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BIOLOGY 108 TEST #4 > Regulation of Gene Expression > Flashcards

Regulation of Gene Expression Flashcards

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1
Q

Can bacteria tune its metabolism to changing envirnment and food sources?

A

Yes, this is a selective advantage.

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2
Q

What is tryptophan? How does E. coli regulate its tryptophan synthesis?

A

Tryptophan is an amino acid.

E. coli can synthesize its own typrtophan from a precursor when the environment is lacking and it also can turn this synthesis off when there is tryptophan available in the environment.

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3
Q

What are the two levels that metabolic control can occur on? What is an example of each? Which is faster?

A
  1. Adjusting activity of metabolic enzymes: allosteric regulation - in tryptophan production, when tryptophan accumulates in the cell this excess with stop th already present enzymes in the cell that synthesize trytophan from functioning. FASTER.
  2. Regulation of genes that encode metabolic enzymes: regulation of transcription so that certain genes aren’t expressed. SLOWER.
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4
Q

What is an operon? What are these composed of?

A

Consists of:

  1. Operator
  2. Promoter
  3. Genes for metabolizing enzymes

These things compose an operon which is located on DNA and can be turned on or off to control particular metabolic pathways.

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5
Q

What is an operator?

A

This is the On/Off switch region of the operon.

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6
Q

What is the promoter

A

The region where RNA polymerase attaches on the operon.

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7
Q

What attaches to operator to switch the operon off?

A

A repressor.

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8
Q

What is the function of a corespressor?

A

This is a small molecule that attaches to a repressor in to allow it to attach to operator to switch operon off,

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9
Q

Look at the picture of this operon. How does each enzyme get created separately if the genes are transcribed onto the same strand of mRNA? What is the function of the regulatory gene? What happens when a repressor is rendered inactive?

A

There are stop codons located on the mRNA that cleaves each polypeptide chain to ensure each enzyme is produced separately.

The regulatory gene transcribes the mRNA that translates to the repressor for the operon

When a repressor is rendered inactive it can’t bind to the operator to switch the operon off, so the operon genes are transcribed.

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10
Q

Look at this picture and understand the function of a corepressor. Notice what acts as the corepressor.

A

Tryptophan acts as the corepressor in this picture.

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11
Q

What is the difference between a repressible and an inducible operon? What is an example of each?

A

Repressible - Usually on, but can be shut off when repressor binds to operator. Trp operon is an example of this. Usually involved in anabolic pathways.

Inducible - is usually off, an inducer can bind to the repressor and render it inactive so it can’t bind to operator. This allows transcription of the operon. Lac is an example of an inducible operon. Repressors are made in their active form.

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12
Q

Describe the Lac operon. Why is it inducible? What acts as the inducer?

A

Allolactose acts as the inducer, it attaches to the repressor and inactivates it.

Normally bacteria use glucose as their source of energy, but, when glucose levels are low and there is a high level of lactose available the operon is induced to make enzymes that metabolize lactose for energy.

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13
Q

What is the difference between inducible and repressible enzymes?

A

Inducible enzymes - synthesis is induced. Lac.

Repressible enzymes - synthesis can be repressed if needed. Trp.

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14
Q

What type of metabolic pathways do inducible versus repressible enzymes work in?

A

Inducible - usually function in catabolic pathways.

Repressible - usuallt function in anabolic pathways.

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15
Q

What is meant by saying the the trp and lac operons can be regulated via NEGATIVE CONTROL?

A

This means that they are switched off by the active form of the repressor.

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16
Q

Describe what goes on in positive control.

A

A stimulatory protein increases the transcription (expression) of the genes.

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17
Q

What is an example of a activator protein?

A

Catabolite activator protein (CAP)

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18
Q

How and where does CAP (activator) bind to the promoter to enhance transcription?

A

cAMP binds to inactive CAP to make it active, it then binds to the promoter of that operon and enhances the binding of RNA polymerase to the operon.

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19
Q

Describe the different situations in relation to glucose and lactose levels and when positive and negative control are effected for the lac operon.

A

High glucose and low lactose – Lac operon not expressed

High glucose and high lactose – lac operon expressed but no activator for positive control.

Low glucose and high lactose – lac operon activated and activator (CAP) positively controls transcription of operon

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20
Q

Understand this picture that describes what happens to the lac operon when glucose levels rise again.

A

When glucose levels rise, cAMP levels fall and CAP detaches from Lac operon and stops positive control.

THIS IS ASUSMING THAT THE LACTOSE LEVELS REMAIN HIGH

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21
Q

What two features of the eukaryotic genome present a challenge in information-processing?

A
  1. The typical genome is much larger than prokaryotes.
  2. Different cells are specialized and the expression of genes differs.
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22
Q

How does chromatin differ in prokaryotes and eukaryotes?

A

Eukaryotes chromatin is ordered into higher structural levels than in prokaryotes.

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23
Q

Must organisms regulate the genes that are expressed at a given time?

A

YES

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24
Q

What percentage of genes might a human cell express at a given time?

A

around 20%

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25
Q

What is cell differentiation?

A

This is when a cell specializes in form and function.

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26
Q

How many different cell types does the human body have?

A

200

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27
Q

All cells in an organism contain the same genome, so how do we have differentiated cells?

A

By differential gene expression.

Each differentiated cell has its own unique subset of genes in the genome expressed.

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28
Q

Where are genes of organisms most commonly regulated? What are they commonly regulated by?

A

At the level of transcription

In response to external signals.

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29
Q

What stages in gene expression can be regulated in a eukaryote? Look at picture.

A
  1. Chromatin modification.
  2. Transcription
  3. RNA processing
  4. Degradation of mRNA
  5. Translation
  6. Protein processing and protein degradation
30
Q

When modifying chromatin structure to regulat gene expression what can be done? Describe histone acetylation, phosphorylation, and DNA methylation.

A
  • When genes are within highly packed chromatin they are usually not expressed due to lack of access.
  • Chemical modifications of histones and DNA influence the chromatin structure and in turn expression.

Acetylation: negative acetyl groups (COCH3) are attached to positive HISTONE TAILS, this loosens chromatin structure by decreases the histone tails from reacting with one another. Permitting transcription.

Methylation: addition of methyl (CH3) group to DNA can lead to increased condensation of chromatin, decreasing transcription.

Phosphorylation: phosphorylation next to a methylated area can help to loosen the chromatin again.

31
Q

Go more in-depth on DNA methylation. Can this be a long-term effect? Where have you heard of DNA methylation before?

A

This is the addition of methyl groups to certain bases in DNA that USUALLY causes reduced transcription.

This can be long-term, for example in cellular differentiation these specialized cells have permanent methylation in some cases to reduce transcription of specific genes.

You have heard of this in genomic imprinting, where methylation turns off either the maternal or paternal allele by methylation at the beginning of development.

32
Q

Look at this picture or DNA methylation and histone acetylation and understand it.

A

DO IT.

33
Q

Can alterations in chromatin structure be passed on from generation to generation?

A

YES

34
Q

What is epigenetic inheritance?

A

The inheritance of traits transmitted by mechanisms that don’t directly affect the nucleotide sequence.

NO CHANGE IN NUCLEOTIDE SEQUENCE

35
Q

Direct DNA mutations are permanent, can chromatin modification be reversed however? Do we understand this yet?

A

Yes it can

No we dont understand this.

36
Q

What is the function of control elements of genes? Are these important in being precise in gene expression in different cell types?

A

These are segments of noncoding DNA sequences that help to regulate transcription by binding certain proteins including transcription facotrs.

YES, VERY CRITICAL.

37
Q

Do enzymes that modify chromatin structure provide the initial control of gene expression? How?

A

YES

By controlling access to gene by transcriptional machinery to start expression.

38
Q

What must be present in eukaryotes for RNA polymerase II to bind to DNA promoter?

A

Transcription factors

39
Q

What is the difference between a general and a specific transcription factor?

A

General - required for the transcription of all protein encoding genes, leads to a few RNA transcripts being made.

Specific - used for high levels of transcription of PARTICULAR genes.

40
Q

Do all transcription factors bind to DNA?

A

NO, some bind to other proteins including other transcription factors.

41
Q

What is the different between proximal and distal control elements (control elements are sites for transcription factors and other proteins to bind)?

A

Proximal - located close to the promoter

Distal - further upstream from the promoter, groups of these form enhancers.

The rate of gene expression is strongly controlled by the binding of proteins (activators or repressors) to the control elements.

42
Q

What is an activator? What do they do?

A

An activor is a specific transcription factor that binds to an enhancer to stimulate transcription of a gene.

43
Q

What does a specific transcription factor that acts as a repressor do?

A

Inhibits the expression of particular gene.

44
Q

What is an indirect way that specific activator or repressor transcription factors can act to effect gene expression?

A

Their binding can influence chromatin structure by recruiting proteins that acetylate or deacetylate histones near the promoters of specific genes.

45
Q

What is the function of architectural (DNA-bending) proteins?

A

These can bend DNA - this is how the distal control elements can be so far away from the gene that they affect.

SEE PICTURE FOR CLARITY

46
Q

Do eukaryotes have operons?

A

NO

47
Q

If eukaryotes dont have operons, what does this mean for a group of genes that make products of the same metabolic pathway? Think about coordinative control.

A

each have their own promoter and control elements that are coordinately controlled, meaning that these gene common to a group have the same regulatory sequences that allows recognition by the same specific transcription factors.

48
Q

What is an enhancer?

A

This is the area that contains the distal control elements, found upstream of the gene it is controlled.

49
Q

Do control elements contain many nucleotide sequences?

A

Surprisingly not

50
Q

How many distal control elements are typically contained within an enhancer? How do these play a part in regulating transcription of certain genes (think combinatorial control)?

A

There are approximately 10 control elements in an enhancer.

The specific combination of these control elements regulate the expression of the gene.

51
Q

What is the significance of combinatorial control of gene transcription in eukaryotes?

A

This allows for fewer activators necessary to have to ability to specify what genes are turned on.

52
Q

Do post-transcriptional regulation methods of gene expression exist? What is the main purpose of them?

A

YES

This is a RAPID way for the cell to fine-tune gene expression in response to environmental changes.

53
Q

Describe alternative RNA splicing. Does this occur before or after transcription? How does this work?

A

After transcription

This is when different mRNA are made from the same primary tanscript

This works by changing which segments of the primary RNA transcript are treated as exons or introns.

Notice what happen during RNA splicing when exon 3 or 4 are treated as introns in the picture.

54
Q

Does the life of an mRNA molecule in the cytoplasm help to determine the pattern of protein synthesis in a cell?

A

YES

55
Q

What are the 4 forms of post-transcriptional regulation of gene expression?

A

RNA processing (alternative RNA splicing)

Initiation of translation

mRNA degredation

Protein processing and degradation

56
Q

Does the life span of prokaryotes vs eukaryotes differ?

A

YES

Prokaryotes - typically last minutes after synthesis before being degraded by enzymes.

Eukaryotes - survive from hours to weeks.

57
Q

Describe how mRNA degradation can help determine the pattern of protein synthesis.

A

Prokaryotes can quickly adapt to their environmental changes because their mRNA degrades, this means the new mRNA is constantly being made so they can quickly adapt.

Eukaryotes have long living mRNA that is repeatedly translated. Like in RBCs the mRNA for hemoglobin polypeptides live for a long time and are repeatedly translated.

58
Q

What portion of the mRNA molecule determines its life span?

A

The untranslated region (UTR) at the 3’ end.

59
Q

How might translation of selected mRNAs be blocked? How can translation of ALL mRNAs of a cell be blocked?

A

Regulatory proteins bind to sequences or structures of the UTR at the 5’ or 3’ end that prevent to attachment of ribosomes.

ALL can be regulated via activation or inactivation of translation initiation factors. For example in some egg cells the polyA tails are too short to permit translation, but at a certain time an enzyme if turned on that adds A to the tail to initiate translation.

60
Q

What are two things that cna happen after TRANSLATION that help in regulation of gene expression?

A

Protein processing

Protein degradation

61
Q

Give an example of protein processing.

A

Often eukaryotic polypeptides have to be processed to become functional.

Insulins initial polypeptide is cleaved to form the functioning hormone.

Also adding or removing phosphate groups can activate or inactivate proteins. And proteins headed for the cell surface acquire sugars.

62
Q

What is the function of a proteasome? What is the function of ubiquitin?

A

Proteasomes bind to protein molecules and degrade them into protein fragments. These fragments are further broken down outside of the proteasome to amino acids to be used for other proteins.

Ubiquitin tag proteins so the proteasomes know what proteins to degrade.

63
Q

What are the two types of non-protein coding RNAs (ncRNAs) that play crucial roles in regulating gene expression? Single or double standed?

A
  1. microRNA (miRNA)
  2. small interefering RNA (siRNA)

Single stranded

64
Q

How much of the human genome code for protein?

A

1.5%

65
Q

What is the shape of a primary miRNA transcript? is this single stranded? How does this attach to mRNA and what does it do?

A

Single stranded, shaped like multiple hairpins with multiple strands of miRNA.

Each miRNA is around 22 nucleotides long and has AT LEAST 7-10 complementary base pairs of its target mRNA via its miRNA protein complex.

Once it attached:

  • If the entire miRNA is complementary is degrades the mRNA
  • If only a portion of the miRNA is complementary, then translation is blocked.
66
Q

What does a dicer do? How does the single strand of the primary miRNA transcript get its shape?

A

Dicer is what cuts the miRNA from its transcript

Hydrogen bonding gives its shape.

67
Q

Where does the single stranded siRNA molecule come from?

A

A much larger DOUBLE STRANDED RNA transcript.

68
Q

What is the blocking of transcription by siRNA? What is this used for?

A

This is called RNA interference (RNAi),

This is used in research to diable genes to assess their function.

69
Q

How did scientists discover siRNA?

A

They injected an siRNA precursor into the cell and they were processed into siRNAs and inhibited transcription of certain genes.

70
Q

How do siRNAs and mRNAs really differ? Do they both do the same thing?

A

They differ via their precursors.

They both do essentially the same thing, which is BLOCKING TRANSLATION

siRNAs can also block transcription in the formation of heterochromatin, like the example that was used in yeast.

71
Q

LOOK AT FIGURE 18.15 ON P. 378 IN THE BOOD AND HAVE AN IDEA ABOUT IT. What is it ultimately showing?

A

DO IT.

It is showing how siRNA is formed in yeast and how it is used to condensation chromatin at the centromere.

72
Q

How can eukaryotes regulate their gene expression? LIST ALL 6 ways.

What is the only way prokaryotes can regulate their expression?

A

said we should be able to draw this picture.

Prokaryotes can only regulate at the level of transcription.

BIOLOGY 108 TEST #4 (5 decks)

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