Comprehensive Study Notes

The Chemistry of Life

Organizing Life

Early life consisted of unicellular prokaryotes. Organisms are classified into three Domains: Archea, Bacteria, and Eukarya.

• Archea: Often extremophiles, thriving in harsh environments.
• Bacteria: Common prokaryotic organisms.
• Eukarya: Includes organisms with eukaryotic cells; can be unicellular or multicellular.

Key distinctions among domains include:

• Cellularity (unicellular vs. multicellular).
• Cell type (prokaryotic vs. eukaryotic).
• Presence/absence of a cell wall.
• Mode of reproduction (sexual vs. asexual).
• Mode of obtaining nutrition (autotrophic vs. heterotrophic).

Phylogenetic trees and cladograms illustrate evolutionary relationships.

Viruses

Viruses are not considered alive but require a host cell to replicate, acting as a vector. They contain either DNA or RNA.

Water

Structure

Water (H_2O) is a polar molecule with partial positive charges on the hydrogen atoms and a partial negative charge on the oxygen atom.

Properties

1. Universal Solvent: Due to its polarity, water can dissolve charged or polar substances. Free water is not attracted to solutes, while bound water is.
2. Cohesion: Water molecules bond to each other, resulting in surface tension.
3. Adhesion: Water molecules are attracted to charged surfaces.
4. Capillary Action: Combination of cohesion and adhesion allows water to move in thin tubes (e.g., xylem in trees).
5. High Specific Heat: Water requires a significant amount of energy to change temperature, helping to stabilize Earth's temperature.
6. States of Matter: Ice floats, providing insulation for bodies of water and allowing life to persist underneath.

Reactions and Water

1. Dehydration (Condensation) Reaction: Building a polymer by removing water (H_2O). This is an anabolic reaction.
2. Hydrolysis: Breaking a polymer by adding water (H_2O). This is a catabolic reaction.

Reactions can be spontaneous (exergonic), releasing net energy, or non-spontaneous (endergonic), requiring net energy input.

Organic Chemistry

Life is based on organic compounds, characterized by carbon-hydrogen (C-H) bonds.

Types of Bonds

• Covalent bonds: Sharing of electrons (can be polar or nonpolar).
• Ionic bonds: Transfer of electrons, forming ions.
• Hydrogen bonds: Intermolecular forces based on attraction.

Isomers

1. Structural Isomers: Atoms arranged differently around a single bond.
2. Geometric Isomers: Atoms arranged differently around a double bond.
3. Enantiomers (Mirror Image Molecules): Stereoisomers that are mirror images of each other.

Macromolecules

Carbohydrates

Composed of carbon, hydrogen, and oxygen in a 1:2:1 ratio (CH_2O). Names often end in "-ose". Monomer: monosaccharide (e.g., glucose). Used for energy storage.

• Disaccharide: Two monosaccharides joined (e.g., sucrose = glucose + fructose).
• Polysaccharide: Many monosaccharides joined.
  • Starch: Glucose chain with all glucose oriented the same way (alpha linkage - α).
  • Cellulose: Glucose chain with alternating orientation (beta linkage - β).
  • Glycogen: Branched chain of glucose (α linkage), produced by animals and digestible by animals.
  • Chitin: Similar to cellulose but also contains nitrogen (N).

Lipids

Composed of carbon, hydrogen, and oxygen (CHO), but not in a 1:2:1 ratio. Lipids are not true polymers; they consist of small individual units. Function as energy storage.

• Fats/Oils:
  • Fats: Solid at room temperature, often from animals. Saturated fats have hydrocarbon tails that are saturated with hydrogen.
  • Oils: Liquid at room temperature, often from plants. Unsaturated fats contain double bonds.
• Steroids: Involved in cell signaling and structure. Characterized by 4 fused rings. Small, nonpolar, and can easily pass through cell membranes.
• Phospholipids: Contain phosphorus (P) in addition to C, H, and O. Make up cell membranes. Amphipathic, having a polar head and a nonpolar tail.

Nucleic Acids

Composed of C, H, O, N, and P. Monomer: nucleotide, consisting of a sugar, phosphate group, and a nitrogenous base. Polymers: RNA and DNA. 5 Flavors of nitrogenous bases: A, C, G, T, U.

Proteins

Composed of C, H, O, N, and sometimes S. Polymers: polypeptides. Monomer: amino acid, with a central carbon, amino group, carboxyl group, and a variable R group. The R group gives each amino acid its unique identity.

• Levels of Protein Structure:
  1. Primary (1^o): String of amino acids.
  2. Secondary (2^o): Hydrogen bonding, forms α-helices and β-pleated sheets.
  3. Tertiary (3^o): Overall 3D globular structure.
  4. Quaternary (4^o): Multiple polypeptides forming a protein complex.

Protein folding and breaking (denaturing). Primary structure is broken by hydrolysis, while 2^o, 3^o, 4^o are broken by environmental changes.

Cell Structure & Function

Prokaryotes vs. Eukaryotes

• Origins: Prokaryotes came first, lacking membrane-bound organelles. Eukaryotes evolved later and are generally larger.
• Shared Structures:
  • Cell membrane
  • Cell wall (in some)
  • Cytoplasm
  • Ribosomes
• Additional Eukaryotic Structures:
  • Nucleus: Holds DNA.
  • Rough Endoplasmic Reticulum (RER): Contains ribosomes for protein synthesis.
  • Smooth Endoplasmic Reticulum (SER): Makes lipids and detoxifies.
  • Golgi apparatus: Modifies proteins.
  • Lysosome: Contains digestive enzymes.
  • Mitochondria: Produces energy (ATP).
  • Chloroplast: Uses sunlight to create sugar (in plants).
• Endosymbiotic Theory: Mitochondria and chloroplasts have their own DNA and ribosomes, suggesting they were once independent prokaryotes.

The Cell Membrane

Structure

The cell membrane primarily consists of a phospholipid bilayer.

Proteins in Membrane

• Peripheral proteins: Located on one side of the membrane.
• Integral proteins: Embedded in the membrane.
• Transmembrane proteins: Span the entire membrane.

Cholesterol

Maintains membrane fluidity.

Cytoskeleton

Attaches to membrane proteins for structural stability and transport assistance.

Endomembrane System

Modifies and transports lipids and proteins within the cell.

Transporting Materials In and Out of Cell

What Needs to Be Transported

The cell membrane controls the movement of solutes across itself.

• Water (H_2O): Small polar molecules that can pass through slowly; aquaporins (channel proteins) facilitate faster transport.
• Steroids: Small nonpolar molecules that do not require protein assistance.
• Ions: Small charged particles that need protein channels.

Passive Transport

Requires no energy input; movement from high to low concentration.

• Simple diffusion: No protein required.
• Facilitated diffusion: Requires a protein channel.

Active Transport

Requires energy (ATP) to move substances from low to high concentration or to move large materials via vesicles.

Osmosis

Diffusion of water (H_2O) to reach equilibrium.

• Hypertonic: Higher solute concentration.

• Hypotonic: Lower solute concentration.

• Isotonic: Equal solute concentration.

• Animal Cells: Want outside to be isotonic.

• Plant Cells: Want outside to be hypotonic.

Water Potential

Ability of water to cross a semipermeable membrane.

\Psi = \Psip + \Psis

• \Psi = Water potential
• \Psi_p = Pressure potential
• \Psi_s = Solute potential

Cell Size

Cells are tiny because:

1. Redundancy is protective.
2. Smaller cells move materials more efficiently in and out.
3. Want a high surface area to volume ratio.

Cell Metabolism

Enzymes

General Info

Biological catalysts (usually proteins, but can be RNA) that reduce the activation energy (Ea) of a reaction. They are not consumed or altered by the reaction and are very specific to their substrates. Random molecular motion brings enzymes and substrates together.

Ways for Enzymes to Lower Ea

1. In catabolic reactions, the active site can flex to stress bonds, exposing them.
2. Active site holds substrates in optimal orientation for reaction.
3. Provides a favorable environment for the reaction.

Catabolic (Breaking) Reactions

Spontaneous and exergonic (release energy).

Anabolic (Building) Reactions

Require energy input (endergonic).

Changing Effectiveness of Enzyme

Environmental changes affect enzyme activity. All enzymes have optimal temperature, pH, and salinity.

Inhibition

• Competitive: Inhibitor binds to the active site.
• Noncompetitive: Inhibitor binds to an allosteric site, changing the enzyme's shape.

Feedback Loops

• Negative: Product inhibits its own production.
• Positive: Product promotes its own production.

Cellular Respiration

General Info

Digestion of food at a cellular level to transfer chemical energy from food. The first stage is Glycolysis, which all living things do this.

Occurs in the cytoplasm and mitochondria.

The overall equation for cellular respiration is: C6H{12}O6 + 6O2 \rightarrow 6CO2 + 6H2O + ATP

The process can be aerobic or anaerobic depending on available oxygen.

Glycolysis

Produces 2 ATP and 2 NADH.

Anaerobic Fermentation

Two types: produces ethanol or lactic acid. The purpose is to regenerate NAD^+.

Aerobic Citric Acid Cycle (Krebs Cycle)

Occurs in the mitochondria and produces 2 ATP, 2 FADH2, 6 NADH, and 6 CO_2.

Electron Transport Chain

Located in the inner mitochondrial membrane. Makes approximately 30 ATP and creates an H+ gradient.

Photosynthesis

General Info

• Stomata: These are openings in leaves that control water loss and gas exchange. When guard cells are turgid, the stomata open, allowing water to evaporate and O2 to exit. When guard cells are flaccid, the stomata close, reducing water loss and gas exchange.

The overall equation for photosynthesis is: 6CO2 + 6H2O + Light Energy \rightarrow C6H{12}O6 + 6O2

• Two stages:
  1. Light Reactions
  2. Calvin Cycle

Light Reactions

Occur in the chloroplast's thylakoid membrane. Uses light and water (H2O) to produce energy (ATP and NADPH) and waste oxygen (O2).

Calvin Cycle

Occurs in the stroma. Requires ATP and NADPH from the light reactions to produce sugar.

Cellular Communication & Cell Cycle

Signal Transduction

Involves signaling, reception, transduction, and response. Can involve secondary messengers.

• Types of Signaling:
  • Autocrine: Cell signals itself.
  • Juxtacrine: Cell signals an adjacent cell.
  • Paracrine: Cell signals a nearby cell.
  • Endocrine: Cell signals a faraway cell.

The Cell Cycle

1. G1 (Gap 1): Cell grows and makes organelles.
2. S (Synthesis): DNA replication.
3. G2 (Gap 2): Cell grows more.
4. M (Mitosis): Division of DNA into two nuclei:
   • Prophase
   • Metaphase
   • Anaphase
   • Telophase
5. Cytokinesis: Cells divide to form two cells.

Cancer

Tumors result from the cell cycle being incorrectly completed. Cells divide too fast without enough time to grow. Signals and density-dependent inhibition rules are ignored.

Heredity

Human Heredity

• Somatic cells: Non-sex cells are diploid (2 sets of chromosomes).

• Gametic cells: Sex cells are haploid (1 set of chromosomes).

• Homozygous vs. Heterozygous: Having the same or different alleles for a gene.

• Dominant vs. Recessive: Alleles that are expressed or masked, respectively.

• Atypical Chromosome Number: Aneuploidy is often lethal.

• Autosomal Inheritance: Genes found on autosomes (non-sex chromosomes).

• Sex-linked Inheritance: Genes found on sex chromosomes.

Karyotypes are images showing chromosomes.

Meiosis

Biological mechanism to create haploids.

The cell cycle is changed a bit for meiosis like so:

G1 -> S -> G2 -> Meiosis I (Prophase I, Metaphase I, Anaphase I, Telophase I, Cytokinesis) -> Meiosis II (Prophase II, Metaphase II, Anaphase II, Telophase II, Cytokinesis).

Note that G and S phases aren't repeated. Also, crossing over (genetic mixing) occurs in Prophase I.

Mendelian Inheritance

• Genotype vs. Phenotype: Genetic makeup vs. physical expression.
• Dominant vs. Recessive: Alleles that are expressed or masked, respectively (functional protein vs. no functional protein).
• Punnett Squares: Used to predict inheritance patterns.
• Rule of Multiplication: When asked for the probability of two things happening, multiply the probabilities together.

Non-Mendelian Inheritance

• Incomplete Dominance: Red + White = Pink.
• Codominance: Blood types (both alleles are expressed).
• Polygenetic Inheritance: Multiple genes affect a phenotype.
• Lethal Alleles: Cause death.
• Mitochondrial Inheritance: Passed from woman only to all kids.
• Linkage: Assume it's this when ratios are unexpected.
• Sex-linkage
• Epistasis: One gene can influence the expression of another gene.
• Epigenetics: Environmental impacts on gene expression.
• Mutations: Can change phenotype.

Pedigrees

Family trees showing genetics.

Chi-Square

Determines the plausibility of a numerical outcome.

\chi^2 = \sum \frac{(o-e)^2}{e}

• o = observed outcomes
• e = expected outcomes

Look at the chi-square chart to see if likely. If the value you get is smaller than the value on the chart for your degrees of freedom, fail to reject the null hypothesis.

Gene Expression & Regulation

DNA Structure

Double helix, antiparallel.

• Base Pairing: A pairs with T (or U in RNA); G pairs with C.

DNA Replication

1. Helicase unzips (breaks hydrogen bonds) the double helix.
2. Topoisomerase/gyrase prevents DNA tangling.
3. DNA polymerase (primary DNA replication enzyme) needs primase to start; it can only add to a 3' OH group.
4. Continuous replication occurs on the leading strand; discontinuous replication occurs on the lagging strand.
5. Ligase fixes missing covalent bonds in the sugar-phosphate backbone.
6. Telomeres are located on either end of DNA.

Gene Expression

Central dogma: DNA -> transcription -> RNA -> translation -> protein -> trait.

Transcription

Starts at the promoter. RNA polymerase makes a copy of the template strand. RNA polymerase needs transcription factors to activate. Before leaving the nucleus, mRNA gets edited:

1. 5' cap
2. 3' poly-A tail
3. Cut out introns and splice together exons.

Translation

Occurs in the ribosome. Starts at a start codon and ends at a stop codon.

In prokaryotes, translation and transcription happen at the same time.

Mutations

Changes in the DNA code that occur during the S phase.

Types of Point Mutations (single nucleotide is altered)

1. Substitution: Swapping a letter.
   • Missense: Alters an amino acid.
   • Same-sense: Produces the same amino acid.
   • Nonsense: Creates a new stop codon.
2. Insertion: Adds an extra nucleotide, causing a frameshift.
3. Deletion: Deletes a nucleotide, causing a frameshift.

Gene Regulation in Prokaryotes

Operons control the production of proteins:

1. Inducible: Normally turned OFF, can be turned ON (e.g., Lac Operon).
2. Repressible: Normally turned ON, can be turned OFF (e.g., Trp Operon).

Biotechnology

PCR (Polymerase Chain Reaction)

Replicating DNA in vitro (needs heat and enzymes).

Gel Electrophoresis

DNA visualization. Bigger DNA fragments move slower; smaller fragments move faster.

Restriction Enzymes

Enzymes that cut DNA at specific locations in bacteria.

Natural Selection

Historical Ideas

• Linnaeus: Taxonomy structures.
• Cuvier: Catastrophism.
• Lyell: Gradualism; Earth is old.
• Lamarck: Epigenetics (inheritance of acquired characteristics).

Phylogenetic trees and cladograms show evolutionary relationships.

Mutation is the ultimate source of variation.

• Bacteria go through transformation, conjugation, and transduction, which allow them to swap DNA.
• Viruses replicate via the lytic or lysogenic cycle:
  • Lytic cycle: Virus hijacks the cell, makes new copies, and the cell lyses, releasing new viruses.
  • Lysogenic cycle: Viral DNA becomes part of the bacterial DNA; bacteria copy viral info every time it replicates, then sometimes goes to the lytic cycle.

Evidence for evolution includes:

• Fossils
• Analogous structures
• Homologous structures
• Vestigial structures
• Embryology
• Biogeography

Reproductive Isolation

• Sympatric vs. Allopatric Speciation:

  • Sympatric: Genetic mutation prevents breeding with the original species.
  • Allopatric: Population is physically split into smaller groups that cannot reach each other, evolving differently due to different pressures.

• Prezygotic vs. Postzygotic Isolation:

  • Prezygotic: Occurs before offspring are produced.
    • Geographic isolation
    • Temporal isolation
    • Behavioral isolation
    • Mechanical isolation
    • Gametic isolation
  • Postzygotic: Occurs after hybrid offspring is produced.
    • Hybrid breakdown
    • Reduced hybrid fertility

Gradualism vs. Punctuated Equilibrium

Gradualism involves slow changes, while punctuated equilibrium involves changes that are very fast.

Hardy-Weinberg Equilibrium

Predicts whether a species is evolving for a specific trait.

• p + q = 1
• p^2 + 2pq + q^2 = 1

Genetic Drift

Random, non-adaptive changes.

• Bottleneck Effect: A portion of the population is killed randomly.
• Founder Effect: A small group of founders affects allele frequencies.

Ecology

Dispersion

• Clumped: Patches.
• Uniform: Evenly spaced.
• Random.

Population Curves

• Type I: Humans.
• Type II: Constant mortality rate.
• Type III: High juvenile mortality rate.

Population Growth

Two models for population growth:

• Exponential: Ideal conditions, dN/dt = r_{max}N
• Logistic: When populations reach carrying capacity, dN/dt = r_{max}N(\frac{K-N}{K})

Life History

Traits that affect life, when reproduction begins, how often an organism can reproduce, number of offspring produced.

• Density-dependent vs. Density-independent Factors:
  • Density Dependent: K selection, food availability, competition.
  • Density Independent: R selection, natural disasters, weather.

Behavior

Innate vs. Learned.

Innate behaviors are fixed action patterns (unchangeable).

Trophic Levels

Producers -> Primary Consumers -> Secondary Consumers -> Tertiary Consumers

Relationships

• Competition: -/-
• Predation: +/-
• Herbivory: +/-
• Parasitism: +/-
• Mutualism: +/+
• Commensalism: +/0

Species Diversity

Protecting against invasive species.

To calculate species diversity, use the formula: \frac{\text{# of species}}{\text{# of all organisms}}

Keystone Species

Species that are relied on in an ecosystem.

Pathogens

Cause diseases.