Biology 1 Notes
Intro and properties of life
Core Concepts for Biological Literacy
 Evolution: the diversity of life evolved over time by processes of mutation, selection, and genetic
change
 Structure and function: basic units of structures define the function of all living things
 Information flow, exchange, and storage: the growth and behavior of organisms are activated through
the expression of genetic information in context
 Pathways and transformation of energy and matter: biological systems grow and change by process
based upon chemical transformation pathways and are governed by the laws of thermodynamics
 Systems: living systems are interconnected and interaction
Biology: the scientific study of living organisms and how they have evolved
Characteristics of Living Organisms
 Cells and Organization:
o Organisms maintain internal order
 Energy Use and Metabolism:
o Energy required of maintain order
o Energy utilized via metabolism
 Response of Environmental Change
o Organisms react to stimuli
 Regulation and Homeostasis
o Maintain relative stable internal condition
 Growth, Development, and Reproduction
o Genetic material (DNA) causes offspring to have traits like their parents
 Evolution
o Population of organisms change over generations
o Evolution results in traits that promote survival and reproductive success
Characteristics of Life
 DNA
 Organized
 Grow & Develop
 Reproduce
 Adapt & respond to the environment
 Cells
 Energy
"Scale of Life" Scala Naturae
 Great Chain of Being establishes man as dominate and perfect form of life
 The earth and its creatures are the result of special creation, that they have not changed since they were
created
Scientific Names
 Carolus Linnaeus: Classified organisms into nested hierarchies based on shared similarities
 Binomial nomenclature (two-word names)
o Universal
o Latin
 First word represents genus
 Second word is specific epithet of a species with a genus
o Always italicized or underlined
Classification = Taxonomy
 Rules of identifying the classifying organisms
 Hierarchical levels based on hypothesized evolutionary relationships (phylogeny)
 A level usually includes more species than the level below it, and fewer species than the one above it
Evolutionary Theory
 "It is not the strongest of the species that survive, nor the most intelligent, but the one most responsive to
change” Charles Darwin (1809–1882)
 Adaptation = Any modification that makes an organism better suited to its way of life
 Descent with Modification = Biological Evolution
o Populations of organisms change over generation
o Evolution results in heritable traits that promote survival and reproductive success
Scientific Method
Science "scientia"
 The intellectual and practical activity encompassing the systematic study of the structure and behavior of
the physical and natural world through observation and experiment
Characteristics of Science
 is guided by natural law
 is testable against the natural world
 the conclusion of science are tentative
 is falsifiable
Scientific Method: objective way of thinking about the world
 Hypothesis: a tentative testable explanation for what was observed: "educated guess"
 Prediction: the expected result of an experimentation if a hypothesis is supported; "if/then" statement
Discovery of Penicillin (1928 | Alexander Fleming)
 Observation: no bacteria growing near mold
 Hypothesis: Penicillium may release a substance that kills nearby bacteria
 Experiment: Grew penicillium in liquid medium; applied liquid to uncontaminated bacterial cultures
 Results: Bacteria killed by liquid
Scientific Theory
 Related set of well-supported hypotheses that form a broad-ranging testable explanation about
fundamental aspects of the natural world
o Complex dynamic
o ex. cell, genes, evolution
Chi-square test
 Observed ration may deviate from expected ratios by chance
 Chi-square tests the null hypothesis (Ho)
o there is no significant difference between expected and observed
o 0: observed value
o e: expected value
o df = number of categories - 1
(0 − 𝑒)2
2
𝑥 =∑
𝑒
Basic Chemistry and Bonds
Chemical Elements: 99% of living organisms are composed of C, H, N, O, P, S, Ca
Atoms: smallest function units of matter that cannot be broken down
 Protons (+): in nucleus
 Neutrons (neutral): in nucleus
 Electrons (-): orbiting nucleus
Isotopes: atoms of the same element where proton # stays
the same but the neutron # is different
 Radioisotopes (some isotopes spontaneously decay)
 Tracers: Reveal a pathway or destination of a substance
 that has entered a cell, the human body or an ecosystem
Fossil Dating (Radiometric Dating), Half-Life
 The length of time required for half (½) the atoms (parent) to change into something else (daughter
product)
 Unaffected by temperature, light, pressure, etc
 All radioactive isotopes have a dependable half life
Orbitals and Shells
 Electrons occupy regions of space called orbitals
 Atoms with more than two electrons have at least two orbitals
 Bohr model - electron shells as concentric circles around nucleus
Octet Rule - Distribution of Electrons
 Each shell has one or more e- orbitals
o Innermost shell has 1 orbital, 2 eo The next two shells can have a max of 8 eo Atoms with fewer than 8e- in outermost shell are reactive
 Electrons available to combine with other atoms = valence electrons
o ≤ 3e- tendency to donate
o ≥ 5e- tendency to receive
Chemical Bonds
 Atoms can combine with one another to form molecules, which are held together by chemical bonds
 Molecule stability occurs when atoms of the molecule share enough electrons to occupy the outermost
energy level
 Octet rule: Atoms tend to combine so that they have 8 electrons in their outer shell; full = most stable
 The number of valence electrons affects the number of bonds that can be formed
 Types of Bonds: Covalent & Ionic
Covalent: When 2 atoms share one or more pairs of valence electron
 Electrons are not permanently transferred from one atom to another
 A pair of electrons from the outer shell will “time share” with each atom
 2 or 3 pairs of electrons can be shared (double or triple covalent bond)
 Polar Covalent Bons
o Electrons that are shared between two atoms are not equally shared
 Nonpolar Covalent Bonds
o Atoms share electrons equally
Ionic Bonds: An attraction between atoms (ions) with opposite electrical charges
 e- acceptor = Anion (Cl-)
 e- donor = Cation (Na+)
 Ionic Compound is electrically neutral
Electrolytes: ions that carry electrical current in solution; common in body, dissolve in fluids
Free Radical: Atom with a single, unpaired electron in its outer shell
 Unstable
 Reacts with other molecules to “steal” electrons
 Creates new free radical in “donor” molecule
 Initiates chain reaction
 Oxidative Stress
 Formed by exposure of cells to radiation
 Some molecules donate electrons to free radicals without becoming reactive
Water
Water Chemistry
 Water is a polar molcule
 Water is a good solvent
o Molecules can be described as hydrophilic or hydrophobic depending on how they react with
water
 The pH of water is 7
o pH is a measurement of the concentration of protons in solution
Water & Temp.
 Water is less dense when solid (frozen) than when liquid
 Water resists decreases or increases in its temperature because in order for its temperature to change
hydrogen bonds must be broken
Solvent: In water, the partial positive charge on the hydrogen ions associate with the negative charge on the
chloride ions, and the partial negative charge on the oxygen ions associates with the positive charge on the
sodium ions
Cohesion & Adhesion
 Cohesion: water is attracted to water
 Adhesion: water is attracted to non-water molecules
Summary properties of Water
 Polar
 High heat capacity
 Less dense as a solid
 Excellent solvent
 Cohesive and adhesive
Biomolecules
Organic vs. Inorganic
 Inorganic: chemistry of elements other than carbon
o + & - ions
o ionic bonding
o few atoms
o often nonliving matter
 Organic: carbon-based chemistry
o contain carbon and hydrogen
o covalent bonding
o large, with many atoms
o typically living systems
Macromolecules
Function
Example
Carbohydrates
Energy Storage
Molcules
Glucose
Protein
Lipid
Monomer types
Diagram
Dehydration and Hydrolysis
 Dehydration: removal of water molecule (synthesis)
o Used to connect monomers together to make polymers
 Hydrolysis: addition of water molecule
o Used to disassemble polymers into monomer parts
Carbohydrates
 C, H, O: often in ratio of 1:2:1
 Universally used as an immediate energy source
 Energy storage molecules
 Structural component of cells
 Most abundant organic molecules on earth
 Monosaccharides (simple sugars)
o single sugar molecule, foundation for others
o quite soluble and sweet to taste
o ex. ribose, glucose, etc
 Disaccharides
o Contain two monosaccharides joined during dehydration reaction
o Soluble, sweet to taste (table sugar, maple, milk )
o Important in transport of sugars, glycocalyx
o ex. glucose + fructose → sucrose
Nucleic Acid

Polysaccharides
o Polymers of monosaccharides
o Branched and unbranched form
o Low solubility
o Not sweet to taste
o Structural component
o Short-term energy storage
o ex. starch, glycogen, cellulose
Lipids
 Insoluble in water; not polymers
 Long chains of repeating CH2 units (also with O, P, N)
 Renders molecule nonpolar
 Structural in cells, energy reserves, messenger, insulation, cushioning
 Types: fats, oils, phospholipids, steroids, waxes
 Triglycerides (neutral fats, Triacylglycerols)
o Long-term energy storage
o Backbone of one glycerol molecule
 three-carbon alcohol (each with OH- group)
o Three fatty acids attached to ach glycerol molecule
 Long hydrocarbon chain
 Saturated no double bonds between carbons
 Unsaturated 1 double bonds between carbons
 Fats are solid and oils are liquid
o Polyunsaturated fats tend to be liquid at room temperature
o Saturated fats tend to be solid
 Phospholipids
o Glycerol backbone with:
 2 fatty acids – hydrophobic
 1 phosphate group – hydrophilic
o In water:
 Polar phosphate “heads” near water
 Nonpolar fatty acids “tails” overlap and exclude water
 Spontaneously form double layer & sphere
 Steroids
o Skeletons of 4 fused C rings + polar groups
o Cholesterol: animal cell membranes
o Sex hormones: testosterone, estrogen, progesterone
o Vitamin D
 Eicosanoids
o Local hormones produced by all cell of human body (essential)
o Blood pressure, childbirth, inflammation
 Waxes
o Long-chain fatty acid bonded to a long-chain alcohol, very nonpolar
 High melting point
 Waterproof
 Resistant to degradation
Proteins
 Some of most abundant organic molecules in living systems 20% human body weight
 C, H, O, N, and sometimes S
 Diverse function
 Proteins are polymers of amino acids
 Each amino acid has a central carbon atom to which are attached:
o Hydrogen atom
o Amino group -NH2
o Carboxylic acid group -COOH
o One of 20 different types of -R groups
 Fibrous vs. Globular Proteins
o Fibrous – Structural: stringy, tough, water insoluble, elongated rod-like proteins
o Globular – Functional: spherical, water soluble, polar groups on outside, enzymes, hormones
 Denaturation
o Exposure of proteins to harmful agents (heat, pH, chemicals)
o Disorganization of protein structures
 Protein Folding Diseases = Proteinpathies
o Assembly of AA’s into protein extremely complex
o Process overseen by “chaperone” molecules
 Cystic Fibrosis (CF)
o Autosomal recessive
o Inherited
o Mutations in gene CF transmembrane regulators (CFTR)
Nucleic Acids
 Polymers of nucleotides
 Large complex organic molecules
o DNA (deoxyribonucleic acid)
o RNA (ribonucleic acid)
 Nucleotides
o Phosphate group
o Pentose sugar (ribose or deoxyribose)
o Nitrogenous base (4 kinds in DNA, 4 kinds in RNA, 3 in both)
 RNA
o Nucleotide subunits connected end-to- end to make a nucleic acid
o Sugar of one connected to the phosphate of the next
 ATP (adenosine triphosphate)
o Composed of adenine, ribose, and 3 phosphates
Cells
Cell Theory
 All organisms are composed of cells
 Life processes of metabolism and heredity occur within these cells
 New cells come only from preexisting cells
 Smallest unit of life
Microscopy
 Magnification: ration between size of image produced and actual size
 Resolution: measure of clarity of image
 Contrast: how different objects looks from adjacent structures
 Optical: lenses focus light, compound, stereo confocal laser scanning
 Electron: TEM, SEM
Cell Size
 Most much smaller than on millimeter (mm)
 Some as small as one micrometer (um)
 Size restricted by surface/volume ratio
o Surface is membrane across which cell acquires nutrients and expels wastes
o Volume is cytoplasm, which demands nutrients and produces wastes
o As cells grows, volumes increases faster than surface
Prokaryotic Cells
 Lack a membrane-bound nucleus
 Structurally simple and small
 Two domains:
o Bacteria: ubiquitous, some pathogenic, some photosynthetic, some decompose organics
o Archaea: more diverse, some in extreme habitats, closer to eukaryotes
 Cell Shapes:
o Cocci: round cells
o Bacilli: long and thin cells that look like rods
o Spirilla: rod-like shape with a unique curved, corkscrew spiral appearance
o Vibrio: comma looking
Eukaryotic Cells
 Domain Eukarya
o Protists
o Fungi
o Plants
o Animals
 Cells contain
o Membrane-bound nucleus
o Specialized organelles
o Plasma membrane
 Organelles
o Compartmentalization:
 Allows eukaryotic cells to be larger than prokaryotic cells
 Isolates reactions from others
o Two classes:
 Nucleus and endomembrane systems, organelles that communicate with one another via
membrane channels and vesicles
 Energy related organelles, mitochondria and chloroplasts, basically independent and selfsufficient
 Chloroplasts
o Bounded by double membrane
o Inner membrane enfolded
o Form disc-like thylakoids, which are stacked to form grana
o Suspended in semi-fluid stroma
o Green due to chlorophyll pigment
o Derived from cyanobacteria
o Chloroplast genome – cpDNA
o Binary fission
o Photosynthesis
 Captures light energy to drive cellular machinery
 Synthesizes carbohydrates from CO2 and H2O
 Mitochondria
o Bounded by double membrane (outer, inner)
 Cristae – enfolding of inner membrane that encloses matrix
 Matrix – inner semifluid containing respiratory enzymes
o Cellular respiration
o Produces most ATP utilized by cell
o Generate heat
o Derived from purple bacteria – proteobacteria
o Mitochondrial genome – mtDNA
o Binary fission
 Plasma Membrane
o Phospholipid bilayer with embedded protiens
 Regulates what does in/out
 Sensitivity, support, protection
 Nucleus (center of cell)
o Separated from cytoplasm by nuclear envelope
o Contains chromatin: has DNA (genes), condenses to form chromosomes
o Composed on rRNA: produces subunits of ribosomes