IB Bio: Human Physiology

Gastrointestinal tract

aka alimentary canal, long continuous tube connecting the mouth and the anus

accessory organs

organs related to digestion not in the GI tract, secrete enzymes and digestive molecules into the GI tract

4 stages of digestion

1. Ingestion 2. Digestion 3. Absorption 4. Transport

mechanical digestion

physically breaking food into smaller units

Mastication

the tongue pushes food around the mouth to be chewed by the teeth, mixes with saliva to create a bolus

Uvula

structure at the back of the mouth, prevents the bolus from entering the nasal cavity

Bolus

a mixture of chewed food and saliva

epiglottis

a structure that prevents bolus from entering the trachea

stomach churning

* the stomach has 3 layers of muscle, all moving in different directions that churn/squeeze the food
* creates chyme by mixing bolus with gastric juices

Chyme

created by the stomach churning the bolus with gastric juices

Cardiac sphincter

valve at the top of the stomach

chief cells

secrete pepsinogen (zymogen of pepsin), present in the stomach

goblet cells

secrete mucus, line stomach to protect it from acid, in small intestine to aid movement

pyloric sphincter

between the stomach and the duodenum of the small intestine

peristalsis

continuous segments of longitudinal smooth muscle rhythmically contract and relax along the oesphagus, moves food in the caudal direction, also present in the small intestine and stomach

caudal direction

movement down the GI tract

segmentation

circular and longitudinal muscle moves food in both directions, performing mechanical digestion and mixing with secreted enzymes

Pulmonary system

blood pumped from right ventricle, to lungs, then returned to left atrium

Systemic blood system

oxygen-rich blood from the left ventricle is pumped all around the body, then returned to right atrium

left ventricle has a thick muscular wall because…

it has to pump to the entire body

arteries structure + function

* carry oxygen-rich blood away from the heart to body tissue
* the thick outer wall contains collagen for stretch and so it won’t rupture
* contains elastin, elastic recoil helps move blood
* the muscular wall allows it to transport blood at high pressures
* autonomic nervous system regulates the lumen diameter using the smooth muscle

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elastic recoil

the movement of arteries, created by the presence of elastin, that helps to pump blood

capillaries structure +function

* one cell thick for efficient exchange
* has a diameter of 1 RBC for efficient exchange
* connects the veins and arteries
* has low blood pressure
* exchanges nutrients and waste

veins structure + function

* has wide lumen to maximize blood flow
* carries oxygen-poor blood to the heart
* carries blood at a low pressure therefore walls are very thin and contain little muscle
* located between skeletal muscle, relies on contraction for blood flow

fenestrated capillaries

has many pores, located in the intestinal villi and endocrine glands

continuous capillaries

have tight junctions which reduces the permeability, located in fat, muscle, and nervous system

discontinuous capillaries

have intercellular gaps so permeable to large molecules and cells, located in liver, bone marrow

myogenic muscle contraction

contracts independent of nervous system, performed by cardiac muscle of the heart

SA node

the sinoatrial node, located in the right atrium, sends electric signals for atria to contract every 0.8 seconds

AV node

the atrioventricular node, located in the septum, receives a signal from the SA node, then transmits a signal for the ventricles to contract with a 0.1 second delay

• sends signals down the septum via a nerve bundle (Bundle of His)

• The Bundle of His innervates nerve fibres (Purkinje fibres) in the ventricular wall, causing ventricular contraction

vena cava

* large vein going back into the heart
* inferior vena cava = lower body
* superior vena cava = upper body

the response of the heart to exercise

* demand to remove CO2 and intake O2, triggers the medulla to send a signal to the SA node through the cardiac nerve to increase heart rate
* when CO2 levels go down, medulla sends a signal through the vagus nerve to decrease the heart rate

Pathogens

any living organism or virus that causes disease (eg. virus, bacteria, fungus, worm, protozoa)

Disease

condition that disturbs normal body functioning (interrupts homeostasis)

Illness

deterioration in the normal state of health of an organism

zoonotic pathogens

• can cross species barrier

• an increasing problem as contact between humans and animals increases via animal husbandry

• eg. west nile virus, rabies

Species specific pathogens

• can infect one species but not another

• based on optimal body temperatures, presence of cell receptor molecules

• eg. frogs cannot suffer from TB

• eg. gonorrhea, polio, syphilis, measles

Primary defence: Skin

• While the dermis is alive with sweat glands, sensory receptors, dermal cells, etc., the epidermis is mainly dead cells on the surface

  • since many pathogens enter living tissues, as long as dead epidermis is intact, it acts as a primary defence

• Sebaceous glands in skin secrete lactic acid and fatty acids which makes the surface of the skin acidic and prevents growth of most pathogenic bacteria

Primary defence: Mucus

• Entry points of the body (urethra trachea, nasal passage, vagina) are heavily lined with goblet cells —the mucus they secrete can trap pathogens

• Cilia may also be present which “sweep” the pathogens out the body

• Lysozomes may be present in mucus, their enzymes can kill bacterial pathogens

Haemostasis

• sealing the hole in a blood vessel to keep pathogens out and prevent blood loss

Platelets

• cell fragments produced by bone marrow

• have no nucleus

• live for 8-10 days

• undergo a structural change when activated to form a sticky plug at the damaged region

Coagulation cascade

• Clotting factors are released by platelets when a blood vessel is damaged

  • they also initiate localised vasoconstriction to reduce blood flow through the damaged region

• they trigger the conversion of inactive zymogen prothrombin to activated enzyme thrombin

• thrombin then catalyzes the conversion of soluble plasma protein fibrinogen into insoluble fibrous form fibrin

• fibrin forms a mesh of fibres around the platelet plugs and traps RBCs to form a temporary clot

Coronary Thrombosis

• Formation of a blood clot within coronary arteries

• occlusion of a coronary artery by a blood clot may lead to an acute myocardial infarction

Atherosclerosis

• Blood clots form in arteries when vessels are damaged as a result of the deposition of cholesterol

• Stenosis - The diameter of the lumen is reduced by atheromas the increased pressure results in fibrous scar tissue forming in damaged areas

• atherosclerotic plaque forms as smooth lining degrades

• if the plaque ruptures, blood clotting forms a thrombus that restricts blood flow —forms an embolus if it is dislodged

Leukocytes

• White blood cells, includes phagocytes and lymphocytes

Phagocytes role in the immune system

• Ingestion of pathogens by macrophages gives non-specific immunity to disease (part of the innate immune system)

  • They do not differentiate between different types of pathogens

  • They are also non-adaptive; they respond to an infection the same way every time

Mechanism of phagocyte’s ingestion of pathogens

• Macrophages circulate in blood and move into body tissue (extravasation) in response to infection (damaged tissues release chemical signals to draw in white blood cells via chemotaxis)

• They recognize that a pathogen is “not-self” based on protein molecules on its surface (generally glycoproteins)

• Use phagocytosis to ingest pathogens —pseudopodia extend from the cell membrane and surround the pathogen, eventually fusing to form an internal vesicle

• This vesicle fuses to a lysosome to form a phagolysosome which contains enzymes to digest the pathogen

• Pathogen fragments (antigens) may then be presented on the surface of a macrophage to form a dendritic cell and stimulate the third line of defence.

Mechanism of inflammation

• tissue damage signals leukocytes called mast cells (localised) and Basophils (circulating) to release histamine

• histamine is recognized by some cells and causes local vasodilation which increases capillary permeability to improve the recruitment of leukocytes to the region

• this also causes increased blood flow (redness/heat) and release of fluids (swelling/tenderness)

Antibodies definition and structure

• specific protein molecules that are produced in response to a pathogen’s specific antigen

• Y shaped, four polypeptides with disulphide bonds between them

• antigen binds to a variable region specific to it

• constant region serves as a recognition site for the rest of the immune system

Antibodies functions

• recognizes and attaches to foreign antigen proteins on non-self cells

• Precipitation: Makes soluble antigens insoluble to aid elimination

• Agglutination: links cell-bound antigens together, causes clumping, restricting mobility

• Neutralisation: Masks dangerous parts of pathogens (eg. exotoxins)

• Inflammation: Triggers histamine release, increases immune mobility

• Complement: complement proteins perforate cell membrane, can lead to cell lysis

• all of these functions aid in destroying pathogens, or enhancing immune system to aid phagocytic leukocyte’s recognition of pathogens

Adaptive immune system description

• 3rd line of defence, differentiates between particular pathogens and targets response specific to the pathogen

• Immunological memory: The adaptive immune system can respond rapidly upon re-exposure to a specific pathogen

Explain the process of forming immunological memory

• Dendritic cells present antigen fragments on their surface, they migrate to the lymph nodes and activate specific helper T lymphocytes by binding to them

• The T_H cells then release cytokines to activate the B cell capable of producing antibodies for the antigen

  • Some of the T cells will then from memory T cell’s (important upon re-exposure)

• Clonal selection: triggered by the cytokine, the specific B cell will then divide and form clones

  • Some of these clones will form mature but short lived plasma cells, which are capable of producing large volumes of the antibody

  • others will form memory B cells which will be able to swiftly produce antibodies upon reexposure (allows for immunity)

Polyclonal activation

often pathogens contain multiple distinct antigenic fragments, so a single pathogen is likely to activate many different T and B cells to produce a variety of antibodies

Mechanism of vaccines

• Contain an attenuated version of a pathogen with a recognizable antigen that will stimulate an immune response (initiate a primary immune response), but not cause the disease

• Memory cells are produced, creating long-term immunity

• Length of time someone is immune after an injection depends on the lifespan of memory cells

Significance of smallpox in vaccination efficacy

• first disease of humans eradicated (disease stops circulating worldwide) via vaccination

  • last case was in 1977

• Possible because: easily identifiable; direct transmission without animal vectors; short infection period; virus did not mutate; population was cooperative

Antibiotics function

• only blocks processes in prokaryotes (only works for bacterial pathogens, not viruses, and doesn’t affect eukaryotes)

• each antibiotic is specific to the pathogen it attacls

• they block processes such as protein/cell wall/nucleic acid synthesis, metabolism, and cell membrane integrity

Penicillin

• First chemical compound found to have antibiotic properties, identified by Alexander Fleming (1928)

• Discovered by unintendingly contaminating a dish with s. aureus,

• penicillin mould growth caused a halo of inhibited bacterial growth around the mould

Florey and chain experiment

• discovered medical applications of penicillin

• eight mice injected with pathogenic bacteria, four treated with penicillin survived

HIV

• human immunodeficiency virus —retrovirus that infects T_H lymphocytes, results in a loss of antibody production.

• following infection, the virus undergoes a period of inactivity (clinical latency) during which T_H cells reproduce

• once the virus becomes active again, it spreads, destroys T lymphocytes in the process (lysogenic cycle)

• Body then becomes susceptible to opportunistic infections -AIDS

AIDs

• Acquired immuno-Deficiency syndrome, a result of HIV

• It describes the inability to produce antibodies some period after an HIV infection

• There is currently no treatment for AIDs (however PrEP is an effective preventative treatment for HIV)

Allergic reactions

• mast cells release histamines that cause inflammation to improve immune response

• allergens are antigens that produce an abnormal immune response fighting a perceived threat

• the abnormal inflammation results in sympmtons in nose/throat and rashes

Monoclonal antibodies description

• antibodies artificially derived from a single B cell clone (ie. identical specific antibodies)

• an animal (usually a mouse) is injected with an antigen and produces antigen-specific plasma cells

• Plasma cells are removed and fused with tumour cells (myeloma cells) capable of endless divisions

• results in a hybridoma cell which is capable of synthesizing large quantities of monoclonal antibody

Therapeutic treatments with monoclonal antibodies

• injecting purified antibodies is an effective emergency treatment for rabies

• can be used to target cancer cells that the body’s own immune system fails to recognize as harmful

Diagnostic uses of monoclonal antibodies

• used in pregnancy tests —tests for the presence of hCG in urine

  • hCG is a hormone produced by women during fetal development

  • uses the enzyme ELISA to identify the substance via a colour change

3 processes of respiration

• external respiration (including ventilation): exchange of gasses b/n air and blood (via alveoli)

• Internal respiration: exchange of gasses b/n blood and cells

• cellular respiration: formation of ATP molecules (using O₂ and producing CO₂)

Ventilation and concentration gradients in alveoli

• process by which the body maintains a concentration gradient in alveoli to facilitate passive respiration

• flow of O₂ into alveoli and removal of CO₂

  • O₂ levels must be higher in alveoli so they diffuse into blood

  • CO₂ levels must be lower in the alveoli so CO₂ diffuses out of the blood into alveoli

• lungs function as a ventilation system by continually cycling fresh air into the alveoli

Pneumocytes

• alveolar cells, line the alveoli and comprise of the majority of the inner surface of the lungs

• divided into type 1 and type 2 pneumocytes

Type 1 pneumocytes

• squamous (flat) and very thin to maximize diffusion

• involved in gas exchange between blood and capillaries

• connected by occluding junctions to prevent leakage of tissue fluid into alveolar air space

• amitotic, but type 2 can differentiate into type 1

• cover around 95% of the alveolar surface

Type 2 pneumocytes

• responsible for the secretion of pulmonary surfactant, which reduces the surface tension in alveoli

• cuboidal shape and contain many granules for storing surfactant components

Pulmonary surfactant

• secreted by type two pneumocytes

• manipulates surface tension (can spread out across moist lining to increase surface tension and slow rate of expansion) so all alveoli inflate at roughly the same rate

Alveolar fluid

• lines the inside of alveoli

• moist surface is conductive to gas exchange (easier for O₂ to dissolve across membranes when dissolved in liquid)

• however, it creates a tendency for the alveoli to collapse and resist inflation (which is counteracted by pulmonary surfactant)

Relationship between pressure and volume in relation to ventilation (think thoracic cavity)

• contraction of respiratory muscles changes the volume of the thoracic cavity

• Boyle’s law P proportional to 1/V

• gasses will move from an area of high P to low P

• Inspiration: When P in thoracic cavity < atmosphere, air moves into lungs

• Expiration: When P in thoracic cavity > atmosphere, air moves out the lungs

Respiratory muscles for inspiration

• Diaphragm contracts, causing it to flatten

• External intercostals contract, pulling rips up and out

Respiratory muscles for exhalation

• diaphragm relaxes causing it to curve upwards

• internal intercostals contract, pulling ribs in and down

• abdominal muscles contract, push diaphragm upwards during forced expiration

Lung cancer causes and symptoms

• since lungs are very vascular, there is an increased probability of metastasis, so most common cause of cancer related deaths

• Risk factors: radiation; aging; pollution; environment; diseases; genetics; occupation; asbestos; tobacco; smoke

• Symptoms: coughing blood; wheezing; respiratory distress; weight loss; chest pain; difficulty swallowing; heart complications

Emphysema causes and symptoms

• chemical irritants (eg. cigarettes) damage cells of alveolar walls, causing them to lose their elasticity

• phagocytes release elastase at damaged region, breaking down elastic fibres

• sometimes caused by a gene mutation

• symptoms: short breath; phlegm; expansion of ribcage; cyanosis, increased susceptibility to chest infections

Dendrites

short branched fibres from the soma that receive chemical information from other neurons or receptor cells and convert it into electrical signals

Axon

elongated fibre to transmit electrical signals to terminal branches to be passed on

Myelin sheath

• in some neurons, the axon is surrounded by a fatty white layer made of glial cells (oligodendrocytes in CNS and Schwann cells in the PNS)

• improves conduction speed of electrical impulses via saltatory conduction

• However, myelination takes up significant space within a closed environment

Saltatory conduction

• propagation of action potentials along myelinated axons, from one node of Ranvier to the next

• increases conduction velocity of action potentials by up to 100x

Resting potential

• difference in charge across the membrane when a neuron is not firing (-70 mV)

• neurons pump sodium and potassium ions across their membranes to generate a resting potential

  • more negative inside the neuron than outside

• maintained by the sodium-potassium pump

Sodium potassium pump

• maintains the resting potential by expelling sodium ions and admitting potassium ions through the hydrolysis of ATP

  • 3 Na+ ions our for every 2K+ in

  • some K+ ions also leak back out of the cell

• This imbalance and the presence on negative ions (eg. chloride ions) and negatively charged proteins in the neuron maintains a negative interior environment

• Creates an electrochemical gradient

Action potential

• rapide changes in charge across the membrane that occur when a neuron is firing

• caused by depolarisation and repolarisation

• allows the axon to propagate an electrical impulse along its length

Depolarisation

• sudden change in membrane potential from a negative to positive internal charge

• in response to a signal at the dendrite, sodium channels on axon membrane open, causing a passive influx of sodium ions due to concentration/electrochemical gradient

• results in a membrane potential of +30mV

Repolarisation

• restoration of the membrane potential following depolarisation (restoring negative internal charge)

• potassium channels open following the sodium ion influx (triggered by a change in voltage), causing a passive potassium efflux

• causes voltage to reach -80 mV

Refractory period

• period of time following a nerve impulse before a neuron is able to fire again

• sodium-potassium pump actively transports sodium ions out and potassium ions in to restore the resting potential of -70mV

Threshold potential

• minimum stimulus to open voltage-gated channels; combined stimulus from dendrites must exceed minimum level of depolarisation

• an action potential of the same magnitude will always occur no matter the magnitude of the stimulus provided the threshold potential is reached

self-propagation of nerve impulses

• action potentials that move along that length of the axon act as a self-propagating wave of depolarisation

• the ion channels that occupy the length of the axon are voltage-gated (open in response to changes in membrane potential)

• hence depolarisation in one point of the axon triggers the opening of ion channels in the next segment

Synapses

• gaps that separate neurons and other neurons/receptors/effector cells

• electrical signals are converted to chemical signals to transmit a message across the synapse

Description of process of synaptic signal transfer

• Action potential arrives at the axon terminal of the pre-synaptic neuron

• depolarisation causes voltage-gated channels to open, Ca2+ ion rushes in and signals to synaptic vesicles to move and fuse to the membrane

• neurotransmitters are released by exocytosis and diffuse across the synaptic gap

• specific neurotransmitters bind to specific receptors on the post-synaptic neuron

• sodium channels on the post-synaptic neuron open, causing a sodium ion influx and depolarisation

  • action potential is initiated, leads to propagation of nerve impulse if above threshold potential

• enzymes in synaptic gap break down neurotransmitters and the products are reuptaken by pre-synaptic neuron by active transport

neurotransmitters

• chemical messengers released from neurons

• bind to receptors on post-synaptic neuron to trigger (excitatory) or prevent (inhibitory) response

acetylcholine functions and structure

• used by both CNS and PNS, commonly released at neuromuscular junctions to trigger muscular contractions and also commonly released by autonomic nervous system to promote parasympathetic response (rest and digest)

• created in the axon terminal by combining choline with an acetyl group and stored in a vesicle

• binds to either a nicotinic muscarinic receptor on post-synaptic neuron

• must be continually removed from the synaptic cleft bc overstimulation leads to fatal convulsions and paralysis

• broken down by acetylcholinesterase (AChE) which is either released into synapse or embedded in the membrane of post-synaptic neuron

• liberated choline can reform acetylcholine when returned to pre-synaptic neuron

Neonicotinoid pesticides

• irreversibly bind to nicotinic acetylcholine receptors to trigger a sustained response

• AChEs cannot break them down, so they lead to fatal convulsions and paralysis

• insects have more acetylcholine receptors which bind to neonicotinoids more strongly so they are more toxic to insects than mammals

• linked to reduced honey bee populations and bird populations (since insects are their food source)

• has been restricted in some countries

endocrine system

collection of glands that produce hormones that regulate homeostasis and essential life processes

Secretion of thyroxin and target cells

• secreted by the thyroid in response to signals initially from the hypothalamus when thyroxin levels or temperature levels are low

• hypothalamus stimulates thyroxin release at low temperatures and inhibits it at high temperatures

• requires iodine from the diet, if iodine levels are too low, the thyroid cannot complete the synthesis of thyroxin, so will store intermediary molecule which forms goiter

• targets all cells

Functions of thyroxin

• regulates metabolic activity (eg. rate of cellular respiration) and body temperature

• increases basal metabolic rate (amount of E used by body at rest) by stimulating carb and lipid metabolism via oxidation of glucose and fatty acids

• heat is a consequence of increased metabolism, so thyroxin is released in response to decreased body temperature

Secretion of leptin and target cells

• secreted by adipose (fat tissue) and targets hypothalamus cells

Functions of leptin

• regulates appetite and metabolic activity, as well as fat stores

• binds to receptors in the hypothalamus to inhibit appetite

• overeating causes more adipose cells to from, hence more leptin is produced; inverse with starvation

Uses of leptin therepeutically

• cured obesity in a group of mice that genetically could not produce leptin

• not applicable to humans, however, because most people do produce leptin, but are just desensitized to it and leptin resistance develops with age

Secretion of melatonin and target cells

• secreted by pineal glands in response to signalling from cells in the SCN (suprachiasmatic nucleus) in the hypothalamus when blue wavelengths are removed

• target cells, many cells of the body and brain