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Intro Microanatomy 9/29/2011 10:01:00 AM
1) Name the components that make up cells, tissues and organs.
Cellsare comprised of three domains:
Nucleus Intracisternal (inside organelles) Cytosol (Cytoplasm contains organelles Intracisternal space)
o Contains cytoskeletal elementsTissues: Cells + ECM(Extracellular Matrix)
4 Types of Tissueo Epithelial:closely linked cells form a liningo Connective Tissue: Supportive tissue can be flexible or rigid
(cartilage vs bone)
o Nervous Tissue: Specialized for conductiono Contractile Tissue:Muscles with contractile protein fibers
Organs:Comprised of Multiple Tissue Types (Usually all 4)
Complex structureOrgan Systems
2) List common features of cells
- Domains(i.e Organelles) have specific functions and are Separated by
Membranes
Know:
(1)nucleolus(2) nucleus
(3)ribosomes
(4)vesicle
(5) roughendoplasmic reticulum(ER)
(6)Golgi apparatus
(7)cytoskeleton
(8) smooth ER
(9)mitochondria
(10)vacuole
(11)cytosol
- Different from Inclusions which are substances stored in cell (Glycogen,
Fat)
http://en.wikipedia.org/wiki/Ribosomeshttp://en.wikipedia.org/wiki/Ribosomeshttp://en.wikipedia.org/wiki/Ribosomeshttp://en.wikipedia.org/wiki/Vesicle_(biology)http://en.wikipedia.org/wiki/Vesicle_(biology)http://en.wikipedia.org/wiki/Vesicle_(biology)http://en.wikipedia.org/wiki/Endoplasmic_reticulumhttp://en.wikipedia.org/wiki/Endoplasmic_reticulumhttp://en.wikipedia.org/wiki/Endoplasmic_reticulumhttp://en.wikipedia.org/wiki/Golgi_apparatushttp://en.wikipedia.org/wiki/Golgi_apparatushttp://en.wikipedia.org/wiki/Golgi_apparatushttp://en.wikipedia.org/wiki/Cytoskeletonhttp://en.wikipedia.org/wiki/Cytoskeletonhttp://en.wikipedia.org/wiki/Cytoskeletonhttp://en.wikipedia.org/wiki/Mitochondrionhttp://en.wikipedia.org/wiki/Mitochondrionhttp://en.wikipedia.org/wiki/Mitochondrionhttp://en.wikipedia.org/wiki/Vacuolehttp://en.wikipedia.org/wiki/Vacuolehttp://en.wikipedia.org/wiki/Vacuolehttp://en.wikipedia.org/wiki/Cytosolhttp://en.wikipedia.org/wiki/Cytosolhttp://en.wikipedia.org/wiki/Cytosolhttp://en.wikipedia.org/wiki/Cytosolhttp://en.wikipedia.org/wiki/Vacuolehttp://en.wikipedia.org/wiki/Mitochondrionhttp://en.wikipedia.org/wiki/Cytoskeletonhttp://en.wikipedia.org/wiki/Golgi_apparatushttp://en.wikipedia.org/wiki/Endoplasmic_reticulumhttp://en.wikipedia.org/wiki/Vesicle_(biology)http://en.wikipedia.org/wiki/Ribosomes7/27/2019 Microanatomy -
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Membranes:Phospholipid Bi-layer establishes compartmentalization /
domains
Restricts / Regulates movement in and out of cell Fluid-Mosaic Model: Membrane has lipid and protein components
o Small polar or charged molecules move via Protein MediatedTransport
o Large Molecules move through vacuoles through Endocytosisand Exocytosis
o Integral Membrane Proteins: contain hydrophobic domainsare require detergent to remove from membrane
o Peripheral Membrane Proteins: Do not completelypenetrate bi-layer and are only temporarily associated with
membrane
Glycoconjugates:Sugars associated with membrane proteinso Cell-cell interactions
Recognitiono Cell-matrix interactionso Almost Exclusively on Non-Cytosolic Side
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Polarity: Non-Random distribution of organelles
Tight-Junctions cause polarity in Membrane proteins3) Explain the basic processes of tissue preparation and microscopy for
histological preparations
1) Fixation: Cross linking of proteins with formaldehyde. Need stronger
fixatives like glutaraldehyde preserves ultrastructure
2) Sectioning: Fixed sample is sliced so light can pass through it on a slide
< 50 microns thick for light microscopy (hair is 100 microns) Electron microscopy needs 60 nanometers
o Black and White Use Microtome Plane of Section
3) Staining
Hematoxylin: Stains basophilic subtances blueo DNA, Rough ER
Eosin: Stains acidophilic substances pinko Mitochondria, Cytoplasm
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Protein Structure and Function 9/29/2011 10:01:00 AM
Prior Review
1. pH of strong and weak acids
Stronger acids have a lower pH than weak acids. Weak acids tend to have
better buffering properties, especially when mixed with weak bases.
2. pK, buffers (Henderson-Hasselbach), titration curvepKa is the acid dissociation constant, pKb is the base dissociation constant.
Stronger acids have a larger pKa. As stolen from wikipedia,
if an acid dissociates like HA
Then the
The Henderson-Hasselbalch Equation states that
Namely, the pH of a solution depends on the extent of dissociation of its
dissolved acid (a similar equation exists for basic solutions).
A buffer solution resists change in pH from the addition of acids or bases up
to a certain point. Its usually a mixture of a weak acid and weak base. As
more acid is added to the buffer, the weak base dissociates to raise the pH.
When all of the base has dissociated, the buffer breaks. The reverse is
true, of course, when the weak acid dissociates to resist an increase in pH.
3. General Properties of Amino Acids
An amino acid has a carboxyl (COO-) end, an amino (NH2-) end, and a side
chain.
Each side chain has its own pKa. Depending on the pH, this will give the
chain a charge. The isoelectric pointis the pH at which a specific side
chain will have no charge. In general, amino acids are assigned a charge
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based on standard body pH, although there are environments in the body
with extremely low and high pH.
4. Structure of the peptide bond
The peptide bond links together amino acids from carboxyl end to amino endvia dehydration synthesis. Its a covalent bond and difficult to break.
Learning Objectives
1. General Properties of proteins
Functions:Seen in table below.
Catalysis
Regulation
Transportation
Contractile elements
Defense
Structural elements
Size: molecular weight ranges from 6000 to 40,000,000
Shape: Globular
Fibrous
Conjugated: Protein and Sugar/Lipid/RNA covalently linkedCharge: Depends on amino acids on surface of protein.
Solubilitiy: Depends on location in body. Blood proteins are water soluble,
membrane proteins lipid soluble. Some proteins are amphipathic.
2. Levels of Protein Structure
Primary: Amino acid chain derived directly from gene translation. Each unit
is connected via peptide bonds
Determines higher orders of foldingSecondary: Smallest possible structure, connection by weak hydrogen
bonds. Most common structures are the alpha helix and beta pleated sheet.
H-bonds localized
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Tertiary: Three-dimensional structure of a single protein chain. Stabilized by
hydrogen and ionic bonds. Folding usually needs to be done exactly right in
order for protein to function properly. Chaperoninproteins exist to refold
damaged proteins correctly, usually by presenting them with a rapidly
alternating hydrophobic and hydrophilic environment. Ribonucleases always fold correctly after denaturation insulin is irreparable when denatured.
Quaternary: The conjugation of multiple tertiary protein structures.
Stabilization by hydrogen, ionic, and hydrophobic interactions. For example,
hemoglobin, collagen.
3. Protein folding and denaturation
Discussed above.
4. Structure-function relationships
Protein structure is related to function. Globular proteins usually have
hydrophobic center and hydrophilic surface. Enzymes have a unique active
site that binds to a specific substrate.
Examples given in class:
A point mutation on a B-chain of hemoglobin results in a long chain insteadof a globular protein. The protein loses its solubility and sickle cell results.
A mutation in CFTR makes it unable to transport Cl- and cystic fibrosis
results.
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Enzymes 9/29/2011 10:01:00 AM
1. General properties of enzymes:
-Enzymes are a class of proteins that increase the rate of a chemical
reaction.
-Because enzymes control the rates of reactions, they are used to regulate
the activity of the cell.-Enzymes have a specific distributionwithin subcellular compartments
and within specific organs.
*As proteins, enzymes are sensitive to changes in temperature and pH and
require a relatively stable environment in order to function.
*Enzymes are often kept in the inactive state, where it is called the
zymogen orproenzyme. This allows enzyme activity to be strictly
regulated.
Example: Many proenzymesrequire s short sequence on the N-terminus to
be cleaved in order to become active. For example, pepsinogen is translated
and released by chief cells in the stomach. Trypsin then cleaves the N-
terminus, converting the proenzymeto its active form pepsin.
2. Interaction of enzyme with substrate:
-Substrates bind to a relatively small region of an enzyme called the active
site. The bound substrate fits in a specific orientation and is fitted through
ionic bonds, hydrogen bonds, and hydrophobic interactions.
- No covalent boding to enzyme-The act of the substrate binding to the enzyme can cause a
conformational changein the enzyme. This is also called induced fit.
- Enzymes dont affect the Thermodynamics, they do effect the kinetics
3. Enzyme catalysis; Michaelis-Menten equation
-Enzymes have no effect on the thermodynamic properties of a given
reaction and therefore always move the chemical reaction towards
equilibrium. Instead, enzymes lower the energy of activation, an energy
barrier required in order for a reaction to proceed, and thereby increase the
speed of a reaction.
-Enzymatic reactions can proceed in the forward or backward reactions
depending on where the chemical equilibrium lies.
-The Michaelis-Menten equationallows one to predict the rate of reaction
given a specific amount of substrate.
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*During catalysis, the enzyme remains unchanged after the reaction has
taken place. In many cases, the enzyme forms a covalent intermediate.
However, this covalent bond is not involved in substrate-enzyme binding.
4. Enzyme inhibition-Competitive inhibitorsdirectly compete with the substrate to bind at the
active site.
-A competitive inhibitor will increase the Km, the concentration required for
half the enzymes to be bound to substrate, because the competitive
inhibitors will always occupy a specific portion of active enzymes.
-A competitive inhibitor will leave vmax unchanged because adding an
infinite amount of substrate will allow the enzyme to bind to the substrate
more often than to the competitor.
-Noncompetitive inhibitors, also called allosteric inhibitors, bind to a
site on the enzyme somewhere other than at the active site.
-Non-competitive inhibitors will occupy a given portion of enzymes at any
given time, thereby reducing vmax regardless of substrate concentration.
*It is hypothesized that the noncompetitive inhibitor binds to the enzyme
and prevents it from achieving a specific conformational state, thereby
making the enzyme non-functional.
5. Mechanism of enzyme reactions
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-Enzymes can have a high specificity to a given substrate or can be more
non-specific (digestive enzymes).
-In a given reaction with an enzyme, two reactants need to bump into each
other with the proper orientation in order for the reaction to take place. An
enzyme binds to these substrates, thereby increasing effective proximity andplacing the substrates into the
proper orientation.
*An enzyme remains unchanged after performing the appropriate chemical
reaction.
6. Regulation of enzyme activity
-Isozymesare multiple forms of the same enzyme, often with different
kinetic properties.
ex/ -Lactate dehydrogenase is given as a specific example where the
distribution of lactate dehydrogenase is specific to different organs.
-Phosphorylation can activate or deactivate a given enzyme.
-Positive and negative modulators can demonstrate cooperativity
(speeding up reaction) or inhibition in order to alter the kinetics of the
reaction.
*indicates relevant information covered in other lectures but not this one
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DNA Replication 9/29/2011 10:01:00 AM
DNA REPLICATION
1. Compare and contrast DNA replication in Prokaryotes and Eukaryotes
Phase Prokaryotes Eukaryotes
Initiation DNA Abinds to OriC(only
origin of replication) and
melts DNA
Helicase(?) binds to origin of
replication (many)
DNA B(helicase) unwinds
DNA Helicase (?) unwinds DNA
Topoisomerase Ineeded to
nick 1 strand of DNA to
relieve torsional stress (bc
continuous circle)
Single Strand Binding
Proteins(SSBs) bind to
prevent DNA from re-binding
to other parent strand
RPAs bind to prevent DNA
from re-binding to parent
strand
Priming Primaserecruited to
replication fork and adds RNA
primer to leading strand,
then to lagging strand further
down DNA
Primase recruited to
replication fork and adds RNA
primer to leading strand, then
to lagging strand further down
DNA
DNA Pol adds a few DNA
nucleotides to primer
Elongation DNA pol IIIthen binds
(tethers with beta clamp) to
polymerize DNA in 5-3
direction (leading strand in
DNA pol then binds
(tethers w PCNA) to replicate
in 5'-3' (leading strand in
continuous manner, and
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continuous manner, and
lagging strand in
discontinuous manner w
Okazaki fragments)
lagging strand in
discontinuous manner w
Okazaki fragments)
DNA Pol III can backtrack
and proofread in 3-5
direction
DNA pol can backtrack and
proofread in 3'-5' direction
DNA Pol Ireplaces DNA Pol
III to remove RNA primers
Fen-1removes primers and
DNA pol replaces gaps w
DNA
DNA ligasejoins strands DNA ligasejoins strands
Termination Terminator sequences trap
replication fork near origin
site and bing TUS proteins
Telomerasecreates RNA
template to extend lagging
strand with junk DNA
2nd TUS Protein does not
allow DNA B to pass through,
and elongation is stopped T-loops formed at ends
Topoisomerase ivunlinks
the catenated strands
2. Examples of diseases that occur due to replication defects
a. Mutation in RNA telomerase --> Dyskeratosis congenity:
Developmental delay
b. Low telomerase levels --> no T-loops = genomic instability =
increased cancer risk
c. Fragile X syndrome excess CGG
d. Muscular dystrophy
e. Spinocerebellar ataxia
f. Huntingtons Disease: In coding sequence
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Mutations in UTR, introns and coding sequence
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DNA Mutation and Repair 9/29/2011 10:01:00 AM
1. Describe the relationship between DNA damage, DNA repair, DNA
replication and mutagenesis
Mutagenesis: the permanent alteration of DNA
2. State the major sources of DNA damage and the major types of DNA
repair
Sources of DNA Damage
1. Endogenous Sources DNA Replication Errors (misincorporation, slippage)
Deamination (cytosine to uracil, 5-methylcytosine to thymine) Depurination
(creates abasic site) Reactive Oxygen Species (strand breaks, base damage)
DNA Recombination Errors
2. Environmental Sources:
-Ionizing Radiation (IR) increases reactive species (Indirect Mechanism)-Ultraviolet Radiation (UV) generates pyrimidine dimers (Direct Mechanism)
-Chemical Mutagens (e.g. alkylation by MNNG, MNU O6-methylguanine,
pairs like A)
Repair least to most serious
Proofreading during replication. error rate:10^-4 10^-8
Post Replication Mismatch excisionrepairafter replication. Error rate
10^-8 10^10
Error recognition strand discrimination->excision->resynthesis->ligation
Base excision repair: DNA glycosylase flips and removes base AP
endonuclease cuts phosphodiester bond -> DNA polymerase -> ligase
- can create abasic site that can be premutagenic if not repaired on time
Direct reversal: MGMT destroys itself to get rid of methylation of guanine
bases
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Nucleotide excision repair:Damage recognition Nuclease cleavage
removal with helicase Pol, Pol DNA ligase
removes bulky dimmers/unrecognizable bases/
note: DNA ligaserepairs single-strand breaks > 100,000 / day very efficient
Homologous Recombinationless errors, only available during mitosis
when sister chromatid is around. Reliable repair of double strand breaks
exonuclease cuts to make stick endstrand invasion by sister chromatidDNA
synthesis/sister chromatid exchangeunwindig/ligation(BLM helicase)
Non-homologous RecombinationMore error prone, available any time
of cell cycle. Unreliable possible error in relegation, clean up step is
wasteful
synapse formation to hold ends together by Ku70 and Ku80 DNA PKs clean
up staggered ends Ligation by LIG4 and XRCC4 proteins
3. Describe the clinical consequences of mutagenesis and of defects in DNA
repair
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Nuclear Structure and Function 9/29/2011 10:01:00 AM
1. Make a simplified schema of the basic structural components of the
nucleus (nuclear envelope, pores, nucleolus, chromatin, nuclear matrix).
2. Explain the structure and function of the nuclear envelope and nuclear
matrix.
Nuclear Envelope: Is a 2-membrane system which forms a barrier between the
nucleus and the rest of the cell to:
- Maintain unique protein and nucleotide environment
- Sequester mRNA synthesis from Translational machinery
- Protect / Contain DNA
Outer Membrane and Inner Membraneare separated by the Perinuclear
cisterna. It is perforated by Nuclear Porescontaining NPC(Nuclear Pore
Complexes). The inner membrane is supported by the Lamina
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Nuclear Matrix: A protein lattice made of fibers (similar to cytoskeleton) which:
- Anchors DNA replication
- Anchors transcription complexes
- Reinforces nuclear envelope --> stability
3. Explain the importance of the structure of nuclear pore complexes and
how this plays a role in nucleocytoplasmic exchange.
Nuclear Pore Complex: (80-100 nm diameter) is the site of selective
nucleocytoplasmic exchange. It creates a selective barriers for the transport
of macromolecules across the nuclear envelope (not as selective for smaller
molecules). Has a 3-ring Structurethat has 8 spokes with a hole in the
center.
- Cytoplasmic Ring:(8-subunits) with protusions into cytoplasm formediating import
- Middle Ring:8 subsunits protrude into Perinuclear spaceo Transport proteins
Nucleoplasmic Ring: Fibrous proteins protrude into nucleoplasm
Serves as a dock for importins and exportins.o Importin / exportin mediated transport requires energy
4. Describe the organization of chromatin and its role in synthesis,
processing and storage of DNA and RNA.
Chromatin is highly compacted DNA + Packing Proteins:
- Heterochromatin: highly coiled and less active
Genes not transcribed in cell
- Euchromatin: less coiled, more active DNA
Composition:
Nucleosome:(10 nm) DNA wrapped around 8 Histones(166 bp/ histone)
Forms Beads on a StringCoiled Nucleosome: (30 nm) coiled nucleosomes
H1 Histone: Activity affects density of nucleosome coil
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The density of chromatin packing determines the availability of the genes for
transcription. Histone tails are sites for activating the exposing / coiling of
local DNA
5. Have a general concept of the cell cycle and its control as well asapoptosis.
G1: Cell Growth
S phase: DNA replication
G2 phase:Interval before mitosis (valuable for DNA lesion repair)
Mitosis
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RNA Transcription 9/29/2011 10:01:00 AM
Transcription and Control of Transcription Learning Objectives
1. Describe the basic transcription machinery, the basic structure of
genes (including promoters) and transcription units, and the basic
mechanism of transcription in eukaryotes.
a. Basic machinery neededi. RNA pol(to read your template 3-5)
ii. Some bases(ATP, GTP, CTP, UTP, all ribonucleotides of course)
iii. DNA topoisomerasesto unwind the helix
b. Basic structure of genes, w/promoters & txpn units
ii. Promoter regiono 1. Where proteins bind to begin transcription. This
includes:
o 2. Initiator sequence(which includes the)o 3. TATA boxo 4. A mix of enhancer and silencer sequences
a. Can be in other places other than right before thetranscribed gene (ex. Behind, in the intron, etc.)
b. Fxn: assist regulation by allowing a specific txpnfactor to bind to it
c. This leads to activation/repression of transcription d. Environmental conditions can control the binding of
txpn factors to these enhancer/silencer elements e. Ultimately, the binding will lead to actions such as
phosphorylation or binding/dissociation of another
protein that is related to the txpn factor
iii. Transcribed gene
Exon: leaves the nucleus as mature mRNA afte modification
Intron: Kept inside the nucleus (although problems with the introncould later contribute with mutations and problems with the mature
mRNA)
c. Basic mechanism of euk txpn
- RNA pol transcribes the DNA
- Depending on the RNA we are attempting to transcribe, we will use a
corresponding polymerase
- Basal txpn factors assist pol in recognizing the promoter and initiating txpn
-NOTE: Mitochondria (have RNA pol that is similar to prok pol, and
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transcribes their own DNA into their own rRNAs, mRNAs, and tRNAs)
2.Discuss the roles of transcriptional activator proteins, enhancer elements,
coactivators, and chromatin in regulation of eukaryotic transcriptiona. Transcriptional activator proteins
- Bind basal txpn factors associated with RNA pol 2 to get it over to the
promoter
- Recruit coactivatorsto perform 2 functions
Coactivators are proteins that increase gene expression by bindingto an activator or txpn factor which contains a DNA binding domain,
facilitating the txpn of a desired gene
Alter chromatinstructure (like unwind it from the histone) to makepromoter region more accessible
Recruit RNA pol II and its basal transcription factors- Enhancer elements(gene sequences far upstream/downstream for the
gene or nearby) are brought closer to the gene we want to transcribe
through complexes of transcriptional activator proteins, coactivators,
and other transcription factor proteins in preparation for transcription by
RNA pol II
3. Describe the cellular response (or signal transduction) pathway used
by steroid hormones and list the major hormones which interact with
members of the nuclear rece with the steroid receptor protein family also
known as the nuclear receptor family
Glucocorticoids, Mineralcorticoids, Estrogens, Androgens, Progestin Can also interact with steroid-related vitamins, amino acid
derivatives, and other molecules yet to be discovered
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b. Pathway
- Steroid comes into the cell and is bound by a steroid receptor
- This creates a steroid-protein complex that enters the nucleus, which binds
to a hormone enhancer element on DNA
Steroid Receptor can be stabilized as dimmers after binding Steroid- The bound complex + enhancer sequence will fold up/join the promoter
region, which will now begin to bind txpn factors, coactivators, and Pol II
onto the promoter region. The TATA box is illustrated in the example above
to give a frame of reference.
- Now the desired gene can be transcribed into mRNA
- The mRNA is then modified and packaged so it can exit the nucleus and be
translated into protein
- This protein will in turn create a physiological response
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4. Explain why agnoists promote gene activation by steroid receptors,
but antagonists inhibit steroid receptor function
Agonist binding steps Antagonist binding steps
1. Agonist molecule binds to a receptor. In
our notes, the receptor is a steroid
receptor.
1. Antagonist molecule binds
to a receptor
2.Receptor binds to enhancer sequence on
DNA
2.Receptor binds to enhancer
sequence on DNA
3.Receptor undergoes a conformational
change, yielding a new binding spot
3.Receptor undergoes a
conformational change, BUT
there is NO new binding site
4.A coactivator protein will bind to this new
spot, and with this binding, will recruit thebinding of other transcriptional factors and
RNA Pol 2
4.Coactivator has no place to
bind, the txpn apparatusnever sets up
5.Now transcription can occur :) 5.No transcription occurs :(
Conclusion: promotion of activity Conclusion: inhibited acitivity
5.Discuss the roles of steroid receptors and their agonist/antagonists in the
etiology and/or treatment of breast cancer
Breast tissue development is triggered by estrogen Therefore, estrogen is an agonist for breast tissue/breast cancer
growth
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Tamoxifen, an anti-cancer drug, is an antagonist, changingconformation and inhibiting txpn by denying coactivators and txpn
factors a binding site (see question 4)
This prevents the growth of breast cancer cells
6. Explain how the cAMP signaling pathway can regulate txpn of specific
genes
a. Ex. Glucagon pathway (which signals that we need to make glucose)
i. Protein or steroid from outside the cell binds to a receptor.
ii. The receptor activates a G protein, which activates adenylyl cyclase
iii. Adenylyl cyclase releases cAMP, which binds to protein kinase A
iv. Protein kinase A enters the nucleus via nuclear pore, phosphorylating
CREB (cAMP response element binding) protein. Now this is just like
question 3!
v. CREB now binds to its enhancer region, CRE (cAMP reponse element)
vi. NOT in the notes, but I thought this was helpful: a coactivator called
CBP (CREB-binding protein) then binds to CRE
vii. Now txpn is activated
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9/29/2011 10:01:00 AM
---------------------------------------Regulation of Transcription-----------------
---------------------
Initiation
Can have multiple promoter and start sites
Creates diversity by including/excluding exonsAlso changes the UTR length and potential for regulation
Capping: Guanine cap
Capped by inverted guanine
Some groups are methylated
Done by capping enzymes associated with polymerase as it transcribes
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- recognized by nuclear pores, necessary for proper export
- prevents exonuclease degradation
- promotes circularization and translation
Polyadenylation- Transcription ends when it recognizes termination sequence AAUAAA
- Also can have multiple termination sites
provides 3 end diversityOnce termination sequence is recognized, mRNA is cut 30 bp down and 200
adenosines are added
- Necessary for export of the mRNA --> proteins bind poly A tail
Link to cap to help promote translation Prevents 3 end exonuclease degradation
Splicing
Introns out, Exons in
Alternative splicing creates great biodiversity (when intentional)
Temporal/spatial regulation
Consensus site is strong for introns
Excised structure is termed lariat
When accidental or mis-spliced, can be harmful to cell Dominant negative forms Protein complexes (snRNPs) remain on mRNA, cells can tell if intron
is left in --> Tend not to be exported
Cryptic sites- sites (sometimes mutations) that become splice
acceptor/donor sites that are not the normal sites
Ex/ Portuguese family with cystic fibrosis cryptic splice site >> frameshift
mutation
- Burkitts Lymphoma
- chromosomal translocation shortens 3 UTR, removing sequences
necessary for mRNA downregulation
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RNA Translation 9/29/2011 10:01:00 AM
1) Describe the principle of mRNA translation and explain the degeneracy
of genetic code
a. mRNA is read in groups of three in two-unit ribosome complexes where
tRNA match the mRNA and bring the appropriate amino acids. They formpeptide bonds to form the primary structure of the protein
b. Degeneracy: There are 64 possible combinations of 3 basepairs, and
only 20 amino acids. Each amino acid is coded by 2-6 codons
2) Understand and be able to summarize the general steps of translation
a. Scanning and initiation (2 ATP for aa-tRNA synth; 1 GTP required to
unwind 5 UTR)
i. Aminoacyl-tRNA synthetasescouple amino acids to the
correct tRNA
ii. 40S ribosomal subunit binds to 5 cap and starts scanning 5-3
iii. Finds AUG start codon (ACCAUGG = Kozak sequence usually
start)
iv. tRNA recognizes codon & brings in Met
v. 60S ribosomal subunit joins for protein synthesis
b. Elongation (2 GTP / amino acid)
i. AAs bind to A site, then P site as new peptide bonds form.
(Leave via E site)1. This is called Translocation
ii. N terminus = 5, C = 3
c. Termination (1 GTP)
i. Occurs when encounters stop codon
ii. Requires Release Factor R + GTP
iii. Polypeptide released
iv. Likely a physical link bw cap and poly A tail --> ribosome
recycling
3) Explain how aberrant translation can play a role in human:
a. Splicing mutations/ frameshift changes
i. Occurs if introns not removed or exons are skipped & not
matched up correctly
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ii. Frameshift will change all subsequent amino acids & will result in
incorrect protein
iii. Only a frameshift of 3 amino acids would be less problematic but
may still cause a problem w the protein
b. The role of nonsense-mediated mRNA decayi. A frameshift mutation will likely cause an early stop codon
ii. If a stop codon is encountered, the ribosome releases a release
factor that scans for exon/exon junction complexes (EJCs) 50+ bp upstream
of stop codon
iii. If a protein is encountered, the mRNA is signaled for destruction
iv. This is important for cells because dominant negative proteins
can be very detrimental to cells (eg beta thalassemia = shortened beta
subunit of hemoglobin ruins all hemoglobin)
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Protein Secretion and Trafficking 9/29/2011 10:01:00 AM
1) Describe the general mechanism of protein synthesis, and where
it takes place in epithelial cells.
Protein synthesis takes place on ribosomes.
The ribosome life cycleRibosomal RNA synthesized in nucleolus
Ribosomal proteins synthesized in cytoplasm
Ribosomal proteins imported to nucleolus, two subunits assembled
(The two eukaryotic ribosomal subunits are 40s and 60s, useful to
remember. Also useful numbers for the CF sweat test: 60mosm is positive.)
Ribosomal subunits are transported to cytoplasm.
Small subunits identify and bind to mRNA
Large subunits join to complex to form the ribosome.
(The two eukaryotic ribosomal subunits assemble to form an 80s
protein. Minimum sweat needed for the sweat test is 75 mg.)
FROM 2011 FIRST AID FOR THE USMLE STEP 1
Protein Synthesis
Initiation
Activated by GTP hydrolysis, initiation factors help assemble the 40s
ribosomal subunit with the initiator tRNA and are released when the mRNAand the ribosomal subunit assemble with the complex.
Elongation
Aminoacyl-tRNA binds to A site (except for initiator methionine)
Ribosomal rRNA (ribozyme) catalyzes peptide bond formation, transfers
growing polypeptide to amino acid in A site.
Ribosome advances 3 nucleotides toward 3 end of RNA, moving peptidyl
RNA to P site (translocation)
Termination
Stop codon is recognized by release factor, and completed protein is
released from ribosome.
Mnemonics
Eukaryotes: 40S+60S=80S (Even)
prOkaryotes: 30S+50S=70S (Odd)
ATP = tRNA Activation
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GTP = tRNA Gripping and Going places (translocation)
Clinical Relevance
Many antibiotics act as protein synthesis inhibitors
Aminoglycosidesinhibit formation of the initiation complex and cause
misreading of mRNAChloramphenicolinhibits 50S peptidyltransferase
Macrolides and clindamycinbind 50S, blocking translocation.
Ribosome location
Free ribosomes in cytoplasm vs. Bound ribosomes on ER.
Both form polyribosomes (polysomes).
2) Diagram and list the basic functions of the RER, SER, and Golgi
complex.
Rough Endoplasmic Reticulum
FROM 2011 FIRST AID FOR THE USMLE STEP 1
Nissl Bodies (RER in neurons) synthesize enzymes (e.g. ChAT) and peptide
neurotransmitters.
Mucus-secreting goblet cells of small intestine and antibody-secreting
plasma cells are rich in RER.
Smooth Endoplasmic Reticulum
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Irregular network of membrane-bound tubules. Functions in steroid
hormone synthesis, drug detoxification, andrelease and recapture of
calcium ions for muscle contraction.
FROM 2011 FIRST AID FOR THE USMLE STEP 1
Liver hepatocytes and syeroid hormone-producing cells of the adrenal cortexare rich in SER.
Golgi Complex
FROM 2011 FIRST AID FOR THE USMLE STEP 1
Golgi apparatus
Distribution center of proteins and lipids from ER to plasma membrane,
lysosomes, and secretory vesicles.
Modifies N-oligosaccharides on asparagine.
Adds O-oligosaccharides to serine and threonine residues
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Addition of mannose-6-phosphate to specific lysosomal proteins --> targets
the protein to the lysosome
Proteoglycan assembly from core proteins
Sufation of sugars in proteoglycans and of selected tyrosine on proteins.
Vesicular trafficking proteins:COPI:Retrograde, Golgi --> ER and more
Constituitive secretion Intercisternal transport
COPII:Anterograde, RER -> Golgi
Clathrin:trans-Golgi --> lysosomes, plasma membrane --> endosomes
3) Distinguish between regulated and constitutive secretory
pathways.
Constitutive Secretion (default pathway): Usually continuous, needs no
special stimulus. Can be upregulated or downregulated. (cop 1)
Regulated Secretion: Requires an extracellular stimulus. Until then,
proteins to be secreted are concentrated into secretory granules.
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Cytoskeleton 9/29/2011 10:01:00 AM
Actin
Microfilaments
Tubulin
Microtubules
Intermediate
Filaments
Subunits Made from
globular (g) actin
Made from tubulin
dimers (alpha andbeta)
Various elongated
proteins, oftenhelical
Primary
Structures
Form filamentous
actin (f-actin) in a
coiled
microfilament
Dimers align to
form
protofilaments.
Dimers and
tetramers
Higher order
structures
F-actin MFs can
run parallel oranti-parallel,
branch, be
capped, anchored,
or severed (via
protein partners)
Protofilaments
(13) assembleside-side to form
hollow tubules
Coiled-coil (likely
not important)
Size ~7 nm ~25 nm (hollow) ~10 nm
Use
nucleotide?
ATP GTP Nope.
Polarity assembly usually
occurs on (+) end,
disassembly on
the (-) end
(-) is anchored
centrally to the
MTOC, or to the
basal body.
Assembly usually
occurs on (+) end
extending towards
cell periphery
None
Dynamics Fast Fast Very slow
Motors Myosin Kinesin (+) and
dynein (-)
?
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Found in: -Cell peripheries,
for cell shape and
motility
(lamellipodia,
projections)
-Microvilli
-Cleavage furrow
of cytokinesis
-Sarcomeres
-Cell interior, for
rigidity and
vesicular transport
-Mitotic spindles
-Cilia, flagella
-Nuclear lamins,
for nuclear
structure
-In cytoplasm for
support
-ECM (i.e.
keratin) for
mechanical
support
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Endocytosis and Lysosomes 9/29/2011 10:01:00 AM
Endocytosis:General phenomenon of cellular uptake via mechanisms
involving membranes (not channels or pumps)
Pinocytosis (cell drinking)
-Macro/microMediated by caveolin, causing cell invaginations
Non-specific, but not really random; tend to be positive/neutralmolecules
Phagocytosis (cell eating)
Can be specific (receptor-mediated) or non-specific Contents go through endosomal system
Endosomal system
Consists of variable membranous structures (vesicles, tubules,MVBs), differing in shape and sizes
Involves progressive acidification of interior , initially by H+ pumps(pH goes down Enzymes are tagged with mannose-6-phosphate (M6P) in cis-Golgi
- Receptors for M6P (M6PR) binds and sorts these enzymes at the trans-
Golgi, bud as lysosomes to traffic to endosomes
- Acidification causes cargo release, and M6PR receptors are recycled- Primary lysosomes are newly minted, have not combined
- Secondary lysosomes have combined with endocytic cargo
- Hydrolytic enzymes protected by glycosylation
*If contents are undegradable, cell removes what it can and then
condenses/sequesters material into a residual body
-Progression can be generally categorized as early (near periphery) vs.late
(near Golgi) but really is a functional continuum
Ex: LDL receptor-mediated endocytosis
LDL recognized by receptor (LDLR) and these complexes will startto cluster
Clathrin, previously free in the cytoplasm, associates with theseclustered receptors at their cytoplasmic ends
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Coated pits form and pinch off to form vesicles. Clathrindisassociates and is recycled
Acidification causes LDLR to release LDL, receptors are recycledback to plasma membrane
Combines with primary lysosome, so that contents can be actedupon
Vesicle membranes can be recycledHeterophagy: uptake of external materials
Autophagy:digestion of cellular components for turnover (proteins,
ribosomes, mitochondria)
Clinical Correlates:
Hypercholesterolemia: Defective receptor-mediated endocytosis of LDL
(at the receptor level or trafficking level) causes extreme fatty deposits in
various locations of body.
-Premature atherosclerosis & heart attacks
Infection
-Many infectious agents use receptors as cellular entry points- have the
ability to escape or neutralize lysosomal degradation>i.e. diphtheria toxin, almost every virus, parasites
Inclusion cell disease
Defective enzyme responsible for tagging lysosomal enzymes Lysosomal enzymes traffic through constitutive pathway out of the
cell (secreted)
Extra (?)
Secretory lysosomes
Conventional lysosome whose contents are also secreted
Immunity
-Cytotoxic T-cells release cytolytic proteins against cancer cells
-MHC presentation of degradatory products
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-Histamine from mast cells
Albinism
-Secretion of melanin from melanocytes
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Peroxisomes and Mitochondria 9/29/2011 10:01:00 AM
Lecture 6: Peroxisomes and Mitochondria
Explain the role of peroxisomes in detoxification, catabolism, and
biosynthesis.
Peroxisomes (aka microbodies)producing and breaking down hydrogen peroxide
Detoxification
Alcohol in liver and purines in kidney (abundant in organs)Catabolism
Oxidase breaks down long chain fatty acids, H2O2 side productCatalase degrades H2O2H2O + O2
Biosynthesis
Gets membranes from the ER Myelin precursor, bile acids, cholesterol
Other notes:
Replicate by fission
Peroxins transport proteins from cytosol (receptor for PTS), important for
biogenesis
PTS (peroxisome targeting signals) at the C and N terminus on these
proteins
Diseases:
Long chain fatty acid accumulation and low myelinPeroxisome biogenesis disorder (more severe) (eg: Zellweger syndrome:
severe, peroxin mutations that lead to virtually no peroxisomes, fatal w/I 1st
yr of life)
Demyelination and accumulation of long-chained fatty acid
Very flaccid and no muscle contraction
Peroxisomal enzyme deficiencies (eg: X linked adrenoleukodystrophy, gene
mutation of fatty acid transport into peroxisomes, death 1-10yrs after onset)
Demyelination and fatty acid accumulation
Lorenzos oil
2. Explain the role of mitochondria in ATP production, catabolism, calcium
homeostasis, and apoptosis.
Mitochondria
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ATP production: electron transport chain makes intermembrane acidic to
drive ATP synthas
(I) NADH dehydrogenase: H+intermebrane, e-ubiquinone
(II) FADH2 dehydrogenase (succinate): FADH22H + FAD-+e-(ubiquinone)
(III) Cytochrome C reductase: H+ intermembrane, e- (ubiquinone)cytochrome c
(IV) Cytochrome c oxidase: H+ intermembrane, e- used to reduce O2 to
water
ATP synthase: H+ returns to matrix
Catabolism: long chain fatty acid oxidation, pyruvateacetyl CoAoxidation
Calcium homeostasis: sequesters excess cytosolic Ca (refer to muscles)
Apoptosis: mito releases cytochrome c and activates a caspase cascade to
induce apoptosis
*NOT the same as necrosis (inflammation, uncontrolled release of cell
contents)
Other:
Inner membrane is impermeable to small ions
Tubular and can form networks
Acetyl CoA Citric Acid cycle ETC (ATP synthase)
Mt protein import (general): proteins contain mt targeting sequence
Proteins bind the TOM and TIM (transfer protein of outer/inner mitochondrial
membrane) and binding allows import into mitoThere are also secondary sequences which target inner membrane,
intermembrane space, outer membrane
Identify peroxisomes and mitochondria in electron micrographs.
Compare and contrast the structure, function, and genetics of peroxisomes
and mitochondria.
Peroxisomes Mitochondria
Structure 0.5-1m
Lipid bilayer; single membraneGranular matrix; oxidase,
catalase
Nonhumans have a nucleoid
structure in the middle (big black
spot)
0.5-10m
Inner membrane (cristae e-transport)
Outer membrane
Intermembrane space (high
H+)
Matrix: mtDNA, ribosome,
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tRNA, TCA enzymes
Function Biosynthesis (bile acid,
cholesterol, myelin)
Detoxification of alcohol and
purines
oxidation of fatty acids (very
long chain)
breakdown H2O2
ATP synthesis
Ca homeostasis
Regulation of apoptosis
oxidation of fatty acids
Genetics Binary fission replication
Membranes from the ER
No endogenous DNA
Binary fission replication
Inherited from egg (gamete)
mtDNA (can have defects)
autosomal mtprotein defects
Disease biogenesis disorders are moresevere
Neurological myelination
diseases
Zellweger syndrome (no
peroxisome; buildup of very long
chain fatty acids)
X linked adrenoleukodystrophy
(no fatty acid transport into
peroxisomes)
Mt enzyme deficiencyMitochondrial DNA defects
Autosomal DNA defects for mt
proteins
Lebers hereditary optic
neuropathy (loss of central
vision, affects mostly males,
optic nerve degeneration)
Identify maternal inheritance by pedigree analysis; explain how
mitochondrial diseases can be maternally or autosomally transmitted;
explain heteroplasmy.
Maternal inheritance: Mitochondrial DNA defects (13 mt proteins, 22 tRNA,
2rRNA)
Autosomal inheritance: nuclear DNA defects that code for mt proteins
Heteroplasmy: mixture of mutated and normal mitochondria redistributeunevenly during development, so this is the occurrence of cells having
different mitochondria and may occur within one individual
Eg: Lebers hereditary optic neuropathy (lossof central vision, affects mostly
males, optic nerve degeneration because not enough functional mito
produce energy to maintain cells)
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Microanatomy 7: Cell Differentiation
1. Describe the main characteristics of differentiated cells and
understand that it is a result of differential gene expression, not
gross changes in the genome itself.
Differentiated cells are cells that have become
morphologically/structurally, biochemically, and functionally
specialized. Since nearly all cells of the body have genomic equivalence
i.e., they all possess the same full genome cell differentiation typically
results from changes in gene expression, not any changes in the DNA itself.
Exceptions:Gametes (sperm and egg cells); immune system (B cells, T
cells splicing of immunoglobulin genes in order to generate antibody
diversity)
Once a cell is differentiated, the changes are often permanent and
heritable, such that the cells produced through divisions of this
differentiated cell have the same specialized characteristics that it does.Terminally differentiated cells (ex. neurons) lose their capacity for mitotic
division entirely.
In short, differentiation = restriction of cell fate
2. Describe the general properties of stem cells and compare them to
differentiated cells.
Properties of stem cells:
- Capable of self-renewal or differentiation
- May give rise to transit amplifying cells with limited division capacity
- Often lack specialized organelles, and show high nucleus/cytoplasm ratio
- Long-lived express telomerase
- Slow to divide, few in number
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- May be restricted spatially to specific zones or niches
- Respond to signals that will regulate their growth and proliferation
Stem cells vs. differentiated cells seems pretty obvious just by extrapolating
from the above properties, so a finer distinction to make might be stem cellsvs. progenitor cells:
Stem cellscan divide an unlimited number of times, and can give rise to
more stem cells (self-renewal) as well as differentiate into specialized cells of
any of the three germ layers (pluripotency).
Progenitor cellshave a limited number of divisions and do not maintain
their ability to self-renew, are considered to be at a further stage of
differentiation than stem cells, and are more limited in the variety of cell
types into which they can differentiate (multipotency or oligopotency).
*Note: These two terms are sometimes used interchangeably, and the
distinction between the two is still contested, since some stems cells (ex.
adult stem cells) are also only multipotent, oligopotent, or unipotent. The
best criterion to go by for distinguishing the two seems to be the self-
renewalaspect, which is exclusive to stem cells.
3. Distinguish determination and differentiation.
Differentiation= the process by which different, specialized cells
(morphologically, biochemically and functionally) arise from a homogeneous
group of unspecialized cells.
Determination= the commitment of a cell to differentiate into a certain
cell type at some later time. Determination generally occurs as a step (or a
series of steps) that is prior to, and separate from, differentiation. Cells can
be determined a long time before they differentiate (at least by histological
criteria). Two major ways that cells can become committed are by: 1)
possession of special cytoplasmic determinants localized within the egg or
early embryo, and 2) interaction with other cells or the factors secreted by
other cells. Cytoplasmic determinants are components localized to a
particular region of the egg or embryo that, when segregated to a cell or cell
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lineage cause those cells to become determined, i.e., to adopt a particular
cell fate.
First column: Normal pattern of differentiation; cells in region A differentiate
into one type of cell, cells in region B into another typeSecond column: Sample of region B cells labeled and transplanted into
region A early on, before they have become determined transplanted cells
differentiate into region A type cells
Third column: Sample of region B cells labeled and transplanted into region
A later on, when they are already determined transplanted cells
differentiate into region B type cells
[Fourth column is not relevant to this objective, but is basically
demonstrating that region B cells that are specified (specification = early,
reversible/changeable step of determination, so not fullydetermined) will
still differentiate into region B type cells in an isolated environment.]
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4. Explain the potency of stem cells and understand it in the context
of differentiation stages.
Cell potency = amount of differentiation potential; the following are listed
from least differentiated stage (have the most differentiation potential) tomost differentiated stage (have the least differentiation potential)
Definition Example
Totipotent
Can differentiate into
any cell type (ectoderm,
mesoderm, and
endoderm) as well as
extra-embryonic tissue
such as the placenta
Human zygote is
totipotent up through
the 8-cell stage.
Pluripotent
Can differentiate into
any cell type (ectoderm,
mesoderm, and
endoderm), but cannot
produce full embryo
Embryonic stem cells
(which originate from
the inner cell mass of
the human blastocyst)
are pluripotent.
Multipotent
Can differentiate into a
limited number of cell
types
Progenitor cells; also,
hematopoietic stem
cells (a type of adult
stem cell) can
differentiate into various
blood cells (RBCs, white
blood cells, platelets,
etc.) but not other
mesodermal cell types.
OligopotentCan differentiate into
very few cell types
Progenitor cells; some
adult stem cells
Unipotent
Can differentiate into
only one cell type;
however, unipotent
stem cells can still self-
renew
Skin cells
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Terminally
differentiated
Have fully differentiated
and can no longer divide
via mitosis
Neurons
5. Explain inductive interactions and epigenetic controls in cell
differentiation.
Induction= process by which surrounding cell or environment guide the
cell differentiate process; can be mediated through cell-cell, cell-matrix, or
diffusible growth factor interactions; can be instructive(signal itself causes
target cell to differentiate) or permissive(cell already committed, induction
creates conducive environment for differentiation); timing of induction is
crucial (see objective #6 on temporal specificity).
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Epigenetic controlscontribute to maintenanceof differentiation through
heritable alterations in chromatin structure (ex. DNA methylation) and
transcription factor expression.
6. Draw a diagram that demonstrates the principle of temporalspecificity in induction.
7. List the sources of stem cells for use in research and medicine.
Type Pros Cons
Adult stem cells Easily obtained; no
controversy
Multipotent or
unipotent, so have
limited usefulness
Embryonic stem cells Pluripotent Political/ethical
controversy; potential
for aberrations leading
to tumor formation
during culturing stageCord blood stem cells Mostly multipotent
(peripheral blood stem
cells, or PBSCs), but
also some pluripotent
stem cells; less
(None mentioned in
lecture)
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controversial
Induced pluripotent
stem cells (iPSCs)
Derived from non-
pluripotent cell, ex.
adult skin cells, so also
no controversy; can be
reprogrammed to regain
pluripotency and even
totipotency
Chances of aberrations
tumor formation in
origin cells, and during
reprogramming and
culturing stages; require
more research
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Intro to Tissues 9/29/2011 10:01:00 AM
Intro to Tissues
Dr. Wood 9.1.2011
Generalities:
All cells have:-Nuclei,EXCEPT RBCs or mitotic cells
-Cytoplasm
-Plasma membrane
**They may be hard to see, due to abundance or plane or section
Common cell shapes:
Squamous
Cuboidal
Columnar
Spherical
Spindle
Stellate
When talking about tissues, dont forget to think about the ECM associated
with the cells
Epithelial tissue
-Lines free surfaces, both externally and internally (i.e. skin, sweat glands,
GI, kidney tubules)
-Supported by connective tissue
-Serves as barriers
-Cells tend to be tightly packed (look for high density of nuclei) with
little ECM
-Avascular
-Tend to be polarized
Connective tissue
-Provide structural support for many other types of tissue
-Tend to have few cells (sparse density of nuclei) with lots of ECM
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-Fibroblasts are the most common type of connective cell
>Stellate/spindle shape, constitutively secreting ECM (collagen)
-Classified as loose (more cells/water, less protein/fibers) or dense (more
protein/fibers, less water/cells)
-Blood is connective tissue-Also fat, bone, tendon, cartilage
Contractile tissue
-Specialized for rapid movement, responsive to electrical signals
-Striated (cardiac, skeletal) vs. smooth muscle
-Voluntary (skeletal) vs. involuntary (cardiac, smooth)
-Many tubular structures (vasculature, GI tract) have contractile tissue
*Smooth muscle can often look like connective tissue. Try looking at how
many nuclei there are- more nuclei usually signals smooth muscle
Nervous tissue
-Neurons are large cells responsive for conveying electrical stimuli
-Glia are smaller supporting cells (50:50 90:10)
-Neuropil is cellular (not extracellular) material between cell bodies- cell
processes of glia and neurons
Origins of tissues from germ layers
Ectodermal Origin Mesodermal Origin Endodermal Origin
Epidermis of skin Dermis of skin GI (stomach, intestines,
epithelial lining) but
NOT including muscle
layers
Nervous system Circulatory (heart,
vascular epithelia)
Lungs and epithelial
lining
Cornea Kidney tubule epithelia LiverLens Skeletal muscle,
skeleton
Pancreas
Connective tissue Bladder/urethral lining
Lymphatic systems
Excretory system
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(kidneys and bladder,
excluding lining of
bladder)
Lining of body cavity
(mesothelium?)
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Epithelium 9/29/2011 10:01:00 AM
1) Explain how epithelia establish barriers and control exchange between
different environments
Epithelium lines the free surfaces of the body, so material (ions, proteins,
oxygen, sugars) needing to pass between tissues of the body and luminalspaces (lungs, gut, ducts) needs to pass through the epithelium. Epithelial
cells are densely packed and connected to neighboring epithelial cells
through:
Tight junctions: forms a ring around the cell that maintains polarity of
transport proteins between apical and basolateral faces. Not anchored by
cytoskeletal elements
Adhering Junctions: forms a ring around the cell, connected to actin
Desmosomes: Spot welds connected to intermediate filaments
This most commonly happens in a transcellular pathway, although there
are examples of paracellular transport through the tight and adhering
junctions. Because of cellpolarity, different transporters on apical and
basolateral surfaces can regulate directionality of transport and create
downhill gradients across the cell.
The apical side of epithelium in the trachea are coated in cilia that facilitate
transfer of mucus out of the airway
Keratinized stratified squamous epitheliumprovides a particularly
strong barrier with a thick layer of dead, denucleated squamous cells that
are continuously regenerated as they are sloughed off.
2) Classify Epithelium based on cell layers and cell morphology
Simple Squamous Epithelium: fried egg morphology, can have elongated
cytoplasm. (endothelium, alveoli, mesothelium, portions of kidney tubule)
Simple Cuboidal epithelium:cuboidal, regular (or just not columnar or
squamous) morphologyshape. (kidney tubules and ducts)
Simple Columnar Epithelium:Tall cells, usually with apical surface
specialization (gut, intestine, respiratory tract, oviduct
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Stratified Squamous Epithelium: Only top living layer has to be
squamous. Usually serves to protect underlying tissue. Can be keratinized
(skin cells) or non-keratinized (mouth, vagina, esophagus)
Transitional Epithelium: Stratified epithelium thatlines urinary system
from center of kidney (Renal calyx) to bladder. Allows stretching.
-rounded (bumpy) surface is identifying characteristic
Pseudostratified epithelium (Respiratory Epithelium): All cells contact
the basement membrane, but not all are exposed to the lumen
3) Explain replacement of epithelium:
Determined cells can undergo mitosis to form new cells (liver, endothelium)
or stem cells can undergo mitosis and determination (intestines, skin). In
stratified epitheliums, the new cells are generated near the basement
membrane and migrate to the top as cells are sloughed off.
4) Explain different types of glandular secretion:
Merocrine:secretory granule fuses with the PM and dumps it contents intothe ECF
Apocrine:secretory granule leaves cell where its contents are still enclosed
in plasma membrane (i.e. mammary glands secreting milk)
Holocrine:Whole cell lyses and dumps contents (ex/ sebaceous gland)
Paracrine: Cell releases contents that then signals nearby cells. Commonly,
this occurs with signaling molecules that degrade quickly and can thus only
act on nearby cells.
Autocrine: Cell releases contents that then binds to same cell (B-cells)
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Cell-cell/Cell-matrix interactions 9/29/2011 10:01:00 AM
Multicellularity allows cells to specialize and carry out more tasks
simultaneously
To become multicellular:
- Contact and communicate with other cells
- Regulate passage of environmental substances into and out oforganism
- Recognize self/non-self
Occluding/tight junctions: do not involve cytoskeletal elements
Formed by claudin and occludin (transmembrane proteins)
associations
Form tight seal that that not allow most molecules to pass through
Found usually on apicolateral surface of cells (epithelial usually)
Anchoring junctions: do involve cytoskeletal elements
Actin Microfilament
associated
Intermediate
Filament associated
Cell-cell junction
(mediated by
cadherins)
Adherens junctions Desmosomes
Cell-matrix junction
(mediated by
integrins)
Focal adhesions Hemidesmosomes
Homophilicvs. heterophilicbinding
Cadherin family:
Calcium-dependent adhesion molecules
Low Ca++: cadherins are largely disorganized
~1mM Ca++: Dimers form extracellularly, nucleates other dimers molecular zipper
Adherens Junctions: Desmosomes:
E-, N-, VE-cadherins (classical) Desmocollin, desmoglein
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Linked to actin cytoskeleton Linked to IF via
plakoglobin/desmoplakin
via / catenin
*Cadherins mediate cell-cell sorting where cells expressing the samecadherins (hemophilic binding) associate with each other and organize into
structures
Other adhesion molecules:
Ig superfamily:
Ca-independent family of proteins that are weaker than cadherins and can
be both homophilic and heterophilic
Selectins
Ca-dependent group of adhesion molecules that bind oligosaccharide lectins
(heterophilic)
Low affinity binding. Responsible for leukocyte rolling
ECM
Hydrated, polysaccharide gel substance with fibrous proteins embedded,
important for physical stability and diffusion of important substances.
Usually formed via fibroblasts. The basal lamina is a specialized form of ECMlaid down by epithelial cells.
ECM components
Glycosaminoglycans(GAGs):
Unbranched, repeating disaccharide units.
Hydrophilic, highly negatively charged- responsible for resisting
compressive forces
Ex: hyaluronan
Proteoglycans:
Protein + GAG = proteoglycan
Formed by a tetrasaccharide link
Structral and cell-cell signaling roles
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Fibrous proteins:
Collagen long inflexible fibers providing strength
Elastin - mesh-like fibers that provide flexibility
Fibronectin recognized by attachment proteins
Laminin - recognized by attachment proteins
Integrins
Transmembrane receptors (heterodimeric) with affinity for RGD motif in
fibronectin.
Linked to actin/IF cytoskeleton via talin.
Can communicate bi-directionally.
ECM cell: Leukocyte recruitment
Cell ECM: ECM remodeling for pathfinders
Communicating junctions: mediate chemical or electrical signals from one
cell to another
Gap junctions
Mediated by membrane channels called connexons, which are formed by 6
connexin proteins
Permeability affected by pH and Ca++ (open with high pH, low Ca++)
Chemical synapsesFast type of paracrine signaling
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Blood 9/29/2011 10:01:00 AM
Element Function
Identifying
characteristic
Abund
ance Lineage
Erythrocyte
transport O2,
transport a little
CO2
no nucleus or other
organelles, biconcave
shape, appear
electron dense
most
abundant
proerythroblasts ->
erythroblasts ->
reticulocytes (no
nucleus) -> RBCs (left
bone marrow, no more
RNA)
Thrombocyte
(platelets)
trigger thrombi
to limit blood
loss at injury
site; aggregate
w/ platelets,
alter blood flow,
initiate
coagulation
cascade
discoid, small
fragments (small
specks interpsersed
w RBCs) many
megakaryoblast -
>megakaryocyte (in
bone marrow) -->
1000 platelet clumps
(made of cytoplasm)
Neutrophil
phagocytosis &
destruction of
bacteria
multilobed; clear or
light pink granules 60-70% myeloid cell
Eosinophil
destroy larger
parasites /
modulated
allergic
response
multi-lobed (2);
pink/orange granules 1-3%
myeloid cell
Basophil
release
histamine &
heparin
(anticoagulation
)
S-shaped nucleus,
blue/black granules phagocytosis
irregular, kidney-
shaped nucleus; no
granules 4-10%
lymphoid cell: enter
lymphoid organs -->
macrophages (Myeloid
lineage)
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Lymphocyte
B cells -->
plasma cells; T
cells -->
immune rxns
large, round, dark
nucleus 20-30%
myeloid cell: B cells --
> plasma cells
Megakaryocyte
produce
platelets;
located in bone
marrow
largest cell; has
clusters of
proplatelets
Reticulocytes
produce RBCs;
located in bone
marrow
look like RBCs but
still have RNA (blue
stain in cytoplasm)
Plasma cells
found in
connective
tissue; secrete
targeted
antibodies
lots of rough ER that
is dilated; clumps of
heterochromatin; no
storage vessicles
Macrophages
found in
connective
tissue;
phagocytic; act
as antigen-
presenters
many cytoplasmic
processes, numerous
lysosomes
Remember: Never Let Monkeys Eat Banas
7/27/2019 Microanatomy -
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9/29/2011 10:01:00 AM
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