Intro to Biology - Flashcards 3

Learning Objectives

Define biology
List and describe the seven characteristics of life that distinguish living organisms from non-living matter
Differentiate between prokaryotic and eukaryotic cells
Define homeostasis
Define adaptive evolution and identify examples of adaptations
Define metabolism
Describe the levels of biological organization from molecules to the biosphere, noting the interrelationships between levels
Define emergent properties
Define taxonomy and compare the 3 domains of life
Explain key themes in biology, such as evolution, energy transfers and matter transformations, information flow, structure and function
Explain how evolution describes the unity and diversity of life
Explain the central dogma
Compare the dynamics of nutrients and energy in an ecosystem
Define science, explain the scientific method, and apply it to daily living as an inquisitive individual

What is life? and Seven Characteristics of Life

Biology is the scientific study of life.
What is life? A system is considered alive if it shows the seven characteristics of life: order, reproduction, growth and development, energy processing, regulation, response to the environment, evolutionary adaptation.
These characteristics distinguish living matter from non-living matter.

Seven Characteristics of Life (overview)

Order: organisms are organized in a hierarchical fashion; cells are the structural and functional units of life. All organisms are composed of at least one cell; cells combine to form tissues, organs, etc.
Reproduction: all living organisms contain genetic material and reproduce. Reproduction can be sexual (meiosis, fertilization) or asexual (e.g., binary fission).
Growth & Development: organisms grow and develop via cell division (mitosis) and developmental processes.
Energy Processing (Metabolism): organisms obtain and use energy from the environment; metabolism encompasses all chemical reactions inside an organism.
Regulation (Homeostasis): organisms regulate internal conditions to maintain stability; involves feedback loops.
Response to Environment: organisms respond to stimuli via receptors and signaling pathways.
Evolutionary Adaptation: populations change over generations in response to the environment through heritable traits.

Homeostasis and Regulation

Homeostasis: the maintenance of a stable internal environment despite external changes.
Negative feedback loops: reduce the initial stimulus to return to a set point.
Positive feedback: end products speed up their own production (less common in biology).
Example: insulin-glucose regulation involves a negative feedback loop controlling blood glucose levels.

Reproduction, Growth, and Development (brief details)

Sexual reproduction: involves genetic material from two parents; offspring inherit a combination of genes; meiosis produces gametes (eggs and sperm).
Asexual reproduction: produces genetically identical offspring; e.g., binary fission in bacteria.
Growth & development: involves cell division (mitosis) and differentiation; development leads to mature form and function.

Evolutionary Adaptation and Adaptive Evolution

Evolution: change in species/populations over time due to environmental pressures and genetic variation.
Adaptation: a heritable trait that increases an organism’s chance of survival and reproduction in a given environment (e.g., camouflage).
Mechanism: natural selection acting on heritable variation over many generations leads to population-level changes.
Example: camouflage in prey or signaling in mating displays.

Hierarchy of Life and Emergent Properties

Hierarchy (from small to large): atoms → molecules → organelles → cells → tissues → organs → organ systems → organism → population → community → ecosystem → biosphere.
Emergent properties: at each higher level, new properties emerge that are not present at the lower levels (e.g., properties of water emerge from H and O atoms).
Emergent properties example: a molecule’s characteristics differ from its constituent elements (e.g., water is H2O, not H or O alone).

The Three Domains of Life and Taxonomy

Taxonomy: science of classifying, describing, and naming organisms.
8 taxonomic ranks; mnemonic example: Did King Philip Come Over For Good Soup.
Scientific binomial nomenclature: Homo sapiens is the two-part name for humans; ~1.8 million species named; estimates range from 10 million to over 100 million total species.
3 Domains of Life: Bacteria (prokaryotes), Archaea (prokaryotes), Eukarya (eukaryotes).
Eukaryotes can be unicellular or multicellular and possess membrane-bound organelles and a nucleus; prokaryotes lack a nucleus and membrane-bound organelles.

Phylogeny and the Tree of Life

The tree of life divides life into Bacteria, Archaea, and Eukarya; common ancestors connect all life.
Endosymbiotic theory (evolutionary theme): mitochondria and chloroplasts originated as free-living prokaryotes that were incorporated into early eukaryotic cells; evidence includes similar DNA, ribosomes, and bacterial-like replication.

Central Dogma and Information Flow

Theme: Life depends on the flow of information.
DNA stores genetic information and programs cellular activities by providing blueprints for proteins.
Central Dogma: DNA → RNA → Protein
Representation: ext{DNA}
ightarrow ext{RNA}
ightarrow ext{Protein}
Transcription: DNA sequence is copied into messenger RNA (mRNA).
Translation: mRNA is used as a template to synthesize proteins at ribosomes.

Structure and Function; Energy and Matter Transfer

Theme: Structure and function are related at all levels; protein structure determines function (e.g., hemoglobin transports oxygen).
Theme: Life depends on the transfer and transformation of energy and matter.
Ecosystems involve producers (autotrophs), consumers (heterotrophs), and decomposers; energy flows in one direction (sunlight → chemical energy → work/heat); matter cycles through ecosystems via chemical cycles (C, N, etc.).
Producers convert solar energy to chemical energy; consumers obtain energy by consuming others; decomposers recycle nutrients.
Example energy flow: sunlight → chemical energy in plants → consumed by animals → heat loss to the environment.
Nutrient cycling: CO2, H2O, nutrients move through producers, consumers, and decomposers; matter returns to the environment.

The Process of Science

Science is a way of knowing: observations, hypotheses, predictions, tests, analysis, conclusions, and sharing results.
A hypothesis must be testable; science relies on evidence and falsifiable explanations.
Controlled experiments: use independent variable (manipulated) and dependent variable (measured); include experimental and control groups.
Examples: mice models in habitat matching studies; vitamin effects on hair growth in humans require control groups.
Theory: a well-supported explanation with extensive evidence.

pH, Buffers, and Water Chemistry

pH measures acidity/basicity via hydrogen ion concentration: ext{pH} = -\log [ ext{H}^+]; each unit change represents a 10-fold change in \[H^+\].
Most biological fluids have pH ~6–8; buffers stabilize pH by accepting/donating H+.
Buffer example: bicarbonate system helps maintain blood pH.
Water properties: polarity; cohesive and adhesive properties; high specific heat; high heat of vaporization; excellent solvent.
Hydrogen bonds: weak bonds between partially positive H and electronegative atoms (e.g., O). These bonds give water many of its characteristic properties.
Hydrophilic/polar/ionic substances interact with water; hydrophobic/nonpolar substances do not mix well with water.

Organic Chemistry Basics for Biology

Carbon as the backbone: carbon can form four covalent bonds, creating diverse organic compounds.
Hydrocarbons: molecules composed of C and H; hydrophobic/nonpolar generally.
Carbon skeletons: length, branching, presence of rings; double bonds affect geometry (cis/trans) and function.
Functional groups: key to molecular properties and reactivity; examples include hydroxyl (-OH), carbonyl (C=O), carboxyl (-COOH), amino (-NH2), sulfhydryl (-SH), phosphate (-OPO3^2-), methyl (-CH3).
Polarity and polar functional groups influence solubility and interactions in biological contexts.

Macromolecules: Four Classes

Macromolecules (polymers) are built from monomers; four classes: carbohydrates, proteins, nucleic acids, lipids. Lipids are not true polymers.
Monomers link via dehydration (condensation) reactions to form polymers; polymers are broken by hydrolysis; enzymes mediate these reactions.
Dehydration synthesis: links monomer A and monomer B, releasing a water
Hydrolysis: breaks a bond via addition of water.

Carbohydrates

Roles: energy storage, structural components, cell identity/signaling.
Monosaccharides: simple sugars with general formula ext{Cn}( ext{H}2 ext{O})n; often isomers (e.g., glucose vs. fructose).
Disaccharides: two monosaccharides linked by glycosidic bonds (e.g., maltose from glucose + glucose).
Polysaccharides: starch (plant energy storage, α-1,4 linkages with some α-1,6 branches), glycogen (animal energy storage, highly branched), cellulose (structural in plants, β-1,4 linkages), chitin (structural in arthropods and fungi).
Glycosidic bonds: α-1,4 and β-1,4 linkages; geometry determines structure (helices vs sheets) and function.
Polysaccharide structures influence digestibility and energy storage; lactose intolerance is a human example of lactose metabolism genetics.

Lipids

Lipids are diverse hydrophobic molecules; main types: fats (triglycerides), phospholipids, steroids.
Triglycerides: glycerol + three fatty acids; energy-dense (≈ 9 kcal/g). Saturated fats have no double bonds; unsaturated fats have one or more cis double bonds causing kinks and a lower melting point.
Phospholipids: glycerol + two fatty acids + a phosphate group; amphipathic; form bilayers that make up membranes.
Steroids: four fused carbon rings (e.g., cholesterol); components of membranes and precursors to hormones.
Membrane structure: phospholipid bilayer with hydrophilic heads facing water and hydrophobic tails inward; membrane proteins and cholesterol modulate fluidity and function.

Nucleic Acids

DNA stores hereditary information; RNA participates in protein synthesis and other roles.
Nucleotides: sugar (deoxyribose in DNA, ribose in RNA) + phosphate + nitrogenous base.
Bases: DNA uses A, T, C, G; RNA uses A, U, C, G.
Polynucleotides: nucleotides linked by phosphodiester bonds (5' to 3' direction) forming sugar-phosphate backbone.
Base pairing: A pairs with T (or U in RNA); C pairs with G via hydrogen bonds.
DNA structure: double helix with antiparallel strands; stability from base pairing and hydrophobic interactions in the core.
Gene expression: DNA transcribed into RNA, which is translated into proteins; transcription occurs in the nucleus; translation occurs at ribosomes in cytoplasm or on ER.
RNA structure: often single-stranded; can form stems and loops via intramolecular base pairing; ribozymes (RNA with catalytic activity) support the RNA world hypothesis.

Proteins

Proteins perform enzyme catalysis, transport, defense, signaling, regulation, receptors, structure, and storage roles.
Amino acids: monomers with amino group, carboxyl group, hydrogen, and R group (side chain); R groups determine properties (nonpolar, polar, charged).
Protein structure levels:
- Primary: sequence of amino acids linked by peptide bonds.
- Secondary: patterns like α-helix and β-pleated sheets held by backbone hydrogen bonds.
- Tertiary: overall 3D shape from interactions among R groups and backbone.
- Quaternary: multiple polypeptide subunits forming a functional protein.
Peptide bonds: formed by dehydration synthesis between carboxyl of one amino acid and amino group of the next.
Denaturation: disruption of protein structure due to heat, pH, salt; function often lost.
Example classes of proteins: enzymes, transport, antibodies, hormones, receptor proteins, contractile proteins, structural proteins (e.g., collagen).
Importance of side chains: polar, nonpolar, charged; affect folding, interactions with water, and bonding (ionic, hydrogen, van der Waals).
Protein design: quaternary structure (e.g., hemoglobin has multiple subunits); mutations (e.g., one amino acid change) can profoundly affect function (e.g., sickle-cell disease).

Nucleic Acids Revisited: DNA/RNA and Gene Expression

DNA stores information; RNA translates DNA information into proteins.
Transcription: DNA sequence → mRNA; Translation: mRNA → polypeptide chain (protein).
In eukaryotes, transcription occurs in nucleus; mRNA travels to cytoplasm for translation at ribosomes; ribosomes are composed of rRNA and proteins.

Carbohydrates, Monosaccharides, and Isomerism

Monosaccharides: examples include glucose and fructose; isomers share molecular formula but differ in arrangement.
Disaccharides: maltose (glucose-glucose) is an example formed by a glycosidic bond; dehydration linkage releases a water molecule.
Polysaccharides: linear forms (starch) and branched forms (glycogen), or structural (cellulose, chitin).

ATP and Energy Currency

ATP hydrolysis provides energy for cellular processes: ext{ATP} + ext{H}2 ext{O} ightarrow ext{ADP} + ext{P}i + ext{energy}.

The Cell: Tour of the Cell (Key Organelles and Concepts)

Cells are the smallest units of life; all life is cellular; cells arise from pre-existing cells (cell theory).
Eukaryotic cells: larger (5–100 μm), membrane-bound nucleus, and various organelles; can be unicellular or multicellular.
Prokaryotic cells: smaller (1–10 μm), lack membrane-bound organelles, no true nucleus; include bacteria and archaea.
Endomembrane system: nucleus, ER (rough and smooth), Golgi apparatus, lysosomes, vesicles, and plasma membrane are interconnected; roles include synthesis, modification, packaging, and transport of cellular products.
Rough ER: ribosomes on surface synthesize membrane and secretory proteins; protein folding and quality control occur here.
Golgi apparatus: modifies, sorts, and ships products from the ER; has cis (receiving) and trans (shipping) faces; glycosylation and tagging occur here.
Lysosomes: digestive compartments with hydrolytic enzymes; break down ingested materials and damaged organelles.
Vacuoles: storage and maintenance; plant cells have a large central vacuole for storage and growth.
Mitochondria: site of cellular respiration; generate ATP; have inner membrane, intermembrane space, and matrix containing DNA and ribosomes.
Chloroplasts: site of photosynthesis in plants and algae; contain thylakoids (grana) and stroma; contain DNA and ribosomes; convert light energy to chemical energy.
Cytoskeleton: network of microfilaments, intermediate filaments, and microtubules; provides shape, moves organelles, enables cell movement, and organizes contents.
Plasma membrane: selective barrier; phospholipid bilayer with hydrophilic heads and hydrophobic tails; embeds proteins that control transport and signaling.
Plant cells vs animal cells: plant cells have cell walls (cellulose), plasmodesmata (cytoplasmic channels through cell walls), and chloroplasts; animals have ECM, tight/desmosomal/gap junctions, and lack cell walls.
Extracellular matrix (ECM): network of glycoproteins (e.g., collagen, laminin) and proteoglycans; anchors cells to each other and to the ECM; integrins connect ECM to cytoskeleton; ECM participates in signaling and tissue organization.
Cell junctions in animals: tight junctions (seal sheets), desmosomes (anchoring junctions), gap junctions (cytoplasmic channels); in plants: plasmodesmata connect plant cells for transport and signaling.

Plant-Specific Structures

Plant cell walls: cellulose network provides rigidity and protection; plasmodesmata allow transport and communication between adjacent plant cells.
Chloroplasts: photosynthesis; contribute to energy capture in plants and algae.

Endosymbiotic Theory and Evidence

Mitochondria and chloroplasts likely originated as free-living bacteria engulfed by an ancestral eukaryote.
Shared features with bacteria: circular DNA, ribosomes similar to bacterial ribosomes, and replication by binary fission.
This endosymbiotic origin explains why these organelles have their own DNA and ribosomes and are semi-autonomous.

Evolution Connections: Lactase Persistence as an Example

Lactase persistence in adulthood is a recent human adaptation in some populations (e.g., East Africa, certain European groups).
Mutations in regulatory regions of the LCT gene (and nearby MCM6) keep lactase expression on; appears as a convergent adaptation in different cultures with dairy farming histories.
This highlights how genetic regulation underlies evolutionary changes in metabolism and diet.

Origin of Life and Early Earth

Early Earth (~4.6 billion years ago) featured a hot, volatile environment with volcanic activity, UV radiation, and lightning.
Atmosphere was reducing; oceans formed as Earth cooled and water vapor condensed.
Evidence of early life includes stromatolites (3.5 billion years ago) with photosynthetic prokaryotes.
Four-stage hypothesis for the origin of life:
1) Abiotic synthesis of small organic molecules (amino acids, nitrogenous bases).
2) Joining of small molecules into polymers (proteins, nucleic acids).
3) Formation of protocells (lipid-based compartments).
4) Emergence of self-replicating molecules enabling inheritance.
Miller–Urey experiments demonstrated abiotic synthesis of organic molecules under early-Earth-like conditions.
RNA world hypothesis proposes that RNA could have stored genetic information and catalyzed replication before DNA-based life.

Lactose Tolerance: Genetics and Evolution Connection

Lactase persistence results from regulatory mutations in the LCT gene region (and MCM6) enabling continued lactase expression beyond infancy.
Different populations show different mutations leading to the same functional outcome (tolerance to lactose), illustrating convergent evolution driven by dairy farming practices.

The Central Dogma and Information Flow (Recap)

DNA stores genetic information; transcription creates RNA; translation builds proteins.
DNA stores information to run cells; RNA's function is to make proteins; proteins do the cellular work.
Formally: ext{DNA}
ightarrow ext{RNA}
ightarrow ext{Protein}

Equations and Key Notations (selected)

pH balance: ext{pH} = -\log [ ext{H}^+]
ATP hydrolysis: ext{ATP} + ext{H}2 ext{O} ightarrow ext{ADP} + ext{P}i + ext{energy}
Dehydration synthesis (example): monomers join with loss of water; polymers form.
Hydrolysis (example): water is used to break bonds in polymers.

Connections to Foundational Principles and Real-World Relevance

Evolution provides a unified explanation for the unity and diversity of life; natural selection acts on heritable variation.
Structure and function relate across all levels of biology—from atomic bonds to macromolecular folding to organelle function, to tissues and organisms.
Understanding energy transfer and matter transformation is essential to explain how ecosystems sustain themselves and how human activities impact climate, carbon cycles, and biodiversity.
The scientific method underpins all biology: observation, hypothesis, experimentation, data analysis, and theory formation.

Quick References and Examples

Central Dogma: DNA → RNA → Protein
Major macromolecule classes: carbohydrates, proteins, nucleic acids, lipids
Endosymbiosis evidence: organelles contain their own DNA and ribosomes similar to bacteria
Lactose tolerance: regulatory mutations enabling lactase persistence in adults
Water properties: high specific heat, solvent abilities, cohesive/adhesive behavior, polarity, hydrogen bonding
pH and buffers: homeostatic maintenance of pH in biological fluids
Glycosidic linkages: α-1,4 and β-1,4 linkages in starch/glycogen vs cellulose/lactose
Membrane structure: phospholipid bilayer with hydrophobic tails and hydrophilic heads; membrane proteins modulate transport
ECM and cell junctions: ECM provides structural support and signaling; tight, desmosomal, and gap junctions coordinate tissue integrity and communication
Plant vs animal cells: cell walls and plasmodesmata in plants; ECM and junctions in animals
Origin of life stages and Miller–Urey: abiotic synthesis under reducing atmosphere with energy input

Summary Takeaways

Biology seeks to explain life through a set of core themes: evolution, information flow, energy and matter transformation, and the relationship between structure and function.
Life is organized hierarchically, with emergent properties at each level.
Cells are the fundamental units of life; eukaryotes and prokaryotes differ in nucleus and organelles.
Macromolecules drive all biological processes; their structures dictate functions.
Organ systems, organelles, and molecules all participate in energy flow, matter cycling, and information processing that define living systems.
The origin of life involves a continuum from simple molecules to proto-cells, with RNA potentially playing a pivotal role in early biochemistry.
Real-world examples (lactose tolerance, climate interactions, and disease-related protein folding) illustrate how biology connects to health, ecology, and evolution.