Module 3 (special topics)

Question 1

Major developments of week 2

Answer 1

Trophoblast development and embryonic disk, development of amnion and yolk sac, gastrulation, notochordal process, structures derived from the three primary germ layers and neurulation (development of somites)

Question 2

Major developments of week 1

Answer 2

Fertilisation, cleavage of zygot, formation of morula and blastocyst and implantation

Question 3

Pattern formation

Answer 3

Developmental process by which cells acquire different identities depending on their relative special positions in the embryo

Question 4

Germ layers formation name and types

Answer 4

Gastrulation generates the three germ layers: endoderm, mesoderm and ectoderm

Question 5

Mesoderm

Answer 5

Internal (between); body systems include: integumentary, skeletal, muscular, endocrine, cardiovascular, lymphatic, urinary, reproductive and miscellaneous (lining of pericardial, peritoneal and pleural and CTs that support organ systems); shown as red

Question 6

Ectoderm

Answer 6

Skin (outside); body systems include integumentary, skeletal, nervous, endocrine, respiratory and digestive; shown as blue

Question 7

Endoderm

Answer 7

Inside; body systems include endocrine, respiratory, digestive, urinary and reproductive; shown as yellow

Question 8

Fertilisation

Answer 8

Sperm is directed toward egg with chemotactic/thermotactic cues; one sperm enters egg and haploid gametes fuse to make diploid zygote; meiosis occurs after; occurs within uterine tube 2-24 hours after ovulation

Question 9

Path of sperm cell at egg

Answer 9

Corona radiata: somatic cells surrounding egg that came from ovary during egg release; protect egg and release hormones which act as a chemoattractant for the sperm
Zona pellucida: fibrous mat on exterior of egg, allows sperm to bind to egg; once sperm is bound, it burrows into protective mat until it reaches cytoplasm of egg
Plasma membrane of secondary oocyte
Cytoplasm of secondary oocyte

Question 10

Cleavage and formation of blastocyst (5 days)

Answer 10

Day 1: cleavage of zygote (2 cell stage); cell divides and gives rise to two smaller blastomeres
Day 2: cleavage of zygote (4 cell stage); further cell division, cells don’t get bigger, same volume
Day 4: ball of cells called a morula, no cavity; loosely-packed ball of cells form a blastocyst; cells huddle closer and adhesion has increased to form first epithelial layer; active sodium pumps pumping Na into cavity inside cells to encourage water to flow in by osmosis
Day 5: two distinct cell types; outside (layer of cells; trophoblast which give rise to placenta) and inside (inner cell mass which give rise to embryo); blastocyst cavity formed allows space for cells to move around

Question 11

Egg movement

Answer 11

Egg is released from ovary every month, travels down fallopian tubes (where it may be fertilised) with help from cilia and muscular movements; at days 3-4, it is still packaged within zona pellucida as a morula to prevent ectopic pregnancies (cannot develop placenta if implantation occurs in fallopian tube); implantation occurs after about 6 days after fertilisation

Question 12

Endometrium

Answer 12

Internal layer of uterus which sheds if pregnancy does not occur after egg has been released each month (menstruation); if egg is fertilised, implantation will occur in this layer

Question 13

Trophoblast and development

Answer 13

Extra embryonic tissues which give rise to the placenta (combination of maternal tissues and tissues from the embryo itself); trophoblast cells differentiate into the syncytiotrophoblast cells and cytrophoblast cells; trophoblast cells eventually give rise to the chorion (extra embryonic part of embryo); occurs about 1 week after fertilisation

Question 14

Syncytiotrophoblasts

Answer 14

Type of trophoblast cell; loosely packed cells which secrete enzymes to to allow blastocyst to implant into uterine lining; gives rise to chorion

Question 15

Cytotrophoblast

Answer 15

Distinct cells which secrete human chorionic gonadotrophin that helps maintain the uterine lining in a secretory state so that no menstruation occurs (hormone detected in pregnancy tests); gives rise to chorion

Question 16

Chorion

Answer 16

Made from both types of trophoblast cells; contributes to the embryonic portion of the placenta; important for creating an interface between the mother and child, allows for exchange of materials between them; villi within chorion create a large surface area to facilitate this

Question 17

Bilaminar embryonic disc development

Answer 17

Loosely packed inner cell mass forms 2 layers; epiblast is the primitive ectoderm and hypoblast is the primitive endoderm which are together called the bilaminar disc; occurs at approximately days 5-6; after 2 weeks it is connected to the trophoblast cells by a connecting stalk

Question 18

Amniotic cavity development

Answer 18

Once embryo is buried deep within endometrial layer, amniotic cavity which is initially just on top of the embryonic disc begins to enlarge and surrounds entire embryo; single layer of squamous epithelium forms a dome above the epiblast (amnion) and the cavity fills with amniotic fluid; occurs around 12 days after fertilisation

Question 19

Amniotic fluid

Answer 19

Inside the amnionic cavity (amnion); buffers the embryo, helps regulate temperature, prevents embryo from dying out and prevents it to sticking to other surfaces; can be used to test foetal cells for abnormalities and infections

Question 20

Yolk sac development

Answer 20

Hypoblasts proliferate and migrate around inner wall of blastocyst wall until they cover it entirely at day 9; hypoblasts form a new thin membrane and yolk sac develops, so that the embryo sits between the yolk sac and the amnion
At day 12, embryo has completely embedded itself into endometrium; syncytiotrophoblasts divide, expand and the formation of lacunar networks occurs due to small holes developing in the syncytiotrophoblast layer

Question 21

Yolk sac

Answer 21

Provides a bit of energy for the developing embryo; source of blood cells and nutrients in early development; contributes to formation of the gut

Question 22

Lacunar networks

Answer 22

Spaces which eventually fuse with the maternal blood network creating the placenta which delivers a source of nutrients to the embryo and a route for waste disposal out of the embryo

Question 23

Extraembryonic mesoderm cells

Answer 23

Formed around day 12 after fertilisation; along with trophoblast cells will give rise to the chorion

Question 24

Gastrulation

Answer 24

Germ layers are laid down; first evidence is the formation of the primitive streak which occurs on the dorsal surface of epiblast and elongates from the posterior to anterior of embryo (where head and tail will be); it starts a faint groove which elongates
Invagination occurs where cells from epiblast (ectoderm/bilaminar disc) migrate to lie below primitive streak, displacing the hypoblast, to form the mesoderm which is a loosely organised connective tissue and is between the endo and ecto derm layers; occurs at about 16 days after fertilisation
Hypoblast cells become endoderm and epiblast cells become ectoderm, both being tightly packed cells

Question 25

Names of directional views of an embryo

Answer 25

Anterior: head; posterior: tail; dorsal: back; ventral: tummy

Question 26

Notochordal process

Answer 26

Mesodermal cells migrate down from the primitive node of the primitive streak towards the anterior and form a hollow tube of cells in the midline called the notochordal process; occurs underneath the ectoderm at about 16 days after fertilisation but by day 22-24, it becomes a solid rod of cells (notochord)

Question 27

Notochord

Answer 27

Solid rod of cells formed by day 22-24; defines backbone of organism; induces surrounding tissue to develop in certain ways to give rise to specialised cells by releasing a chemical substance which influences neighbouring tissues

Question 28

What effects does the notochord have on neighbouring tissues?

Answer 28

Mesodermal cells: develop into ventral bodies | Ectoderm cells above it: form the neural plate

Question 29

Neurulation

Answer 29

Day 17-19: neural plate thickens and depresses to form neural groove Day 20: edges of neural groove rise up to form neural folds Day 21: eventually sinks down and pinches off as a seperate tube (neural tube)

Question 30

Neural tube at 3-4 weeks

Answer 30

The anterior end of the neural tube gives rise to 3 enlarged areas which will give rise to the brain (hindbrain, midbrain and forebrain) Somite formation induced by notochord at 22 days; mesoderm on the sides of the neural tube form cuboidal structures, in pairs, on each side of the neural tube; by the end of the 5th week there are 42-44 pairs

Question 31

Somite division

Answer 31

Divide into 3 sections as they mature; Top: dermatome which forms CT Middle: myotome which develops into the skeletal muscles of neck, back and limbs Bottom: sclerotome which gives rise to vertebrae and ribs

Question 32

Embryonic folding

Answer 32

2D disc now forms a 3D structure which occurs over days 22-26; embryo becomes completely surrounded by amniotic cavity Dorsal endodermal layer is continuous with the amnion and endodermal ventral layer is continuous with the yolk sac; connecting stalk is precursor to the umbilical cod which connects embryo to placenta Different growth rates across embryo causes it to fold and form a curved structure (head at one end and tail at the other); simultaneous lateral folding of the ectoderm is occurring, it folds down and around central column where it surrounds the mesodermal layer with the endoderm in the middle (which forms foregut, mid gut and hind gut through gastrulation)

Question 33

Pharyngeal arches development

Answer 33

6 bulges (4 obvious and 2 less obvious) form either side of future head and neck; seen at 28 days Within each pharyngeal arch there are all three germ layers which contain blood vessels, cranial nerve tissue and muscle Each arch will give rise to unique regions of the head and jaw

Question 34

Digestive enzyme/catalytic protein

Answer 34

Break down nutrients in food; amylase, lipase, pepsin

Question 35

Transport protein

Answer 35

Carry substances throughout body in blood or lymph; haemoglobin

Question 36

Structural protein

Answer 36

Build different structures; actin, keratin, tubulin

Question 37

Hormone signalling protein

Answer 37

Coordinate activity of different body systems; insulin, glucagon

Question 38

Immunilogical protein

Answer 38

Protect body from foreign pathogens; antibodies

Question 39

Contractile protein

Answer 39

Muscle contraction; myosin

Question 40

Storage protein

Answer 40

Provide food for early development of embryo or seedling; legume storage proteins

Question 41

Toxin proteins

Answer 41

Used by pathogens or other organisms to cause disease; cholera toxin, botox

Question 42

What is a protein and how does it work?

Answer 42

A chain/polymer of amino acids linked by peptide bonds; short polypeptides are called peptides; individual amino acids in a protein are called residues Can adopt complex structures to facilitate varied functions; shape determines function; binding a substrate in an active site can cause conformational changes which provide a function or strengthen interaction

Question 43

What is an amino acid made of?

Answer 43

Composed of an amino (base) group, side chain, carboxyl (acid) group and central alpha carbon Zwitterionic form is the dominant form: amino group has a positive charge from an additional H+ and the carboxyl group has a negative charge from a loss of an H+

Question 44

Peptide bond formation

Answer 44

Amide bond; condensation reaction/dehydration synthesis reaction

Question 45

Peptide bond properties

Answer 45

Ridged and cannot rotate due to resonance; O-C-N-H of peptide bonds are essentially co-planar; rotation can occur at the single bonds between the alpha-carbon and it's neighbouring atoms; N terminus to C terminus

Question 46

Amino acid side chains and special cases

Answer 46

Chemical structure determines the behaviour; some may be acidic/basic, polar/non-polar Proline: R group folds back and creates weird conformations in polypeptide and may result in strange structural constraints in a protein Cystein: has a sulphur in it, can be used to create covalent linkages to other cystine residues and can put constraints on the protein structure

Question 47

Lock and key vs induced fit

Answer 47

Lock and key: defined binding pocket allows substrates to bind to the protein Induced fit: where the binding process facilitates a conformational change that locks the substrate down

Question 48

Primary structure

Answer 48

Unique sequence of amino acids of a protein driven by the DNA gene encoding it; can deduce the primary structure by knowing the DNA sequence only

Question 49

Secondary structure

Answer 49

Localised folding of the polypeptide driven by H-bonding interactions within its backbone; common types are Beta pleated sheets and alpha helices; can fairly accurately predict regions of secondary structure in a protein knowing only the DNA sequence

Question 50

Beta pleated sheets

Answer 50

Can be parallel (N-C in same direction) or non/anti-parallel (N-C in opposite direction), driven by H-bonding between backbone amine group on one strand and backbone carbonyl group on another strand Large aromatic residues and B-branched amino acids are favoured in B-strands

Question 51

Alpha helices

Answer 51

Right-handed helix, normally each turn is 3.6 amino acids, driven by H-bonding between backbone amine group and a backbone carbonyl group 3-4 residues earlier; tightly packed with almost no free space within the helix; side chains protrude out from helix Methionine, alanine, leucine, glutamate and lysine like to form helices; proline and glycine don't, as they are helix breakers and are usually found at the end of a helix

Question 52

Tertiary structure

Answer 52

3D shape of protein primarily driven by side chains and their interactions (H-bonding, ionic bonding, dipole-dipole interactions and Van der Waals forces); hydrophobic groups of nonpolar amino acids cluster in protein interior and hydrophilic groups lie on proteins surface outside to interact with water and maintain solubility In membrane spanning proteins the hydrophobic groups may be on the outside interacting with lipid tails

Question 53

Cystine tertiary structure

Answer 53

Can form covalent linkages with each other (disulphide bonds); thiol groups are oxidised, H is removed and a covalent linkage is formed between the two sulphur atoms

Question 54

Bond interaction strengths

Answer 54

Disulphide > Ionic > hydrogen > Van der Waals

Question 55

Cofactors in a tertiary structure

Answer 55

Some proteins (particularly enzymes) can coordinate a cofactor (prosthetic group) within protein using the R groups; may be essential for function and/or structure; common examples: metal ions (Mg, Mn, Zn, Fe, Ca), organic molecules or vitamins

Question 56

Quaternary structure

Answer 56

Proteins comprised of more than one polypeptide chain; multiple folded protein subunits driven by ionic interaction, H-bonding and hydrophobic interactions (rarely disulphide bonds); may be dynamic where one protein comes off/on another or moves around

Question 57

Types of quaternary structures

Answer 57

Homooligomers: protein with 2 or more subunits of the same protein and a ring is formed Heterooligomers: protein with 2 or more different polypeptides which form one functional unit

Question 58

Protein structure categories

Answer 58

Globular, fibrous and membrane proteins

Question 59

Globular protein properties

Answer 59

Typically soluble in water; often enzymes, transport, immune (floating around cell); often irregular sequence and secondary structure; moderate or no quaternary structure (2 or 3 different polypeptides); lower stability; en e.g. enzymes, haemoglobin, antibodies

Question 60

Fibrous protein properties

Answer 60

Typically insoluble in water; often structural; often repetitive primary and secondary structure (have a repeated amino acid sequence; may have a lot of helices one after another); high level of quaternary structure (1000's of polypeptides); highly stable (e.g. heat, pH) due to them forming long fibres that soluble e.g. keratin, actin, collagen, silk

Question 61

Membrane protein properties

Answer 61

Transverse through a lipid bilayer; transport (small molecules and other proteins), receptors (surface of cells), signalling, adhesion (attachment to other cells or surfaces); high degree of non-polar (hydrophobic) amino acids which have to interact with a lipid environment, so side chains face out toward membrane; polar (hydrophilic) side chains face inwards Transmembrane portion of protein can be a single alpha-helix or alpha-helix bundle; exception is mitochondria and Gram negative bacteria also have B-barrel (proteins made of a series of B-sheets form a barrel) transmembrane proteins

Question 62

Protein structure folding

Answer 62

A newly synthesised (or denatured) protein may not correctly fold without help; it needs the correct environment (solute, salt conc., pH, temp, macromolecular crowding); depends on temporal aspect - co-translational folding as the polypeptide is coming out of the ribosome (N term folds before C term); chaperones - other proteins which bind to and prevent misfolding of parts of the protein; enzymes involved in disulphide bond forming

Question 63

Studying protein structure

Answer 63

Experimental lab determination is very time consuming and often impossible; ~1% of structures of DNA proteins are known Methods used are X-ray Crystallography, Nuclear Magnetic Resonance (NMR) and Cyro-Electron microscopy

Question 64

X-ray crystallography

Answer 64

Crystallise pure protein (dehydrate until saturated) and use the short wavelength of X-rays and basic principles of diffraction in a crystal lattice to deduce atomic structure of protein; most widely used method for structural determination; highest resolution (atomic); crystallisation is slow and prone to failure; sometimes don't tell us much about how they move Can be done on soluble proteins, some membrane proteins

Question 65

Nuclear Magnetic Resonance (NMR)

Answer 65

Sample dissolved in water, need a 13C/15N labelled protein, use illuminating radiation type with smaller wavelength (wavelength of accelerated electron beam is very small); electron optics are complex and not ideal, so current max practical resolution is about 0.5nm; closer to real protein structure but larger proteins cannot be resolved Can be done on small soluble proteins and peptides, dynamic proteins

Question 66

Cyro-Electron Microscopy

Answer 66

Rapidly emerging technique where purified protein is frozen in its native state in thin layer of virtuous ice, shoot with electron microscope and protein particles randomly distribute in ice at all different orientations (projection of all particles observed); near-atomic resolution, fast sample preparation; can gain insights in to protein dynamics/movements (tease out multiple conformations in one sample) Can be done on soluble proteins, membrane proteins and large protein complexes (which would never crystalise), dynamic proteins

Question 67

Resolution

Answer 67

The distance corresponding to the smallest observable feature; if two objects are closer than this distance, they appear as one combined blob rather than two seperate objects

Question 68

Protein structure model types

Answer 68

Backbone model (traces polypeptide backbone), ribbon model (assign secondary structures; spirals and arrows), wire model (backbone with chemical structure shown) and space-filling model (assign each atom its size)

Question 69

Cyro-EM tackling Covid-19

Answer 69

From DNA to structure in 2 weeks, including structure of the spike protein bound to human receptor; structures being used to help inform response, design drugs and antibodies to block binding of virus to receptor or tread patient; identify candidate regions of spike protein fro vaccine design

Question 70

Human skin functions

Answer 70

Protection/barrier against the environment, chemicals, pathogens, heat, UV and water loss; blood reservoir (can hold 8-10% of the total blood volume); thermoregulation: sweat glands (evaporation of sweat cools the body) and blood vessels (vessel constriction in the dermis reduces the blood flow and reduces heat loss; vasodilation in dermis increases blood flow and increases heat loss Sensation: touch/pressure, pain and temperature Vitamin D synthesis: vit D precursor requires modification by UV before active form can be made in the liver (need UV)

Question 71

Layers in skin structure

Answer 71

Epidermis, dermis and hypodermis (usually in contact with muscle, bone or tissue)

Question 72

Epidermis

Answer 72

``` Top layer of skin; provides a barrier and continued renewal; no structural strength; mainly consists of layers of keratinocytes (dead or dying keratinocytes); no CT in epidermis to provide strength to this tissue; no vasculature (all nutrient supply and waste removal through dermis) Thin skin (most skin) has 4 layers Thick skin (fingertips, palms and soles) has 5 layers - 5th layer is the Stratum lucidum ```

Question 73

Keratinocytes

Answer 73

Cells which make up the epidermis; produce keratins which are important for the barrier function of the epidermis

Question 74

Epidermis stratification

Answer 74

Crucial for barrier function and continued renewal of epidermis; Stratum corneum, Stratum lucidum, Stratum granulosum, Stratum spinosum, Stratum basale; also includes epidermal ridge and corpuscle of touch in dermal papilla

Question 75

Stratum basale

Answer 75

Bottom layer of epidermis; keratinocyte stem cells are reservoirs of cells for a lifetime of renewal (can divide: one cell remains a stem cell and the other becomes a transit amplifying keratinocyte); transit amplifying keratinocytes proliferate a lot to provide cells for the top layers (only capable for a limited number of cel divisions before they die)

Question 76

Stratum spinosum

Answer 76

Above stratum basale and below stratum granulosum; 8-10 layers of cells; keratinocytes begin to flatten out; keratin intermediate filaments and desmosomes form, together they hold cells together for barrier formation

Question 77

Stratum granulosum

Answer 77

Above stratum spinosum and below stratum corneum/lucidum (thick skin); flattened keratinocytes undergo apoptosis; lamellar granules fuse to plasma membrane and release lipid rich secretions to help form barrier; keratohyalin (dark granules) help form keratin intermediate filaments into keratin (final formation of keratin, holds keratinocytes tightly together which is important in the barrier formation)

Question 78

Stratum lucidum

Answer 78

Above stratum granulosum and below stratum corneum; only present in thick skin and is found on the fingertips, palms and soles

Question 79

Stratum corneum

Answer 79

Top layer of epidermis; 25-30 layers of flattened, dead keratinocytes (finished undergoing apoptosis) which overlap like snake scales; barrier formed to keep moisture in and the outside world out

Question 80

Stratification process

Answer 80

Proliferating keratinocytes on the bottom of the epidermis push cells up and away from the dermis and undergo programmed cell death; complete epidermal turnover occurs over approximately a month

Question 81

Basement membrane and potential problems

Answer 81

Interface between dermis and epidermis; made of Collagen IV, Perlecan, Nidogen, Laminin 332; important for epidermal (keratinocytes in basal layer) attachment to dermis Mutation in BM proteins can result in Epidermolysis; if keratinocytes cannot attach properly to BM, epidermis can be easily detached by sheer force

Question 82

Rete ridges

Answer 82

Dermal papillae/rete ridges; contour of BM provides resistance to sheer forces If interface between dermis and epidermis was flat, less sheer force would be required to seperate the two layers

Question 83

Pigmentation

Answer 83

Melanocytes make melanosomes which contain melanin

Question 84

Melanocytes

Answer 84

Reside at BM on epidermal side; responsible for pigmentation of skin; make melanosomes (vesicles) which contain melanin pigment, transferred to keratinocytes though dendrites (arms which make contact with keratinocytes) of melanocytes; contacts on average 36 keratinocytes

Question 85

Melanin

Answer 85

Pigment which gives skin its colour; pheomelanin is yellow-red and eumelanin is brown-black; protects from UV by absorbing it; keratinocytes concentrate myosomes in the melanin on top of their nuclei for protection

Question 86

Langerhan's cells

Answer 86

Immune cells which surveil the epidermis for foreign organisms; if barrier of epidermis is broken or bacteria gets through, the cells will find the foreign organisms, move into the dermis and find help from the WBCs

Question 87

Dermis

Answer 87

Dense matrix made up of collagen and elastic fibres (CT); strong and supple; thickness varies (thickest on palms and palms); very stable and turnover is minimal Vasculature: supply nutrients and remove waste for both dermis and epidermis; laminin 1+2 lines vessels of vasculature system and alpha-SMA is a contractile protein

Question 88

Fibroblasts

Answer 88

Produce collages (strength) and elastin (elasticity); long and spindle-like; found in dermis

Question 89

Layers of dermis

Answer 89

Papillary: high cell density, loose CT (lower density) Reticular: low cell density, dense CT (high density)

Question 90

Types of wound types

Answer 90

Superficial, partial thickness and full thickness

Question 91

Superficial wounds and healing

Answer 91

Damage to epidermis only Healing occurs by migration of keratinocyte from the wound edges and dermal appendages (sweat glands, hair follicles, sebaceous glands); once all keratinocytes are in contact on all sides, stratification can occur to reform epidermis

Question 92

Partial thickness wounds and healing

Answer 92

All of the epidermis and some of the dermis is destroyed; still have some skin appendages Four healing stages: inflammatory (immune cells/pathogens come in and clean up the wound), migratory (keratinocytes migrate from around wound edge and appendages, fibroblasts migrate in to the clot and make collagen fibres), proliferative (keratinocytes proliferate once they have covered the dermal surface), maturation (epidermal stratification/reformation occurs and then scab falls off)

Question 93

Full thickness wound; healing and intervention

Answer 93

All of epidermis and dermis is destroyed, hypodermis can be destroyed too (exposing bone and muscle) Difficult to heal due to all reservoirs of epidermal stem cells being destroyed; keratinocytes have to migrate from the wound edges and intervention is required to increase outcomes Split thickness skin graft is used where all of the epidermis and part of dermis is removed from a healthy donor site (undamaged skin) and the skin graft covers the wound; donor site heals in 10-14 days

Question 94

White Island eruption example

Answer 94

Lots of patients with mixture of wound types, having burns on 30-80% of their body surface; first surgery is to remove all burnt skin which is critical for skin graft success (any residual neurotic tissue will negatively affect skin graft take); next surgery is receiving split thickness skin grafts on as much of the surface area wounds as possible, cadaver skin temporarily placed on other sites until more skin grafts can be taken from donor site

Question 95

Engineered skin

Answer 95

Permanent wound coverage solution that could reduce time to complete wound coverage Digest sample of patient skin with enzymes, isolate and grow fibroblasts and keratinocytes (in a cell culture they will thrive in), grow large sheets of autologous, full thickness skin Currently no full thickness, autologous skin product available for treating wounds

Question 96

Engineered skin limitations

Answer 96

No pigmentation, hair follicles, sweat glands or sebaceous glands; lack of function will impact patient outcomes in the long term