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.

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

Similar to box and whisker plots, violin plots display the median value and interquartile range (25th to 75th percentile) but adds a rotated kernel density plot on each side to show the probability density of the data at different values. They are useful for visualizing the distribution and identifying modes (peaks) in the data.

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 and the strength of the intramolecular bonds.

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

A graphical representation illustrating the physical states of water (solid, liquid, gas) under varying conditions of temperature (X-axis) and pressure (Y-axis). Notably, the slope of the line separating the liquid and solid phases is negative, indicating that water is denser in its liquid form than in its solid form (ice), which explains why ice floats.

Molarity

Most common means of looking at solute concentration, used for most solutions. Measures moles of solute per volume of solution in liters (total).

Molality

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

pH

The negative log concentration of hydrogen ions (from dissociation of water) which indicates acidity of a certain solution.

The Henderson Hasselbalch Equation

pH = pKa + log (conjugate base/acid)

Applications of the Henderson Hasselbalch Equation

Used to calculate the pH of a solution within its buffer zone where weak acids and bases are in equilibrium. Useful in understanding amino acid behavior during titration, predicting pH changes, and maintaining stable pH conditions in biological systems.

Buffer Zone

The buffer zone, occurring during titration, is the region where weak acids and weak bases coexist, facilitating the exchange between their ionized and deionized forms.

Most common form of polymerization

Dehydration synthesis

Ester Linkages in Translation

Notably the binding site between tRNA molecule and amino acids within the ribosome.

How sugars become hydrolyzed and seperated

Excess electrons from oxygen will attack hydrogen ion, creating an unstable intermediate and thus fracturing the two molecules.

Carbohydrates

Carbon chained molecules with formula CnH2nOn capable of having the water taken out and becoming pure carbon.

Number of carbon atoms in a typical carbohydrate monosaccharide

3-7 Carbons (rarely larger than this)

How do sugars of the same length differ

Sugars of the same length can differ due to variations in the arrangement of atoms around their chiral centers. Because these molecules are asymmetrical, different arrangements lead to different stereoisomers. Sugars that differ in configuration at only one chiral center are called epimers.

The monosaccharide that was no chiral center

Dihydroxyacetone which does not have an asymmetrical carbon (only carbon that would be assymetrical has a carbonyl so it cant)

How to calculate steroisomers

For every chiral center you have you have 2^n stereoisomers (where N is the chiral centers)

How to Differentiate Between L and D Forms of Monosaccharides

Chirality of the carbon that is most distant from the carbonyl

The form of monosaccharides primarily prevalent in the kingdom of animalia and humans, notably

D Carbohydrates

Aldose

Carbohydrate with a carbonyl attached at the end

Ketose

Carbohydrate with a carbonyl in the center of the molecule

The Fischer Projection

Way biological molecules are drawn (croissant that curves away from you with ribs coming towards you)

Form Monosaccharides are Typically Found In

Ring form

Difference between Hemiacetals and Hemiketals

Hemiacetals are reducing because they possess a reactive hydroxyl group and a hydrogen atom attached to the same carbon, allowing them to donate electrons (reduce other substances). Hemiketals, while structurally similar, are less prone to oxidation due to the carbon atom of the carbonyl group being bonded to two carbon-containing groups, making them non-reducing under typical conditions.

Reducing Tests

Tests that employ the addition of ions that can be reduced to detect hemiacetals. Color change can be observed. Hemiketals will not react because in standard conditions they will not give up electrons.

Which ketose is reducing

Fructuose can interconvert itself into glucose by forming an acyclic anion → ene-diol intermediate → glucose. Thus it is a reducing agent. This reaction occurs in the presence of base so adding more acid to your solution can counteract this.

Barfoeds Test

Barfoed's Test is a chemical test utilized to detect the presence of monosaccharides (reducing sugars) in a sample. Conducted under weakly acidic conditions using copper(II) acetate, monosaccharides reduce the copper(II) ions to copper(I) oxide, forming a brick-red precipitate. Disaccharides react more slowly because they need to be hydrolyzed into monosaccharides first, leading to a delayed or weaker reaction.

Notable feature of polysaccharides

Some polysaccharides have a reducing end because the hemiacetal end of the chain is not bonded both ways and thus can reduce other compounds.

Storage Polysaccharides

Starch (never branches, only in plants and least evolutionary common, alpha 1-4 connections occasional alpha 1-6 connections)

Glycogen (same connection structure as starch except higher abundance of alpha 1-6 connections)

Cellulose (beta 1-6 connections, allows hydrogen bonding within strands, which gives strength between strands)

Lugols Iodine Test

Test for presence of polysaccharides with potassium iodine (positive is black, negative is orange-y). This is also used in gram stain procedure, iron supplement and various medications.

Lipids

Chemically not monomeric so debatable whether they are macromolecules. Hydrophobic tails joined to a hydrophilic head through an ester linkage formed through dehydration synthesis. Fatty acid tail can both be saturated or unsaturated with hydrogen atoms. Double bonds (unsaturated) make hydrophobic tails kinky, which creates a physical obstruction that keeps them as liquid with low melting point (i.e. olive oil).

How Fatty Acids Are Characterized

Seperated into odd and even, which changes the breakdown reaction because you use beta oxidation which takes out two carbons at a time.

The type of fatty acid humans can synthesize

Even chained fatty acids

Sudan Test

Tests for the presence of lipids. Becomes red in the presence of lipids because sudan shifts from one form of the molecule to the other and changes the pigment.

Paper Bag Test

Alternative to the Sudan Test. Oil makes paper bag translucent, water does not (just darker).

Four Types of Membrane Lipids

Glycerophospholipids, Galactolipids, Sulfolipids, Sphingolipids

Membrane Lipids

Membrane lipids are amphipathic molecules characterized by a glycerol backbone linked to two fatty acid tails, which provide a hydrophobic barrier. Instead of a third fatty acid, a polar head group is attached to the glycerol, creating a hydrophilic region.

Glycerophospholipids

Most common class of membrane lipid and notably includes phosphatidylserine which is a simple membrane lipid. One of two very common classes of lipids.

Galactolipids

A relatively rare membrane protein found in chloroplast membranes.

Sulfolipids

A very rare membrane protein with high quantity of sulfur.

Sphingolipids

A class of membrane proteins oftentimes found in lipid rafts. One of two very common classes of lipids. Contains three classes.

Cardiolipin

Inner mitochondrial membrane lipid that is also a signalling molecule for apoptosis.

Diphytanyl Tetraether

A type of monolayered membrane lipid only archaea possess.

Cholesterol

Steroid composed of four conjugated carbon rings (three of which are six carbon, one of which is five carbon) that is imbedded in plasma membranes to maintain liquidity and is all around very useful.

Form Amino Acids are Found In

Only found in the L form

Alipathic/Non-Polar Amino Acids

Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine

Helix Breakers

Proline and Glycine both prevent the formation of alpha helices

Polar Amino Acids

Serine, Threonine, Cysteine, Asparagine, Glutamine

Aromatic (Non-Polar) Amino Acids

Phenylalanine, Tyrosine, Tryptophan (All of which can absorb light)

Basic (Positively Charged) Amino Acids

Aspartate and Glutamate

Acidic (Negatively Charged) Amino Acids

Lysine, Arginine, Histidine

Ninhydrin Test

Test to detect individual amino acids by reacting with the amine groups on amino acids. Technique does not work for proteins because they are joined together via amine groups.

Titration of amino acids

Amino acids possess ionizable R-groups that dictate their charge at various pH levels. During titration, different R-groups undergo ionization at varying pH values. This process involves gradual addition of acid or base, enabling the precise determination of the amino acid's pKa values.

Disulfide Bridges

Type of bond between two cysteine amino acids that determined protein structure. Two cysteines form a cystine (twin has an I).

Protein Folding Determinants

Protein folding is influenced by environmental factors such as pH and temperature. Proteins tend to fold into a conformation that minimizes their free energy (Gibbs Free Energy \Delta G ), leading to a stable and functional three-dimensional structure.

Chaperonins

Chaperonins are specialized protein complexes that assist in the proper folding of other proteins within a cell, preventing aggregation and misfolding. They often function by providing a protected environment where proteins can fold correctly, particularly useful in stressful conditions or for complex proteins. They are looked at as a potential treatment for prion diseases because they refold denatured proteins.

Polypeptide Sequencing

A process used to determine the order of amino acids in a polypeptide chain. While gene knockout techniques can identify a protein's function, they do not reveal its sequence. Edman Degradation is a common method used. This method involves using phenylisothiocyanate (PITC), also known as Edman's reagent, to selectively label and remove the N-terminal amino acid of the polypeptide. This process can be repeated to sequentially identify each amino acid in the chain. Mass spectrometry is an alternate approach that is based on the mass-to-charge ratio of peptide fragments to infer the sequence.

Ramachdran Plot

A protein visualization tool that plots the ϕϕ (phi) and ψψ (psi) angles of amino acid residues in a protein structure. These angles represent the rotational freedom around the alpha carbon in the polypeptide backbone.

Column Chromatography

A diverse set of methods in which you drip a solution containing your chosen protein into a column and let the proteins separate. You can do this via size, ionization, etc.

Alpha Helices

Secondary structure involving hydrogen bonding of backbone. Hydrogen bonds between the fourth residue create alpha helices.

Beta Sheets

Secondary structure involving hydrogen bonding of backbone. Favors large aromatic amino acids in the center and can occur with crossover or no crossover.

Collagen

Prime example of quaternary structure between its 3 distinct alpha helix chains interact to create a very strong makeup. Most abundant protein in the animal kingdom.

Furanose

Ring structure of a ketose

Puranose

Ring structure of an aldose

Benedicts test

Tests for hemiketals by quantifying the conversion of Cu2+ → Cu+ in the presence of carbohydrates

Tollens Test

Tests for hemiketals by quantifying the conversion of Ag+ → Ag in the presence of carbohydrates

Sphingomyelin

Class of sphingolipids with a phosphacoline head

Glycosphingolipids

Class of sphingolipids only found in the outer leaflet that have a sugar attached to them. Two notable glycosphingolipids are cerebrosides and globosides.

Gangliosides

Class of sphingolipids that have complex oligosaccharides

Difference between Cerebrosides and Globosides

Cerebrosides have 1 sugar and are present in nervous cells. Globosides have 2+ sugars and play a role in cell recognition, adhesion, and signal transduction

Non-Coded Amino Acids

There are 300 total amino acids including intermediates and non-proteogenic molecules. Hydroxyproline and pyrolysine are used to make proteins. N-methyllysine is found in myosin for contracting. Gamma carboxyglutamate is found in prothrombin to help bind calcium. Desmosine is found in elastin. Selenocysteine is also uncoded for and rare.

Hybridization

SP3 and SP2 hybridization. SP3 is tetrahedral (4 atoms attached) and SP2 is planar (3 atoms attached (double bonds count as one)).

Formal Charge

Hypothetical charge of a molecule if each bond was shared equally (1/1 split)

Formal Charge Equation

formal charge (q) = V - L - (B/2)

valence electrons - electrons in lone pairs - electrons in bonds/2

negative charges show up on electronegative atoms such as oxygen

Resonance (in organic chemistry)

Distribution of electrons across an entire molecule

Types of arrow pushing

From bond to bond, from bonds to atom, atom to bond

Always move two electrons at a time

Conjugation

When long molecules with alternating single and double bonds have arrow pushing behaviors

Allylic Lone Pairs

Allylic carbons are the carbons adjacent to a double bond. If there is a lone pair on an allylic group it will be pushed onto the double bond and then onto one of the other allylic groups.

Allylic Carbocations

Positive charge is transferred from one carbocation to another by shifting the electron density of an adjacent double bond (similar as allylic lone pair).

Lone Pair Next to Carbocation

Arrow pushing shift from a lone pair with a negative formal charge to a carbocation, making a double bond to distribute the formal charge.

Pi Bonds Between Atoms of Difference in Electronegativity

Same process as lone pair next to carbocation in reverse, sends double bond from two atoms and gives those two atoms a formal charge