Download Chapter 3—The Cell I. Cell Theory. a. Organisms are made of 1 or

Chapter 3—The Cell
I.
II.
III.
IV.
V.
Cell Theory.
a. Organisms are made of 1 or more cells.
b. The cell is the smallest unit having the properties of life.
c. All cells come from pre-existing cells.
Cell structure and function.
a. Prokaryotic cells—single celled organisms (Domains Bacteria and Archaea) that don’t have a
nucleus or other membrane bound organelles; they do have a plasma (cell) membrane. Fig. 3.1.
i. They do contain non-membrane bound organelles (ribosomes, cytoskeletal elements);
their DNA is dispersed loosely within the cell’s cytoplasm (the watery environment
inside the cell).
b. Eukaryotes (Domain Eukarya)—more complex cell forms. All eukaryotic cells share these
features: Fig. 3.2.
i. Plasma membrane—allows cellular reactions to proceed in a controlled environment.
ii. A variety of membrane bound organelles, which carry out specific cellular functions.
iii. Nucleus—membrane bound organelle that contains DNA.
iv. Cytoplasm—water based environment that includes all substances/organelles within the
cell, except the nucleus.
c. Table 3.1 provides a nice summary eukaryotic vs. prokaryotic cellular features.
Cell size and microscopy. [First sentence in book contains a typo: “…micrometers (µm), which are
equal to 1/1000 millimeter (mm).”]
a. Units of measurement:
i. 1 m = 1000 mm
ii. 1 mm = 10-3 m = 1000 µm
iii. 1 µm = 0.000001 m = 10-6 m = 10-3 mm
iv. 1 nm = 0.000000001 m = 10-9 m = 10-6 mm
v. 1000 nm = 1 µm
vi. 0.001 µm = 1 nm
vii. Typical eukaryotic cells = 10 µm to 500 µm.
viii. Typical prokaryotic cells = 1 µm to 10 µm.
ix. Typical virus = 20 nm to 1000 nm.
b. Surface area to volume ratio: Fig. 3.3.
i. As a cell increases in size, its surface area increases at a slower rate that its volume
increases.
c. Most cells are too small to be seen with the naked eye. Fig. 3.4.
Cell structure and function. Fig. 3.5.
a. The structure of a cell reflects its function. Examples:
i. Sperm cell.
ii. Egg cell.
iii. Red blood cell.
iv. Cardiac muscle cell.
Plasma (cell) membranes—arranged in a phospholipid bi-layer. Fig. 3.6.
a. Outside the plasma membrane is the extracellular (interstitial) fluid, while the cytoplasm resides
on the inner side of the plasma membrane.
i. Embedded within the phospholipid bi-layer are proteins and other molecules
(carbohydrates, glycoproteins, lipoproteins, enzymes, etc.).
ii. Fluid mosaic model:
1. Fluidity is displayed by the lipids as they move about (rotational, side to side).
2. Mosaic—proteins are interspersed within the bi-layer.
b. Plasma membrane functions.
i. Maintains the cell’s structural integrity.
VI.
ii. Controls movements of substances into and out of the cell, maintaining critical
concentration gradients.
iii. Proteins within the phospholipid bi-layer include:
1. Transport proteins—bind molecules or ions on one side of the cell membrane and
release them on the other.
2. Receptor proteins—bind hormones or other chemical signals that trigger changes
in cellular activities.
3. Recognition proteins—identifies a cell as a specific type.
4. Adhesion proteins—aids some cells in remaining together at specific locations.
Movement across the plasma membrane.
a. Cell membranes are selectively permeable; some substances are not allowed to cross, while
others may cross at certain times in certain ways.
i. Small non-polar solutes freely cross the cell membrane (CO2, O2).
ii. Water may also cross, even though it is polar.
iii. Large polar molecules do not cross by themselves; a transport protein within the cell
membrane must bring them across.
b. Concentration gradients and diffusion.
i. Concentration gradient—difference in the number of molecules or ions of a particular
substance in two adjoining regions.
ii. Molecules move from a region where they are highly concentrated to a region where they
are less concentrated. This is called diffusion.
iii. In solutions where more than one solute is present, both diffuse down their own
concentration gradient.
iv. Charged solutes (ions) also diffuse down an electric gradient, which may oppose its
concentration gradient.
v. A pressure gradient (difference in pressure between two adjoining regions) also impacts
the diffusion of solutes.
c. Simple diffusion. Fig. 3.7.
i. Solute molecules move down their concentration gradient until equilibrium is reached.
1. The solute may or may not be moving across a plasma membrane.
2. No energy input is required for this to occur; just the existence of a gradient.
d. Facilitated diffusion. Fig. 3.8.
i. Large molecules and polar molecules/ions can’t cross cell membranes on their own.
1. The interior of the membrane is hydrophobic, which repels ions and polar
molecules.
ii. The solute diffuses down its concentration gradient through the inside of a transport
protein spanning the phospholipid bi-layer. No energy input is required for these
transport mechanisms to occur.
iii. Transport proteins allow one type of solute to pass, but not others.
e. Osmosis—diffusion of water across a selectively permeable membrane in response to solute
concentration gradients. No energy input is required for osmosis to occur. Fig. 3.9.
i. Tonicity—the relative concentration of the solutes in two fluids, including fluids
separated by a semi-permeable membrane.
1. Isotonic solutions—when the two fluids contain equal concentrations of solute, no
net movement of water across the membrane occurs.
2. When solute concentration is not equal across a semi-permeable membrane, one
fluid is hypotonic (has fewer solutes) and the other fluid is hypertonic (has more
solutes).
3. Because water moves down its concentration gradient, it moves from a hypotonic
to a hypertonic solution.
VII.
4. Osmotic pressure is a result of water passing from a hypotonic solution to a
hypertonic solution through a selectively permeable membrane. Water moves
into the region where solutes are more concentrated.
5. Hydrostatic pressure—mechanical pressure, such as a plasma membrane’s
resistance to stretching.
f. In "active transport" a solute crosses the cell membrane through a transport protein against its
concentration gradient. For this to occur, energy (ATP) is required. Fig. 3.10.
i. Na+/K+ pumps constantly work to pump K+ into your cells and Na+ out, against the
concentration gradients for these ions. (3 Na+ out, 2 K+ in).
g. Bulk movement of materials across a membrane is accomplished by vesicles (small membrane
bound sacs).
i. Endocytosis—the cell membrane sinks inward and seals itself, trapping some fluid and
substances from the exterior.
1. Phagocytosis—when organic matter is brought in. Fig. 3.11a.
2. Pinocytosis—when liquids are brought in. Fig. 3.11b.
ii. Exocytosis—a vesicle made inside the cell fuses with the cell membrane and releases its
contents to the cell's exterior. Fig. 3.12.
h. Table 3.2 provides a nice summary of the processes listed above.
Organelles.
a. Eukaryotic cells contain organelles; each serves a specialized function within a cell.
i. Membrane bound organelles provide a physical barrier that separates incompatible
reactions. They allow for interconnected reactions to occur at different times. They
include:
1. Nucleus.
2. Endoplasmic reticulum.
3. Golgi body.
4. Vesicles.
5. Lysosomes.
6. Peroxisomes.
7. Mitochondria.
ii. Non-membrane bound organelles include:
1. Ribosomes.
2. Cytoskeleton.
b. Nucleus—contains the DNA, and keeps it separated from other parts of the cell. Fig. 3.13.
i. Nucleolus—location of active protein and rRNA synthesis.
1. Proteins are assembled due to the action of ribosomes and RNA.
ii. Nuclear envelope—a pair of lipid bi-layers. The outer one is continuous with the
endoplasmic reticulum. Transport proteins span the bi-layers.
iii. Chromosomes—each is an individual molecule of DNA and associated proteins;
chromatin is all the cell's DNA and associated proteins. Fig. 3.14.
c. Endoplasmic reticulum (ER)—extension of the nuclear envelope that curves into the cytoplasm.
Fig. 3.15.
i. Rough ER—appears as stacked flattened sacs with ribosomes attached on the outer
surface; ribosomes assemble proteins.
1. Newly formed proteins enter the internal space of the rough ER for further
processing and modification.
2. These proteins are then enclosed in vesicles that bud from the rough ER and are
sent to the Golgi complex for further processing (discussed below).
3. In addition to ribosomes that stud the outer surface of the rough ER, free
ribosomes exist within the cell’s cytoplasm.
ii. Smooth ER—no ribosomes are found here. Smooth ER is the main site of phospholipid
synthesis and drug/toxin detoxification.
VIII.
IX.
1. Phospholipids synthesized here are used to replenish those lost due to the
formation of vesicles from the rough ER.
d. Golgi complex—enzymes found here modify newly formed lipids and proteins arriving from the
rough ER. They are then sorted and sent out in vesicles. Fig. 3.16.
i. Golgi complex is composed of a series of flattened membranous sacks.
e. Lysosomes—digest intracellular materials. Form by budding from the Golgi complex.
i. Fig. 3.17 shows a summary of how some vesicles form within the cell.
ii. Fig. 3.18 shows how lysosomes function within the cell.
f. Peroxisomes—break down fatty acids and amino acids. They break down approximately half of
all consumed alcohol. Operate in a fashion similar to lysosomes.
g. Mitochondria—construct ATP from energy derived from the breakdown of glucose and other
organic molecules. Oxygen is required for this to occur. Fig. 3.19.
i. Has a double membrane with the inner membrane folded in a labyrinthine fashion =
cristae. On the inside of the inner membrane is the matrix (inner compartment).
ii. Resembles a bacterium.
1. Has its own DNA and ribosomes.
2. It divides on its own.
3. Was once a free-living organism.
a. Endosymbiotic theory.
h. Table 3.3 provides a nice summary of the membrane bound organelles.
Cytoskeleton—system of fibers, threads, and lattices within the cell. Composed of microtubules,
microtubule organizing centers that contain the centrioles, intermediate filaments, and
microfilaments.
a. Gives cells their shape.
b. Provides for internal organization of the cell.
c. Gives some cells the ability to move.
d. Provide pathways for vesicles and organelles to travel on within the cell.
e. Participate in cell division.
f. Can be organized into highly motile structures. Fig. 3.21.
i. Flagella—relatively large, single whip-like structure that propels many free-living
eukaryotic cells. Sperm.
ii. Cilia—shorter than flagella, and one ciliated cell typically has many cilia that beat in a
regular, coordinated motion.
Cellular respiration and fermentation in the generation of ATP.
a. Metabolism—the use of energy to build, store, break up, and eliminate substances in a controlled
manner. ATP is the energy currency inside the cell that that links reactions that require energy
input to reactions that release energy.
b. Metabolic pathway—reactions proceeding one after another in orderly steps, mediated by
enzymes.
i. Biosynthetic (anabolic) pathway—small molecules are assembled into larger molecules
of higher energy content. Condensation (dehydration) synthesis reactions…
ii. Degradative (catabolic) pathway—large molecules are broken down to products of lower
energy content. Hydrolysis reactions…
c. Substrates (reactants or precursors) are substances that enter a reaction.
d. Intermediates—substances formed between the start and end of a metabolic pathway.
e. End products—substances present at the end of a metabolic pathway.
f. Enzyme—speeds up the reaction rate of, and lowers the activation energy of a specific chemical
reaction. (Enzyme vs. Catalyst).
i. Enzymes are proteins, but some RNA molecules show enzymatic properties.
ii. All enzymes share these features:
1. They don't cause a reaction to occur that wouldn't occur on its own.
2. They are not permanently altered or consumed in the reaction.
X.
XI.
3. An enzyme sometimes can catalyze a reaction in both directions.
4. Each enzyme is highly selective about its substrate.
iii. An enzyme has one or more "active sites"—crevices and pockets in the enzyme surface
where substrates interact with the enzyme and where a specific biochemical reaction is
catalyzed.
iv. Enzymes work best within a specific temperature and pH range.
v. Control of Enzymes.
1. Rate of enzyme synthesis.
2. Hormonal control to stimulate or inhibit enzymes.
3. Competitive inhibition.
4. Non-competitive inhibition.
5. Feedback inhibition.
g. Coenzymes and cofactors—organic molecules or metal ions that:
i. Assist enzymes.
ii. Transport electrons.
iii. Transport atoms.
iv. Many coenzymes are complex organic molecules derived from vitamins.
1. NAD+ and FAD transfer electrons from one site to another. When loaded with
electrons (and protons), they are abbreviated NADH and FADH2.
2. Some metal ions (ferrous iron Fe++) also serve as cofactors.
h. Energy carriers—donate energy to substances by transferring functional groups to them. The
major energy carrier for humans is ATP.
i. ADP/ATP cycle.
i. In aerobic cellular respiration, energy input drives the attachment of Pi (inorganic
phosphate = PO4-3) to ADP to form ATP. When ATP releases a phosphate group, it
becomes ADP. (ATP  ADP + Pi).
j. Oxidation-reduction reactions (Redox).
i. When a molecule or substance gives up one or more electrons, it is said to be "oxidized."
ii. When a molecule or substance accepts electrons, it is said to be "reduced."
iii. LEO the lion goes GER.
1. Electrons don’t exist in isolation; protons (H+) follow…
a. 1 electron + 1 proton = 1 hydrogen atom…
Capturing energy in ATP.
a. The transfer of a phosphate group from ATP to another molecule is called a phosphorylation
reaction.
b. Cells make ATP by breaking covalent bonds of carbohydrates, lipids, proteins and nucleic acids;
electrons are removed from intermediate compounds and the energy associated with these
electrons drives the formation of ATP.
Cellular respiration—may be aerobic or anaerobic. The metabolic reactions involved in both include
glycolysis, an intermediate step/transition reaction, the Krebs (citric acid) cycle, and the electron
transport chain (ETC).
a. Aerobic cellular respiration—metabolic pathway of ATP formation where oxygen is the final
electron acceptor.
b. Anaerobic cellular respiration—pathway where some other substance (not oxygen) is the final
electron acceptor.
i. Only parts of the Krebs (citric acid) cycle and ETC operate in anaerobic respiration.
c. Fermentation is a separate metabolic process from cellular respiration.
i. Some books mistakenly label fermentation as anaerobic respiration.
ii. Although fermentation does not use oxygen, and is therefore an anaerobic process, it is
not the same thing as anaerobic cellular respiration.
iii. The final electron acceptor is always a derivative of pyruvate (pyruvic acid).
d. The cellular respiration (aerobic and anaerobic) pathways and fermentation pathway all begin
with glycolysis.
e. Glycolysis—series of reactions in which glucose is broken down into pyruvate (pyruvic acid)
with a net yield of 2 ATP molecules. Fig. 3.22.
i. Takes place within the cytoplasm.
ii. Oxygen plays no role.
iii. For glycolysis to occur, energy (2 ATP) is required to start the reactions.
iv. 2 ATP phosphorylate the glucose molecule, raising its energy content.
v. The phosphorylated glucose then goes through a series of reactions where 4 ADP
molecules each bond to a phosphate group to form 4 ATP molecules = substrate level
phosphorylation.
vi. Net energy yield is 2 ATP.
vii. Electrons and hydrogen ions (H+) released during the reactions are transferred to the
coenzyme NAD+ to form NADH. These are destined for the electron transport chain.
1. NAD+ is the oxidized form of the coenzyme, NADH is the reduced form.
viii. 2 pyruvate (pyruvic acid) molecules are left at the end of glycolysis.
f. Transition reaction/intermediate step. Fig. 3.23.
i. Pyruvate (pyruvic acid) formed by glycolysis may enter a mitochondrion.
ii. Within the mitochondrial matrix the aerobic cellular respiration pathway continues.
iii. In the transition reaction/intermediate step, pyruvate (pyruvic acid), coenzyme A, and
NAD+ come together to form CO2 , NADH, and Acetyl-CoA.
g. Krebs (citric acid) cycle. Fig. 3.24.
i. Acetyl-CoA bonds to oxaloacetate, which is the entry point of the Krebs cycle, where
more steps in the breakdown of the original glucose molecule take place.
ii. These reactions serve three functions:
1. NAD+ and FAD pick up hydrogen ions (H+) and electrons to become NADH and
FADH2.
2. 2 molecules of ATP are produced by substrate level phosphorylation.
3. Intermediates of the Krebs cycle are rearranged into oxaloacetate so the cycle may
continue.
iii. These reactions form 2 ATP and load many coenzymes (NAD+ and FAD) with hydrogen
ions (H+) and electrons for transport to the sites of the final stage of the aerobic pathway.
h. Electron transport chain (ETC) = Oxidative phosphorylation. Fig. 3.25.
i. This is the generation of ATP within a mitochondrion in a reaction sequence that requires
coenzymes and consumes oxygen.
ii. The key reactions occur in the electron transport system, a series of proteins in the inner
membrane of the mitochondrion, where electrons are transferred from one protein to
another, in a specific sequence, via a series of oxidation-reduction reactions.
iii. These reactions set up hydrogen ion (H+) concentration and electrical gradients, which
ultimately drives the formation of ATP from ADP and unbound phosphate.
iv. Oxygen is the final electron acceptor; protons = hydrogen ions (H+) also bind to oxygen.
This results in the production of metabolic water.
i. Glycolysis and aerobic respiration of a single glucose molecule typically yields 36 ATP (net) but
some cells can make 38 ATP (net). Fig. 3.26.
i. For each glucose molecule processed:
1. 2 (net) ATP are gained from glycolysis.
2. 4 (or 6) ATP are gained from the NADH (generated in glycolysis) from ETC.
3. 2 ATP from the Krebs (citric acid) cycle by means of an intermediate (GTP).
4. 28 ATP from NADH and FADH2 (from the Krebs cycle) via oxidative
phosphorylation in the ETC.
ii. Table 3.4 summarizes the production of ATP in aerobic cellular respiration.
j. ATP from anaerobic cellular respiration.
i. Glycolysis proceeds as previously described.
ii. Only portions of the Krebs (citric acid) cycle and the ETC operate. Therefore, the yield
of ATP is less than what is produced in the aerobic pathway.
1. More than 2 but less than 38 ATP are produced, depending on the organism.
2. Final electron acceptor is something other than oxygen; nitrate, sulfate, carbonate
ions.
k. Fermentation.
i. Glucose can also be used as a substrate for fermentation pathways.
ii. Glycolysis proceeds as discussed earlier, with pyruvate (pyruvic acid) as the end product.
iii. In lactate (lactic acid) fermentation (in muscle cells) pyruvate (pyruvic acid) accepts
hydrogen ions (H+) and electrons from NADH, which converts the pyruvate (pyruvic
acid) into lactate (lactic acid).
1. This regenerates NAD+ so it can participate in another round of glycolysis.
2. This is good for short bursts of energy only, because glucose reserves within
muscles are used quickly.
3. Lactate (lactic acid) produced by muscle cells diffuses into the blood and is
converted back to pyruvate (pyruvic acid) after exercise ends.
l. Alternative energy sources.
i. When food intake exceeds daily energy expenditures, ATP synthesis and the resulting
concentration of ATP can inhibit glycolysis. Instead of being broken into pyruvate,
glucose is converted into glycogen (a storage molecule).
ii. When blood glucose levels fall, glycogen reserves are broken down into glucose-6phosphate, which enters the glycolysis pathway. Liver cells can also convert it back into
glucose, which is released into the blood.
iii. 1% of stored energy in an adult is stored as glycogen.
iv. 78% is stored as fats.
v. 21% is stored as proteins.
vi. Excessive food intake results in the formation of fats—no matter what kind of food
consumed.
vii. Stored triglycerides are broken into:
1. glycerol, which is converted into PGAL (glycolysis intermediate).
2. fatty acids, which are broken down and converted to acetyl-CoA (Krebs cycle).
viii. The body doesn’t store the proteins it doesn’t use. Instead, the amino group (NH3) is
removed from each amino acid, with the carbon backbones being converted to fats or
carbohydrates; or, amino acids may enter the Krebs cycle, where the amino groups are
converted to urea, which is excreted in the urine.
ix. Nucleotides can also be used as reactants at various points in the aerobic pathway.
Study suggestions for this chapter: In the textbook at the end of the chapter, the sections entitled 1)
Highlighting the Concepts, 2) Recognizing Key Terms, and 3) Reviewing the Concepts are all good for you to
gauge your comprehension and focus your study efforts.