Biology 1406 Morris
Review for Exam #2: Chapters 5-8
Chapter 5: The Cell
Know the differences between a prokaryotic cell and a eukaryotic cell
Chloroplasts: photosynthesis; the light reactions take place in the thylakoid membranes (a stack
is called a granum); the Calvin Cycle takes place in the stroma
 Mitochondria: cellular respiration: takes place mainly in the mitochondrial matrix, but also on the
inner mitochondrial membranes (the folds are called cristae)
 Ribosomes: make protein
o Free ribosomes: make protein for use in the cytoplasm
o Bound ribosomes: make protein for use in membranes or export
 Rough ER: make protein for use in membranes or export
 Smooth ER: Synthesize lipids, detoxify poisons; stores calcium for muscle contraction, and does
carbohydrate metabolism
 Lysosomes: contain hydrolytic enzymes; do intracellular digestion of macromolecules; recycle
monomers; and programmed cell death; If lysosomal enzymes are missing or non-functional,
leads to Storage Diseases
 Peroxisomes: break down toxins, poisons, and lipids to make hydrogen peroxide, which the
peroxisome must break down to water and oxygen
 Nucleus: contains DNA (chromatin or chromosomes) and the nucleolus/nucleoli; bounded by a
PL bilayer called the nuclear envelope which has pores for material transport in and out of the
nucleus (like the ribosomal subunits, like mRNA, etc)
 Nucleolus: makes ribosomal subunits; may be more than one per cell if the cell needs to make a
lot of protein
 Golgi body: modifies, stores, and routes products of ER (glycoproteins and glycolipids)
 Centrosome: microtubule organizing center (when in animals, also contains centrioles)
 Centrioles: important in animals for cell division; it is made of microtubules; 9 sets of triplets in a
ring at right angles to each other
 Cilia/Flagella: made of microtubules in a 9 + 2 pattern (9 doubles plus 2 in the middle)
 Cytoskeleton: network of fibers throughout cytoplasm; microtubules, intermediate filaments,
microfilaments; familiarize with table in the book
 Communicating channels: allows material to pass from one cell to the other
o Plasmodesmata: in plants through the cell walls
o Gap junction: in animals
 Anchoring junctions:
o Tight junctions: belts that secure adjacent animal cells close together
o Desmosomes: rivets that anchor adjacent animal cells close together
 Central vacuole: storage compartment for plants
o Tonoplast: name of the central vacuole membrane
 Extracellular Matrix (ECM): meshwork of macromolecules found outside of plasma membranes
of animal eukaryote cells only
 Cell Wall: found outside the plasma membrane of all prokaryotes (bacteria) and some
eukaryotes (like plant eukaryotes)
o In bacteria (prokayotes): made of peptidoglycan
o In plants (eukaryotes): made of cellulose
o In fungi (eukaryotes): made of chitin
All Cells: have a plasma membrane; ribosomes; DNA/chromatin
Prokaryotes only: have a capsule; cell wall; pili/flagella (animals also have a flagella)
All Eukaryotes: microtubules/microfilaments, nucleus; mitochondria; rough or smooth ER,
peroxisomes; Golgi body; centrosomes; nucleolus
Plant Eukaryotes only: cell wall (but also in bacteria); central vacuole, tonoplast; chloroplast,
plasmodesmata
Animal Eukaryotes only: gap junction, centrioles; cilia/flagella, lysosomes, tight junctions,
desmosomes, ECM
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Dr. Solti, 2014
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Biology 1406 Morris
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Dr. Solti, 2014
Chapter 5: Membranes
Function of plasma membrane: to physically separate all living cells from the external
environment and to be selectively permeable
o All cells have a plasma membrane as a boundary
Know the Fluid Mosaic Model for plasma membranes: Know what a plasma membrane looks
like: phospholipid bilayer that is fluid and contains embedded proteins bobbing in it. The head
groups of the PL molecules are hydrophilic and turn outward, while the fatty acid tails are
hydrophobic and turn inward.
Know the functions of plasma membrane proteins
Know the function of glycoproteins and glycolipids in the membrane: cell recognition
Know the function of cholesterol in the membrane: fluidity
Understand the selective permeability of the plasma membrane:
o Cross the membrane easily: passive transport: nonpolar (hydrophobic) molecules such
as hydrocarbons and O2, as well as small polar molecules such as H2O and CO2.
o Difficulty crossing the membrane: large polar molecules such as glucose, as well as all
ions such as Na+ or K+. These need specific transport proteins to cross. See below
regarding facilitated diffusion and active transport. Study Review Figure 8.16.
Know the definitions of:
o Diffusion: spontaneous, net movement of a substance DOWN its concentration gradient.
Substance moves from a higher concentration to a lower concentration. Spontaneous,
passive process, - delta G. Needs no energy input.
o Osmosis: diffusion of water through a membrane
o Exocytosis: release of very large molecules out of cell
o Endocytosis: import of very large molecules into cell
o Phagocytosis: cell eating
o Pinocytosis: cell drinking
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Review for Exam #2: Chapters 5-8
o Hypotonic/Hypoosmotic: solution with low solute concentration compared to the cell
o Hypertonic/Hyperosmotic: solution with a high solute concentration compared to the cell
o Isotonic/Isoosmotic: equal solute concentrations
Know the water balance of living cells
o Animal cells have no cell walls:
 therefore in an isotonic solution, they are normal (water goes in and out)
 in a hypertonic solution, they shrivel or crenate (lose water)
 in a hypotonic solution, they lyse or burst (gain water)
o Plant cells HAVE cell walls:
 therefore in an isotonic solution, they are flaccid or limp (water goes in and out)
 in a hypertonic solution, they plasmolyze or shrivel (lose water). This is lethal to
the plant.
 in a hypotonic solution, they become turgid or normal (gain water)
Understand Facilitated Diffusion: This is a passive transport, so no ATP needed: but needs
transport proteins for diffusion of large polar molecules and ions to go DOWN the gradient
Understand Active Transport: This is an active transport (pumping) that needs ATP to pump
AGAINST the gradient. Needs transport proteins. Pumps mainly ions.
Cotransport: Couples “uphill” pumping with “downhill” diffusion.
Chapter 6: Metabolism
Metabolism: an organism’s complete chemical processes: manages the “chemicals” and
“energy” of cells
Catabolic pathway: Break down process which releases energy; examples :breaking down
complex macromolecules; cellular respiration
Anabolic pathway: Build up process which requires energy and then stores it; examples:
building up macromolecules; photosynthesis
Energy: the ability to do work
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Biology 1406 Morris
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Review for Exam #2: Chapters 5-8
Dr. Solti, 2014
o Kinetic energy: energy of motion
o Potential energy: energy of position (stored energy)
o Least useful form of energy: heat or thermal energy
1st Law of Thermodynamics: Conservation of Energy: energy can be transferred or transformed,
but not created or destroyed
2nd Law of Thermodynamics: Every energy transfer leads to an increase in the entropy (chaos or
disorderliness) of the universe
Free energy (delta G): energy available to do work; At equilibrium, delta G =0 and the cell dies.
Exergonic reactions: spontaneous, - delta G, the reactant does more work than the product,
similar to catabolic reactions, releases energy; example cellular respiration
Endergonic reactions: non-spontaneous, + delta G, the product does more work than the
reactant, similar to anabolic reactions; stores energy, example photosynthesis
ATP: adenosine triphosphate, similar to RNA nucleotide but with 2 additional phosphate groups;
ATP is the product of cellular respiration and it is critical for energy; used to couple exergonic
reactions (that give off energy) with endergonic reactions (that need energy)
o How does it work? Last phosphate group is hydrolyzed off ATP, then transferred to an
intermediate; the phosphorylated intermediate is very reactive and will do the chemical
work, lastly the phosphate leaves and you are left with ADP and Pi (which needs to be
regenerated again to ATP by cellular respiration).
Enzymes: are proteins that act as biological catalysts: they speed up chemical reactions without
changing the reaction or getting used up
o How do enzymes work? By lowering the energy of activation
o Enzymes are unique to their substrate
 Active site of enzyme: binds to the substrate; called an induced fit
Chapter 7: Cellular Respiration
Catabolic process, exergonic, - delta G, slowly releases energy to produce ATP, the ultimate
electron acceptor is O2.
Summarized as: C6H12O6 + 6O2 --------------------- > 6CO2 + 6H2O + energy (ATP)
ATP= adenosine triphosphate: works by transferring last phosphate to an intermediate
Redox reactions:
o Oxidation: loss of electrons (H+)
o Reduction: gaining of electrons (H+)
In cellular respiration:
o Glucose is oxidized to CO2
o Glucose (ultimately) gives its electrons to O2 (uses electron carriers first)
o Oxygen is reduced to H2O.
NAD+ = electron carrier that receives electrons from glucose and holds them until Stage 4 (ETC);
once it is carrying the electrons, it is NADH.
Stage 1: Glycolysis
o Occurs in cytoplasm
o The 1st 5 steps are energy requiring: splits the glucose into 2-3carbon glyceraldehyde 3
phosphates (G3P), needs 2 ATP
o The 2nd 5 steps are energy producing: re-organize the 2-G3P into 2-pyruvates, makes 4
ATP and 2NADH
o Partially oxidizes glucose to 2 – 3carbon pyruvates. Most of the energy of glucose
remains in the 2 pyruvate molecules.
o Makes no CO2.
o No oxygen required (takes place under aerobic or anaerobic conditions)
o Makes a net 2 ATP by substrate-level phosphorylation (5% of total ATP)
o Makes 2 NADH (to go to ETC)
Fate of pyruvate
o Depends on the presence or absence of O2
o If O2 available, pyruvate goes into mitochondria for Stage 2
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Biology 1406 Morris
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Review for Exam #2: Chapters 5-8
Dr. Solti, 2014
o If O2 is not available, the 2 pyruvates stay in cytoplasm and do anaerobic fermentation
Stage 2: Oxidation of Pyruvate
o Occurs in mitochondrial matrix (only if pyruvate sees O 2 available)
o Oxidizes the 2 pyruvates into 2 acetyl CoA
o Also makes 2 CO2 and 2 NADH
o Makes no ATP
Stage 3: Krebs Cycle
o Occurs in mitochondrial matrix
o Finishes glucose oxidation by oxidizing the 2-acetyl CoA’s into the 4 remaining CO 2
o Need 2 turns of Krebs/glucose (due to the 2 acetyl CoA’s)
o Makes 4 CO2
o Makes 6NADH, 2FADH2 (this is the only stage that uses FAD as an electron carrier)
o Makes 2 ATP by substrate level phosphorylation (other 5% of total ATP)
o Starts the cycle with oxaloacetate; ends the cycle with oxaloacetate
Stage 4: ETC and OxPhos
o ETC is the electron transport chain: found in the inner mitochondrial membranes (in the
cristae)
o OxPhos is oxidative phosphorylation: also found in inner mitochondrial membranes
o ETC receives the electrons from all of the NADH’s and FADH2’s, passes them from one
cytochrome protein to the next, until they reach O2 and oxygen is then reduced to H2O.
o This also allows for a slow release of energy, which allows the next set of steps to occur
o Chemiosmosis: linking step: links the exergonic ETC with the endergonic OxPhos;
consists of making a proton gradient across the inner mitochondrial membranes
 Starts as proton pumping (from low to high protons)
 Continues as a diffusion of protons back across the membranes
o Stage 4 ends with OxPhos, which is putting the phosphate back onto ADP to make ATP.
Allowed to happen due to energy released from ETC and chemiosmosis. The proton
diffusion goes through the enzyme, ATP Synthase, in order for OxPhos to occur.
(OxPhos is how the cell makes 90% of ATP)
Cellular respiration is the catabolism of the carbohydrates, lipids, and proteins that you eat; Only
nucleic acids are not involved in cellular respiration.
Fermentation: anaerobic catabolism of organic nutrients (no oxygen is available)
o Takes place in cytoplasm, instead of (aerobic) cellular respiration
o Glycolysis will occur whether you continue on with cellular respiration (yes O2) or
fermentation (no O2). Therefore, during fermentation, you only have the 2 ATPs from
glycolysis.
o Alcohol fermentation: occurs in bacteria and yeast; the only ATP made was by substrate
level phosphorylation in glycolysis previously; pyruvate is reduced to ethanol (pyruvate is
electron acceptor, NOT oxygen)
o Lactate fermentation: occurs in human muscle cells, yogurt, cheese; the only ATP made
is by substrate level phosphorylation previously in glycolysis; pyruvate is reduced to
lactate (pyruvate is electron acceptor, because there is no oxygen).
Chapter 8: Photosynthesis
Anabolic process; requires energy(sunlight) and stores energy; +delta G; transforms light energy
into chemical bond energy in glucose; sunlight is the energy source; CO2 is the carbon source
6CO2 + 6H2O +light energy --- C6H12O6 + 6O2
o H2O is oxidized (donates electrons to CO2); becomes O2
o CO2 is reduced (accepts electrons); becomes glucose
Leaves: major organs of photosynthesis
Chlorophyll: green pigment in the thylakoid membranes in the chloroplasts. Gives leaves its
color; absorbs sunlight
Mesophyll: cells in the green tissue of leaves that have chloroplasts
Stomata: openings on the underside of leaves which allow CO 2 in, and O2 out
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Biology 1406 Morris
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Review for Exam #2: Chapters 5-8
Dr. Solti, 2014
Sunlight is electromagnetic energy
o Has wave-like and particle-like behavior
o Visible light: 750 to 380 nm wavelengths; remembered as ROYGBIV; red at 750 nm to
violet at 380 nm; these are the wavelengths important for photosynthesis
o Sunlight consists of packets of energy called photons. As the wavelength increases, the
energy of the photons decrease (inverse proportion). Therefore, red has longest
wavelength and least energy.
o Pigments: molecules that absorb visible light; wavelengths that are absorbed disappear
 A leaf appears green because chlorophyll absorbs red and blue, and reflects
back green light
Two groups of pigments used in PS: carotenoids and chlorophylls; chlorophyll a is the primary
pigment, chlorophyll b is the accessory. For both chlorophylls, wavelengths between 500-600 nm
are not absorbed (green light)
Photoexcitation: when light hits chlorophyll
o absorbs photon of light, boosts electrons of chlorophyll's Mg to excited state, then
trapped by primary electron acceptor; goes to photosystem's reaction center chlorophyll
a molecule
Photosystem I: reaction center chlorophyll a molecule is P700
Photosystem II: reaction center chlorophyll a molecule is P680
Linear Electron Flow: primary light reactions in plants and algae; the flow of electrons occurs in
both PS I and PS II in thylakoid membranes; produces NADPH and O 2; makes ATP by linear
(noncyclic) photophosphorylation of ADP and Pi; have chemiosmosis where redox reactions of
ETC generates a H+ gradient across the membrane. ATP Synthase uses this gradient to make
ATP.
Comparison of ETC/chemiosmosis in mitochondria for CR and chloroplasts for PS
o In both, the ETC generates a proton (H+) gradient across the membrane
o Then, ATP Synthase uses the proton force to make ATP in both CR (called Oxidative
Phosphorylation) and PS (called Light Reactions or Linear Photophosphyorylation)
Summary of Light Reactions:
o Occur in the thylakoid membranes of chloroplasts (where chlorophyll is)
o Initially converts sunlight energy into temporary energy in ATP and NADPH
o Oxidizes H2O into O2
o Makes NADPH from NADP+ (electrons given by H2O)
o Makes ATP from ADP and P by noncyclic photophosphorylation
Summary of Calvin Cycle:
o Occurs in the stroma
o Reduces CO2 into glucose
o uses electrons from NADPH and energy from ATP to convert CO2 to sugar
o Takes 3 CO2s (3 turns of Calvin) to make 1 molecule of G3P
o Takes 6 CO2s (6 turns of Calvin) to make 1 molecule of glucose
o Also called the “Dark Reactions”, because they don’t need light
o Puts CO2 into existing organic molecule ribulose bi-phosphate or RuBP (called carbon
fixation) and then reduces it to glucose
o Needs NADPH from Light Reactions for reducing power
o Needs ATP from Light Reactions for energy (because now the process doesn’t use
sunlight)
o Actual final product is glyceraldehydes 3-phosphate (G3P), a 3 carbon molecule
o Takes 3 turns of Calvin to make 1 molecule of G3P
o Takes 6 turns of Calvin to make 1 molecule of glucose
o Regenerates NADP+ and ADP and P, all to be used again in the Light Reactions
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