Understanding Phylogeny and Cell Biology Concepts Save

Phylogeny

The evolutionary history of species or genes, reconstructed using phylogenetic trees.

Node

Represents a divergence event (e.g., speciation, gene duplication).

Root

Common ancestor of all taxa on the tree.

Branch

Represents lineage.

Taxon

A named species or group (e.g., humans, mammals).

Clade

A monophyletic group (ancestor + all descendants).

Homologous Traits

Inherited from a common ancestor.

Homoplastic Traits

Traits that appear similar due to convergence or reversal, not inheritance from a common ancestor.

Convergent Evolution

Independent evolution of similar traits (e.g., bird and bat wings).

Evolutionary Reversals

Return to an ancestral state (e.g., fins in cetaceans).

Synapomorphies

Shared derived traits indicative of common ancestry.

Ancestral Traits

Shared by ingroup and outgroup, predating the divergence of the ingroup.

Derived Traits

Evolved within the ingroup and not present in the outgroup.

Ingroup

Species of primary interest.

Outgroup

A species used to determine ancestral traits.

Parsimony

Simplest explanation with the fewest evolutionary changes is preferred.

Maximum Likelihood

A model for analyzing molecular data.

Molecular Clocks

Measure divergence time based on mutation rates in DNA or proteins.

Binomial Nomenclature

Genus + species (e.g., Homo sapiens).

Monophyletic Groups

Include all descendants of a common ancestor.

Polyphyletic Groups

Exclude the common ancestor (invalid in taxonomy).

Paraphyletic Groups

Exclude some descendants of a common ancestor (incomplete group).

Shared, derived traits

Indicate evolutionary relationships.

Binomial Nomenclature

Genus + species (e.g., Homo sapiens). Follows strict rules to avoid ambiguity.

Cell Theory

Cells are the fundamental units of life. All living organisms are composed of cells. All cells arise from preexisting cells. Modern cells share a common ancestor.

Cell Size

Small size ensures efficient nutrient exchange and waste removal. Surface area-to-volume ratio decreases as size increases.

Cell Membranes

Selectively permeable. Maintain homeostasis and mediate communication between cells.

Light Microscopes

Used for live cells.

Electron Microscopes

High resolution but require dead samples.

Prokaryotic Structure

Components: Cell membrane, Nucleoid (DNA region), Cytoplasm and ribosomes.

Prokaryotic Cell Size

1-10 µm, generally smaller than eukaryotic cells.

Cell Wall

Provides support; made of peptidoglycan in bacteria.

Capsules

Protect against desiccation and immune responses.

Flagella

Aid in movement.

Internal Membranes

Enable photosynthesis or specialized reactions.

Eukaryotic Cell Features

Membrane-bound organelles compartmentalize cellular functions. Generally larger than prokaryotic cells (10-100 µm).

Cytoskeleton

Provides structural support and intracellular transport.

Nucleus

Houses DNA; site of transcription and nucleolus (ribosome synthesis).

Rough ER

Studded with ribosomes; protein synthesis.

Smooth ER

Lipid synthesis, detoxification.

Golgi Apparatus

Modifies, sorts, and packages proteins.

Mitochondria

Site of ATP production; contains its own DNA.

Chloroplasts

Photosynthesis in plants; contains chlorophyll and its own DNA.

Lysosomes

Contain hydrolytic enzymes for digestion.

Peroxisomes

Break down toxic substances like hydrogen peroxide.

Vacuoles

Store nutrients and waste; maintain turgor pressure in plants.

Microfilaments

Actin-based, maintain cell shape.

Intermediate Filaments

Provide structural stability.

Microtubules

Tubulin-based, enable organelle transport and cell division.

Fluid Mosaic Model

Membranes consist of a phospholipid bilayer with embedded proteins. Fluidity is influenced by lipid composition and temperature.

Passive Transport

Diffusion along a concentration gradient (no energy required).

Simple Diffusion

Small, nonpolar molecules (e.g., O₂, CO₂).

Facilitated Diffusion

Uses channel or carrier proteins.

Active Transport

Moves substances against a gradient, requires energy (e.g., Na⁺/K⁺ pump).

Endocytosis

Uptake of materials via vesicles (e.g., phagocytosis, pinocytosis).

Exocytosis

Release of materials outside the cell.

Kinetic Energy

Energy of motion.

Potential Energy

Stored energy (e.g., chemical bonds).

First Law of Thermodynamics

Energy cannot be created or destroyed.

Second Law of Thermodynamics

Energy transformations increase entropy (disorder).

ATP

The primary energy currency.

Metabolic Pathways

Highly regulated to maintain efficiency and homeostasis.

Enzymes

Function as biological catalysts.

Activation Energy

Lowered by enzymes for reactions without being consumed.

Enzyme-Substrate Complex

Formed when substrate binds to the enzyme's active site.

Factors Influencing Enzyme Activity

Temperature and pH affect enzyme structure and efficiency.

Competitive Inhibitors

Bind to the active site.

Noncompetitive Inhibitors

Bind elsewhere, altering enzyme shape.

Allosteric Regulation

Activators or inhibitors bind to sites other than the active site.

Glycolysis

Glucose → Pyruvate, producing ATP and NADH (in cytoplasm).

Pyruvate Oxidation

Converts pyruvate to Acetyl-CoA (in mitochondria).

Citric Acid Cycle

Produces ATP, NADH, and FADH₂ (in mitochondria).

Oxidative Phosphorylation

Electron transport chain (ETC) generates a proton gradient.

ATP Synthase

Produces ATP through chemiosmosis.

Anaerobic Respiration

Occurs without oxygen; includes fermentation (e.g., lactic acid or alcohol fermentation).

Light Reactions

Occur in thylakoid membranes of chloroplasts; convert light energy into chemical energy (ATP and NADPH).

Calvin Cycle

Occurs in the stroma of chloroplasts; uses ATP and NADPH to fix CO₂ into glucose.

Autocrine Signals

Affect the cells that release them.

Paracrine Signals

Affect nearby cells.

Endocrine Signals

Hormones travel through the bloodstream to distant targets.

Reception

A signal molecule (ligand) binds to a receptor.

Transduction

The signal is amplified through a cascade of intracellular events.

Response

The cell activates specific genes or proteins.

Ion Channel Receptors

Open or close ion channels in response to a signal.

Protein Kinase Receptors

Activate or deactivate proteins through phosphorylation.

G Protein-Coupled Receptors (GPCRs)

Ligand binding activates a G protein, which activates downstream targets.

Second Messengers

Small molecules like cyclic AMP (cAMP) and calcium ions mediate signal transduction.

Interphase

The phase of the cell cycle that includes G₁, S, and G₂.

M Phase

The phase of the cell cycle that includes mitosis and cytokinesis.

Prophase

Chromosomes condense; spindle fibers form.

Metaphase

Chromosomes align at the metaphase plate.

Anaphase

Sister chromatids separate to opposite poles.

Telophase

Nuclear envelope reforms; chromosomes decondense.

Cell Cycle Regulation

Controlled by checkpoints (e.g., G₁/S, G₂/M) and regulated by cyclins and cyclin-dependent kinases (CDKs).

Apoptosis

Programmed cell death ensures damaged cells are eliminated.

Structure of DNA

Double helix composed of nucleotides: Sugar (deoxyribose), phosphate group, nitrogenous base (A, T, G, C).

DNA Replication

Semi-conservative process involving helicase, DNA polymerase, and ligase.

Meiosis Overview

Reduces chromosome number from diploid (2n) to haploid (n) and produces four genetically distinct gametes.

Independent Assortment

Random distribution of homologous chromosomes.

Crossing Over

Exchange of genetic material between homologs.