1. Cell Structure and Function
Chapter 7
Biology

2. Cell
Cells are the basic unit of structure and functional unit of living things.
English scientist named Robert Hooke made a simple microscope. He observed small, box-shaped structures, called cellulae (meaning small room)
The cell is the simplest component considered to be living. Cells can differ substantially from one another based on their function. (structure = function)

3. Cell Theory All living things are made of one or more cells.
Cells are the basic unit of structure and function in the organization of living things.
All cells come from pre-existing cells.
The cell is the simplest component considered to be living. Cells can differ substantially from one another based on their function. (structure = function)

4. Eukaryotic vs. Prokaryotic Cells
Eukaryotic cells contain DNA in the nucleus. Prokaryotic cells contain DNA in a concentrated region called the nucleoid.
Which domains (ABE) are prokaryotes? Which are eukaryotes?
We will talk more about prokaryotic cells later.
Cells share basic features:
All cells are bound by a plasma membrane
contains cytosol that has organelles suspended in it.
All cells contain chromosomes which have genes in the form of DNA
All cells have ribosomes that make proteins according to instructions from genes.
Nucleus is bounded by a double membrane, nucleoid is not membrane enclosed.
Eu = tru, karyon = kernel referring to the nucleus. Prok = before nucleus, reflecting that prokaryotic cells evolved before eukaryotic cells- tomorrow we will talk about how that happened
Within the cell is the cytoplasm. In eukaryotes, organelles are suspended in the cytosol of the cytoplasm. These organelles (with the exception of the ribosome) are not found in the prokaryotic cell. Prokaryotes are generally much smaller than eukaryotes.

5. Basic Structure of every Organism
Based on 1 of 2 types of cells
Prokaryotic
‘pro’ =before
‘karyon’ = kernel
Eukaryotic
‘eu’ = true

6. Basic Structure of every Organism
Based on 1 of 2 types of cells
Prokaryotic
Only exist in domains of Bacteria or Archaea
Eukaryotic
Protists, fungi, animals, and plants

7. Eukaryotic Cell (plant)

8. Eukaryotic Cell (animal)

9. Prokaryotic Cell (Bacteria)

10. Basic Common Feature of Both
Bound by selective barrier (plasma membrane)
Have cytosol (jellylike substance)
Where organelles and other components are found
Contain chromosomes
Carry genes in the form of DNA
Have ribosomes

11. Different Features of Both
Location of DNA
Eukaryotes
Most DNA is in nucleus
Nucleus is bound by double membrane
“true kernel”
Prokaryotes
DNA is concentrated in region not membrane-enclosed
Nucleoid

12. Different Features of Both
Cytoplasm
Eukaryotes
Region between the nucleus and plasma membrane
Contains a variety of organelles of specialized form and function
Prokaryotes
Interior of prokaryotic cell

13. Different Features of Both
Organelles
Eukaryotes
Membrane- bound organelles are Present
Specialized form and function
Prokaryotes
Absence of organelles

14. Different Features of Both
Size
Eukaryotes
Generally Larger than prokaryotes
Size relates to function
10 – 100um in diameter
Metabolic requirements limit size practicality of cells
Prokaryotes
Smallest cells known
1 – 5 um in diameter

15. Plasma Membrane
Acts as a selective barrier
Allows sufficient passage of oxygen, nutrients, and wastes to service entire cell

16. The Plasma Membrane
Plasma Membrane- a selective barrier (semipermeable) that allows passage of enough oxygen, nutrients, and wastes to and from the cell.
The plasma membrane is a lipid bilayer embedded with diverse proteins.
The logistics of carrying out cellular metabolism (coded in the DNA) sets lower limits on cell size. Metabolic requirements also impose theoretical upper limits on cells size At the boundary of the cells, the plasma membrane allows passage of nutrients. These organelles have a specialized structure and function. (cytosol is the fluid like portion of the cytoplasm)

17. Fluid Mosaic Model
Fluid Mosaic Model- membrane is a fluid structure with a “mosaic” of various proteins embedded in or attached to a phospholipid bilayer. (lipids and proteins are amphipathic)
Phospholipids form the cell membrane and are amphipathic- meaning they have a hydrophilic and hydrophobic region. Most of the proteins within membranes are amphipathic also.
Scientists began building models of the membrane long before they were ever seen with the EM. They had isolated membranes from RBCs and chemically analyzed them to determine presence of lipids and proteins.
Fluid Mosaic Model- proposed by SJ Singer and G. Nicolson in still the accepted model today.

18. Nucleus: Information Central
Nucleus- contains cellular DNA which includes most of the genes in the cell. The nucleus is surrounded by the nuclear envelope.
**Most of the genes in the cell? Where are the other genes? Where there is more DNA! Where is that? Mitochondria and chloroplast. The nucleus is usually the most conspicuous organelle in the cell (that means the one you can see the best- because it is usually the largest). Nuclear pores are lined with proteins called the pore complex that actually helps with movement in the nucleus.
Lipid bilayer includes proteins.
Also thought to be a nuclear matrix, protein fibers extending through the inside of the nucleus that helps organize genetic material so it functions efficiently.

19. Nucleus: Information Central
Chromosomes- structures that carry genetic information (DNA). Each chromosome contains one long DNA molecule.
Each eukaryotic species has a distinct number of chromosomes.
Chromatin- the complex of DNA and protein making up chromosomes.
Nucleolus- helps synthesize rRNA (ribosomal RNA) and ribosomes.
Within the nucleus, DNA is organized into discrete units called chromosomes.
The DNA molecule is associated with many proteins. Some of them help coil the DNA molecule of each chromosome, reducing its length and allowing it to fit into the nucleus.
When the cell is not dividing, chromatin is a diffuse mass, and chromosomes cannot be distinguished from one another. When cells begin to divide, the chromatin condenses, and chromosomes become visible.
Fruit flies have 8 chromosomes.
Sometimes there are more than 1 nucleoli.
Proteins enter the nucleolus from the cytoplasm and are assembled with rRNA into large and small subunits of ribosomes. These subunits then exit the nucleus through the nuclear pores, to the cytoplasm, where a large subunit and a small subunit can assemble into a ribosome.

20. *What else do you see in this picture of the nucleus that wasn’t discussed in the others? RER and ribosomes
3 places ribosomes are found- on nucleus, on RER, and free floating in the cytoplasm.

21. Ribosomes: Protein Factory
Ribosomes- made of rRNA and proteins- carry out protein synthesis.
Ribosomes exist as either free ribosomes (suspended in cytosol) or bound ribosomes (attached to the Rough ER or nuclear envelope)
The nucleus helps direct protein synthesis by synthesizing mRNA according to instructions in the DNA. The mRNA is then transported to the cytoplasm where ribosomes translate the mRNA genetic message into the primary structure of a specific polypeptide.
Cells that have high rates of protein synthesis, have a higher number of ribosomes, which also make them more likely ot have more or more prominent nucleoli, b/c nucleoli help make ribosomes. ***What kind of cells would these be? Muscle cells. Pancreas cells have a few million ribosomes. They secrete digestive enzymes.
Bound and free ribosomes are structurally identical and they can alternate between the two roles. Most of the proteins made on free ribosomes function in the cytosol (ie: enzymes that catalyze reactions to breakdown sugar), whereas bound ribosomes generally make proteins that are destined for insertion in membranes, or for export from the cell (secretion).

22. Endoplasmic Reticulum: Biological Factory
Endoplasmic Reticulum- consists of membranous tubules, and sacs, called cisternae.
Smooth ER- lacks ribosomes. Functions lipid synthesis, detoxification, and storing calcium ions.
Rough ER- has ribosomes on surface. Continuous with the nuclear envelope. Synthesizes glycoproteins and other secretory proteins.
Endomembrane system- includes nuclear envelope, ER, golgi, lysosomes, and vassicles and vacuoles and the plasma membrane
Smooth- helps synthesize oils, phospholipids (membranes) and steroids (sex hormones- testosterone and estrogen).
***considering that the smooth ER is used in detox, what organs in the body might contain a large amount of smooth ER? (liver) what other cells might contain lots of smooth ER? (sex cells- sperm and egg, cells in the ovaries and prostate.
Alcohol and some other drugs increase the rate of smooth ER proliferation, which causes quicker detox and requires more of the substance to experience the same effect. This could ultimately lessen the effect of antibiotics and other medications (because of increased tolerance). Part of the way that the smooth ER detoxifies is by adding a hydroxyl group
*What is a hydroxyl group? Is it polar or non polar? What does that mean about its solubility? This makes them easier to flush from the body.
Calcium ions are important for muscle contraction.
Rough- many cells secrete proteins produced by ribosomes attached to rough ER. For example, certain pancreatic cells synthesize the protein insulin in the ER and secrete to bloodstream. As a polypeptide chain grows from an ER ribosome, it is threaded into the lumen of the ER through a pore in the ER membrane (made of protein complexes) When polypeptide enters lumen it folds into native shape. (Discuss protein folding again- chaperonins). Most proteins synthesize are glycoproteins. Carbohydrate attached to protein. This occurs by enzymes in ER membrane.
The RER is responsible for making its own membrane. Like the smooth ER, it also makes membrane phospholipids- also transported via vesicles.

23. After secretory proteins are formed, ER keeps them separate by moving them to the transitional ER. They depart wrapped in the membranes of a vesicle.

24. Golgi Apparatus: Shipping and Receiving
Golgi Apparatus- made of flattened membranous sacs called cisternae. Has 2 sides the cis face (receiving) and the trans face (shipping).
When leaving ER, many transport vesicles travel to the Golgi- sorts, receives, ships, and some manufacturing.
Golgi has structural directionality- stacks on opposite sides differ in thickness and molecular composition. Cis face is usually locatd near the ER as much of the receiving is from the ER (via transport). A vesicle that comes from the ER can fuse with the cis face of Golgi.
Products of ER are typically modified between cis and trans regions. (maybe the carbs in a glycoprotein, or phospholipids altered) Many polysaccharides are made in golgi (for plant cell walls, etc). The cisternae on the cis face are less mature than the trans face. Most delicate modifications happen there. Before departing trans face, golgi sorts and identifies destination. (by adding specific phosphate groups, external molecules that recognize docking sites on certain organelles, etc) May also go to plasma membrane for secretion.

25. Lysosomes: Digestive Compartments
Lysosome- contains hydrolytic enzymes used to digest molecules.
Phagocytosis- “cell eating”- lysosome digesting food
Autophagy- lysosome breaking down damaged organelles.
Have an acidic environment, ideal for these enzymes. If a lysosome breaks open, these enzymes are not very active in cytoplasm because it has neutral pH (and enzymes have optimal pH and temperature where they thrive). Excessive leakage can cause cell death via self-digestion.
The hydrolytic enzymes and lysosomal membrane are made by the Rough ER and transported to the lysosome via the Golgi. These molecules may be sugars, amino acids, monomers, etc.
Many amoeba and protists eat by phagocytosis. Macrophages are white blood cells that do phagocytosis, by engulfing and destroying bacteria and invaders.
Autophagy- recycle the cell’s own material. These damaged organelles become surrounded by a membrane (unknown origin). Organic monomers returned to cytosol for reuse.
Lysosome helps the body to restore itself. Human liver cell recycles half of its macromolecules each week!
Tay Sachs- lysosomal storage disease- lipids build up in brain- inactive or lacking lipid digesting enzymes- genetic.

26. Vacuoles: Storage Centers
Vacuole- functions vary depending on cell type.
Food Vacuole
Contractile Vacuole
Central Vacuole
Pumps water to help maintain solute concentration. Some vacuoles can help store proteins or other cell stockpiles. In plants some contain poisonous materials to protect them from predators. Some vacuoles hold pigments for plant coloration. Some contain hydrolytic enzymes and function as lysosomes.

27. Mitochondria: Chemical Energy Supercenter
Mitochondria- site of cellular respiration.
Cellular Respiration- the process that uses O2 to generate ATP by extracting energy from sugars, fats, and other fuels.
*What is ATP?
Which cells need the number of ATP or have the highest metabolic activity that would have the highest number of mitochondria. Membranes have phospholipid bilayer with proteins. Inner membrane space is between the membranes. The matrix contains the mitochondrial DNA, and ribosomes and enzymes. Enzymes in the matrix help catalyze some of the reactions in cell respiration. (including atp synthase which helps make ATP). The foldings of the cristae enhance the surface area thus making cellular respiration more efficient.
Mitochondria can move around, change shapes, fuse, and divide.

28. Chloroplast: Light Energy Capturer
Chloroplast- found in plants and algae- the site of photosynthesis. Contain the green pigment chlorophyll.
Is a member of the plastid family- a group of plant organelles.
*Think back to secondary productivity diagram. Leaf makes energy, caterpillar eats leaf. What determines how much energy is available for caterpillar?
Stroma contains chloroplast DNA and ribosomes as well as enzymes.
Chloroplasts are mobile. They grow and pinch in two- reproducing themselves. They move around the cell along tracks of the ckytoskeleton.
Amyloplast- stores starch (amylose) in plants
Chromoplast- contains pigments that gives fruits orange and yellow pigments.

29. Peroxisomes: Oxidation
Peroxisomes- contain enzymes that remove hydrogen atoms and transfer them to oxygen, producing hydrogen peroxide (H2O2).
Some peroxisomes break down fatty acids into smaller molecules that can be used by the mitochondria as fuel for respiration. Some can detoxify in the liver by removing hydrogen. Peroxide itself is toxic to cells, but the peroxisomes compartmentalize it, and an enzyme inside break down peroxide to water. Specialized peroxisomes are found in plant seeds and store enzymes that convert fatty acids to sugar for emerging seedlings to use for energy until they can produce their own via photosynthesis. They can divide and make new peroxisomes.

30. Cytoskeleton
Cytoskeleton- a network of fibers extending throughout the cytoplasm- plays a major role in organizing the structure and activities of the cells.
Motor Proteins- allows for cell movement.
Cytoskeleton is composed of three types of structures: Microtubules, Microfilaments, and Intermediate Filaments
Main function of cytoskeleton is to give mechanical support to the cell and maintain its shape. Especially important for animal cells- bc they lack rigid cell walls.
Cytoskeletal elements and motor proteins allow whole cells to move along fibers outside the cell. Motor proteins also help bend and move flagella and cilia by gripping microtubules in those organelles and moving them against one another. A similar action causes muscle cells to contract. Motor proteins allow vesicles to move from RER to golgi and from there to other places in cell or plasma membrane for secretion. Cytoskeleton manipulates the plasma membrane making it bend inward to form food vacuoles or other phagocytic vesicles.

31. Cytoskeleton
Microtubules- the thickest cytoskeletal fiber, provide a track that organelles with motor proteins can move along. Help separate chromosomes during mitosis. Form flagella and cilia.
Centrosome- region where microtubules are organized. Contains a pair of centrioles. Only in animal cells.
Microtubules are hollow tubes constructed from a protein called tubulin- a dimer made of 2 subunits, alpha and beta tubulin, which are added to grow the length of the tubulin. Can also be disassembled to build microtubules somewhere else in the cell.
Cilia lining trachea (windpipe) sweeps debris out of lungs. In reproductive tract- cilia help move egg toward uterus.
Before animal cells divide, centrioles replicate. Centrioles help organize microtubule assembly in animal cells. They are only present in animal cells. Fungi and protein don’t have centrosomes with centrioles, but have well organized microtubules, so they have another organelle that plays this role.
Cilia may also act as a signal-receiving antenna which is important in early brain function and embryonic development. Transmit signals from cells environment to the interior, signaling pathways that may lead to changes in cell activities. Basal body anchors flagella or cilium to cell. Many times basal body in sperm flagella enters the egg and becomes a centriole. (structurally similar to centriole)

32. Cytoskeleton
Microfilaments- the thinnest fiber. Actin and myosin filaments help muscle cells contract. Aide in pseudopodia movement by converting cytoplasm from a liquid to a gel.
Cytoplasmic Streaming- circular flow of cytoplasm within cells. Speeds distribution of cell materials.
Sometimes called actin filaments- actin is a protein. The microfilament network forms just inside the plasma membrane and gives it a gel consistency, rather than the cytosol liquid consistency in the inner portions of cell. Microfilaments make up microvilli (found in intestinal cells). They help muscle cells contract by sliding past one another an shortening the cell. Microfilaments form a cleavage furrow that pinches a dividing anima cell in two. Cytoplasmic streaming is caused by gel sol transformations.
Microtubules and microfilaments are found in all eukaryotes.

33. Cytoskeleton
Intermediate Filaments- more permanent fixtures, fix the position of organelles and shape of the cell. Include keratin proteins.
Intermediate diameter. Bigger than microfilaments but smaller than microtubules. Microfilaments and microtubules break and reform, intermediate filaments do not. They maintain their shape even after cells die (ie: external skin cells)

34. Cell Wall
Cell Wall- extracellular structure of plant cells. Protects the cell, maintains its shape, and prevents excessive uptake of water. Holds the plant up against gravity.
Primary Cell Wall, Middle Lamella, Secondary Cell Wall
Plasmodesmata-perforations in the plant cell wall that allows cytoplasm to be continuous between neighboring plant cells.
Extracellular implies that it lies outside of the plasma membrane. Prokaryotes, fungi, and some protists also have cell walls. Sugars and proteins (such as cellulose) are secreted to extracellular space to help make plant cell walls strong. Embedded in a matrix of proteins and sugars.
Primary cell wall- thin and flexible- secreted by a young plant
Middle Lamella- thin layer rich in pectins (sticky polysacc) that glues adjacent cells together. Pectin is used as a thickening agen in jams and jellies.
When cell matures and stops growing, it strengthens its wall. Some plant cells doe this by secreting hardening substances into the primary wall. Others add a secondary wall between the plasma membrane and primary wall. Secondary wall is very strong. Plant cell walls are usually perforated by channels called plasmodesmata.

35. Passive Transport
Passive Transport- moves solute from high to low concentration. DOES NOT requires energy.
Passive transport occurs when the solute moves down its concentration gradient- thus requires no energy. Facilitated diffusion speeds up the process, but does not alter the direction of transport.
Ex: animal cells has a higher concentration of K+ ions and a lower concentration of NA+ ions on the inside than the outside. The membrane helps maintain this by pumping Na+ out and K+ in.
Discuss how ATP provides energy by breaking phosphate bond.
One way that ATP can power active transport is by transferring the terminal phosphate group to the transport protein. This causes the protein to change its shape in a way that transports the solute across the membrane (See picture)
Na/K in animal cells.

36. Diffusion
Diffusion- movement of molecules of any substance until they spread out evenly in the available space. (equilibrium).
Diffusion is a spontaneous process, needing no energy input.
Rule of Diffusion: in the absence of a force, a substance will diffuse from high concentration to low concentration.
Molecules have heat energy because of their constant motion.
Dynamic Equilibrium- molecules crossing the membrane at equal rates.
*Discuss concentration gradient. Diffusion down vs. against the gradient.
*Diffusion assumes that the membrane is permeable. Much of cellular transport, including update of oxygen. Diffuses into cell because of concentration gradient.

37. Diffusion
A substance diffuses down its own concentration gradient, unaffected by the concentration of other substances.
Diffusion is a form of passive transport- movement that does not require the cell to use energy.
The concentration gradient itself represents potential energy and drives diffusion.
What types of molecules diffuse with most ease? Small, nonpolar molecules.

38. Osmosis
Osmosis- the diffusion of water. Water diffuses from the region of lower solute concentration (higher water concentration) to the area of higher solute concentration (lower water concentration)- until equilibrium is reached.
Pores in this membrane are too small for sugar molecules to pass through, but large enough for water molecules.
Free water concentration- some of the water molecules are tied to the sugar molecules because water is polar. Those water molecules are unable to cross the membrane.

39. Osmosis
Tonicity- the ability of a surrounding solution to cause a cell to gain or lose water.
Hypertonic- concentration of solution is more than the cell. Cell will lose water, shrivel, and probably die.
Hypotonic- concentration of solution is less than the cell. Water will enter the cell and the cell will swell and lyse (burst).
Isotonic- concentration of solutions is the same on both sides of the membrane. No net movement of water = stable volume.
One reason that an increase in salinity can kill animals. If the lake becomes hypertonic to the animal cells, then the cells might shrivel and die. Taking up too much water can be equally hazardous.

40. Facilitated Diffusion
Facilitated Diffusion- passive transport aided by proteins.
Frequently involves polar molecules.
Ion Channels- channel proteins that transport ions down the concentration gradient. No energy required.
Gated Channels- open or close in response to a stimulus.
Most transport proteins are very specific- transporting some substances but not others.
2 types: channel proteins and carrier proteins- channel provide hydrophilic passageways allowing water molecules to diffuse very quickly (aquaporins- found in large quantities in plant cells, RBCs, and kidney cells, because these move a lot of water.) Kidney cells reclaim water from urine before it is excreted. If the kidneys did not do this function, you would pee about 180 L of urine per day and have to drink and equal volume.
Many ion channels are gated channels. Some of which respond to an electrical stimulus. Sometimes they open or close when a specific substance binds to the channel. These are functions of the nervous system.

41. Active Transport
Active Transport- moves solute from low to high concentration. Requires energy (usually ATP). Uses carrier proteins.
Active transport allows a cell to have an internal concentration different from its surroundings.
Sodium-Potassium Pump- an example of active transport that exchanges Na+ for K+ across the plasma membrane.
Passive transport occurs when the solute moves down its concentration gradient- thus requires no energy. Facilitated diffusion speeds up the process, but does not alter the direction of transport.
Ex: animal cells has a higher concentration of K+ ions and a lower concentration of NA+ ions on the inside than the outside. The membrane helps maintain this by pumping Na+ out and K+ in.
Discuss how ATP provides energy by breaking phosphate bond.
One way that ATP can power active transport is by transferring the terminal phosphate group to the transport protein. This causes the protein to change its shape in a way that transports the solute across the membrane (See picture)
Na/K in animal cells.

42. One way that ATP can power active transport is by transferring the terminal phosphate group to the transport protein. This causes the protein to change its shape in a way that transports the solute across the membrane (See picture)

43. Diffusion- hydrophobic molecules (nonpolar) and polar (hydrophilic) molecules at a very slow rate
Facilitated- polar (hydrophilic) molecules at a very fast rate. Channel proteins are for facilitated diffusion only. Carrier proteins for facilitated diffusion or active transport.
Active- ATP, carrier proteins
*Does each of these go with or against the concentration gradient?

44. Endocytosis/Exocytosis
Exocytosis- the secretion of large molecules by the fusion of vesicles with the plasma membrane. Requires energy.
Endocytosis- cell takes in molecules by forming new vesicles from the plasma membrane.
Phagocytosis- cell eating
Pinocytosis- cell drinking
Receptor-Mediated Endocytosis
The cell secretes large molecules by the fusion of vesicles with the plasma membrane. This includes proteins polysaccharides, etc. They generally cross in bulk. Requires energy.
When the vesicle membrane and plasma membrane come in contact, specific proteins rearrange the lipids of the bilayers so that the two membranes fuse. The contents then spill outside the cell and vesicle membrane becomes part of plasma membrane. Ex; pancreas cells secrete insulin via exocytosis. When plants are making cell walls, exocytosis delivers proteins tot eh outside of the cell. Neurons release neurotransmitters that signal other neurons or muscle cells.
*Where do those proteins come from? Golgi vesicles.
*How does the food vacuole get digested? *Lysosome.
One adds to plasma membrane- one takes away- over time evens out.

45. Endocytosis/Exocytosis
Humans use receptor mediated endocytosis to take in cholesterol for membrane synthesis and the synthesis of other steroids. Cholesterol travels in the blood in a form called LDL (low density lipoprotein) and binds to receptors on plasma membranes and enter the cells by endocytosis. (they must bind to the receptor to enter the cell).
Ligands- any molecule that binds specifically to a receptor site on another molecule. In this case, LDL.
In hypercholesterolemia (inherited) cholesterol in the blood cannot enter the cells because receptor proteins are defective or missing. Thus cholesterol accumulates in the blood where it contributes to early atherosclerosis. Impeding blood flow.