dna (eg, hiv) are not site specific but have site preferences.

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3
Q

What are processed genes?

A

DNA elements that are NOT viruses and cantransport themselves in and out of host genom, effecting neighboring sequences. –) also known as Jumping DNA/ genes. (They effect evolution.
Eg. Alu family

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4
Q

What do precessed genes consist of?

A

They consist of DNA sequences, nearly identical to those of RNA for the appropriate gene product
-They have: -5’ nontranslatet region
-coding region without intron representation
-3’poly A tail
- Have short terminal repeats
The arrangement of their structure, or components must have resulted from reversed transcription of m RNA from which intron had already been removed

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5
Q

Whats a Pseudogene

A

A processed gene that has been altered randomly through evolution and that now contains nonsense codons, thus has lost its ability to encode any functional protein

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6
Q

Describe gene conversion

Főrstár ej helt

A

When homologous and nonhomolgous chromosomes that normally, occasionally comes together to eliminate any mismatch sequences between them, accidentally fixate a repetative sequence of one family , thus homogenizing the sequence of the member of repetative DNA

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7
Q

Which re the 3 mechanisms that effect rapid chnge in genetic material?

A

Unequal Cross over
Transposition
Gene conversion

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8
Q

Explain sister chromatid exchange

A

Cross over between homologous sister chromatids.

Occurs After S-Phase when the cell contains tetraploid DNA.

each of these sister chromatids are generally identical so when crossing over occurs it ill have no genetic consequences as long as it isnt an unequal cross over

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9
Q

Immunoglobin gene rearrangement

A

Kolla upp

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10
Q

Which are the steps of DNA replication in Eukaryotes?

A

1) identification of origin
2) ATP- Hydrolysis driven Unwinding of dsDNA to provide ssDNA since replication only can occur from a singe strand template
3) Formation of replication fork
4Initiation of DNA synthesis and elongation
5)Formation of replication Bubbles of newly synthesized DNA segments
6) re- formation of the chromaton structure –) nucleosomes.

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11
Q

What can be found at the origin of replication (Ori)

A

an association of sequence specific dsDNA- binding proteins with a series of direct repeat DNa sequences.

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12
Q

Origin site of E.coli?

A

Ori C, bound by the protein dnaA forming a complex which consists of 150-250 Bp of DNA multimers of the DNA-binding protein. this leads to local denaturation and unwinding of adjecent AT rich region of DNA.

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13
Q

Whats the origin replication eliment (ORE)?

A

11BP sequence of ars in yeast

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14
Q

What does a replication fork consist of?

A

four components that forms in following sequence ;

1) DNa Helicase unwinds
2) primase initiates
3) DNa pol. initiates the elongation
4) ssBproteins bind to ssDNA to keep the strands separated.

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15
Q

Which gene does DNA Pol III come from

A

Its a product of dnaE gene.

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16
Q

Wich are the polymerase accessory factors wich polymerase III forms a complex with in order to bind to the DNA for replication?

A

beta, gamma, delta, delta’ grekiskt T

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17
Q

What is the role of Helicase

A

unwinds DNA in a 5’-3’direction. it associates with primase complex (With dnaA and dnaB) to get proper access to the template.
Without the action of helicase DNA pol cant initiate the elongation.

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18
Q

Which are the 3 properties that all DNA polymerases share?

A

1) Chain elongation ( in nucleotides/sec)
2) Processivity (how many nucleotides it can add before letting go of the template strand)
3) Proofreading (identifying and correction of errors)

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19
Q

Name all the DNA polymerases in E.coli and explain their functions.

A

Pol I; Gapfilling following replication, repair and recombination.
Pol II; Proofreading and repair
Pol III; Elongation; processive leading strand synthesis. (analogous with e in eukaryotes)
DnaG; Primase (analogous with alpha in eukaryotes)

MER INFO FRÅN SHERLEYS

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20
Q

whats the role of the Beta subunit of Pol II

A

Sliding clamp -increases the processivity and stability of the complex, as well as elongation rate.

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21
Q

Whats the roles of DNA Pol I and Pol II Of prokaryotes?

A

Mostly involved in proofreading and repair.

However pol TA MER INFO FRÅN SHERLEYS

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22
Q

Whats the reason the rate of replication in Eukaryotes is slower than that of Eukaryotes??

A

Packed in nucleosemes

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23
Q

Which enzymes catatyzes the formation of Primers in -eukaryotes and Prokaryotes respectively?

A

Pro; DnaG

Euk; Pol alpha

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24
Q

explain how the first nucleotide is added onto he primer

A

DNA pol III in prokaryotes and DNA Pol E or delta in eukaryotes catalyses will brong the first nucleotide. the 3´ hydroxyl group of the rna primer will carry out nucleophilic attack on the phosphate of the newly arrived deoxy triphosphate nucleotide ( at its alpha moiety) and this requires cleavage of two acid anhydrade bonds. a pyrophosphate is released in the process. Obs. in replication the ppi will be progen down into two pi´s thus the reaction is irreversible.

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25
Q

explain how the second dna nucleotide is added

A

triphosphate nucleotide will enter and ita alpha phosphate will be attacked by the carboxyl of the deoxyribonucleotide monophosphate of the previou nucleotide.

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26
Q

what dictates which nucleotide that will be added to the chain?

A

hydrogen bondin, which also hoøds it in place while nucleophilic attack is carried out

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27
Q

What is the role of Ligase?

A

ligase is an enzyme which joins the nicks after removal of primers on okazaki fragments (done by Pol I in pro) or after repair. it does this through formation of new phosphodiester bond in a 3 step process.

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28
Q

Which are the 3 steps in which the enzyme Ligase joins nicks in prokaryotes?

A
  • Ligase binds to NAD+ and forms a complex know as Ligase-NMN (Releases a pyrophosphate in the process).
  • Ligase MNM then reacts with the free 5’ phosphate at the nick and Ligase is released.
  • The OH group at the 3’ end is then free to carry out nucleophilic attack on the 5’ end the rest of the complex is released.
29
Q

Explain the process in which nicks are joined by Ligase in Eukaryotes

A

sam as Prokaryotes but with ATP insted of NAD+

30
Q

What are the functions of ligase?

A

Joins Okazaki fragments
Closes linear DNA into circular
Closing nicks in DNA repair and recombination

31
Q

How does Eukaryotes make up for their slow replication?

A

Multiple replication bubbles and bidirection.

32
Q

Which proteins promote separation of dsDNA during replication inProkaryotes and Eukaryotes, respectively?

A

Pro; SSB proteins
Euk; Replication protein A (RPA)

They all bind cooperatively and stoichiometrically without interfereing with ability of template. and bind ones every 10 nucleotides.

33
Q

Another name for helicase?

A

DNA B protein (is hexametric)

34
Q

Which enzyme unwinds the DNA during replication in Eukaryotes?

A

MCM protein

35
Q

What counteracts the unwinding of DNA during replication to release stress from the molecule?

A

Swivel function. “swivels” are interspersed into molecule by Topiomerases. They do so bu introducing nicks in one strand of the double helix.

36
Q

What are the roles of the Topiomerases?

A

Top I ; KOLLA SHERLIES, VEM SOM GØR VAD!

Top II;

37
Q

Define supercoiled DNA

A

i higher ordered structure occuring in circular DNA molecules when they wrap around a core, or around their own axis.

38
Q

What is reverse transcriptase?

A

Class of enzymes; species of Animal virus (Retro virus) that are capable of synthesizing a DNA molecule from a single strand of RNA.

39
Q

Explain the steps in which the Reverse transcriptase can produce DNA from RNA.

A

1) Synthesis of DNA-RNA hybrid from a single RNA strand template.
2) RNase H, a specific virus encoded nuclease will then degrade the hybridized template RNA strand leving only a single DNA strand. (remember degration of RNA easier than DNA due to extra hydroxyl group on ribose)
3) The ssDNA can now be used as a template for the syntesis of a ds DNA (done just like each strand in replication, semiconservative)

Voila!! bam boom DNA is born!

40
Q

What is the role of histone chaperones?

A

They are proteins that work in samførstånd med chromatin assembly and remodeling complexes to reassemble the randomly distributed old and new histones into nucleosomes as soon as the DNA has been replicated.

41
Q

When does replication of human genome occur?

A

S-Phase (synthetic phase)

42
Q

What occurs in each of the phases of the Cell cycle?

A

G1 ;preparation for DNA synthesis in form of synthesis of proteins required for the process etc.
Cell can reversely leave the cell cycle at G1 by entering a non replicative state (G0) if any errors have occured. When the cell is back to normal then it reenters G1 and contines as normal.
S- phase ; Replication of DNA, this can only occur at this stage and thats how the cell regulates the DnA synthesis, by only allowing it once.
In this phase there will be a greater content on Polymerases.
G2 ; Preparation for Mitosis (cell division)

  • if te cell detects any DNA damage at either G1 or G2 the cell cycle will not be completed (enters Go) if damage isn’t repairable then programmed cell death (apoptosis) will occur.
43
Q

What are cyclins?

A

A family of proteins that govern the transition from one Phase of the cell cycle to another, through increase and decrease of concentration.
They are able to activate different Cyclin Dependent Protein Kinases (CDK) through their concentration change.

44
Q

What is the role of cyclin D?

A

In mammals it allows the transition beyond the restriction phase (to enter s-phase). When it increases its concentration in late G1 phase it allows for transition by activation of protein kinases. its a nuclear protein.

45
Q

Which nuclear proteins does Cyclin D activate?

A

CDK4 and CDK6, which both are synthesized during g Phase. The three nuclear proteins will assemble as a Cyclin CDK complex, an active serine-threonine protein kinase.

46
Q

Wwhich is the important substrate of the Cyclin CDK complex and what is its role?

A

Retroblastoma protein (Rb). its a cell cycle regulator that binds to and inactivates the transcription factor E2F, which is necessary for the transcription of certain protein essential for DNA synthesis (eg. Histones and DNA replication proteins)

47
Q

How does CDK4&CDK6 enable the ransition to s phase in cell cycle?

A

They can Phosphorylate the Rb from its repressor thus releasing the E2F, and transcription of important proteins and progression into next phase then follows.

48
Q

Which proteins will CDK2 form complexes with, and when?

A

CDK2 will form complex first with Cyclin E in late G1 as well, however this complex degenerates fast and CDK 2 forms complex with Cyclin Aright after instead.
This sequence is important for initiation of DNA replication.
How it’s important, well no one fucking knows!!

49
Q

What are oncoviruses?

A

cancer causing viruses and oncogens. samma som oncogenes?? fattar nooollllll fuck me

50
Q

Oncogenes are?

A

Cancer producing genes that are capable or disrupting the apparent restriction that normally regulates the entrance to s-phase in mammals.

51
Q

In which ways can disruption lead to abnormal or restrained cell division? (cancer??)

A
  • Excessive production of Cyclins.
  • loss of spec. CDK inhibitor.
  • Activation or inhibition of Rb, CDK’s or Cyclins at inappropriate time.
52
Q

bcl oncogene associated with B-cell lymphoma = Cyclin D1 gene.

A

noll aning om vad jag menar men passss!

53
Q

What are oncoproteins?

A

Transforming proteins produced by several DNA viruses that target Rb repressors.
they can; 1) inactivate repressor, causing uncontrolled cell division =) Cancer
2) keep repressor on, causing uncontrolled cell growth =) tumor formation

54
Q

Describe the process of Replication licensing

A

Process in which a chromatin that has been replicated in S-Phase of a certain cell cycle is “marked” so that it wont be replicated until it passes through mitosis again.

55
Q

What does the “marking” of replicated chromatin in cell cycle involve?

A

Dissociation and/ or cyclin-CDK phosphorylation ans subsequent degradation of several origin binding proteins that play critical role in replication initiation complex formation etc.

56
Q

How many check point controls are there?

A

4

57
Q

What is the function of the checkpoint controls?

A

Monetoring of the DNA and chromosomal integrity during cell cycle.

58
Q

What happens if any errors are detected in one of the four checkpoints of cell Cycle?

A

Progression through cell cycle is interrupted and halted until the damages can be repaired. however if the cell isn’t able to restore its condition to normal, programmed cell death will occur.

59
Q

What kind of regulator is P53, where does it act?

A

A tumor repressor which play role in the check point controls in G1 and G2. Its a DNA binding transcription factor.

60
Q

Family of P53?

A

P63 P73.

61
Q

Explain about P53’s stability?

A

Normally relatively unstable but somehow becomes stabilised in response to DNA damage. Maybe bcs of direct DNA interaction.

62
Q

What happens when the concentration levels of P53 is increased?

A

increace of its concentration activates the transcription of an asemble of genes that collectively delays the transcription through the cell cycle.

63
Q

Name the important induced proteins that serves to delay cell cycle.

A

P21 -

64
Q

What is the role of P21?

A

-Delays cell cycle.

Its a CDK-cyclin inhibitor and is capable of inhibiting all CDK-cyclins.

65
Q

Which compound is responsible for Apoptosis and how?

A

P53 induces the activation of a collection of genes that induce apoptosis.

66
Q

What happens to cells that lack P53?

A

They fail to undergo apoptosis…….

67
Q

Which histone isotope types can be incorporated in repair?

A

H2AX (into nucleosomes at damaged sites)

PARP

68
Q

Which are the damage specific Histones?

A

Dimethylated lysine 20 histone H4 (H4K20Me2)

69
Q

fattade ej resten kolla sida

A

391 i harp.

Biochem K (10 decks)

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