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From Flashcardlet > Micro Exam 2_ Rev > Flashcards

Micro Exam 2_ Rev Flashcards

1
Q

Septum

A
  • partition
  • inward growth, where bacilli pinches
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2
Q

FtsZ Role

A
  • Polymerizes to form a Z ring.
  • Cell’s division plane
  • Related to Tubulin
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3
Q

FtsA

A
  • Anchors Z ring to cyto membrane
  • ATPase
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4
Q

FtsK

A
  • pulls apart Kromosomes
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5
Q

FtsL

A
  • Cross-Linking
  • Penicillin binding, lose catalytic activity.
  • Transpeptidation
  • Burst Cell Wall
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6
Q
  • FtsZ Midpoint Determination
A
  • Spiral structure on inner surface of membrane.
  • Oscillates back & forth. Middle is most free space
  • by MIN proteins
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7
Q

MIN proteins

A
  • prevent FtsZ ring from being placed near mid cell & nuclear material
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8
Q

When does binary fission replication occur?

A
  • before FtsZ ring forms
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9
Q

MreB

A
  • Directs synthesis/insertion of pepti building in, to allow length of bacteria
  • recruits other proteins, form cell’s wall growth
  • controls width of rods, also helical
  • NO MreB if SPHERICAL
  • similar to Actin, ancestor of Cytoskeletal elements
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10
Q

Crescentin

A
  • shape of curved rods
  • bulges up when no pepti
  • similar to Keratin
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11
Q

Autolysins

A
  • clip small holes @ Z ring
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12
Q

Bactoprenol

A
  • brings pepti to fill in holes
  • must be hydrophobic
  • Bonds to NAT/NAM/pepti
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13
Q

Identify phases Growth.

A
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14
Q

Lag Phase

A
  • Step 1
  • Adjustment
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15
Q

Exponential phase

A
  • Step 2
  • Logarithmic growth every generation time
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16
Q

Stationary Phase

A
  • Step 3
  • Some dies, some replicate.
  • Steady
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17
Q

Death Phase

A
  • Step 4
  • Depletion of nutrients
  • closed system
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18
Q

Final # of Cells

A
  • # of Cellsi x 2#of genes
  • N= No x 2x
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19
Q

N=

A

Final # of cells

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20
Q

of Generations

A
  • n= t / g
  • duration of exponential growth/gen time
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21
Q

g=

A

generation time

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22
Q

t=

A

duration of exponential growth

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23
Q

Growth Rate

A
  • regulated by dillution
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24
Q

Cell Density

A
  • regulated by limiting nutrients
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25
Q

Chemostat

A
  • oxygen makes it go faster
  • controlled by cell’s density & cell’s growth rate
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26
Q

Cell Count Limitations x4

A
  1. Can’t distinguish between dead/live cells
  2. Small cells are difficult to see
  3. Low density bacteria difficult to count
  4. Motile cells are difficult
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27
Q

Where are cell counts performed?

A
  • phase contrast microscopy
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28
Q

Spread Plate

A
  • Sample spread over agar
  • Pipetting/Mixing affect accuracy
    • quick, few materials required
    • 0.1 mL or less, makes it hard
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29
Q

Pour Plate

A
  • Sterile medium added to samle, mixed well
  • pipetting/mixing affect accuracy
    • limited in agar on top
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30
Q

10 Fold Seriel Dillution

A
  • Count cells in original sample
  • # of cells = plate count x Dilution Factor/mL dilution plated
  • Transfer 3x (min) 1:10–> 1:100
    • easier to perform
    • more materials/time
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31
Q

Appropriate # of Colonies present in a plate count

A

30-300

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32
Q

CFU

A
  • Colony Forming Unit, cluster
  • Each cell by division of pre-existing cell similarities
  • thru 2 cells in a sexual process
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33
Q

Great Plate Count Anomaly x3

A
  • Direct Count more organisms than plate count
  1. only measure viable cells
  2. must be able to support all types of cells
  3. Clumping lowers counts
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34
Q

Turbidity

A
  • muddiness/cloudiness
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35
Q

Spectrophotometer x4

A
  • Measures unsscattered light/turbidity
  1. higher conc= higher turbidity
  2. more cells= more scattered light
    • dillution is unecessary
    • cheap/ fast / doesn’t destroy sample
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36
Q

Optical Density

A
  • high density = less accurate
  • how much light was scattered
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37
Q

Psychrophile x5

A
  • Grow at 15oC
  1. Alpha Helix flexi
  2. fewer bonds
  3. fewer hydrophobic AA’s
  4. shorter fatty acid chains
  5. double bonds= unsaturated fatty acids (oil)
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38
Q

Mesophile

A
  • grow at body temp 37oC
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39
Q

Thermophile x3

A
  • Grow at 45oC
  1. More beta sheets (rigid)
  2. more ionic bonds
  3. opposite of psychrophile
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40
Q

pH

A
  • H+ = 10-1 ; OH- = 10-13;
  • H+ = 10-2 ; OH- = 10-12
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41
Q

How aerobes grow in lab

A
  • jar with gaspak
  • generates H2 + CO2
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42
Q

How Microaerophiles grow in lab

A
  • Heat in trapped jar CO2 incubation
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43
Q

Reducing Agent

A
  • Thioglycolate
  • Reduce Oxygen
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44
Q

3 Types of Oxygen Toxic to cells

A
  1. Superoxide
  2. Hydrogen Peroxide
  3. Hydroxyl Radical
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45
Q

Catalase vs Peroxidase

A
  • C= Decomposes peroxide to water & hydrogen
  • P= Decomposes hydrogen to water & NAD+
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46
Q

Superoxide Reductase vs Superoxide Dismutase

A
  • R= decompses superoxide to less toxic hydrogen peroxide. Peroxide turned into water by Rubrerythin.
  • D= decomposes superoxide into oxygen & water. Present in Facultative/Aerobes
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47
Q

Transcription

A
  • First step
  • DNA copied to RNA by RNA poly.
  • makes mRNA
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48
Q

Translation

A
  • mRNA is decoded to Amino Acid Chain
  • Ribosomes create proteins
  • Begins at 5’ end
  • Blocked when Riboswitch binds
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49
Q

DNA template

A
  • strand used to make complementar daughter strand
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50
Q

Complementary DNA

A
  • 2 polynucleotide strands
  • Double strand
  • A-T, G-C
  • Has a methal group (T)
  • missing an OH
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51
Q

Complementary RNA

A
  • single strand
  • A-U
  • T-A
  • C-G
  • Has Ribose instead of deoxyribose
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52
Q

Why are bases paired? x3

A
  • A-G would develop 4 rings
  • Hydro Bonds wouldn’t match
  • Primidine pairs with Purine b/c of space constraints
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53
Q

Hydrogen Bonds & Base Pairs

A
  • C-G= 3 H bonds
  • A-T= 2 H bonds
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54
Q

Prymidine

A
  • One ring
  • C= DNA only
  • T= DNA/RNA
  • U= RNA only
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55
Q

Purine

A
  • Two rings
  • A
  • G
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56
Q

Deoxyribose/Ribose Number of Carbon (sequential)

A
  • High Five at the end HOCH2
  • 5 Carbon Sugar
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57
Q

3’

A
  • OH
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58
Q

5’

A
  • PO4
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59
Q

Antiparallel

A
  • One strand runs 5’ - 3’
  • Another strand runs 3’ - 5’
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60
Q

Size of E. Coli

A
  • 4,640,000 bP
  • 1.58 mm
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61
Q

Supercoiling

A
  • How long length of DNA fits into Cell
62
Q

Negative supercoiling

A
  • DNA twisted opposite sens from rt handed double helix
63
Q

DNA Gyrase

A
  • Negative supercoiling
  • cuts a double helix & passes through
  • Link 2 in each enzymatic step
64
Q

Topoisomerase I

A
  • relaxation of supercoil
65
Q

5’ Deoxyriboducleotide Triphosphate

A
  • precursor of new nucleotide in growing DNA Chain
66
Q

DNA Chain grows in?

A
  • 5’ to 3’ b/c polymerase requires OH on 3’ as active site
  • Pol 1 & Pol 3
67
Q

Events of the DNA replication (label)

A

*

68
Q

Helicase

A
  • separetes DNA strands.
  • Unwinds double helix
  • When transcription is initiated
69
Q

Single Stranded Binded Protein

A
  • binds to single-stranded regions to keep strands apart
70
Q

Primer

A
  • Required for replication
  • Initiate synthesis of DNA strand
  • enzymes can only add nucleotides to an existing strand
71
Q

Primase

A
  • RNA poly adds an RNA primer
72
Q

Proofreading

A
  • Both Pol 1 & Pol 3 can do this
  • 3’ to 5’
  • DNA poly reverses mistake by one base pair
73
Q

DNA Poly 1

A
  • 5’ to 3’ Exonuclease activity to remove primer
  • fills gap with DNA
  • Proofreading
74
Q

DNA Poly 3

A
  • Synthesizes leading strand 5’ to 3’
  • cannot remove primer
  • proofreading
75
Q

Okasaki Fragment

A
  • short DNA frag
  • formed on lagging template strand
  • form short double bonded DNA section b/c must be synthesized in opposite direction from helicase opening
76
Q

Ligase

A
  • Joins Okasaki Fragments to form 1 pc. of DNA
77
Q

Replisome

A
  1. 2 copies of Pol 3, helicase, primase and ssbp
  2. unwinds double strand into 2 single strands
78
Q

TUS

A

Terminates forks

79
Q

3 Types of RNA transcribes

A
  1. Transfer RNA
  2. Ribosomal RNA
  3. Message RNA
80
Q
A
  • Promotors are Double Strand DNA (-35 sequence + Pribnow Box)
  • Template —> 5’ to 3’ mRNA
  • Start- mRNA
  • 35 sequence= up stream; Pribnow box= downstream
81
Q

Whiche direction does RNA poly move along template

A

3’ to 5’

82
Q

Promoters

A
  • double strand
  • -35 sequence, Pribnow Box
  • bind RNA poly (like operator)
83
Q

Sigma Proteins x6

A
  1. Recognize promoter
  2. positions RNA core @ initiation site
  3. accompany genes needed for a task
  4. Regulate transcription
  5. Diff sigma recognize diff promoters
  6. conserve energy/resources
84
Q

Strength of a promoter

A
  • affinity for RNA poly
  • stronger if transcribed more
85
Q

Xmas tree reason

A
  • nucleolus is growing RNA chains
  • many polys operate on same transcription unit
86
Q

Termination Signal for RNA Poly

A

base sequence

87
Q

Open Reading Frame

A
  • contains no stop codons
  • transcription termination is located after ORF
88
Q

How a stem loop structure forms

A
  • Inverted repeats in transcribed DNA
  • Terminates transcription when followed by a run
  • Operator
89
Q

Polycistronic

A
  • Chem blue print
  • carries ORF’s translated to polypeptide
  • made by mRNA
90
Q

Operon

A
  • Groups of genes encoding m RNA. Transcribed together, as single gene.
91
Q
A
  • Where operator is located with respect to promoter
92
Q

Operon vs Regulon

A
  • Regulon= many Operons on diff location of x-somes with 1 regulon
93
Q

Why genetic code is degenerate

A
  • 43 = 64 codons
  • 20 amino acids
  • not all will generate, some AA’s are coded by more than 1
94
Q

Shine Dalgarno Sequence x4

A
  1. holds ribosomes in correct starting place
  2. 3-9 nucleotides
  3. upstream of start codon
  4. complementary to 3’ of 16S rRNA in 20 30S Subunit
95
Q

F-met

A
  • first Amino Acid added to growing prokaryotic protein
96
Q

Anti Codon Calculation

A
  • Codon = CGA
  • Complement= GCU (3’-5’)
  • Answer = UCG (5’-3’)
97
Q
A
  • Amino acids are linked at 3’ End
98
Q

Steps for Amino Acid to Transfer RNA (x5)

A
  1. AA + ATP= Aminoacyl Amp
  2. Catalyzes
  3. AMP + RNA = Aminoacyl to tRNA
  4. AA attached at 3’ end
  5. Each AA has its own. AMP to tRNA synthase
99
Q

Large Subunit

A

50S

100
Q

Small Subunit

A
  • 30S
101
Q

Initiation of Complex forms x4

A
  1. 16S rRNA/30S Binds to Shine Dalgarno
  2. tRNA & f-met bind to AUG codon
  3. 50 S creates E,P,A Sites,
  4. AUG codon aligns with P-site
102
Q

E-site

A
  • Exit Site,
  • created by 50S
103
Q

P-Site

A
  • peptide
  • created by 50S
  • aligns with AUG codon
104
Q

A-site

A
  • acceptor created by 50S
105
Q

Translation Initiation

A
  • tRNA carriet “Met”
  • bind to small unit first
  • use energy from GTP to promote large unit
  • starts in P-site
106
Q

Polysomes

A
  • cluster of ribosomes
  • bond to mRNA molecule
  • catalysts for polypeptide bond formation
107
Q

Process for Elongation

A
  1. tRNA binds with A-site
  2. 23S rRNA on 50S catalyzed peptide bond formation
  3. Fmet released from its tRNA
  4. hiccup, ribos moved DOWN on mRNA
  5. tRNA moves into A-site
  6. continues until receives STOP codon
108
Q

Sec A

A
  • contains signal sequence
  • bind proteins across c-membrane
109
Q

Signal Sequence x5

A
  1. Keeps protein from folding
  2. 15-20 residues
  3. variable
  4. binds Sec A or sig Recognition Particle
  5. Proteins in/thru membranes
110
Q

Signla Recognition Particle

A
  • Binds to proteins being insterted into membranes
111
Q

TAT

A
  • Twine Arginine Translocase
  • Thru Proton Motive Force
  • function in periplasm
  • short signal sequence
112
Q

Half Life & Regulation

A
  • very short (few min)
  • Allows for quick response to change
  • if we don’t need it, they can stop
  • production will not occur unless mRNA is made
113
Q

Constituitive

A
  • under all growth conditions
  • proteins & molecules that are needed at the same level
114
Q

Housekeeping Genes

A
  • always on
  • constituitive
  • required for maintenance of cell function
115
Q

Allosteric

A
  • Repressor
  • Regulates enzyme/protein by bind to site
116
Q
A
  • helix turn helix
  • most common motif in prokaryotes
  • form homodimes. resemebles clothespin
  • clothespin can bind in other major grooves of the DNA
117
Q

Negative Transcription

A
  • Turn gene off
  • top rNA Poly
118
Q

Repression

A
  • Negative Transcription
  • Anabolic- construct molecules from smaller units
119
Q

Induction

A
  • Positive Transcription
  • Made when lac operon is present
  • Catabolic- breaks down molecules into smaller units to release energy
120
Q

Arg Operon & Repressor

A
  • arginine absent- repressor Not bind- Transcription Proceeds
  • Corepresson-repressor binds-transcription blocked
121
Q

Repressor & Lac Operon

A
  • When lac absent- Transcription blocked
  • when lac is present, transcription proceeds
122
Q

Corepressor

A
  • an effector
  • repressor binds
123
Q

Repressor

A
  • alters shape when effector binds
    • downstream
124
Q

Inducer

A
  • an effector
  • repressor cannot bind when present
125
Q

Activator

A
    • upstream
126
Q

Catabolie Repression

A
  • Positive regulation
  • allow sigma to bind to promoters
  • grow faster in glucose
127
Q

Diauxic Growth

A
  • Resulte of Catabolite Repressor
  • double growth
  • 2 sugars on a culture frowth media
128
Q

Role of cAMP

A
  • when no Glucose
  • lactose must be presnet
  • CRP-cAMP
  • sigma binds to weak promoter
129
Q

Lac Operon Positive

A
  • Metabolit Repression
  • CRP binds to CRP binding site
130
Q

Lac Operon Negative

A
  • Must be present as inducer
  • lactose repressor doesn’t block transcription
131
Q
A
132
Q

Attenuation

A
  • Simultaneous
  • Translation & Transcription
  • Example: TRP Operon
  • Terminates Transcription
133
Q

Tryptophan

A
  • UGG codon
  • essential protein for human life
134
Q

Ribosomes and Attenuation x5

A
  1. Ribos stall at TRP codon/ Limiting TRP
  2. enter s.loop at 2 & 3
  3. continues transcription
  4. each structural gene has start site for ribo
  5. structural genes are transcribed then translated
135
Q

Component of Leader Sequence

A
  • encodes 2 TRP AA’s
  • has stop codns
  • run of UUUUU’s
136
Q

Excess TRP x5

A
  1. s.loop forms at end of leader sequence
  2. run of UUUUUs
  3. Ribos translate to leader stop codon
  4. bas pairing in 3 & 4 region
  5. Poly terminates
137
Q

Translation of Downstream

A
  • Tryp gets made
  • stall RNA
  • 2 Alternate stem loops form
138
Q

What happens when Riboswitch binds

A
  • forms a different s.loop
  • shine dalgarno blocked
  • no translation
139
Q

Riboswitch, Abundant vs Blocked (nclued Shine Dalgarno)

A
  • see image
140
Q

Progress toward Protocell

A
  • RNA Over 100oC
  • hyperthermophiles
  • take in nucleotides quickly at high temp
  • build RNA faster at low temp
  • Heat causes strands to pull apart , allow new RNA molecule to function
141
Q

RNA world Hypothesis

A
  • RNA were precursors to current life
  • Self Replicating
142
Q

Kinase

A
  • phosphorylates w/ ATP
143
Q

Phosphotase

A
  • Repressor Released
  • clips phophate
144
Q

What resets Signal Transduction

A

phosphotase

145
Q

2 component regulatory system (see image)

A
  1. Sensory
  2. Response Regulator
146
Q

Environment and Signal Transduction

A
  • phosphorylates itsel
  • phosphryl groups is transferred to 2nd component
  • response to regulator
147
Q

Flagella

A
  • regulated by Signal Transduction
148
Q

Quorum Sensing

A

AHL diffuses freely across membrane

149
Q

Quorum Sensing Regulating

A
  • transcription of genes
  • Bacteria can count
  • makes sure suficient # of cells
  • require density
  • Positive inside the cell
  • UPSTREAM
150
Q

A molecule that regulates Quorum sensing must be able to do?

A
  • must be diffusible via passive transport through the membrane
  • That is how the cell can “sense” when other organisms also are making this product and causing a buildup inside the cell.
151
Q

Biofilm

A
  • Microbe Colonies encased in adhesive.
  • Polysaccharide

From Flashcardlet (35 decks)

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