AP BIO

UNIT 1: THE CHEMISTRY OF LIFE

• Macromolecules

  • Carbohydrates

    • Sugars: Simple carbohydrates, also known as saccharides, which include monosaccharides like glucose and fructose, and disaccharides like sucrose and lactose.

    • C,H,O - 1:2:1 ratio

    • Cellulose - found in plant walls

    • Chitin - found in fungi cell walls and exoskeletons of arthropods

    • Starch/Glucose - found in plants/animals for storage

  • Proteins

    • C,H,O,N,S

    • Monomer - Amino Acid

      • Amino, Hydrogen, Carboxyl, and R group

      • Bonded by peptide bonds (between carboxyl and amino groups)

    • Structure:

      • Primary:

        • Peptide bonds between amino caids

        • String of amino acids

      • Secondary:

        • Hydrogen bonds between backbone

        • Alpha helix or beta pleated sheet

      • Tertiary:

        • ANY bonds between R groups

        • Final 3D structures

      • Quaternary:

        • ANY bonds between R groups of different polypeptides

    • R Groups:

      • Hydrophilic - Exterior

      • Hydrophobic - Interior

      • Charged - Exterior

  • Nucleic Acids

    • C,H,O,N,P

    • Monomer - Nucleotide

    • Phosphate group + pentose sugar + nitrogenous base

    • Phosphodiester linkage bond between phosphate and hydroxyl group

    • Directionality - 5’ to 3’ (Antiparallel)

    • Purine:

      • Double ring

      • A and G

    • Pyrimidine

      • Single ring

      • C, U, and T

    • DNA - deoxyribose and double stranded

    • RNA - ribose and single stranded

  • Lipids

    • C,H,O,P (in phospholipids)

    • No monomer (no repeating structure)

    • Fats:

      • Glycerol stuck to 3 fatty acids

      • Saturated - All single bonds, each carbon saturated by hydrogen

      • Unsaturated - At least one double bond

      • Not all carbons are saturated by hydrogen

    • Phospholipids:

      • Phosphate head attached to glycerol attached to 2 fatty acids

      • Hydrophilic head attracted to water

      • Hydrophobic fails repelled by water

• Water Properties

  • Polar:

    • Polar covalent bonds between oxygen and hydrogen IN the water molecule

    • Leads to hydrogen bonds as oxygen is more electronegative than the hydrogen atoms

    • Water acts as a universal solvent to anything that is polar

    • Cohesion - water molecules attracted to other water molecules

    • Adhesion - water molecules attracted to other polar substances

    • Capillary action - water pulls other water molecules, when water transpires it pulls the next water molecule within a plant stem

    • Surface tension - cohesion develops a “surface” based on the interaction of hydrogen bonds

  • Less Dense when Solid:

    • Hydrogen bonds constantly break and reform when temp is high

    • When hydrogen bonds are stable (cold/iced) the bonds form a uniform structure taking up more space

  • High Specific Heat:

    • Water must absorb or release a large amount of energy to change 1 gram of water by 1 degrees Celsius (due to hydrogen bonds)

    • Evaporative cooling - release water on surface of organism to absorb heat energy from body (and break the bonds cooling down the organism)

  • pH:

    • pH = -log[H+]

    • As the concentration of hydronium/hydrogen ion increases, the pH decreases

• Extra:

  • Hydrolysis - adding H20 to cleave bonds between polymers

  • Dehydration - removing H20 between polymer/monomers to create/link polymers

UNIT 2: THE CELL

• Cellular Organelles

  • Nucleus:

    • Double membrane (nuclear envelope) with pores

    • Stores genetic information (DNA)

    • Synthesis of RNA

    • Ribosome subunit assembly

  • Rough ER:

    • Membrane studded with ribosomes attracted to nuclear envelope

    • Site of membrane bound protein and secreted protein synthesis

    • Cell compartmentalization

    • Mechanical support

    • Role in intracellular transport

  • Smooth ER

    • Folded, tubelike structure (cisternae)

    • Detoxification

    • Calcium storage

    • Lipid synthesis

  • Golgi Complex

    • Membrane-bound structure composed on flattened sacs (cisternae)

    • Folding and chemical modification of synthesized proteins

    • Packaging protein traffic

  • Ribosomes

    • Composed of rRNA and protein

    • Large and small subunits

    • Bound or free (cytoplasmic)

  • Mitochondria

    • Double membrane (outer: smooth; inner: highly folded)

    • Intermembrane space, ribosomes inside the matrix, 2 membranes, DNA also inside matrix

    • Site of oxidative phosphorylation (cristae/inner membrane)

    • Site of Krebs Cycle (matrix)

  • Lysosome

    • Membrane-enclosed sacs that contain hydrolytic enzymes

    • Intracellular digestion (recycles cell organic materials and programmed cell death: apoptosis)

  • Chloroplast

    • Double outer membrane (thylakoid sac stacked: grana and fluid: stroma)

    • Site of photosynthesis

    • Thylakoid: Light Reactions

    • Stroma: Calvin-Benson Cycle

  • Vacuole

    • Membrane-bound sac

    • Storage and release of macromolecules and cellular waste products

    • Central: water retention - turgor pressure

    • Contractile: osmoregulation (protist)

    • Food: phagocytosis, fuse with lysosome

• Surface Area: Volume

  • Smaller cells typically have a higher surface area-to-volume ratio and more efficient exchange of materials with the environment

• Membrane Transport

  • Plasma Membrane

    • Composed of:

      • Phospholipids

      • Membrane proteins

      • Glycolipids/Glycoproteins

      • Cholesterol

  • Simple Diffusion

    • Passive transport, no energy

    • Down concentration gradient

    • Small, nonpolar

    • No transport protein needed

    • Examples: CO2, O2, N2, steroids

    • Small amount of H20 can leak through membrane

  • Facilitated Diffusion

    • Passive transport, no energy

    • Down concentration gradient

    • Small molecules

    • Requires transport proteins

      • Channel vs. Carrier protein

    • Examples: Water, Na+, K+, Ca+

  • Active Transport

    • Requires input of energy

    • Against concentration gradient

    • Requires transport proteins (carrier proteins)

    • Examples: Na+, K+, Ca+, H+

  • Endocytosis

    • Import of materials

    • Phagocytosis: cellular eating

    • Pinocytosis: cellular drinking

    • Receptor-Mediated: endocytosis

  • Exocytosis

    • Export of materials

    • Rough ER (synthesize) $\rightarrow$ Golgi complex (package/modification) $\rightarrow$ Plasma membrane

• Osmosis

  • Hypertonic Solution

    • HIGH solute concentration

    • LOW free water concentration

    • GAINS water from hypotonic solution

  • Isotonic Solution

    • EQUAL solute concentration

    • EQUAL free water concentration

    • Equal water movement into and out of solution

  • Hypotonic Solution

    • LOW solute concentration

    • HIGH free water concentration

    • LOSES water to hypertonic solution

UNIT 3: CELLULAR ENERGETICS

• Gibbs Free Energy and Reactions

  • Gibbs Free Energy - Energy available to do work (deltaG = deltaH - TdeltaS)

  • Endergonic Reaction

    • Not spontaneous

    • ABSORBS energy

    • Example: ADP+ P1 $\rightarrow$ ATP

  • Exergonic Reaction

    • Spontaneous

    • RELEASES energy

    • Example: ATP $\rightarrow$ ADP + P1

• Enzymes

  • Biological catalyst

  • Speeds up chemical reactions

  • Reduces the activation energy

  • Enzymes are proteins

  • NOT consumed by the reaction

  • Has no effect on the change in Gibbs Free Energy

  • Inhibitors

    • Competitive - Binds to active site

    • Noncompetitive - Binds to allosteric site

  • Denaturation

    • Environmental Temperatures

    • pH (outside of optimal range)

    • Salinity

• Cellular Respiration

  • Glycolysis

    • Located in Cytosol

    • Starts with Glucose

    • Products:

      • 2 Pyruvate

      • 2 NADH

      • 2 ATP

  • Krebs Cycle

    • Located in mitochondrial matrix

    • Starting material - Acetyl CoA

    • Products:

      • 2 CO2

      • 3 NADH

      • 1 FADH2

      • 1 ATP

  • Oxidative Phosphorylation

    • Located in mitochondrial cristae

    • Starting material - NADH/FADH2 (electrons)

    • Product:

      • ATPs

    • 2 parts: Electron Transport Chain (ETC) and Chemiosmosis

      • Electron Transport Chain:

        • Protons pumped into IM space

        • Generates proton gradient

        • Final electron acceptor: OXYGEN

      • Chemiosmosis

        • ATP synthase uses proton gradient

        • Synthesizes ATP

• Photosynthesis

  • Light Reactions

    • Located in Thylakoid Membrane

    • Starting Material:

      • Water (electrons)

      • Photons (energy)

    • Products:

      • ATP

      • NADPH

    • Linear Electron Flow

      • PS I and PS II

      • Synthesizes ATP and NADPH

    • Cyclic Electron Flow

      • PS I ONLY

      • Synthesizes ATP ONLY

  • Calvin Cycle

    • Located in Stroma (cytosol of chloroplast)

    • Starting Material:

      • 3 CO2

      • 9 ATP

      • 6 NADPH

    • Products:

      • G3P

• Fermentation

UNIT 4: CELL COMMUNICATIONS AND CELL CYCLE

• Cellular Communication

  • Reception

    • Ligand (signaling molecule) binds to a receptor

    • Causes confirmational shape change

      • Ex. G protein coupled receptor, Tyrosine kinase receptor

    • Steroid Hormone

      • Release: simple diffusion

      • Receptor: intracellular

      • Ex. Testosterone, Estrogen

    • Protein Hormone

      • Release: exocytosis

      • Receptor: extracellular

      • Ex. Insulin

  • Transduction

    • Signaling cascades relay signals from receptors to cell targets, often amplifying the incoming signals

    • Phosphorylation cascade

      • Protein kinase

      • Phosphorylate relay molecules

    • Secondary Messengers

      • Ca²+

      • cAMP

  • Response

    • Cell growth

    • Secretion of molecules

    • Gene expression

    • Alters cell function/phenotype

    • Apoptosis

• Cell Cycle   

  • Interphase (cell grows through all the different phases of interphase)

    • G1:

      • Duplication of cell organelles

      • Synthesis of proteins, RNA, and building blocks

    • S:

      • Replication of genetic material and centrosomes

    • G2:

      • Synthesis of proteins and RNA

      • Makes organelles

      • Reorganizes cellular contents

  • Mitosis:

    • Prophase

      • Cell prepares to divide

      • Centrosomes organizes, nuclear envelope starts to disappear

    • Metaphase

      • Sister chromatids line up in the middle

    • Anaphase

      • Sister chromatids pulled apart to opposite poles

    • Telophase

      • Two new nuclei are formed

    • Cytokinesis

      • Division of the cytoplasm

• Checkpoints

  • G1 - determines whether to complete the cell cycle:

    • Growth factor

    • Adequate reserves

    • Check for DNA damage

    • If cell does not pass, it enters G0 (nondividing state)

  • G2 - checks that all DNA is replicated and not damaged

    • If problems are detected with DNA, the cell cycle is halted to complete DNA replication or to repair the damaged DNA

  • M - checks that sister chromatids are attracted to the spindle microtubules

UNIT 5: HEREDITY

• Meiosis

  • Prophase I

    • Chromatin condenses

    • Sister chromatids/homologous chromosomes align

    • CROSSING OVER

  • Metaphase I

    • Homologous chromosomes align on the metaphase plate

    • Independent assortment

      • Homologs separate independently of other homologs

  • Anaphase I

    • Homologous chromosomes separate to opposite poles

  • Telophase I

    • 2 haploid cells

    • Nuclear envelope forms around the haploid daughter cells

  • Prophase II

    • Chromatin condenses

    • Sister chromatids align

  • Metaphase II

    • Sister chromatids align on the metaphase plate

  • Anaphase II

    • Sister chromatids separate to opposite poles

  • Telophase II

    • Nuclear envelope forms around the haploid daughter cells

• Mitosis vs. Meiosis

  • Mitosis:

    • Parent cell - diploid

    • 1 round of DNA replication

    • 1 round of nuclear division

    • Daughter cells - diploid

    • No crossing over

    • No independent assortment

  • Meiosis

    • Parent cell - diploid

    • 1 round of DNA replication

    • 2 rounds of nuclear division

    • Daughter cells - haploid

    • Crossing over and independent assortment occurs

• Inheritance Patterns

  • Compete dominance

    • Homozygous dominant and heterozygous look the same

    • 3:1 ratio

  • Codominance

    • Heterozygous is both dominant traits in organism

    • 1:2:1 ratio

  • Incomplete dominance

    • Heterozygous is a blend between the two dominant traits

    • 1:2:1 ratio

  • Dihybrid

    • Heterozygous for 2 traits

    • Complete dominance:

      • 9:3:3:1 ratio

    • Incomplete or codominance:

      • 6:3:3:2:1:1

  • Autosomal inheritance

    • Allele is located on an autosome (non-sex chromosome)

  • Sex-Linked

    • Allele is located on a sex chromosome

  • Maternal inheritance

    • Allele is located on the DNA found in a mitochondrial or chloroplast

• Chromosomal Inheritance

  • Genetic Variation

    • Crossing over

    • Independent assortment

    • Law of segregation

      • Diploid organisms possess 2 alleles for each trait which separate during meiosis so that each gamete receives only 1 allele

    • Random fertilization

  • Chromosomal basis of inheritance

    • Concept that genes are located on chromosomes and are passed from parent to offspring during reproduction

  • Human genetic disorders

    • Single affected/mutated allele

      • Sickle cell disease

      • Tay Sachs disease

      • Huntington’s disease

    • Chromosomal changes

      • Downs Syndrome/Trisomy 21

      • Klinefelter Syndrome/XXY

      • Turner Syndrome/XO

• Environmental Effects on Phenotype

  • Phenotype Plasticity

    • Result of environmental facts influencing gene expression

    • Individuals with the same genotype exhibit different peoples in different environments

UNIT 6: GENE EXPRESSION AND REGULATION

• Central Dogma: DNA $\rightarrow$ RNA $\rightarrow$ Polypeptide

  • Replication:

    • Located in nucleus for eukaryotes

    • Located in nucleoid for prokaryotes

    • Multiple linear in eukaryotes

    • Single circular in prokaryotes

    • Sidedness

      • 5’ end: phosphate

      • 3’ end: hydroxyl group

    • Directionality

      • Read 3’ to 5’

      • Synthesize 5’ to 3’

    • Important Enzymes:

      • Helicase unwinds the DNA strands

      • Topoisomerase relaxes supercoiling in front of the replication fork

      • Primase synthesizes the RNA primer (DNA polymerase requires RNA primers to initiate DNA synthesis)

      • DNA polymerase synthesizes new strands of DNA continuously on the leading strand and discontinuously on the lagging strand

      • Ligase joins the fragments on the lagging strand

  • Transcription

    • Located in nucleus for eukaryotes

    • Located in nucleoid (cytosol) for prokaryotes

    • RNA made of:

      • Nitrogenous base (A,U,C,G)

      • Pentose sugar (ribose)

      • Phosphate group

      • 5’ end: phosphate

      • 3’ end: hydroxyl group

    • Directionality:

      • Reads 3’ to 5’

      • Synthesizes 5’ to 3’

    • Template strand (noncoding strand, minus strand, or antisense strand)

    • Important Enzymes and Components:

      • RNA polymerase synthesizes molecules in the 5’ to 3’ direction by reading the template DNA strand in the 3’ to 5’ direction

      • Promoter: site where RNA polymerase binds to start transcription

      • Transcription Factors: activators/inhibitors to turn on/off the gene expression

  • Post-Transcriptional Modifications

    • 5’ Guanine Cap

      • Signals the “start” o the mRNA transcript for ribosome to bind

      • Facilitates export from nucleus

    • Splicing

      • Removal of introns from pre-mRNA transcript

    • Poly-A Tail

      • Inhibits degradation from hydrolytic enzymes in cytosol

  • Translation

    • Located in cytosol/rough ER for eukaryotes

    • Located in cytosol for prokaryotes

    • Initiation: start codon AUG

    • Elongation: base pair between tRNA/mRNA with amino acid added

    • Termination: stop codon (UAG UAA, UGA)

    • A site: amino acid added in (tRNA carries next amino acid to be added to the polypeptide chain)

    • P site: holds the tRNA that is attached to the growing polypeptide chain

    • E site (exit): binds the deacylated tRNA that has released its amino acid, preparing it for release from the ribosome

  • Mutations

    • Point Mutations - mutation at one nucleotide base pair

      • Silent: no change in amino acid

      • Missense: change from one amino acid to another amino acid

      • Nonsense: change from amino acid to a STOP codon

      • Frameshift: insertion/deletion of 1 or 2 nucleotide base pairs

        • shifts the reading frame for codons

    • Chromosomal mutations

      • Rearrangement of parts of chromosomes or chromosome number

        • Rearrangement

          • Insertion

          • Deletion

          • Duplication

          • Inversion

          • Translocation

        • Changes in Chromosome Number

          • Nondisjunction

          • Polyploidy

• Operons - Gene regulation found in prokaryotes

  • Promoter

    • Site where RNA polymerase binds

  • Operator

    • Site where repressor binds

  • Genes

    • DNA

  • Repressible Operon

    • Ex. Trp Operon (synthesizes tryptophan)

    • Starts ON

    • Repressor - INACTIVE

    • If trp is present…

      • Trp binds to repressor to activate

      • Repressor binds to operator to turn the operon OFF

  • Inducible Operon

    • Ex. Lac Operon (synthesizes enzymes to break down lactose)

    • Starts OFF

    • Repressor - ACTIVE

    • If lactose is present…

      • Lactose binds to repressor to inactivate

      • Repressor no longer binds to operator to turn the operon ON

• BioTechnology

  • Gel Electrophoresis - Separates molecules based on size and charge

    • Apply electrical current to move molecules (DNA moves towards positive charge)

    • smaller molecules move faster and father than larger ones

    • allows for analyzation of DNA fragments, identifying PCR products, and purifying samples for sequencing

  • Polymerase Chain Reaction (PCR) - Makes multiple copies of DNA fragments

    • 1. Heating

    • 2. Cooling

    • 3. Annealing

  • Bacterial Transformation - Introduce genetic material (plasmid) to bacteria

    • Bacteria takes up foreign DNA (usually plasmids) enabling bacteria to express new genes for applications

    • Useful for experimentation and production of new applications such as medicine

  • DNA Sequencing - Use radioactive nucleotides to determine the sequence of a DNA strand

    • Involves breaking DNA into smaller pieces and attaching adapters

    • Can be use to read 100% of a genome

UNIT 7: NATURAL SELECTION

• Selection

  • Natural Selection

    • Developed by Charles Darwin

    • Establishes that due to variation in the population and competition for resources organisms with more favorable traits are most likely to survive and pass on their traits to the next generation

      • Ex. Peppered moths - antibiotic resistance

    • Disruptive Selection

      • Selection for the two extreme phenotypes

      • Selection against the intermediate phenotype

    • Stabilizing Selection

      • Selection for the intermediate phenotype

      • Selection against the two extreme phenotypes

    • Directional Selection

      • Selection for an extreme phenotype

      • Selection against the other phenotypes

  • Artificial Selection   

    • Organisms with certain traits are bred until population has that trait

    • Humans affect variation in the population

    • Ex.    

      • Dog breeds

      • Corn from maize

      • Wild mustard $\rightarrow$ cauliflower, broccoli, cabbage, kale, and kohlrabi

• Hardy-Weinberg

  • Five Fingers of Evolution

    • Extremely large population size

    • Random mating

    • No mutations

    • No gene flow (immigration/emigration)

    • No natural selection

  • Genetic Drift

    • Founder’s effect

      • Small population is isolated from original population

    • Bottleneck effect

      • Population is reduced by a natural disaster (fire, flood, etc.) where there was no selection based on traits

    • Both reduces the population size and could decrease genetic diversity making them more susceptible to environmental impact or could fix harmful alleles

  • Equations

    • Variables:

      • p = frequency of dominant allele

      • q = frequency of recessive allele

      • p² = frequency of homozygous dominant

      • 2pq = frequency of the heterozygous

      • q² = frequency of the homozygous recessive

    • Hardy-Weinberg Equilibrium

      • p + q = 1

      • p² + 2pq + q² = 1

      • Only works if population is in equilibrium

    • If genotype numbers are all given, we must use the counting alleles method:   

      • p = (2AA+Aa)/(2 x # of individuals)

      • q = (2aa+Aa)/(2 x # of individuals)

        • Count each allele individually and divide by total number of alleles

• Phylogeny

  • Biochemical

    • DNA or protein

    • Comparison of the number of differences

  • Morphological

    • Homologous structures: similar structures due to common ancestry

      • Ex. Bat wing and cat arm

    • Ancestral/Derived traits: characteristics derived from ancestor or from descendants

    • Analogous structures are due to convergent evolution

  • Biogeography

    • Distribution of species and ecosystems in geographic space and through geological time

• Speciation

  • Two organisms are of the same species if they can INTERBREED and produce FERTILE, VIABLE offspring

  • Prezygotic - before zygote is created

    • Behavioral

      • 2 organisms have different mating rituals

    • Temporal

      • 2 organisms mate at different times

    • Geographic

      • 2 organism are separated by a geographical barrier

    • Habitat/Ecological

      • 2 organisms in different ecological environments

    • Mechanical

      • 2 organisms incompatible anatomically

    • Gametic

      • 2 gametes are unable to fuse

  • Postzygotic - after zygote is created

    • Reduced Hybrid Viability

      • Hybrid is not healthy/viable

    • Reduced Hybrid Fertility

      • Hybrid is not fertile

    • Hybrid Breakdown

      • Subsequent hybrid starts decreasing viability and fertility

  • Sympatric

    • New species from a surviving ancestral species while both continue to inhabit the same geographic region

      • Habitat isolation, behavioral isolation, sexual selection, polyploidy

  • Allopatric

    • Occurs when biological populations of the same species become isolated due to geographical changes

UNIT 8: ECOLOGY

• Energy Flow - Organisms use energy to maintain, organize, grow, and reproduce

  • Body Temperature

    • Endotherm - maintains body temperature through metabolism

    • Ectotherm - maintains body temperature through behaviors (bask in sunlight, aggregation)

  • Trophic Structure

    • Autotroph - captures energy from physical or chemical source

      • Photosynthetic (sunlight)

      • Chemosynthetic (small inorganic molecules in environment, sometimes without oxygen)

    • Heterotroph - captures energy present in carbon compounds produced by other organisms

      • Metabolizes carbohydrates, lipids, and proteins (notice: not nucleic acids) for energy through hydrolysis

  • Changes in Availability

    • Changes in energy resource - affects number and size of trophic levels

    • Change in producer level - affects number and size of trophic levels

• Animal Behavior

  • Communication - signaling allows for changes in behaviors of organisms to allow for differential reproductive success

    • Types of communication:

      • Visual

      • Auditory

      • Electrical (tactile)

      • Chemical

    • Functions:

      • Indicate dominance

      • Foraging

      • Establish territory

      • Ensure reproductive success

  • Altruistic Behaviors

    • Reduces individual fitness but increases inclusive fitness

  • Intersexual Selection

    • Reproductive behaviors to attract a mate

    • Individuals of sone sex choose members of the opposite sex

      • Examples:

        • Blue footed booby - mating dance (visual)

        • Frogs - croaking (auditory)

        • Pheromones - (chemical)

  • Intrasexual Selection

    • Reproductive behaviors to indicate dominance and compete access to mates

    • Examples:

      • Deer: antler size

      • Horned beetles: strength and size of “horn”

• Population Ecology

  • Exponential Growth

    • Unlimited growth of population

    • r = b - d

    • rate of increase = birth rate - death rate

    • dN/dt = rN

  • Logistic Growth

    • Population size limited by carrying capacity

    • dN/dt = rN((K-N)/K)

  • Density Dependent Factors

    • Factors that intensifies as population increases

    • Ex. competition, predation, disease

  • Density Independent Factors

    • Factors that affect all individuals regardless of size, population, density

    • Ex. natural disasters, human activity

• Community Ecology

  • Species Diversity

    • Simpson’s Index: measures biodiversity (species composition and diversity)

    • 1 - Σ(n/N)²

    • n = total number of organisms of particular species

    • N = total of organisms of all species

    • Higher index indicated greater biodiversity and a balanced, healthy ecosystem

  • Interactions

    • Predator/Prey (+/-)

    • Herbivory (+/-)

    • Competition (-/-)

    • Symbiosis:

      • Parasitism (+/-)

      • Mutualism (+/+)

      • Commensalism (+/0)

  • Invasive Species

    • Organism that is not indigenous, or native, to a particular area with no natural predators and unlimited resources

    • Ex. Zebra mussel (clogging water ways), Lionfish (venomous species)