micro exam 2

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fimbriae and pili

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1

fimbriae and pili

  • short, thin hairlike protein appendages up to 1,000 per cell

  • can mediate attachment to surfaces, motility, and DNA uptake

  • is regulated by how many copies of the gene you have

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sex pili

  • longer, thicker, less numerous where there is 1-10 per cell

  • genes for the formation on plasmids

  • required for conjugation/ movement of DNA

  • send to another cell to be able to send a plasmid and make genes from that same plasmid

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3

structures similar to pili used by pathogens to secrete effector proteins in to or around the cells

what is a plasmid transfer?

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4

flagella

  • threadlike, locomotor appendage extending outward from the plasma membrane and cell wall

  • helps with motility, attachment to surfaces, and may have virulence factors

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monotrichous

one flagellum

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polar flagellum

flagellum at end of cell

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amphitrichous

one flagellum at each end of cell

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8

lophotrichous

cluster of flagella at one or both ends

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peritrichous

spread over entire surface of the cell

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  • thin, rigid protein structures that cannot be observed with bright-field microscope unless specially stained

  • ultrastructure composed of three parts

    • filament extends from cell surface to the tip

    • hook links filament to basal body

    • basal body is series of ring that drive flagellar motor

what is different about bacterial flagella?

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flagellar synthesis

  • complex process involving many genes/gene products

  • new flagellin molecules transported through the hollow filament using Type III-like secretion system

  • filament subunits self-assemble with help of filament cap at tip, not base

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12

rotates like a propeller

how does the bacterial flagella move?

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13

counterclockwise (CCW)

what is the general rotation for the flagella to have a run motion?

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clockwise (CW)

what rotation disrupts run to cause the cell to stop and tumble?

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help to avoid and move direction

what can tumbling of the flagella do?

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2 part motor producing torque

how many parts is the flagellum made up of?

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17

rotor and stator

what are the two parts that help with the motor of the flagellum?

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Rotor

C (FliG protein) ring and MS ring turn and interact with stator

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19

Mot A and Mot B proteins to help get through plasma membrane

what is the stator made up of?

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stator

  • form channel through the plasma membrane

  • protons move through Mot A and Mot B channels using energy of proton motive force

  • torque powers rotation of the basal body and filament

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swarming

  • move out from the center in a branched, defined pattern

  • occurs on moist surfaces as a type of group behavior by bacteria

  • have peritrichous flagella

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spirochete motility

  • multiple flagella form axial fibril to wind around the cell

  • flagella remain in periplasmic space inside outer sheath

  • corkscrew shape exhibits flexing and spinning movements

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twitching and gliding motility

  • occurs on solid media

  • no flagella

  • have Type IV pili and slime

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twitching

  • pili at ends of cell

  • short, intermittent, jerky motions

  • cells are in contact with each other and surface

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gliding

smooth movement

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26

chemotaxis

  • movement toward a chemical attractant or away from chemical repellent

  • changing concentration of chemical attractants and chemical repellents bind chemoreceptors of chemosensing system

  • behavior of bacterium altered by temporal concentration of chemical

  • presence of attractant/repellent, tumbling frequency is reduced’ runs toward/away from compound are longer

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27

sessile cells

  • bare minimum to survive

  • hibernations to shut down everything not needed for survival in times of stress

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spore formation

releasing small seed to make things again in a less stressful environment

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endospore

  • complex, dormant structure

  • can form in various locations within the cell

  • resistant to numerous environmental conditions

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  • calcium complexed with dipicolinic acid

  • small, acid-soluble, DNA-binding proteins\

  • dehydrated core

  • spore coat and exosporium protect

why are endospores resistant to numerous environmental conditions?

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endospore structure

  • spore surrounded by thin covering called exosporium

  • thick layers of protein form the spore coat

  • cortex, beneath the coat, thick peptidoglycan

  • core has nucleoid and ribosomes

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sporulation

  • process sof endospore formation

  • occurs in a few hours

  • commences when growth ceases due to lack of nutrients

  • complex multistage process

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  • activation

  • germination

  • outgrowth

types of formations of vegetative cell

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activation

  • prepares spores for germination

  • results from treatments like heating

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35

germination

  • environmental nutrients are detected

  • spore swelling and rupture of absorption of spore coat

  • increased metabolic activity

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outgrowth

emergence of vegetative cell to go back to normal cell size

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37
  • macleod and mccarthy showed that the transforming principle was DNA

  • so there is a smooth strain of colony where the S strain has a capsule that killed the mouse

  • there was an R strain that was rough with no capsule where the mouse was unharmed

  • however, when they heat killed the S strain, there was no harm to the mouse

  • finally, the thing is when they put the heat-killed S strain with the live R strain where they will both come together to form the S strain to kill the mouse, hence saw DNA as genetic material

how did scientists find out DNA is genetic material?

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38

change of non-virulent organisms into virulent ones via transformation

what did Griffith discover in 1928?

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39

transforming principle to prove that DNA is the genetic material

  • type R cells with the type S DNA extract will make DNA through transformation

  • when there is DNase with the Type R cell and the type S DNA extract, the DNA can be destroyed

  • however, if protease or RNase is used, there will be DNA still transformed but either no protein or RNase

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40

adenine, guanine, cytosine, and thymine

what are the nucleotide bases for DNA?

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41
  • bases

  • deoxyribose sugar

  • phosphate esterified to sugar carbon

what forms nucleotides for DNA?

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42

covalent bonds between the 3’-hydroxyl of one sugar and a 5’-phosphate attached to an adjacent sugar

what bonds are formed for the sugar phosphate backbone?

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43

major groove allows things to come through and to it easier

difference between minor groove and major groove?

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44
  • bases

  • ribose sugar

  • phosphodiester bonds

what are the parts to make nucleotides for RNA?

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45

adenine, guanine, cytosine, and uracil

what are the bases of RNA?

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46
  • messenger RNA (mRNA)

  • ribosomal RNA (rRNA)

  • transfer RNA (tRNA)

  • noncoding RNA ( ncRNA, snRNA, snoRNA, sRNA)

what are the four different types of RNA with different functions, site of synthesis, and structure?

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47

it is read to make proteins

what is coding?

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48

peptide bonds

what bonds do proteins have to link amino acids together?

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49
  • carboxy group (C-terminal)

  • amino group (N-terminal)

  • side chain (R)

what are the parts of amino acid?

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50

polar, non-polar, or charged depending on the side chain, environment, and such

what can amino acids be?

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51

synthesis is semi-conservative where each daughter cell obtains one old and one new strand

how is the DNA synthesis like?

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52

you need to mutate it where it can’t start, so you have OR

how can you prove that the OR is where replication starts?

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53

mainly circular

how is DNA like in bacteria?

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54

bidirectionally from a single origin replication fork where the DNA is unwound and will wait until both sides are done to separate

how does DNA replication occur in bacteria?

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55

replicon

origin and is replicated as a unit (entire genome in bacteria)

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56

DNA gyrase

relieves supercoiling of DNA produced as DNA strand are separated by helicases; separate daugther molecules in final stages of replication

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57

DnaA (initiator protein)

initiation of replication; binds origin of replication (or/C)

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58

DnaB

helicases (5’ to 3’); breaks hydrogen bonds holding two strands of double helix together; promotes DNA primase activity; involved in primosome assembly

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59

SSB proteins

bind single-stranded DNA after strands are separated by helicases

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60

DnaC

helicase loader; working with DnaA, directs DnaB (helicase) to DNA template

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61

DNA primase

synthesis of RNA primer; component of primosome

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DNA polymerase III holoenzyme

catalyzes most of the DNA synthesis that occurs during DNA replication; has 3’ to 5’ exonuclease (proofreading) activity

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DNA polymerase I

removes RNA primers; fills gaps in DNA formed by removal of RNA primer

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removes RNA primers

ribonuclease H

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DNA ligase

seals nicked DNA, joining DNA fragments together

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Tus

termination replication

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67

topoisomerase IV

separation of chromosomes upon completion of DNA replication

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68

DNA polymerase

what catalyzes synthesis of complementary strand of DNA?

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69

5’ to 3’ to form phosphodiester bonds

what direction does DNA synthesis go?

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70
  • a template to direct synthesis of complementary strand

  • a primer from either DNA or RNA strand

  • dNTPs (dATP, DTTP, DCTP, dGTP)- deoxynucleotide triphosphates

what do polymerases require?

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71

5; polymerase III

how many DNA polymerases does E. coli have and what polymerase plays the major role in replication?

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72

DNA polymerase holoenzyme

  • complex of 10 proteins

  • 3 proteins form core enzyme

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73

2 core enzymes in each polymerase

  • catalyze DNA synthesis

  • proofreading for fidelity

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74

topoisomerase

breaks one strand of DNA; relieves tension from rapid unwinding of double helix, prevents supercoiling

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75

primase

synthesizes short complementary strands of RNA primers needed by DNA polymerase

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76

DnaA proteins bind oriC (origin of replication ) causing bending and separation of strands

what is the first event at the replication fork in E. coli?

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77

DnaB and other helicases

what helps separate the strands of DNA in E. coli to allow SSB attach?

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78

primase

what will synthesize RNA primer for the E. coli?

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79

DNA polymerase I

what removes the RNA primers and fills those gaps with DNA?

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80

yes

can multiple codons code for the same amino acid?

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81

Proofreading (making sure it is all good)

what is carried out by DNA polymerase III?

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82

removal of mismatched base from 3’ end of growing strand by exonuclease activity of enzyme

what happens during proofreading?

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83
  • replisome reaches the termination site (ter) on DNA

how does DNA replication in E. coli stop?

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84

catenanes

what forms when two circular daughter chromosomes do not seprate

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  • use topoisomerase and catanenes

  • cross-over occurring at the ter site

ways to break apart daughter chromosomes in the bacteria

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86

5’ to 3’

what does the mRNA read?

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87

tRNA, mRNA, rRNA

what RNAs used to help with the translation of mRNA

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88

template strand of DNA and read in 3’ to 5’ direction

what directs RNA synthesis and how is it read?

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89

promoter

  • located at the start of the gene

  • recognition/binding site for RNA polymerase

  • functions to orient polymerase

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90

leader sequence

  • transcribed into mRNA but not translated into amino acids

  • shine-delgarno sequence is needed for initiation of translation

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91

N-formylmethionine, a modified amino acid used to initiate protein synthesis in bacteria

what does AUG code for?

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92

genes

DNA sequences that code for tRNA and rRNA

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93

single, large precursor

genes coding for rRNA are transcribed as what?

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94

spacers

what is removed between coding regions of transcription, either by special ribonucleases and ribozymes?

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95

no

do prokaryotes have introns and exons?

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96

polycistronic mRNA

  • found in bacteria and archaea

  • contains directions for >1 polypeptide catalyzed by a single RNA polymerase

  • has a shine degarno sequence

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97

initiation, elongation, termination

steps of transcription

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98

5 chains and catalyzes RNA synthesis

what are core enzymes composed of in most bacterial RNA polymerases?

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99

sigma factor

what has no catalytic activity but helps the core enzyme recognize the start of genes?

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100

holoenzyme

core enzyme + sigma factor; only this can begin transcription

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