Microbio exam 3

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129 Terms

1

genome

the total of all genes in an organism whether they are found on a single chromosome or distributed among multiple replicons

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2

genes

the units of heredity (most are located on chromosomes)

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3

transformation

the internalization of free DNA from the environment into bacterial cells

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4

what kind of chromosomes do most archaea and bacteria have?

circular

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enhancer

a noncoding DNA regulatory region in eukaryotes that can lead to activation of transcription when bound by an appropriate transcription factor. It location on the chromosome can be far removed from the regulated gene.

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promoter

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

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nucleobase

(also called a nitrogenous base) forms a nucleotide of nucleic acids (U, A, C, G, T)

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phosphodiester bond

the phosphoryl bond that includes ester links with two adjacent nucleotides in a nucleic acid

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9

antiparallel

oriented such that the two strands are in opposite directions (5’-to- 3’ and 3’-to-5’)

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10

purines

nitrogenous bases with fused rings ( adenine and guanine)

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11

pyrimidines

single-ring nitrogenous bases (cytosine, thymine, and uracil)

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12

denature

to lose secondary or tertiary structure in a protein or nucleic acid because of high temperature or chemical treatment

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13

nucleoid

the looped coils of a bacterial chromosome

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14

topoisomerases

the enzymes that change DNA supercoiling

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15

quinolone antibiotic

antibiotic that inhibits DNA synthesis by targeting bacterial topoisomerases such as DNA gyrase

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16

positive supercoils

tightening of the coil

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17

negative supercoils

unwinding of the coil

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18

what kind of supercoils do most bacteria, eukaryotes, and archaea possess?

negatively supercoiled DNA

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19

how do bacteria replicate their DNA quickly and minimize errors?

replication efficiency

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20

semiconservative replication

each daughter cell receives one parental strand and one newly synthesized strand; allows for each daughter duplex to be checked for accuracy against its parental strand

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replications fork

parental strands are seperated while extending the new growing strands

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DNA replication

1.) initiation: the melting (unwinding) of the helix and the loading of DNA polymerase enzyme complex

2.) elongation: the sequential addition of deoxyribonucleotides to a growing DNA chain, followed by proofreading

3.)termination: the DNA duplex is completely duplicated,the negative supercoils are restores, and key sequences of new DNA are methylated

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23

replication from a single origin

replication in bacteria begins at a single defined DNA sequence called the origin

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24

catenane

a pair of linked rings of DNA that occurs as a by-product of replication of circular chromosomes

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25

homologous recombination

the exchange of strands between two molecules of DNA; exchange occurs within extensive regions of identical or nearly identical sequence

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plasmids

extrachromosomal elements found in bacteria, archaea, and eukaryotic microbes; usually circular and negatively supercoiled; much smaller than chromosomes and encode only a few genes

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secondary chromosome

carries at least one essential gene; smaller than primary chromosome

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28

telomeres

ends of eukaryotic chromosomes

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29

transcription

the copying of DNA to RNA

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30

RNA polymerase (DNA-dependent RNA polymerase)

an enzyme complex that carries out transcription, making RNA copies of a DNA template

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DNA template strand

specifies the base sequence of the new complementary strand of RNA

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32

RNA polymerase consists of:

core polymerase and a sigma factor (holoenzyme)

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core polymerase

contains the proteins required to elongate an RNA chain

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sigma factor

a protein needed only for initiation of RNA synthesis, not for its elongation

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A bacterial core RNA polymerase is a complex of four different subunits:

2 alpha, 1 beta, 1 beta-prime

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beta-prime subunit

houses the Mg 2+ which contains the catalytic site for RNA

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alpha subunit

assembles the beta and beta-prime subunits into a functional complex. It also communicates through physical “touch” with various regulatory proteins that can bind DNA

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38

sigma factor proteins

used to guide RNA polymerase to the beginning of each gene whose expression is needed under certain conditions.

  1. binds to RNA polymerase through the beta and beta-prime subunits

  2. the bound sigma factor recruits the core enzyme to the promoters, marking the beginning of a gene

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39

consensus sequence

consists of the most likely base (or bases) at each position of the predicted promoter. some positions in a consensus sequence are highly conserves, meaning that the same base if found in that position in every promoter

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sequences identified and bound by E.coli sigma -70

located at -10 and -35 bp upstream of the transcription start site

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open reading frame (ORF)

protein-coding region

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polygenic

containing both operon genes

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monocistronic

(referring to RNA products of transcription) RNA encodes the product of a single gene. This gene has its own promoter and transcription terminator

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polycistronic

(referring to RNA products of transcription) RNA encodes the products of one or more adjacent genes in one contiguous RNA molecule

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operon

the combination of the regulatory regions and all the genes that are cotranscribed in the polycistronic message

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3 stages of transcription

  1. Initiation

  2. Elongation

  3. Termination

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initiation

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

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elongation

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

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termination

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

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50

Rho factor

binds to an exposed region of RNA after the ORF at C-rich sequences that lack obvious secondary structure; used for termination in some genes

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51

rifamycin B

selectively target bacterial RNA polymerase and bind to the polymerase’s beta subunit near the Mg2+ active site, this blocking the RNA exit channel

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rifampicin (rifampin)

used for treating tuberculosis, leprosy, and bacterial meningitis

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53

actinomycin D

its phenoxazone ring is a planar structure that inserts, or intercalates, between GC pairs within DNA

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54

messenger RNA (mRNA)

the class of RNA molecules that encode proteins; doomed to a short existence due to their degradation by intracellular RNases

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55

ribosomal RNA (rRNA)

forms the scaffolding on which ribosomes are built; forms the catalytic center of the ribosome; has unusual bases

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transfer RNA (tRNA)

ferry amino acids to the ribosome; has unusual bases

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small RNA (sRNA)

do not encode proteins but used to regulate the stability or translation of specific mRNAs into proteins; contain untranslated leader sequences that precede the actual coding region

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tmRNA

has properties of both tRNA and mRNA

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catalytic RNA

also called ribozymes; associated with proteins; the enzymatic (catalytic) activity resides in the RNA portion of the complex rather than in the protein

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60

RNA stability

measured in terms of half-life

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61

half-life

the length of time the cell needs to degrade half the molecules of a given RNA species

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codons

triplets of nucleotides

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stop codons

trigger a series of events that dismantle ribosomes from mRNA and release a completed protein

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anticodons

RNA sequences that match and bind to specific codons on the mRNA being translated

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65

aminoacyl-tRNA synthetases

enzymes that match and attach the correct amino acid to the correct tRNA

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ribosomes

catalyze the linkage of amino acids during translation using mRNA as the code and charged tRNAs as the source of amino acids

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start codons

mark where translation starts and set the correct reading frame

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ribosome-binding site (Shine- Dalgarno sequence)

purine-rich sequence located four to eight bases upstream of the start codon

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69

aminoacyl-tRNA acceptor site (A site)

(first position) where the incoming aminoacyl-tRNA enters the complex and its anticodon binds the codon of the mRNA

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peptidyl-tRNA site (P site)

(second position) binds the tRNA that is attached to the growing polypeptide

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exit site (E site)

(third position) where the tRNA will be jettisoned from the ribosome after giving up its amino acid to the polypeptide chain

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72

initiation factors for E.coli

IF1, IF2, IF3

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73

polysome

multiribosome structure that is the result of an mRNA molecule with multiple ribosomes moving along its length at once

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74

most ribosomes are located at the poles of what cells?

rod-shaped cells

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75

translation terminates when:

a stop codon is reached. A release factor enters the A site and triggers peptide bond formation, thus freeing the completed protein from tRNA in the P site

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76

glycoproteins

involved in important microbial processes such as biofilm formation, virulence, and colonization of the human gut

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mass spectrometry

experimentally determines the exact mass of an unknown protein or peptide fragment.

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78

chaperones

helper proteins that aid in the folding of other proteins

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79

heat-shock proteins (HSPs)

more resistant to heat denaturation than the average protein

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80

mutation

any permanent, heritable alteration in a DNA sequence, whether harmful, beneficial, or neutral

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point mutation

a change in a single nucleotide

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82

transition

replacing a purine with a different purine or a pyrimidine with a different pyrimidine

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transversion

swapping a purine for a pyrimidine

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84

insertions/ deletions

the addition or subtraction of one or more nucleotides, making the sequence either longer of shorter than it was originally

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85

inversion

when a fragment of DNA is flipped in orientation relative to the flanking DNA on either side

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86

duplication

produces a second copy of a sequence fragment on the DNA molecule, usually adjacent to the original copy

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87

transposition

the movement of a sequence fragment from one location to another

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88

reversion

restores a mutated sequence to its original sequence

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89

silent mutations

mutations that do not change the amino acid sequence of a translated open reading frame (ORF)

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90

missense mutation

changes the amino acid sequence of the protein

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91

loss-of-function mutation

the decrease or elimination of the activity of a protein by a missense change

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92

gain-of-function mutation

when a protein gains a new activity, such as an expanded substrate specificity or a completely different substrate specificity.

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knockout mutation

a mutation that eliminates function

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94

nonsense mutation

a point mutation that changes an amino acid codon into a translation termination codon (ex. UCA to UAA)

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95

truncated proteins

the result of a nonsense mutation; truncations can completely knock out the function of proteins, especially in cases where the mutation occurred early in the ORF; degraded by cellular proteases

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frameshift mutation

when the number of bases inserted or deleted is not a multiple of three and the reading frame of translation changes; cause the ribosome to encounter a premature stop codon

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97

genotype

the genome sequence of an organism

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98

phenotype

the observable characteristics of an organism

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99

mutagens

chemical agents or forms of electromagnetic radiation that can damage DNA

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100

tautomeric shifts

the change in the bonding properties of amino (-NH2) and keto (C-O) groups; if occurring during DNA replication, number of mutation events will increase

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