AP Biology

Covalent Bonds

form cell's molecules

strong bonds

Ionic Bonds

quick reactions/responses

weaker bond (esp. in H2O)

Hydrogen Bonds

H bonds to other electronegative atoms

weaker than ionic and covalent

pH

-log(H+) or -log(H3O)

Monomers/Polymers/Macromolecules

Macromolecules are made of 2 or more polymers

Polymers are made of monomers

amino acid --> peptide --> polypeptide --> protein

Building/breaking polymers

Build: dehydration synthesis (remove H2O)

Break: hydrolysis (add H2O)

Orders of protein structure

Primary: amino acids in polypeptide chain

Secondary: local folded structures (α helix & β pleated sheet)

Tertiary: overall 3D shape

Quaternary: multiple chains

Amino Acid

Nonpolar side group (only C & H) = hydrophobic

Polar side group (O, N, S) = hydrophilic

Ionic = acidic (- charge) or basic (+ charge)

Nucleotide

Monomer of DNA & RNA (nucleic acids)

Deoxyribose (DNA) is missing an O in the sugar

Nucleoside (base + sugar) & phosphate group

Carbohydrates

Sugars that contain only C, H, O

General Formula: Cₙ(H2O)ₙ

Name: (# of C) + (-ose), (# of rings) + (-saccharide)

Lipids

Nonpolar

Steroids: multiple rings

Fatty Acids: hydrocarbon chains with a carboxyl (COOH) group, store energy

--Saturated: no double bonds

--Unsaturated: double bond(s)

Properties of Water

Adhesion: stick to another surface

Cohesion: stick to each other --> surface tension

High specific heat (lots of heat needed to raise temp)

Lower density when frozen

Evaporation of sweat cools body

Extracellular matrix and cell wall

Extracellular matrix: space outside cells

-Contain collagen for structural integrity

Cell wall is made of cellulose

Facilitated vs nonfacilitated diffusion vs active transport

Non: Only small, uncharged substances (water passes thru slowly)

Facilitated: Transport proteins let polar/ions pass

Active: Use ATP & carrier proteins, against concentration gradient

Path of Information in Neuron

Dendtrite --> axon --> synapse

Information Processing

sensory input --> integration --> motor output

Types of Neurons

Sensory: external stimuli/internal conditions

Interneurons: connect neurons, integration of sensory input

Motor: transmit signals to muscles

Nervous System Structure

Nerve: bundle of axons

CNS: brain, spinal cord

PNS: ganglia (nerve clusters)

Both have glia: support/protect neurons

Resting potential

Membrane potential of resting neuron (-70 mV)

More K+ and less Na+ & Cl- inside

NaK pump takes out 3 Na & takes in 2 K

Hyperpolarization

Stimulus --> voltage-gated K channels open --> K+ leaves --> cell more negative

Depolarization

Stimulus --> voltage-gated Na channels open --> Na+ enters --> cell less negative

Action Potential Process

Depolarization increases membrane potential past threshold (-55 mV) --> volted-gated Na channels open --> Na+ enters

Rising Phase: further depolarization --> more channels open (postive feedback loop, depolarizes neighboring region)

Falling Phase: Na channels become inactivated, K channels open --> cell becomes negative

Undershoot

Resting State: Na & K channels closed

Refractory Period

Na channels inactivated, stimulus won't trigger actional potential

Prokaryotic vs. eukaryotic cells

Eukaryotic cells have nucleus, membrane-bound organelles, & linear chromosomes

Plant vs. animal cell

Endoplasmic Reticulum

Rough: has ribosomes (make proteins), package proteins into vesicles for transport

Smooth: synthesis of carbohydrates, lipids, and steroid hormones, stores calcium ions

Golgi apparatus

Protein/lipid sorting, tagging, packaging, and distribution

Lysosomes

Digestion, Recycling, Self-Destruction

Vacuoles

central vacuole stores water and wastes

Endosymbiosis

Pre-eukaryotic cells absorbed prokaryotes

Evidence: Mitochondria & chloroplasts have DNA, membrane, & reproduce independently

Cell Membrane

Large SA:V better for chemical exchange

Amphipathic Phospholipid Bilayer: hydrophilic head, hydrophobic tail

Selective permeability: no ions or large polar molecules

Hypertonic (high solute), hypotonic (low solute), isotonic

Water Potential

the potential energy of a volume of water, expressed as a pressure

high --> low

Enzymes 🍔

Lower reaction's activation energy (amt of E needed to begin)

Substrates (reactants) bind to active sites

Affected by temperature, pH, regulatory molecules (activators/inhibitors), & enzyme/substrate concentrations

Reusable ♻️

PHOTOSYNTHESIS🌿☀️🌧️

Glucose can be used to make ATP and provides carbon to be fixed (incorporated into organic molecules)

Includes light-dependent reactions and Calvin cycle

LIGHT-DEPENDENT REACTIONS💡

Use light energy to make ATP & NADPH (in thylakoid membrane of chloroplasts)

1. Light absorbed in Photosystem II --> boosts an e⁻ to a high energy level

2. e⁻ is passed to acceptor molecule & replaced with e⁻ from water (releases O2)

3. e⁻ releases energy --> creates H+ gradient

4. H+ flow down gradient through ATP synthase --> drives ATP production

5. In PSI, e⁻ boosted to high energy level

6. Passed to NADP+ --> NADPH

CALVIN CYCLE🩲

Light-independent, Carbon fixed into sugars, (in stroma)

1. Carbon fixation: CO2 combines with RuBP, (catalyzed by rubisco)

2. Reduction: ATP & NADPH used to reduce to G3P

3. Regeneration: Some G3P molecules go to make glucose

CELLULAR RESPIRATION🫁

1. Glycolysis: glucose converted into 2 pyruvate (ATP is made, NAD+ converted to NADH

2. Pyruvate oxidation: pyruvate enters mitochondrial matrix, converted to acetyl CoA (CO2 released, NADH generated)

3. Krebs Cycle: ATP, NADH, FADH2 produced

4. Oxidative phosphorylation: NADPH & FADH2 deposit electrons in ETC

Lactic Acid Fermentation

NADH transfers its electrons directly to pyruvate, generating lactate as a byproduct

Types of Signaling

Paracrine: nearby

Synaptic: neurotransmitters diffuse across synapse

Endocrine: hormones in body fluids

Autocrine: targets itself

Juxtacrine: touching

Stages of Cell Signaling

Signal Reception: ligand binds to receptor protein

Signal Transduction: converts signal to a form that can bring about a cellular response

-Pathway: activates proteins through protein kinase --> phosphorylation cascade, amplifies signals, easier regulation

Cellular Response

Endocrine Glands

Hypothalamus: regulates anterior pituitary, which releases hormones -- tropic hormones stimulate other glands

Pancreas: Insulin & Glucagon

Thyroid: metabolic processes

Adrenal glands: blood sugar, metabolism

Ovaries: estrogen

Testes: androgen

Innate Immunity

Barrier Defenses: mucous membranes, skin

Phagocytes (type of white blood cell, engulf): macrophages, neutrophils

Natural Killer cells (release cytotoxic molecules)

Dendritic cells capture/present antigens to T cells

Mast cells release histamine

Adaptive Immunity

B cells differentiate into plasma cells that produce antibodies, activated by helper T cells

Helper T cells release cytokins that signal other immune cells, activated by antigen-presenting cells

Cytotoxic T cells kill infected cells

Memory cells

Antibodies

Proteins produced by B cells that bind to specific antigens on pathogens, marking them for destruction

Major Histocompatibility Complex (MHC)

Molecules on cell surfaces that present antigens to T cells

Active vs Passive Immunity

Active: body produces its own antibodies against pathogens

Passive: receive antibodies from other source (i.e. breast milk)

Lymphatic System

Lymphatic vessles transport white blood cells & remove waste/pathogens from tissues

Lymph nodes trap pathogens to be destroyed by lymphocytes (WBCs)

Redox Process

photosynthesis is a redox process in which H2O is oxidized and CO2 is reduced

Laws of Thermodynamics

1: energy can't be created/destroyed

2: heat flows from hotter to colder regions, every energy transfer increases the entropy of the universe & reduces the amount of usable energy available

Hydrolysis of ATP

P_i is an inorganic phosphate group

Reversing this requires energy

Reaction coupling

an energetically favorable reaction is directly linked with an energetically unfavorable (endergonic) reaction, a product (shared intermediate) of one reaction is "picked up" and used as a reactant in the second reaction

Anabolic and catabolic pathways

Anabolic: build complex molecules from simpler ones and typically need an input of energy

Catabolic: breakdown of complex molecules into simpler ones and typically release energy

Leaf Structure

Stomata let CO2 in and O2 out of mesophyll

Mesophyll > chloroplasts > grana > thylakoids > chlorophylls

Stroma: space around grana

Pyrimidine vs Purine Nitrogenous bases

Pyrimidines: 1 ring (T, U, C)

Purine: 2 rings (A & G)

Connected by H bonds

DNA vs RNA

DNA has deoxyribose (missing hydroxyl group)

RNA has ribose, T replaced with U (binds w/ A)

DNA/RNA Directionality

DNA created in 5' to 3' direction

Antiparallel: coding strand runs opposite to template strand

Prokaryote DNA

Found in the nucleoid.

Single circular chromosome.

Plasmid: rings of non-essential DNA outside the chromosome, can be transferred to other prokaryotes in a population

DNA Replication

Semiconservative

Leading strand: made continuously

Lagging strand: made in Okazaki fragments

Enzymes involved in DNA Replication

Polymerase III: synthesizes and proofreads in 5' to 3' direction (of the strand being made), require a primer

Polymerase I: replaces primers w/ DNA

Primase: creates primers

Helicase: separates strands

Ligase: joins strands

Transcription

Initiation: RNA Polymerase II binds to promoter & seperates strands

Elongation: reads template strand from 3' to 5' & makes mRNA transcripts from 5' to 3'

Termination: terminator sequences cause RNA polymerase to release transcript

RNA Modifications

Protection: 5' cap & poly-A tail (3' end) --> pre-mRNA

Splicing: spliceosome removes introns --> primary mRNA

Alternative Splicing

pre-mRNA can be spliced in multiple ways depending on which exons are kept

Translation

Initiation: ribosome assembles around mRNA, tRNA carrying met attaches to AUG codon

Elongation: admino acids added

Termination: UAA/UAG/UGA --> release polypeptide chain

Eukaryotic vs Prokaryotic RNA Processing

Eukaryotes: transcription takes place in nucleus, mRNA goes through protection and splicing, protein synthesis takes place in cytosol

Prokaryotes: transcription and translation in cytosol (no nucleus)

Operon

Group of genes w/ on/off switch

-Promoter: where RNA polymerase attaches

-Operator: controls access of RNA polymerase

Inducible vs Repressible

Inducible: usually off, turned on by inducer (lac)

Repressible: usually on, turned off by corepressor (trp)

Transcription Factors

Proteins that help turn genes on/off by binding to DNA

Activators boost transcription.

Repressors decrease transcription.

Groups of transcription factor binding sites called enhancers and silencers can turn a gene on/off.

Chromosomal Rearrangements

Duplication: part is repeated

Deletion: part is removed

Inversion: region is flipped around

Translocation: a piece of one gets attached to another

Genetic variation in prokaryotes

Transformation: takes up DNA from environment

Transduction: virus moves DNA from one to another

Conjugation: DNA transferred through tube between cells

Transposable elements: chunks of DNA that jump from one place to another

Mutations

Point: any mutation involving a single base

Insertion/Deletion --> frameshift

Gel Electrophoresis

Small fragments move farther than large ones

Polymerase chain reaction

Laboratory technique to amplify specific DNA sequences, by making copies of a fragment

Genetic Drift

Allele frequencies change over generations due to chance.

Strongest effects in small pop. -- bottleneck effect or founder effect (split off)

--> loss or fixation (100% freq.) of alleles

Microevolution & Macroevolution

Micro: Change in allele frequencies

Macro: large-scale

Polygenic traits

traits determined by many genes, typically form a spectrum

Three types of selection

Stabilizing: intermediate more fit than extreme

Directional: one extreme more fit

Disruptive: two extremes more fit

Hardy-Weinberg assumptions

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

Mechanisms of evolution correspond to violations of the assumptions

Hardy-Weinberg equilibrium

Homologous vs Analogous features

Homo: from a common ancestor --> vestigial structures

Ana: from convergent evolution

Homologous genes

"Same" inherited gene, use DNA differences to determine relation

Biological Species Concept

A group of organisms that can potentially mate to produce viable, fertile offspring.

Prezygotic barriers (reproductive isolation)

Habitat

Temporal (times of day/year)

Behavioral (courtship rituals)

Gametic (egg/sperm cells can't combine)

Mechanical (reproductive structures don't fit)

Postzygotic barriers

Often related to the hybrid embryo's mixed set of chromosomes, which may not match up correctly or carry a complete set of information.

Allopatric vs Sympatric Speciation

Allopatric: geographic separation

Sympatric: reamining in one location (common in plants through polyploidy --> diff #s of chromosomes)

Adaptive Radiation: a single species or small group of species rapidly diversifies into many new species

Hypotheses for the Origins of Life

Oparin-Haldane: arose from inorganic molecules forming “building blocks” like amino acids then complex polymers

Miller-Urey experiment: organic molecules could be formed from inorganic components

RNA World: first life was self-replicating RNA

Metabolism-first: first life was self-sustaining networks of metabolic reactions

Innate vs. Learned Behaviors

Innate: genetically hardwires, inherited

Learned: develop from experience

Partly both: genetically programmed to develop a behavior, but the form the behavior takes depends on the individual's experience

Reflex

involuntary and rapid response to a stimulus

Kinesis and taxis

Kinesis: changes movement in a non-directional way (ex: speed)

Taxis: movement towards/away from stimulus

Fixed action patterns

predictable series of actions triggered by a cue; automatic and involuntary

Types of learned behaviors

Habituation: stops responding to stimulus after repeated exposure

Imprinting

Conditioned

-Classical: neutral stimulus paired w/ a one w/ a natural response

-Operant: awards/punishment, doesn't rely on existing stimulus/response

Cognition: awareness, reasoining, recollection, judgement

Social Learning: observe others

Types of Signals in Animal Communication

Pheromones

Visual

Tactile

Auditory

Metabolism & metabolic rate

sum total of the biochemical reactions that take place in an organism's body

how quickly fuels (such as sugars) are broken down to keep the organism's cells running

Endotherms vs Ectotherms

Endotherms use metabolic heat to keep a stable body temperature (BMR), while ectotherms do not (SMR).

Torpor, hibernation, and estivation

Torpor: state of decreased activity to conserve energy

-Hibernation

-Estivation (hot/dry)

Autotrophs vs. Heterotrophs

Autotrophs: make own food

-Photoautotrophs

-Chemoautotophs

Heterotophs: eat organisms/byproducts

Density-(in)dependent limiting factors

Dependent: competition, predation, disease, parasites, waste accumulation

Independent: natural disaster, weather, pollution

interspecific interactions

Competition -/-

Predation +/-

Herbivory +/-

Mutualism +/+

Commensalism +/0

Parasitism +/-

competitive exclusion principle

two species can't coexist if they occupy exactly the same niche (competing for identical resources) --> resource partitioning

Species Richness & Diversity

Richess: # of species

DIversity: depends on # of species and relative abundances

Foundation and keystone species

Foundation: create & define community (kelp/coral)

Keystone: large effect on community relative to biomass/abundance