Preliminary Exam

What is microscopy?

The scientific practice of using microscopes to observe objects not visible to the human eye due to small size

What is used to focus the electrons when using an electron microscope?

An electromagnetic lens

What is the most commonly used type of microscopy?

Light/brightfield microscopy

If you were examining virus attachment to the surface of a cell, what type of microscope would be the best option? Explain.

Scanning Electron Microscope (SEM). It is ideal for this purpose because it scans the specimen's surface with a focused electron beam, producing detailed, three-dimensional (3D) images of the topography and morphology of both the cell and the virus attachment.

If the ocular of a microscope is 20x and the objective is 100x, what is the total magnification?

(Eye Lens) * (Objective)

What is the best footwear to use in the lab?

Closed-toe, non-perforated, and made of fluid-resistant materials like leather or synthetic leather, featuring non-slip soles. Shoes should cover the entire foot to protect from spills etc.

Why should we not add water to a solution containing concentrated acids?

The reaction is highly exothermic, releasing intense heat that can cause the water to boil instantly, causing acid to splatter or splash. You should add the concentrated acids to water.

What is a common feature of all biosafety cabinets?

A common feature of all biosafety cabinets (BSCs) is the use of High-Efficiency Particulate Air (HEPA) filtration for their exhaust air, which removes harmful aerosols and microorganisms (bacteria and viruses) before the air is discharged.

How should hazardous materials be stored?

Hazardous chemicals must be stored in clearly labeled, tightly sealed containers in well-ventilated, secure, and dry areas, separated by compatibility (e.g., separating acids from bases and flammables from oxidizers). Chemicals should be stored below eye level, away from direct sunlight/heat, and utilize secondary containment.

You examine a bottle of liquid in the lab with no labels, what is the next appropriate step?

1. Do Not Handle: Avoid moving or opening the bottle, as the contents are unknown and potentially hazardous.

2. Secure the Area: Keep others away from the area to prevent accidental exposure.

3. Notify Authority: Report the discovery to a responsible authority (e.g., PI, Lab Manager).

4. Label as "Unknown": If necessary to move it to a safe location, label the container as "UNKNOWN - HAZARDOUS WASTE" and contact the Environmental Health and Safety (EHS) office for proper disposal.

Upon completion of laboratory work, what steps should you follow exiting the lab?

1. Clean and Decontaminate: Wipe down all benches and surfaces with appropriate disinfectants or cleaning agents.

2. Waste Management: Dispose of waste materials in the appropriate containers (e.g., biohazardous bags, chemical disposal).

3. Equipment Shutdown: Turn off electrical devices, instruments, water faucets, and gas burners.

4. Remove PPE: Remove gloves (inside out) and lab coats before leaving the lab area. Do not wear PPE in common areas like offices or cafeterias.

5. Personal Hygiene: Always wash hands with soap and water after removing gloves and before leaving.

6. Secure the Lab: Close all windows, check refrigerators/freezers, and lock the main exit door if required.

7. Check Shared Spaces: Ensure all equipment in shared labs or fume hoods is cleaned and turned off.

You are conducting an experiment with a 10% NaCl solution, and it contacts your bare skin. Should you

Simply rinse your hands in the sink. Can cause mild skin irritation and should be avoided, it is generally not classified as a severely corrosive or hazardous substance requiring a full emergency shower.

What is a p value?

The p value (probability value) is used in statistics to assess how well the observed data align with the null hypothesis

What is the difference between a T-Test and ANOVA?

ANOVA (Analysis of Variance) is used when comparing the means of three (3) or more groups. T-Test compares the means of two (2) groups.

What is the relationship between correlation and causation?

Correlation measures the strength and direction of a relationship between two variables, while causation indicates that one variable directly causes the other to change. Correlation does not imply causation.

When interpreting research data, why is the p-value important?

A small p value (<0.05) suggests strong evidence against the null hypothesis (consider rejecting the null hypothesis), while a large p value suggests weak evidence against the null hypothesis (consider not rejecting the null hypothesis).

What are the different types of peer review?

• Single-blind (reviewer anonymous),

• double-blind (both anonymous),

• open peer review (identities revealed).

• Other types include collaborative reviews, where reviewers work together, and post-publication reviews, where comments occur after the paper is published.

What are the main outcomes of peer review?

• Acceptance without changes,

• accept with minor revisions,

• accept with major revisions,

• revise and resubmit (The paper is rejected in its current form but invited for resubmission as a new manuscript after significant improvements),

• rejection

What leads to rejection after peer review? (7)

• Lack of novelty or innovation,

• poor study design,

• poor quality data,

• inadequate literature review,

• poor language and readability,

• unsupported conclusions,

• submission errors

Why is the peer review process necessary in science? (3)

• credibility,

• integrity of published research,

• acts as a quality control mechanism for scientific literature

What does it mean if someone is the first author to a publication?

They are the primary contributor/lead researcher

List the steps a manuscript goes through to be accepted for publication. (8)

• Pre-submission preparation,

• submission,

• desk review,

• peer review,

• author revisions,

• editorial decision,

• acceptance to production,

• online publication

What is activation energy, and why is it needed in chemical reactions?

Activation energy is the minimum amount of energy required to initiate a chemical reaction, acting as a barrier between reactants and products. It is essential for breaking existing chemical bonds and allowing reactants to collide with enough force to form new bonds. It determines reaction rates and is often provided as heat.

How do enzymes lower the activation energy of chemical reactions? (3)

• use their active sites to bind substrates in optimal orientations

• strain bonds to initiate breakage,

• create favorable electrostatic environments, allowing reactions to occur at lower temperatures than otherwise required.

Name six amino acids.

Leucine, Isoleucine, Valine, Arginine, Lysine, Glycine, Histidine, Methionine, Phenylalanine, Threonine, Tryptophan, Alanine, Asparagine, Aspartic Acid, Cysteine, Glutamic Acid, Glutamine, Proline, Serine, Tyrosine

What are monosaccharides? Give two examples.

1. A monosaccharide is the simplest form of sugar and the basic unit of carbohydrates, which cannot be hydrolyzed further into simpler sugars. 

1. glucose (blood sugar)

2. fructose (fruit sugar)

3. galactose

What is ATP and explain how it is used by the cell.

Adenosine triphosphate (ATP) is the primary energy carrier and "energy currency" of all living cells, providing readily releasable energy to fuel biological processes. It stores energy in high-energy phosphate bonds, releasing it when converted to ADP (adenosine diphosphate) to power muscle contraction, molecule transport, and protein synthesis.

Define Homeostasis. Use examples in your description and explain how negative and positive feedback mechanisms are related to homeostasis.

• Homeostasis is the human body’s ability to perform regulatory functions despite the external environments changing surroundings.

• Negative feedback is when the body downregulates a stimulus, bringing it back to its original state. (Sweating)

• Positive feedback upregulates a stimulus, pushing it further from its original state. Both mechanisms maintain homeostasis. (Oxytocin/Breastfeeding)

What are the basic components of the membrane of a cell?

The cell membrane (plasma membrane) is a dynamic, fluid mosaic primarily composed of a phospholipid bilayer, proteins, cholesterol, and carbohydrates.

Among the cellular structures identified in the eukaryotic cells, which organelle is the site for protein synthesis?

Ribosomes are the primary cellular organelles responsible for protein synthesis in eukaryotic cells. They translate messenger RNA (mRNA) into chains of amino acids, assembling them into proteins. They function either freely in the cytosol or attached to the rough endoplasmic reticulum.

Describe passive transport across a biological membrane.

1. The spontaneous movement of substances across a biological membrane along a concentration gradient—from high to low concentration—without requiring cellular energy (ATP). Driven by diffusion, it allows small, nonpolar, or lipid-soluble molecules to move until equilibrium is reached.

2. Key types of passive transport include:

   1. Simple Diffusion: Substances pass directly through the phospholipid bilayer, such as oxygen, carbon dioxide, or small nonpolar molecules.

   2. Osmosis: The specific diffusion of water molecules across a selectively permeable membrane.

   3. Facilitated Diffusion: Polar or charged substances (e.g., ions, glucose) use membrane proteins—channel or carrier proteins—to move down their gradient without energy.

An alternative form of a gene is referred to typically as a(n) ______.

Allele

Which special chemical represents a distinct organic molecular compound required for heredity function?

Deoxyribonucleic acid (DNA) is the distinct organic molecular compound, specifically a nucleic acid, that acts as the primary carrier of genetic information for heredity.

List and describe the stages of mitosis.

1. (P)rophase - Chromosomes condense, the nucleolus disappears, and the mitotic spindle begins to form. The nuclear envelope begins to break down.

   1. Prometaphase - The nuclear envelope fully breaks down and microtubules attach to kinetochores

2. (M)etaphase - Chromosomes line up along the equator of the cell (metaphase plate). Spindle fibers attach to the centromere of each chromosome.

3. (A)naphase - Sister chromatids separate and are pulled toward opposite poles of the cell.

4. (T)elophase - Nuclear membranes re-form around each set of separated chromosomes. The chromosomes begin to decondense (uncoil).

   1. Cytokinesis - Divides the cytoplasm and separates the two daughter cells.

Explain (in short) how the process of DNA to a functional protein is carried out.

1. Transcription (Nucleus)

   1. RNA polymerase reads the DNA sequence of a gene and synthesizes a complementary messenger RNA (mRNA) molecule. This mRNA is processed (e.g., removing introns) before leaving the nucleus.

2. Translation (Cytoplasm)

   1. The mRNA binds to a ribosome, which reads the genetic code in triplets called codons. Transfer RNA (tRNA) molecules match specific amino acids to each mRNA codon, allowing the ribosome to assemble a polypeptide chain.

3. Folding and Maturation

   1. The polypeptide chain folds into a specific three-dimensional structure and may undergo post-translational modifications to become a fully functional protein.