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BIO230 > Lecture 1 and 2 > Flashcards

Lecture 1 and 2 Flashcards

1
Q

3 primary branches of the Tree of Life

A

Bacteria, Archae and Eukaryotes

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2
Q

Features of prokaryotic organisms

A

① Eubacteria and Archaea
② Single called
③ Lack nucleus and organelles

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3
Q

Features of eukaryotic organisms

A

① Plants, fungi, animals and humans
② Single celled or multicellular
③ Have nuclei or organelles

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4
Q

What does our microbiodata include?

A

Bacteria, archaea, fungi, protests and viruses

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5
Q

Microbial cell: human cell ratio

A

1:1

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6
Q

Microbioma

A

Combined genome of nicrobiota

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7
Q

Genome

A

It encodes the information to construct and maintain an organism.

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8
Q

What are genomes made of?

A

Most are made of DNA but some viruses have RNA genomes.

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9
Q

The first product of genome expression

A

Transcriptome

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10
Q

What is the transcriptome?

A

All the RNA present in a cell at a particular time

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11
Q

What is used to analyze the transcriptome?

A

DNA microarray

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12
Q

DNA microarray

A

It gives a snapshot of the transcriptome. It analyses RNA, not DNA!!!

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13
Q

How is the DNA microarray read?

A

It is read as a table. Red - lots of RNA, Green- less RNA, and Black- medium RNA.

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14
Q

How is the transcriptome maintained?

A

Through the process of transcription. DNA to RNA.

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15
Q

The second product of genome expression

A

Proteome

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16
Q

Proteome

A

The collection of all proteins in a cell, it defines the biochemical functions of the cell.

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17
Q

How is the proteome analyzed?

A

2D Gel Electrophoresis

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18
Q

How is 2D Gel electrophoresis read?

A

As a graph
x-axis- isoelectric point (goes from acidic to basic)
y-axis- molecular weight (goes from low to high)

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19
Q

How is the proteome maintained?

A

Through the process of translation. (RNA to protein)

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20
Q

‘Central Dogma’ of molecular biology

A

Genome (DNA) to Transcriptome (RNA) to Proteome (Protein)

21
Q

How do we produce different cell types?

A

Through differences in genome expression. At any one time only 30-60% of genes are expressed.

22
Q

Why is the regulation of gene expression crucial?

A
  1. Defining cell types (multicellular organisms)
  2. Responses to extracellular stimuli (both multicellular and unicellular organisms)
23
Q

Promoter

A

Region of DNA that positions RNA polymerase and indicates transcription start site.

24
Q

RNA polymerase holoenzyme

A

Sigma factor + core enzyme

25
Q

When is the sigma factor released?

A

Once approximately 10 nucleotides are synthesized.

26
Q

How is gene expression in both prokaryotes and eukaryotes regulated?

A

Gene regulatory proteins (transcription factors) which bind to the regulatory regions of DNA (CIS elements)

27
Q

What can Gene Regulatory proteins do?

A

They can turn genes on (positive regulators- activators) and off (negative regulators- repressors)

28
Q

How were gene regulatory proteins discovered?

A

Bacterial genetics

29
Q

E. coli

A
  1. Unicellular prokaryote
  2. It has one chromosome of circular DNA
  3. It encodes about 4300 proteins
  4. Many genes are transcriptionally regulated by food availability
30
Q

Operon

A

A system where multiple genes can be transcribed into a single RNA molecule

31
Q

The Tryptophan (Trp) Operon

A

It encodes enzymes for tryptophan biosynthesis.
transcription regulated by a single promoter.
contains 5 genes.

32
Q

2 potential bound states of the Tryptophan operon promoter

A
  1. Bound by RNA polymerase - Trp gene expression on
  2. Bound by a tryptophan repressor protein - Trp gene expression off
33
Q

Where does the Trp repressor bind?

A

On a specific DNA sequence of the promoter called an operator

34
Q

Tryptophan repressor

A

it blocks promoter access so that RNA polymerase cannot bind and it thus negatively regulates Trp expression.

35
Q

How is the tryptophan repressor DNA binding activity regulated?

A

The repressor must bind two molecules of tryptophan to bind to DNA.

36
Q

What is the structure of the tryptophan repressor?

A

It contains a helix-turn-helix DNA binding motif which binds in the major groove of the DNA double helix.

37
Q

What does tryptophan binding induce?

A
  1. Conformational change
  2. Protein fits into the major groove
38
Q

E. coli Lac operon

A
  1. Here, three genes are required for the transport of lactose into the cell and its catabolism
  2. it enables the use of lactose when there is high lactose and low glucose.
39
Q

lac operon activator

A

catabolite activator protein (CAP)
it promotes lac expression: low glucose/high lactose
it binds to the CIS regulatory sequence for CAP

40
Q

lac operon repressor

A

lac repressor protein
it inhibits lac expression: low lactose
binds to the lac operator

41
Q

What does the 1st gene of lac operon encode?

A

It encodes beta-galactosidase; to break down lactose to glucose and galactose

42
Q

How is lac operon regulated (lactose)?

A
  1. when lactose levels are low, the lac repressor is bound to the operator
  2. lac operon gene expression is off
43
Q

Biomolecular explanation for how lac operon is regulated for lactose

A

increases in lactose increases levels of allolactose (related to lactose), and requires beta-galactosidase.
Allolactose then binds to the lac repressor

44
Q

What happens after allolactose binds to the repressor?

A
  1. Conformational change
  2. DNA binding activity reduces
  3. The repressor is released from the operator
45
Q

Why is an activator needed for RNA pol binding to lac promoter?

A
  1. RNA pol binding is inefficient to the lac promoter.
  2. the activator - CAP - is needed for efficient binding.
  3. CAP contains a helix-turn-helix binding domain
46
Q

Biomolecular explanation for how lac operon is regulated for glusoce

A
  1. CAP DNA binding activity is regulated by low glucose.
  2. Decreasing glucose levels increases the levels of signaling molecule cyclic AMP
  3. cAMP will bind CAP protein, there will be a conformation change, increase in DNA binding activity and it will bind to the CAP binding site.
  4. RNA pol will then bind
47
Q

what does a decrease in glucose cause?

A

increase in levels of signaling molecule cyclic AMP.

48
Q

what happens after cAMP binds to the CAP protein?

A
  1. conformaitonal change
  2. increase in DNA binding activity
  3. it will bind to the CAP binding site

BIO230 (2 decks)

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