Amoebas are very small
Oh ah ee oo there's absolutely no strife
living the timeless life
I don't need a wife
living the timeless life
If I need a friend I just give a wriggle
Split right down the middle
And when I look there's two of me
Both as handsome as can be
Oh here we go slithering, here we go slithering and squelching on
-Incredible string band, A very cellular song

Cell Biology

Assignment
Audesirk, Audesirk & Byers Chapter 4

Today's musical selection
Five blobs - The blob

Figure E42a
Euglena complex Eukaryotic cell - self sufficient, swim, see, photosynthesize

Figure 4-20
Prokaryote

Figure 4-3
Eukaryote

Figure E42c
Protozoan (Paramecium)
vs. Metazoan complex, starts as 1 cell.

Figure 4-10
divide (Mitoses) - daughter cells
become specialized

control of gene expression (in multicellular organism):
(1) different genes turned on in different cells (and at different times)
(2) ALL CELLS HAVE SAME GENES - CELLS DIFFERENT BY WHICH GENES ARE TURNED ON
(3) but this can be fairly permanent, developmental change in gene regulation

Figure 4-1
Microscopy:
gives relative sizes and emphasizes the importance of light and electron microscopy.

Dyes (that absorb light) are used to highlight substructures in cells. Consider, for instance, the word "chromosome" which translates to "colored body."

Similarly, electron dense materials, heavy metals like osmium, uranium and lead create an electron density in the EM.

Since I have done some EM, I offer these pictures to give you a feeling of how EM is done. Sections are cut with an ultramicrotome using a diamond knife and sections, floated onto water are picked up on small copper grids. The grid is put into an evacuated column in the EM (like Figure E41c), and, at low magnification, a ribbon of sections can be seen.

Figure. 4-2
The cell membrane is a selective barrier to polar, charged, hydrophilic molecules and ions. These need to be pumped at the expense of energy or come through specific channels (pore molecules) through the membrane (more later in membrane coverage).

Eukaryotic cells have specific little bodies that are the small cell parallel of organs in the body, and hence they are called "organelles."

Figure 4-4
plant cell, note cell wall, plasmodesmata, chloroplasts and large vacuole.

Figure 4-3 (again)
animal cell. Below, we will go through the following structures one at a time: nucleus, endoplasmic reticulum (rough and smooth), Golgi apparatus, flagellum

Figure 4-9a
Nucleus - double envelope with pores

Figure 4-12
Ribosomes & RER (rough endoplasmic reticulum) where mRNA is translated into protein, "rough" describing the ribosomes that can be seen in the electron microscope. Also, here is an EM from my work showing RER.

Figure 4-12 (continued)
There is also smooth ER where reactions other than protein synthesis take place, such as steroid hormone synthesis, detoxification of substances in liver. Liver hepatocytes detoxify. Barbiturates induce an increase in the "microsomal fraction," smooth ER as seen after grinding and spinning down in a centriguge tube

Figure 4-11
Also free ribosomes and polysomes in the cytoplasm that make proteins that go to different places.
Protein synthesis - goes at 10 amino acids per second

Figure 4-13
Golgi apparatus receives vesicles from ER (at cis face) and send secretory products that bleb off (from trans side) reactions after protein synthesis (post-translational modification of proteins) take place in Golgi complex.

Figure 4-14
It is very interesting to consider the different routings for different proteins in the cell.
this figure ("sidedness of the plasma membrane") reminds us that inside the ER, Golgi complex, or vesicle is outside the cell, much like inside the gut is outside the body.

FigureE4-2d
Figure 4-17
Mitochondria has a inner and outer membranes, the inner one with shelves called cristae.
The function of the mitochondrion in ATP production

Theory that mitochondria (and chloroplasts), with their double membranes, are evolved from prokaryotes, engulfed into eukaryotic cells; They have some genes.

Also mitochondria are intimastely involved in programmed cell death (apoptosis)

Figure 4-18
chloroplast with 2 membranes plus granum with thylakoid membranes, frets and stroma. Note that the pigmernts for photosynthesis, in order to be absorbed by light, are deployed in multiple layers of membranes.

Figure 4-15
Lysosomes, need to introduce phagocytosis (phag - eat as in hyperphagic, eating too much, or bacteriophage, a virus that infects bacteria)
Lysosomes merge and digest.
This also applies to autophagy, where cell eats itself in a process of turnover of its components.
Here is a picture from my own work of lysosomes merging with recycled membranes in the Drosophila visual receptor,

Figure 4-7
Microtubules
flagella and cilia - "9 + 2" arrangement
Paramecia swimming cilia - beat reverses when bump

Figure 4-8
sperm flagella, cilia to clear mucus from trachea

Figure 4-6
Microfilaments
(will be covered in muscle lectures)
also many other functions, streaming and anchoring of cytoplasm

Questions used in 2007 and 2008 relating to this outline

Posttranslational modifications are changes that are made to
(a) phage.
(b) cells when they are being prepared for microscopy.
(c) bacterial DNA.
(d) mitochondria.
*(e) proteins.

The Golgi apparatus receives vesicles from
(a) chromosomes.
(b) the nucleolus.
*(c) the rough endoplasmic reticulum.
(d) the cell wall.
(e) autophagy.

To "attack" antigens, an antibody
(a) uses phagocytosis.
(b) injects its RNA into the cell.
(c) must be polyunsaturated
(d) must reside within the lysosome.
*(e) is put out of the cell by exocytosis.

The primary structure of a protein
(a) depends on whether it is a "self" vs. a "non-self" protein.
(b) has to do with whether there is an alpha helix or a beta sheet.
*(c) depends on the sequence of amino acids.
(d) depends on glycosylation.
(e) is exemplified by the alpha and beta chains in hemoglobin.

ATP, is made
(a) by chopping out fragments from a protein.
*(b) in cytoplasm and mitochondria.
(c) during apotosis.
(d) by plasmids.
(e) by smooth endoplasmic reticulum.

Euglena
(a) have a cell wall made of chitin.
(b) are metazoans with different genes active in different cells of the body.
(c) are so small that they can only be seen in the electron microscope.
*(d) have photosynthesis.
(e) are prokaryotes.

Mitochondria and chloroplasts are thought to have originated about 1.5 billion years ago
(a) when the microsomal fraction assembled into the smooth endoplasmic reticulum.
(b) as vesicles that blebbed off of the Golgi apparatus.
*(c) when prokaryotes became engulfed into the primordial eukaryotic cell.
(d) because of a mass extinction.
(e) because of genetic drift.

Ribosomes exist as free ribosomes, polysomes, and
(a) attached to the basal body.
(b) attached to the Golgi complex.
(c) attached to the chromosomes.
*(d) attached to the rough endoplasmic reticulum.
(e) in the spindle apparatus.

In phagocytosis, a food vacuole (endosome) merges with
*(a) a lysosome.
(b) a cilium.
(c) a microfilament.
(d) plasmodesmata.
(e) a nephridium.

Ribosomes are the site of synthesis of
A) DNA.
B) phagocytosis.
C) ATP.
D) nucleoli.
*E) proteins.

Which of the following is associated with rough endoplasmic reticulum?
A) chlorophyll
*B) ribosomes
C) cholesterol
D) microtubules
E) mitosis

What is not characteristic of a prokaryotic cell?
A) a cell membrane
*B) a nuclear membrane
C) a cell wall
D) plasmids
E) DNA

Receptors are membrane proteins that would be synthesized on ribosomes
*A) on the rough endoplasmic reticulum
B) on the smooth endoplasmic reticulum
C) on the Golgi complex
D) in the chloroplast
E) in the nucleus

Which organelle does one expect to be most abundant in cells that need lots of biological energy like cardiac muscle cells?
A) vacuoles
B) lysosomes
C) Golgi complexes
D) smooth ER
*E) mitochondria

If all the lysosomes within a cell suddenly ruptured, what could occur?
A) If it were a prokaryotic cell, it would become a eukaryotic cell.
B) If it were a Paramecium, it would swim backwards.
*C) The macromolecules in the cell cytoplasm would be broken down.
D) Antibody proteins would be exocytosed.
E) Proteins would be translated from DNA in vesicles.

Cells that primarily produce steroid hormones, as well as liver cells that destroy toxins, have large quantities of
A) apoptosis.
*B) smooth endoplasmic reticulum.
C) cell walls.
D) heavy metals.
E) flagella

The Golgi packages materials into ________ for transport or exocytosis.
A) cilia
B) plasmids
*C) vesicles
D) vacuoles
E) nucleoli

Which organelle would a white blood cell use to destroy a bacterium it has phagocytosed?
A) nucleus
B) mitochondrion
*C) lysosome
D) polysome
E) flagellum

Which order describes the flow between endoplasmic reticulum (ER), exocytotic vesicles, and Golgi apparatus in the export of protein from the cell?
A) From Golgi to ER to vesicle.
*B) From ER to Golgi to vesicles.
C) From vesicles to Golgi to ER.
D) From Golgi to vesicle to ER.
E) From vesicles to ER to Golgi.

Questions used in 2002 relating to this outline (and other outlines)

Ribosomes might be situated (A-where?) and serve (B-what function?).
(a) A in the nucleus; B to store genetic information.
(b) A in the Golgi apparatus; B to deliver energy.
*(c) A in the rough endoplasmic reticulum; B to synthesize proteins.
(d) A in the plasmalemma; B to mediate transcription.
(e) A in the desmosome; B to carry the genetic code for each protein.

Lysosomes would function to
(a) make glucose from CO2 and H2O using energy from light.
(b) modify proteins coming from the endoplasmic reticulum.
(c) allow cells to move ("swim").
*(d) break down membrane-enclosed cellular waste or food.
(e) carry oxygen from the lungs to the tissues.

In which cellular organelle is most of the ATP produced from thorough glucose catabolism?
(a) nucleus
(b) rough endoplasmic reticulum
*(c) mitochondrion
(d) flagellum
(e) chloroplast

If a biochemist grinds up liver and isolates microsomes as fraction in the centrifuge tube, what would this organelle with enzymes for detoxifying alcohol, drugs or toxins, be as seen in an electron microscope?
*(a) smooth endoplasmic reticulum
(b) tight junction
(c) nuclear envelope
(d) microtubules
(e) contractile vacuole

When you see dark areas in transmission electron microscopy or what appear to be membrane proteins in freeze-fracture, you are actually seeing
(a) colored dyes such as those that make chromosomes to appear as colored bodies.
*(b) heavy metals such as osmium, lead, uranium and platinum.
(c) individual molecules.
(d) the effects of radioactive isotopes.
(e) covalent and ionic bonds.

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