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Bio 302 > Chapter 8 > Flashcards

Chapter 8 Flashcards

1
Q

How is gene expression controlled in different lives?

A

Bacterium: expresses genes selectively to make enzymes needed to digest food only when it is available.
Multicellular plants and animals: under more elaborate control.
Embryonic development: fertilized egg cell gives rise to many cell types that differ dramatically in both structure and function.

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2
Q

How is cell differentiation achieved?

A

Changes in gene expression

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3
Q

What are housekeeping proteins?

A

Structural proteins of chromosomes.
RNA polymerases.
DNA repair enzymes.
Ribosomal proteins.
Enzymes involved in glycolysis and other basic metabolic processes.
Many proteins that form cytoskeleton.

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4
Q

Where is hemoglobin made in mammals?

A

Reticulocytes

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5
Q

How can a cell control the proteins it makes?

A
  1. Controlling when and how often a given gene is transcribed
  2. Controlling how an RNA transcript is spliced or otherwise processed
  3. Selecting which mRNAs are exported from the nucleus to the cytosol.
  4. Selectively degrading certain mRNA molecules.
  5. Selecting which mRNAs are translated by ribosomes.
  6. Selectively activating or inactivating proteins after they have been made.
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6
Q

What is the main site of control for most genes?

A

step 1: transcriptional control

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7
Q

What is transcription controlled by?

A

Proteins binding to regulatory DNA sequences

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8
Q

What does the promoter region of a gene do?

A

Attracts enzyme RNA polymerase and correctly orients the enzyme for transcription

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9
Q

What does the promoter region include?

A

Initiation site where transcription actually begins, and a promoter sequence of about 50 nucleotides that extend upstream from the initiation site, required for the binding of RNA polymerase.

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10
Q

Where does a transcription regulator bind?

A

Major groove of DNA helix

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11
Q

How many contacts does the protein-DNA interface consist of?

A

10 - 20, each involving a different amino acid and each contributing to the strength of the protein-DNA interaction

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12
Q

What does the protein form with the edges of the base?

A

Hydrogen bonds, ionic bonds, and hydrophobic interactions

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13
Q

What is a homeodomain?

A

A structural motif found in many eukaryotic-DNA binding proteins that consists of 3 consecutive alpha helixes.

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14
Q

What is the zinc finger motif built from?

A

Alpha helix and beta sheet, held together by a molecule of zinc

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15
Q

What is a leucine zipper motif formed from?

A

2 alpha helices, each contributed by a different protein molecule

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16
Q

What does dimerization do?

A

Doubles the number of protein-DNA contacts

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17
Q

What do transcription switches allow?

A

Cells to respond to changes in the environment

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18
Q

What are all of the enzymes needed to synthesize?

A

Amino acid trytophan

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19
Q

What is an operon?

A

Cluster of genes transcribed as a single mRNA molecule that is common in bacteria

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20
Q

What does an operator do?

A

Regulatory DNA sequence that controls expression of the trytophan operon within the promoter

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21
Q

What can switch genes on and off?

A

Repressor proteins

22
Q

What happens if the concentration of trytophan inside the cell is low?

A

RNA polymerase binds to the promoter and transcribes the 5 genes of the trytophan operon

23
Q

What happens if the concentration of trytophan inside the cell is high?

A

The repressor protein becomes active and binds to the operator, where it blocks the binding of RNA polymerase to the promoter.

24
Q

What happens when the concentration of intracellular tryptophan drops?

A

Repressor releases its tryptophan and falls off the DNA, allowing the polymerase to again transcribe the operon

25
Q

What does an activator protein do?

A

Binds to a regulatory sequence on the DNA and then interacts with the RNA polymerase to help it initiate transcription

26
Q

What happens without the activator?

A

Promoter fails to initiate transcription efficiently

27
Q

What do glucose and lactose concentrations control?

A

Initiation of transcription of the Lac operon through their effects on the Lac repressor protein and CAP

28
Q

What happens when lactose is absent?

A

The Lac repressor binds the Lac operator and shuts off expression of the operon

29
Q

What happens when there is an addition of lactose?

A

Increases the intracellular contraction of a related compound, allolactose. Allolactose binds to the Lac repressor, causing it to undergo a conformational change that releases its grip on the operator DNA

30
Q

What happens when glucose is absent?

A

Cyclic AMP is produced by the cell and CAP binds to DNA. LacZ, the first gene of the operon, encodes the enzyme beta-galactosidase, which breaks down lactose to galactose and glucose.

31
Q

What attracts RNA polymerase and general transcription factors to the promoter?

A

Activator protein bound to DNA

32
Q

What does looping of the DNA permit?

A

Contact between the activator protein bound to the enhancer and the transcription complex bound to the promoter

33
Q

What does the broken stretch of DNA signify?

A

The length of DNA between the enhancer and the start of transcription varies, sometimes reaching tens of thousands of nucleotides

34
Q

What can activator proteins recruit to the promotor region of a gene?

A

Histone-modifying enzymes and chromatin-remodeling complexes, which renders the DNA packaged in chromatin more accessible to other proteins in the cell, including those required for transcription initiation. In addition, the covalent histone modifications can serve as binding sites for proteins that stimulate transcription initiation

35
Q

What do many transcription activators attract?

A

Histone acetylases, which attach an acetyl group to selected lysines in the tail of histone proteins

36
Q

What do many transcription repressors attract?

A

Histone deacetylases- enzymes that remove the acetyl groups from histone tails, thereby reversing the positive effects that acetylation has on transcription initiation

37
Q

What is the most important control point of gene expression?

A

Transcription initiation

38
Q

What are the two major ways eukaryotic transcription regulators act?

A
  1. Directly affect the assembly process of RNA polymerase and the general transcription factors at the promoter.
  2. Locally modify the chromatin structure of promoter regions
39
Q

Can a positive feedback loop create cell memory?

A

Yes, all of the descendants of the original cell will remember that the progenitor cell had experienced a transient signal that initiated the production of the protein

40
Q

How do combinations of a few transcription regulators generate many different cell types during development?

A

A decision to make a new regulator is made after each cell division.
Eight cell types (A-H) are created using only three different transcription regulators.
Each of the 8 cell types would then express different genes.

41
Q

What do transcription regulators do to control the expression of a eukaryotic gene?

A

Work together as a committee:
- general transcription factors are the same for all genes transcribed by RNA polymerase II
- transcription regulators and locations of their binding sites relative to the promoters are different for different genes
- combinatorial control refers to the way that groups of regulatory proteins work together to determine expression of a single gene

42
Q

What is the second way of maintaining cell type?

A

Through faithful propagation of a condensed chromatin structure from parent to daughter cell

43
Q

What is the third way cells can transmit information about gene expression to their progeny?

A

Through DNA methylation, which can be faithfully inherited.

44
Q

Post-transcriptional control

A

A riboswitch controls purine biosynthesis genes in bacteria.
- majority of genes are regulated by switching on or off transcription initiiaton.
- post-transcriptional controls regulate gene expression after transcription initiation
- riboswitches: short sequences in a number mRNAs change their conformation when bound to small molecules to regulate own transcription and translation

45
Q

What does an miRNA target?

A

A complementary mRNA transcript

46
Q

What does siRNAs do to foreign RNAs?

A

destroy them

47
Q

What is a dicer?

A

Nuclease that cleaves foreign double stranded RNAs

48
Q

What are siRNAs

A

small interfering RNAs, which are double stranded fragments

49
Q

What can RNAi trigger?

A

RNA interference can trigger transcriptional silencing. RNAi can selectively shut off the synthesis of foreign RNAs by the host’s RNA polymerase

50
Q

What are RITS?

A

RNA-induced transcriptional silencing; protein complex that uses single stranded siRNA as a guide to attach itself to complementary RNA sequences as they exit from an actively transcribing RNA polymerase

51
Q

What are IncRNA?

A

Long noncoding RNAs that are no longer than 500 nucleotides in length

Bio 302 (4 decks)

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