Research Methods: Data, Reasoning, and Hypotheses

• Chapter 1 covers data types, reasoning, hypotheses, and experimental groups

Qualitative vs. Quantitative Data

• Qualitative data is descriptive and subjective
• Quantitative data is numerical and objective.
• Qualitative data explores new phenomena and generates hypotheses
• Quantitative data tests hypotheses and confirms/refutes theories

Inductive vs. Deductive Reasoning

• Inductive reasoning makes generalizations from specific observations
• Deductive reasoning makes specific predictions from general principles
• Inductive reasoning is used early to find patterns and form hypotheses
• Deductive reasoning is used later to test hypotheses and develop theories

Hypothesis Characteristics

• A hypothesis is a testable explanation for a phenomenon/observation set
• A good hypothesis is clear, concise, and specific and must be falsifiable
• Testable hypotheses can be supported/refuted by evidence
• Falsifiable hypotheses can be proven wrong
• Parsimonious hypotheses are the simplest that account for observations
• Fruitful hypotheses lead to new predictions/discoveries

Experimental and Control Groups

• Experimental groups are subjects exposed to independent variables being manipulated
• Dependent variables gauge effects of independent variables.
• Control groups are subjects not exposed to independent variables
• Results from the experimental and control groups are compared

Controlled Experiment

• Only one variable changes at a time
• This ensures observed effects stem from manipulated variables.
• They're used in scientific research to test hypotheses
• Controlling variables increases certainty in experiment results

Scientific Theory Attributes

• A scientific theory requires a well-substantiated explanation of the natural world

• Theories must have repeated confirmation through observation/experimentation

• Theories get revised/updated as new evidence emerges, but core principles are accepted

• Chapter 2 covers electron configuration, chemical bonds, and electronegativity

Electron Configuration

• The electron configuration of atoms is the electron distribution among orbitals
• Electron configuration determines chemical behavior
• Atoms with the same number of valence electrons have similar chemical properties

Chemical Bonds

• Chemical bonds are attractive forces between 2+ atoms formed when atoms share/transfer electrons
• Covalent bonds form when atoms share electrons
• Ionic bonds form when atoms transfer electrons
• Hydrogen bonds are weak, covalent bonds between a hydrogen atom and an electronegative atom

Polar vs. Nonpolar Covalent Bonds

• Covalent bonds are polar if electrons are shared unequally between atoms
• It occurs when one atom is more electronegative
• Covalent bonds are nonpolar if electrons are shared equally between atoms
• It occurs when the electronegativity between the two atoms is the same

Electronegativity

• Electronegativity gauges an atom's capacity to attract electrons

• The higher the electronegativity, the stronger the attraction

• Chapter 3 covers hydrogen bonding, water properties, and its role in life

Hydrogen Bonding

• Hydrogen bonds result from polar covalent bonds in water molecules
• Water is polar with slightly positive and negative ends
• Oxygen is more electronegative than hydrogen
• Electrons in water's covalent bonds are shared unequally
• Oxygen attracts electrons, giving hydrogen a slightly positive charge
• Positive hydrogen atoms attract negative oxygen atoms in other molecules

Water's Unique Properties

• Hydrogen bonds give water unique properties
• Cohesion and high specific heat (heat without changing temp) make water essential for life
• Water is an excellent solvent and regulates temperature
• It also transports nutrients and participates in reactions

Moderating Temperatures

• Water has a high specific heat, meaning it absorbs much heat without changing temperature
• Water absorbs heat from the sun during the day and releases it at night to moderate temperature

Water as a Solvent

• Water dissolves substances due to its polarity
• Polar molecules have slightly positive and negative ends
• Water surrounds and dissolves polar molecules and ionic compounds

Acids and Bases

• Acids donate protons (H+) and, when dissolved in water, raise H+ concentration

• Bases accept protons (H+) and, when dissolved in water, reduce H+ concentration

• Buffers resist pH changes, made of weak acid/conjugate base or weak base/conjugate acid

• Buffers neutralize small amounts of added acid or base

• Chapter 4 covers Miller's experiments and carbon's properties

Miller's Experiments

• Stanley Miller and Harold Urey's experiments in the 1950s showed that organic molecules formed from inorganic materials on early Earth
• They created a closed system with water, methane, ammonia, and hydrogen
• They applied an electric spark to simulate lightning
• Amino acids (protein building blocks) formed
• The experiments show that organic molecules may have had a role in forming life on early Earth

Carbon's Versatility

• Carbon forms diverse molecules because it has four valence electrons and forms four covalent bonds and single, double, and triple bonds allowing varied shapes and sizes
• Carbon is the backbone of biological macromolecules, including carbohydrates, lipids, proteins, and nucleic acids
• Molecules with the same chemical formula but different structures = isomers

Isomers Types

• There are structural isomers, cis-trans isomers, and enantiomers
• Structural isomers share molecular formulas but have different connectivity
• Butane and isobutane are structural isomers of C4H10
• Amines have an amino group

Functional Groups

• Functional groups determine a molecule's characteristic reactions

• Examples include hydroxyl (OH), carbonyl (C=O), carboxyl (COOH), amino (NH2), sulfhydryl (SH), phosphate (PO4), and methyl (CH3)

• Chemical properties depend on structure/atoms

• Hydroxyl groups are polar and attract water, making alcohols soluble

• Chapter 5 covers protein structure and biological macromolecules

Protein Structure

• There are amino acids in proteins
• Amino acid sequences are called primary structure
• Secondary structure is the polypeptide backbone's local structure
• Alpha helices and beta sheets indicate secondary structure
• Tertiary structure involves 3D overall shape with hydrophobic interactions, van der Waals forces, hydrogen, and disulfide bonds
• Quaternary structure involves multiple polypeptide chains
• Not all proteins have quaternary structure

Biological Macromolecules

• The four main macromolecules are carbohydrates, lipids, proteins, and nucleic acids
• Carbohydrates store energy and provide structural support
• Lipids store energy, insulate, and signal cells
• Proteins catalyze reactions, transport substances, and provide structural support
• Nucleic acids store/transmit genetic information

Monomers

• Carbohydrate monomers are monosaccharides

• Protein monomers are amino acids

• Nucleic acid monomers are nucleotides

• Chapter 6 covers microscopy and cell structure

Light vs. Electron Microscopes

• Light microscopes use visible light and are inexpensive/easy to use
• Electron microscopes use electrons and have higher resolution but are expensive/difficult to use

Scanning vs. Transmission Electron Microscopes

• Scanning electron microscopes (SEMs) scan surfaces with electrons for 3D images
• Transmission electron microscopes (TEMs) transmit electrons through specimens for 2D internal structure views

Domains and Cell Types

• The three life domains include Bacteria, Archaea, and Eukarya
• Bacteria and Archaea are prokaryotic cells
• Prokaryotic cells may lack a nucleus or other membrane-bound organelles
• Eukarya are eukaryotic cells
• Eukaryotic cells may have a nucleus and other membrane-bound organelles

Key Cell Components

• All cells have a plasma membrane, cytoplasm, and ribosomes
• The plasma membrane is the barrier separating the inside of the cell from the outside environment
• Cytoplasm is a jellylike substance containing organelles
• Ribosomes synthesize proteins

Cell Size and Types

• Cell size is limited by the surface area to volume ratio
• Larger cells = lower area to volume ratio
• Prokaryotic cells lack a nucleus/membrane-bound organelles
• Eukaryotic cells have multiple organelles
• Free ribosomes in the cytoplasm synthesize proteins for use within the cell

Endomembrane System

• The endomembrane system is a network of membranes in eukaryotic cells
• It includes the endoplasmic reticulum, Golgi apparatus, lysosomes, and vesicles

Distinguishing Eukaryotic Cells

• Prokaryotic cells are smaller, and they also lack a nucleus and other membrane-bound organelles.
• Eukaryotic cells have multiple organelles

Organelles

• The nucleus contains DNA

• This makes it the cell control center

• Mitochondria produce ATP

• They're the powerhouses of the cell

• Chapter 7 covers membrane structure and transport

Fluid Mosaic Model

• The fluid mosaic model describes the plasma membrane
• There's a phospholipid bilayer with proteins
• The bilayer is fluid, allowing phospholipids/proteins to move constantly through
• The membrane is a mosaic of molecules with different structures and functions

Membrane Components

• Plasma membranes consist of phospholipids, proteins, and carbohydrates
• Phospholipids form a bilayer with hydrophilic heads facing out and hydrophobic tails facing in
• This creates a barrier permeable to some molecules
• Proteins get embedded in the bilayer and transport molecules and catalyze reactions
• Proteins also signal to other cells
• Carbohydrates on surfaces play a role in cell adhesion
• Small, nonpolar molecules move through membranes most easily via the hydrophobic interior

Solutions

• Isotonic solutions have the same solute concentration as cells
• Water moves into and out of those cells the same rate, so cells keep form
• Hypertonic solutions have higher solute concentrations than cells, moving water out and causing shrinkage
• Hypotonic solutions have lower solute concentrations than cells, moving water in and causing swelling

Solutions Ideal for Plants and Animals

• A hypotonic solution is ideal for plant ells
• A cell wall prevents plants from bursting in hypotonic conditions
• An isotonic solution is ideal for animal cells
• Animal cells don't have a cell wall for protection and thus will swell

Aquaporins

• Aqauporins are proteins and form channels in the plasma membrane
• Channels facilitate water movement across the cell membrane and regulate water balance

Sodium-Potassium and Electrogenic Pumps

• The sodium-potassium pump transport sodium ions out of the cell and potassium ions into to cell
• This manages electrochemical gradients for nerve impulse transmission and contraction
• Electrogenic pumps transport ions to create electrochemical gradients, essential for cellular processes
• The electrogenic process includes nerve impulse transmission and muscle contraction

Membrane Potential

• Membrane potential is the difference in potential across the plasma membrane

• This is created by unequal ion distribution.

• It helps with nerve impulse transmission and contraction

• Chapter 8 covers thermodynamics

Laws of Thermodynamics

• The first law of thermodynamics states that energy cannot be created or destroyed, only transferred/converted
• The second law of thermodynamics states that the universe's entropy (disorder) constantly rises

Free Energy

• Equations calculate the change in free energy (ΔG = ΔH - TΔS)
• ΔG is the amount of energy to do work
• ΔH is the change in enthalpy (total energy)
• T is temperature in Kelvin
• ΔS is the change in entropy

Spontaneous Chemical Reaction

• A reaction is spontaneous if ΔG is negative and occurs without energy input
• It's nonspontaneous if ΔG is positive and needs energy input

ATP

• ATP is the cell's energy currency, powering muscle contraction, protein synthesis, and transport
• ATP does cellular work via phosphorylation (moving a molecule phosphate group)

Enzymes

• Enzyme activity is affected by temperature, pH, and substrate concentration
• Enzymes have optimal temperatures and pH, with activity decreasing otherwise
• High substrate concentrations saturate enzymes and level off reaction rates

Enzymes and Inhibitors

• Enzymes are can get competitively or non-competitively inhibited

• Competitive inhibitors bind to the active site, like a lock, preventing substrate binding

• Noncompetitive inhibitors site alter the shape of the enzyme, also preventing substrate binding

• Allosteric regulation increases or decreases activity

• Chapter 9 covers cellular respiration

Oxidization

• Cellular respiration oxidizes organic fuel molecules
• Cellular respiration breaks down glucose and organic molecules to produce ATP
• Glucose is oxidized and loses electrons during cellular respiration
• Electrons get transferred to carriers such as NAD+ and FAD

Electron Flow

• The carriers transfer electrons to the electron transport chain to generate ATP

Stage of Cellular Respiration

• The main stages are glycolysis, the citric acid cycle, and oxidative phosphorylation

Glycolysis

• During glycolysis, glucose breaks down into two pyruvate molecules in the cytoplasm of the cell

Citric Acid Cycle

• With the citric acid cycle, pyruvate oxidizes to produce CO2 in the mitochondrial matrix

Oxidative Phosphorylation

• Oxidative phosphorylation generates ATP from electrons carried by NADH/FADH2 in the inner mitochondrial membrane

Fermentation

• During fermentation, pathways recycle NAD+ by transferring electrons to pyruvate to create ATP without oxygen
• NADH transfers electrons to regenerate NAD+ and continue glycolysis

Types of Fermentation

• There are two main types of fermentation
• Alcoholic fermentation
• Lactic acid fermentation

Cellular Respiration and Oxygen

• Oxygen acts as the final acceptor in final the electron transport chain
• Without oxygen, the electron transport chain cannot function and so cannot generate ATP

Citric Acids

• CO2 releases during the citric acid cycle
• Substrate-level phosphorylation directly transfers a phosphate group to ADP to product ATP
• Oxidative phosphorylation generates ATP using energy from electrons carried by NAD+ and FAD

NAD+

• NAD+ is recycled during fermentation by transferring electrons from NADH to pyruvate

Explore qualitative vs. quantitative data, inductive vs. deductive reasoning, and the characteristics of a good hypothesis. Learn how to form testable explanations and make predictions. Understand data analysis and testing methods.