Sunday, June 17, 2012

Biological Sciences 5 (Generalized Eukaryotic Cell)

Generalized Eukaryotic Cell

Day 8:


For some eukaryotic cell not specifically any animal or plant, just a concept of typically multicellular life...

The National Science Foundation Virtual Cell Tour

A. Nucleus and Other Defining Characteristics

The nucleus of the cell contains DNA, the DNA must be copied (transcription) into RNA (mRNA, tRNA, rRNA), mRNA is spliced to remove introns and the exons are spliced together, then pre-mRNA gets a methylated cap and poly-A tail, then the mRNA leaves the nucleus through a nuclear pore.

1. Defining Characteristics (Membrane-Bound Nucleus, Presence of Organelles, Mitotic Division)
The DNA in a eukoryote is in a nucleus with a membrane (except during part of mytosis) , organelles with membranes (like mitochondria) are in the cytoplasm, mitosis occurs, replacing dead cells with exact copies of living cells.

Mitosis usually takes 80 minutes and occurs every 24 hours in most cells.

The National Science Foundation Mitosis Video

2. Nucleus (Compartmentalization, Storage of Genetic Information)
Genetic information (stored in DNA/chromosomes) has its own room (the nucleus), all the other organelle just crash on the couch in the living room (cytoplasm).

3. Nucleolus (Location, Function)
Like a desk in a bedroom (the nucleus), most of the writing (transcription of rRNA) takes place there. It is seen as a dark circle in the nucleus.

4. Nuclear Envelope, Nuclear Pores
The nuclear envelope are the walls surrounding the nucleus (there are an inner and an outer wall) and the nuclear pores are the doors (transcription factors go in and RNA comes out).

B. Membrane-Bound Organelles

A membrane separate from the cell membrane is what constitutes an organelle. Vacuoles don't even have to have anything in them.

This Video Reviews Most Oraganelles

1. Mitochondria
 All mitochondria are provided by the mother in humans, thanks mom (for that much).

Mitochondria are enslaved photosynthetic purple bacterium:

A. Site of ATP Production
ATP is made in mitochondria (see cool video on "Molecular Biology: Enzymes and Metabolism" post under the Electron Transport Chain section). The inner-membrane space is H+ saturated, the matrix is H+ deficient. Mitochondria replicate independently (during G2).

B. Self-Replication; Have Own DNA and Ribosomes
Mitochondria have their own DNA, genome, and ribosomes because they were once a separate organism (endosymbiosis theory). 

Exercise does have a positive effect on causing more mitochondria to be produced thus providing more natural energy, as opposed to unhealthy energy drinks. Read the study by Elizabeth Menshikova and friends in the National Library of Medicine:

C. Inner and Outer Membrane
The inner membrane surrounds the matrix, folding into cristae (nooks and crannies), between the outer and inner membrane is the intermembrane space (ATP synthase hangs out there getting high on protons), the outer membrane separates the mitochondria from everything else. 

2. Lysosomes (Vesicles Containing Hydrolytic Enzymes)
The digestive sac of the cell. Can rupture and kill the cell under certain circumstances. Made in the Golgi Apparatus. Kill old mitochondria and foreign invaders.

Normal pH 5. Contains over 40 enzymes including proteases, nucleases and phospholipases.

3. Endoplasmic Reticulum
Transport highway of the cell.

Endoplasmic Reticulum (A. Hugh Pelham, B. Petra Boevink and Chris Hawes)

A. Rough (RER) and Smooth (SER)
Smooth endoplasmic reticulum lacks ribosomes, rough endoplasmic reticulum has ribosomes. How are ribosomes are like crack whores? They are found in rough areas. SER produces fat and steriods, and consumes carbohydrates and drugs. Eating carbohydrates is the number one reason Americans are the fattest on the planet, 47.7% overweight in 2012. The smooth ER can turn the unneeded carbohydrate right into fat. Obesity will cost $957 billion by 2030 according to the American Heart Association. Is it worth the profit Wonder Bread and Pillsbury? Is it really? Maybe the health care system should pay the bread and chip companies to not sell their products...

RER folds, modifies, exports and synthesis protein. 
SER in muscles stores and regulates calcium.

B. RER (Site of Ribosomes)
The ribosomes are on the outside of the tubes and deposit protein inside the lumen. 

C. Role in Membrane Biosynthesis: SER (Lipids), RER (Transmembrane Proteins)
SER makes walls of fat (lipids)
RER makes signs (transmembrane proteins)

Day 9:

D. RER (Role in Biosynthesis of Transmembrane and Secreted Proteins that Cotranslationally Targeted to RER by Signal Sequence)
The ER captures proteins from the cytosol. Proteins may be transmembrane proteins (partialy translocated across the ER membrane) or water-soluble proteins (fully translocated across the ER membrane and released into the ER lumen). Import is a co-translational process. The protein is never released into the cytosol, so chaperone proteins are not needed. A signal sequence at the beginning of a transmembrane protein recruits a signal recognition particle that drags it to the RER, at the end the signal sequence is clipped off when the protein is done.

4. Golgi Apparatus (General Structure; Role in Packaging, Secretion, and Modification of Glycoprotein Carbohydrates)
It is funny to know that Camillo Golgi was kind of an ass. 

He (left) and Santiago Cajal (right) had differing viewpoints about neurons and in 1906 when they were jointly awarded the Nobel Prize. Golgi told everyone that Cajal's theory was wrong (which it was not) at the ceremony is Stockholm. It's part of a video produced by the Nobel Prize Organization, about the history of neuroscience and the study of memory.

History of Neuroscience Video -->

The golgi apparatus looks like a stack of pancakes, it functions to secrete macromolecules from the ER, via exocytosis. Glycoprotein is protein with sugar (saccharides). Goli apparatus can glycosylate proteins as well as modify them affecting structure, function and protect it from degradation.

The National Science Foundation Golgi Protein Trafficking Video

The National Science Foundation Golgi Protein Modification Video

C. Plasma Membrane (Phospholipid Bilayer)

1. General Function in Cell Containment
The cell must have a border to be distinct, the plasma membrane surrounds the cell allowing somethings in (food, oxygen) and somethings out (waste, hormones). The cell is mostly water, the cell membrane is mostly fat.

2. Protein and Lipid Components, Fluid Mosaic Model
The membrane has signal and transport proteins as well as the lipids. The fluid mosaic model refers to the fact that proteins float around unfixed within the lipid membrane.

3. Osmosis
Water can diffuse from area of low concentration to area of high concentration across any membrane. Osmosis is due to molecules bumping into each other and separating as a result of kinetic energy.

4. Passive and Active Transport
Passive transport is used to help move things across the membrane with out energy, like trash (ions) through a storm drain (ion channel). Active transport is used to help move things across the membrane using energy, like taking the bus (transport protein) into the city (cell).

5. Membrane Channels
Membrane channels do not require energy and are used mostly for ions.

6. Sodium–Potassium Pump
Sodium-potassium pump: 3 sodium (Na+) out help 2 potassium (K+) come in, therefore the cell maintains a negative resting potential.

7. Membrane Receptors, Cell Signaling Pathways, Second Messengers

  • Membrane Receptors: Hormones can not cross the plasma membrane, they bind to receptors on the outside of cell membranes, which triggers the production of second messengers, which cause a change inside the cell (using a protein kinase cascade).
  • Cell Signaling Pathways: contact signaling uses physical contact, chemical signaling uses a receptor as a trigger (neurotransmitters or hormones). Electrical signaling uses a change in membrane potential as a trigger (causing contraction in muscles and release of neurotransmitters into synapse).
  • Secondary messengers relay signals from receptors on cell membranes to targets inside the cell. Earl Wilbur Sutherland Jr. discovered second messengers (Nobel Prize 1971). They can be hydrophobic, hydrophilic or gases.

8. Membrane Potential
The resting potential of the cell membrane is negative, due to the sodium-potassium pump.

9. Exocytosis and Endocytosis
Exocytosis throws out cell contents.
Endocytosis takes in cell contents.

10. Cell–Cell Communication (General Concepts of Cellular Adhesion)
Cells communicate with surrounding cells.

A. Gap Junctions
Connect cells, allowing signals to flow between the cells.

B. Tight Junctions
Holds cells together like snaps, but doesn't allow signals to flow between the cells.

C. Desmosomes
Connect cells by linking their cytoskeleton, provides mechanical strength.

Day 10:

D. Cytoskeleton

The substance of a cell. Cells are not empty, they have a structure supporting the gel of the cytoplasm, the cytoskeleton.

1. General Function in Cell Support and Movement
The shape of a cell is produced by the cytoskeleton. Movement of cells or of cell components is caused by the cytoskeleton.

2. Microfilaments (Composition; Role in Cleavage and Contractility)
Microfilaments are made of actin, cause cytokinesis, support cell shape by bearing tension.

3. Microtubules (Composition; Role in Support and Transport)
Microtubules are made of tubulin, form the mitotic spindle, cilia/flagella, cause intracellular transport of organelles and vesicles, support cell shape by bearing compression.

4. Intermediate Filaments (Role in Support)
Intermediate filaments are made of various components, support cell shape by bearing tension.

5. Composition and Function of Eukaryotic Cilia and Flagella
Cilia (used to move, sense pressure and clear mucus) and flagella (used to move) are made of microtubules.

6. Centrioles, Microtubule Organizing Centers
Centrioles are microtubule organizing centers. Microtubules radiate out of these centers, which are also made of microtubules.

E. Cell Cycle and Mitosis

The cell does its normal function most the time, then it divides into 2 cells to compensate for cells that naturally die.

Mitosis Video (This website has really pretty biological animation sequences)

1. Interphase (G1, S, G2) and Mitosis (Prophase, Metaphase, Anaphase, Telophase)
Interphase is when the cell can function normally. During G1 the cell grows and replicates organelles. During pre-S mitochondria are replicated. During S DNA is copied. During G2 cells spindle begins to form. During prophase, the nuclear membrane breaks down, chromatin condenses, mitotic spindles assemble, centrioles move toward opposite poles of the cell. During metaphase chromosomes line up on an equatorial plane. During anaphase sister chromatids get pulled apart. During telophase chromosomes return to normal, the nuclear membrane forms and the mitotic spindle dissolves.

2. Mitotic Structures and Processes
Centrioles create microtubules (asters and spindles) that move around DNA giving half to each new cell (one copy each of every gene).

A. Centrioles, Asters, Spindles
Centrioles are the main centers, asters are star shaped located at each pole, spindles are the microtubule fibers that arrange and move the chromosomes.

Mitotic Structures

B. Chromatids, Centromeres, Kinetochores
Chromatids form half a chromosome, centromeres connect the 2 chromatids forming a chromosome, kinetochores connect centromeres and spindle fibers.

C. Nuclear Membrane Breakdown and Reorganization
The nuclear membrane dissolves during prophase and reforms during telophase.

D.Mechanisms of Chromosome Movement
Microtubules connected to the kinetochores cause the chromosome movement.

3. Phases of Cell Cycle (G0, G1, S, G2,M)
G0: no cell replication Ex. muscles and nerves.
G1: growth, organelles are replicated.
S: DNA replicated, centrioles are replicated.
G2: growth, mitotic spindles form.
M: mitosis.

4. Growth Arrest
The cell stops growing (in M phase) due to mutation/damage, due to contact inhibition (crowding), or due to lack of food.

F. Apoptosis (Programmed Cell Death)

Programmed cell death, caused for caspases digesting the cell from within, macrophages clean up the debris, triggered by development or immune response.

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