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Biotechnology > Chapter 4 > Flashcards

Chapter 4 Flashcards

1
Q

What does the term “electrophoresis” mean?

A

to carry with electricity

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2
Q

How do you run a gel?

A
  • DNA fragments are loaded into an agarose gel
  • gel is placed into a chamber filled with a conductive buffer solution
  • a direct current is passed through
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3
Q

How does DNA pass through the gel?

A

since DNA fragments are negatively charged, they are drawn towards the positive pole, or electrode

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4
Q

What is the relationship between the rate at which a DNA fragment migrates and the size of its base pairs?

A

inversely related

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5
Q

Which travel further: smaller or larger DNA fragments?

A

smaller

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6
Q

What does TAE stand for?

A

Tris/acetic acid/EDTA

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7
Q

At what temperature does TAE need to be cooled before pouring?

A

55 C

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8
Q

What are other names for DNA size standards?

A

standards, ladders, rulers, or markers

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9
Q

How were the original DNA standards made?

A

made from bacteriophage cut with specific restriction enzymes that yielded DNA fragments of known number and size

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10
Q

Why is lambda phage DNA useful?

A

it covers a broad range of DNA sizes when cut with HindIII enzyme

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11
Q

Can you find the amount of DNA in a band if you have the intensity or thickness of the band? How?

A

yes, they are proportional

compare the intensity of the band to the intensity of bands in the DNA control to estimate the quantity of DNA

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12
Q

What are molecular mass rulers?

A

standards that are engineered to prod bands of evenly distributed molecular mass

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13
Q

What are other names for horizontal gel electrophoresis chambers?

A

gel tanks, gel boxes

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14
Q

what does molecular biology refer to?

A

it is the study of biology and the molecular level, also refers to a set of tools and techniques that have revolutionized biology.

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15
Q

what is the central dogma of molecular biology?

A

refers the the normal flow of genetic information from DNA to RNA and then to protein.

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16
Q

What two studies does molecular biology bridge between?

A

genetics and biochemistry

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17
Q

What are some molecular biology techniques?

A

restriction enzyme digestion analysis, ligation, bacterial transformation, and the polymerase chain reaction

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18
Q

What are some of the ways that microbiology has benefitted society?

A

scientists used molecular biology to trace the anthrax poisonings of 2001, pharmaceutical industries (Genentech and Amgen), exonerate wrongly accused criminals

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19
Q

What are horizontal gel electrophoresis chambers made from?

A

acrylic plastic; they have a positive electrode at one end and a negative electrode (cathode) at the other

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20
Q

What is sample loading buffer mixed with?

A

an agent such as glycerol or FicoII to increase the density of the sample so that it sinks into the well, and a dye to monitor migration of the samples

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21
Q

How long and at what voltage do gels typically run at?

A

100V for 30mins to 1 hr

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22
Q

What are restriction enzymes used for?

A

used extensively in recombinant DNA technology: involves moving DNA fragments from one location to another

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23
Q

What are restriction fragment length polymorphisms?

A

genetic differences/genetic variations among individuals, including mutations in restriction sites such that the sites are no longer recognized by the restriction enzyme
it generates a banding pattern unique for each individual

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24
Q

How does one perform RFLP analysis?

A

the DNA is digested with a restriction enzyme and the fragments generated are analyzed by agarose gel electrophoresis

25
Q

What is Southern blotting?

A

genomic DNA is resolved on an agarose gel, denatured so that is single-stranded, and transferred onto a solid membrane of nylon or nitrocellulose
DNA bands are trapped inside the membrane and form a replica of the original gel
a probe is incubated in the membrane and is modified with a radioactive or fluorescent label so that it can be detected
the probe anneals to the single-stranded target DNA
the location of the site is visualized using fluorescence technology

26
Q

who invented the central dogma of molecular biology?

A

Francis Crick

27
Q

What happens in DNA replication?

A

an enzyme called DNA polymerase copies both DNA strands and makes a brand new copies of the DNA

28
Q

What happens in DNA transcription?

A

enzyme RNA polymerase copies one DNA strand into messenger RNA, reads 3 prime to 5 prime

29
Q

What happens in DNA translation?

A

the seqquence of bases on the MRNA is read and the information is converted into a polypeptide chain composed of amino acids, which folds into a protein

30
Q

Special circumstances in which genetic information flows differently!

A

For ex, RNA viruses such as the influenza virus can replicate their own DNA. HIV can copy RNA into DNA, this is known as a retrovirus that uses reverse transcriptase.

31
Q

What are DNA strands comprised of?

A

polymers of nucleotides, consisting of a sugar, a phosphate, and a nitrogenous base

32
Q

What are the four nitrogenous bases?

A

Thymine, Guanine, Cytosine, and Adenine

33
Q

Guanine and Adenine are…

A

Purines, two nitrogen bases

34
Q

Thymine and cytosine are…

A

pyrimidines, one nitrogen base

35
Q

A-T and G-C are

A

base pairs

36
Q

what is the basis of PCR and DNA sequencing

A

complementarity

37
Q

How many carbons does the sugar part of the DNA strand have? What does this mean it is called?

A

5; pentose

38
Q

how are nucleic acids synthesized?

A

synthesized in vivid only in a 5’ to 3’ direction

39
Q

what do the terms sense and antisense mean?

A

sense means 5’ to 3’, and antisense means 3’ and 5’

40
Q

when DNA is transcribed , the antisense strand…

A

serves as the template for the synthesis of mRNA.

41
Q

recombinant DNA technology…

A

based on the premise that dNA is virtually the same in all cells and can be acted on in other cells. the foundation of modern biotechnology.

42
Q

example of genetic engineering

A

cotton plants, expresses a bacteria gene that makes them resistant to agricultural pests, in the pharmaceutical industry, recombinant proteins are produced in bacteria and eukaryotic cells.

43
Q

restrictions enymes serve what purpose?

A

able to precisely cut DNA and enabled scientists to move genes from the genome of one organism into another genome of another, discovered by Werner Arber and Hamilton Smith and Dan Nathans

44
Q

bacteriophages

A

invading viruses that inject their DNA, stopped by restriction enzymes, methyl groups prevent own DNA from being cut

45
Q

enzyme name is derived from

A

bacterial genus, species, and then strain, name uses the first initial of the genus and the first two letters of the species name followed by the order in which the enzymes were discovered

46
Q

restriction enzymes are more accurately known as

A

restriction endonucleases (endo means within, nuclease means an enzyme that cutes nucleic acids)

47
Q

how is the DNA broken?

A

restriction enzymes cut the DNA at certain areas, stop sliding when they reach a certain combo, enzymes hydrolyze the sugar-phosphate bond, thus breaking the strand

48
Q

blunt vs sticky ends

A

blunt-no unpaired ends, sticky-staggered cutes in the DNA, restriction sites are palindromic

49
Q

separation of DNA with restriction enzymes can be separated using what

A

electrophoresis in an agarose gel

50
Q

what is the function of ligase?

A

joins together one new cut piece of DNA to another genome by reforming the phosphate bonds that were broken by the restriction enzymes.

51
Q

where is ligase seen in nature?

A

used in DNA replication to ligate the Okazaki fragments made on the lagging strand of DNA

52
Q

What is more efficient, sticky ends with ligase or blunt end?

A

sticky end

53
Q

What is likely to happen when putting a ligase into a plasmid?

A

re-circularizing is more likely, mostly because open ends of the plasmid chicken near each other

54
Q

what happens to prevent plasmids from self-ligating?

A

the phosphate on the 5’ end of the plasmid is removed using an enzyme known as phosphatase in a process called dephosphorylation

55
Q

dephosphorylation prevents what type of bond from forming?

A

phophdiester bond, can only circulate if fragment is inserted

56
Q

what was the original supplier of enzymes for genetic engineering?

A

New England BioLabs

57
Q

how is enzyme concentration denoted?

A

units of activity (U) rather than the concentration of the protein, definition is provided by the supplier, also supplied with a reaction buffer

58
Q

unit of restriction enzyme

A

the amount of enzyme need to digest 1 microgram of lamda phase in 1 hour at 37 degrees

59
Q

enzymes should be stored at, other conditions

A

-20 degrees celcius, do not heat/cool repeatedly, if working with them directly keep at -4 celsius

Biotechnology (1 decks)

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