Micro Lab Exam 1

Cetrimide agar (CA)

A selective medium used to select for Pseudomonas aeruginosa.

Tryptic soy agar (TSA)

A nutrient or general-purpose medium used to grow many types of bacteria.

What does TSA stand for?

Tryptic soy agar.

What type of medium is CA?

Selective medium.

What type of medium is TSA?

Nutrient or general-purpose medium.

What does CA select for?

Pseudomonas aeruginosa.

What is the rhizosphere?

The soil directly surrounding plant roots that is influenced by the plant.

What is bulk soil?

Soil that is away from the direct influence of plant roots.

What is the O soil horizon?

The organic surface layer containing dead and decomposing material.

What is the A soil horizon?

Topsoil containing minerals and organic matter with high biological activity.

What is the B soil horizon?

Subsoil where minerals from upper soil layers accumulate.

What is the C soil horizon?

Weathered parent material beneath the B horizon.

What is the R soil horizon?

Bedrock beneath the soil.

What is the order of the soil horizons?

O → A → B → C → R.

What are prokaryotes?

Organisms whose cells do not have a membrane-bound nucleus.

What organisms are prokaryotes?

Bacteria and archaea.

What are eukaryotes?

Organisms whose cells contain a membrane-bound nucleus.

Are viruses prokaryotes or eukaryotes?

Neither because viruses are not cells.

What are the three common bacterial cell shapes?

Coccus bacillus and coccobacillus.

What is a coccus?

A round or spherical bacterial cell.

What is a bacillus?

A rod-shaped bacterial cell.

What is a coccobacillus?

A short rounded rod-shaped cell that is between a coccus and a bacillus.

What does staphylo- mean?

Cells arranged in clusters.

What does strepto- mean?

Cells arranged in chains.

What does diplo- mean?

Cells arranged in pairs.

What shape is a coccus?

Round or spherical.

What shape is a bacillus?

Rod-shaped.

What shape is a coccobacillus?

Short and rounded rod-shaped.

What is a serial dilution?

A stepwise dilution used to reduce the concentration of microorganisms.

Why are serial dilutions used?

To reduce microbial concentration so colonies can be counted.

What is microbial growth?

An increase in the number of microbial cells.

What are media?

Substances used to grow microorganisms in the laboratory.

What is culture-dependent testing?

Studying microorganisms after growing them in the laboratory.

What is culture-independent testing?

Studying microorganisms without growing them in the laboratory often using DNA.

What is a pure culture?

A culture containing only one species of microorganism.

What is a colony-forming unit (CFU)?

A viable microorganism or group of microorganisms capable of producing a colony.

What does one visible colony approximately represent?

One CFU.

Can one colony sometimes come from multiple cells?

Yes multiple cells can sometimes form one colony.

Who was Selman Waksman?

A scientist associated with the discovery and study of antibiotics from soil microorganisms.

Who was Alma Whiffen?

A microbiologist known for her work with antibiotic-producing microorganisms.

What is nutrient media?

Media designed to provide nutrients needed for many microorganisms to grow.

What is selective media?

Media designed to allow certain microorganisms to grow while inhibiting others.

What is the difference between TSA and CA?

TSA is a nutrient medium while CA is a selective medium.

What are photoautotrophs?

Organisms that use light energy to make their own organic compounds.

What are chemoautotrophs?

Organisms that obtain energy by oxidizing inorganic chemicals and make their own organic compounds.

What is another name for chemoautotrophs?

Chemolithotrophs.

What are chemoheterotrophs?

Organisms that obtain energy and carbon from organic compounds.

What is the main difference between photoautotrophs and chemoautotrophs?

Photoautotrophs use light for energy while chemoautotrophs use chemicals for energy.

What is a zone of inhibition?

The clear area around an antibiotic where bacterial growth has been inhibited.

What does a larger zone of inhibition generally indicate?

Greater inhibition of bacterial growth by the antibiotic under the test conditions.

What are antibiotics?

Substances that kill bacteria or inhibit bacterial growth.

What is a class of antibiotics?

A group of antibiotics that share similar chemical structures or mechanisms of action.

What are biosynthesis pathways?

Cellular pathways used by organisms to build important molecules.

Why can antibiotics target biosynthesis pathways?

Blocking an important biosynthesis pathway can prevent bacterial growth or survival.

What is a mechanism of action?

The specific way an antibiotic affects or damages a bacterial cell.

What are antibiotic targets?

Specific bacterial structures or processes that antibiotics interfere with.

What is peptidoglycan?

A structural material that makes up the bacterial cell wall.

Where is peptidoglycan found?

In bacterial cell walls.

How does Gram-positive peptidoglycan compare with Gram-negative peptidoglycan?

Gram-positive bacteria have a thick peptidoglycan layer while Gram-negative bacteria have a thin peptidoglycan layer.

What major structure does Gram-negative bacteria have that Gram-positive bacteria do not?

An outer membrane.

What do beta-lactam antibiotics target?

Bacterial cell wall synthesis.

How do beta-lactam antibiotics affect bacteria?

They interfere with peptidoglycan cell wall synthesis.

What do tetracyclines target?

The 30S ribosomal subunit.

What do macrolides target?

The 50S ribosomal subunit.

What do aminoglycosides target?

The 30S ribosomal subunit.

What do fluoroquinolones target?

Enzymes involved in bacterial DNA replication.

What do sulfonamides target?

The bacterial folate biosynthesis pathway.

Why is the bacterial cell wall a good antibiotic target?

Bacteria need the cell wall for structure and survival and human cells do not have peptidoglycan cell walls.

What does PCR stand for?

Polymerase chain reaction.

What is PCR?

A technique used to make many copies of a specific DNA sequence.

What is the purpose of PCR?

To amplify a specific DNA sequence so it can be studied.

What is a DNA template?

The DNA molecule that provides the sequence being copied during PCR.

What is Taq polymerase?

An enzyme that adds nucleotides during PCR.

Why is Taq polymerase used in PCR?

It can withstand the high temperatures used during PCR.

What are primers?

Short pieces of DNA that bind to the target DNA and provide a starting point for DNA synthesis.

What are the two primers used for the 16S rRNA PCR?

27F and 1492R.

What is primer 27F?

A forward primer used to begin amplification of the 16S rRNA gene.

What is primer 1492R?

A reverse primer used to begin amplification from the opposite side of the 16S rRNA gene.

What are dNTPs?

The DNA nucleotides used to build new DNA.

What four nucleotides are included in dNTPs?

A G C and T.

What is the purpose of the PCR buffer?

It provides optimal conditions for Taq polymerase to amplify DNA.

Why is water included in a PCR reaction?

It provides the liquid needed for the reaction and helps bring the reaction to the correct volume.

What is the 16S rRNA gene?

A gene commonly used to identify and compare bacteria.

Why is the 16S rRNA gene useful for bacterial identification?

Its sequence can be compared between bacteria to determine evolutionary relationships.

What is molecular phylogeny?

The study of evolutionary relationships using molecular information such as DNA sequences.

How is molecular phylogeny different from morphological characterization?

Molecular phylogeny uses DNA information while morphological characterization uses physical characteristics such as Gram stain results.

What is a Gram stain?

A differential staining technique used to distinguish Gram-positive bacteria from Gram-negative bacteria.

What are the four main Gram stain reagents?

Crystal violet Gram's iodine 95% alcohol and safranin.

What is the first reagent used in the Gram stain?

Crystal violet.

What is the second reagent used in the Gram stain?

Gram's iodine.

What is the third reagent used in the Gram stain?

95% alcohol.

What is the fourth reagent used in the Gram stain?

Safranin.

What is the purpose of crystal violet?

It is the primary stain that initially stains bacterial cells purple.

What is the purpose of Gram's iodine?

It acts as a mordant and helps hold the crystal violet in the cells.

What is the purpose of 95% alcohol?

It decolorizes cells during the Gram stain.

What is the purpose of safranin?

It is the counterstain that stains decolorized cells pink or red.

What color are Gram-positive bacteria after Gram staining?

Purple.

What color are Gram-negative bacteria after Gram staining?

Pink or red.

Why do Gram-positive bacteria remain purple?

They have a thick peptidoglycan layer that retains the crystal violet-iodine complex.

Why do Gram-negative bacteria become pink or red?

Their thin peptidoglycan layer does not retain the crystal violet-iodine complex after alcohol treatment and they take up safranin.