Organ Systems 1 Exam 1 Flashcards

Question

Protein synthesis on the ER

Answer 1

Protein synthesis on the ER • If the protein the ribosome is forming contains an N-terminal ER signal sequence, it will be directed to the ER membrane • ER signal is cleaved off by signal peptidase after protein is inserted into the ER

Answer 2

ER signal sequence on the growing protein directs the ribosome to a translocator that forms a pore through which the protein is inserted. • Signal sequence is cleaved during translation by a peptidase, and the remaining protein is inserted into the lumen of the ER

Answer 3

Protein insertion into rER As proteins are synthesized, they are secreted into the rER lumen In the rER, proteins are modified into glyco- or lipoproteins by resident enzymes. Proteins inserted into rER are then transported within vesicles to form Golgi apparatus

Answer 4

Protein insertion into rER As proteins are synthesized, they are secreted into the rER lumen In the rER, proteins are modified into glyco- or lipoproteins by resident enzymes. Proteins inserted into rER are then transported within vesicles to form Golgi apparatus

Answer 5

GOLGI APPARATUS • Proteins transported into rough endoplasmic reticulum (rER) combine with oligosaccharides and lipids • ER vesicles containing proteins fuse to form Cis Golgi layers • Proteins are sorted into types • Trans Golgi releases vesicles: – Fuse to form lysosomes – Fuse with cell membrane to insert resident membrane proteins – Secrete proteins into into the extracellular space

Answer 6

Protein secretion • Golgi vesicles fuse with cell membrane and release contents by two mechanisms • Unregulated mechanisms – Proteins are inserted continually into the membrane or secreted from the cell – Lipids from Golgi membrane are inserted into cell membrane • Regulated mechanisms – Proteins are secreted from the cell in response to extracellular signal (eg. pancreatic acinar cells)

Answer 7

• Types of proteins synthesized include, eg. – Metabolic enzymes – Histones (proteins around DNA) – Transcription & regulatory factors – Structural proteins • Cell adhesion molecules (CAM) • Receptors • Ion channels • Cytoskeleton – Secreted proteins • Extracellular matrix • Signaling factors

Answer 8

Areas of protein functions we will cover here are: 1. Enzymes – Cellular energy is derived from metabolism – Proteins act as enzymes to facilitate metabolic reactions 2. Differentiation – Proteins are used as internal and external signals to induce cell division plus changes in structure and function

Answer 9

Proteins as Enzymes • All cellular reactions require an activation energy to convert one substrate into another • What about just heating it? • Enzymes lower the activation energ

Answer 10

• Mechanisms that lower activation energy include – proper orientation – using charged groups to alter distribution of charges in substrate – changing substrate shape • Enzymes are very specific; they bind only to particular substrates • Enzymes activity can be affected by – Inhibitors such as drugs and poisons – Activators such as other proteins – Temperature, pH, substrate concentration

Answer 11

Enzymes often need coenzymes or cofactors to facilitate reactions • Coenzymes can be metals or small molecules ATP, Adenosine triphosphate (same as in DNA) • one of many examples of coenzymes • has a high energy bond between the 2nd and 3rd phosphate group used to drive energetically unfavorable reaction

Answer 12

Energy for cell functions, including protein synthesis, comes from foodstuffs. Food is processed in metabolism via two opposing streams of reactions Catabolism • Involves the breakdown of foodstuffs into intermediate products and ultimately CO2 & H2O and heat • Catabolic pathways are energetically favorable and are facilitated by enzymes • The intermediates created are used in synthesis of larger molecules (anabolism) Anabolism: • Synthesis of new molecular structures uses anabolic reactions which are energetically unfavorable. • They require both enzymes & activated carrier molecules (eg. ATP) for energy

Answer 13

• ATP is an activated carrier molecule produced by catabolic reactions: – Energy from of foodstuffs   ADP + P  ATP • ATP temporarily holds its energy so it can be used by anabolic reactions to build molecules: ATP  ADP + P – ATP is a coenzyme that helps enzymes construct patterns and structures with synthetic pathways • Molecular synthesis increases the orderliness in cell organization (negative entropy). – Entropy is a measure of disorderliness or dispersal of useful energy • Development of orderliness and cellular structure is an example of self organization

Answer 14

6. What sort of proteins bind at protein coding genes? What are the promoter and the TATA box? What is the function of RNA polymerase? Is mRNA transcribed at all genes? PROTEIN CODING GENES Protein synthesis begins with assembly of RNA transcription proteins at promoter region, which includes the TATA site Various proteins “dog pile” into a transcription complex and attach to the promoter region of DNA • RNA polymerase • Transcription factors – assemble at promoters • Transcription regulators – activators and suppressors that attach to regulatory genes distant from the promoter and regulate transcription factors

Answer 15

MESSENGER RNA (mRNA) • Transcription complex unravels DNA and uses one strand at a time to transcribe code into mRNA • mRNA is then used to translate the code into protein synthesis

Answer 16

A living cell is an open, self organizing, dissipative structure, far from equilibrium * Open systems permit influx and efflux of energy * In open, self-organizing systems, the internal organization increases in complexity without being guided or managed by an outside source and typically display emergent properties. – Complexity refers to the degree of emergent properties stemming from element interactions, not the total number of elements. * Anabolic syntheses of complex structures or development patterns in gastrulation are emergent properties produced by the interaction of the elements of the system, eg. small molecules, enzymes, genes, etc. * Interactions can be either direct or indirect, eg. if the behavior of one component modifies the environment and thus affects the behavior of another component.

Answer 17

Dissipative structure 2nd Law of Thermodynamics • Dissipative structure: The continuous flow of matter and energy and release of heat (dissipation) allows the system to self organize and exchange entropy with the environment – Formation of structures within the cell creates and maintains the orderliness of the cell (decreases entropy) relative to the outside – Heat released from these synthetic reactions decreases orderliness (increases entropy) outside the cell Second Law of Thermodynamics: Entropy of the universe increases – With heat released from the cell, the increase in order (decreased entropy) internally is more than compensated by a greater decrease in order (increased entropy) externally.

Answer 18

A system that is “far from equilibrium “ contains potential energy, an energy capable of doing work. * This is reflected in the higher level of negative entropy (orderliness) within the cell. * Potential energy in a cell is partly due to the thousand-fold concentration gradient of ATP over ADP, created by metabolism in oxidative phosphorylation – This could produce a significant release of energy for the cell – At equilibrium, where ATP follows its energetically favorable path to ADP, and there are no uphill reactions creating negative entropy, ADP would exceed ATP. And the cell would be dead.

Answer 19

The Bottom Line * The same self-organizing principles seen in cells apply to the whole hierarchy from molecules to organism, within each level and among levels * The interrelations among hierarchical levels produce emergent properties unpredicted by the properties of individual structural levels. This creates greater complexity as the hierarchical range increases. Grizzi F, et al. Theor Biol Med Model 2005, 2:26 * Organismal complexity is contingent on order, i.e. the synthesis of structures and their interrelations that reduces entropy relative to the external world

Answer 20

Regulation of Gene Expression Determining which proteins are translated and how much is synthesized is regulated at many possible steps between RNA transcription and protein translation. Two examples are: • Regulation of mRNA transcription (1) • Regulation of mRNA activity and protein translation (4,5)

Answer 21

Regulation of Gene Transcription & Transcription Factors TRANSCRIPTION FACTORS , TF Proteins that BIND to promoter or regulatory regions of DNA • General (basal) transcription factors (eg. TFIIA) bind to either the promoter region or to the RNA polymerase and regulate its activity – Small number of them; will not be discussed further • Gene regulatory proteins are transcription factors that bind to regulatory genes and alter RNA transcription at the promoter site • I will call all of these Transcription Factors (TF)

Answer 22

Transcription factors TF • Located throughout the cytoplasm and the nucleus • Activated and regulated by various other factors (coregulators) such as local enzymes (JNK/MAPK) and signaling from outside sources

Answer 23

Most transcription factors (TF) are GENE REGULATORY PROTEINS that bind to REGULATORY GENES – (other authors, eg. Alberts et al., call them just regulatory proteins or transcription regulators ) • Regulatory genes do not code for either RNA or protein; they only bind gene regulatory proteins • TF are translated from 10% of the 25,000 genes that encode proteins • TF Influence transcription rate of coding genes by regulating the following: – Help position RNA polymerase – Separate DNA strands to permit transcription – Release RNA polymerase from promoter (TATA region) once transcription begins • Regulatory genes provide fine control of differentiation and morphogenesis.

Answer 24

• DNA looping permits contact between regulatory TFs and other TFs nearer to the promoter • Regulatory TF also act as DNA bending proteins

Answer 25

Regulatory Genes: Enhancer Silencer Regulatory TF: activators repressors

Answer 26

Competition among activator and repressor regulatory proteins provides flexibility in both the direction (activate, suppress) and the overall degree of gene expression

Answer 27

SOURCE OF TRANSCRIPTION FACTORS Homeotic genes – encode TF that generate the body plan and organ development; several subtypes with specific functions Hox genes encode TF that determine development of body segmentation – Homeobox genes – subset of hox genes that encodes the homeodomain sequence within TF protein that binds to regulatory genes in order to regulate patterns of gene expression PAX6 produces TF for development of the eye Other homeotic genes include Sox, POU, Lim, T-Box, etc – all of which produce TF

Answer 28

4. What is chromatin? What are histones and histone tails? What are nucleosomes? What is the difference between euchromatin and heterochromatin? 1. CHROMATIN REMODELING AND HISTONE MODIFICATION Histone alteration regulates access of transcription factors and regulators to target genes Histone structure • Most DNA is bound to histones and inaccessible to transcription and regulatory factors • Nucleosomes consist of DNA wrapped around histone octomers in two forms: o Euchromatin o Heterochromatin • TFs can reversibly interconvert eu- and heterochromatin

Answer 29

5. What is the difference between chromatin remodeling and histone modification? What is the transcriptional impact of single acetyl or methyl groups attached to histone tails? What are the names of the enzymes that do this? In order to open the chromatin for access to DNA, transcription factors need to: * Open chromatin by chromatin remodeling * Label and subsequently identify which genes to bind to by modifying histone proteins

Answer 30

CHROMATIN REMODELING Regulation of DNA-histone binding • DNA-histone coupling and decoupling can occur spontaneously due to instability • DNA-binding proteins (chromatin remodeling complex) separate DNA from histones • TFs are accompanied by chromatin remodeling complexes (eg. SWI-SNF) that loosen DNA from histone • Thus, unwinding histones and binding TFs to DNA occur in the same step

Answer 31

5. What is the difference between chromatin remodeling and histone modification? What is the transcriptional impact of single acetyl or methyl groups attached to histone tails? What are the names of the enzymes that do this? \>\>Histone Modification HISTONE MODIFICATION • methyl and acetyl groups bind to histone “tails” OPEN CHROMATIN * Acetylation by histone acetyl transferase (HAT) * Trimethylation by methyl transferase * Forms euchromatin and opens gene to TF binding CLOSE CHROMATIN * Methylation by methyl transferase * Deacetylation by histone deacetylase (HDAC) * Forms heterochromatin, closing the gene.

Answer 32

5. What is the difference between chromatin remodeling and histone modification? What is the transcriptional impact of single acetyl or methyl groups attached to histone tails? What are the names of the enzymes that do this? \>\>Histone Modification \>Names of enzymes that do this! Histone acetylation is directed by transcription factors * In development, morphogens such as growth factors first recruit transcription factors (TF) in a large population of cells. * TF approaches a gene combined with histone acetyl transferase (HAT) and other proteins – TF-HAT open the gene for transcription – HAT reconfigures the genes into a stable form by adding epigenetic acetyl tags to histone tails • Type of epigenetic tag that marks which genes are available fro transcription

Answer 33

2. DNA METHYLATION CpG islands = DNA methylation site • Repeated cytosine-phosphate- guanosine pairs • Occurs in 60% of gene promoters DNA Methylation • Cytosines are methylated by DNA methyltransferases (DNMTs) • Usually SUPPRESSES gene expression (but can sometimes activate them) • DNA methylation patterns essential for mammalian development and normal functioning in adulthood. Disturbed methylation sequences can lead to chronic illness, eg. cancer DNA methylation is not universal * methylation-resistant CGIs bind TFs that prevent methylation of house keeping genes that must remain open * methylation-prone CGIs bind tissue– specific transcription factors – associated with development, differentiation and cell communication – facilitates histone deacetylation by HDACV (histone deacetylase) – lead to formation of heterochromatin

Answer 34

9. How does miRNA impact protein synthesis? Is it at the transcriptional or translational level? Micro RNA (miRNA) see mRNA degradation control (4) on first slide • • Reduces translation of mRNA into proteins by degrading mRNA or blocking translation process TF family determines which miRNAs are transcribed and hence determines which proteins are diminished. Lack of miRNA will permit more expression of another type of protein (yin-yang). FYI: Several miRNAs are directly involved in lung, breast, brain, liver, colon cancer, and leukemia * miRNAs operate by either cleaving mRNA or inhibiting translation in concert with RISC (RNA-induced silencing complex). * Overexpression of miRNAs—for instance, by amplification of the miRNA-encoding locus—could decrease expression of the target, such as a tumor suppressor gene. * Underexpression of miRNAs—for instance, by deletion or methylation of the miRNA locus—could result in increased expression of a target such as an oncogene.

Answer 35

7. Describe DNA methylation in terms of: where does it occur? What enzymes are involved? What impact it has on gene transcription? How does it compare to other factors in determining the stability of gene transcription? 2. DNA METHYLATION CpG islands = DNA methylation site • Repeated cytosine-phosphate- guanosine pairs • Occurs in 60% of gene promoters DNA Methylation • Cytosines are methylated by DNA methyltransferases (DNMTs) • Usually SUPPRESSES gene expression (but can sometimes activate them) • DNA methylation patterns essential for mammalian development and normal functioning in adulthood. Disturbed methylation sequences can lead to chronic illness, eg. cancer

Answer 36

8. How are the epigenetic markers maintained through the cell cycle? What is cell memory? Maintenance of the epigenome during cell division • Cell division propagates epigenetic code by maintaining the epigenetic tags on DNA and histones. Cell memory - Maintenance of epigenetic code Maintenance of the Epigenetic code * Identifies which genes will be expressed and what type of a cell it will be. * How are epigenetic tags maintained across many generations of cell division? Cell cycle of mitosis * GO, the resting state, can be interrupted by a stimulus that elicits cell division * G1, the cell manufactures all the proteins and RNA to produce a new cell and a duplicate set of DNA * S, duplication of the DNA takes 6-8 hours. This is also where epigenetic codes are duplicated • G2, the cell manufactures all the structural elements that the duplicate cell will need.

Answer 37

2. What is meant by asymmetric division? Asymmetric division * Earliest developmental stages: asymmetric distributions of transcription factors in the cytoplasm * During mitosis, TFs are divided unequally and produces cells with different patterns of gene expression

Answer 38

3. How do signaling factors induce differentiation between two offspring cell? Induction by signaling factors * Signaling factors specify patterns of gene expression of TF and epigenetic markers * Concentration gradients of signaling factors determine the degree of differentiation * Dominant mechanism of differentiation throughout development * Positive feedback interaction between cells or intracellular transcription factors enhances difference between cells – lateral inhibition

Answer 39

5. Describe what is meant by: signaling factor, receptor, signal transduction. OVERVIEW OF SIGNALING FACTORS AND THE CELL SIGNALING SYSTEM Signaling factors • Include: growth factors, peptides (eg. insulin, glucagon) & proteins, epinephrine, acetylcholine, histamine, ATP, steroid and thyroid hormones, prostaglandins, nitric oxide (NO) Receptors • Membrane bound or intracellular proteins that bind signaling factors Signal transduction • • Chemical messages conveyed from receptors regulate TF activity on gene expression Changes in gene expression regulate level of cell activity – Up regulation: increased cell function – Down regulation: decreased cell function

Answer 40

Be able to recognize the major families of growth factors. Growth factor is a specific type of signaling factor necessary for cell growth and development Families of growth factors • TGF (transforming growth factor) – tissue regeneration, cell differentiation, embryonic development and regulation of the immune system • FGF (fibroblast growth factor) – Development of mesoderm , limb and neural development; regulation of angiogenesis, keratinocyte organization, and wound healing in adult tissue • Wnt – wingless types • Hedgehogs (Sonic, desert, Indian, tiggy-winkle) – Regulates embryonic development of digits on limbs and the brain, plus cell division of adult stem cells

Answer 41

8. Be able to give a general and brief description of how miRNA interacts with epigenetic markers of DNA and histones. Role of miRNA in differentiation • Recall how TF families determine the types of miRNA transcribed and how they constrain the number of mRNA’s that will be translated into protein • miRNAs facilitate transitions in development by reducing protein production from mRNAs inherited from an earlier developmental stage **miRNA and epigenetic mechanisms form a mutually inhibiting control system** **• miRNAs control the relative expression of DNA methyltransferases and histone deacetylases thereby determining the amount of gene product** **• DNA methylation and histone modification in turn regulate the expression of miRNAs. • Disruption of the circuit can contribute to various disease processes.**

Answer 42

9. What is morphogenesis? Be able to recognize the different ways that cells interact to generate body forms and structures. What is lateral inhibition? MORPHOGENESIS Development of tissue/organ form and shape that involves 1. Morphogens: signaling factors that act on a population of cells 2. Changes in spatial distribution of cells (i.e. environment) due to morphogenetic mechanisms including: – Lateral inhibition – Differential adhesion – Cell polarity – Morphogen gradient – Segmentation Morphogenesis involves a change in scale from individual cells to multicellular populations LATERAL INHIBITION * Early differentiating cells signal to adjacent cells to become something different * Asymmetric division creates a lead cell which in turn inhibits differentiation of neighboring cells by the Notch-Delta pathway * Process of self organization that produces heterogeneous cell populations in structural development as well as functional specialization in post natal life

Answer 43

9. What is morphogenesis? Be able to recognize the different ways that cells interact to generate body forms and structures. What is lateral inhibition? MORPHOGENESIS Development of tissue/organ form and shape that involves 1. Morphogens: signaling factors that act on a population of cells 2. Changes in spatial distribution of cells (i.e. environment) due to morphogenetic mechanisms including: – Lateral inhibition – Differential adhesion – Cell polarity – Morphogen gradient – Segmentation Morphogenesis involves a change in scale from individual cells to multicellular populations LATERAL INHIBITION * Early differentiating cells signal to adjacent cells to become something different * Asymmetric division creates a lead cell which in turn inhibits differentiation of neighboring cells by the Notch-Delta pathway * Process of self organization that produces heterogeneous cell populations in structural development as well as functional specialization in post natal life

Answer 44

9. What is morphogenesis? Be able to recognize the different ways that cells interact to generate body forms and structures. What is lateral inhibition? How do morphogen concentration gradients impact pattern formation? ## Footnote MORPHOGEN CONCENTRATION GRADIENTS • • • Signaling factors spread by diffusion Signal gradient determines the degree of impact on the target cell Mutual inhibition

Answer 45

1. Where does fertilization occur? Where does implantation occur? What stage implants in the uterus? Fertilization occurs in the uterine tube. The blastocyst begins in implant in the uterine endometrium. FIRST WEEK • Fertilization • Cleavage • Morula • Blastula • Cavity (blastocoel): created by secretion of Na+ & water via Na-/K+ ATP-ase • Blastocyst = blastula plus – Inner cell mass (embryoblast) – Trophoblast surface

Answer 46

2. What is an ectopic implantation and where do they occur? An ectopic pregnancy, or eccysis, is a complication of pregnancy in which the embryo implants outside the uterine cavity.[1] With rare exceptions, ectopic pregnancies are not viable. Furthermore, they are dangerous for the mother, since internal haemorrhage is a life-threatening complication. Most ectopic pregnancies occur in the Fallopian tube (so-called tubal pregnancies), but implantation can also occur in the cervix, ovaries, andabdomen. An ectopic pregnancy is a potential medical emergency, and, if not treated properly, can lead to death.

Answer 47

3. What are the characteristics of the zygote, morula, blastula, blastocyst? And where are they found? Zygote: A zygote (from Greek ζυγωτός zygōtos "joined" or "yoked", from ζυγοῦνzygoun "to join" or "to yoke"),[1] is **the initial cell formed when two gametecells are joined by means of sexual reproduction**. In multicellular organisms, it is the earliest developmental stage of the embryo. In single-celled organisms, the zygote divides to produce offspring, usually through mitosis, the process of cell division. Location: Uterine tube Morula: A morula (Latin, morum: mulberry) is an embryo at an early stage ofembryonic development, consisting of cells (called blastomeres) in a solid ball contained within the zona pellucida.[1]. Location: uterine tube Blastula: The blastula (from Greek βλαστός (blastos), meaning "sprout") is a hollow sphere of cells, referred to as blastomeres, surrounding an inner fluid-filled cavity called the blastocoele formed during an early stage of embryonic development in animals.[1] Embryo development begins with a sperm fertilizing an egg to become a zygote which undergoes many cleavages to develop into a ball of cells called a morula. Only when the blastocoele is formed does the early embryo become a blastula. The blastula precedes the formation of the gastrula in which the germ layers of the embryo form.[2]. Location: Uterine cavity Blastocyst: The blastocyst is a structure formed in the early development of mammals. It possesses an inner cell mass (ICM) which subsequently forms the embryo. The outer layer of the blastocyst consists of cells collectively called thetrophoblast. This layer surrounds the inner cell mass and a fluid-filled cavity known as the blastocoel. The trophoblast gives rise to the placenta. In humans, blastocyst formation begins about 5 days after fertilization, when a fluid-filled cavity opens up in the morula, a ball consisting of a few dozen cells. The blastocyst has a diameter of about 0.1-0.2 mm and comprises 200-300 cells following rapid cleavage (cell division). After about 1 day, the blastocyst embeds itself into the endometrium of the uterine wall where it will undergo later developmental processes, including gastrulation.

Answer 48

4. Describe the epigenetic changes that occur in the morula and blastula and what is their significance? What is the significance of de novo methylation after implantation? FIRST WEEK • Fertilization • Cleavage • Morula • Blastula • Cavity (blastocoel): created by secretion of Na+ & water via Na-/K+ ATP-ase • Blastocyst = blastula plus – Inner cell mass (embryoblast) – Trophoblast surface Blastocyst formation[edit] The morula, which precedes the blastocyst, is an early embryo composed of 16 undifferentiated cells. Shortly following the morula's entry into the uterus from the Fallopian tube, the morula becomes the blastocyst through cellular differentiation and cavitation. The morula's cells differentiate into two types: an inner cell mass growing on the interior of the blastocoel and trophoblast cells growing on the exterior.[2] The animal pole refers to the side of the blastocyst where the ICM resides, while the vegetal pole is on the opposite side. Cavitation is the process by which a fluid cavity forms inside the embryo. The trophoblast cells pump sodium ions into the center of the embryo, which causes water to enter through osmosis. This forms an internal fluid-filled cavity called the blastocoel. This distinguishable blastocoel cavity in addition to cellular specification are both hallmark identities of the blastocyst.[3] Implantation[edit] Implantation is critical to the survival and development of the early embryo. It establishes a connection between the mother and the early embryo which will continue through the remainder of the pregnancy. Implantation is made possible through structural changes in both the blastocyst and endometrial wall.[4] The zona pellucida surrounding the blastocyst breaches, referred to as hatching. This removes the constraint on the physical size of the embryonic mass and exposes the outer cells of the blastocyst to the interior of the uterus. Furthermore, hormonal changes in the mother, specifically a peak in luteinizing hormone (LH) prepares the endometrium to receive the blastocyst and envelope it. Once bound to the extracellular matrix of the endometrium, trophoblast cells secrete enzymes and other factors to embed the blastocyst into the uterine wall. The enzymes released degrade the endometrial lining, while autocrine growth factors such as human chorionic gonadotropin(hCG) and insulin-like growth factor (IGF) allow the blastocyst to further invade the endometrium.[5] Implantation in the uterine wall allows for the next step in embryogenesis, gastrulation, which includes formation of the placenta from trophoblastic cells and differentiation of the ICM into the amniotic sac and epiblast.

Answer 49

4. Describe the epigenetic changes that occur in the morula and blastula and what is their significance? What is the significance of de novo methylation after implantation? Embryological DNA methylation and “Epigenetic reprogramming” begin in early stages • Unmethylated primordial germ cell DNA become methylated as cells develop postnatally into sperm or ova (gametogenesis) • After fertilization, general demethylation of the maternal and paternal genomes continues until implantation • After implantation, de novo DNA methylation of specific genes that epigenetically determines cell lineage = reprogramming – How do they know this? • Transgenerational epigenetic inheritance via “germ line differentially methylated regions” (gDMRs) = imprinting from parents

Answer 50

5. Describe how the epiblast and hypoblast arise. How are the amniotic cavity and yolk sac formed? SECOND WEEK Inner cell mass divides into two epithelial layers that form spaces • Epiblast – amniotic cavity • Hypoblast (endoblast) – yolk sac – primary and secondary Trophoblast -\> placenta Cavities: • Amniotic • Yolk sac Becoming bilaminar[edit] The zygote first transformed into a morula through cleavage and then more divisions lead to a blastocyst that consisted of just a trophoblast, and an embryoblast. By the end of the first week, the embryoblast has begun separating into two layers: the epiblast and hypoblast also called the primitive endoderm. At the embryonic pole of the blastocyst, the amniotic cavityfinds a home between the epiblast and the hypoblast. The epiblast stretches to surround the cavity very quickly and this layer of the epiblast becomes known as the amnion, which is one of the four extraembryonic membranes. The rest of thehypoblast and epiblast, not including the amnion, is what contributes to the bilaminar embryonic disc (bilaminar blastoderm/blastocyst), which sits between the amniotic cavity and the blastocyst cavity. The embryo proper and extramembryonic membranes are later derived from the embryonic disc.[3] Establishment of the amniotic cavity[edit] Beginning on day 8, the amniotic cavity is the first new cavity to form during the second week of development.[3] Fluid collects between the epiblast and the hypoblast, which splits the epiblast into two portions. The layer at the embryonic pole grows around the amniotic cavity, creating a barrier from the cytotrophoblast. This becomes known as the amnion, which is one of the four extraembyonic membranes and the cells it comprises are referred to as amnioblasts.[5] Although, theamniotic cavity starts off small it eventually grows to be larger than the blastocyst and by week 8, the whole embryo is encompassed by the amnion.[3] Yolk sac during development[edit] Like the amnion, the yolk sac is simply an extraembryonic membrane that surrounds a cavity. Formation of the definitiveyolk sac happens after the extraembryonic mesoderm splits, and it becomes a double layered structure with hypoblast-derived endoderm on the inside and mesoderm surrounding the outside. The definitive yolk sac contributes greatly to the embryo during the 4th week of development and it executes critical functions for the embryo. One of which being the formation of blood, or hematopoiesis. Also, Primordial germ cells are first found in the wall of the yolk sac. After the 4th week of development, the growing embryonic disc becomes a great deal larger than the yolk sac and its presence usually dies out before birth. However, seldom will the yolk sac remain as deviation of the digestive tract named Meckel's diverticulum.[3]

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6. What is the fate of the epiblast? The hypoblast? Inner cell mass divides into two epithelial layers that form spaces • Epiblast – amniotic cavity • Hypoblast (endoblast) – yolk sac – primary and secondary Trophoblast -\> placenta Cavities: • Amniotic • Yolk sac THIRD WEEK • Gastrulation • Notochord formation • Neurulation GASTRULATION is the formation of the three germ layers • Midline epiblast cells differentiate, separate, migrate and form the mesoderm and endoderm layers Epiblast cells during gastrulation[edit] The third week of development and the formation of the primitive streak sparks the beginning of gastrulation.[3] Gastrulationis when the three germ cell layers develop as well as an organism’s body plan.[6] During gastrulation, cells of the epiblast, a layer of the bilaminar blastocyst, migrate towards the primitive streak, enter it, and then move apart from it through a process called ingression.[3] Definitive endoderm development[edit] On day 16, epiblast cells that are next to the primitive streak experience epithelial-to-mesenchymal transformation as they ingress through the primitive streak. The first wave of epiblast cells takes over the hypoblast, which slowly becomes replaced by new cells that eventually constitute the definitive endoderm. The definitive endoderm is what makes the lining of the gut and other associated gut structures.[3] -- Overview[edit] In amniotes, gastrulation occurs in the following sequence: (1) the embryo becomes asymmetric; (2) the primitive streakforms; (3) cells from the epiblast at the primitive streak undergo an epithelial to mesenchymal transition and ingress at theprimitive streak to form the germ layers.[4]

Answer 52

7. Describe how the three germ layers are formed in gastrulation THIRD WEEK • Gastrulation • Notochord formation • Neurulation GASTRULATION is the formation of the three germ layers • Midline epiblast cells differentiate, separate, migrate and form the mesoderm and endoderm layers -- Endoderm and mesoderm formed in two phases • Formation of endoderm and fate of hypoblast • Formation of mesoderm Remaining epiblast becomes ectoderm and notochord Three layer embryo : ECTODERM MESODERM ENDODERM

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8. What is the epithelial-mesenchymal transition? TISSUE DIFFERENTIATION BY EMT AND ITS REVERSIBILITY • Mesenchymal cells migrate away from epiblast and re-aggregate into secondary epithelium • Secondary epithelium either remains epithelium or differentiates into various types of CT via EMT. Transcription factors are indicated. • In adult stage, secondary epithelia can transform into tumors that undergo EMT to metastasize. Also, renal tubules can change from epithelium into CT to generate FIBROSIS of the kidney.TISSUE DIFFERENTIATION BY EMT AND ITS REVERSIBILITY • Mesenchymal cells migrate away from epiblast and re-aggregate into secondary epithelium • Secondary epithelium either remains epithelium or differentiates into various types of CT via EMT. Transcription factors are indicated. • In adult stage, secondary epithelia can transform into tumors that undergo EMT to metastasize. Also, renal tubules can change from epithelium into CT to generate FIBROSIS of the kidney.

Answer 54

9. Be able to recognize which general structures arise from the three germ layers. ECTODERM gives rise to brain and external layer of body, the skin • Central nervous system, CNS – Brain & spinal cord; glia • Neural crest – Peripheral nervous system, PNS – Dermal pigmented cells – Bone & CT of face/neck • Epidermis, hair, nails, teeth enamel, etc MESODERM gives rise to middle level structures such as muscle & connective tissue • Connective Tissue: bone, cartilage, CT, blood • Muscle: striate, smooth, cardiac • Glands: kidney, gonads, adrenal cortex • Pleura, pericardium, peritoneum ENDODERM gives rise to the deep level structures of the gut tube and its derivatives • GI, Liver, pancreas • Lungs • Bladder/urethra

Answer 55

10. Where is the notochord and how does it impact the development of the nervous system? What signaling factor is involved? Notochord • Forms within mesoderm • Induces formation of CNS and somites. • Differentiation into nucleus pulposus Sonic hedgehog (Shh) • Notochord signaling molecule that activates TF in neural plate • Morphogenetic cylinder formation • Contraction of actin filaments in apical region of polarized cell

Answer 56

11. What are the morphogenetic steps that generate the cylinder that will form the central nervous system? What are some of the peculiar fates of neural crest cells? ECTODERM gives rise to brain and external layer of body, the skin • Central nervous system, CNS – Brain & spinal cord; glia • Neural crest – Peripheral nervous system, PNS – Dermal pigmented cells – Bone & CT of face/neck • Epidermis, hair, nails, teeth enamel, etc -- Neurulation • Neural tube created by fusion of neural folds, bordering the neural groove. • Neural crest pluripotent cells migrate Neural crest cells migrate into mesoderm to form: • Peripheral nervous system: sensory neurons, glia, autonomic postganglionic cells including adrenal medulla and enteric nervous system in the gut. • Pigmented skin cells, skull bones, etc

Answer 57

11. What are the morphogenetic steps that generate the cylinder that will form the central nervous system? What are some of the peculiar fates of neural crest cells? II Notochord • Forms within mesoderm • Induces formation of CNS and somites. • Differentiation into nucleus pulposus

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13. Describe how food deprivation during early embryogenesis can impact levels of gene methylation, such as IGF2? Would folate supplementation be a good idea in early pregnancy if you suspect a mother was not eating right? Epigenetic impact of the Dutch Hunger Winter • Individuals who were prenatally exposed to famine during the Dutch Hunger Winter in 1944–45 had, 60 years later, hypomethylation of IGF2 (a maternally imprinted gene implicated in growth and development) compared with their unexposed, same-sex siblings. • The association was specific for periconceptional (but not late gestational) exposure, thus very early development is a crucial period for establishing epigenetic marks that persist throughout life. • F1 famine exposure in utero was associated with increased F2 neonatal adiposity and poor health in later life implying that the increase in chronic disease after famine exposure in utero is not limited to the F1 generation but persists in the F2 generation. A typical daily ration distributed by the local authorities in the famine-struck western part of the Netherlands consisted of two slices of bread, two potatoes and piece of sugar beet. The newspaper in the background announces the closure of the soup kitchens. Hypomethylation may be related to a deficiency in methyl donors, such as the amino acid methionine, folate, etc. • In sheep, offspring with periconceptional B vitamin and methionine restricted diet, 4% of 1,400 CpG sites had altered methylation and numerous phenotypic alterations, such as increased body mass, altered immune responses to antigenic challenge, insulin resistance, and elevated blood pressure. Predictive adaptive response • Poor maternal nutrition may signal to the fetus that nutrients are scarce; the fetus may then adapt its metabolism to conserve energy demands, increase its propensity to store fat and accelerate puberty. • If the epigenetic prediction is correct (poor nutrition), the metabolism of the organism will be matched to the environment and have a low risk of disease. If the prediction is incorrect and the offspring is mismatched with the environment (over nutrition), then it is at risk of metabolic disease: Insulin resistance, central fat deposition, etc. This phenotype is advantageous in a food deprived environment, because it conserves resources via reduced growth, and diverts substrate from metabolism to fat deposition to provide energy stores. The phenotype is highly appropriate to any mammal with restricted food supply See Gluckman and Hanson on PubMed for more studies, esp Adaptive value of epigenetically transmitted familial susceptibility to cardiovascular disease, obesity and other non-communicable diseases

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What are the "regulatory proteins"? Examples include Activators & Repressors (and they bind to regulatory genes :)

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How do signaling factors induce differentiation between 2 offspring cell? Signaling factors differentiate between 2 offspring cells since they create different TFs that create different genes.

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How do TF ensure that they are the primary or dominant factors that determine which genes will be expressed? TFs go down the DNA strand and recognize/detect where coding genes are.

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6. What are the primary pathways the signaling factors use in reaching their target cells? Which ones are more likely to be used in an embryo consisting of only a few hundred cells? Signaling factors communicate from one cell to another in various ways. Some examples: 1. Endocrine: transport through circulatory system • peptides (eg. insulin, glucagon) & proteins, epinephrine, steroid and thyroid hormones 2. Paracrine: diffuse from cell to cell through the extracellular fluid • Growth factors (FGF), histamine, nitric oxide (NO), ATP 3. Neuronal: move across synapse • Acetylcholine, norepinephrine 4. Contact dependent: cell surface molecule (signaling factor) binds to receptor molecule on adjacent cell • Delta

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9. What is morphogenesis? Be able to recognize the different ways that cells interact to generate body forms and structures. What is lateral inhibition? How do morphogen concentration gradients impact pattern formation? Even if it's the same signaling factor, the amount of signaling factor can determine what muscle or organ will be formed.

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12. Describe what happens to the following during the folding of the embryo: amniotic cavity, yolk sac, intraembryonic coelom. The amniotic cavity gets pulled to the sides, stretched out and then eventually disappears. The intraembryonic coelem becomes the bursae and allows the guts to rub against each other, and the yolk sack becomes the lining of the digestive track.

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1. Briefly describe the differences among the four types of tissues. Despite the body’s complexity, there are only 4 type of tissues: • Epithelium • Interconnected cells • Functions • Connective tissue (CT) • Constituents: cells, matrix (ground substance & collagen) • Types & Functions • Nerve • Cell types • Communication • Muscle • Function & types • Similarity to nerve

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2. Compare and contrast the properties of the following cell junctions: occluding, adhering, communicating TIGHT (or OCCLUDING) JUNCTIONS (Zonula occludens) • Nearest to apex • Diffusion barrier: impermeable to large molecules, variably permeable to water and ions • Maintains polarity of cell constituents • Claudin determines permeability to water and other molecules ADHERING JUNCTIONS - Zonula adherens and macula adherens, i.e. DESMOSOME • Interconnect epithelial cells • Cadherin: • Adhesion between cells; resists physical disruption • Connect to intracellular actin; intracellular communication GAP (COMMUNICATING) JUNCTIONS • Channels permit direct passage of signaling molecules and ionic current between cells • Connexons

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3. What is the basement membrane and how does it differ from basal lamina? Where do you find basement membranes? Basal Domain BASEMENT MEMBRANE – Protein filled layer between epithelium and CT • Basal lamina • thin, acellular layer of proteins eg. integrin, laminin (a glycoprotein) secreted by the epithelial cells • forms flexible layer that supports overlying epithelium • barrier for transport of substances between blood and cells • Reticular lamina • layer of collagens secreted by underlying CT • connects epithelium and the basal lamina to underlying CT B

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4. What are microvilli and how do they compare to cilia? What is the role of cilia in respiratory epithelium? APICAL DOMAIN Microvilli • Brush border • Increase surface area; actin interacts with myosin II to adjust microvilli length and rigidity Stereocilia (not shown) • Microvilli of unusual length found in only a few tissues: epididymis, ductus deferens, sensory cells of ear Cilia • Microtubules derived from basal body • Movement: dyneins form cross bridges on microtubules, bending the cilia

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5. What are the types and some examples of simple epithelium? What is pseudostratified epithelium? EPITHELIAL TYPES Simple & stratified SIMPLE 1. Simple squamous epithelium 2. Simple cuboidal epithelium 3. Simple columnar epithelium 4. Pseudostratified • Appears multiply layered, but is a single layer of cells. • Ciliated and non-ciliated forms EX: Respiratory epithelium is pseudostratified

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6. What are the types and some examples of stratified epithelium? STRATIFIED EPITHELIUM 1. Stratified squamous • Keratinized, eg. skin 2. Stratified squamous • non-keratinized • Eg. lining of mouth, esophagus 3. Stratified cuboidal • Glandular ducts, eg sweat gland 4. Stratified columnar • Glandular ducts, eg mucus gland duct in tongue 5. Transitional • Expandable type of stratified • bladder

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7. What are the basic constituents of CT? What are the types of “proper” CT? CONNECTIVE TISSUE, CT Cells Extracellular matrix Fibers Ground substance CT CELLS Those derived from mesenchyme: • Fibroblasts • Adipocytes • Mesenchymal stem cells • Some remain in adult tissue to become myofibroblasts during wound healing. They have characteristics of both fibroblast and smooth muscle cell types and can contract EXTRACELLULAR MATRIX, ECM • Fibers • Ground Substance COLLAGEN FIBERS • Flexible, strong glycoprotein fibers • Helical α chains form collagen fibrils • CT turnover, collagen is degraded by • Matrix metalloproteinases (MMPs) • Phagocytosis by fibroblasts and macrophages CONNECTIVE TISSUE TYPES • CT proper  Loose (areolar) CT  Reticular, elastic  Adipose  Dense - regular & irregular • Special CT (seen in other lectures)  Blood  Cartilage  Bone

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8. Compare loose with dense CT. Compare regular and irregular CT. Loose CT • Contains various cells, type 1 collagen fibers, abundant ground substance, deep to skin, epithelia • Viscous gel-like consistency • Diffusion of O2 , CO2 and nutrients Dense CT • Higher concentration of type I collagen compared to loose CT Irregular dense CT: • collagen bundles are oriented in various directions, eg. submucosa in the GI tract Regular dense CT Picture: Left is irregular, right is regular) • collagen bundles are densely arranged in parallel, eg. tendons, ligaments

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9. What type of cells are found in CT? What do they do? • Connective tissue (CT) • Constituents: cells, matrix (ground substance & collagen) • Types & Functions CT CELLS Those derived from mesenchyme: • Fibroblasts • Adipocytes • Mesenchymal stem cells • Some remain in adult tissue to become myofibroblasts during wound healing. They have characteristics of both fibroblast and smooth muscle cell types and can contract

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10. In the ECM, what is collagen? What is elastic CT and how does it compare to loose and reticular CT? EXTRACELLULAR MATRIX, ECM • Fibers • Ground Substance COLLAGEN FIBERS • Flexible, strong glycoprotein fibers • Helical α chains form collagen fibrils • CT turnover, collagen is degraded by • Matrix metalloproteinases (MMPs) • Phagocytosis by fibroblasts and macrophages Elasticity • Elastic fibers enable many types of CT to snap back with stretch • Hydrophobic elastin uncoils and recoils with stretch up to 1.5 times their length • In matrix of CT (skin, nuchal lig), cartilage (ear, nose, larynx, auditory tube), bronchial tree, blood vessel smooth muscle • Elastic fibers function without replacement throughout lifetime • Half-lives of types I and II collagen in human skin, articular cartilage and intervertebral disc are 15, 95 and 117 years • Elastin degraded MMP in age-related inflammatory conditions: emphysema, atherosclerosis, excess UV exposure, etc Reticular CT • Type III collagen fibers: thin, unbundled, flexibility • Holds together the parenchyma of various organs: liver, kidney, spleen, lymph nodes, bone marrow and adipose tissue Loose CT • Contains various cells, type 1 collagen fibers, abundant ground substance, deep to skin, epithelia • Viscous gel-like consistency • Diffusion of O2 , CO2 and nutrients

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11. Describe the constituents of ground substance. What are glycosaminoglycans? Proteoglycans? What is hyaluronic acid? What does it do? GROUND SUBSTANCE • Viscous, high water content, • Consists of mainly: Glycosaminoglycans GAG • Polysaccharide chains: attract water • Proteoglycans: GAG attached to proteins • Transported into the ECM • Repeating disaccharides of different types yield various forms of GAG: chondroitin, dermatan, etc Proteoglycans attach to: • Collagen fibers • Hyaluronan • Cell membranes Hyaluronan (hyaluronic acid) • Large GAG formed on the exterior surface of the cell membrane • Attracts water to form hydrated gel • Provides ECM rigidity to resist compression and provide structural integrity of matrix