Cell Biology Lab Final Exam

In traditional pipetting, what position should you press the plunger before aspirating the sample?

First stop

Which size micropipette would be appropriate to accurately measure 15 uL?

P20

Why is it important to store micropipettes in an upright position when not in use?

To prevent liquid from flowing back into the piston and causing damage or contamination.

Why should pipettes never be laid down or inverted while a tip contains liquid?

It causes liquid to flow back into the pipette, potentially damaging or contaminating the piston.

What is a potential consequence of letting the plunger snap back quickly after aspirating liquid?

Dispensing an incorrect sample volume due to turbulence or air bubbles.

What is the purpose of pre-wetting a pipette tip several times before delivering a sample?

To condition the tip with the sample which improves accuracy and precision.

What is the purpose of pressing the plunger to the first stop during the traditional pipetting method?

To aspirate the sample fluid by creating a vacuum.

Key difference between traditional and reverse pipetting?

Reverse pipetting presses the plunger past the second stop before aspiration and dispenses only to the first stop.

Why should all sample fluids and equipment reach room temperature before pipetting?

Temperature differences affect liquid volume and pipetting accuracy.

What chemical in the Bradford Assay is responsible for shifting its absorption spectrum upon binding to protein?

Coomassie Brilliant Blue dye

Why is the Bradford Assay preferred over other protein quantification methods?

It is faster and has fewer steps.

T/F: The absorbance peak shift observed in the Bradford Assay is a direct consequence of laser-induced fluorescence.

False

Which type of spectroscopy is utilized in the Bradford Assay?

Absorbance spectroscopy

T/F: The Bradford Assay exclusively uses laser light for protein detection.

False

T/F: The Bradford Assay requires a standard curve generated with a known protein to accurately determine unknown protein concentrations.

True

Which step is critical to ensure reproducibility in Bradford Assay measurements when reviewing scientific literature?

Use of consistent incubation times and reagent volumes.

How does the principle of absorbance linearity in the Bradford Assay relate to the principles of spectroscopic quantification in optical imagine modalities?

Both rely on Beer-Lambert law to correlate absorbance with concentration.

T/F: The Bradford Assay can directly measure protein localization within a cell when combined with fluorescence microscopy.

False

How does the Bradford Assay exemplify the application of light and optics principles in biological assays?

By utilizing absorption of visible light to quantify biomolecules.

In light-based protein assays, how does solvent polarity affect the colorimetric response?

It causes a shift in the absorption peak due to changes in dye-protein interactions.

Why is it important to understand the photophysical properties of dyes used in the Bradford Assay?

The dye’s properties affect light absorption and assay accuracy.

Why is it important to understand the limitations of the Bradford Assay in biophotonic research?

Its sensitivity and potential for interference from various chemicals can affect the accuracy of protein measurements, which can influence experimental conclusions.

How does the Bradford Assay facilitate the study of protein interactions in a biological sample using optical biosensors?

By measuring changes in light absorbance due to protein-dye binding.

T/F: The Bradford Assay can be utilized to quantify proteins in samples that also contain high concentrations of detergents without interference.

False

What is the purpose of using secondary antibodies in indirect detection?

To amplify the signal around the antigen.

T/F: Immunofluorescence assays use fluorescently labeled antibodies to detect specific microorganisms.

True

What role does incubation temperature play in a manual ELISA protocol?

It affects the antibody-antigen binding kinetics and assay sensitivity.

What is NOT a type of diagnostic test mentioned in the ELISA document?

Polymerase chain reaction

T/F: Acquired immunity does not require an initial contact with the invader to be activated.

False

What is a characteristic of killed vaccines?

They are safer for immunocompromised individuals.

An advantage of using recombinant DNA tech to produce therapeutic antibodies for patient treatment?

It allows for the creation of “humanized” antibodies, reducing the risk of adverse immune reactions.

Key characteristics and examples of killed vaccines:

Made from microorganisms that have been inactivated by heat or chemicals; generally safer than live vaccines, but provide a weaker immune response; Includes vaccines for rabies, cholera, and the Salk polio vaccine.

Type of immunity characterized by the production of antibodies that circulate the bloodstream?

Humoral immunity

T/F: The charge density of a molecule is determined by its electrical charge divided by its molecular weight.

False

SDS-PAGE is a technique used to separate proteins by their ___________ after denaturation with SDS.

Molecular weight

T/F: Proteomics is considered less complex than genomics because it deals with fewer variables.

False

T/F: The term “proteomics” was coined to draw an analogy with genomics.

True

Primary role of SDS in the Tris-glycine-SDS running buffer used in electrophoresis?

To maintain the denaturation of proteins in the gel.

Modifications to mRNA, such as capping with a 7-methylguanosine nucleotide, __________ its stability and protein expression levels.

Increases

Protein diversity cannot be fully characterized by _______________ analysis alone, making proteomics essential.

Gene expression

Gels can be transferred directly into Bio-Safe Coomassie stain after ___________ is complete.

Electrophoresis

The molecular weight markers are bound to __________ molecules to make them visible on the gel.

Colored

What is the primary factor affecting protein migration in SDS-PAGE?

Molecular weight

T/F: Myofibrils are the basic contractile elements of muscle cells.

True

T/F: Laemmli sample buffer contains Tris buffer, SDS, Bromophenol Blue, and glycerol.

True

From the positions of the bands we can determine the size and relative _______ of the proteins.

Abundance

Linnaean taxonomy

The method of grouping organisms according to common physical characteristics.

Convergent evolution

Where two species from different ancestors independently develop similar traits due to environmental pressures.

What is DNA barcoding and its components?

DNA sequences can be used to identify different species by using a short genetic marker; DNA barcoding consists of a genetic sequence unique to a species and a database that can provide the identity of a species by reading and matching the barcode to a library of reference barcodes.

What makes an ideal DNA barcode?

It should be present in most organisms of interest, readily amplified without using species-specific PCR primers, and should exhibit few nucleotide differences among members of the same species but larger variation between species.

What genes are used to generate DNA barcodes from different taxonomic kingdoms?

The cytochrome c oxidase subunit for animals (from mitochondrion), ribulose-1,5-bisphosphate carboxylase and maturase K for plants (from chloroplasts), and the nuclear ribosomal internal transcribed spacer region for fungi (from the nuclear ribosome).

What is the BOLD database?

The Barcode of Life Data Systems reference library that stores all the high-quality reference DNA barcode records.

What is Sanger sequencing?

A DNA sequencing technique in which numerous cycles of primer extension are used with modified nucleotides to determine the sequence.

Why does each newly synthesized strand include only one ddNTP in the sequence?

Most of the nucleotides incorporated are standard nucleotides, as they are in excess. When a ddNTP is incorporated, DNA synthesis stops.