FINAL EXAM FLASHCARDS / NEW MATERIAL Flashcards by Izzie Oberhauser

Regulating ___________ is another level of transcription regulation.

Enzyme synthesis

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

Homodimeric

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_________________ is the most common conformation for DNA binding proteins.

Helix-turn-helix

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

Helix - turn - helix
Zinc Finger
Leucine Zipper

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In the Helix-turn-helix:

1st Helix =
Turn =
2nd Helix =

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

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

Zinc

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

Intertwining

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

Inverted repeats

Major groove

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DNA binding proteins can act in a ___________ or ___________ fashion

Activator

Repressor

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Repression is an _____________ reaction

Anabolic

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Activation is a ____________ reaction

Catabolic

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

Repression

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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.

Activation

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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 _____________

Negative control

Effector protein (co-repressor)

Operator

Promoter

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

Positive

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

Promoting

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

Activator binding site

Upstream

Weak

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

Activator protein

Activator binding may alter DNA, to help promoter sequence get recognized
Activator may interact with RNA polymerase to pull it in

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

Presence

Activator binding site

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Negative control

What is involved
1A: Upstream or downstream of promoter
1B: Location of binding
What does it use
What are the two methods

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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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

What are the two methods

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

Operon

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

Regulon

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

Glucose

Catabolite repression

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

- Positive control - Cyclic AMP receptor protein (CAP) - AMP - Cyclic AMP

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

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

If glucose is absent = (INHIBITION / NO INHIBITION) on adenylate cyclase ______________ stays inside the cell, binds to ____________, which binds the ____________, and ____________ binds leading to transcription.

No inhibition on adenylate cyclase cAMP stays inside the cell Binds to CAP Binds to Activator Protein Binds RNA Polymerase = Transcription

Glucose and Lactose present = lactose Repressor is BLANK Glucose w/o lactose present = lactose Repressor is BLANK

Present = ON Absent = OFF

Catabolite repression leads to _________ growth

Diauxic Growth

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?

GLUCOSE LACTOSE The lag occurs as we shut down glucose genes and turn on the lactose genes Diauxic growth

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

Two Component Regulatory System

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

1. Sensor Kinase Protein 2. Response Regulatory Protein

_________________ 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 ____________.

Sensor Kinase Protein Autophosphorylation Histidine Residue Response regulatory protein

Kinases ____________ proteins

Phosphorylate

What are some common Kinases we see as sensor kinase proteins

Serine-Threonine kinases Tyrosine Kinases Histidine Kinases

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

Cytoplasm DNA binding protein Phosphate from a Sensor Kinase Protein

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.

Phosphatase Response regulatory protein

__________ is used at high osmotic pressures ___________ is used at low osmotic pressures

OmpC = high OmpF = low

How do genomes change?

Mutations

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

Mutation

Why are mutations rare?

Repair mechanisms Cells try to prevent mutations

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

- No backup copy of gene (haploid) - Much faster / more replication

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

Mutant strain

What are the two types of mutations ?

Point mutations Frameshift mutations

What are the 3 types of Point mutations ?

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)

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

Frameshift mutations

Different sequences but creates the same AA.

Silent mutation

Adds in a stop codon, creating an incomplete protein

Nonsense mutation

Creates a a different amino acid, causative for evolution

Missense mutation

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

Reversion mutation

What are the two types of reversion mutations?

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

How do mutations occur? (2 ways)

1. Spontaneous mutations 2. Induced mutations

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

Spontaneous Mutations

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

Induced Mutations

What are the three types of Induced mutations?

1. Base analogs 2. DNA-modifying agents 3. Intercalating agents

- 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.

Base analogs

- 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

DNA-modifying agents

- 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)

Intercalating agents

What are the two types of radiation?

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

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 = ____________

- Atoms - Ultraviolet radiation - Pyrimidine bases forming Pyrimidine dimers - Wavelength = 260nm

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)

- Orbital electrons - Ions - Gamma rays (most) - X-rays - Cathode rays (least) - DNA Breaks

What are the two types of Excision repair ?

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

What are the two main types of repair mechanisms?

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

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

Endonuclease

NUCLEOTIDE EXCISION REPAIR: BLANK repairs the section that was cut out, cannot make the last connection

DNA Polymerase I

NUCLEOTIDE EXCISION REPAIR: ____________ makes the final connection that DNA Pol.1 cannot

DNA ligase

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

Photolyase Pyrimidine

What is the last ditch effort if mutations keep occurring?

SOS repair system

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

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

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

LexA

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)

RecA

What are some of the SOS genes that are made?

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)

What are the two ways to isolate a mutant?

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

Used to detect autotrophic mutations, like a nutritional mutation.

Replica plating

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

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

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

- Master plate - Velveteen stamp - Complete plate - Minimal plate

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

- Genetic Recombination - Homologous recombination

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

Homologous recombination

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

True

Eukaryotes use __________ transfer. This occurs during ________.

Vertical Meiosis

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

Horizontal gene transfer 1. Transformation 2. Transduction 3. Conjugation

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

- 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)

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

- Type IV pilus - Double stranded DNA - Single stranded DNA - Single-stranded DNA binding proteins

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

Competent

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

- Bacillus - Streptococcus - Haemophilus - Neisseria - Acinetobacter

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

True

What are two methods of forcing bacteria to become competent?

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

BLANK is the DNA transfer that is mediated by a bacteriophage

Transduction

What are two types of bacteriophage (virus)

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)

What are the two methods of transduction?

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

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

ALLLOOOOOO

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

AAAALLLOOOO

__________ Plasmids can be transferred from one cell to another.

Conjugative plasmids

Conjugative plasmids: Must contain a specific set of genes called the ________ region - _________ = nicking enzyme - Relaxosome - __________ = allows genetic exchange - __________ = injuects DNA into the pilus

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

What are some common types of Conjugative plasmids?

- 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

BLANK is the transfer of DNA by direct cell contact

Bacterial conjugation

Bacterial conjugation is BLANK transfer

One way transfer f

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

- Pilus - Nicked - F+ to F- cell - F+ cell

HFR =

High frequency of recombination

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

HFR

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

TRUE

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

Transposable elements

T/F: transposable elements have an origin of replication

False

Who discovered Transposable elements?

Barbara McClintock

What are the two major types of Transposable elements?

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

What do both Insertion sequences and transposons require?

- Gene that encodes for transposase - Short inverted repeats at their ends

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

Transposase

What is a good way to search for transposable elements?

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

What are the two mechanisms of transposition ?

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)

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

Enzymes Synthesizing proteins

Viruses are considered obligate intracellular parasites. Why?

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

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

Yes 22 to 250nm

T/F: Bacterial structure is more simple than viral

False, virus structure is more simple

What are the components of a virus?

- Envelope (presence or absence) - Capsid - Genetic material

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

Host cell membrane Viral proteins

What are the two arrangements of a capsid ?

- Helical - Icosahedral

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

- Atypical / Complex

What is an example of a complex virus?

- Poxvirus - Bacteriophage

What makes the Poxvirus atypical?

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

What makes the bacteriophage atypical?

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

Can viruses contain both DNA and RNA?

What are the 4 possibilities for genetic material in a virus

1. DNA double stranded 2. DNA single stranded 3. RNA single stranded 4. RNA double stranded

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 ___________

- Postive sense - Negative sense - DNA phase - Segmented

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

- International committee - 2000

How does the international committee classify bacteria?

Order, family, genus, and species

How many orders are there for 2000 viruses?

3 orders

Orders always end with BLANK

Viralis

Families have the suffix BLANK

Viridae

Genus ends with BLANK

Virus in the name

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

Virus - like “measles virus”

The BLANK system focuses mainly on the genome and RNA

Baltimore system

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

Genome RNA Seven

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

1. Adsorption 2. Penetration

What happens in adsorption?

Virus attaches to its host by binding to specific cell receptors

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

Tropism - immunoglobulin family

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

Host Tropism

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

Tisssue / cellular tropism

What are the two methods of Penetration in animal virus replication

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

DNA viruses stay in the BLANK RNA viruses stay in the BLANK

Nucleus cytoplasm

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

Negative sense - RNA-dependent - Viral capsid - Cytoplasm