Unit 1 - Chemistry of Life 🧪

INTRO TO MACROMOLECULES

• monomers are the building blocks of polymers

• in dehydration synthesis, one monomer forms a covalent bond to another monomer & releases a water molecule

• carbs, nucleic acids, & proteins all contain multiple types of monomers

  • composition & sequence important to function

• hydrolysis - bond is broken by adding a water molecule

  • one molecule gains "H", the other gains "OH"

  • generally releases energy

CARBOHYDRATES

• made of carbon, hydrogen, and oxygen

• monosaccharides - simple sugars, contain 3-7 carbon atoms (ex: glucose, fructose, galactose)

  • isomers of each other - differ in organization of their atoms

• disaccharides - form when two monosaccharides bond via dehydration synthesis (ex : lactose, maltose, sucrose)

• polysaccharides - long chains of monosaccharides linked by glycosidic bonds (ex : starch, glycogen, cellulose, chitin)

  • chain may be branched or unbranched

• starch - stored form of sugars in plants

• glycogen - storage form of glucose in humans

PROTEIN STRUCTURE

• primary structure - sequence of amino acids

• secondary - due to interactions of the peptide backbone

  • beta-pleated sheets - hydrogen bonding

    • parallel - backbones interact & sequence match

    • anti parallel - opposite sequences & backbones interact

  • alpha helix - hydrogen bonds between different layers of the helix

• tertiary - due to interactions of side chains

  • hydrophobic & hydrophilic retract each other

  • hydrogen bonds might form

• quaternary (more than 1 polypeptide) - arrangement of multiple chains together

TRIGLYCERIDES (FATS)

• fatty acids - carbon chains (HYDROPHOBIC) & an acidic carboxyl group

  • glycerol can bond with 3 other fatty acids through dehydration synthesis

    • results in a triglyceride

    • ester bonds

• saturated fat - saturated by hydrogen

  • solid at room temp

  • unhealthy - butter

  • dense

  • no double bonds

• unsaturated - less hydrogens

  • liquid at room temp

  • Kinks formed - less dense - healthier

  • ex : oils

NUCLEIC ACIDS

• DNA is found in the nucleus in eukaryotes

  • chromosomes - DNA is broken up into long linear pieces

• chromosomes contain tens of thousands of genes

• located in the nucleoid of prokaryotes

  • chromosomes are smaller & often ring-shaped

• monomers=nucleotides

  • when combined the resulting chain is called a polynucleotide

• made up of: nitrogen - containing ring (NITROGENOUS BASE), five-carbon sugar, at least one phosphate group

• purine: adenine & guanine - two rings

• pyrimidine: thymine, uracil, & cytosine - single ring

• DNA's sugar: deoxyribose - 2nd carbon has a hydrogen

• RNA's sugar: ribose - 2nd carbon has a hydroxyl group

• polynucleotide chain has directionality

  • 5' - phosphate group

  • 3 ' - hydroxyl of the last nucleotide

• DNA sequences written in 5' to 3' direction

• DNA chains found in a double helix - two complementary chains stuck together

  • sugar - phosphate backbone

  • bases interior - bound to each other by hydrogen bonds

  • two strands have opposite directionality - anti parallel orientation

• RNA is single-stranded

  • mRNA - an intermediate between a protein coding gene & its protein product

  • rRNA - help accelerate chemical reactions, helps mRNA bind to the right spot

  • tRNA - bring amino acids to the ribosome

• RNA is involved in protein synthesis & gene regulation

Unit 2 - Cell Structure and Function 🦠

EUKARYOTIC CELLS

• Lysosomes maintain acidic pH for waste disposal.

• Peroxisomes carry out oxidation reactions and produce hydrogen peroxide.

• Eukaryotic cells have a membrane-bound nucleus, multiple organelles, and linear chromosomes.

ENDOMEMBRANE SYSTEM

• Includes endoplasmic reticulum, Golgi apparatus, lysosomes, and plasma membrane.

• Rough ER has ribosomes for protein synthesis, while smooth ER synthesizes lipids.

• Golgi apparatus tags, packages, and distributes lipids and proteins.

• Lysosomes act as recycling facilities and digest foreign particles.

MITOCHONDRIA AND CHLOROPLASTS

• Mitochondria break down molecules for energy.

• Chloroplasts use photosynthesis to build sugars.

PLASMA MEMBRANE STRUCTURE

• Phospholipid bilayer with cholesterol in the core.

• Integral membrane proteins anchor to the core, while peripheral proteins are on the surface.

• Carbohydrates form cell markers for recognition.

PROKARYOTE AND EUKARYOTE DIFFERENCES

• Eukaryotes have linear DNA, membrane-bound organelles, and are larger.

• Prokaryotes have circular DNA, no nucleus, and are smaller.

ENDOSYMBIOSIS THEORY

• Scientific concept where one organism lives inside another.

EXTRACELLULAR MATRIX (ECM) AND CELL WALL

• Animal cells release materials into the extracellular space forming ECM.

• ECM consists of proteins and carbohydrates, with collagen being a major component.

• Collagen provides strength and structural integrity to tissues.

• Fibronectin acts as a bridge between integrins and collagen.

• Cell wall surrounds and protects the cell, with cellulose being a major component.

• Other polysaccharides found in the cell wall include hemicellulose and pectin.

PASSIVE TRANSPORT

• Does not require energy.

• Involves diffusion from high to low concentration.

• Small, uncharged substances can easily diffuse across the cell membrane.

• Charged ions or large molecules require different transport mechanisms.

ACTIVE TRANSPORT

• Requires energy input, usually from ATP.

• Involves moving substances against the concentration gradient.

• Carrier proteins assist in the process.

BULK TRANSPORT

• Involves enclosing substances in membrane-bound vesicles.

• Endocytosis moves particles into the cell, while exocytosis moves materials out.

CELL SIZE

• Cells have a limitation on how small they can get due to the need for complex materials and organelles

• Surface area needs to process inputs and outputs efficiently

  • Larger surface area to volume ratio (or larger surface area) is more efficient

FACILITATED DIFFUSION

• Involves channel proteins or carrier proteins

• Allows charged or polar molecules to pass through hydrophobic regions

OSMOSIS AND TONICITY

• Osmosis is the movement of water across a semipermeable membrane

• Osmolarity refers to the total concentration of solutes in a solution

• Hyperosmotic, hypoosmotic, and isosmotic solutions have different solute concentrations

  • if a cell is placed in a hypotonic solution, there will be a net flow of water

    into the cell - cell will GAIN VOLUME

  • if a cell is placed in a hypertonic solution, there will be a net flow of water

    out of the cell - cell will LOSE VOLUME

  • if a cell is placed in an isotonic solution,

    there will be no net flow of water into

    or out of the cell - volume will remain stable

Unit 3 - Cellular Energetics ⚡️

ACTIVATION ENERGY

• Reactions with negative ∆G require activation energy (Ea) to proceed.

• Bonds must be contorted into an unstable shape to reach a high-energy state.

• Ea always has a positive value.

• Heat is a common source of activation energy.

• Higher Ea leads to slower reactions.

ENZYMES

• Enzymes bind to reactants to facilitate bond-breaking and bond-forming.

• Enzymes do not change whether a reaction is energy-releasing or energy-absorbing.

• Enzymes lower the energy of the transition state.

EFFECTS OF TEMPERATURE AND PH

• Higher temperature leads to a higher rate of reaction.

• Extreme temperatures can denature enzymes.

• pH affects the ability of substrates to bind to enzymes.

ENZYME REGULATION

• Cofactors and compartmentalization are important for enzyme function.

• Feedback inhibition controls key metabolic enzymes.

TYPES OF INHIBITION

• Competitive inhibition reduces reaction rate with fewer substrates.

• Noncompetitive inhibition prevents the reaction from reaching maximum rate.

METABOLISM

• Metabolic pathways involve building up (anabolic) and breaking down (catabolic) processes.

PHOTOSYNTHESIS

• Carbon fixation incorporates carbon into organic molecules.

• Photoautotrophs use light for self-feeding.

• Heterotrophs obtain fixed carbon from other organisms.

LIGHT DEPENDENT REACTIONS AND THE CALVIN CYCLE

• Light-dependent reactions occur in the thylakoid membrane and produce ATP and NADPH.

• The Calvin Cycle takes place in the stroma and uses ATP and NADPH to fix carbon dioxide and produce glucose.

ATP SYNTHESIS

• Electron transport chains drive ATP synthesis in photosynthesis.

• Photosystems absorb light and transfer energy to produce ATP and NADPH.

CYCLIC PATHWAY

• Chloroplasts switch to a cyclic pathway under certain conditions.

• The cyclic pathway may play a photoprotective role in cells with high ATP needs.

REDUCTION

• ATP & NADPH convert a 3-pod molecule into 3-carbon sugar (G3P).

REGENERATION

• Some G3P molecules make glucose, while others are recycled to regenerate the RuBP acceptor.

CELLULAR RESPIRATION AND REDOX

• Catabolic reactions break down large molecules to extract energy.

• Electron carriers pick up and drop off electrons.

• NAD+ & FAD gain hydrogen atoms when picking up electrons.

• They go back to their original form when dropping off electrons.

• LEO (lose electrons oxidized) GER (gain electrons reduced) principle.

• Energy is released as electrons move to a lower energy level during glucose breakdown.

STEPS OF CELLULAR RESPIRATION

• Glycolysis: Glucose converted to pyruvate, ATP is made, NADH is converted to NADH.

• Pyruvate Oxidation: Pyruvate converted to acetyl CoA, releasing carbon dioxide and generating NADH.

• Citric Acid Cycle: Acetyl CoA undergoes a cycle of reactions, producing GTP, NADH, and FADH2.

• Oxidative Phosphorylation: NADH & FADH2 deposit electrons in the electron transport chain, generating ATP.

ELECTRON TRANSPORT CHAIN

• Series of proteins in the mitochondria where electrons are passed down via redox reactions.

• Energy released is captured as a proton gradient to produce ATP in chemiosmosis.

• Oxygen accepts electrons at the end to form water.

ULTIMATE ATP YIELD

• Direct products at each stage contribute to a total ATP yield of 30-32.

FERMENTATION AND ANAEROBIC RESPIRATION

• Some organisms perform anaerobic respiration using alternative electron acceptors.

• Fermentation involves glycolysis and regenerates NAD+ from NADH.

• Lactic acid fermentation and alcohol fermentation are two types.

• Facultative anaerobes can switch between aerobic and anaerobic pathways, while obligate anaerobes only grow in the absence of oxygen.

Unit 4 - Cell Communication and the Cell Cycle 🔄

CELL SIGNALING

• Cells produce proteins (chemical signals) that are secreted into the extracellular space.

• Target cell must have the right receptor for the signal molecule to bind.

• Ligands are molecules that bind specifically to receptors.

• Signaling can occur through paracrine, synaptic, autocrine, and endocrine mechanisms.

• Quorum sensing in bacteria involves monitoring population density through chemical signals.

CELL JUNCTIONS

• Plasmodesmata in plant cells allow direct cytoplasmic exchange between cells.

• Gap junctions in animal cells allow transport of ions and water.

• Tight junctions create a watertight seal between adjacent animal cells.

• Desmosomes act like spot welds between epithelial cells.

LIGANDS AND RECEPTORS

• Intracellular receptors regulate gene activity.

• Cell-surface receptors have extracellular, hydrophobic, and intracellular domains.

• Ligand-gated ion channels and G-protein coupled receptors are common types of receptors.

SIGNAL RELAY PATHWAYS

• Phosphorylation alters protein activity by adding a phosphate group.

• Second messengers like calcium ions relay signals within the cell.

• GPCRs involve G-proteins and second messengers like cAMP.

• Response to signals can lead to changes in gene expression, cell growth, or apoptosis.

HOMEOSTASIS

• The body maintains stable internal conditions through negative feedback loops.

• Examples include temperature regulation through blood vessel constriction/dilation and sweat gland activity.

• Diabetes is caused by a disrupted feedback loop involving insulin and glucose regulation.

• Positive feedback loops amplify the starting signal in processes like childbirth and fruit ripening.

• Negative feedback loops maintain homeostasis

CELL CYCLE

• The cell cycle in eukaryotic cells consists of interphase and mitotic phase.

• Interphase includes G1 phase, S phase, and G2 phase where the cell grows, makes copies of organelles and DNA, and prepares for division.

• Mitotic phase involves mitosis where chromosomes are separated and cytokinesis where the cytoplasm divides.

• During prophase, chromosomes condense and the mitotic spindle forms.

• In metaphase, chromosomes align at the metaphase plate and spindle checkpoint ensures correct alignment.

• Anaphase involves sister chromatids separating and being pulled towards opposite ends of the cell.

• Telophase sees the formation of two new nuclei and decondensation of chromosomes.

• The cell cycle is regulated by checkpoints including cell size, nutrients, growth factors, DNA damage, and spindle checkpoint.

• Cyclins and cyclin-dependent kinases (CDK’s) drive cell cycle transitions by activating or inactivating target proteins.

CANCER

• Cancer is a disease of uncontrolled cell division with characteristics like replicative immortality, metastasis, and angiogenesis.

• Most cancers arise from mutations that allow cells to divide quickly, escape controls on division, and avoid programmed cell death.

• Benign tumors do not invade other tissues, while malignant tumors can invade other tissues and metastasize.

• Cancer development is promoted by overactivation of proto-oncogenes and inactivation of tumor suppressor genes.

Unit 5 - Heredity 👨👩👶

MEIOSIS

• Meiosis is the process of cell division for the production of gametes (sex cells)

• Daughter cells have half the number of chromosomes as parent cells.

• Sperm and egg join to form a complete diploid set.

• Homologous chromosomes are similar but not identical chromosome pairs.

• Meiosis 1 and meiosis 2 involve separation of homologue pairs and sister chromatids respectively.

• Meiosis results in four gametes

• Genes are found at specific locations on chromosomes.

• Law of independent assortment states that chromosome pairs are sorted into gametes independently.

  • crossing over is in prophase 1

• X-linked inheritance involves genes present on the X chromosome.

• Genetic linkage and mapping involve estimating the relative distance apart of genes on a chromosome.

• Recombination frequency is used to measure the linkage quantitatively.

PEDIGREES

• Pedigree charts show the presence or absence of a trait within a family across generations.

• They can be used to determine dominant or recessive traits.

• Autosomal and sex-linked traits can be determined using pedigrees.

• Inheritance of mitochondrial and chloroplast DNA is also shown in pedigrees.

• Differences between nucleus DNA and mitochondrial DNA include high copy number and random segregation

• Single-parent inheritance and the impact of mutations in mother's mitochondria on genetic disorders are also discussed.

• Polygenic inheritance, environmental effects, variable expressivity, incomplete penetrance, and phenotype plasticity are all factors related to genetic traits and inheritance.

• Aneuploidy, euploidy, and polyploidy are also covered.

• Chromosomal rearrangements such as duplication, deletion, inversion, and translocation are explained.

Unit 6 - Gene Expression and Regulation 🧬

• Eukaryotes have DNA found in the nucleus, while prokaryotes have DNA enclosed in a plasma membrane and located in the nucleoid region

• Prokaryotic chromosomes are smaller and circular

• The central dogma involves the progression from DNA to RNA

• DNA consists of nitrogenous bases (adenine, guanine, cytosine, and thymine) and is written in the 5' to 3' direction

• RNA has uracil instead of thymine and is single-stranded

• Prokaryotes belong to Bacteria and Archaea, lack a nucleus, organelles, and have a single circular chromosome

• DNA replication is semi-conservative and involves leading and lagging strands, DNA polymerase, primer, helicase, topoisomerase, and ligase

• Transcription involves initiation, elongation, and termination, and is the process of copying DNA to make an RNA molecule

• Translation decodes mRNA to build a protein with a specific sequence of amino acids, involving initiation, elongation, and termination

• Gene regulation in bacteria involves operons, repressors, activators, inducers, and corepressors

• Gene regulation in eukaryotes involves responding to growth factors, transcription factors, and various processes such as chromatin accessibility, transcription, RNA processing, translation, and protein activity

• Biotechnology techniques include DNA cloning, polymerase chain reaction, gel electrophoresis, and DNA sequencing

Unit 7 - Natural Selection 🐀

EVOLUTION AND NATURAL SELECTION

• Evolution involves species changing over time, giving rise to new species, and sharing a common ancestor.

• Natural selection occurs because resources are limited in nature, where organisms with heritable traits that favor survival and reproduction leave more offspring.

• Traits increase in frequency over generations due to natural selection based on observations such as heritable traits, offspring variation, and more offspring being produced than can survive.

ARTIFICIAL SELECTION

• Humans select desired traits in animals or plants, such as the domestication of wolves resulting in the loss of aggressive traits.

GENETIC DRIFT

• Mechanism of evolution where allele frequencies change in a population due to chance.

• Effects are strongest in small populations, especially after a bottleneck event or when a small group splits from the main population.

NATURAL SELECTION IN POPULATIONS

• Natural selection acts on phenotype to cause microevolution in a population.

• Fitness is a measure of how organisms survive and reproduce, depending on predation and mate preference.

• Types of selection include stabilizing, directional, and disruptive selection.

HARDY-WEINBURG EQUILIBRIUM

• When a population is in equilibrium for a gene, it is not evolving, and allele frequencies remain the same.

• Assumptions include no mutation, random mating, no gene flow, infinite population size, and no selection.

• p² + 2pq + q² = 1

EVIDENCE FOR EVOLUTION

• Evidence includes shared ancestry, molecular biology, biogeography, anatomy, fossils, and vestigial features.

• Phylogenetic trees show the relationship between species based on common ancestors.

SPECIES AND SPECIATION

• Speciation is the process by which new species form, with allopatric speciation occurring due to geographical separation and sympatric speciation occurring without separation.

• Prezygotic and postzygotic barriers prevent reproduction between different species.

Unit 8 - Ecology 🌳

BEHAVIOR

• Innate Behaviors:

  • Hardwired in an organism's genes and inherited.

  • Predicted and performed similarly across members of the same species.

  • Includes reflex actions, kinesis, taxis, and fixed action patterns.

• Learned Behaviors:

  • Developed through experience.

  • Animals capable of problem-solving and constructing mental maps.

  • Includes habituation, imprinting, and conditioned behaviors.

  • Result of associative learning such as classical and operant conditioning.

ANIMAL COMMUNICATION

• Transmits information using changes in the receiving animal.

• Helps animals find mates, establish dominance, defend territory, care for young, and coordinate group behavior.

• Signals include pheromones, auditory cues, visual cues, and tactile cues.

METABOLIC RATE

• Metabolism is the total of biochemical reactions in an organism.

• Metabolic rate determines how quickly fuels are broken down.

• Endotherms generate metabolic heat to maintain internal temperature, while ectotherms rely on the environment.

• Strategies for temperature regulation include thermogenesis, vasoconstriction, and vasodilation.

LIFE HISTORY STRATEGIES

• Reflects how species distribute resources among offspring.

• Short-lived species reproduce earlier, while long-lived species reproduce later.

• Influenced by natural selection and survival events.

FOOD CHAINS AND WEBS

• Energy transfer between trophic levels is inefficient.

• Producers make their own food, consumers eat other organisms, and decomposers break down organic material.

• Follows the 10% rule of energy transfer and can exhibit exponential or logistic growth patterns.

POPULATION REGULATION

• Influenced by limiting factors such as competition, density-dependent and density-independent factors.

• Cyclical oscillations in population size can result from predation, parasites, and food availability.

INTERACTIONS IN COMMUNITIES

• Community includes all populations of different species in a particular area.

• Interspecific interactions include competition, predation, mutualism, commensalism, and parasitism.

• Niche, competition exclusion principle, and resource partitioning play roles in community structure.

COMMUNITY STURCTURE

• Species richness and diversity influence community stability.

• Foundation species modify the environment to support other organisms.

• Keystone species have a large effect on community structure relative to their abundance.

INVASIVE SPECIES AND HUMAN IMPACTS ON ECOSYSTEMS

• Invasive species can alter community structure by outcompeting native species.

• Human impacts include land-use change, pollution, introduced species, and resource exploitation.