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Prokaryotic Biology > Exam 2 > Flashcards

Exam 2 Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

transcription

A

the synthesis of RNA complementary to a DNA template

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2
Q

RNA polymerase

A

an enzyme that produces RNA complementary to a DNA strand

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3
Q

sigma factor

A

protein needed only for initiation of RNA synthesis, not for elongation; in bacteria, binds RNA polymerase to DNA

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4
Q

bacterial core RNA polymerase is a complex with four different subunits:

A

two alpha subunits, one beta subunit, and one beta’ subunit

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5
Q

a fifth subunit of bacterial RNA polymerase is ______ but not needed for transcription

A

sigma

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6
Q

random transcription initiation occurs at ______ levels along the chromosome

A

low

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7
Q

how does a sigma factor bind RNA polymerase?

A

through the beta and beta’ subunits
- recruits core enzyme to a promotor

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8
Q

promotor

A

a noncoding DNA regulatory region immediately upstream of a structural gene that is needed for transcription initiation

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9
Q

sigma factors generally contain ____ highly conserved amino acid sequences

A

four

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10
Q

how to sigma factors recognize specific DNA sequences when the DNA is a double heix?

A

proteins can recognize side groups of the bases that protrude from the grooves

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11
Q

_____ marks the DNA base where the mRNA transcript starts

A

+1

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12
Q

open reading frame

A

a DNA sequence predicted to encode a protein

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13
Q

untranslated regions

A

the leader and trailer sequences around a gene; not translated

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14
Q

monocistronic RNA

A

RNA that encodes the product of a single gene; has its own promoter and terminator

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15
Q

polycistronic RNA

A

encodes the products for one or more adjacent genes in one contiguous RNA molecule; starts at the promoter of the first gene and terminated at the end of the last gene

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16
Q

operon

A

a collection of genes that are in tande on a chromosome and are transcribed into a single RNA

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17
Q

transcription: initiatoin

A

RNA polymerase binds to the promoter, melts open the DNA helix, and catalyzes placement of the first RNA nucleotide

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18
Q

transcription: elongation

A

the sequential addition of ribonucleotides to the 3’ OH end of a growing chain

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19
Q

transcription: termination

A

whereby sequences trigger release of the polymerase and the completed RNA molecule

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20
Q

Rho-dependent termination

A

relied on a protein called Rho; Rho factor binds to an exposed C-rich region of RNA, contact between Rho and RNA polymerase causes termination

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21
Q

Rho-independent termination

A

contact between hairpin, NusA protein, and RNA polymerase causes termination

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22
Q

to be useful in medicine, all antibiotics must meet two fundamental criteria:

A
  1. must kill or inhibit the growth of a pathogen
  2. must not harm the host
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23
Q

rifamycin B

A

selectively target bacterial RNA polymerase and bind to the polymerase’s beta subunit near the magnesium active site, blocking the exit channel

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24
Q

actinomycin D

A

its phenoxazone ring is a planar structure that inserts between GC base pairs within DNA; blocks elongation
- binds to ANY DNa, can also be used to treat human cancers

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25
Q

mRNA

A

encodes proteins
approx. half-life: 3-5 min

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26
Q

rRNA

A

synthesizes protein as part of the ribosome
approx. half-life: hours

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27
Q

tRNA

A

shuttles amino acids
approx. half-life: hours

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28
Q

sRNA(b)

A

controls transcription, translation, or RNA stability
approx. half-life: variabe

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29
Q

tmRNA

A

frees ribosomes stuck on damaged mRNA
approx. half-life: 3-5 min

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30
Q

catalytic RNA

A

carries out enzymatic reactions
approx. half-life: 3-5 min
aka ribosyme

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31
Q

why do half-lives of RNA vary within the cell?

A

Microbes face extremely rapid changes in their environment, so they must be able to act quickly and halt synthesis of things no longer needed and begin synthesis to counteract the changes.

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32
Q

What do our white blood cells detect as a sign of invading bacteria?

A

fMet

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33
Q

what does a protein’s function depend on? (2)

A

3D shape and chemical properties

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34
Q

adenylylation

A

the covalent attachment of adenosine 5’-monophosphate; can regulate glutamine synthetase

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35
Q

lipidation

A

covalent attachment of lipids to proteins; can anchor proteins to the membrane

36
Q

glycosylation

A

covalent addition of mono- or polysaccharides to generate glycoproteins

37
Q

heat-shock proteins

A

a chaperone protein who’s synthesis is triggered by higher temperatures

38
Q

start codon

A

Met, AUG

39
Q

stop codons (3)

A

UAA, UAG, and UGA

40
Q

what amino acid only has a single codon that codes for it?

A

trp

41
Q

anticodons

A

three nucleotides in the middle of tRNA that pairs with codons in the mRNA

42
Q

extremophiles

A

an organism that grows only in an extreme environment- an environment including one or more conditions that are ‘extreme’ relative to the conditions of human life

43
Q

polyextremophiles

A

extremophiles that are suited for multiple extreme environments

44
Q

metagenomic analysis

A

includes random screening for and sequencing of genes that encode ribosomal RNA from a mixed environmental sample

45
Q

bioinformatic analysis

A

uses the DNA sequence of a gene to identify the probable function of it’s protein product

46
Q

hyperthermophile

A

lives above 80 deg C

47
Q

thermophile

A

lives between 50 deg C and 80 deg C

48
Q

mesophile

A

lives between 15 deg C and 45 deg C

49
Q

psychrophile

A

lives below 15 deg C, as low as -10 deg C

50
Q

alkaliphile

A

lives above pH 9

51
Q

neutralphile

A

lives between pH 5 and pH 8

52
Q

acidophile

A

lives below pH 3

53
Q

halophile

A

lives in high salt; > 2M NaCl

54
Q

halotolerant

A

high salt environment not required, but able to grow up to 2M NaCl

55
Q

strict aerobe

A

only lives in O2 rich environments

56
Q

facultative microbe

A

can live with or without O2

57
Q

microaerophile

A

only lives in O2 poor environments

58
Q

strict anaerobe

A

lives only in environments without O2

59
Q

why is temperature so important to microbes?

A

they cannot control their temperature; temperature impacts every aspect of microbial physiology including membrane fluidity, nutrient transport, DNA stability, RNA stability, and enzyme structure and function

60
Q

what are growth limits (partly) imposed by?

A

thousands of proteins in a cell which function within the same temperature range

61
Q

In general, microbes that grow at _____ temperatures can achieve _____ rates of growth

A

higher, higher

62
Q

mesophiles

A

typical “lab rat” microbes; optimum growth range is between 20 deg C and 40 deg C

63
Q

psychotrophs

A

a cold-resistant organisms that can grow at temps. between 0 deg C and 7 deg C, but show optimal growth between 20 deg C and 35 deg C

64
Q

Why do these microbes do so well in the cold?

A

one reason is the proteins of psychrophiles are more flexible than those of mesophiles and require less energy to function (aka heat)

65
Q

Why do psychrophiles grow poorly at temps above 20 deg C?

A

their membranes are more fluid at lower temperatures, but at higher temps their membranes are TOO flexible and fail to maintain cell integrity

66
Q

why are thermophiles adapt to the heat?

A

they often have specially adapted membranes and protein sequences; enzymes do not unfold as easily as mesophiles; contain low amounts of glycine

67
Q

how do thermophile membranes withstand the heat?

A

the membranes of thermophiles manage to “glue” together parts of the two hydrocarbon layers that point toward each other, making them more stable (more linear lipids)

68
Q

what makes a monolayer membrane so speacial?

A
  • built for extremophiles living
  • heat stable because long hydrocarbon chains directly tether glycerophosphates on opposite sides of the membrane
69
Q

heat-shock response

A

a coordinated response of cells to higher-than-normal temps; includes changes in the membrane and expression of heat-shock proteins

70
Q

barophile (piezophiles)

A

require high pressure to grow

71
Q

most barophiles are also _____

A

psychrophilic; average temp at the ocean floor is 2 deg C

72
Q

how do barophiles tolerate the pressure?

A

not as well known; thought increased hydrostatic pressure and cold temps decrease membrane fluidity, so they have high levels of polyunsaturated fatty acids to increase fluiditywa

73
Q

water activity

A

a measure of the water that is not bound to solutes and is available for use by organisms

74
Q

osmolarity

A

a measure of the number of solute molecules in a solution

75
Q

compatible solutes

A

a small molecule that does not disrupt normal cell metabolism even at a high intracellular concentrations

76
Q

halophiles

A

an organism that requires a high extracellular sodium chloride concentration for optimal growth

77
Q

aquaporins

A

membrane channel proteins that allow water to move quickly across membranes to equalize internal and external pressures

78
Q

mechanosensitive channels

A

leak solutes out of the cell when internal pressure rises

79
Q

neutralophiles

A

generally grow between pH 5 and pH 8; most human pathogens

80
Q

acidophiles

A

bacteria and archaea that live in extreme acidic environments; between pH 0 and pH 5

81
Q

How can acidophiles grow at such low pH?

A

partly due to altered membrane lipid profiles that decrease proton permeability and to ill-defined proton extrusion mechanisms

82
Q

alkaliphiles

A

grow best at pH 9 to pH 11

83
Q

how do alkaliphiles survive in such high pH environments?

A

the cell-surface barrier that sequesters fragile cytoplasmic enzymes away from the harsh extracellular environment;

84
Q

anaerobic

A

lacking oxygen

85
Q
A

Prokaryotic Biology (5 decks)

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