Fundamentals of Biology: The Essentials of Life
Characteristics of Living Organisms
Kingdom
Cell Wall
Nutrition
Complexity
Yield: Net 2 ATP and 2 NADH.
Protists
Variable
Both
Unicellular/Mult
i
Citric Acid Cycle (TCA): Occurs in the mitochondrial matrix. Oxidizes
Composition: Composed of a common set of chemical elements (C,
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Cellular Basis: Made up of cells, the fundamental units of life.
Elements: C, H, O, N, P, S make up 98% of living tissue .
Genetic Information: Contain universal genetic code to specify their
Carbon: Central to life; can form up to 4 covalent bonds.
organization and function.
Homeostasis: Maintain internal continuity while responding to
external environmental changes.
Evolution: Populations of organisms evolve over time through
Mendelian Laws:
Anaerobic Pathways:
Segregation: Homologous pairs separate during meiosis.
Energy Definition: The capacity to do work or cause change.
2. All living organisms are composed of cells.
Potential Energy: Stored energy (e.g., chemical bonds,
Fermentation: Recycles N AD in the absence of oxygen to keep
+
glycolysis running.
Lactic Acid: Produces lactate (muscles, some bacteria).
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First Law of Thermodynamics: Energy can be transferred or
Produces ATP and NADPH for the Calvin Cycle.
heat.
Free Energy (G): The portion of a system's energy available to do
Energy is released via hydrolysis to ADP and Inorganic Phosphate
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Nature of Mutations
hydrolysis) drive non-spontaneous endergonic reactions.
Definition: Changes in the sequence, structure, or composition of a
Enzymes: Biological Catalysts
genome; the primary source of genetic variation.
Function: Speed up reactions by lowering activation energy (Ea )
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prokaryotes.
Cambrian Explosion (541 mya): Rapid diversification; appearance of
most major animal groups.
without altering the ΔG or equilibrium constant.
Active Site: A specific region where substrates bind.
Mechanisms: Orienting substrates, straining bonds, or providing a
Prokaryotes vs. Eukaryotes
favorable microenvironment.
Prokaryotes (Bacteria/Archaea):
Models: Lock and Key (rigid fit) vs. Induced Fit (enzyme changes
shape upon binding).
No membrane-bound organelles.
DNA located in a nucleoid (not a nucleus).
Cofactors: Non-protein helpers (e.g., metal ions, organic coenzymes
Cell wall typically contains peptidoglycan.
like vitamins).
Possess flagella (flagellin) and pili for attachment/DNA exchange.
Regulation:
Competitive Inhibition: Inhibitor binds to the active site, competing
Eukaryotes (Plants, Animals, Fungi, Protists):
Contain a nucleus and membrane-bound organelles.
DNA packaged as chromosomes in the nucleus.
with the substrate.
Non-competitive Inhibition: Inhibitor binds to an allosteric site ,
changing the enzyme's shape.
Complex flagella made of microtubules.
Feedback Inhibition: The end product of a metabolic pathway
Kingdoms of Life
inhibits an upstream enzyme to prevent overproduction.
Kingdom
Cell Wall
Nutrition
Complexity
Plants
Cellulose
Autotroph
Multicellular
Animals
None
Heterotroph
Multicellular
Fungi
Chitin
Heterotroph
Multicellular
Cellular Respiration and Metabolism
Metabolism: The sum of Catabolism (breaking down, exergonic) and
Anabolism (building up, endergonic).
Glycolysis: Occurs in the cytoplasm . Converts 1 Glucose into 2
Pyruvate.
(CAM).
Genetics: Mutations and Inheritance
Reaction Coupling: Spontaneous exergonic reactions (like ATP
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Eukaryotic Life (2.1 bya): Result of prokaryotes absorbing other
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Gene Interactions
Additive Traits: Multiple genes contribute independently to a single
phenotype (e.g., pigment density).
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(Pi).
Ozone Layer (O3 ): Formed as UV light split O2 into radicals. This
allele.
photorespiration by isolating CO2 fixation spatially (C4) or temporally
Stromatolites: Fossil evidence of ancient cyanobacteria.
barrier against DNA-breaking UV-A/B/C allowed life to move onto land.
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C4/CAM Plants: Evolutionary adaptations to minimize
Endergonic: ΔG > 0 (non-spontaneous, energy required).
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Trans: Each chromosome has one dominant and one recessive
Uses ATP and NADPH to convert CO2 into G3P (sugar).
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ATP (Adenosine Triphosphate): The primary energy currency.
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Cis: Both dominant alleles on one chromosome, both recessive on
the other.
Carbon Fixation: Catalyzed by Rubisco.
(wasteful).
Exergonic: ΔG < 0 (spontaneous, energy released).
Cyanobacteria (3.5 bya): First organisms to perform photosynthesis.
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Configuration:
Calvin Cycle (Light-Independent): Occurs in the stroma.
Photorespiration: Occurs when Rubisco binds O2 instead of CO2
work.
Liquid Water: Essential medium that arose 3.5 billion years ago;
serves as a universal solvent.
observable RF is 50% .
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Second Law of Thermodynamics: Every energy transfer increases
the entropy (disorder) of the universe; some energy is always lost as
Earth.
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Map Units: 1% RF equals 1 centimorgan (cM). The maximum
Water is split (photolysis), releasing O2 .
Two Primary Theories:
2. Extraterrestrial Origin: Meteorites carried organic molecules to
gametes
Recombination Frequency (RF): RF = No. of recombinant
× 100
Total gametes
Light Reactions: Occur in thylakoids.
transformed, but cannot be created or destroyed.
formed on primitive Earth and joined into complex life.
tend to be inherited together, violating independent assortment.
Location: Chloroplasts (specifically thylakoids and stroma).
Origin of Life: Occurred approximately 4 billion years ago.
1. Spontaneous Formation: Monomers (proteins, carbs, nucleic acids)
Linkage: Genes located close together on the same chromosome
Photosynthesis
Kinetic Energy: Energy of movement that does work.
Independent Assortment: Alleles of different genes on different
chromosomes distribute independently, producing a 9:3:3:1 ratio in
dihybrid crosses.
Gene Linkage and Mapping
Alcoholic: Produces ethanol and CO2 (yeast).
concentration gradients).
Origins and Timeline of Life
type).
Final Electron Acceptor: Oxygen (forms water).
Bioenergetics and Thermodynamics
4. Modern cells evolved from a common ancestor.
Codominance: Both alleles are expressed equally (e.g., AB blood
Chemiosmosis: ATP Synthase uses the proton-motive force to
Ionic: Electronegativity difference > 1.9 (electron "theft").
1. Cells are the fundamental units of life.
3. All cells come from pre-existing cells.
Incomplete Dominance: Heterozygote shows an intermediate
phenotype.
Bonding Types:
Non-polar Covalent: Difference < 0.4 (equal sharing).
Cell Theory
through complexes, pumping H + to create a gradient.
synthesize ATP.
Polar Covalent: Difference 0.4 − 1.9 (uneven sharing).
natural selection .
Dominance Variations:
Electron Transport Chain (ETC): Electrons from NADH/FADH₂ pass
Increases across a period; decreases down a group.
molecules to synthesize new ones.
Alleles: Variant forms of a gene at a specific locus.
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Oxidative Phosphorylation:
Electronegativity: The attraction of a nucleus to its outer electrons.
Metabolism: Extract energy from the environment to do work; use
Ploidy: Number of sets of chromosomes (e.g., diploid 2n vs.
haploid n).
Acetyl CoA.
Yield per turn: 2 CO2 , 3 NADH, 1 FADH2 , 1 ATP/GTP.
Chemical Foundations
H, O, N, P, S).
Oxygenation Event: Photosynthesis converted CO2 and CH4 into O2
, allowing for aerobic respiration.
Patterns of Inheritance
Selectively Neutral Mutations: Often occur in non-coding intergenic
Epistasis: An allele at one locus masks the phenotypic expression of
an allele at a second locus.
Typical modified Mendelian ratio: 9:4:3.
Gene Regulation and Expression
Control Points in Eukaryotes
Regulation is more complex in eukaryotes because transcription
regions or are "silent," meaning they do not alter the resulting protein's
(nucleus) and translation (cytoplasm) are spatially and temporally
function.
separated .
Impact on Fitness: More mutations are deleterious than beneficial.
Large-scale changes often disrupt "gene balance."
mRNA stability, Translational, and Post-translational.
Levels of Control: Transcriptional, Processing (splicing), Transport,
Spontaneous vs. Induced:
Epigenetics and Transcription
Spontaneous: Occur via rare DNA replication errors or chemical
DNA Methylation: Addition of a methyl group to Cytosine (forming
5-methylcytosine).
changes like deamination.
Induced: Caused by external mutagens such as radiation or
chemical agents.
Small-Scale vs. Large-Scale Mutations
Point Mutations (SNPs): Affect a single nucleotide.
Indels: Small insertions or deletions that can cause a frameshift if
not in multiples of three.
Large-Scale Chromosomal Changes:
Deletion/Duplication: Loss or gain of entire chromosome
segments.
Inversion: A segment is flipped 180 degrees.
Translocation: Non-homologous chromosomes swap regions.
High methylation at CpG islands typically decreases transcriptional
activity.
Regulatory Proteins:
Activators: Recruit/stabilize RNA polymerase (Positive regulation).
Repressors: Block/destabilize RNA polymerase (Negative
regulation).
The Lac Operon (Prokaryotic Model)
Components:
lacZ: β -galactosidase (breaks down lactose).
lacY: Permease (lactose entry).
lacA: Transacetylase.
Mechanism:
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No Lactose: LacI repressor binds to the operator, blocking
transcription.
Growth Patterns:
Primary Growth: Longitudinal growth from apical meristems
Lactose Present: Allolactose binds the repressor, changing its
shape so it releases the DNA; transcription occurs.
Glucose Influence: Low glucose increases cAMP, which activates
CAP (activator) to maximize expression.
(protoderm, ground meristem, procambium).
Secondary Growth: Radial thickening via lateral meristems
(vascular cambium and cork cambium).
Embryogenesis and Tissue Differentiation
Multicellularity and Complex Transport Systems
Cell Potency:
Origins and Transition
Totipotent: Can form all cell types (zygote).
Molecular Clock: Technique estimating divergence of life forms
Pluripotent: Can form all embryo cells (Inner Cell Mass).
based on DNA mutation rates; suggests multicellularity arose at least 6
Multipotent: Can form multiple related types (adult stem cells).
times.
Gastrulation: Massive cell movement converting a blastula into a
Stages of Transition:
gastrula with three germ layers:
1. Aggregation of cells into a cluster.
1. Ectoderm: Nervous system, epidermis.
2. Intercellular communication and cooperation.
3. Transitory specialization (cells can still function independently).
4. Permanent specialization (loss of independent viability; formation
of tissues).
Volvocine Algae Model: Shows transition from single cells switching
2. Mesoderm: Muscle, blood, skeletal system.
3. Endoderm: Lining of digestive and respiratory tracts.
Homeostasis: Maintenance of a steady state via negative feedback
loops (e.g., Insulin/Glucagon regulating blood glucose).
between swimming and division phases to multicellular colonies where
outer cells handle movement and inner cells specialize in reproduction.
The Problem of Size and Diffusion
SA:V Ratio: As volume increases, the Surface Area to Volume ratio
decreases, limiting gas and nutrient exchange.
P2
Fick’s Law of Diffusion: Q = DA P1 −
Where Q is rate of diffusion, A
L
is surface area, (P1 − P2 ) is partial pressure gradient, and L is diffusion
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distance.
Solutions: Evolution of thin, branched, or folded exchange surfaces
(lungs, gills, spongy mesophyll) and bulk flow transport systems to
bypass diffusion limits.
Animal Circulatory Systems
Open Circulatory System: Hemolymph flows openly through body
cavities (sinuses).
Found in: Insects, many molluscs.
Characteristics: Lower pressure, less energy-intensive, but less
control over flow distribution.
Closed Circulatory System: Blood is confined to vessels, separate
from interstitial fluid (IF).
Vertebrate Evolution: Transition from single circuits (fish) to partial
double (amphibians) to complete double circuits (birds/mammals),
allowing high-pressure delivery to the body and low-pressure to lungs.
Starling Forces in Capillaries:
Filtration: Driven by Capillary Hydrostatic Pressure (CHP ) pushing
fluid out; dominant at the arteriole end.
Reabsorption: Driven by Blood Osmotic Pressure (BOP ) pulling
fluid back via plasma proteins; dominant at the venule end.
Plant Transport and Development
Water Potential (Ψ): Water moves from high to low potential. Ψ =
Ψs + Ψp Where Ψs is solute potential (negative) and Ψp is pressure
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potential (turgor).
Xylem (Water/Minerals): Dead tracheids and vessel elements. Driven
by the Transpiration-Cohesion-Tension mechanism (negative pressure).
Phloem (Sugars): Living sieve tube elements and companion cells.
Driven by the Mass Flow Hypothesis : active loading of sucrose at the
"source" creates high osmotic pressure, pushing sap toward the "sink."
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