Biology II Lab Practical Exam

Define science

Science is both a body of knowledge and a process through which we gain understanding of the natural world. This process involves observing, testing, and refining ideas to explain phenomena in nature. While science is grounded in evidence and facts, it is also dynamic, with new discoveries constantly reshaping our understanding.

Compare scientific theories and hypotheses

Scientific theories are well-substantiated explanations based on a body of evidence and broad principles, while hypotheses are testable predictions or assumptions that can be investigated through experiments.

independent and dependent variables

Independent variables are factors that are manipulated in an experiment to observe their effect on dependent variables, which are the outcomes measured to determine the effects of the independent variables.

Four parts of the scientific method

• Exploration and discovery

• Testing ideas

• Community analysis and feedback

• Benefits and outcomes

Exploration and discovery

The first phase of the scientific method where questions are generated through observations, research, and prior knowledge, leading to the formulation of hypotheses for further investigation.

Testing ideas

The stage of the scientific method where hypotheses are tested through experiments and observations to gather data and validate or refute the original idea.

Community analysis/feedback

The process of gathering and evaluating data from scientific experiments and studies, often involving collaboration and critique from peers to improve and validate findings.

Societal benefits and outcomes

The final phase of the scientific method that involves sharing research findings with the community to assess impact, gather additional insights, and inform future research directions.

Scientific arguments must be supported by what?

empirical evidence and data.

Compare hypothesis-driven versus observational/discovery science

Hypothesis-driven science tests predictions based on existing theories, while observational/discovery science explores phenomena without preconceived hypotheses, leading to new insights.

What role does peer-review play in the process of science?

Peer review ensures the quality and validity of research by evaluating the study's methodology, results, and conclusions before publication, promoting accurate scientific communication.

Differences between an original research article versus a review

An original research article presents new findings, including methodologies and data, while a review article summarizes and analyzes existing research on a particular topic.

Example of a CSE Name-year format for one author

(Smith 2020)

Example of a CSE Name-year format for two authors

(Smith and Jones 2020)

Example of a CSE Name-year format for more than two authors

(Smith et al. 2020)

If you wanted to find a peer-reviewed journal article online, where would you start?

the Clarkson Library and Google Scholar.

How many mililiters in a microliter?

0.001

How many microliters in a mililiter?

1,000

How many microliters in a liter?

1,000,000

How many mililiters in a liter?

1,000

What is the range of magnification of a compound microscope?

Between 40x and 1,000x.

What is the range of magnification of a stereoscopic microscope?

Between 8x and 35x

Magnification

The ratio between the size of the image produced by a microscope compared to its actual size. The units for magnification are x, which stands for times magnification

Resolution

The ability to differentiate between two different points on a specimen. Images with higher resolution have better clarity

Depth of field

The thickness of the specimen or the range of distance within which the object appears acceptably sharp. It is the vertical distance in the sample that remains in focus at a given time.

Field of view

The area of the specimen that is visible through the microscope at any given moment. It is the portion of the sample that can be observed when looking through the eyepiece or camera, typically expressed in terms of diameter (e.g., millimeters or micrometers).

How do you calculate the total magnification of a compound light microscope if given the magnification of the ocular and objective lenses?

To calculate the total magnification of a compound light microscope, multiply the magnification of the ocular lens by the magnification of the objective lens.

Images under a compound microscope are __________ and ________

upside down, inverted

Describe when you would use the coarse versus fine focus knob on the compound microscope

The coarse focus knob is used for initial focusing and bringing the specimen into general view, while the fine focus knob is used for precise focusing and enhancing image clarity.

Under which objective lens should you to use the coarse focus knob?

4x only

Describe the relationship between the diameter of the field of view and total magnification

As total magnification increases, the diameter of the field of view decreases. This means that higher magnification allows you to see smaller areas of the specimen but in greater detail.

Compare the type of specimens that you would view under the compound versus stereoscopic microscope

The compound microscope is used for viewing smaller, thinner specimens such as bacteria or slides of cellular material, while the stereoscopic microscope is suited for larger, three-dimensional specimens like insects or plants.

Range of a P10 micropipette

0.5 to 10 µL

Range of a P100 micropipette

10 to 100 µL

Range of a P1000 micropipette

100 to 1000 µL

Explain the function of the first and second stops of the plunger on a micropipette.

The first stop is used to withdraw the set amount of liquid into the micropipette tip. The second stop is used to release the liquid from the tip.

Compare light and electron microscopy

Light microscopy uses visible light to magnify specimens, while electron microscopy uses beams of electrons for higher resolution imaging.

Compare the prepared slides versus wet mounts

Prepared slides are permanently mounted specimens that are stained and sealed for long-term observation, while wet mounts are temporary slides created by placing a specimen in liquid and covering it with a coverslip for immediate viewing.

What is the purpose of a wet mount?

A wet mount allows for immediate viewing of live specimens in a liquid medium, preserving their natural state and enabling observation of movement and behavior.

Define the abbreviations l.s.

Longitudinal section

Define the abbreviations c.s.

Cross section

Define the abbreviation w.m

Whole mount

Describe the basic differences in cellularity between the following groups of organisms - prokaryotes (bacteria) and eukaryotes (protists, plants, fungi, and animals)

Prokaryotes are unicellular organisms without membrane-bound organelles, while eukaryotes can be unicellular or multicellular and have complex cells with membrane-bound organelles.

Compare the movements of ciliates and flagellates in live cultures

Ciliates move using hair-like structures called cilia to propel themselves, while flagellates use one or more long whip-like structures called flagella for movement.

Compare the structure of unicellular, colonial, and multicellular organisms

Unicellular organisms consist of a single cell, colonial organisms are groups of similar cells that live together but function independently, while multicellular organisms are composed of multiple cells that are specialized for different functions, working together as a whole.

Describe the purpose of oil immersion microscopy

Oil immersion microscopy enhances resolution and clarity by using a special oil with a refractive index similar to glass, which reduces light refraction and allows for greater magnification of specimens.

Define enzymes, including the terms substrate and active site

Enzymes are biological catalysts that speed up chemical reactions by lowering the activation energy. They bind to specific molecules called substrates at their active sites to facilitate the conversion of substrates into products.

Describe the effect that the following have on enzyme function:

• Substrate/enzyme concentration

• Temperature

• pH

• Competitive inhibitors

• Substrate/enzyme concentration affects enzyme activity by altering the rate of reaction; increased concentrations typically increase the rate until saturation occurs.

• Temperature influences enzyme activity, with moderate heat often increasing activity, while extreme heat can denature enzymes.

• pH levels can also greatly affect enzyme function, as each enzyme has an optimal pH range for activity.

• Competitive inhibitors decrease enzyme activity by binding to the active site, preventing substrates from attaching.

Explain how the β-Galactosidase Glow model system is used to study enzyme activity, include a description of the enzyme and substrate, as well as the role of fluorescein

The β-Galactosidase Glow model system utilizes the enzyme β-Galactosidase to hydrolyze lactose into glucose and galactose, with fluorescein acting as a substrate that emits fluorescence upon cleavage, allowing for quantitative measurement of enzyme activity.

Define standard curve, and describe how a standard curve was used in this experiment

A graphical representation that shows the relationship between known concentrations of a substance and a measurable response, such as fluorescence, absorbance, or signal intensity. By measuring the response of the unknown sample and finding the corresponding value on the standard curve, you can calculate the concentration of the substance in that sample.

captions go _____ tables and _____ figures

above, below

Define DNA barcoding

A method for identifying species by analyzing short sequences of DNA from a standard region of the genome.

List the pros and cons of using morphological traits versus DNA barcoding to identify species

Morphological traits provide easy observation and are cost-effective but can be misleading due to convergent evolution. DNA barcoding offers precise identification and resolves cryptic species but requires specialized equipment and expertise.

Describe how the centrifuge was used in the DNA extraction steps

The centrifuge separates cellular components by spinning samples at high speed, allowing for the isolation of DNA from other cellular debris and solutions.

What does the acronym PCR stand for? What is the purpose of this technique?

PCR stands for Polymerase Chain Reaction. It is a technique used to amplify specific segments of DNA, producing millions of copies from a small initial sample.

Explain the steps of PCR, including the role of primers, as well as the temperature changes that occur during the denaturing, annealing, and extensions steps in the thermocycler

PCR involves three main steps: denaturation, where the double-stranded DNA is heated to separate it into single strands; annealing, where primers bind to the target sequences at a lower temperature; and extension, where DNA polymerase synthesizes new DNA strands. Primers are short sequences of nucleotides that initiate DNA synthesis during the extension step.

Define mtDNA

Mitochondrial DNA, is the DNA located in the mitochondria of a cell. It is inherited maternally and is often used in studies of genetics, evolution, and ancestry.

Define cpDNA

Chloroplast DNA, which is the genetic material found in the chloroplasts of plant cells. It is involved in photosynthesis and is passed from plant to plant, providing insights into plant evolution and relationships.

What is the purpose of gel electrophoresis?

The purpose of gel electrophoresis is to separate nucleic acids or proteins based on their size and charge, allowing for analysis and comparison of different samples.

Explain the purpose of a DNA ladder

A DNA ladder is a molecular weight marker used in gel electrophoresis to estimate the size of DNA fragments by comparing them to known DNA sizes.

Describe the relationship between the size of a DNA fragment and distance traveled

In gel electrophoresis, smaller DNA fragments travel farther through the gel compared to larger fragments, as they experience less resistance in the agarose matrix.

Explain how a gel should be oriented relative to the electric field in an electrophoresis chamber

The gel should be oriented with the wells closest to the negative electrode, allowing negatively charged DNA or RNA to migrate toward the positive electrode during electrophoresis.

Explain how gel electrophoresis can be used to confirm whether a PCR reaction was successful

Gel electrophoresis allows researchers to visualize the amplified DNA fragments produced by a PCR reaction. By comparing the size of the bands on the gel to a DNA ladder, one can determine if the PCR amplified the target DNA segment successfully.

What is the name of the type of sequencing used in this study?

Sanger sequencing

Sanger sequencing

A method for determining the nucleotide sequence of DNA using selective incorporation of chain-terminating dideoxynucleotides during DNA replication.

Explain what the QS and CRL tell us about the results of a Sanger sequencing reaction

The QS (Quality Score) indicates the confidence level in the accuracy of each nucleotide call, while the CRL (Contiguous Read Length) reflects the length of the longest uninterrupted sequence. Together, they provide insights into the reliability and completeness of the sequencing data.

How do you interpret the results of an electropherogram?

An electropherogram displays the DNA sequence as peaks, with each peak representing a nucleotide. By analyzing the peak height and sequence order, one can assess the quality and accuracy of the sequencing results.

Describe the purpose of the NCBI GenBank Database and BLAST in the context of this study

The NCBI GenBank Database provides researchers with access to a vast collection of genomic data. BLAST (Basic Local Alignment Search Tool) allows users to compare their sequences against those in the GenBank Database to identify similarities and infer functional or evolutionary relationships.

Describe the pros and cons of using DNA barcoding to identify species

Pros include its efficiency and accuracy in distinguishing closely related species, while cons encompass limitations in sequencing depth and the potential for misidentification due to insufficient reference data.

Describe the purpose of scientific posters in the community analysis and feedback step of the process of science

Scientific posters serve to effectively communicate research findings to a broader audience, facilitating discussion, feedback, and collaboration among scientists and the public.