Comprehensive Animal Physiology & Plant Biology: Respiration, Circulation, Metabolism, and Reproduction

Partial pressure

The portion of the total pressure due to a single gas (e.g., O₂). Gases diffuse from higher to lower partial pressure; that gradient is the engine of gas exchange.

Three ways to increase diffusion

Increase surface area, increase the gradient (ΔP), or decrease diffusion distance (thinner barriers). Fick's law: Diffusion ∝ (Area × ΔP) / Distance.

Unidirectional flow

Fish gills, birds' parabronchi: fresh medium flows one way; pro: sustained gradient; con: more complex anatomy.

Why bulk flow, not diffusion, to supply tissues?

Diffusion alone is too slow over organismal distances; bulk flow (ventilation + circulation) rapidly transports gases close to cells, after which diffusion finishes the job.

Why keep flow constant?

Conservation of flow requires velocity ∝ 1 / total cross-sectional area; capillaries have huge area → slow speed → optimal exchange.

Sieve tubes

Sap conduits in phloem.

Xylem

Carries water/minerals from root to shoot.

Phloem

Carries sugars & signals from source to sink (any direction depending on season/tissue).

Flower

Reproduction.

Vertebrate respiratory system parts

Nasal/oral cavity → pharynx → larynx → trachea → bronchi → bronchioles → alveoli (site of exchange). Surrounding capillaries pick up O₂, drop off CO₂.

Tidal ventilation

Most mammals: air in/out same path; easy to protect moist surfaces; con: "dead space" dilutes fresh air.

Cutaneous respiration

Amphibians as supplement: across skin; pro: simple; con: requires moist skin, limited surface/size.

Countercurrent exchange

Water and blood flow in opposite directions across fish gills, maintaining a favorable gradient along the entire lamella—maximizes O₂ uptake.

Bird respiratory order & relevance

Inhalation 1: air → posterior air sacs → Exhalation 1: to lungs (parabronchi) → Inhalation 2: to anterior sacs → Exhalation 2: out. Result: near-constant, unidirectional, high-efficiency gas exchange during both in and out phases.

Tradeoffs: maximizing bulk flow vs exchange

Large tubes/fast flow reduce resistance (better delivery) but reduce surface area and contact time (worse exchange). Conversely, huge, thin exchange surfaces (great exchange) are fragile and create high resistance (poor delivery). Systems balance both.

Qualities for bulk flow vs exchange

Bulk flow: thick, reinforced conduits, smooth lumens, branching pipes. Exchange: ultra-thin epithelium, massive surface area (alveoli/gill lamellae), slow flow for time to equilibrate.

Gas exchange location

Across the alveolar epithelium and adjacent capillary endothelium (the respiratory membrane).

Types of circulatory systems

Open (many arthropods/mollusks): hemolymph bathes organs; low pressure; cheap to maintain; limited fine control. Closed (vertebrates, annelids, cephalopods): blood confined to vessels; higher pressure; precise regulation; costlier.

Flow definition & equation

Flow (Q) = ΔP / R (Ohm's law analogue). Increase pressure difference or decrease resistance to raise flow.

Vessel types, order, area, speed

Aorta → arteries → arterioles → capillaries → venules → veins → venae cavae. Total cross-sectional area peaks in capillaries → lowest speed there (ideal for exchange).

Artery vs vein walls

Arteries: thicker smooth muscle & elastic tissue (withstand/maintain pressure). Veins: thinner walls, valves, rely on skeletal muscle/respiratory pumps.

O₂/CO₂/H⁺ sensors

Peripheral chemoreceptors in carotid and aortic bodies sense O₂, CO₂, and pH (H⁺).

Pulmonary vs systemic circuits

Pulmonary: heart ↔ lungs (gas exchange). Systemic: heart ↔ body (deliver O₂/nutrients, remove wastes).

Three types of vertebrate systems

Fish: single circuit; 2-chamber heart (atrium, ventricle). Problem: low pressure after gills.

Amphibians/reptiles (non-croc)

Double circuit; 3-chamber heart with partial mixing; solve pressure issue; problem: O₂ mixing.

Birds/mammals

Double circuit; 4-chamber heart; complete separation; high efficiency.

Heart parts

Right/left atria, right/left ventricles; two pacemakers: SA node (primary), AV node (relay). Valves: tricuspid, pulmonary semilunar, mitral (bicuspid), aortic semilunar.

Pacemaker cell

Autorhythmic cells with unstable resting potential (slow Na⁺/Ca²⁺ "funny currents") that spontaneously depolarize to set heart rate.

Systole vs diastole

Systole = contraction/ejection. Diastole = relaxation/filling.

Cardiac output

CO = Heart Rate × Stroke Volume. Modulated by autonomic input, venous return, contractility, afterload.

O₂ flow from air → blood → tissue

pO₂: Alveoli (high) → arterial blood → interstitial fluid → cells (lowest). Diffusion follows the descending gradient at each step.

Hemoglobin

Cooperative binding: O₂ binding increases affinity (sigmoid curve). Effects: Low pO₂ favors unloading; low pH (Bohr effect), high CO₂, high temperature shift curve right (reduced affinity) → enhance tissue delivery.

Myoglobin

Monomer in muscle with higher O₂ affinity; acts as an O₂ buffer, improving uptake and storage for active muscle.

Blood flow through the heart + electrical order

Venae cavae → RA → tricuspid → RV → pulmonary valve → pulmonary arteries → lungs → pulmonary veins → LA → mitral → LV → aortic valve → aorta. Electrical: SA node → atria contract → AV node delay → Bundle of His → Purkinje fibers → ventricles contract.

How pacemakers set rate

Rate depends on slope of spontaneous depolarization—modulated by autonomic signals (NE ↑ slope/HR; ACh ↓ slope/HR).

Where can blood flow be closed off?

Arterioles (precapillary sphincters) regulate distribution; can shunt blood away from some beds.

Where does gas exchange occur in circulation?

Across capillary walls.

Why is cooperative binding important?

Enables high O₂ loading in lungs and steep unloading in tissues—efficient transport.

Reading an oxygen dissociation curve

Left shift = higher affinity (loads more, unloads less); right shift = lower affinity (delivers more to tissues). P50 (pO₂ at 50% saturation) summarizes affinity.

EKG parts & heart cycle

P wave: atrial depolarization. QRS: ventricular depolarization (atrial repolarization buried). T wave: ventricular repolarization.

Modifying cardiac output

HR: autonomic tone, hormones, temp. SV: preload (venous return), contractility (sympathetic, Ca²⁺), afterload (arterial pressure).

Aerobic vs anaerobic respiration

Aerobic uses O₂ as final electron acceptor (high ATP yield). Anaerobic uses other acceptors or fermentation (low ATP, quick bursts).

Three processes for energy + ATP yield

Phosphagen/ATP-PCr (anaerobic): seconds, very fast, very low capacity. Glycolysis (anaerobic → lactate): fast, moderate ATP, fuels sprints. Oxidative phosphorylation (aerobic): slowest, highest ATP per fuel.

Macromolecules

Carbs (quick ATP via glycolysis/TCA), lipids (dense ATP via β-oxidation + TCA), proteins (last resort; deaminated, carbon skeletons enter TCA).

Essential nutrients

Cannot be synthesized; must be eaten. Humans have essential fatty acids (e.g., linoleic, α-linolenic) and 9 essential amino acids (11 nonessential).

Essential fatty acids

Fatty acids that are necessary for human health but cannot be synthesized by the body, such as linoleic and α-linolenic.

Essential amino acids

Amino acids that must be obtained from the diet because the body cannot produce them; there are 9 essential amino acids.

Vitamins

Organic cofactors/coenzymes required for various biochemical functions in the body.

Minerals

Inorganic ions that play roles in structure, cofactors, and electrolytes in the body.

Anabolism

The metabolic process that builds molecules and requires energy.

Catabolism

The metabolic process that breaks down molecules and releases energy.

Basal metabolic rate

The minimum energy expenditure at rest, in a thermoneutral state, and post-absorptive.

Dietary macros

Nutrients from food that are digested to monomers, absorbed, and then reassembled into body molecules as needed.

Lactic acid

The end product of anaerobic glycolysis that regenerates NAD⁺ to allow glycolysis to continue when oxygen is limited.

Preferred fuels

Fats are preferred during rest/long duration activities, while carbohydrates are preferred for quick, high-intensity activities.

Citric acid cycle

A metabolic pathway where deaminated amino acids enter at various points, such as α-ketoglutarate and oxaloacetate.

Vitamin synthesis

Humans cannot synthesize many vitamins because they lack the necessary enzymes and pathways that plants and microbes use.

Headgut/foregut

The section of the digestive system responsible for ingestion and initial mechanical and chemical digestion.

Midgut

The section of the digestive system where most digestion and nutrient absorption occurs.

Hindgut

The section of the digestive system responsible for water and electrolyte absorption, feces formation, and housing the microbiome.

Salivary glands

Glands that secrete amylase and lipase to begin the digestion process.

Emulsification

The process by which bile salts break large fat globules into tiny droplets, increasing surface area for lipase action.

Peristalsis

Coordinated circular and longitudinal muscle contractions that propel the bolus or chyme through the digestive tract.

Sphincters

Valve-like smooth muscle rings that regulate one-way flow at various points in the digestive system.

Peyer's patches

Clusters of immune tissue in the ileum that defend against gut microbes as the luminal antigen load increases.

Flora in the large intestine

Microbial communities that ferment fiber, synthesize some vitamins (e.g., K, biotin), train immunity, and compete with pathogens.

Nutrient absorption

Nutrients are primarily absorbed in the small intestine, while many vitamins are also absorbed there, and water is primarily absorbed in the colon.

Meiosis

A type of cell division that results in four non-identical haploid cells, used in the formation of gametes.

Mitosis

A type of cell division that results in two identical diploid cells, primarily used for growth and repair.

Asexual reproduction

Fast, low diversity; includes budding, fission, parthenogenesis.

Sexual reproduction

Slower, high diversity, adaptation; includes internal/external fertilization.

r-strategy

Many, low-investment offspring.

K-strategy

Few, high-investment offspring.

Male anatomy

Includes testes (spermatogenesis, testosterone), epididymis (storage/maturation), vas deferens, accessory glands (seminal vesicles, prostate), urethra, penis.

Female anatomy

Includes ovaries (oogenesis, hormones), oviducts (fertilization site), uterus (implantation), cervix, vagina, external genitalia.

Ovulation process

Fimbriae draw oocyte into oviduct; sperm undergo capacitation, chemotaxis, and meet egg in ampulla of fallopian tube.

Conditions favoring asexual reproduction

Stable, low-mate environments favor asexual (rapid colonization).

Conditions favoring sexual reproduction

Variable environments favor sexual (genetic diversity).

Primary challenges for males

Produce/deliver huge numbers of viable sperm.

Primary challenges for females

Protect gametes, secure fertilization, support gestation, prevent infection.

Vaginal properties against microbes

Acidic pH (lactobacilli), mucus, epithelial turnover, immune factors.

Testes location

Spermatogenesis requires cooler temperatures than core body temp.

Cell wall

Provides support in plant cells.

Chloroplast

Site of photosynthesis in plant cells.

Vacuole

Storage and turgor in plant cells.

Plasmodesmata

Facilitates cell-cell transport in plant cells.

Mitochondria

Responsible for respiration in plant cells.

Rubisco

Carbon-fixing enzyme of Calvin cycle; can bind CO₂ (desired) or O₂ (photorespiration—wasteful).

Stomata

Adjustable leaf pores for gas exchange/transpiration.

Lenticels

Stem bark pores for gas exchange in woody tissues.

PEP carboxylase

Fixes CO₂ to form 4-C acids in C₄/CAM plants; high CO₂ affinity, no O₂ binding—reduces photorespiration.

Transpiration

Water loss driving upward pull in xylem.

Nitrogen fixation

Conversion of N₂ to NH₃ by bacterial nitrogenase.

C₄/CAM

Save photorespiration/water but cost extra ATP.

C₃

More energy-efficient under mild temps, high CO₂, and adequate water.

Xylem conduits

Dead at maturity.

Phloem sieve elements

Living (with companion cells).

Macronutrients

N, P, K, Ca, Mg, S.

Micronutrients

Fe, Mn, Zn, Cu, B, Mo, Cl, Ni.

Extensive, high-SA roots

To intercept scarce ions/water in heterogeneous soils.