Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

BIOL-M 250 > Exam 4 > Flashcards

Exam 4 Flashcards

(118 cards)

Start Studying
1
Q

How are large deletions repaired

A

Bring in fresh copy of genetic sequence with all missing info
Recombination and gene replacement
DNA comes from external source and once its inside it can be either destroyed by restriction (defense) or recombined into chromosome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What is recombination

A

If incoming DNA strand is similar to chromosome, it may replace old sequence. Sequence must base pair over some of their length for replacement

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What protein facilitates homologous recombination

A

RecA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Vertical Transfer

A

Requires Cell division

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Horizontal transfer

A

requires 2 cells

`

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What is Transformation

A

Uptake of free DNA directly from the environment (“com” machinery)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What are the proteins involved with transformation?

A

com machinery

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What are the steps of transformation?

A

1) dsDNA binding
2) digested to single strand
3) single strand uptake by com system
4) recombination

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What are the possible benefits of transformation?

A

1) sample genetic environment for beneficial genes
2) repair damaged DNA gene sequences
3) eating DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is conjugation

A

cell interaction facilitated by sex pilus

Donor cells have fertility factor (F Factor)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is the F Factor

A

plasmid encoded with sex pilus, tra machinery (for DNA transfer) and independent origin of replication (oriT)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What are the steps involved with conjugation

A

1) pilus extends
2) recognizes and binds to a receptor on surface of recipient
3) pilus retracts to bring cells into contact
4) plasmid replication begins at oriT via rolling circle mechanism and transferred through Tra machinery
5) recipient gains copy of F factor plasmid and can now be a donor for other bacteria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is the type of replication required for plamids

A

Rolling circle: one replication complex, unidirectional migration, synthesizes continuous strand, makes many copies, indefinite

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is transduction

A

phage accidentally packages bacterial chromosomal DNA and transfers DNA to another bacterium

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What are the two types of transduction

A

Generalized: mispackaged bacterial DNA can come from any location on the bacterial chromosome

Specialized: mispackaged DNA can only come from part of bacterial chromosome adjacent to prophage integration site (att site)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What are bacteriophages

A

tiny viruses that infect bacteria
phages use host to make copies of themselves
Lack ribosomes and cannot make their own energy
Parasites

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

How does generalized transduction occur

A

Phage mispackages random fragment of bacterial DNA instead of phage DNa

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What is lysogeny

A

Phage DNA is stably integrated into host chromosome and remains dormant as a prophage

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

How does specialized transduction occur

A

phage will package adjacent bacterial DNa in all particles from that cell
only genes near the att site

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

OOTW: Agrobacterium tumefaciens

A

Plant pathogen
creates tumors (galls)
transfers Ti plasmid to plant by conjugation
Ti plasmid directs production of 1) growth hormone 2) octopine synthesis
genetic engineering of plants

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Is blocking attachment similar to innate or adaptive immunity

A

Innate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

How do bacteria block phage attachment?

A

Capsules/slime layers: blocks phage from attaching by masking phage receptors

Phase variation: altering protein expression to evade immune system

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Is blocking DNA entry innate or adaptive

A

innate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What is a mechanism for blocking DNA entry

A

Phage exclusion: prophages block similar related phages from infecting DNA into same cells

Superinfection immunity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
What is a prophage
when a phage gets integrated into the DNA of the host
26
Is replication modification innate or adaptive
innate
27
What are restriction enzymes
Recognize patterns of dsDNA and cut incoming DNA into pieces Defense agains foreign DNA
28
How is the bacterial chromosome protected from restriction enzymes
DNA methyltransferase methylates old strand so it can be identified
29
Is abortive infection similar to innate or adaptive
innate
30
How does abortive infection protect from phage infection
bacterial cell sacrifices itself to protect surrounding clonal bacterial cells
31
Is CRISPR-Cas adaptive or innate
adaptive
32
What does CRISPR-Cas stand for
``` Clustered Regularly Interspaced Short Palindromic Repeats ```
33
What is Cas
endonuclease that recognizes foreign DNA using spacers and cut DNA
34
What are the 3 stages for CRISPR-Cas based immunity?
Adaption crRNA biogenesis Interference
35
What is swimming
Individual movement powered by rotating flagella that takes place in liquid
36
How are Flagella organized
monotrichous: single flagella lophotrichous: multiple flagella at one pole amphitrichous: multiple flagella at both poles petritrichous: multiple flagella along cell body
37
How is flagellum built
from the inside out
38
How is a flagellum powered
PMF
39
What is swarming
surface motility, social/ group behavior, requires flagella and surfactant to reduce surface tension, cells become hyperflagellate (requires more energy and creates more flagella on their bodies)
40
How is swarming different from swimming
social group behavior | moves on surface
41
How is swarming similar to swimming
requires flagella
42
What is twitching motility
surface motility, pilus extends and attaches to surface, pilus retracts and pulls cell along, jerky movement over surfaces
43
What structure is required for twitching
type IV pilus
44
What is gliding?
requires slime/ surfactant, no visible surface structures, trail following, very slow
45
How does the cell move
Focal adhesion complexes: bind surfaces Internal helical track moves relative to adhesion complex moves like a tank
46
What is floating
gas vesicles inflate to rise, deflate to shrink
47
What structure is required to float
gas vesicles
48
OOTW: Borrelia burgdorferi
Causative agent of Lime disease, spirochete, endoflagellum, rotates cell body to push through viscous environment, requires no iron, has linear chromosome
49
What is chemotaxis
Directed movement with respect to a chemical gradient. Gradient is essential
50
How do you measure chemotaxis
Plate assay and the use of chemo attractants and repellents to observe movement and response
51
What are chemo-attractants and cheme-repellents
Chemo-attractant: migration up a chemical gradient (Food sources) Chemo-repellent: migration down a chemical gradient (toxic compounds)
52
What is random walk
only 2 behaviors: run and tumble With each new tumble a new random direction is required Statistically no net displacement
53
What is biased random walk
directed movement with respect to chemical gradient tumbles discouraged as long as concentration of attractant increases increasing attractants indirectly favors runs Direction still completely random
54
How do bacteria sense a chemical gradient
TIME not space. They sample the enviroment every 4 seconds
55
What is adaption with respect to chemotaxis
Inhibition of behavioral response in presence of constant stimulus essential for all sensory systems
56
What proteins are involved in sensing and signaling to the flagella? How?
CheA phosphorylates CheY response regulator Ground state: MCP partially inhibits CheA so that CheY is partially phosphorylated Excitation: MCP fully inhibits CheA to make cell run. CheY is unphosphorylated
57
What is a chemoreceptor and where are they located
located on the skin and help mediate movement and direction
58
what are the 3 stages of biofilm development
attachment, growth and detachment
59
how is the switch between motility and biofilm formation modulated
cyclic-di-GMP 2GTP get converted to c-di-GMP and then suppress motility and express EPS (biofilm) development GGDEF makes c-di-GMP
60
What is the role of EPS in biofilm formation
helps stick ells to each other and other surfaces
61
How do bacteria control gene expression in biofilms
different levels of biofilm express different genes
62
What are the advantages of biofilms
1) concentrate digestive enzymes. Many bacteria eating as one 2) Persist in favorable environment: prevent cells from being flushed out of environment 3) Aids collaborative metabolism between different species 4) EPS provides for chemical diffusion barrier to antibiotics and engulfment defense 5) maintains high cell density to facilitate a variety of processes; quorum sensing
63
Some examples of good biofilms
rhizosphere (growth on plant roots) cyanobacterial mats/blooms ("pond scum") marine snow normal body flora
64
Some examples of bad biofilms
``` "bathtub scum" on the hulls of ships biocorrosion plaque and dental carries contaminate medical supplies virulence and pathogenesi ```
65
OOTW: Myxococcus xanthus
``` mistaken for eukaryote due to complex multicellular behavior gliding motility: mobile biofilm only eats AA predator of other bacteria multicellular fruiting bodies sporulation makes antibodies and anti-cancer drugs ```
66
Why were biofilms only recently discovered
we selected against biofilm production in lab strains | Domestication
67
What is the role of autoinducers in quorum sensing
extracellular signaling molecule that cells can directly sense and group
68
How are autoinducers synthesized
LuxI => autoinducer synthase (enzyme)
69
How are autoinducers detected by LuxR proteins
high concentrations of autoinducer | LuxR binding site
70
What role does quorum sensing play in vibrio fischeri
Regulates luciferase production
71
How does quorum sensing control gene expression with regard to population density
at critical cell density the concentration of autoinducer reaches threshold to activate gene expression
72
Compare and contrast intraspecies and interspecies autoinducers
Inter: between cell species Intra: within cell species LitR activates LuxR
73
What is the interspecies autoinducer? Why is this unique?
AI-2 | passive diffusion
74
What are the two signaling systems used by vibrio fisheri
LuxPQ LuxO
75
OOTW: Vibrio Cholerae
Causes cholerae 7 historic pandemics Lives in brackish water mode of infection: ingestion of contaminated water Life cycle: pathogenic at low population densities Form biofilm after binding and growing then release and resume motility cycle continues
76
What is pathogenesis
nutritional strategy to take nutrients away from other cells
77
Compare and contrast mutualism, commensalism and parasitism
mutualism: both partners benefit commensalism: one benefits, one is unharmed parasitism: one benefits, one is unharmed
78
Colonization
persistence of a microbe in a specific site within the host body
79
infection
colonization of host body by pathogen
80
pathogen
mircoorganism or agent able to cause disease
81
Disease
defect in body function caused by infection
82
Pathogenicity or virulence
ability to cause disease
83
Virulence factors
bacterial products that contribute to pathogenicity
84
What are Koch's postulates
1) Isolate organism from infected individual 2) culture in lab 3) re-infect new individual and reproduce disease 4) re-isolate organism
85
Problems with Koch's postulates
not all infectious diseases are culturable not all agents can be deliberately re-introduced into host not all hosts react the same way to an agent Not all diseases are caused by only one organism
86
How do we measure pathogenicty
ID50 and LD50
87
ID50
number of bacteria that results in infections in 50% of hosts
88
LD50
number of bacteria that results in leathality in 50% of hosts
89
What are the human defenses against pathogens
Dry environment: resistant to infection (skin, lungs, stomach) Flushing: tears, mucus, urine Enzyme: lysosyme in tears destroys peptidoglycan and saliva and stomach acid have suites of digestive enzymes Native Microbial Flora: harmless bacteria cover outside surfaces Iron sequestration: body starves invaders of iron Macrophages: WBC that protects body Antibodies: proteins made by immune system that bind to antigens
90
Virulence Factors: Motility
aids in migration to target tissues
91
Virulence Factors: Adhesion, Pili
attachment at site of infection, resists flushing
92
Virulence Factors: Capsules
Also attach at site of infection, resist flushing and also protect from H2O2, block engulfment by macrophages, shield surface antigens from antibodies and form biofilms
93
Virulence Factors: Siderophores
switch between versions of antigens
94
Exotoxins
secreted enzymes that disrupt host cell structure or processes
95
hemolysins
protein secreted by bacteria that creates holes in host cell membranes. Host cells burst
96
phospholipases
lest bacteria escape from endolytic vesicle and breaks phospholipid bilayer
97
Proteases
degrades antibodies and prevents them from targeting bacteria
98
A/B toxins
Self injecting secreted toxin complex A= toxin B=Delivery vesicle
99
Endotoxins
structures released from dead bacteria that hyperstimulate immune system
100
OOTW: Streptococcus pneumonia
infects the lungs makes com machinery antigenic variation: 90 different capsules to evade immune system mimicry: some capsules look like host cell sugars
101
OOTW: Yersinia pestis
causes bubonic plague carried bn rodents and people by fleas wide variety of virulence factors encoded on plasmids (pMT1: encodes pili, pPCP1: encodes proteases, pCD1: encodes toxins and type 3 secretion machine) Injects toxins directly
102
What did the Avery and Griffith experiments demonstrate
capsule genes (virulent) transferred to avirulent strain during co-infection by natural competence (transformation)
103
Penicillin
Fungus, inhibited the growth of a bacterium | antibiotic dose decreases as it gets farther away
104
Static
suspend growth while antibiotic is present
105
cidal
actually kill bacteria
106
assay
lawn of bacteria
107
What is Minimal inhibitory concentration (MIC)
lowest concentration of antibiotic required to inhibit an organism different fore each combination of antibiotic and organism less antibiotic does not kill less, just less needed to kill
108
What are ideal (general) targets for antibiotics
Target systems bacteria require to grow Target pathways humans do not use Target enzymes for which humans have similar but substantially different variation Complex multistep processes provide many targets
109
OOTW: Streptomyces coelicolor
``` mistaken for eukaryotic fungus linear chromosome hyphal growth, cell division is rare multiple chromosomes per cell developmental cycle, sporulation, polyketide antibiotics (produces naturally) ```
110
Examples of antibiotics produced by streptomyces coelicolor
erythromycin globomycin vancomycin
111
Where does antibiotic resistance come from
Bacteria make antibiotics to kill other bacteria antibiotic produces contain genes that encode resistance to their own antibodies Antibiotic resistance genes get passed to other bacteria by genetic transfer mechanisms Resistance genes often found on plasmids
112
What antibiotic resistance strategies exist
Exclusion: a) prevent antibiotic from entering, passive b) actively pump; antibiotic out. transporter genes Inactivation: a) enzymatically destroy antibiotic. enzyme genes b) enzymatically modify antibiotic Immunity: modify cellular target. spontaneous mutations in target
113
How do we prevent resistance
Make new antibiotics only take antibiotics for bacterial infections when sick take your full prescription of antibiotics Take a combination of antibiotics stop using antibiotics on farm animals hiatus on particular antibiotics
114
DNA polymerase III proofreading
DNAPIII backs up one base and excises the mismatch and then proceeds with replication
115
Which proteins are involved in methyl-directed mismatch repair, how do they function?
MutS: recognizes and binds to DNA distortion MutL: "Linker protein" recruits MutH to MutS MutH: endonuclease, nicks DNA near damaged base DNAPI: repair polymerase Damaged DNA is excised and repair DNAP1 loads and fills the gap
116
How does the cell know which base is the right and the wrong one to get rid of
older, original DNA strand is modified by methylation and newer strand lacks methyl groups
117
What protiens are involved in SOS repair
RecA: binds to damaged base and becomes activated RecA* LexA: transcriptional repressor DNA binding protein that inhibits SOS genes (RecA* causes cleavage of LexA and expresses SOS genes)
118
What genes are under SOS control? how do they function?
SulA: inhibitor of FtsZ (blocks Zring formation undil DNA damage has been resolved) UvrABC: DNA excision repair (detects chemically damaged base) Pol IV: error prone polymerase (fills in gap)

BIOL-M 250 (11 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions