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bio > Organisation And Contorl Of Euk Genome > Flashcards

Organisation And Contorl Of Euk Genome Flashcards

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Biology 101 flashcards
1
Q

What is a euk cell ? (Features)

A
  • larger in size 10-100 000Mb
  • contains membrane bound organelles
  • consists of 2 or more linear chromosomes bound by nuclear membrane in nucleus
  • each chromosome consists a double-stranded, linear DNA molecule associated with histones
  • multiple origins of replications
  • coding sequence is interrupted by non-coding introns located between exons
  • 80s ribosomes
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2
Q

How is euk genome packed (first level) ?

A

Negatively charged DNA (2nm helix diameter) is wound around groups of eight positively charged core histone proteins (histone octamer) - produce ‘bead-like’ structure called nucleosome / ‘beads on a string’ (10nm)
Remainder DNA not wound around histones (Linker DNA) joint adjacent nucleosomes
Histone H1 proteins binds to the core histones and DNA, securing the nucleosome

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3
Q

How is euk genome packed (2nd level) ?

A

Coiling of beads into helical structure known as 30nm chromatin / solenoid fibre with histone H1 proteins facing towards the centre where they form a polymer
Solenoid structure form looped domains (supercoils 300nm) which further coil and fold and associate with central nuclear matrix scaffold proteins to form a condensed chromosome (700nm - 1 sister chromatid) at mitosis

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4
Q

What are the two types of chromatin?

A

Euchromatin
Heterochromatin

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5
Q

Features of euchromatin

A

Less condensed form of chromatin
Appears as lightly stained regions
Contains genes which are actively transcribed or destined to be transcribed

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6
Q

Features of heterochromatin

A

Highly condensed form of chromatin
Appear as darkly-stained regions
Contain repetitive sequences that are transcriptionally inactive - resistant to being expressed as heterochromatin is unusually compact
Concentrated in specific areas of the chromosome
eg. telomeres and centromere

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7
Q

What is the structure of chromosomes?

A

Condensed structure which consists of two identical sister chromatids joined at the centromere, tips of the chromosome are telomeres

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8
Q

What are the 6 non-coding DNA in euk?

A

Introns
Control elements : Promoter, enhancer, silencer
Centromeres
Telomeres

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9
Q

What are introns ?

A

Sections of non-coding DNA, allows one gene to code for more than one polypeptide (alternative splicing)
Intron sequences tend to start with ‘GT-‘ and end with ‘-AG’

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10
Q

What is a promoter in eukaryotes ?

A

A specific nucleotide sequence located just upstream of a gene, which general transcription factors and RNA polymerase attach, to initiate transcription
- TATA box

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11
Q

What is an enhancer?

A

Specific nucleotide sequence located far away from transcription start site, which activator proteins bind to to activate transcription
- DNA has to bend to brig enhancer close to transcription factors (DNA bending protein)

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12
Q

What is a silencer?

A

Specific nucleotide sequence located far away from transcription start site which repressor protein bind to to suppress transcription

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13
Q

What is a centromere? What are its functions?

A

Centromere: constricted region of chromosome about 220 nucleotides in length, composed of highly repeated sequences
- not always positioned at centre (metacentric)

Functions :
Sister chromatid adhesion
Kinetochore formation
- kinetochore : complex of proteins that forms at each centromere, serves as attachment point for spindle fibres that will separate the sister chromatids
- abnormal centromeric function = improper chromosomal alignment and segregation = aneuploidy

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14
Q

What are telomeres? What are its functions?

A

Specialised DNA sequences which form the ends of linear DNA of euk genome, consisting many copies of a repeated DNA sequence (5’ - TTAGGG - 3’)

Function :
- protect genes from being eroded (end replication problem, telomeres act as buffer) via successive rounds of replication
- maintain the integrity of chromosomal end
- limit the lifespan of cells

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15
Q

How does telomeres protect genes from being eroded?

A

Telomeres don’t prevent shortening of DNA but postpone the erosion of genes near the end of DNA molecule
Non-coding regions, act as buffer to prevent loss of crucial genes as chromosome shortens after rounds of replication
They also help prevent ends of linear DNA molecule from degradation by deoxyribonucleases - special enz meant to breakdown unwanted genetic material, targets DNA with loose/no telomeres

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16
Q

How does telomeres maintain integrity of chromosomal end?

A

They prevent fusion of chromosomal ends with the ends of other chromosomes (chromosomal mutation)
- fusion could disrupt regulation of genes on adjoined chromosomes

Broken chromosomes that lack telomere are recognised as defective by cellular DNA repair machinery which remedies the situation by putting broken ends together - telomere prevents this recognition

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17
Q

How does telomeres limit the life span of cells?

A

Cells undergo apoptosis (programmed cell death) after a limited number of rounds of cell division when critical length is reached - Hayflick’s limit

This limits the extent of accumulated mutations and prevents the development of cancerous cells

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18
Q

How are telomeres extended?

A

By enz telomerase, only active in germ (sex) cells and inactive in somatic cells
It contains a short RNA molecule which has a complementary sequence to ‘TTAGGG’ repeats on telomere thus allowing extension of the parental strand

  1. Short RNA molecule of telomerase pairs up with telomere sequence (complementary base pairing)
  2. Enz telomerase reverse transcriptase (TERT) then uses the short RNA molecule as a template to extend telomere length by RNA template DNA synthesis
    - Telomerase catalyses the formation of the phosphodiester bonds between the existing 3’OH group of existing DNA overhang and 5’ phosphate group of incoming deoxyribonucleotide
  3. Then primase makes an RNA primer near the end of the telomere. DNA polymerase adds nucleotides to the 3’OH end of the primer and hence synthesizes a complementary strand . The nick is then sealed by ligase. The RNA primer is eventually removed.
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19
Q

Why is there a need for gene regulation ?

A

Regulation of gene expression plays a critical role in directing development of organisms and maintaining homeostasis

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20
Q

What are housekeeping genes ?

A

Genes involved in general cell maintenance and activity, code for proteins required for common and essential functional and structural purposes in most cells
Are continuously expressed

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21
Q

What is differential gene expression?

A

Each cell type of a multi-cellular organism is differentiated to serve different specialised functions (stem cells)
Some genes are only expressed in a certain stage of their life cycle (temporal regulation) or in a certain cell type (spatial regulation)

22
Q

What are the 5 main methods to control gene expression in euk?

A
  1. Chromatin remodelling : regulates if genes in a region of chromatin are expressed
    - histone acetylation and methylation
    - DNA methylation
  2. Transcription : regulate timing and rate of transcription
    - specific transcription factors interact with control elements
  3. Post-transcription : regulate which mature mRNA is produced
    - 5’ capping
    - 3’ polyadenylation
    - alternative splicing
  4. Translation : timing and rate
    - half-life of mRNA
    - translation initiation
  5. Post-translation : regulate functionality of protein and amount of protein
    - biochemical modification
    - proteolytic cleavage
    - protein degradation
23
Q

How is gene expression regulated at chromatin level?

A

Packaging of DNA into chromatin can affect transcription, by changing the packaging (chromatin remodelling) transcription can be regulated

Close packing of DNA wound around histones prevents the binding of general transcription factors and RNA polymerase onto the promoter
- formation of transcription initiation complex is prevented
- also prevents leaky/basal transcription

24
Q

Access to the promoters of the genes by general transcription factors depend on the packing of nucleosomes, how is this controlled?

A
  1. Post-translational modification of the histones : histone acetylation and methylation
  2. Modification of residues within the DNA : DNA methylation
25
Q

Describe the process of histone acetylation (addition of acetyl groups)

A

Histones undergo acetylation of free lysin residues at the N-terminal of the histone molecules, catalysed by histone acetylase / histone acetyltransferase (HAT)
Net positive charge of histones decrease, lowering affinity between histones and DNA which is negative charged
Chromatin threads unravel and become less condense, forming euchromatin

26
Q

How does histone acetylation regulate gene expression?

A

Allows greater accessibility of the general transcription factors and RNA polymerase to the underlying DNA sequence
Greater accessibility facilitates assembly of general transcription factors and RNA polymerase at the promoter and allows binding of additional gene regulatory proteins to the other control elements

Transcriptionally active regions of the chromatin usually contain histones that are modified via acetylation

27
Q

What is histone deacetylation?

A

Removing of acetyl groups catalysed by histone deacetylase resulting in histones reverting back to their positively charged nature
Greater affinity of these histones to negatively charged DNA
Chromatin thread becomes more condensed, forming heterochromatin

Expression of genes is switched off due to lower accessibility of protein to the DNA = transcriptionally inactive regions

28
Q

What is DNA methylation and its significance?

A

DNA methylation modifies DNA structure with the addition of methyl groups, catalysed by DNA methyltransferase, without altering DNA sequence
DNA methylation occurs mostly on recognition sites rich in cytosine (specifically CpG-rich sites)

Significance : it is observes in most transcriptionally inactive regions of the genome which suggest a role in gene silencing

29
Q

What are the 2 effects of DNA methylation?

A
  1. Block binding of transcription factors
    - many transcription factors bind to DNA at CpG rich sites thus DNA methylation at these sites block their binding and thus results in suppression of transcription initiation
  2. Induce heterochromatin formation
    - DNA methylation induces histone deacetylation as protein like histone deacetylase recognises and binds to regions with methylated DNA
    - leads to chromatin remodelling, chromatin is more closely packed resulting in transcriptionally inactive regions
30
Q

(Transcriptional control)
What are control elements?

A

Specific non-coding DNA sequences.that regulatory proteins (specific transcription factors) bind to to regulate rate of transcription

31
Q

What are the three types of control elements?

A
  1. Promoter
  2. Enhancer
  3. Silencer
32
Q

(Euk)
What are the features of the promoter?

A

location : proximal (close to) gene it regulates, upstream of gene (left)

type of transcription factor : general transcription factors

Sequence of events :
- general transcription factos recognise and bind to the promoter via the TATA box
- they then recruit RNA polymerase to the promoter, forming the transcription initiation complex

Effects : transcription initiated

33
Q

What are the features of enhancer?

A

Location : distal (far away) to the gene it regulates, can be upstream or downstream

Type of transcription factors : specific transcription factor - activators

Sequence of events : (same as silencer)
- activators binding to specific enhancers triggers a DNA looping mechanism aided by DNA bending proteins
- this brings the activator close to the promoter to interact with the transcription initiation complex (TIC)

Function :
- activator up-regulates the activity of RNA polymerase
- facilitate assembly and correct positioning of TIC on promoter

Effects : increased rate of transcription

34
Q

What are the features of the silencer?

A

Location : distal (far away) form gene it regulates, can be up or down stream

Type of transcription factors : specific transcription factor - repressor

Sequence of events : (same as silencer)
- repressor binding to specific silencers triggers a DNA looping mechanism aided by DNA bending proteins
- this brings the repressor close to the promoter to interact with the transcription initiation complex (TIC)

Function :
- repressor down-regulates the activity of RNA polymerase
- blocks assembly of TIC or prevent release of RNA polymerase from assembled TIC

Effects : decreased rate of transcription

35
Q

What are the two domains of transcriptional factors (structure)?

A
  1. DNA binding domain - for recognition and binding to specific DNA sequence
  2. Activation domain - for interaction with the other proteins of transcriptional machinery
36
Q

How is the euk repressor proteins different from the prok repressor proteins?
What are some of the mechanisms of euk repressor proteins?

A

Euk repressor proteins do not directly block the binding of RNA polymerase to the promoter or prevent the movement of RNA polymerase downstream to transcribe the genes

  1. Competitive DNA binding - blocks binding of activator protein to enhancer sequence as binding site for both repressor and activator overlaps
  2. Masking the activation domain of an activator protein - prevents activator from interacting with TIC
  3. Direct interaction with general transcription factors - block further assembly or prevent release of RNA polymerase
  4. Recruitment of repressive chromatin complexes - package whole regions of euchromatin into heterochromatin
  5. Recruitment of histone deacetylase - condense chromatin into heterochromatin
37
Q

What is combinational control and why is it significant?

A

A particular gene may be regulated by multiple enhancers or silencers, each active at a different time or in a different cell type or location in an organism

The specific combinations of control elements associated with a particular gene have a more significant effect than the presence of a single unique control element in regulating transcription (temporal and spatial regulation)
- even though all somatic cells have the same genetic material, they express different genes specific for their location and function

38
Q

How does post-transcriptional control regulate gene expression

A

In euk after transcription, pre-mRNA undergoes post-transcriptional modification
- 5’ capping, splicing and 3’ polyadenylation

39
Q

What is alternative splicing?

A

A regulated process ( controlled by the cell) which can result in a single gene coding for more than one protein
- particular exons may be included or excluded from the mature mRNA produced
- results in the protein being translated from the alternatively spliced mRNAs to have different AA sequences and thus different biological functions

Allows different cell types to produce different proteins from the same gene

40
Q

How does translational control regulate gene expression?

A

Translational rate is controlled to regulate amount of proteins synthesised
- half-life mRNA
Initiation of translation

41
Q

How does half-life of mRNA affect gene expression?

A

The longer the half-life the more stable an mRNA is, the longer it remains in the cytoplasm and the more time it can serve as a template for the translation of more proteins

42
Q

What is half-life influenced by ?

A
  1. Presence of 5’ cap
    - 5’ cap shields mRNA against degradation by 5’ exonucleases, increasing half-life and allows mRNA to be translated more and produce more proteins
  2. Length of 3’ poly-A tail
    - poly-A tail acts as a buffer against degradation by 3’ exonucleases, longer tail = mRNA remains functional longer

specific proteins that bind to 3’ UTR can mark the mRNA for rapid degradation thus limiting the number of times mRNA can be used for translation (longer tail=more stability against degradation)

certain hormones can also stimulate/retard rate of degradation of mRNA therefore decreasing/increasing availability of mRNA for translation

43
Q

Why is 5’ capping and 3’ polyadenylation in both post-transcriptional and translational control?

A

They both occur as part of post-transcriptional modifications but their effects in terms of regulation of gene expression are seen at the translational level

44
Q

How is translation initiation regulated?

A

Sequence-specific RNA binding proteins (translational repressor) or complementary RNA molecule bind to the 5’ UTR of mRNA and prevent ribosomes binding and formation of translational initiation complex

45
Q

How does post-translation control regulate gene expression?

A

Post-translational modification that control the functionality of synthesised proteins (biochemical modification and proteolytic cleavage)
Protein degradation that control amount of the protein

46
Q

What is biochemical modification?

A

Post-translational modifications to form functional proteins through the addition of chemical groups :
Glycosylation - addition of short carbohydrate chains
Phosphorylation - addition of phosphate groups
Acetylation - addition of acetyle groups
Methylation - addition of methyl groups
Hydroxylation - addition of hydroxyl groups

47
Q

What is proteolytic cleavage?

A

Some polypeptides needs to be cleaves/cut after translation in order for them to be able to fold into functional proteins

Eg. Insulin maturation
- removal of signal peptide from the translated pre-pro insulin via proteolytic cleavage forms proinsulin
- further formation of disulfide bonds and removal of C-chain via proteolytic cleavage results in active insulin molecule

48
Q

What is protein degradation?

A

Proteins that have fulfilled their functions and are no longer required need to be removed to prevent excessive protein functions and to recycle raw materials
Cells must be able to dispose of faulty or damaged proteins rapidly (high turnover rate)

49
Q

How are proteins degraded in euk?

A

By ubiquitinylation (destabilise protein) and proteasome action
- a small protein, ubiquitin, is covalentes added to the N-terminus of the protein to be degraded marking the protein for degradation by a protease complex (proteasome)

50
Q

Why is euk genome packed?

A

The packing of the very long eukaryotic DNA ensures that it fits into the nucleus and that it does not get entangled and break

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