Scientific Method + Molecular Biology Lecture Flashcards

2025 Baology Course (Lectures 1 and 2)

Scientific Method

Widely agreed upon method by which scientists operate to formulate and test hypotheses through observation, experimentation, and analysis (discovery based research does not count, you must have a question to concur with the method).

Inductive Reasoning

Begins as a series of observations that evolve into a hypothesis

Deductive Reasoning

Begins as a theory that is then backed by experimentation, observation and finally a confirmation of said theory

Basic Hypothesis Setup

If X then Y because Z

If soda is carbonated then the carbon can be released because the gases will equilibrate

Positive Control

A group in an experiment that receives a treatment with a known response to ensure that the experimental setup is capable of producing results.

Negative Control

A group in an experiment that does not receive the treatment, allowing researchers to observe any changes outside of the experimental variable.

Binary Data

Data that can take on two possible outcomes, often represented as 0 or 1, true or false. Truly a yes or no situation.

Float Data

A type of data that can take on a nearly infinite number of values within a given range, often used in experiments to represent measured quantities such as weight or volume. More rare in molecular biology papers (thus, less common on USABO)

Important Considerations for Histograms

Picking bin size, the arrangement of data for effective visualization and representation of frequency distribution.

Flow Cytometry

A technique used to analyze the physical and chemical characteristics of cells or particles in a fluid as they pass through a laser and automatic cell sorter. It is commonly used for sorting and counting cells in biological research. Gating is a method used to isolate specific populations based on their characteristics. Machine will put those cells with those properties in one section.

Side and Forward Scatter (SSC and FSC)

Determines how much light is splitting off, allowing identification of cell size (FSC) and internal complexity (SSC) in flow cytometry.

FSC Height and FSC Area

Refers to measurements in flow cytometry that provide information about the size and granularity of cells. FSC Height indicates the peak value of light scatter based on cell size, while FSC Area represents the total light scatter, useful for cell population analysis.

Manhattan Plot

Plots location on the chromosome with correlation to a certain trait. Set the cutoff for correlation based on sample size and certainty you have the trait is correlated. Seen on Genome Wide Association Studies, which are not particularly useful.

FRET

Technique where you use one fluorescent molecule to react with another fluorescent molecule (which would subsequently fluoresce) to detect interaction between the two. Overlap region where one will simulate the other is measured by sample ones emission and sample twos absorption. Always test the end of both spectra for accuracy.

The Joy Plot

Stacked line histograms together. Researcher will elect to organize them to reveal ranked order. If something such as time is on the X-Axis it can be very useful.

Principal Component Analysis

A method for reorienting data (IE gene sequencing) to understand clustering, can collapse most salient features into two/three dimensions. Can combine certain traits (component compression). Consider what the groupings mean biologically and what is being highlighted.

Box and Whisker Plot

Box portion shows median value, interquartile range (25th to 75th percentile) and whiskers demonstrate minimum and maximum value (MIN/MAX plus/minus IQR*1.5).

Violin Plot

A more advanced box and whisker plot that shows a live histogram

The Reason Why Emergent Properties of Water Occurs

High heat capacity, cohesion, adhesion, surface tension, and evaporative cooling are all due to hydrogen bonding networks (intramolecular forces).

Gravity Versus Surface Tension Trade-Off

Small organisms are not hindered by gravity, yet are unable to escape the surface tension of water.

Transpiration

Product of waters emergent properties of cohesion and adhesion. Water travels from the roots of plants to shoots (much more notable in trees). Water sticks to itself and the sides of water conducting cell walls to push the water up.

Water Phase Diagram

Diagram with temperature as X-Axis and pressure as the Y-Axis. Slope of line between liquid and solid is negative. Water is more dense as a liquid than solid (why ice floats).

Molarity

Most common, used for any solution. Measures moles of solute per volume of solution in liters (total).

Molality

Less common. Measures moles of solute per kg of solvent. Affects the colligative properties (freezing and boiling post, osmotic pressure, and vapor pressure).

pH

Negative log concentration of hydrogen ions which indicates acidity of a certain solution.

The Henderson Hasselbalch Equation

pH = pKa + log (conjugate base/acid)