Micro410_Exam2_Myterms

Front 1

In the genus Bacillus, what are the 7 stages (w/distinctions) of sporulation and what

Back 1

1. DNA condensation, axial filament.
2. asymmetric cell division Fts proteins developing endospore.
3. Forespore formationEndospore septum grows around protoplast (engulfment).
4. Exopsporium appears primordial cortex is formed between two membranes, Dehydration.
5. Coat Layers, Ca2+ incorporation further deydration, production of SASPs and dipicolinic acid. Coat layers are formed. (difficult to stain cause dehydrated).
6. Mature endospore, Development of resistance to heat and chemicals, cortical layers.
7. Lysis.. of cell and release of free endospore with it's core and Exosporium.

Front 2

What are properties of endospores that distinguish them from vegetative cells. (3 and 3)

Properties of spore forming Species..

Back 2

Triggered by C,N, P limitations
* 1. Heat Resistance 2. Radiation Resistance 3. Resistance to chemicals ie. H2O2.
* (+ for veget. cell and - for Endospore) = 1. Enzyme activity 2. Metabolism O2 uptake 3. Macromolecular synthesis.

Bacillus and Clostridium, gram+.

Front 3

What are 8 properties of Heterocyst?

Back 3

* Formation triggered when cells limited for fixed nitrogen.
*Cell wall of heterocyst limits or prevents O2 and other gases from entering
*Photosystem II non-functional.
*Photosystem I directed at producing ATP not NADPH
*heterocyst no longer able to fix CO2
*Nitrogenase in heterocyst fixes N2 to NH3.
NH3 is converted to glutamine in heterocyst and exported to neighboring photosynthetic cells... for these processes to occur, the photosynthetic neighbors must provide heterocyst with an electron donor and glutamic acid.
*Heterocyst is differentiated forever.

Front 4

Enzymes involved inassimilation of ammonia into organic carbon: (3)

Key ingredient in for Heterocyst NH3 dispersion...

Back 4

* L-glutamate dehydrognase (GH)
* L-glutamine synthetase (GS) and glutamate synthetase (GOGAT)

Glutamate is the key ingredient that's pased down to other cells in a gradient.

Front 5

Two Mechanisms of Assimilation of Inorganic Nitrogen:

Back 5

1. Glutamic dehydrogenase
α-ketoglutarate + NH3 -----> glutamic acid
2. Second mechanism uses a 2 enzyme system: L-glutamine
synthetase and glutamate synthetase or
GOGAT enzyme.
Glutamic acid + NH3 + (16 - 24)ATP -------> glutamine
Glutamine + α-ketoglutarate --------> 2 glutamic acids

Front 6

Name three things during sporulation that contribute to differential gene expresison

Back 6

1. Sigma subunits of RNA polymerase.
2. Activation of sigma F and E in forespore and mother cell compartment respectively
3. Cross-talk between forespore and mother cell leads to mature endospore.

Front 7

Characteristics of Rhizobia bacteria (3)
1. properties of Bact.
2. properties of symb. forms of bact.
3. Genes expressed... including functions of nod and nif genes.

Back 7

1. Obligately aerobic g.neg... only will fix N2 in symbiosis w legume roots.
2. Bacterial cells that carry out the N2 fixation are differentiated and they are contained in nodules.
3. Bacterial cells express genes important for causing the plant nodules to form (nod genes) and genes that code for the N2 fixation enzymes (nif genes)

Front 8

Root nodulation and establishment of symbiosis (5)
1. How attach to root hairs?
2. Specificity, how?
3. Nod factors do what?
4. ...then what?
5. Describe bacterioids..

Back 8

* Attachment to root hairs via specific binding proteins such as rhicadhesins (bacterial) and lectins (plant).
* Host plant specificity determined (in part) by bacterial nod factors which detect plant flavonoids
* Nod factors induce root hair curling, growth of an infection thread, and proliferation of root cortical cells to form a nodule.
* Bacterial cells in infection thread are eventually enclosed within intracellular symbiosomes.
* Bacteroids are terminally differentiated, non-growing bacterial cells that express nif genes within symbiosomes.

Front 9

Nodule Metabolism (4) ..
*fixed N2 is released as...
*host plant regulates ...
*Boundary layer cells do what?...
*What acts as an O2 buffer and who produces it?

Back 9

* Organic acids from plant provide energy and reducing power for nitrogen fixation; fixed nitrogen is released from bacteroids as ammonia.
* Oxygen tension is regulated by the host plant.
* Boundary layer cells surround the nodule and act as a diffusion barrier.
* Leghaemoglobin is produced cooperatively by both partners to act as an O2 buffer in nodules.

Front 10

Myxobacteria: (3)
1. characteristics...
2. development cycle...
3. Genomic requirements for lifestyle...

Back 10

* Obligately aerobic, Gram-negative soil bacteria that feed primarily on lysed cells of other bacterial species.
* Undergo multicellular developmental cycle.
* Complex lifestyle seems to require a large genome (9.5 Mb for Myxococcus xanthus).

Front 11

Vegetative growth. (3)
1. What do they eat?
2. What community do they require?
3. How do they move?

Back 11

* Enzymes and antibiotidcs secreted by myxobacteria lyse other bacteria in environment and help to digest the released nucleic acids, proteins (nucleases and proteases)and lipids; these used by myxobacteria for growth.
* Lifestyle requires high cell density-- "the microbial wolf pack."
* Vegetative cells are motile by gliding motility (does not involve flagella), with individuals moving in "slime trails" left by other cells.

Front 12

Fruiting body and myxospore formation..(4)
1. Aggregation leads to what and what?....
2. How are endospores different from myxospores?
3. Where do myxospores form in the fruiting body? what%
4. Germination of what leads to what?

Back 12

* Aggregation of cells leads to formation of fruiting body, and differentiation of individual cells into myxospores.
* Myxospores are fundamentally different from endospores, both in their formation and in their properties once formed.
* Myxospores form in the head of fruiting body ~1%.
* Germination of myxospores from a fruiting body leads directly to the formation of a new swarm of vegetative cells.

Front 13

What are some Non-legume plants and the Bacteria associated with them?

Back 13

1. Alders and Frankia bacteria
2. Azolla (water ferns) and Anabaena azolla (cyanobacteria)

Front 14

What are some Legume plants and the Bacteria associated with them?

Back 14

1. Soybean and Bradyrhizobium japonicum, B. elkanii and R. fredii bacteria.
2. Alfalfa and Sinorhizobium meliloti bacteria.
3. Clover and Rhizobum legum and R. trifolii bacteria.

Front 15

5 steps in nodule formation:

Back 15

Step 1: Bacteria attracted and swim to the root.
• Step 2: Plant flavonoids induce bacterial nod genes, leading to formation of infection tube.
• Step 3: Nod factors also lead to plant cortical cell division.
• Step 4: Differentiation of nif- expressing bacteroids
• Step 5: Plant membrane surrounds bacteroids, forming symbiosome,

Front 16

1. In Symbiotic bacteria, the NH3 is grabbed by what?.. from plant.

2. ATP synthesis for nitrogenase comes from?

Back 16

1. Glutamine synthatase to make Glutamine or Asparagine.

2. Bacteroid relies on organic acids coming from plant for ATP synthesis

Front 17

Gliding motility:
1. How
2. How fast compared to flagellar motility?

Back 17

1. For use on surface.. contractile pili (only M.xanthus)in front and propellar jets that squirt slime to push fwd.
2. 1-5um/min. compared to Flagellar motility ~10-20um/SEC!

Front 18

Properties of myxospores (5)

Back 18

1. Go directly from vegetative to myxospore (bypass fruiting body and mother cell)
2. Cell shape more round, more cross linking of glycans.
3. Few specific spore proteins.
4. Resistant to desiccation, heat and survive long periods of time but are not as refractory as endospores.
5. Tend to remain together in fruiting body/cyst. Will get germination as a group and immediately form a swarm.. find fruiting bodies on dung pellets.

Front 19

Purine bases:
Pyrimidine bases:

Back 19

1. Purine bases = Adenine and Guanine
2. Pyrimidine bases = Cytosine and Thymine (Uracil)

Front 20

DNA replication occurs at what site? Is regulated by what?.. daughter start site immediately does what?

Back 20

Initiation occurs at a specific site called oriC and regulated by DnaA protein. While the original oriC is bound in the middle, the daughter cells' oriC sites immediately aggregate to the poles.

Front 21

Primary polymerase enzyme that synthesizes DNA strands bidirectionally

Back 21

DNA pol III Has exonuclease activity.

Front 22

RNA primer requires.....

Back 22

primase and helicase.

Front 23

Lagging strand requires....

Back 23

Multiple primases, primers, DNA pol III. But ALSO DNA pol I and DNA ligase.

Okazaki frabments ~1000bp initiated by new RNA priming event.. helps prevent folding back on eachother and replication error.

Front 24

DNA replication rate vs RNA transcription rate

Back 24

DNA replicates at 750 - 100 bases/sec and accurate at 1 mistake in every 10^-8 or 10^-10. RNA is transcribed at 20/30 bases/sec. .. (maybe because of simultaneous translation)

Front 25

DNA termination occurs at ____ site

Back 25

Ter site

Front 26

DNA pol I

Back 26

contains a 5' exonuclease that clips off the RNA primer contained immediately upstream from the site of DNA synthesis in a 5' --> 3' manner. Pol I then synthesizes DNA nucleotides in place of the RNA primer it had just removed. DNA polymerase I also has 3' to 5' exonuclease activity which is used in editing and proofreading DNA for errors. (act from DNA or RNA)

Front 27

DNA pol III
Acts as complex of ....
It is the primary _______

Back 27

Acts as a complex of 2 enzymes.
Being the primary holoenzyme involved in replication activity, the DNA Pol III holoenzyme also has proofreading capabilities that correct replication mistakes by means of exonuclease activity working 3'->5'. DNA Pol III is a component of the replisome, which is located at the replication fork. Bases of added dNTP are ocmplementary to template base with new strand with 5'end with -PiPiPi and 3' end with -OH

Front 28

Role of Topoisomerases

Back 28

1. To condense the DNA supercoiling.
2. Relieve torsional stress during replication (Gyrase)
3. Decatenation of two daughter chromosomes and restoring supercoiled structure to molecule.

Front 29

Protein - DNA complexes at oriC:

Back 29

*oriC is ~300bp
* control frequency of initiation of replication: cells can initiate a new round of replication before completing first round of replication.
* control segregation of chromosomes into daughter cells

Front 30

Linear DNA replicated by using what kind of primer?

Back 30

protein primer

Front 31

DNA primase does what?

Back 31

Adds short stretches of RNAprimers(before DNA pol III comes along).. Synthesizes RNA primers

Front 32

DNA helicase does what?

Back 32

Unwinds dsDNA from ATP Hydrolysis to break the H bonds in 5'-3'direction.. that breaks open bond.

Front 33

DnaA does what?

Back 33

Creats ssDNA at oriC. Multiple copies ofDnaA (~ 20-40!)bind to specific 9bp oriC sequences, AT-rich dsDNA adjacent to DNAA binding is distorted and becomes ss

Front 34

DNA polymerases III pauses due to....

Back 34

Probably due to mismatch (abnormal H bonding) Takes step back and takes out incorrect dNTP.

Front 35

Polycistronic mRNA

Operons identified by their...

Back 35

Polygenic (multiiple gene ic) operons

Operon will be transcribed from a single promoter. -10 and -35 conserved regions upstream from start codon. Region recognized by RNA pol holoenzyme.

Front 36

Dry Weight % macromolecules/cell.:
1. rRNA
2. tRNA
3. mRNA
4. DNA
5. protein

Back 36

1. rRNA = 20% (1/2 life of hours)
2. tRNA = 3% (1/2 life of hours)
3. mRNA = 2% (1/2 life of mins.)
4. DNA = 2%
5. proteins = ~50%

Front 37

RNA pols (enzymes) in
1. Eubacteria synthesis
2. Eukaryote RNA synthesis
3. Archeabacteria RNA synthesis

Back 37

1. 1 RNA polymerase Core enzyme
2. 3 RNA enzymes
3. 8-10 subunit enzymes

Front 38

1. Core RNA pol (eubacteria) consists of .....
2. Holoenzyme consists of....

Back 38

1. a2bb' core.
2. a2bb' and a sigma subunit. (several different subunits in the cell help core RNA pol specifically recognize promoters.

Front 39

Initiation:
1. binding...
2. Then,...
3. Then, 2rNTPs joined.....90%..
4. Short ____bp RNA is polymerized then ..
5. ______ is released.

Back 39

RNA pol holoenzyme binding to dsDNA at promoter; 12-18 bp are unwound. First two rNTPs are joined; approximately 90% of time, first base is purine. Short RNA is polymerized, then, after 5 or 6 nucleotides, s subunit is released from RNA pol (leaving core).

Front 40

Elongation:
6. _____ are added.
7. RNA core moves down and ....
8. Transcription rate...

Back 40

Subsequent NTPs are added to growing RNA chain. RNA pol (core) moves down DNA and unwinds another region of 12 bp DNA. Within transcription bubble, RNA/DNA heteroduplex. Transcription continues at approximately 20 nt/sec, with RNA pol, pausing occasionally

Front 41

Termination:
2 kinds:
1. Intrinsic ..formation of...rich in...stop translation on what side... termination do to what...

2. Rho ...binds to ....goes to... similar to..only at...

Back 41

1. Intrinsic terminators formation of hairpin that's rich in G-C stem loop forms on 3' side of stop translation (after stop) Formation of UUUU followed by stem destabilizes RNA-DNA duplex in transcription bubble allowing pol core to dissociate from DNA
2. Rho (rho-dependent terminators) they are proteins that bind tightly to C-rich rut site on RNA (5' to 3'translocation until it gets to RNA polymerase) and collision causes RNA/DNA heteroduplex falls apart, and RNA pol falls off DNA. Rho protein hexamer similar to DNA helicase.. only at transcriptional pause site.

Front 42

4 critical elements of promoters:

Back 42

* -35 seqeuence
* -10 sequence (also called Pribnow box)
* spacing between -35 (6bp seq.) and -10 (6bpseq) sequence
* RNA start site is +1

Front 43

DNA polymerase vs
RNA polymerase

vs Linear chromosomes

Back 43

In contrast to DNA polymerase that needs a primer for the 3' -OH, RNA polymerase can take two ribonucleotidetriphosphates and join those two together, making the first phosphodiester bond in an RNA molecule.

Linear Bacteria: Tyrosine rsidue provides -OH group for polymerase... also common for plasmids and bacteria phage with linear... Some bacteria have internal origins and hairpin loops on ends of telomeres.

Front 44

Linear or Circular?
One or two?
1. E.coli
2. Rhodobacter sphaeroides
3. Deinococcus radiodurans
4. Borrellia burgdorferi
5. A tumefaciens

Back 44

1. E.coli, circular, one.
2. R.sphaeroides (photosynthetic), circular, two.
3. D.radiodurans (resistant to gamma radiation), circular, two in multiple copies..in case one gets zapped.
4. B.burgdorferi (Lyme disease), linear, One, up to 25 small linear and circular plasmids.
6. A.tumefaciens (plant pathogen), circular and linear, one and one.

Front 45

Factor, Cellular use, spacing.
1. Sigma 70
2. Sigma 28
3. Sigma 54

Back 45

1. o70, normal use, 16-18bp
2. o28, Motility(flagellar) Chemotaxis use, 16-17bp.
3. o54, Nitrogen Regulation, 6bp.

Front 46

Sequence elements of bacterial promoters related to gene expression... Lower/Higher...

Back 46

Genes or operons that need to be expressed at lower levels will be more likely to have changes at some of these important regions. TT--C- in 35 and TA---T in 10. rRNA promoters with strong promoter sequence can easily vary the efficiency of a promoter by 100fold.

Front 47

Characteristics of tRNAs
...size?
...regions?
...aa attaches to?

Back 47

range in size from 73-93 nucleotides long, with substantial duplex regions and elaborate structure Contain anticodon loops with specific sequence that will base-pair with the codons on mRNA. 3' end is the site where the appropriate amino acid will be attached.

Front 48

What makes mRNA easier to degrade by nucleases and what are the advantages to having short life?

Back 48

Linear format makes it easier to degrade mRNA (vs rRNA with covalent bonds and lots of base pairing interactions) Short 1/2 life makes cell very nimble and adept at responding to different environmental conditions by changing the profile of genes that are translated to proteins.

Front 49

Stop codons are: (3)
.. are not recognized by?
... some cases, the third base is?

Back 49

UGA, UAA, UAG are stop (or nonsense) codons and are not recognized by any tRNAs. In some cases the third codon does not participate in precise base-pairing interactions with the anticodon called wobble base pairing.

Front 50

Peptide bond formation is catalized by what? Inbetween the __ site and the __ site.

Back 50

Peptide bond formation is catalyzed by the 23s rRNA unit in the 50s ribosome inbetween the P site (where the aa's COOH is open and vunerable to the incoming) A site tRNA with an aa attached to the 3' site of tRNA strand where the NH3 is oriented toward the other aa's COOH.

Front 51

Translation; Elongation and Termination:
1. The ribosome translocates ___ codon at a time down the mRNA in the _____ direction.
2. Translation stops at the ____ where there is an empty A site and
3. ______ ______ bind to the A site of the ribosome.
4. The bond between the _____ and the _____ cleave.
5. The _____ disassociates into _____.

Back 51

The ribosome translocates 1 codon at a time down the mRNA molecule (proceeding from the 5' towards the 3' end of the mRNA). Translation continues until the ribosome reaches a stop codon. The polypeptide chain is attached to the tRNA in the ribosome's P site. Release factors bind to the A site of the ribosome, allowing the bond between the polypeptide chain and the tRNA to be cleave. The polypeptide and the tRNA are released from the ribosome. The 70S ribosome disassociates into the 50S and the 30S subunits.

Front 52

Initiation of Translation:
Depends on ____ binding initiation factors and ______ .
First, the ____ identifies the appropriate start codon, usually _____ with a ____ ____ sequence complementary to the 3' end of the ________. Then the tRNA and _______ binds the mRNA.
Finally, the _____ binds to the _____ and translation con proceed once a charged _____ binds to the _____ site.

Back 52

Initiation depends on the 30S ribosomal subunit binding initiation factors and tRNA-f-Met. This complex then binds the mRNA, forming the 30S preinitiation complex. This preinitiation complex identifies the appropriate start codon--usually an AUG codon with a Shine Dalgarno sequence complementary to the 3' end of the 16S rRNA. Finally, the 50S ribosomal subunit binds to the 30S subunit, and translation can proceed once a charged tRNA binds to the A site of the ribosome.

Front 53

Characteristics of tRNAs
1. Each ___ coded by a diff ___.
2. All with same 3' sequence ____ where _____ attaches
3. Anticodon loop bpairs with _____.

Back 53

1. Each different tRNA coded by a different gene.
2. All with same 3' sequence (CCA) where aa attaches (3' OH covalently attached)
3. Anticodon loop will bp with mRNA.

Front 54

"Charging" of tRNA
....tRNA synthetase is?
...first step is?
... secondly?
which makes it ...?

Back 54

..Enzyme that attaches correct amino acid with an appropriate tRNA
...First step a ATP is covalently attached to aa at COOH by tRNA synthetase.. ATP--> AMP.
...Secondly, this makes oyxgen very reactive and the tRNA synthetase transfers the aa from AMP to 3' OH end of tRNA.
... this Activating of COOH for aa peptide bond formation makes it "charged"

Front 55

Leu is most common aa in protein because...

Back 55

Leucine has 6 diff tRNA codon codes:
UUA, UUG, CUG, CUC, CUU ..

Front 56

In bacteria, what charged tRNA always binds first?

Back 56

the f-Met tRNA because AUG is the "start" codon indicator for the 50s subunit to join the 30s ribosome subunit and it locates f-Met in the P site... GUG or CUG are occationally the "start" sites, but there are special dedicated tRNA's that associate with f-Met.

Front 57

GTP hydrolysis allows for?

Back 57

Allows translocation of ribosome along mRNA 5' --> 3'

Front 58

Translation initiation Part 1
1.
2.
3.

Back 58

1. 30s acts alone with IFI and IF III to bind mRNA and finds start site AUG using 16s rRNA.
2. f-Met and RNA complex bind
3. The 50s Binds to initiation complex to make the 70s ribosome initiation complex.

Front 59

Shine-Dalgarno variability

Back 59

Variety of purine rich sequences often 5-10 bp tothe 5' side of start codon act as RBS

Front 60

Site of action for: Streptomycin

Back 60

Inhibits translation initiation at 30s complex

Front 61

Site of action for: Chloramphenicol

Back 61

Inhibits translation elongation.

Front 62

Site of action for: Tetracycline

Back 62

Prevents aa-tRNA binding

Front 63

Site of action for: Rifamycin

Back 63

Inhibits RNA polymerase - affects a2BB' transcription

Front 64

Site of action for: Ampicillin

Back 64

Inhibits cell wall synthesis

Front 65

Site of action for: Novobiocin or Nalidixic Acid

Back 65

Gyrase, Topoisomerase

Front 66

A molecular chaperone is what?1
Interacts with what? 2
Prevents and enables what? 3
20% of what end up where? 5

Back 66

1.A protein for proper folding or for assembly into larger complexes.
2. Interacts with a newly synthesized (nascent) polypeptide (N-terminus) before it folds or with an improperly folded or unfolded protein (often caused by environmental stress like heat shock)
3. Prevents aggregation of proteins and enables efficient aquisition of proper folded conformation.
4. Chaperones often hydrolyze ATP during folding
5. 20% of all polypeptides ultimately localized outside the cytoplasm

Front 67

Cytoplasmic membrane proteins have what characteristics that are how long?

Back 67

Polypeptides with stretches of ~20 hydrophobic amino acids.. that fold into a-helices long enough to span the cytoplasmic memb lipid bilayer.

Front 68

Signal Sequences are what and do what?1 What are the characteristic arrangements? 2
Is removed how? 3

Back 68

1. Are preprotein regions of a translated protein that are destined for lfinal localization outside the cell (or pplasm.memb. gram-) recognized by export machinery.
2. Proteins destined to cross the cytoplasmic
membrane for final localization outside the
cell (or in the periplasm/outer membrane of
Gram neg. bacteria) have an N-terminal
• N-terminal domain, 18-25 aa’s 8nm(longer in G+)
• First, region of 3-8 residues with 1-3 (+)aa (Lys,Arg)
• Next, hydrophobic core of 15-18 aa’s
3. SS cleavage site C-terminal to hydrophobic
core (after Gly/Ala; sometimes more “polar”) by LepA, Leader peptidase.

Front 69

Name the key translocase apparatus from lecture. 1
What does it do? 2
What are it's core components? 3

Back 69

1. Sec apparatus and post-translational export.
2. Sec A sees SS precursor binds to it and stops it from folding, Sec B also associates and Sec A is drawn to Sec EYG pore where Sec A cleaves ATP and pulls the unfolded protein through. LepA cleaves the ss at the (+)Gly or Ala site after the Hydrophobic core.
3. SecA SecEY and Lep

Front 70

Transmembrane hydrophobic aa's have what sort of folding? 1
Why is it important for hydrophobicity and a helices?

Back 70

Hydrophobic aa's enriched in transmembrane a-helices but domains on either side of membrane with "normal" distribution of aa's It's important that there isn't any requirement for H bonding between the polypeptide chain and hydrophobic membrane.

Front 71

Cytoplasmic destined proteins vs proteins destined for translocation (3).

Back 71

Cytoplasmic destined proteins don't have ss and tend to fold very quickly with or without chaperone so there's no mistaking it with one bound for memb. Proteins destined for transport outside tend to remain unfolded because 1. they're being antagonized by chaperones. 2. Some SS actively prevent folding and 3. Cell slows synthesis to prevent folding/allow chaperones to recognize.

Front 72

SRP in Bacteria 1
SRP in Eukaryotes 2

Back 72

1. Signal Recognition particle composed of both RNA and proteins, is the site of co-translation.. it can associate with some bacterial proteins and transport to cytoplasmic membrane. 2. Is a major protein secretion apparatus in Eukaryotes since they don't have SecA and secretion apparatus is located on ENDOPLASMIC RETICULUM.

Front 73

Archaea protein export apparatus

Back 73

Similar to Bacterial Sec like SecYEB, but no SecA.

Front 74

What are the two classes of mutations?

Back 74

Microlesions = one or a few bases changed for another new base (point mut.)
Macrolesions = Addition or deletion of hundreds and thousands of bases

Front 75

Spontaneous Mutation #1
Tautomeric shifts

Back 75

All core bases f DNA exist in 2 isomer forms. Amino and keto vs. imino and enol. Results in redistribution of electrons and mismached basepair.

Front 76

Spontaneous Mutation #2
Deamination of Cytosine

Back 76

Cyosine is deaminated and becomes Uracil. If this happens, then it's a point mutation.

Front 77

Spontaneous Mutation #3
Slippage and frameshift errors:

Back 77

Loop out of bases on template strand results in addition of a single base or more. Loop out of bases in the sense strand results in deletion.

Front 78

Spontaneous Mutation #4
Recombination, 4 types:

Back 78

1. Site specific
2. Replicative Recomb.
3. Homologous recomb (legitimate)
2. Non-homologous recomb (legitimate)

Front 79

Homologous Recomb.
Legitimate. 2 things you need.

Back 79

Have to have certain degree of homology, Have to have RecA. Endonuclease (RecBCD) nicks DNA and Rec A recombines.

Front 80

Non-homologous Recomb.
Illegitimate. (spontaneous)

Back 80

Recombination between dissimilar genes, Do not have to have RecA.
Results in Deletion of genes or duplication of genes... and can either have DNA looping on itself or linear.

Front 81

Mutagens: 3 types

Back 81

Are not specific to a gene or group of genes.
Increase frequency of mutations.
1. Chemical - Modifying agents, -Base analogs, - Intercalating agents.
2. Radiation - Ionizing and Non-Ionizing light
3. biological (Transposable genetic elements) IS and Tn.

Front 82

Wavelengths of Radiation can create....

Back 82

Thymine dimers

Front 83

Transposable Genetic Elements IS and Tn

Back 83

(IS) Insertion Sequences ~800-2000bp insert inverted repeats at both ends and gene coding for transposase.
(Tn) Transposons are larger than 2000bp+ and can insert genes along with transposase.... Transposon only takes place once/cell.

Front 84

Mechanisms of DNA repair:
Six examples

Back 84

1. Proof-reading of DNA polymerase I and III
2. Light, Photoreactivation, Repair
3. Excision Repair
a. Damaged Base or Wrong Base Repair
b. Nucleotide Excision Repair (Dark Repair)
4. Recombination Repair
5. Methyl Directed Mismatched 6. Base Repair
SOS Repair

Front 85

Light (Photoreactivation) Repair. Uses what enzyme that does what?

Back 85

Uses photolyase..Enzyme scans DNA associates with thymine dimers requires visible light for activity and breaks two bonds and strands assume original shape. (only repairs pyrimadine)

Front 86

Glycosylases.. DNA repair. What are two examples and what are the methods?

Back 86

O6-methylguanine transferase is a glycosylase that removes methyl groups from G and transfers it to itself and then it dies.
Example 2. Uracil-DNA glycosylase goes to identify mismatched base, AP endonuclease introduces nick and DNA pol 1 and ligase finish job.

Front 87

What does Dark Repair do?

Back 87

Uvr ABC protein Complex scans DNA look for Damage repair thymine dimer helicase displaces SS molecule.

Front 88

What is Post replication Repair?

Back 88

RecA sees gap that polymerase jumped over (thymine dimer) and goes to other ds DNA that is homologous, cuts one piece exchanges undamaged segment with damaged one... DNA pol 1 and ligase finish job.

Front 89

What does Methyl directed mismatch repair system do? What does MutS,H and C do?

Back 89

With a mismatched base pair, the mutS will scan DNA looking for mismatching, the mutH will then scan around DNA wher mutS is looking for CH3, mutL will associate with mutS and mutH using ATP to introduce nick in complementay strand.. exonuclease chews up strand past mistake and DNA pol1 and ligase finish job.

Front 90

SOS repair...How?
What are the roles of LexA, RecA, UvrA, and UmuD?

Back 90

LexA represses SOS repair. When RecA protease inactivates LexA, that allows for expression of uvrA,B and C to repair error free and then umuD that encode for DNA pol IV and V with no proofreading ability.

Front 91

What is an Auxotrophic mutant? -

Back 91

A cell that has an added growth requirement as a result of a mutation that parent cell did not have... Like a mutant that no longer has the ability to synthesize Histadine.

Front 92

Flagellar movement when swimming?
When Tumbling?

Back 92

Swimming = counterclockwise Flagellar
Tumbling = clockwise flagellar.

Front 93

3 different classes of chemoreceptors

Back 93

Periplasmic, Methyl Accepting and Enzyme II

Front 94

4 Components of a sensory system?

Back 94

• Stimulus (i.e., chemoeffector molecule).
• System to detect chemoeffector (chemoreceptor).
• System to process signal (which must include a way to
measure and compare present with the past environment).
• Production of an appropriate output response, either a CW
(cell tumbles) or CCW (cell swims) rotation of the
flagellum(a).

Front 95

Four classes of MCP's: What do they identify and how many copies etc?
1. MCP 1
2. MCP II
3. MCP III
4. Tap gene
Each of these proteins will have what in the absence of any chemoeffector?

Back 95

Methyl Accepting Proteins (Transducer Proteins)
• MCP 1 (Tsr gene product)- serine plus certain repellents (weak
acids/indole/leucine); 2000 copies/cell, 6 methylation
sites/molecule.
• MCP II (Tar gene product)- maltose/aspartate, repellents Co+2
and Ni+2, ~1000 copies/cell, 4 methylation sites/molecule.
• MCP III (Trg gene encoded)- ribose/galactose, 100-200
copies/cell, ~5 methylation sites/molecule.
• Tap gene- In E. coli used to detect dipeptides.
Each of these proteins will have an inherent level of methylation in the absence of any chemoeffector.

Front 96

1. Transient component associated with MCP II
2. Temporal component associated with MCP II

Back 96

1. The amount of chemoeffector-binding protein
associated with MCP II is a measure of the cells present environment.
2. The level of methylation
of MCP II is a measure of the cells past environment.

Front 97

Maltose binding protein:
1. What is it's function?
2. What does it indicate?

Back 97

1. MBP is an allosteric protein non covalent association that undergoes a conformational change when associated with maltose, It delivers maltose to transporters and MCPII.

Front 98

CheW, what is it's role in chemotaxis?

Back 98

CheW senses maltose MCPII has had a conformational change because certain glutamic acid residues are exposed and it signals to the Processing unit that sends signal to flagella to decrease frequency of tumbling.

Front 99

Three types of chemoreceptors:

Back 99

1. Periplasmic binding protein
2. Methyl accepting membrane
proteins (MCP’s)
3. Enzyme II of the PTS
-no methylation involved
-transport required to elicit chemotatic response
-unphosphorylated form of enzyme 1 of PTS system inhibits autophosphorylation of CheA

Front 100

Signal processing in
Chemotaxis MCPII...
1. What happens with repellents? Frequency of what does what? Methylation does what?
2. What are the steps?

Back 100

1. When a repellant is sensed by chemoreceptor and CheW acknowledges that a repellent is present, Frequency of tumbling goes UP because more phospho-cheY to bind to FliM and level of metylation goes down.
2. CheWtells CheA to phosphorulate itself (expense of ATP), Phosphate group of CheA is used to phosphorulate CheY, PhosphoCheY binds to a protein at the base of flagellum called FliM that is the switch that says to turn in clockwise direction.

Front 101

Signal processing in Chemotaxis MCPII...
1. What happens with attractants? Frequency of what does what? Methylation does what?
2. What are the steps?

Back 101

1. Frequency of tumbling goes down and level of methylation goes UP (because there's no CheB to take off methyl groups that CheR and SAM are adding)
2. When there is an attractant, there is not as many CheW telling CheA to phosphorulate.. so less phospho-CheA means less phospho-CheY and less phospho-CheB groups to remove methyl groups added to MCPII by CheR the methyl transferase that methylates using donor from SAM.