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Biology > 19 Gene Expression in Eukaryotes > Flashcards

19 Gene Expression in Eukaryotes Flashcards

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0
Q

How many base pairs of DNA are in a typical human cell?

A

6billion

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1
Q

Differential gene expression

A

Is responsible for creating different cell types, arranging them into tissues, and coordinating their activity to form the multicellular society we call an individual

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2
Q

How long would a fully stretched DNA molecule be in humans?

A

2meters (6.5feet)

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3
Q

What is the nucleus diameter?

A

5 micrometers

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4
Q

Chromatin layers of organization

A
  1. DNA wrapped around 8 histones to form nucleosomes
  2. Nucleosomes are packed into 30nm fibre
  3. 30nm fibre attached to protein scaffold
  4. entire assembly folded into a highly condensed structure observed during cell division
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5
Q

H1 protein function

A

Seals DNA to each nucleosome

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6
Q

Linker DNA

A

Short chain of DNA that links nucleosome to another nucleosome.

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7
Q

Central idea is that the chromatin must

A

Decondense to expose the promoter so RNA polymerase can bind to it

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8
Q

Function of DNase?

A

Enzymes that cut DNA

  • cleave DNA at random locations
  • cannot cut efficiently if tightly wrapped with proteins
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9
Q

Harold Weintraub and Mark Groudine

A

DNA of actively transcribed genes is in an open configuration

  • compared chromatin structures of two genes, β-globin and ovalbumin, in chicken blood cells.
  • β-globin is protein in haemoglobin found in red blood cells, ovalbumin is a protein found in egg white.
  • in blood cells, β-globin is transcribed at high levels, but ovalbumin is not at all.
  • then treated cells with DNase
  • found that the β-globin gene was cut more readily
  • CONCLUSION: chromatin of the actively transcribed β-globin was decondensed, conversely, the chromatin of ovalbumin was condensed.
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10
Q

Histone gene repression

A

The absence of histone-DNA interactions promotes transcription
The presence of normal histone-DNA interactions prevents it

Data suggest that in their normal, or default state, eukaryotic genes are turned off.

Different form of negative control

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11
Q

DNA methylation

A
  1. Enzyme DNA methyltransferase adds methyl group (-CH3) to cytosine residues in DNA.
  2. In mammals, the sequence recognized is a C next to a G in one strand of DNA. Abbreviated CpG
  3. Methylated CpG sequences are recognized by proteins the trigger chromatin condensation.
  4. Actively transcribed genes usually have low levels of methylated CpG
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12
Q

Histone modification

A

Large set of enzymes adds a variety of chemical groups to specific amino acids of histone proteins.

  • phosphate groups
  • methyl groups
  • short polypeptide chains
  • acetyl groups (-COCH3)
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13
Q

Histone code hypothesis

A

Postulates that particular combinations of histone modification set the stage of chromatin condensation for a particular gene

Important role in regulating transcription

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14
Q

Histone acetyltransferase

A

(HATs) Adds acetyl groups to the positively charged lysine residue in histones

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15
Q

Histone deacetylases

A

(HDACs) remove acetyl groups

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16
Q

Acetylation

A

The adding of acetyl groups to histones

-usually results in decondensed chromatin, state associated with active transcription

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17
Q

How can acetylation of histone promote decondensation?

A

When HATs add acetyl groups, the acetyl group neutralizes the positively charges lysine residue loosens close association of nucleosomes with the negatively charged DNA.

The addition of the acetyl group also creates a binding site for other proteins to help open the chromatin.

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18
Q

Chromatin-Remodeling complexes

A
  1. Enzymes form macromolecule machines called chromatin-remodeling complexes.
  2. These machines use ATP to reshape chromatin
  3. causes nucleosomes to slide along the DNA
  4. in some cases, knocks out the histone completely off the DNA
  5. Opening up stretches of chromatin and allow gene transcription
19
Q

Gene associated with diabetes?

A

Hnf4a gene

20
Q

Promotor

A

Is a site in DNA where RNA polymerase binds to initiate transcription

21
Q

Eukaryote promotors

A

Are more complex than bacterial promotors

Containing two to three conserved sequences that serve as binding sites

22
Q

Most extensively studied promotor

A

TATA box

23
Q

After chromosome remodeling, what binds to the TATA box?

A

TATA-binding protein (TBP)

Does not guarantee that the gene will be transcribed

24
Q

Who discovered regulatory sequence?

A

Yasuji Oshima

25
Q

How do yeast cells control the metabolism of the sugar galactose?

A

When galactose is absent, yeast cells produce very little enzymes required to metabolize it. When present these enzymes increase by a factor of 1000

They found mutant that could not produce any of the five enzymes

  1. The five genes are regulated together, even though they are not on the same chromosome
  2. Normal cells have an activator protein that exerts positive control over the five genes
  3. The mutant cells have a mutation that completely disables the activator protein.
26
Q

Promoter-proximal elements

A

Regulatory sequences located close to the promoter and bind regulatory protein

Unlike the promoter itself, they have sequences unique to specific sets of genes. This way they express certain genes wanted but not others

27
Q

Enhancers

A

Regulatory sequences that are far from the promotor and activate transcription - positive control

  • can be more than 100,000bases away
  • can be located on introns or untranscribed sequences
  • can be on either 5’ or 3’ side of gene
  • many different types exist
  • usually have binding sites for more than one protein
  • can work even if their 5’-3’ orientation is flipped
  • can work if they are moved to a new location
28
Q

Transcriptional activators

A

Regulatory proteins that bind to enhancers beginning transcription

29
Q

Silencers

A

Regulatory sequences that inhibit transcription.

30
Q

Repressors

A

Regulatory protein that bind to silencers shutting down transcription

31
Q

Collective term for promotor-proximal elements, repressors and transcriptional activators

A

Regulatory transcription factors

Transcription factors

32
Q

What causes cell differentiation

A

Different cell types express different genes depending on the transcription factors.

Multicellular organisms can have transcriptional factors produced by signals from other cells (early in embryonic development)

33
Q

How do transcriptional factors recognize the specific DNA sequences?

A
  • DNA sequences are partially exposed in the major and minor grooves.
  • Depending on the base pairing, there are different shapes and composition of atoms.
  • Transcriptional factors can recognize these different shapes and composition.
34
Q

Basal transcription factors

A

These are proteins that interact with the promoter and are not restricted to particular genes or cell types.

Are necessary for transcription to occur but do not provide much in the way of regulation

Eg. TATA-binding protein (TBP)

35
Q

Large complex proteins that act as a bridge between regulatory transcription factors, basal transcription factors and RNA polymerase II

A

Mediator

36
Q

Steps of initiation of transcription in eukaryotes

A
  1. Transcriptional activators bind to DNA and recruit chromatin-remodeling complexes and histone acetlytransferases (HATs)
  2. The chromatin-remodeling complexes and HATs open a swath of chromatin that includes promoter, promoter-proximal elements and enhancers.
  3. Other transcriptional activators bind to the newly exposed enhancers and promoter-proximal elements. Basal transcription factors bind to the promoter and recruit RNA polymerase II
  4. Mediator connects the transcriptional activators and basal transcription factors that are bound to DNA. This step is made possible through DNA looping. RNA polymerase II can now begin transcription
37
Q

RNA interference

A

Occurs when a tiny, single-stranded RNA held by a protein complex binds to a complementary sequence in an mRNA. This event unleashes either the destruction of the mRNA or a block in the mRNA’s translation.

38
Q

RNA interference steps

A
  1. RNA interference beings when RNA polymerase transcribes genes that code for RNAs that double back on themselves to form a hairpin.
  2. Some of the RNA is trimmed by enzymes in the nucleus; then the double stranded hairpin that remains is exported to the cytoplasm.
  3. In the cytoplasm, another enzyme cuts out the hairpin loop to form double-stranded RNA molecules that are only about 22nucleotide long
  4. One of the strands from the short RNA is taken up by a group of proteins called RNA-induced silencing complex (RISC). The RNA hold by a RISC is a microRNA (miRNA)
  5. Once it is part of a RISC, the miRNA binds to its complementary sequence in a target mRNA
  6. If the match between a miRNA and an mRNA is perfect, an enzyme, in the RISC, destroys the mRNA by cutting it in two
  7. If th match is not perfect the mRNA is not destroyed but translation is inhibited.
39
Q

Proteasome

A

Recognizes protein with ubiquitin tag and destroy it

40
Q

Compare DNA packaging between bacteria and eukaryotes

A

Eukaryote DNA must decondense for basal and regulatory transcription factors to gain access to genes and for RNA polymerase to initiate transcription. The tight packaging of eukaryote DNA means that the default stage of transcription is off

In contrast, bacteria lack histone histones and have freely accessible promoters, so may be on in default stage.

Therefore, chromatin structure of eukaryotes provide a mechanism of negative control not found in bacteria.

41
Q

Compare complexity of transcription between bacteria and eukaryotes

A

Much more complex in eukaryotes

The sheer number of proteins involved in regulation transcription dwarves that in bacteria, as does the complexity of their interactions

42
Q

Compare coordinated transcription between bacteria and eukaryotes

A

In bacteria, genes that take part in the same cellular response are often organized into operons and are transcribed together by the same promotor

In eukaryotes, like bacteria many genes can be expressed together, however, use regulons that have physically scattered genes expressed together (may not even be in the same chromosome) and regular transcription factors trigger the transcription of genes with the same DNA regulatory sequence

43
Q

Compare the reliance on post-transcriptional control

A

Eukaryotes make greater use of post-translational control, such as alternative splicing. Alternative splicing allows eukaryotes to produce many different proteins from the same gene. They also make microRNAs and regulate the stability of mRNA.

These post transcriptional controls are seldom seen in bacteria

44
Q

What two classes of genes that when mutated may lead to cancer?

A
  1. Genes that stop or slow the cell cycle

2. Genes the trigger cell growth and division by initiating specific phases in the cell cycle

45
Q

What gene is most linked human cancers?

A

p53 - codes for regulatory transcription factors - halting cell cycle when DNA is damaged

When a mutant form of p53 is formed enhancers cannot bind. DNA damage cannot arrest the cell cycle.

The cell cannot kill itself and damage DNA is replicated

46
Q

Results that support the model function of p53

A
  1. p53 activates many different genes, including genes for cell cycle regulation, DNA repair and apoptosis
  2. X-ray crystallography studies show that p53 binds directly to DNA regulatory sequences of the genes it controls
  3. Virtually all p53 mutations associated with cancer are located in the proteins DNA-binding region and alter amino acids that interfere with p53’s ability to bind to regulatory DNA sequences

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