Unit 2 prokaryotes and identification STUDY THIS FOR FINAL

Chpt 8 = Central Dogma of Biology, mutagens, operons and genes

Degeneracy

Is why different mRNA combos can equal the same amino acid

What is required for DNA replication (their are 7 things)

helicase

Primase

DNApolymerase

DNA nucleotides

RNA nucleotides (primers)

Both current DNA strands

Gyrase

topoisomerases

What components are required for transcription (their are 5 things)

RNA nucleotides

RNA polymerase

DNA template strand

Promoter region

Terminator region

What RNA is involved in translation

tRNA(deceivers the proper amino acid to the ribosome), mRNA(is the message that will be translated), and rRNA (restricts certain mRNAs from being translated)

Stem loop

A structure that forms at the end of an mRNA translation

Causes the RNA to hydrogen bond with itself to pull off the DNA template strand

What would increase the concentration of a particular polypeptide in a cell?

An increase in transcription (leads to a more frequent translation)

What direction is the DNA read during transcription?

3’ to 5’

What direction is the mRNA synthesized during transcription?

3’ to 5’

What are the 3 stages of translation?

Initiation ( the finding of the reading frame through AUG codon)

Elongation (the continuation of amino acids bonding to a polypeptide chain

Termination ( when the ribosome hits a stop codon)

What is the start codon

AUG (mRNA) MET (Amino Acid)

What are each of the sites for a ribosome

A site (Amino Acid site)

P site (polypeptide site or bonding site)

E site (exist site)

During the initiation step of translation, the fMet charged tRNA assembles in which site of the ribosome?

P site

When does tRNA become uncharged during translation?

After the amino acid binds to the polypeptide chain (the P site and E site)

How is translation terminated?

When a protein called a release factor enters and binds to the A site

(Stop codon is hit and calls in the factor)

How do repressors work on a lac operon?

They stop mRNA polymerase from bonding to the operator region of the gene

What is the difference between generalized transduction and specialized

Generalized transduction is initiated during lytic cycle of a virulent bacteriophage; specialized transduction is initiated during the lysogenic cycle of a temperate bacteriophage.

How does an F⁺ cell differ from an Hfr cell?

Hfr strains have the F plasmid integrated into the chromosome and can give a small part of that chromosome and extras to F - cells.

Which of the following is a characteristic of an F⁺ cell?

Ability to synthesize sex pili, presence of a fertility factor, and ability to mate with an F^- cell

Leading strand being built

3’ 5’ direction (template 5’ 3’)

Lagging strand direction

5’ 3’ (template is 3’ 5’)

Topoisomerease and gyrase

Helps unwind DNA before it reaches Helicase

Specific Transduction

takes a VERY SPECIFIC set fo DNA from the host and transfers it into another cell

General Transduction

takes any DNA it can take and transferring it to a bacteria

Conjugation

Creates a bridge between both cells where one sends DNA to another

Cells must have an F plasmid for this to be initiated

The bridge to the cell is made by the pilus reaching out to the other cell

(Think hfr and F- cell interactions)

Tranfromation

When a cell runs into some DNA that it is comparable with

Needs to take DNA from the outside, that could be hindered by DNAases

(Think Griffith experiment and virulent DNA changing non-virulent cells)

Auxotrophic

lacks the ability to make essential molecules, nutrients need to be found in the environment or else they will die

Prototrophic

Can make their own essential molecules, their genome has the enzymes into the essential nutrient ( some cells can create certain nutreient wile they need to find others)

Mutagens

external stressors such radiation, and chemical agents (think UV light for radiation, bromouracil in the case of chemical)

What causes a thymine dimer? Is it repaiarable? By what?

UV light, In most cases, yes, it is repaired via nucleotide excision repair (takes damaged nuclueotides and extras, then resynthesizes the cut out part)

Frame shift mutagens

chemical in nature, these mutagens can embed themselves into DNA groves and case DNA distortion

1. DNA replication stops

2. DNApolymerase makes a mistake and adds additional bases to the daughter cells (insertions)

3. DNApolymerase skips a base that the mutagen is in between (deletion)

Ames Test

A test that looks for a suspected mutagens and possible carcinogens. It starts with 2 tubes, one with the mutagen and one control (both have liver enzymes to activate mutagen) that are added to a plate that has histidine, an amino acid that the cell cannot break down, if the plates shows growth then the cell was mutated to be able to break down the histidine and the suspected substance is a mutagen

Enzymes that are produced only when needed in the cell are called

Inducible enzymes

Positive (direct) selection

Positive (direct) selection involves the detection of mutant cells by rejection of the unmutated parent cells.

It enables detection of a rare mutant from a population containing an extremely large number of bacteria.

The mutant will grow on the selective medium, so there is no need for replica plating.

Nucleotide Analog

is a type of mutagen that is similar to it’s nucleotide counterpart in structure but not base pairing, meaning that when DNA replication is being done and the analog taken, it will not base pair with it’s complement.

Give 3 different pieces of an operon and tell me what they do

Promoter (lets the RNApolymerase link to the DNA strand, Operator (the part that is repressed and stops the polymerase unless a condition is met), and Structural genes ( the genes that create stuff)

Genes whose products are produced constantly are known as

Constructive genes (not regulated)

Repressible genes

Genes that are turned off (needs to have a condition satisfied to be turned back on)

Inducible genes

Genes that are turned on (their products are needed by the cell)

Which of these are auxotrophic?

1, 2, 3, and 9

Snapping division

when a cell elongates after cell division and ultimately begins to snap once both sides get to big

Reproductive spores

Think dandelion in for how this works, a cell builds up a ton of small sporeium and then bursts. Then these small sporeiums then go some where far to recreate a similar structure to their parents

Budding

Think of a cactus growing it’s’ arms, it allows for a young bud to form after DNA synthesis then separates after a certain amount of time

Viviparity

think similar to how a bacteriophage works but instead of lysis due to phages, it is because of offspring that the cell has inside it

Arhcaea

Are prokaryotic cells

Lack peptidoglycan in cell walls

Cytoplasmic membrane lipids are branched or ringform hydricarbon chains (helps them survive in low pH and high temp environments)

Use AUG like eukaryotic cells

Crenarchaeota

Methanogens

Largest group of archaea

Makes most of the methane gas

Lives in colons of animals

Which of these are prototrophs

only 5 (is on plate with both streptomycin and valine

What does low G + C gram positive mean?

It means that Guanine and cytosine are below 50%

They have similar 16S rRNA sequences

Are rod-shaped, obligate anaerobes

Clostriadia

Rod-shaped, obligate anaerobes

Produce toxins that cause disease in human

Has endospores that survive in harsh conditions

Are low G + C gram-positive

Mycoplasma

Facultative or obligate anaerobes

Lack cell walls • Smallest free-living cells

Colonize mucous membranes of the respiratory and urinary tracts of animals

Are low G + C gram-positive

Bacillus

Endospore-forming aerobes and facultative anaerobes

Many common in soil

Listeria

low G + C gram-positive

Contaminates milk and meat products

Capable of reproducing under refrigeration

Survives inside phagocytic white blood cells

Rarely causes disease in adults (can kill fetus in preg women)

Lactobacillus

Grows in the human mouth, stomach, intestinal tract, and vagina

Rarely causes disease

Inhibits the growth of pathogens within the body

Used in the production of various foods

low G + C bacilli

Streptococcus and Enterococcus

low G + C bacilli and cocci

Cause numerous diseases in humans

Various strains of multi-drug-resistant streptococci

Staphylococcus

low G + C bacilli and cocci

One of the most common inhabitants of humans

Produces toxins and enzymes that contribute to diseases

High G + C Gram positive Bacteria

cells that have more G and C than other nucleotides (A and T)

Corynebacterium

High G + C Gram-Positive Bacteria

Pleomorphic aerobes and facultative anaerobes

Produces metachromatic granules

Has vacancies for it

Mycobacterium

High G + C Gram-Positive Bacteria

Has waxy cell walls that let it survive

Aerobic rods that sometimes form filaments

Slow growth, partly due to mycolic acid in its cell walls

Some species are pathogens of animals and humans

Gives lepracy and turbercuosis

Actinomycetes

High G + C Gram-Positive Bacteria

Form branching filaments resembling fungi

Cause disease primarily in immunocompromised patients

Important genera include Actinomyces, Nocardia, Streptomyces

Gram-Negative Proteobacteria

Largest and most diverse group of bacteria

Five classes of proteobacteria

Alphaproteobecteria

Betaproteobacteria

Deltaproteobacteria

Gammaproteobacteria

Epsilonproteobacteria

Alphaproteobacteria

Often capable of growing at low nutrient levels

Some species have extensions called prosthecae

Used for attachment to surfaces and nutrient absorption

Nitrogen fixers

Two genera important to agriculture Azospirillum( helps with nutrient intake), Rhizobium (makes NH4)

Grow in association with the roots of plants

Are pathogenic to humans

Betaproteobacteria

Are gram negative

Are pathogenic to humans

Neisseria

• Inhabits mucous membranes of mammals • Causes numerous diseases

Pathogenic betaproteobacteria

Bordetella

Causes pertussis

Pathogenic betaproteobacteria

Burkholderia

Colonizes moist environmental surfaces and

respiratory passages of cystic fibrosis patients

Pathogenic betaproteobacteria

Thiobacillus

Recycles sulfur in the environment

Zoogloea

Form flocs that assist in the treatment of sewage

non sheath forming

Non sulfur oxidizing Bacteria

Sphaerotilus

Flocs impede flow of waste in treatment plants

Gammaproteobacteria

• Largest and most diverse class of proteobacteria

• Divided into subgroups

• Purple sulfur bacteria

• Intracellular pathogens

• Methane oxidizers

• Glycolytic facultative anaerobes

• Pseudomonads

Are pathogenic to humans

Gammaproteobacteria

Purple sulfur bacteria

• Obligate anaerobes

• Oxidize hydrogen sulfide to sulfur

• Found in sulfur-rich zones in lakes, bogs, and oceans

A single mRNA may have several ribosomes attached.

True, they can!

Assume a cell is grown in a culture medium containing radioactively labeled thymidine. After three cell divisions, what percentage of the cells would contain the radioactive label?

Cells must replicate their DNA before dividing. As DNA is replicated, radioactively labeled thymidine will be incorporated into the new DNA, thus 100% would contain the radioactive label.

When the antibiotic chloramphenicol binds to the 50S portion of the ribosome, the effect is to _____

prevent the ribosome from moving along the mRNA strand

Which of these statements correctly describe RNA processing in eukaryotic cells?

mRNA is processed before is leaves the nucleus

Introns are removed and the remaining exons are spliced together.

Processing involves snRNPs.

What gene would be the most likely to yield a recombinant cell after mating? (Cells)

R factors—antibiotic-resistance genes are plasmids that have significant medical importance. R factors carry genes that confer upon their host cell resistance to antibiotics, heavy metals, or cellular toxins.

How do Hfr cells work and what do they pass on

In E. coli, Hfr cells can pass main chromosome genes to a recipient cell. In some cells carrying F factors, the factor integrates into the chromosome, converting the F⁺ cell to an Hfr cell (high frequency of recombination). When conjugation occurs between an Hfr cell and an F^- cell, the Hfr cell’s chromosome (with its integrated F factor) replicates, and a parental strand of the chromosome is transferred to the recipient cell.

Example of specialized transduction

In specialized transduction, only certain bacterial genes are transferred. In one type of specialized transduction, the phage codes for certain toxins produced by their bacterial hosts, such as diphtheria toxin for Corynebacterium diphtheria, erythrogenic toxin for Streptococcus pyogenes, and Shiga toxin for E. coli O157:H7.

Bacillus

Are gram negative rods

Form endospores

Chlamydias

• Grow intracellularly in mammals, birds, and some invertebrates

• Some are smaller than viruses

• Most common sexually transmitted bacteria in the United States

Gram negative

Uses an elementery body as an infective agent to get to other cells

Spirochetes

• Motile bacteria that move in a corkscrew motion (also looks like it as well)

• Have diverse metabolism and habitats

• Treponema and Borrelia both cause disease in humans

ALL HAVE AXIAL FILAMENTS

Gram negative

Bacteroides

Inhabits digestive tracts of humans and animals

Some species cause infections

Cytophaga

• Aquatic, gliding bacteria

• Important in the degradation of raw sewage

Rickettsias

obligate intercellular parasites

Are alpha-proteobacteria

Induce phagocytosis so that it can get into host cell

Do binary fission in the host’s cytoplasm

Gram Negative Bacillus (or coccobacillus in some cases)

Transmitted by insects and ticks

Cause rashes on humans

Pseudomonas

Aerobic gram negative bacillus

Can metabolize a wide variety of substrates (VERY COMMON IN THE SOIL)

Have lophotirchus flagella (motile)

Is a Gammaprotebacteria

Erwinia

Plant pathogens (cause soft-rot diseases)

Creates enzymes that break down pectin (plant cell walls)

Gram negative

Gammaproteobacteria

Anaerobes

Legionella

Gammaproteobacteria

Causes pneumonia

Don’t normally grow in a lab setting in media.

Found in warm water supply liens and air cooling towers (in AC units)

Can reproduce within aquatic amebrae making it hade to get rid of them in water systems

Burkholderia

Grows on unusual carbon sources and some antiseptics

Capable of degrading more than 100 different organic molecules

Can actually grow in disinfectants!!!!!!!

Gives people cystic fibrosis

Enterics

Are a class of gram-negative facultative anaerobes that are found in the intestines of animals

Member in the order of Enterobacteriales

Usually active fermenters of glucose and carbs (they are anaerobic)

Mycoplasma

are very small bacteria

Has no cell wall (are related to gram positive bacteria tho)

They produce filaments that resemble fungi

Highly pleomorphic (can change shape and structure)

Need an acid fast stain to be seen

What are some bacteria that are found in foodborne illness?

Salmonella

Shigella

Staphylococcus

Campylobacter

Pelagibacter

free living bacteria

Very small cells

Has a small genome

One of the most abundant microorganisms in the marine environment

Borrelia

is a spirochete (has no filaments)

Deltaproteobacteria

have some bacteria that are predators to other bacteria

Important to the sulfur cycle

Are pathogenic to humans

Cyanobacteria

Include both anaerobic and aerobic cells

Also capable of chemoheterotrophic growth

Carry out photosynthesis in the same way that plants do

Non sulfur cells use organic compounds as the source of electrons for reduction of CO2

have gliding motility

Differnet to alge because they are prokaryotes (alge is eukaryotic)

Pseudomnadota

bacteria that contains majority gram negative chemoheterotrophic bacteria

What are some cells that can fix nitrogen?

Rhizobium, Azotobacter, Azospirillum, and some cyanobacteria

They do it by getting nitrogen form the air and turn it into ammonium that is then used by other organisms in the environment

(Important to agriculture)

Rhizobium

Help with plants by forming nodules in plant roots that allow for nitrogen fixation

Known as rhizobia

Lactobacillales

Don’t perform aerobic or anaerobic resperation

Use lactic acid fermentation to survive

There fermentation makes Yogurt, buttermilk and sauerkraut

Streptomyces

best kneeing for helping with the production of many antibiotics

A soil microbe, causes little diseases

Escherichia

Cells that live in your Colin,

Gammaproteobacteria

Spreads through food and water