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Flashcards in Week 5 Deck (95):

What are the three germ layers in the embryo and what parts of the body do they give rise to?

  • Endoderm: visceral organs
  • Mesoderm: connective tissue and muscles (mesenchyme)
  • Ectoderm: epidermis and neural tissue


What are the seven types of connective tissue?

  • muscle tissue
  • nerve tissue
  • bone/cartilage tissue
  • hematopoietic cells
  • vascular tissue
  • fibrous tissue
  • adipose tissue.


What is the major cell of connective tissue and what is its function?

  • Major cell is the fibroblast
    • Function: synthesizes ECM/proteins (collagen/reticular fibers/elastic fibers)


What are the two main subtypes of connective tissue?

  • Name subtypes of these subytypes if any

Loose and Dense (Regular & Irregular)


What is the purpose and location of loose connective tissue?

  • Purpose - anchoring, support, source of cells
  • Location:
    • Underneath epithelium
    • Site of initial attack by bacteria - but will be destroyed by immune cells (i.e. mammary gland, gut epithelium) → swelling/edema


What is the composition of loose connective tissue?

  • Composition
    • Loosely arranged fibers that are irregular/disorganized
    • Sparse collagen fibers
    • Abundant ground substance
    • Abundant cells (immune cells)


What is the purpose and composition of regular dense connective tissue?

  • Purpose - strength
  • Composition

    • Collagen fibers in parallel array and densely packed


What are the three main locations of regular dense connective tissue fibers?

  • Tendon (muscle to bone)
  • Ligaments (bone to bone)
  • Aponeuroses (muscle to muscle)


What is the purpose and composition or irregular dense connective tissue fibers?

  • Purpose - resists stretching and distension (skin dermis/colon)
  • Composition
    • Mostly collagen fibers that are irregular (random orientation)
    • Sparse amounts of cells, mostly fibroblasts 


What is the purpose of the collagen fibers?

Allow for flexiblity with tensile strength


What is the composition of collagen fibers and what is the hierarchy of the structure?

  • Composition: procollagen (triple helix - 3 alpha chains) → collagen molecule (tropocollagen) → fibril → fibers

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Of reticular fibers, what is the:

  • purpose
  • location
  • composition (what type of collagen)
  • synthesizing cell

  • Purpose: provide supportive framework for cells
  • Location: supporting stroma in lymph nodes, spleen
  • Composition: Type III Collagen fibers, mesh-like arrangement (like a cage)
  • Synthesis: by fibroblast mostly


Of elastic fibers, what is the:

  • purpose
  • location
  • composition (what type of collagen)
  • synthesizing cell(s)

  • Purpose: allows tissue to stretch/distend, but return to original shape
  • Location: major part of vertebral ligaments, elastic arteries, larynx)
  • Composition: branching network
    • Central core of elastin
    • Surrounded by fibrillin microfibril - organizes elastin
    • Random coiling → elasticity
  • Synthesis: fibroblasts and smooth muscle cells


What is the extracellular matrix?

What three things does it contain?

  • Extracellular Matrix
    • Network that supports and surrounds cells within connective tissue
    • Contains: collagen, elastic fibers, ground substance (makes up a big component)


What is the description and composition of ground substance?

  • Description: watery substances that allow for the diffusion of oxygen/nutrients from vasculature to cells
  • Composition:
    • Proteoglycans
    • Glycosaminoglycans (GAGs) attached to core protein
    • Multi-adhesive glycoproteins - serve as attachment points within ground substance


What are the two types of connective tissue cells?

  • Resident Cell Population (permanent, non-migratory)
  • Wandering and Transient Cell Population (predominantly cells from the blood)


What are the 5 types of resident cell populations?

  • Fibroblast – main cell of connective tissue; makes collagen etc.
  • Macrophages (Tissue histiocyte) – phagocytic cell
  • Adipose Cells
  • Mast cells
  • Undifferentiated Mesenchymal Cells


What are the types of wandering and transient cell populations?

  • Wandering and Transient Cell Population – predominantly cells from blood
    • Lymphocytes
    • Plasma Cells
    • Neutrophils (PMN’s)
    • Eosinophils
    • Basophils
    • Monocytes


What are the types of collagenopathies (diseases of collagen)

  • Osteogenesis Imperfecta
  • Ehlers-Danlos Syndrome


How does osteogenesis imperfecta occur and what is it a defect in (what subtype specifically)?

  • Inheritable defect (most common autosomal dominant) of collagen Type I
    • Defect in quantity AND quality of collagen
  • Bone is most affected (90% of bone is Type I collagen)
  • Mutations in genes that code for a-1 and a-2 chains of collagen molecules


What are the symptoms associated with osteogenesis imperfecta?

  • Soft, thin, brittle, deformed bones - because of ineffective bone formation
    • Collagen forms abnormally (not parallel)
  • Very prone to repeated fractures with ineffectual healing
  • Blue sclera


How does Ehlers-Danlos Syndrome occur and what is it a defect in (what subtype specifically)?

  • Defect:
    • Collagen Type III
    • mutation in lysyl hydroxylase → abnormal cross-linking of collagen fibers


What tissues are most affected in Ehlers-Danlos Syndrome?

  • Tissues rich in collagen, such as skin and hollow organs (GI and blood vessels) are most affected
    • Tissues lack tensile strength → hyperextensile skin, hypermobile joints
      • joint dislocation
    • Skin is stretchable, fragile, prone to trauma,
    • Internal organs → rupture (GI, great vessels)
    • Rupture of cornea and retinal detachment


What are the two disorders of elastic fibers?

  • Marfan's Syndrome
  • Solar Elastosis of Skin


Where does the defect lie in Marfan's Syndrome?

What function does this defect affect and where is this protein abundant in?

  • Inherited defect in Fibrillin1 (glycoprotein)
  • Fibrillin1 is the scaffolding upon which tropoelastin is deposited to form elastic fibers
    • Particularly abundant in aorta, ligaments, and lens
      • Aortic Rupture


What causes solar elastosis of the skin and where do the defects lie?

  • Repeated exposure to ultraviolet radiation →  premature aging (wrinkling, solar elastosis, irregular pigmentation)
  • UV radiation → degradation of collagen and remodeling of fibrillin microfibrils →  truncated →  nonfunctional elastic fibers →  decreased skin elasticity
  • Seen as irregular fibers and bluish discoloration in dermis


How/Why does a keloid occur?

  • Hypertrophic scar, due to excessive collagen accumulation in response to injury
  • Does not regress on its own but extends beyond boundary of injury


What did Griffith's experiement achieve?

Dicovered the transformation of pathogenic pneumococcal S-bacteria strain to non-pathogenic R-bacteria to kill rats


What did Avery's experiement achieve?

Continuation of Griffith's experiment; Digestion of different macromolecule → proved DNA was the transforming principle


What did Watson and Crick's experiment achieve?

Discovered the basic DNA structure and base pairs


What does replication mean (in regards to DNA)?

Replication: transmission of likeness of DNA


What does information flow mean (in terms of DNA)?

  • Information Flow: DNA provides means for production of all of the cell’s proteins


What is mutability (in terms of DNA)?

  • Mutability: heritable changes in cellular properties


What part of DNA is considered the primary structure? What makes up each of these parts?

  • Mononucleotide Structure
    • Base – purines/pyrimidines
      • i.e. Adenine
    • Nucleoside – base + sugar (via N-glycosyl linkage)
      • i.e. adenosine
    • Nucleotides – base + sugar + phosphates
      • i.e. AMP, ADP, ATP
  • Polynucleotide Structure
    • 3’ → 5’ phosphodiester bond between sugar and phosphate


What makes up the secondary structure of DNA and what are the basic characteristics of this?

  • Helix is right handed
  • Sugar-phosphate backbone
  • A-T, C-G form inside of helix


What re the forces that keep the DNA double helix together?

  • Weak Forces: hydrogen bonds, hydrophobic, and stacking energy


Define the minor and major groove of DNA.

  • Major Groove: occurs where the backbones are far apart
  • Minor Groove: occurs where the backbones are close together


  • What is the conventional notation of DNA and how is it read?
  • What is the RNA transcript and what would it read in relation to the coding strand?
  • What is the DNA template strand and what would it read in relation to the coding strand?

  • Conventional Notation
    • Read 5’ to 3'
  • Coding Strand
    • Will be the strand similar to RNA transcript (opposite of template)
  • RNA Transcript
    • Homologous to Coding Strand, but U subbed for T
  • Template Strand
    • Strand read for RNA replication


Define denaturation (melting) of the double helix and how it occurs.

  • What else can cause denaturation?

  • Denaturation (melting): double helix unravels and separates into single strands by breaking hydrogen bonds
    • Each sequence of DNA has specific melting temperature Tm based on GC ratio
    • Heat, low pH, low salt concentration


Define reannealing.

  • Reannealing: bringing back complementary DNA strands into double helix


Define hybridization.

  • Hybridization: annealing of polynucleotides from unique sources (think PCR primers)


Compare the primary structure of RNA to that of DNA (3 differences).

  • Ribose (RNA) vs. deoxyribose (DNA)
  • Single-stranded (RNA) vs. double-stranded (DNA)
  • Uracil (RNA) vs. thyamine (DNA)


What is special about the primary structure and secondary structure of tRNA?

  • Primary Structure: tRNA utilizes modified bases in its primary structure
  • Secondary Structure: tRNA has 3 hairpin loops and stem structure


Compare the secondary structure of DNA to that of RNA.

  • Fold-back (hairpin) structure (RNA) vs. double helix (DNA)


What are the chemical differences in hydrolysis of RNA compared to those of DNA?

  • RNA is readily hydrolyzed in presence of high [OH-] at 2’-OH group
  • DNA lacks –OH group and is not easily hydrolyzed into mononucleotides


What are nucleases and what subclass is involved with DNA/RNA?

  • Nucleases: break polynucleotides into mononucleotides
    • Phosphodiesterases – class of enzymes which catalyze hydrolysis of phosphodiester linkages


What are restriction endonucleases, how do they function, and what are they used for?

  • Sequence-specific DNAses that cut in the middle of palindromic sites
  • Forms sticky ends that allow for human DNA to be inserted into vector for recombinant technology


  • What is the function of the DNA polymerases and at what side of the DNA strand do they work?
    • How do they work?
    • What do they require to work?

  • DNA polymerases catalyze the addition of nucleotides at the 3’ end; matches incoming nucleotide to the template
    • 3’ hydroxyl group attacks alpha-phosphate of incoming nucleotide
  • Require:
    • Both template nucleotides and a RNA primers


What are the different type of DNA polymerases for mammals and what are their functions?

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How often are mistakes made in DNA synthesis and how are they fixed?

  • A mistake is made about once every billion bases
  • DNA polymerases have 3’ to 5’ exonuclease activity (backwards) that can excise one wrong nucleotide and substitue the correct one.


What is the general description of Fragile X Syndrome and what three nucleotide segment repeats?

  • Fragile X
    • DNA polymerase slippage that causes trinucleotide repeat expansion
    • Repeating nucleotides: CGG


  • What occurs in the initiation step of DNA synthesis?
  • Where does it occur?

  • DNA sequence, called the origin
  • Primase adds an RNA primer to the origin which is extended by DNA polymerase


How is the RNA primer disposed of in humans?

RNA primer is excised and cleaved by endonucleases


  • Describe the leading strand and lagging strand in DNA synthesis and how many origins and primers they require?
    • What are the fragments made by lagging strands called?

  • Leading Strand: only requires one origin and primer
  • Lagging Strand: requires multiple origins and primers (Okazaki fragments)


What is the function of the DNA ligase?

completes gaps between Okazaki fragments


What is the function of the helicase?

opens up double helix following topoisomerase


What is the function of the topoisomerases?

promotes unwinding by removing DNA supercoils


What is the function of single-stranded-binding proteins?

stabilizes the fragments and prevents binding


Which enzymes can change the topology (relaxed vs supercoiled) of DNA?

What are the two types of this enzyme and how do they work?


  • Topoisomerase I
    • Makes a temporary single-stranded break that allows relaxation of a superhelix
  • Topoisomerase II
    • Makes a temporary double-stranded break to pass around another portion of DNA


  • What are toposiomerase inhibitors and what are they used as?
  • What are the two examples? How do they work?

  • Topoisomerase Inhibitors: supercoil accumulation can lead to apoptosis of the cell
    • Doxorubicin: inhibits topoisomerase II, allowing superhelical turns to accumulate and signal apoptosis
    • Etoposide: inhibits topoisomerase II by binding the enzyme-complex and trapping the complex in its cleavable state


How is biological information based down to progeny in humans?

22 pairs of homologous autosomes + 2 sex chromosomes


How are choromosome composed...

in the nucleus?

during metaphase?

  • In the nucleus, the chromatic material is condensed into an indistinguishable mass
  • During mitosis, chromosomes separate into chromatids, which make them easy to identify under the microscope


What stains are used to distinguish chromosomes?

Giemsa stains are used to fix mitotic chromosomes, creating a reproducible banding pattern


What is a karyotype? 


Difference between p and q arms?

Karyotype - the visualization of chromosomes based on number, size, and shape

P - short arm

Q - long arm


How do karyotypes differ between species?

Karyotypes vary between closely related species, but all code for a similar amount of proteins (# of chromosomes are not proportional to amount of genetic info)


What is X-chromosome inactivation?

How does it occur?

One X chromosome is inactivated due to presence of two X chromosomes carrying the same info (XP is paternal and XM is maternal)

Inactivation occurs by Xist RNA, which create Barr bodies that condense randomly chosen chromosomes to heterochromatin thereby inactivating the gene


What is mosaicism?

Mosaic manifestation occurs when XP and XM are inactivated at random embryonic stages causing the appearance of different phenotypes in different areas


Describe origin of replications?

  • Origin of replication ensures precise chromosomal reduplication in the S Phase of the cell cycle
    • DNA deletions in certain regions upstream can cause inactivation of origin of replication


Descirbe centromeres.


What are kinetochores?

  • Centromeres determine chromatid separation during cell division
    • Kinetochores are located at centromeres and are where the microtubules attach



Describe teleomeres.

  • Protect chromosomal ends from shortening during replication
  • Is defined by the sequence: AGGGTT
  • Telomeres shorten with each cell division, and too much shortening can block cell division
  • Telomeres are replenished by telomerases in germ-line cells. They contain RNA-dependent DNA polymerase
  • Telomerases are also found in cancer cells allow for indefinite cell division


Describe SNPs.

SNP (single nucleotide polymorphism): allow for distinguishing of homologous chromosomes (due to different nucleotides)


Stages of mitosis?

How does it work?

  • Mitosis
    • PMAT
    • Occurs with homologous chromosomes and separates them


Stages of meiosis?


How does it work?

  • PMAT x 2
  • Occurs with chromatids, forms tetrads through synapsis and separates them into daughter cells
  • Occurs only in gametogenesis


Define the key concepts in genetic analysis: gene, allele, phenotype, genotype.

  • Gene: basic units of hereditary information that occupy a fixed position (locus) on the genome
  • Allele: variant forms of a gene located at the same locus of a chromosome
  • Genotype: the allelic forms of the genetic info (i.e. Bb, bb)
  • Phenotype: the physical characteristic that is manifested by the genotype (i.e. black hair)


What are the types of genotypes?

  • Heterozygous: one dominant allele and one recessive allele (i.e. Bb)
  • Homozygous: either both dominant alleles or both recessive alleles (i.e. BB or bb)


Describe the role of meiosis in relation to allele segregation.

Alleles segregate during meiosis and new allelic combinations form in the zygote


Explain the law of segregation.

  • Each gamete from each parent (4 total) contains an allele
  • One gamete is chosen from each parent to produce an allelic genotype of the descending generation


How do different genotypes lead to differing phenotypes?

  • Presence of a dominant allele (homozygous dominant or heterozygous dominant) produces a dominant phenotype
  • Homozygous recessive produces a recessive phenotype


What are pedigrees?

How are they used?

  • Circle indicates female, square indicates male
  • Pedigrees can be used to deduce allele possibilities in descending generations
  • Helps determine recessive, dominant, and x-linked mutations based on the individuals in each generation


Explain dominat negative mutations.

Dominant negative mutations: a loss of function dominant mutation that poses a negative effect on the wildtype


Explain reduced/incomplete penetrance.


Reduced/incomplete penetrance: individuals that do not express the trait even though they carry the allele (absence or presence)


Explain variable expressivitiy.

Variable expressivity: refers to a degree of expression rather than its absence or presence


Explain pleiotrophy.

Pleiotropy: a single genotype that affects multiple phenotypes (many body systems are usually affected)


Explain co-dominance.

Co-dominance: Alleles that are presented equally in heterozygous state or dominant state (i.e. blood groups)


Explain mitochrondrial inheritance.


How does it relate to heteroplasmy?

If a mother is affected with a mitochondrial mutation, all her children will inherit the mutation as well - only the maternal mitochondrial DNA is inherited

Heteroplasmy: Daughter cells inherit different versions of the genome (mutated vs normal). Mutations are caused only after mutated mitochondrial DNA accumulates


Explain both sex-linked linkages.


List some related diseases. 

  • Y-chromosome linkage:
    • Affected males will pass mutations onto every single male son
  • X-chromosome linkage:
    • No male to male inheritance
    • Carrier female has a 50% chance of passing gene to her children
      • Daughters who receive the trait will be heterozygous
      • Sons who receive the gene will hemizygous and will manifest the trait
  • Diseases: Hemophilia, Duchenne’s, Fragile X


What type of tissue is the arrow pointing to?

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Loose Connective 



abundant cells in layer and irregular pattern 


What type of tissue is surrounding the black circle?

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Loose Connective 


*Circle is the mammary gland.


abundant cells in layer and irregular pattern 


What type of tissue is depeicted in the image?

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Dense Irregular Connective


Fibers in irregular pattern


What type of tissue is depicted in the image?

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Dense regular connective 


fibers in parrallel pattern


What type of fiber is depicted in the image below?

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Reticular fiber




mesh like structure. 


Identify tissue fiber.

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Elastic fibers


long fibers look like slinky(s)


Identify this picture.  

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Ground substance.





Identify this. 

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Cartilage matrix


Little blue cells with two dots - classical sign of collgen - Caleb


Identify what is around the green circle.

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white globs