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BIOL 1009 > Major Lab Quiz 3 > Flashcards

Major Lab Quiz 3 Flashcards

1
Q

What does PCR stand for?

A

polymerase chain reaction

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2
Q

What does PCR do?

A

Amplifies specific regions of the genome for analysis

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3
Q

What are the three steps of PCR?

A
  1. Denaturation
  2. Annealing
  3. Extension
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4
Q

At what temperature (C) does denaturation occur?

A

95

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5
Q

At what temperature (C) does annealing occur?

A

50-65

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6
Q

At what temperature (C) does extension occur?

A

~72

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7
Q

What is taq polymerase and where did it come from?

A
  • thermostable polymerase (enzyme)
  • comes from thermophilic Thermus aquaticus, which lives in volcanic pools of Yellowstone
  • doesn’t require the addition of fresh enzyme with every PCR cycle
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8
Q

What is gel electrophoresis?

A

Common technique for visualizing and separating DNA fragments based on their size

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9
Q

What direction does DNA run? What property of DNA makes it run that way?

A

Toward the cation (positive) because DNA is negatively charged

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10
Q

Function-based metagenomics involves…

A

screening for a particular function or activity

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11
Q

Sequence-based metagenomics involves…

A

sequencing and analysis of DNA from environmental samples

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12
Q

What is an open reading frame?

A

Sequences that extend from an ATG start codon to a TAG, TGA, or TAA stop codon

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13
Q

What is an antibiotic?

A

Substances that kill microbes or drastically slow their growth

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14
Q

What are antibiotic resistant bacteria?

A

Bacteria that can survive and propagate in the presence of antibiotics

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15
Q

Why is antibiotic resistance a problem?

A

Because they are harder to treat than non-resistant strains

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16
Q

What is a clearing zone?

A

An area where few if any microbial cells can grow (in our lab, E. Coli)

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17
Q

What does a clearing zone tell you?

A

That the bacteria is not resistant to the antibiotic and can be killed or slowed by it

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18
Q

What is bioinformatics?

A

The application of computer science to biological data

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19
Q

What is a distance tree?

A

A type of phylogenetic tree that is a representation of the overall similarity between organisms in the tree.

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20
Q

What is metagenomics?

A

The study of metagenomes, meaning all of the genetic material recovered from all of the species of an environmental sample

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21
Q

What is evolution?

A

A change in the frequencies of alleles from one generation to the next

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22
Q

How can you tell a population is evolving?

A

Observe allele frequencies changing from one generation to the next

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23
Q

What is natural selection?

A

A specific force that can cause evolution. Its driving force is the differential reproductive success of heritable variants.

24
Q

What is fitness?

A

Reproductive output of one genotype

25
Q

Is natural selection the same as evolution?

A

No, evolution is the outcome while natural selection is the process

26
Q

How did we extract DNA?

A

We used the Biorad InstaGene matrix, which breaks the cells open via heating, thereby exposing the DNA.

27
Q

What can metal ions do to DNA? How did we prevent this during DNA extraction?

A

Positive metal ions are required by DNase (an enzyme that degrades DNA). We prevented binding and degradation by using negatively charged Chelex beads to bind with the metal ions.

28
Q

What are the reagents necessary for PCR and what do each do?

A
  • template strand: this is what is being copied
  • thermostable DNA polymerase
  • MgCl2: Mg ions for DNA polymerase
  • primer pair: designed to replicate the sequence of interest
  • deoxynucleotide triphosphates (dNTP): the raw building blocks of DNA
29
Q

What does gel electrophoresis separate DNA by?

A

Lab 6

30
Q

Can you see DNA on the gel under white light? How do we visualize it?

A

No, you see it under ultraviolet (UV) light

31
Q

What did we use to stain the DNA on a gel? The same property that makes this agent useful in lab makes it dangerous to humans- what can it do to humans?

A

Ethidium bromide. It is a mutagen and possible carcinogen.

32
Q

Why did we use a primer specific for the 16S rRNA gene?

A

Because 16S rRNA plays a structural role to keep other components of the ribosome in place, helps select the translation initiation site, and it is highly conserved between different species of bacteria and archaea.

33
Q

Is the 16S rRNA gene found in eukaryotes?

A

nah, just prokaryotes.

Eukaryotes - 18S rRNA

34
Q

What is the purpose of lab six (DNA extraction)?

A

Lab 6

35
Q

How did we use function based metagenomics in lab seven?

A

We were seeing if the DNA we extracted at different sites coded for antibiotic resistance

36
Q

Can you describe how we were testing DNA from different sites within E. Coli?

A

We inserted the DNA from different sites into fosmids then transfected E. Coli with these fosmids.

37
Q

What is the downfall of us using function based metagenomics?

A

Function based metagenomics doesn’t tell you anything about the sequence of the gene, the structure of the protein, or the microbe of origin.

38
Q

What are the advantages and disadvantages of sequence based metagenomics?

A

Advantages: can give you info about the microbial ecology and the genomes of a particular environmental sample
Disadvantages: Can’t tell you if the gene is functional or what they do

39
Q

What was the purpose of lab seven (metagenomics)?

A

Lab 7

40
Q

Are animals closer together on a distance tree more closely related or distant relatives?

A

More closely related

41
Q

What was the purpose of lab 8 (bioinformatics)?

A

Lab 8

42
Q

What is required for evolution to work?

A

Heritable Traits

Variation

43
Q

What is reproductive success?

A

A measure of how well an individual (or specific genotype) reproduces and gains genetic representation in the next generation

44
Q

What are allelic frequencies? Be able to describe data from a graph like we saw in Excel after we pasted data from EvoDots into it.

A

Lab 9

45
Q

Do individuals evolve?

A

NO. Populations evolve, not individuals

46
Q

A1 - 20
A2 - 30
A3 - 40
What is the allelic frequency of A1?

A

20%, 20/100

47
Q

What was the purpose of lab 9? (evolution)

A

Lab 9

48
Q

What is an ecological community?

A

A group of species that live together and interact with each other

49
Q

What types of animals are within a ecological community? (herbivores, etc)

A

Omnivores, predators, herbivores, producers, decomposers

50
Q

What is a dominant species, and how does this relate to competition?

A

The dominant species is the species more abundant in number or biomass that any other.
When a species is competitively dominant it is better at obtaining or holding space than another, or is able to displace another species.

51
Q

What is a keystone species, and how is it different from a dominant species?

A

A single species that controls community structure even though that species may have relatively low abundance. The difference between them and dominant species is that there are less of them, and if you remove the keystone species the community will fall apart, while the dominant species’ removal might have minimal effects.

52
Q

What is a food chain?

A

The progression of what eats what from plant to herbivore to predator

53
Q

What is a food web, and how is this different from a food chain?

A

Food webs are diagrams connecting different species and food chains together based on feeding relationships within a community

54
Q

What are producers?

A

Organisms that use energy from the sun to produce their own food rather than consuming other organisms.
They occupy the lowest trophic level.

55
Q

What are herbivores?

A

Organisms that consume the producers

AKA primary consumers

56
Q

What are predators?

A

Organisms that eat the herbivores

AKA secondary consumers

57
Q

What is the purpose of lab 10 (keystone predator)?

A

Lab 10

BIOL 1009 (7 decks)

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