human biome

Anatomy & Physiology Overview - The Ear

Outer ear 

  • Pinna (auricle) - visible part of the ear outside of the head.  
  • External auditory canal 
  • Ceruminous glands - specialized sudoriferous glands (sweat glands) located subcutaneously in the external auditory canal. They produce cerumen (earwax) by mixing their secretion with sebum and dead epidermal cells.

 Middle ear: air filled 

  • Tympanic membrane -  vibrates in response to sound waves 
  • Malleus, incus and stapes - 3 small bones that transmit vibrations to each other

Inner ear: fluid filled 

  • Mechanoreceptor for hearing and balance 
  • Vesibular apparatus - balance
  • Semicircular canals 
  • Cochlea
  •  • Organ of Cor -  sensory epithelial cell


  • Perilymph = similar in compositon to plasma – Na+ 
  • Endolymph = high in K+ 
  • Organ of Cor: contains hair cells – move due to pressure waves 
  • 50-100 stereocilia on each cell 
  • Longest embedded in tectorial membrane 

In the cochlea that the vibrations transmitted from the eardrum through the tiny bones are converted into electrical impulses sent along the auditory nerve to the brain. 

  • The cochlea is a tapered tube which circles around itself 
  • The basilar membrane divides the tube lengthwise into two fluid-filled canals joined at the tapered end. 
  • ossicles transmit vibration to the cochlea where they attach at the oval window
  • resultant waves travel down the basilar membrane where they are “sensed” by  16-20,000 hair cells (cilia) attached to it which poke up from a third canal called the organ of Corti
  • Organ of Corti transforms the stimulated hair cells into nerve impulses 
  • Waveforms travelling down the basilar membrane peak in amplitude at differing spots along the way according to their frequency 
  • Higher frequencies peak out at a shorter distance down the tube than lower frequencies
  • The hair cells at that peak point give a sense of that particular frequency
  • The distance between pitches follows the same logarithmic distance as our perception of pitch i.e. the placement of octaves are equidistant.

ALSO, here’s a few pages of skull anatomy notes! I drew them in pencil, then went over it with different coloured pens (corresponding to the different bones). I’m definitely not an artist AND it took ages but it helps me to understand and remember everything. 

Neurons - Anatomy Overview

Going to be covering nerves and synapses this week so here’s a recap!

  • Soma (cell body) contains the nucleus which produces RNA to support cell functions, + organelles surrounding the nucleus which are mostly made of up endoplasmic reticulum. Supports and maintains the functioning of the neuron.
  • Dendrites - cellular extensions with many branches ‘dendritic tree’. majority of input occurs via the dendritic spine. The sum of all excitatory (neuron fires) or inhibitory (prevents firing) signals determines whether the neuron fires or not. If firing the action potential is transmitted down the axon.
  • Axon - fine, cable-like projection that can extend thousands of times the diameter of the soma in length. The axon carries nerve signals away from the soma (and also carries some types of information back to it). Can undergo branching - communication with target cells. 
  • Axon hillock - where the axon emerges from the soma. the part of the neuron that has the greatest density of voltage-dependent sodium channels - therefore the most easily excited part of the neuron and the spike initiation zone for the axon - most negative action potential threshold. Can also receive input from other neurons.
  • Axon terminal where neurotransmitters are released into the synaptic cleft to signal the next neuron

Myelin sheath

Myelin is a fatty material that wraps around axons and increases the speed of electrical transmission between neurons. It is broken up by nodes of Ranvier, between which electrical impulses jump. Myelin is produced by schwann cells in the PNS and oligodendrocytes in the CNS.

Classes of neurons

Sensory neurons bring information into the CNS so it can be processed.

Motor neurons get information from other neurons and convey commands to  muscles, organs and glands.

Interneurons,found only in the CNS, connect one neuron to another. 

Types of neuron

Multipolar neurons have one axon and many dendritic branches. These carry signals from the central nervous system to other parts of the body eg muscles and glands.

Unipolar neurons are also known as sensory neurons. They have one axon and one dendrite with branches. Pass signals from the outside of the body, such as touch, along to the central nervous system.

Bipolar neurons have one axon and one dendrite branch. They pass signals from one neuron to the next inside the central nervous system.

Pyramidal neurons have one axon and two main dendrite branches. These cells pass signals inside the brain and tell the muscles to move.

Purkinje neurons are found in the cerebellum, controlling balance, coordination, and timing of actions. They have one axon and a dense and complicated dendrite arrangement.

Antibodies (Human)

  • The ‘foot’ (bottom) of the antibody is known as the Fc fragment - binds to cells, binds to complement = effector function (kills or removes antigen)
  • The top (antigen binding) is the Fab fragment
  • Chains are held together with disulphide binds
  • Associated molecules allow intracellular signalling 
  • Normally 3X constant heavy chain domains per chain and a hinge region (except μ and ε which have 4 and no hinge region)

Classes of Immunoglobulins

The five primary classes of immunoglobulins are IgG, IgM, IgA, IgD and IgE,  distinguished by the type of heavy chain found in the molecule. 

  • IgG - gamma-chains
  • IgMs - mu-chains
  • IgAs - alpha-chains
  • IgEs - epsilon-chains
  • IgDs - delta-chains.

Differences in heavy chain polypeptides allow different types of immune responses. The differences are found primarily in the Fc fragment. There are only two main types of light chains: kappa (κ) and lambda (λ), and any antibody can have any combination of these 2 (variation).


  • monomer
  • Gamma chains
  • 70-85% of Ig in human serum. 
  • secondary immune response 
  • only class that can cross the placenta - protection of the newborn during first 6 months of life
  • principle antibody used in immunological research and clinical diagnostics
  • 21 day half life
  • Hinge region (allows it to make Y and T shapes - increasing chance of being able to bind to more than one site)
  • Fc strongly binds to Fcγ receptor on phagocyte - opsono-phagocytosis
  • Activates complement pathway


  • Serum = pentamer 
  • Primary immune responses - first Ig to be synthesised
  • complement fixing 
  • 10% of serum Ig 
  • also expressed on the plasma membrane of B lymphocytes as a monomer - B cell antigen receptor
  • H chains each contain an additional hydrophobic domain for anchoring in the membrane
  • Monomers are bound together by disulfide bonds and a joining (J) chain.
  • Each of the five monomers = two light chains (either kappa or lambda) and two mu heavy chains.
  • heavy chain = one variable and four constant regions (no hinge region)
  • can cause cell agglutination as a result of recognition of epitopes on invading microorganisms. This antibody-antigen immune complex is then destroyed by complement fixation or receptor mediated endocytosis by macrophages.

In humans there are four subclasses of IgG: IgG1, IgG2, IgG3 and IgG4. IgG1 and IgG3 activate complement.


  • B cell receptor
  • <1% of blood serum Ig
  • has tail pieces that anchor it across B cell membrane
  • forms an antigen specific receptor on mature B cells - consequently has no known effector function (don’t kill antigens, purely a receptor) (IgM as a monomer can also do this)


  • Extra rigid central domain
  • has the most carbohydrates
  • IgE primarily defends against parasitic invasion and is responsible for allergic reactions.
  • basophils and tissue mast cells express very high affinity Fc receptors for IgE - mast cells then release histamine
  • so high that almost all IgE is bound
  • sensitizes (activates) mucosal cells and tissues 
  • protects against helminth parasites

IgE’s main purpose is to protect against parasites but due to improved sanitation these are no longer a prevalent issue across most of the world. Consequently it is thought that they become over activated and over sensitive while looking for parasites and start reacting to eg pollen and causing allergies.


  • Exists in serum in both monomeric (IgA1) and dimeric (IgA2) forms (dimeric when 2 Fcs bind via secretory complex)
  • 15% of the total serum Ig.
  • 4-7 day half life
  • Secretory IgA2 (dimer) = primary defense against some local infections
  • Secreted as a dimer in mucous (e.g., saliva, tears)
  • prevents passage of foreign substances into the circulatory system

Isotype: class of antibody (IgD, IgM etc)

Allotype: person specific alleles 

Idiotype: (hyper) variable region - antibody specificity 

My heart skip skips a beat


The pause is to allow the atria to fully empty into the ventricle.

Heartbeat on an ECG trace

P Interval (Ventricular Diastole)

  • Atria and ventricles are relaxed
  • blood is flowing into the atria from the veins. 
  • Atrial pressure increases above that of the ventricle, AV valves open allowing blood to flow into the ventricle

P Wave (Atrial Systole) P-Q

Signal transduction from SA to AV nodes. 

  • SA node fires 
  • Atria contract causing atrial systole 
  • which forces all blood into the ventricles
  • emptying the atria.

Q Interval (End of Ventricular Diastole)

Depolarisation of interventricular (IV) septum 

  • AV valves remain open - all remaining blood squeezed into the ventricles. 
  • impulse from the SA node reaches the AV node 
  • which spreads the signal throughout the walls of the ventricles via bundles of His and Purkinje fibres
  • R peak is the end of ventricular diastole and the start of systole.

R Interval (Ventricular Systole)

Ventricular contraction

  • All blood is now within the ventricles
  • so pressure is higher than in the atria - AV valves close
  • ventricles start to contract although pressure is not yet high enough to open the SL (semilunar) valves

ST Segment (Ventricular Systole)

Ventricular contraction

  • Pressure increases until it equals Aortic pressure,
  • SL valves open
  • blood is ejected into the Aorta (and pulmonary artery) as ventricles contract
  • At this time the atria are in diastole and filling with blood returning from the veins.
  • plateau in ventricular arterial pressure

T Wave (Ventricular Diastole)

T= moment of Ventricular repolarisation immediately before ventricular relaxation

  • Ventricles relax
  • ventricular pressure is once again less than the aortic pressure 
  • so SL valves close
Antimicrobial Agents - Inhibition of DNA and Protein Synthesis

Bacterial chromosome replication

DNA replication

Bacterial Topoisomerases 

  • maintain DNA in appropriate state of supercoiling 
  • cut and reseal DNA
  • DNA gyrase (topoisomerase II) introduces negative supercoils 
  • Topoisomerase IV decatenates circular chromosomes 
  • these are the targets of the quinolone antibacterial agents 


  • bind to bacterial DNA gyrase and topoisomerase IV after DNA strand breakage 
  • prevent resealing of DNA 
  • disrupt DNA replication and repair 
  • bactericidal (kill bacteria)

Fluoroquinolone is particularly useful against

  • Gram +ves: Staphylococcus aureus, streptococci 
  • Gram -ves: Enterobacteriacea; Pseudomonas aeruginosa 
  • Anaerobes: e.g. Bacteroides fragilis 
  • many applications e.g. UTIs, prostatitis, gastroenteritis, STIs 

Adverse effects

  • Relatively well tolerated
  • GI upset in ~ 5% of patients 
  • allergic reactions (rash, photosensitivity) in 1 - 2% of patients 

Inhibition of Bacterial Protein Synthesis 


  • in 1952: Erythromycin was isolated as the first macrolide (Streptomyces erythreus) 
  • Newer macrolides: clarithromycin, azithromycin 
  • Structurally they consist of a lactone ring (14- to 16-membered) + two attached deoxy sugars 

Mode of action 

  • bind reversibly to bacterial 50S ribosomal subunit 
  • causes growing peptide chain to dissociate from ribosome → inhibiting protein synthesis 
  • bacteriostatic (stops reproduction)

Macrolides’ spectrum of activity

  • good antistaphylococcal and antistreptococcal activity 
  • treatment of respiratory & soft tissue infections and sensitive intracellular pathogens • e.g. Chlamydia, Legionella 

Adverse effects

  • Generally well tolerated
  • nausea 
  • vomiting 
  • diarrhoea 
  • rash 


  • large family of antibiotics produced by various species of Streptomyces (“mycin”) and Micromonospora (“micin”) 
  • include: streptomycin, neomycin, kanamycin, gentamicins, tobramycin 
  • Structure = linked ring system composed of aminosugars and an aminosubstituted cyclic polyalcohol 

Mode of action of aminoglycosides

  • Bind irreversibly to 30S ribosomal subunit 
  • disrupt elongation of nascent peptide chain 
  • translational inaccuracy → defective proteins 
  • bactericidal 

Spectrum of activity 

  • broad spectrum; mainly aerobic G-ve bacilli (e.g. P. aeruginosa) 
  • used to treat serious nosocomial infections (hospital acquired infections)
  • First TB antibiotic
  • Used for cystic fibrosis 

Adverse effects

  • all aminoglycosides have low Therapeutic Index (only a small amount needed to become toxic)
  • renal damage, ototoxicity, loss of balance, nausea 

Chronic obstructive pulmonary disease (COPD) is an umbrella term à emphysema, chronic bronchitis, certain types of bronchiectasis, and sometimes asthma. COPD = leading causes of death in the US - appears to be rising.


  • Persistent cough + wheezing + sputum production
  • Tightness or pain in the chest + shortness of breath
  • (when progressed) Loss of appetite
  • Depression
  • Reduced sexual function
  • Trouble sleeping

Long term smoking is the leading cause of emphysema. Other risk factors include a deficiency of enzyme alpha-1-antitrypsin, air pollution, airway reactivity, heredity, male sex, and age.Most people with emphysema also have chronic bronchitis (inflammation of bronchi)

Hallmarks of Emphysema 

“pursed-lipbreathing.” The person with emphysema struggles to exhale completely, in an attempt to empty trapped air. They purse their lips, leaving only a small opening. Then, when they exhale, the lips block the flow of air, increasing pressure in the collapsed airways, and opening them, allowing the trapped air to empty.

“barrel chest,” where the distance from the chest to the back, which is normally less than the distance side to side, becomes more pronounced. This is a direct result of air becoming trapped behind obstructed airways.


  • causes shortness of breath due to over-inflation of the alveoli
  • the lung tissue around small bronchioles is destroyed/impaired making them unable to hold their shape during exhalation - making it difficult for the lungs to empty and the air becomes trapped in the alveoli.
  • Normal lung tissue looks like a new sponge. Emphysematous lung looks like an old used sponge, with large holes and a dramatic loss of “springy-ness” or elasticity.
  • An abnormal and permanent enlargement of air spaces distal to the terminal bronchioles
  • also severely affects capillaries + blood flow

Cigarette smoke (and other smoke inhalation including dust and air pollution)

  • Destroys lung tissue, which results in the obstruction of airflow, and it causes inflammation and irritation of airways that can add to airflow obstruction.
  • Cigarette smoke causes dysfunction of the cilia.
  • Long-term = cilia disappear from the cells lining the air passages. Without the constant sweeping motion of the cilia, mucous secretions cannot be cleared from the lower respiratory tract.
  • Smoke causes mucous secretion increase – coupled with above causes mucous build up 
  • providing bacteria with a rich source of food –> infection.

Smoking and the immune response

  • Lung immune cells cannot clear many particles (such as tar) that cigarette smoke contains.
  • Increase in susceptibility to lung infection
  • Inflammation caused by the immune system constantly attacking bacteria or tar from smoking leads to the release of destructive enzymes from the immune cells.
  • Over time, enzymes released during this persistent inflammation lead to the loss of proteins responsible for keeping the lungs elastic.
  • In addition, the tissue separating the air cells (alveoli) from one another also is destroyed.


  • Chest X-Ray – changes in lung are physical and visible.  Can also show infections.
  • Lung function tests (how much air your lungs can hold, how quickly your lungs can expel air during expiration, and how much reserve capacity your lungs have for increased demand)
  • Blood test for alpha-1-antitrypsin deficiency – only if family history. 
  • Blood tests for WBC count for infection
  • Arterial blood gas test (O2 + CO2 levels)


Emphysema causes irreversible damage - treatment can only slow progression

  • Stop smoking: halt progression and should improve lung function 
  • Bronchodilators: cause the air passages to open more fully and allow better air exchange, usually the first medications for emphysema - mild cases eg = albuterol (taken with inhaler), fast acting and 1 dose provides relief for 4-6 hours – is a relief medication for periods of shortness of breath, but doesn’t cure. Tiotropium = long acting, more severe. Taken once a day and can extend life expectancy
  • Steroid medications:  decrease inflammation, however not all people will respond to steroid therapy. Orally or inhaled.
  • Surgery if severe eg lung transplant
Physiology of Ageing - Muscles
  • Loss of lean body mass 
  • Infiltration of fat and connective tissue 
  • Altered muscle metabolism 
  • Insulin resistance 
  • Reduced levels of key regulatory hormones 
  • Impaired oxidative defence 
  • Muscle strength peaks at approx. 20-40 years 
  • Strength dictated by muscle cross-sectional area 
  • Age-associated decline in concentric strength (leg > arm
  • Decline in concentric strength occurs earlier than decline in eccentric strength 
  • Power generation ability declines faster than max. strength  


= loss of muscle mass (and strength) due to ageing 

  • Two phases: 
  • ‘slow’ from 25 to 50 years (approx. 10% lost) 
  •  ‘rapid’ from 50 onwards (approx. 40% lost from 50-80) 
  • Deterioration in motor unit remodelling 
  • Reduced cross-sectional area and functionality 
  • Disuse atrophy (ageing is associated with becoming more sedentary(not as active)) may contribute to changes 
  • Reduced regenerative capacity 
  • Stem cell function affected by circulating factors? 
  • ‘Systemic inflammation’ theory of ageing? 
  • Increased apoptosis 
  • Anabolic resistance 
  • Protein degradation (muscle & nerve) 

Motor Unit

  • Entire motor unit affected: 
  • Alpha-motorneuron 
  • Fibres innervated 
  • Shift to predominance of slow-twitch fibres 

Force transfer

  • Network of cytoskeletal proteins align and transmit force produced by actin and myosin along muscle fibres and out to extracellular matrix 
  •  E.g. Costameres = sub-sarcolemmal proteins that connect sarcomere to cell membrane 
  • Found in Z and M lines 
  • Transmit force laterally 
  • Significant decrease in costameres and lateral force in ageing

Muscle protein metabolism in ageing 

  • Basal muscle protein synthesis unchanged 
  • Protein/amino acid feeding leads to increase in muscle protein synthesis in both groups 
  • BUT, response is smaller in the elderly 
  • Resistance exercise leads to increase in muscle protein synthesis AND breakdown 
  • BUT, synthesis rates lower in the elderly 
  • Food + exercise needed for anabolic response 
  • Response delayed in elderly, but can achieve similar rates 

Metabolic Capacity

  • Decrease in Mitochondria 
  • Decrease in capillary density 
  • Reduced ability of muscle to extract O2 from blood 
  • Decrease in enzymes for metabolic pathways 
  • Reduced speed of O2 utilisation 
  • Therefore ↓ (a-v)O2 diff (and ↓VO2max) 


  • Decline in muscle mass and oxidative capacity, plus increased fat mass leads to greater risk of developing: 
  • insulin resistance and/or type II diabetes 
  • hyperlipidaemia 
  • hypertension 
  • Cardiovascular disease
  • Reduced bone mass contributes to loss of functional capacity and risk of injury 
Antimicrobial Agents  - Cell wall inhibitors

Based on mode of action • divided into families based on chemical structure

 Modes of action Interference with: 

  • cell wall synthesis 
  • protein synthesis 
  • nucleic acid synthesis 
  • plasma membrane integrity 
  • metabolic pathway 

Inhibitors of Bacterial Cell Wall (peptidoglycan) Synthesis 

  • The Beta-lactam Family 
  • The Glycopeptides 

Peptidoglycan is composed of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) repeat units, and amino acids.  Each NAM is linked to peptide chain and the peptide chains are cross-linked.


  • Includes penicillin derivatives (penams), cephalosporins (cephems), monobactams, and carbapenems.
  • class of broad-spectrum antibiotics containing a β-lactam ring
  • Bacterial transpeptidase enzymes are responsible for catalysing cross-linking of the peptide chains
  • β-lactam ring bind to these transpeptidases – this inhibits cross-linking between peptide chains and prevents synthesis of stable PG
  • Cell wall synthesis ceases and the bacterial cells eventually die due to osmotic instability or autolysis. 


Polypeptide agents - basic structural elements amino acids 


  • complexes with peptide portion of peptidoglycan’s precursor units 
  • vancomycin is a large hydrophilic molecule able to form hydrogen bonds with the terminal D-alanyl-D-alanine moieties of the NAM/NAG-peptides
  • preventing PG transglycosylation reaction – PG precursor subunits (NAG-NAM+peptide) cannot be inserted into peptidoglycan matrix;
  • Vancomycin also alters bacterial-cell-membrane permeability and RNA synthesis

Uses:  serious Gram positive infections e.g. MRSA wound infection

Adverse effects:

  • damage to auditory nerve 
  • hearing loss (ototoxicity) 
  • “Red man/neck” syndrome - rash on face, neck, upper torso 
Pharmacokinetics Overview

(Absorption and distribution of drugs)

The study of the time course of drugs and their metabolites in the body (what the body does to the drug) consisting of:

  • administration
  • absorption
  • distribution
  • metabolism
  • excretion


Enteral (passes through intestine)

  • oral (mouth)
  • buccal/sublingual (applied in cheek/under tongue)
  • Gastrosomy (surgical opening through the abdomen into the stomach)

Topical (applied directly)

  • Nasal
  • Rectal
  • Ophthalmic (eyes)

Parentral (injection)

  • Intravenous (into veins)
  • intramuscular (into muscles)
  • intradermal (within layers of skin)
  • subcutaneous (under the skin)

Drug molecules move around the body either through bulk flow (bloodstream, lymphatics or cerebrospinal fluid) or diffusion (molecule by molecule over short distances)


Passage of drug from its site of administration into plasma - important for all routes except intravenous injection.


  • IV = fastest route of administration
  • bolus injection = very high concentration of drug
  • rate limiting factors = diffusion through tissues and removal by local blood flow

Drugs need to pass through membranes (cell membranes, epithelial barriers, vascular endothelium, blood-brain barrier, placenta barrier etc) via

  • passive diffusion through lipids
  • carrier-mediated
  • passage through membrane pores/ion channels
  • pinocytosis (ingestion into a cell by the budding of small vesicles from the cell membrane)

Diffusion through lipid

  • non-polar molecules can dissolve freely in membrane lipids
  • the rate is determined by the permeability coefficient (P)(solubility in the membrane and diffusibility) and the concentration difference across the membrane

pH and Ionisation

  • Many drugs are weak acids or weak bases
  • exist in unionised or ionised forms
  • pH = balance between the two forms
  • ionised forms have low lipid solubility
  • uncharged however the drug is usually lipid soluble

ionisation affects:

  • rate of drug permeation through membranes
  • steady state distribution of drug molecules between aqueous compartments if pH difference exists between them


  • urinary acidification accelerates the excretion of weak bases and slows that of weak acids
  • alkalisation has opposite effect
  • increasing plasma pH causes weak acids to be extracted from CNS into plasma
  • Reducing plasma pH causes weakly acidic drugs to become concentrated in CNS, increasing neurotoxicity


  • Bioavailibility (F) indicates the fraction of an orally administered dose that reaches systemic circulation intact, taking into account both absorption and local metabolic degradation
  • determined by comparison between oral and IV absorption

affected by:

  • drug preparation
  • variation in enzyme activity of gut
  • gastric pH
  • intestinal motility

Volume of Distribution

Vd is defined as the volume of fluid required to contain the total amount, Q, of drug in the body at the same concentration as that present in the plasma, Cp

  • determined by relative strength of binding between drug and tissue compared with drug and plasma proteins
  • tight binding to tissue but not plasma –> drug appears to be dissolved in large volume –> large Vd (eg chloropromazine)
  • tight binding to plasma –> V can be very close to blood volume –> low Vd (eg warfarin)
Receptors intro - pharmacology

Drugs act at four different levels

  • Molecular - immediate target for most drugs (eg propanolol binds to B-adregenic receptors)
  • Cellular - biochemical and other consequent effects (eg propanolol reduces Ca2+)
  • Tissue - function altered (eg propanolol decreases myocardial contractility) 
  • System - function altered (eg propanolol reduces need for cardiac output, easing pressure on cardiovascular system)

Most drug targets are proteins 

  • Receptors - for transmitter substances and hormones
  • Enzymes
  • Transport systems - ion channels, active transport
  • Substrates
  • Second messengers 
  • Antibodies 

some drugs act on nucleic acids.


“Receptors are the sensing elements in the system of chemical communication that coordinate the function of all the different cells in the body.”

Upon recognition of ligand (chemical signalling molecule), receptor proteins transmit the signal into a biochemical change in the target cell.

Cell surface receptors

Hydrophilic transmitters act on cell surface receptors

  • peptides
  • most neurotransmitters 
  • other small molecules

All cell surface receptors are transmembrane proteins 

  • Extracellular domain - receptor site
  • transmembrane domain
  • intracellular domain - catalyic/coupling site, only present on certain receptors

Intracellular receptors 

Hydrophobic (lipid soluble) transmitters act on intracellular receptors

  • steroids
  • thyroid hormones
  • vitamin D

Drug interaction with receptors 

  • Agonist - activates receptor
  • Antagonist - binds to receptor without activating, thus presenting activation
  • Affinity - measure of how avidly a drug binds with receptor

Side effects occur when drugs bind to more than one type of receptor. Some bind irreversibly and most bind with weak intermolecular bonds. An equilibrium arises between bound and unbound drug.

(notes on types of receptor to follow - overview:)

Ligand-gated ion channels: open or close upon binding of a ligand

G-protein-coupled receptors: Transmembrane receptor protein that stimulates a GTP-binding signal transducer protein (G-protein) which in turn generates an intracellular second messenger

Nuclear receptors: Lipid soluble ligand that crosses the cell membrane and acts on an intracellular receptor

Kinase-linked receptors: Transmembrane receptor proteins with intrinsic or associated kinase activity which is allosterically regulated by a ligand that binds to the receptor’s extracellular domain

GPCRs/7-transmembrane receptors (7TM receptors)

G-protein-coupled receptors (GPCRs) are the largest and most diverse group of membrane receptors in eukaryotes. 


  • single polypeptide chain comprising of seven transmembrane α-helices
  • extracellular N-terminal domain of varying length, 
  • intracellular C-terminal domain.
  • length of the extracellular N terminus and the location of the agonist binding domain determines family.
  • The long, third cytoplasmic loop couples to the G-protein 
  • Usually particular receptor subtypes couple selectively with particular G-proteins
  • For small molecules, such as noradrenaline, the ligand-binding domain of class A receptors is buried in the cleft between the α-helical segments within the membrane. Peptide ligands bind more superficially to the extracellular loops

G protein system

GPCRs interact with G proteins in the plasma membrane when an external signaling molecule binds to a GPCR, causes a conformational change in the GPCR.  G-proteins comprise a family of membrane-resident proteins
whose function is to recognise activated GPCRs and
pass on the message to the effector systems that generate
a cellular response. 

  • G proteins are specialized proteins with the ability to bind the nucleotides guanosine triphosphate (GTP) and guanosine diphosphate (GDP). 
  • The G proteins that associate with GPCRs are heterotrimeric, (alpha beta and gamma subunits)
  •  alpha and gamma are attached to the plasma membrane by lipid anchors 
  • Trimer in resting state 
  • activated alpha monomer and beta/gamma dimer

Guanine nucleotides bind to the α subunit, which has enzymic activity, catalysing the conversion of GTP to GDP. The β and γ subunits remain together as a βγ complex. All three subunits are anchored to the membrane through a fatty acid chain, coupled to the G-protein through a reaction known as prenylation.

  • G-proteins are freely diffusible so a single pool of G-protein in a cell can interact with several different receptors and effectors 
  • When GPCR is activated by an agonist, a conformational change causes it to acquire high affinity for αβγ (G protein)
  • bound GDP dissociates and is replaced with GTP, which in turn causes dissociation of the G-protein trimer, releasing α-GTP and βγ subunits - the ‘active’ forms of the G-protein
  • which diffuse in the membrane and can associate with various enzymes and ion channels
  • Signalling is terminated on hydrolysis of GTP to GDP through the GTPase activity of the α subunit.
  • resulting α–GDP dissociates from the effector, and reunites with βγ
  • Attachment of the α subunit to an effector molecule increases its GTPase activity
  • GTP hydrolysis is termination –> activation of the effector tends to be self-limiting

Second messenger targets for G proteins

Main targets:

  • Adenylyl cyclase (responsible for cAMP formation)
  • Phospholipase C (inositol phosphate and diacylglycerol (DAG) formation)
  • Ion channels, particularly calcium and potassium channels
  • Rho A/Rho kinase (system controlling the activity of many signalling pathways for cell growth and proliferation, smooth muscle contraction, etc.)
  • Mitogen-activated protein kinase (MAP kinase) system controlling cell functions eg division.

(notes on these coming soon)

Passive Immunotherapy

Active immunotherapies:

  • Cytokines (TNFa IL-2, IFNs)
  • Cancer vaccines
  • tumour CTL and APC
  • DC priming

Passive immunotherapy:

  • Administration of monocolnal (clone derived asexually from a single individual or cell) antibodies which target either tumour-specific or over expressed antigens
  • Generally comprised of antibodies made outside of the body (in a lab)
  • administered to patients to provide immunity against a disease, or to help fight existing disease
  • do not stimulate a patient’s body to ‘actively’ respond to a disease the way a vaccine does
  • immunogen is given several times to induce a strong secondary response
  • blood serum contains many different antibodies to the immunogen
  • most immunogens have multiple antigenic epitopes 
  • each stimulates a different B cell clone/receptor –> polyclonal antibody (PAb) response 

Monoclonal antibody (mAb) therapy is the most widely used form of cancer immunotherapy. Monoclonal antibodies cannot be purified from a polyclonal sample and are derived from a single clone/specific for a single epitope.

Antibodies in cancer therapy:

  • Trigger immune system to attack cancer cells 
  • Block molecules that stop the immune system working (checkpoint inhibitors)
  •  Block signals telling cancer cells to divide 
  • Carry drugs or radiation to cancer cells

Checkpoint inhibitors

  • Immune system uses particular molecules to stop it being over activated and damaging healthy cells  - these are known as checkpoints
  • some cancers make high levels of checkpoint molecules to switch of immune system T cells which would normally attack cancer cells
  • examples of targets include CTLA-4, PD-1 and PD-L1 (programmed death ligand 1)

Blocking cell division signals 

  • Cancer cells often express large amounts of growth factor receptors on their surface –> rapid cell division when growth factors stimulate them
  • some monoclonal antibodies stop growth factor receptors working
  • either by blocking the signal or the receptor itself 
  • cancer no longer gets signal to divide

Carrying drugs/radiation

  • drugs or radioisotopes can be attached to monoclonal antibodies
  • the mAB binds to the cancer cell, delivering directly
  • known as conjugated MABs
Drug Metabolism - kidneys

Drugs and their metabolites are handled in the kidneys via:

  • Glomerular filtration 
  • Reabsorption 
  • Tubule secretions 

Glomerular Filtration

  • Molecules under 20kDa in size are filtered out under positive hidrostatic pressure through pores of 7-8nm in the glomerular membrane 
  • Glomerular filtrate contains about 20% of the plasma volume delivered to glom.
  • Plasma proteins and protein-bound drugs are not filtered
  • Therefore efficiency is influenced by plasma protein binding  


  • Not all glomerular filtrate is lost - some reabsorbed
  • specific tubular uptake processes for carbohydrates, amino acids, vitamins, etc
  • as the tubule to plasma concentration gradient increases only the most polar molecules remain in the urine
  • pH partition between the urine and plasma determines the rate of excretion/absorption 

Tubular Secretion

  • Renal tubule has secretory transporters both on apical and basolateral membrane (organic anion and cation transporters (OATs 1-4 & OCTS 1-3))
  • Some drugs (eg glucuronic acid and sulphate conjugates) may undergo active carrier mediated elimination 
  • secretion rapidly lowers the plasma concentration of unbound drug
  • causing rapid dissociation of any drug-protein complexes
Innate Immunity - intro
  • First line of defence + first to act
  • A primitive response (exists in animals and some plants)
  • Non-specialised and without ‘memory’

Consists of:

  • Physical barriers (eg skin and mucosa//tight junctions, airflow)
  • Chemical barriers (eg enzymes, lung surfactant, antimicrobals)
  • Soluble mediators of inflammation (eg cytokines)
  • Microbal defence (eg commensal competition, secreted antimicrobals)
  • Cells (eg phagocytes)
  • Receptors to recognise presence of pathogen/injury - results in inflammation

Soluble Mediators

Complement Proteins

  • liver-derived 
  • circulate in serum in inactive form
  • activated by pathogens during innate response
  • functions include lysis, chemotaxis and opsonisation

Auxiliary Cells

Mediate inflammation as part of the immune response. The main auxiliary cells involved in the immune response are Basophils, Mast cells and Platelets.


  • Leukocyte containing granules 
  • on degranulation release histamineplatelet activating factor
  • causing increased vascular permeability and smooth muscle contraction
  • also synthesise and secrete other mediators that control the development of immune system reactions

Mast Cells

  • Also contain granules 
  • However they are not circulating cells - found close to blood vessels in all types of tissue especially mucosal and epithelial tissues.
  • rapidly release inflammatory histamine but this is IgE dependant so not innate


  • normally function in blood clotting
  • also release inflammatory mediators

Cytokines and chemokines

Produced by many cells but especially mØ (macrophages), initiate inflammatory response and act on blood vessels 

  • interferons - antiviral protection
  • chemokines - recruit cells
  • interleukines - fever inducing, IL-6 induces acute phase proteins 
  • IL-1 - encourages leukocytes to migrate to infected/damaged tissue
  • as does tumour necrosis factor (TNFa)

Acute phase proteins

  • Liver derived proteins 
  • plasma concentrations increase (positive acute-phase proteins) or decrease (negative acute-phase proteins) in response to inflammation
  • called the acute-phase reaction 
  • triggered by inflammatory cytokines ( IL-1, IL-6, TNFα)
  • help mediate inflammation ( fever, leukocytosis, increased cortisol, decreased thyroxine, decreased serum iron, etc)
  • activate complement opsonisation 



Cytotoxic Cells

  • Eosinophils/natural killer cells, cytotoxic T cells
  • kill target via release of toxic granules 
  • dendritic cell derived IL-12 helps activate NK cells


  • mono-nuclear = long-lived; polynuclear = short-lived
  • engulf, internalize and destroy 
  • phagosome forms around microbe
  • enzyme filled with lysosomes fuses to form phagolysosome
  • organism is digested
  • fragments are either ‘presented’ or exocytosed

phagocytosis requires recognition of microbe via receptors for

  • PAMPs (pathogen associated molecular patterns - eg flagella or capsule) - recognised by toll-like receptors 
  • activated complement
  • antibody

The innate immune response primes for the adaptive 

  • B-cells are primed by activated complement
  • Th1 cell differentiation needs pro-inflammatory cytokines