Module 1/2 ECM And Basics

Question 1

Define gene

Answer 1

A segment of DNA sequence corresponding to a single protein

Question 2

Define genome

Answer 2

Organism’s complete DNA: it dictates nature of cell’s proteins along with when and where they’re made

Question 3

Eukaryotes vs Prokaryotes

Answer 3

Eukaryotes: Bigger, more elaborate, DNA stored in nucleus
Prokaryotes: Unicellular, DNA stored in cytoplasm.

Question 4

Describe the central dogma of cell biology

Answer 4

DNA > Transcription > pre-mRNA> RNA processing> mRNA > translation > protein

Question 5

What is cell specialization?

Answer 5

Certain cells can respond very differently to the same extracellular signal. This is done through changes in chromatin structure and methylation of DNA during development.

Question 6

What is combinatorial gene regulation?

Answer 6

A mechanism which allows for a small number of transcription factors to be combined, helping control the expression of a larger number of genes.

Question 7

What is the property of cell memory?

Answer 7

Pattern of gene expression responsible for identity that must be remembered and passed to daughter cells for divisions.

Question 8

Name the four forms of intracellular signaling

Answer 8

1. Contact-Dependent Signaling: Important during development and immune responses
2. Paracrine Signaling: Secreted molecules are local mediators, which act only on cells in the local environment.
3. Synaptic Signaling: Signaling across the synapse of two neurons.
4. Endocrine Signaling: Uses endocrine cells, which secrete signal molecules called hormones into bloodstream.

*Many use the same molecules but differ in terms of speed and selectivity.

Question 9

Examples of difference cell responses (salivary, cardiac, and muscle) to neurotransmitter acetylcholine.

Answer 9

Cardiac: Decrease rate and force of contraction
Salivary: Stimulates production of saliva
Skeletal: Causes muscle contraction because it also binds to different receptor proteins.

Question 10

How are cells linked? (CHECK THIS)

Answer 10

Attached directly to each other via cell-cell junctions and also within the extracellular matrix (ECM), which is a complex network of proteins and polysaccharide chains that the cells secrete. Examples are epithelial and connective tissue.

Question 11

What are the two main ways in which animal cells are bound together?

Answer 11

Epithelial Tissue: ECM is basal lamina, epithelium has the cells bounded to each by cell-cell junctions and also connected to basal lamina.
Connective Tissue: Examples include bone and tendon, and a formed from an ECM produced by cells that are distributed sparsely in the matrix. It’s a tissue that supports, connects, and separates different types of tissues and organs throughout the body.

Question 12

What is alternative splicing?

Answer 12

A cellular process where exons from the same gene are joined in different combinations, leading to different mRNA transcripts. That allows production of different proteins all from a single gene.

Question 13

What are ways a cell controls the proteins it makes?

Answer 13

Transcriptional control, RNA processing control, RNA transport and localization control, translational control, mRNA degradation control, protein activity control

Question 14

How do cells ensure cell memory?

Answer 14

Positive feedback loops where the cell-type transcription regulator is distributed to the daughter cells to activate it’s own transcription again.

Question 15

What are the main stress-bearing components in connective and epithelial tissue?

Answer 15

Epithelial: Cytoskeletons of the cells themselves.
Connective: The ECM.

Question 16

What are the cell junctions found in epithelial cells?

Answer 16

Tight Junctions: seals gap between epithelial cells

Adherens junctions: Connects actin filament bundle in one cells with that in the next cell

Desmosome: Connects intermediate filament in one cell with that in the next cell

Gap Junction: Allows passage of small water-soluble molecules from cell to cell.

Actin-linked-cell matrix junction: Anchors actin filaments to ECM

Hemidesmosome: Anchors intermediates filaments in a cell to the ECM

Question 17

What are the two transmembrane proteins that link cytoskeletons?

Answer 17

Cadherins: Mediate attachment of cell to cell
Integrins: Mediate attachment of cells to matrix

Question 18

What can appearance and disappearance of specific cadherins tell us?

Answer 18

They correlate with steps in embryonic process where cells regroup and change their contacts to create new tissue structures.

Question 19

What does connective tissue do?

Answer 19

It helps to support, connect, and separate different types of tissues and organs in the body.

Question 20

What are the 3 major classes of macromolecules that construct the ECM?

Answer 20

1. GAGs
2. Fibrous proteins
3. Large classes of non-collagen glycoproteins

Question 21

What is the most anionic (negative) molecules in the animal cells?

Answer 21

Glycosaminoglycan (GAG) chains. This causes it to start attracting positive ions, which attracts H20. Water is critical for the ECM, as this provides cushioning for the joints.

Question 22

What is the role of GAGs in the ECM?

Answer 22

Helps regulating the homing of other cells during injury and regeneration.

Question 23

What are the major proteins of the ECM?

Answer 23

Collagen (limit stretching and prevents tearing), elastin(recoil and stretching), fibronectin(cell attachment to matrix), and laminins.

Question 24

What is scurvy?

Answer 24

Deficiency in making the amino acids in collagen results in scurvy as it’s a lack of Vitamin C, which is one of the building blocks for collagen.

Question 25

What occurs during a mutation in the elastin gene?

Answer 25

Mutations in the elastin gene cause a deficiency of the protein in mice or humans result in narrowing of the aorta or other arteries as a result of excessive proliferation of smooth muscle cells in the arterial wall.

Question 26

What occurs during a mutation in the fibrillin gene?

Answer 26

Mutations result in Marfan’s syndrome, a relatively common human genetic disease affecting connective tissue that are rich in elastic fibers; in the most severely affected individuals, the aorta is prone to rupture.

Question 27

Describe the order of a collagenous fiber (smallest to biggest)

Answer 27

Polypeptide chain > triple helix collagen molecules> microfibril> fibril> collagenous fiber

Question 28

What is the name of a popular specific tripeptide sequence in cell engineering?

Answer 28

Arg-Gly-Asp, or RGD. It helps with cell adhesion to a solid surface.

Question 29

What are the three ways in which the basal laminae are organized?

Answer 29

Muscle, epithelium, and kidney glomerulus.

Question 30

Why is mimicking the ECM important in cell and tissue engineering?

Answer 30

Native tissues exists with a 3D viscoelastic environment (ECM) that guide development and homeostasis.

Question 31

What are the three elements to tissue engineering?

Answer 31

Scaffold, stem cells, biological signals

Question 32

What is one of the major limitations of tissue engineering?

Answer 32

The inability to provide sufficient blood supply in the initial phase after implantation. Vascularization is important or implants will need to just rely on diffusion for nutrients and supplies.

Question 33

What are PEG hydrogels and why is often used in cell/tissue engineering?

Answer 33

Polyethylene glycols (PEG) are hydrophilic polymers with high water content to promote cell viability. They are structurally and mechanically similar to ECM and allow nutrients to move freely between native tissue and cells encapsulated within the hydrogel

Question 34

What is a rheometer?

Answer 34

A laboratory device used to measure the way in which a liquid, suspension or slurry flows in response to applied forces. Storage modulus (G’) is the stored energy, representing the elastic portion.

Question 35

What’s the first step in isolating cells from tissues?

Answer 35

Disruption the ECM and cell-cell junctions via use of proteolytic enzymes such as trypsin and collagenase to digest proteins.

Question 36

Describe what FACs is

Answer 36

It stands for fluorescence-activated cell sorting and it’s a technique to purify cell population based on phenotypes and charges.

Question 37

What are cultures prepared directly from the tissues of an organism called? What does sub cultured mean?

Answer 37

Primary cultures. Subculture is basically making a new cell culture from a previous one.

Question 38

What is the process called when vertebrae cells stop dividing after a finite number of cell divisions in culture?

Answer 38

replicative cell senescence

Question 39

What type of antibodies are secreted by different B cell lineages?

Answer 39

Polyclonal

Question 40

What is a heterokaryon

Answer 40

Multinucleated cell that contains genetically different nuclei

Question 41

Polyclonal vs Monoclonal antibody

Answer 41

Polyclonal: Cheap to produce, mixed population of antibodies, may bind to different areas of target molecules, tolerant of small changes to protein structure
Monoclonal: Expensive to produce, single antibody species, only bind single specific site, may recognize a particular protein form

Question 42

What are some lab techniques used in cell and tissue engineering

Answer 42

SDS electrophoresis, chromatography, western blots, mass spectrometry, epitope tags.

Question 43

What proteins do cells secrete at the site of injury to recruit other cells for the inflammatory response?

Answer 43

Cytokines

Question 44

What is HA?

Answer 44

Hyaluronic acid and it’s the simplest of GAGs. It’s produced in large quantities during wound healing and acts as a lubricant in joint fluid.

Question 45

Name some functions of the ECM material.

Answer 45

Regulate activity of secreted proteins (creating a reservoir), protect proteins from degradation, protein binding and steric blocking, and alter or concentrate protein for presentation to cell surface receptors.

Question 46

What was the Weiss study to detect collagen damage?

Answer 46

Mechanical injury to connective tissue alters function of collagen. The group used CHPs to act as one of the strands in the triple helix that had a signaling protein to notify of the damage.