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Microbiology > FINAL EXAM FLASHCARDS / NEW MATERIAL > Flashcards

FINAL EXAM FLASHCARDS / NEW MATERIAL

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1
Q

Regulating ___________ is another level of transcription regulation.

A

Enzyme synthesis

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2
Q

DNA binding proteins are __________, meaning that the two protein subunits are both the same

A

Homodimeric

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3
Q

_________________ is the most common conformation for DNA binding proteins.

A

Helix-turn-helix

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4
Q

What are the three specific domains for a homodimeric DNA binding protein

A
  1. Helix - turn - helix
  2. Zinc Finger
  3. Leucine Zipper
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5
Q

In the Helix-turn-helix:

1st Helix =
Turn =
2nd Helix =

A

1st Helix = Recognition alpha helix
Turn = 3 amino acids, 1st usually Glycine
2nd Helix = stabilizing helix

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6
Q

The Zinc finger has an alpha helix that binds a ____________ at the end

A

Zinc

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7
Q

Leucine Zipper has leucine residues within the alpha helices that allow ___________, so they can fit tightly like a zipper

A

Intertwining

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8
Q

DNA Binding proteins look for _______________, which are several bases in order, duplicated and opposite. These are found in _____________ areas.

A

Inverted repeats

Major groove

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9
Q

DNA binding proteins can act in a ___________ or ___________ fashion

A

Activator

Repressor

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10
Q

Repression is an _____________ reaction

A

Anabolic

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11
Q

Activation is a ____________ reaction

A

Catabolic

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12
Q

In (Repression / Activation), If the end product is present, the end product will repress the synthesis of enzymes needed to make it

A

Repression

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13
Q

In (Repression / Activation), Enzymes will only be made if their substrate is present, This is usually for something in the environment that we need to break down into usable parts.

A

Activation

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14
Q

Repression is a ___________ control of transcription. A _________ is typically our end product, which binds to the DNA binding protein allosterically. As the end product builds up, it interacts with DNA binding protein = conformational change = allows DNA binding protein to interact with DNA. It then binds to the __________, downstream of the _____________

A

Negative control

Effector protein (co-repressor)

Operator

Promoter

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15
Q

When DNA binding protein acts as an activator, it is considered ___________ control

A

Positive

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16
Q

In positive control by the activator, it is ___________ the initiation of transcription

A

Promoting

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17
Q

Instead of an operator like in negative control, a _____________ is used in positive control, ___________ of the promoter. Also note, the promoter is very __________.

A

Activator binding site

Upstream

Weak

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18
Q

What helps RNA polymerase find the promoter region in positive control of transcription? What are the two ways this can work?

A

Activator protein

  1. Activator binding may alter DNA, to help promoter sequence get recognized
  2. Activator may interact with RNA polymerase to pull it in
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19
Q

Maltose example (positive control): In the (Presence/Absence) of maltose, the ____________ pulls in maltose activator proteins, helping RNA polymerase to attach thus allowing Transcription

A

Presence

Activator binding site

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20
Q

Negative control

  1. What is involved
    1A: Upstream or downstream of promoter
    1B: Location of binding
  2. What does it use
  3. What are the two methods
A
  1. Repressor
    1A: Downstream of promoter
    1B: Binds to operator site

2: Uses Effector / Inducer

3A: Repression (Anabolic) —> Put a Repressor on the operator
3B: Induction (Catabolic) —> Remove the Repressor from the operator

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21
Q

Positive Control of transcription

1A: What is involved
1B: Upstream or downstream of promoter
1C: What site does it interact with?

2: Strength of promoter

  1. What are the two methods
A

1A: Activator proteins
1B: Upstream
1C: Activator binding site

2: Weak promoter

3A: Activator biding may alter DNA to help promoter get recognized
3B: Activator may pull RNA polymerase in

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22
Q

An ___________ is a cluster of genes whose expression is under the control of a single operator.

A

Operon

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23
Q

When more than one operon is under the control of a single regulatory protein, these operons are called a __________

A

Regulon

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24
Q

_____________ is the preferred sugar molecule. We always want to use this first, which is done through the Global regulatory mechanisms called __________________

A

Glucose

Catabolite repression

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25
Q

Catabolite repression is _________ control, using ____________ as an activator protein. ____________ is a common regulatory nucleotide. The effector here is ___________, which control the activator.

A
  • Positive control
  • Cyclic AMP receptor protein (CAP)
  • AMP
  • Cyclic AMP
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26
Q

If glucose is present

(INHIBIT / NO INHIBITION) of _____________ = (PRODUCES / NO PRODUCTION) of _____________. This Stimulates the transport of ___________ out of the cell, causing low levels of _____________.

No cAMP = No binding of the __________= No binding of ____________ = No transcription

A

Inhibition of adenylate cyclase

Produces cyclic AMP

Transport of Cyclic AMP out of the cell

Low levels of cAMP

No cAMP = No binding of the CAP site = no binding of RNA polymerase = No transcription

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27
Q

If glucose is absent = (INHIBITION / NO INHIBITION) on adenylate cyclase

______________ stays inside the cell, binds to ____________, which binds the ____________, and ____________ binds leading to transcription.

A

No inhibition on adenylate cyclase

cAMP stays inside the cell

Binds to CAP

Binds to Activator Protein

Binds RNA Polymerase = Transcription

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28
Q

Glucose and Lactose present = lactose Repressor is BLANK

Glucose w/o lactose present = lactose Repressor is BLANK

A

Present = ON

Absent = OFF

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29
Q

Catabolite repression leads to _________ growth

A

Diauxic Growth

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30
Q

In a closed system, eventually bacteria will exhaust all of the glucose within. Once gone, they switch over to Lactose. We the observe two exponential growth phases. __________ has the steepest exponential growth (most preferred), while __________ will have a slight lag period, then exponential growth but not as steep. WHY is there a lag? What is this growth known as?

A

GLUCOSE

LACTOSE

The lag occurs as we shut down glucose genes and turn on the lactose genes

Diauxic growth

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31
Q

BLANK is a system that links events occurring outside the cell to the regulation of gene expression inside

A

Two Component Regulatory System

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32
Q

What are the two important players in the Two Component Regulatory System

A
  1. Sensor Kinase Protein
  2. Response Regulatory Protein
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33
Q

_________________ is integral within the cell membrane, to interact with the external environment. It will undergo __________ upon recognition of environmental cues. Phosphorylation will occur at the _____________. This response is then later passed onto the ____________.

A

Sensor Kinase Protein

Autophosphorylation

Histidine Residue

Response regulatory protein

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34
Q

Kinases ____________ proteins

A

Phosphorylate

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35
Q

What are some common Kinases we see as sensor kinase proteins

A

Serine-Threonine kinases

Tyrosine Kinases

Histidine Kinases

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36
Q

The response regulatory protein is located in the ____________ and considered a ___________. Binding is initiated by the transfer of a ___________ from a ___________.

A

Cytoplasm

DNA binding protein

Phosphate from a Sensor Kinase Protein

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37
Q

TWO COMPONENT REGULATORY SYSTEM: ___________ is the feedback loop that resets the system, removing a phosphate from _____________ at a constant rate to allow the system to keep going on.

A

Phosphatase

Response regulatory protein

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38
Q

__________ is used at high osmotic pressures

___________ is used at low osmotic pressures

A

OmpC = high

OmpF = low

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39
Q

How do genomes change?

A

Mutations

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40
Q

An inherited change in the nucleotide base sequence of the genome. The driving force of evolution.

A

Mutation

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41
Q

Why are mutations rare?

A

Repair mechanisms

Cells try to prevent mutations

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42
Q

Mutations are seen more readily in prokaryotes than eukaryotes, why?

A
  • No backup copy of gene (haploid)
  • Much faster / more replication
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43
Q

_________ is a strain of bacteria carrying a mutation where the genotype will differ, but the phenotype may or may not.

A

Mutant strain

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44
Q

What are the two types of mutations ?

A

Point mutations

Frameshift mutations

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45
Q

What are the 3 types of Point mutations ?

A
  1. Silent mutation (different sequences but same AA, usually change third base)
  2. Nonsense mutation (Add in stop codon, incomplete protein)
  3. Missense mutation (creates a different amino acid, allow for evolution)
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46
Q

__________ mutations occur when base pairs are deleted or inserted. This alerts the reading frame.

A

Frameshift mutations

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47
Q

Different sequences but creates the same AA.

A

Silent mutation

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48
Q

Adds in a stop codon, creating an incomplete protein

A

Nonsense mutation

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49
Q

Creates a a different amino acid, causative for evolution

A

Missense mutation

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50
Q

BLANK : When an earlier mutation is reversed by a second mutation

A

Reversion mutation

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51
Q

What are the two types of reversion mutations?

A
  1. Same-site (true) reversion: converts the mutant nucleotide sequence back to the original sequence
  2. Second-site reversion: a second mutation occurs at a different site in the DNA and causes the wild-type phenotype to be restored (correct original mutation at a different site)
    —> Second mutation may be found in the same gene or another gene
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52
Q

How do mutations occur? (2 ways)

A
  1. Spontaneous mutations
  2. Induced mutations
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53
Q

A random change in the DNA arising from errors in replication, low rate, inherent or intrinsic mutations.

A

Spontaneous Mutations

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54
Q

Results from exposure to known mutagens which are primarily physical and chemical agents that interact with DNA in a disruptive manner, often result from exposure

A

Induced Mutations

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55
Q

What are the three types of Induced mutations?

A
  1. Base analogs
  2. DNA-modifying agents
  3. Intercalating agents
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56
Q
  • Structurally similar to normal nitrogenous bases and can be incorporated into the replicating chain.
  • Typically exhibit base pairing properties different from the bases they replace, eventually causing a stable mutation.
  • Point mutation
  • Cells must be actively growing.
A

Base analogs

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57
Q
  • Mutagens that change a bases structure, therefore altering its pairing.
  • Attach group to bases that are already in place
  • Does not need to be growing
  • Point mutation
A

DNA-modifying agents

58
Q
  • Planar molecules that insert themselves (intercalate) between the stacked bases of the helix, to induce single nucleotide pair insertions and deletions
  • Disrupts DNA polymerase ability to recognize what is there
  • = Frameshift mutation (deletion/addition)
A

Intercalating agents

59
Q

What are the two types of radiation?

A
  1. Nonionizing (Weaker, thin layer)(changing something)
  2. Ionizing radiation (Stronger, more penetrative)(Breaking something)
60
Q

Nonionizing radiation:

  • Radiation that excites _________ to a higher energy state.
  • Example: ___________ radiation
  • Not as penetrating as ionizing radiation
  • Absorbed by DNA and targets ___________ bases forming ___________dimers
  • Good for tissue cultures
  • Wavelength = ____________
A
  • Atoms
  • Ultraviolet radiation
  • Pyrimidine bases forming Pyrimidine dimers
  • Wavelength = 260nm
61
Q

IONIZING RADIATION:

  • If the radiation ejects _________ from an atom and causes _________ to form
  • Examples: _______ (most penetrating), _________ , ____________ (least penetrating)
  • More likely to see a DNA _________ (Single or full double strand break)
A
  • Orbital electrons
  • Ions
  • Gamma rays (most)
  • X-rays
  • Cathode rays (least)
  • DNA Breaks
62
Q

What are the two types of Excision repair ?

A
  1. Nucleotide excision repair (more general)
  2. Base excision repair (more specific)
63
Q

What are the two main types of repair mechanisms?

A
  1. Excision repair (Nucleotide excision repair, Base excision repair)
  2. Direct Repair (Photoactivation)
64
Q

NUCLEOTIDE EXCISION REPAIR: _____________ detects if we have an issue, then cuts it out. Cuts the problem and area around it. An example is UvrABC

A

Endonuclease

65
Q

NUCLEOTIDE EXCISION REPAIR:

BLANK repairs the section that was cut out, cannot make the last connection

A

DNA Polymerase I

66
Q

NUCLEOTIDE EXCISION REPAIR:

____________ makes the final connection that DNA Pol.1 cannot

A

DNA ligase

67
Q

Photoactivation (light activated repair) uses BLANK, to repair BLANK dimers from UV damage

A

Photolyase

Pyrimidine

68
Q

What is the last ditch effort if mutations keep occurring?

A

SOS repair system

69
Q

What are the two main components within the SOS repair system?

A
  1. LexA = Repressor (negative control of transcription)
  2. RecA = Effector
70
Q

BLANK is normally found on the operator region of the SOS genes. This acts as the Repressor for negative control of transcription.

A

LexA

71
Q

BLANK is the effector, and activated due to stalls in replication, or lots of breakage in DNA. It interacts with LexA to make it cleave itself (prevent binding with operator site)

A

RecA

72
Q

What are some of the SOS genes that are made?

A
  1. UvrABC (repair shit)
  2. SfiA (temporary block on cell division)
  3. Genes for translesion synthesis (lack of template strand, DNA Pol IV and V throw random shit into the gaps, no proofreading)
73
Q

What are the two ways to isolate a mutant?

A
  1. Selection
    - confers some type of advantage to the organism
    - Ex: Antibiotic resistance
  2. Screening
    - involves examining large numbers of colonies for certain types of mutations (non-selectable)
    - Can’t really determine just by growing on a plate
74
Q

Used to detect autotrophic mutations, like a nutritional mutation.

A

Replica plating

75
Q

What is an example of an organism used in replica plating?

A

Auxotroph

(Lysine auxotroph grows only when lysine is supplemented in the media)

76
Q

Process of Replica plating:

  • Grow on a BLANK with a complete medium, put on a BLANK stamp.
  • Stamp the velvet onto a BLANK and BLANK plate.
  • Incubate
  • Observe / compare
A
  • Master plate
  • Velveteen stamp
  • Complete plate
  • Minimal plate
77
Q

BLANK is the physical exchange of genes between genetic elements. BLANK recombination is most common.

A
  • Genetic Recombination
  • Homologous recombination
78
Q

BLANK involves the exchange of two very similar pieces of DNA between different sources. The main enzyme is RecA.

A

Homologous recombination

79
Q

T/F: Homologous recombination occurs in all domains of life

A

True

80
Q

Eukaryotes use __________ transfer. This occurs during ________.

A

Vertical

Meiosis

81
Q

Prokaryotes use BLANK gene transfer. This occurs in three mechanisms, what are they?

A

Horizontal gene transfer

  1. Transformation
  2. Transduction
  3. Conjugation
82
Q

_________ involves the uptake of naked DNA from the environment. (Amount = ________ kb). What is the classic experiment that shows this?

A
  • Transformation (~10 kb)
  • 1920’s Frederick Griffith
    —> Streptococcus pneumonia
    ———> (R strain) = no virulent, no expression of capsule
    ———> (S strain) = virulent, expression of capsule (capsule is like a coat that hides them)
83
Q

Mechanism of Transformation

  • DNA binding complexes resemble a BLANK
    ——> Pull in DNA into the cell
    ——> Typically, one of these strands are degrading
  • Bind BLANK and these are shortened and converted to BLANK (fragments)
  • DNA is stabilized by BLANK
A
  • Type IV pilus
  • Double stranded DNA
  • Single stranded DNA
  • Single-stranded DNA binding proteins
84
Q

A bacteria that can take up DNA and be transformed is known as BLANK

A

Competent

85
Q

Competent bacteria are:
- Genetically determined
- regulated
- variation is seen regarding when and how many bacteria become competent
What are some examples of competent bacteria?

A
  • Bacillus
  • Streptococcus
  • Haemophilus
  • Neisseria
  • Acinetobacter
86
Q

T/F: High-efficiency, natural transformation is rare

A

True

87
Q

What are two methods of forcing bacteria to become competent?

A
  1. Electric shock (electroporation)
  2. Exposure to calcium chloride
88
Q

BLANK is the DNA transfer that is mediated by a bacteriophage

A

Transduction

89
Q

What are two types of bacteriophage (virus)

A
  1. Lytic (get in, multiple and release their copies of lysing)
  2. Lysogenic (two options, lytic or go in and kinda hide for a bit)
90
Q

What are the two methods of transduction?

A
  1. Generalized Transduction (lytic component)(Any piece of DNA)
  2. Specialized transduction (lysogenic only)
91
Q

GENERALIZED TRANSDUCTION:

  • Lytic component
  • Random fragments of disintegrating host DNA are taken up by the phage during assembly
  • Quality control starts to fall behind (checking for right SIZE, not the gene specifically)
  • Bacterial DNA starts to deteriorate
  • Phage will incorporate bacterial DNA on accident if it is the same size fragment, transfers it into a new cell
  • This can also be lysogenic since they can go into a lytic phase
A

ALLLOOOOOO

92
Q

SPECIALIZED TRANSDUCTION:

  • Lysogenic only
  • Highly specific part of the host genome is regularly incorporated into the virus
  • When they cut themselves out, they don’t cut themselves properly
    ——> May grab bacterial genes next to them
    ——> Since we are missing some phage DNA, it is not infection yet can still share with other bacterial cells
A

AAAALLLOOOO

93
Q

__________ Plasmids can be transferred from one cell to another.

A

Conjugative plasmids

94
Q

Conjugative plasmids: Must contain a specific set of genes called the ________ region

  • _________ = nicking enzyme
  • Relaxosome
  • __________ = allows genetic exchange
  • __________ = injuects DNA into the pilus
A

Tra region

TraI = nicking enzyme
- relaxosome
- Pilus = allows genetic exchange
- Type IV secretion system = injects DNA into the pilus

95
Q

What are some common types of Conjugative plasmids?

A
  • R (resistance) Plasmids: Confer resistance to antibiotics and other growth inhibitors (heavy metals) by having genes that encode for proteins that inactivate the substance or inhibit its uptake into the cell. Usually have multiple resistance genes.
  • Virulence Plasmids: Carry genes that allow attachment to specific cells and/or the formation of substances that cause damage to the host
96
Q

BLANK is the transfer of DNA by direct cell contact

A

Bacterial conjugation

97
Q

Bacterial conjugation is BLANK transfer

A

One way transfer f

98
Q

BACTERIAL CONJUGATION:

  • ___________ retracts as soon as the cells make contract.
  • F plasmid __________ in one strand
  • One strand transferred from _________ to _________
    ——> F plasmid simultaneously replicated into _______
  • Synthesis of complimentary strand in recipient cell (F-)
  • cells separate
A
  • Pilus
  • Nicked
  • F+ to F- cell
  • F+ cell
99
Q

HFR =

A

High frequency of recombination

100
Q

Results when plasmid can integrate into the host chromosome and allow plasmid AND chromosomal DNA to be transferred

A

HFR

101
Q

T/F: In HFR, it is possible to exchange a lot of genes, but only a few exchange in reality due to the environment

A

TRUE

102
Q

____________________ are known for recombination due to the movement of DNA sequences from one part of the genome to another part

A

Transposable elements

103
Q

T/F: transposable elements have an origin of replication

A

False

104
Q

Who discovered Transposable elements?

A

Barbara McClintock

105
Q

What are the two major types of Transposable elements?

A
  1. Insertion sequences (Simplistic, shorter, only comprised of transposase and inverted repeats)
  2. Transposons (longer, include additional genes)
106
Q

What do both Insertion sequences and transposons require?

A
  • Gene that encodes for transposase
  • Short inverted repeats at their ends
107
Q

Enzyme that recognizes, cuts, and pastes back in for TE

A

Transposase

108
Q

What is a good way to search for transposable elements?

A

Look for the short inverted repeats at their ends, usually 50 - 100 BP long

109
Q

What are the two mechanisms of transposition ?

A
  1. Conservative
    - cut out and move to another place
  2. Replicative
    - replicate, then move the replicate to a new spot (allows variation and change within cell)
110
Q

Viruses:

  • Lack BLANK for metabolic processes
  • Lack machinery for synthesizing BLANK (no ribosomes)
  • They are not cells (non-living entities)
A

Enzymes

Synthesizing proteins

111
Q

Viruses are considered obligate intracellular parasites. Why?

A

They require a host cell to function. This is due to:

  • Lacking enzymes for metabolic processes, machinery for synthesizing proteins (no ribosomes), and are not cells
112
Q

Are viruses smaller than bacteria? What is the size range?

A

Yes

22 to 250nm

113
Q

T/F: Bacterial structure is more simple than viral

A

False, virus structure is more simple

114
Q

What are the components of a virus?

A
  • Envelope (presence or absence)
  • Capsid
  • Genetic material
115
Q

The envelope of a virus is composed of the ___________. Populated with _________ proteins only.

A

Host cell membrane

Viral proteins

116
Q

What are the two arrangements of a capsid ?

A
  • Helical
  • Icosahedral
117
Q

Viruses that do not fit in the normal categories are considered BLANK

A
  • Atypical / Complex
118
Q

What is an example of a complex virus?

A
  • Poxvirus
  • Bacteriophage
119
Q

What makes the Poxvirus atypical?

A

Tends to have more of a. Polysaccharide capsid/randomness as opposed to a symmetrical structure .

120
Q

What makes the bacteriophage atypical?

A

The bacteriophage has additional structures compared to normal viruses (complex)

121
Q

Can viruses contain both DNA and RNA?

A

No

122
Q

What are the 4 possibilities for genetic material in a virus

A
  1. DNA double stranded
  2. DNA single stranded
  3. RNA single stranded
  4. RNA double stranded
123
Q

RNA:
- ____________ sense (single stranded), which means the RNA virus can act as mRNA.
- ____________ sense, RNA virus cannot act as mRNA, it will be complimentary for what they need (they will need to synthesize mRNA once inside the host cell)
- May have a ___________ phase (retroviruses)
- May be ___________

A
  • Postive sense
  • Negative sense
  • DNA phase
  • Segmented
124
Q

Classification of viruses
- BLANK for the taxonomy of viruses (holistic approach)
- classified about BLANK different species of viruses

A
  • International committee
  • 2000
125
Q

How does the international committee classify bacteria?

A

Order, family, genus, and species

126
Q

How many orders are there for 2000 viruses?

A

3 orders

127
Q

Orders always end with BLANK

A

Viralis

128
Q

Families have the suffix BLANK

A

Viridae

129
Q

Genus ends with BLANK

A

Virus in the name

130
Q

Species has BLANK at the end and is what’s most often used

A

Virus

  • like “measles virus”
131
Q

The BLANK system focuses mainly on the genome and RNA

A

Baltimore system

132
Q

The Baltimore system looks at the BLANK and how they synthesize BLANK. They have a total of BLANK different classes.

A

Genome

RNA

Seven

133
Q

What are the first two phases of replication in an animal virus?

A
  1. Adsorption
  2. Penetration
134
Q

What happens in adsorption?

A

Virus attaches to its host by binding to specific cell receptors

135
Q

Viruses exhibit BLANK, meaning they can only infect cells with that specific receptor. This is typically seen in the BLANK family

A

Tropism

  • immunoglobulin family
136
Q

BLANK Tropism: Receptors are not expressed by everything, ranges between dogs, cats, plants, etc.

A

Host Tropism

137
Q

BLANK tropism: Is it in all cells, specific cells within the host, range, etc.

A

Tisssue / cellular tropism

138
Q

What are the two methods of Penetration in animal virus replication

A
  1. Virus is engulfed or endocytosed and enclosed in a vesicle
  2. Enzymes in the vesicle break down the capsid envelope/capsid then the virus mediates the breakdown of the vesicle, uncoating the genetic material
139
Q

DNA viruses stay in the BLANK

RNA viruses stay in the BLANK

A

Nucleus

cytoplasm

140
Q

BLANK sense RNA needs to make mRNA

Needs to bring with it BLANK RNA polymerase packaged within the BLANK. We have DNA polymerases which they cannot use. This occurs in host BLANK

A

Negative sense

  • RNA-dependent
  • Viral capsid
  • Cytoplasm

Microbiology (30 decks)

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