Module 3 (special topics) Flashcards
Major developments of week 2
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)
Major developments of week 1
Fertilisation, cleavage of zygot, formation of morula and blastocyst and implantation
Pattern formation
Developmental process by which cells acquire different identities depending on their relative special positions in the embryo
Germ layers formation name and types
Gastrulation generates the three germ layers: endoderm, mesoderm and ectoderm
Mesoderm
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
Ectoderm
Skin (outside); body systems include integumentary, skeletal, nervous, endocrine, respiratory and digestive; shown as blue
Endoderm
Inside; body systems include endocrine, respiratory, digestive, urinary and reproductive; shown as yellow
Fertilisation
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
Path of sperm cell at egg
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
Cleavage and formation of blastocyst (5 days)
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
Egg movement
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
Endometrium
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
Trophoblast and development
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
Syncytiotrophoblasts
Type of trophoblast cell; loosely packed cells which secrete enzymes to to allow blastocyst to implant into uterine lining; gives rise to chorion
Cytotrophoblast
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
Chorion
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
Bilaminar embryonic disc development
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
Amniotic cavity development
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
Amniotic fluid
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
Yolk sac development
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
Yolk sac
Provides a bit of energy for the developing embryo; source of blood cells and nutrients in early development; contributes to formation of the gut
Lacunar networks
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
Extraembryonic mesoderm cells
Formed around day 12 after fertilisation; along with trophoblast cells will give rise to the chorion
Gastrulation
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
Names of directional views of an embryo
Anterior: head; posterior: tail; dorsal: back; ventral: tummy
Notochordal process
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)
Notochord
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
What effects does the notochord have on neighbouring tissues?
Mesodermal cells: develop into ventral bodies
Ectoderm cells above it: form the neural plate
Neurulation
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)
Neural tube at 3-4 weeks
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
Somite division
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
Embryonic folding
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)
Pharyngeal arches development
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
Digestive enzyme/catalytic protein
Break down nutrients in food; amylase, lipase, pepsin
Transport protein
Carry substances throughout body in blood or lymph; haemoglobin
Structural protein
Build different structures; actin, keratin, tubulin
Hormone signalling protein
Coordinate activity of different body systems; insulin, glucagon
Immunilogical protein
Protect body from foreign pathogens; antibodies
Contractile protein
Muscle contraction; myosin
Storage protein
Provide food for early development of embryo or seedling; legume storage proteins
Toxin proteins
Used by pathogens or other organisms to cause disease; cholera toxin, botox
What is a protein and how does it work?
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
What is an amino acid made of?
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+
Peptide bond formation
Amide bond; condensation reaction/dehydration synthesis reaction
Peptide bond properties
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
Amino acid side chains and special cases
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
Lock and key vs induced fit
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
Primary structure
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
Secondary structure
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
Beta pleated sheets
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
Alpha helices
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
Tertiary structure
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
Cystine tertiary structure
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
Bond interaction strengths
Disulphide > Ionic > hydrogen > Van der Waals
Cofactors in a tertiary structure
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
Quaternary structure
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
Types of quaternary structures
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
Protein structure categories
Globular, fibrous and membrane proteins
Globular protein properties
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
Fibrous protein properties
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
Membrane protein properties
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
Protein structure folding
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
Studying protein structure
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
X-ray crystallography
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
Nuclear Magnetic Resonance (NMR)
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
Cyro-Electron Microscopy
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
Resolution
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
Protein structure model types
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)
Cyro-EM tackling Covid-19
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
Human skin functions
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)
Layers in skin structure
Epidermis, dermis and hypodermis (usually in contact with muscle, bone or tissue)
Epidermis
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
Keratinocytes
Cells which make up the epidermis; produce keratins which are important for the barrier function of the epidermis
Epidermis stratification
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
Stratum basale
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)
Stratum spinosum
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
Stratum granulosum
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)
Stratum lucidum
Above stratum granulosum and below stratum corneum; only present in thick skin and is found on the fingertips, palms and soles
Stratum corneum
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
Stratification process
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
Basement membrane and potential problems
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
Rete ridges
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
Pigmentation
Melanocytes make melanosomes which contain melanin
Melanocytes
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
Melanin
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
Langerhan’s cells
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
Dermis
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
Fibroblasts
Produce collages (strength) and elastin (elasticity); long and spindle-like; found in dermis
Layers of dermis
Papillary: high cell density, loose CT (lower density)
Reticular: low cell density, dense CT (high density)
Types of wound types
Superficial, partial thickness and full thickness
Superficial wounds and healing
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
Partial thickness wounds and healing
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)
Full thickness wound; healing and intervention
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
White Island eruption example
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
Engineered skin
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
Engineered skin limitations
No pigmentation, hair follicles, sweat glands or sebaceous glands; lack of function will impact patient outcomes in the long term
