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BIO230 Midterm > Week 1 > Flashcards

Week 1 Flashcards

1
Q

What are the primary branches of the tree of life?

A
  • archaea
  • eukaryotes
  • bacteria
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2
Q

How do you tell how recently two species have diverged?

A

the more similar the ribosomal RNA sequences, the more recently the two have diverged from a common ancestor

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3
Q

What is the tree of life?

A

quantifies how closely organisms are related to one another

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4
Q

What are the most abundant biological entities on the planet?

A

viruses

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5
Q

What are the main cell types?

A

prokaryotic and eukaryotic

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6
Q

What are the characteristics of prokaryotic organisms?

A
  • eubacteria and archaea
  • single-celled
  • lack nucleus and membrane-bound organelles
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7
Q

What are the characteristics of eukaryotic organisms?

A
  • plants, fungi, animals, humans
  • single-celled or multicellular
  • tend to be much larger
  • have nuclei and organelles
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8
Q

What kind of organism is the most evolutionary diverse?

A

bacteria

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9
Q

What are the different parts of a prokaryotic cell?

A
  • cell wall (not all but some, protective and tough outer coat)
  • plasma membrane (semi-permeable)
  • DNA (in a nucleoid)
  • ribosomes in the cytosol (protein synthesis)
  • flagellum (not in all, locomotion)
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10
Q

What are some of the different parts of a eukaryotic cell?

A
  • nucleus
  • plasma membrane
  • microtubules (need for a cytoskeleton)
  • membrane-bound organelles (mitochondria)
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11
Q

What does the human microbiota consist of and where do they reside?

A

bacteria, archaea, fungi, protists, and viruses
skin, lungs, mouth, GI tract, etc

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12
Q

What is the microbial cell-to-human cell ratio?

A

at least 1:1

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13
Q

What is a microbiome?

A

the combined genomes of a microbiota

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14
Q

How many more microbial genes are there compared to human genes in the human body?

A

up to 200 times more

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15
Q

What is a genome?

A

encodes the information to construct and maintain an organisms

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16
Q

What are genomes made up of?

A

most are DNA, some viruses have RNA genomes (but viruses aren’t living things)

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17
Q

How is information stored in the genome released?

A

genome expression

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18
Q

What is the first product of genome expression?

A

transcriptome

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19
Q

What is the transcriptome?

A

the repertoire of RNA molecules present in a cell at a particular time

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20
Q

How is the transcriptome measured?

A

DNA microarray gives us a snapshot of the transcriptome

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21
Q

How is the transcriptome maintained?

A

the process of transcription

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22
Q

What is the second product of genome expression?

A

proteome

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23
Q

What is the proteome?

A
  • collection of proteins in a cell
  • defines the biochemical functions of the cell
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24
Q

How is the proteome measured?

A

2D gel electrophoresis

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25
Q

How is the proteome maintained?

A

the process of translation

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26
Q

What is the central dogma of molecular biology?

A

Genome (DNA)–> transcriptome (RNA)–> proteome (protein)

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27
Q

What kinds of genomes do different cell types of a multicellular organism contain?

A

they all contain the same genome

28
Q

How are different cell types produced?

A

genome expression

29
Q

How many genes are in the human genome?

A

~25 000

30
Q

How many genes are expressed at any one time?

A

only 30-60%

31
Q

How is genome expression regulated?

A

at many steps from DNA to protein

32
Q

What is the interactome?

A

all protein-protein interactions

33
Q

What is the metabolome?

A

all small molecule metabolites

34
Q

Why is the regulation of gene expression important?

A
  • defining cell types (multicellular organisms)
  • responses to extracellular stimuli (both muli and unicellular organisms)
35
Q

How is DNA transcribed into RNA?

A

by the enzyme RNA polymerase (in prokaryotes the sigma factor helps bind RNA poly. to the DNA)

36
Q

What are the basic steps for prokaryotic transcription?

A
  1. sigma factor binds to RNA poly.
  2. RNA poly holoenzyme (sigma factor + RNA poly.)
  3. Sigma binds to the promoter region to position RNA poly.
  4. RNA poly. unwinds DNA
  5. transcription begins
  6. once ~10 nucleotides are synthesized, sigma factor is released
  7. transcription elongation
  8. transcription termination
37
Q

How is gene expression regulated in both prokaryotes and eukaryotes?

A

gene regulatory proteins (transcription factors)

38
Q

What do gene regulatory proteins do?

A
  • bind specifically to regulatory regions of DNA (cis-elements)
    they can turn genes
  • on = pos. regulator = activators
  • off= neg. regulator = repressor
39
Q

How were gene regulatory proteins discovered?

A
  • using bacterial genetics
40
Q

What are some properties of E. coli?

A
  • unicellular prokaryote
  • one chromosome of circular DNA
  • encodes about 4300 proteins
  • many genes are transcriptionally regulated by food availability
41
Q

What is one feature of prokaryotes during transcription?

A

they have multiple genes that can be transcribed into a single RNA molecule (operon)

42
Q

What is the Tryptophan Operon?

A

a group of five genes in E. coli that encode enzymes necessary for the biosynthesis of tryptophan, regulated by a single promoter.

43
Q

How does the Tryptophan Repressor function?

A

The Tryptophan Repressor binds to a specific DNA sequence (operator) when tryptophan levels are high, blocking RNA polymerase from transcribing the genes, thus turning off gene expression.

44
Q

What are the potential protein-bound states of the tryptophan operon promoter?

A
  • bound by RNA polymerase (Trp gene expression ON)
  • bound by a tryptophan repressor protein (Try gene expression OFF)
45
Q

How does the Tryptophan Repressor bind to DNA?

A
  • DNA binding activity is regulated
  • the repressor must bind to two molecules of tryptophan
46
Q

What happens when tryptophan levels are low?

A

When tryptophan levels are low, the repressor cannot bind to the operator, allowing RNA polymerase to access the promoter and transcribe the genes needed for tryptophan biosynthesis.

47
Q

What is the significance of the helix-turn-helix motif in the Tryptophan Repressor?

A

The helix-turn-helix motif is a common DNA-binding structure that allows the Tryptophan Repressor to fit into the major groove of DNA, facilitating its binding to the operator.

48
Q

What does the binding of tryptophan induce?

A
  • conformational change
  • protein fits into the major groove
49
Q

Describe the dual regulation of the Tryptophan Operon.

A

The Tryptophan Operon is regulated negatively by the Tryptophan Repressor and can also be influenced by the availability of tryptophan, which determines whether the repressor is active or inactive.

50
Q

What is the Lac Operon?

A

a set of three genes in E. coli that are required for the transport and metabolism of lactose. It enables the use of lactose in the absence of glucose.

51
Q

What are the rules for the Lac Operon?

A
  • E. coli’s first choice is to use glucose
  • when there is low glucose and high lactose, it will then use lactose. Both those conditions must be true to use lacotose
  • the lac operon is what is turned on when it wants to use lactose
52
Q

What are the main regulatory proteins involved in the Lac Operon?

A

the Catabolite Activator Protein (CAP), which acts as an activator (low glucose/ high lactose), and the Lac Repressor Protein, which acts as a repressor (low lactose)

53
Q

What does the first gene of the Lac Operon encode for?

A

beta-galactosidase (breaks down lactose to glucose and galactose)

54
Q

Under what conditions is the Lac Operon activated?

A

under low glucose and high lactose conditions

55
Q

What happens to the Lac Operon when lactose levels are low?

A

the Lac Repressor binds to the operator region, preventing RNA polymerase from binding and thus turning off the expression of the Lac Operon.

56
Q

What happens when glucose is high and lactose is low?

A

The Lac operon is OFF. The Lac repressor binds to the operator, preventing RNA polymerase from binding to the promoter.

57
Q

What happens when glucose is high and lactose is high?

A

The Lac operon is still OFF. Although lactose is present, the high glucose concentration prevents the activation of the Lac operon because cAMP levels are low, which means CAP cannot bind to the promoter.

58
Q

What happens when glucose is low and lactose is low?

A

The Lac operon is OFF. Both the Lac repressor is bound to the operator, and there is insufficient cAMP for CAP to activate transcription.

59
Q

What happens when glucose is low and lactose is high?

A

The Lac operon is ON. Lactose is converted to allolactose, which binds to the Lac repressor, causing it to release from the operator. Low glucose increases cAMP levels, allowing CAP to bind to the promoter and facilitate RNA polymerase binding.

60
Q

What role does cAMP play in the regulation of the Lac operon?

A

AMP levels increase when glucose is low, allowing it to bind to CAP. This complex then binds to the CAP-binding site on the Lac promoter, enhancing RNA polymerase binding and promoting transcription of the Lac operon.

61
Q

What happens when allolactose binds to the Lac repressor?

A
  • conformational change
  • decreases DNA-binding activity
  • release from the operator
62
Q

What is the effect of high glucose on cAMP levels?

A

High glucose levels lead to low cAMP levels, which inhibits the binding of CAP to the Lac promoter, preventing transcription of the Lac operon.

63
Q

Describe the dual regulation of the Lac Operon.

A

The Lac Operon is regulated by both positive control (via CAP) and negative control (via the Lac Repressor). High lactose levels remove the repressor, while low glucose levels activate CAP.

64
Q

Why is an activator needed?

A

(CAP)
- RNA polymerase binding is inefficient to the Lac promoter
- Efficient RNA polymerase binding to Lac promoter requires CAP to be bound
- CAP contains a helix-turn-helix DNA binding domain

65
Q

How is the DNA binding of CAP activated?

A

low glucose because decreasing glucose levels increase the levels of a signaling molecule, cyclic AMP (cAMP)

66
Q

What happens when cAMP binds to CAP protein?

A
  • conformational change
  • increased DNA-binding activity
  • binds to CAP-binding site

BIO230 Midterm (6 decks)

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