Cao, Jasmin

BIOL 151
Prof. Vetrone
9/9/2017
Chapter 1: Cells

A. Cells: Fundamental Units of Life

1. Unity and Diversity of Cells
a. Cells Vary Enormously in Appearance and Function
i. Cells vary in size, chemical requirements, shape, and therefore function.
b. Living Cells All Have a Similar Basic Chemistry
i. In every cell, the long DNA polymer chains are made of the same set of four nucleotides
Central Dogma of Biology: DNA replicates itself, DNA is transcribed to RNA, RNA is
translated into protein
ii. All organisms use the same set of 20 amino acids to make their proteins
Amino acids are linked in different sequences, giving each type of protein molecule a
different three dimensional shape or conformation
c. All Present Day Cells Have Apparently Evolved from the Same Ancestral Cell
i. Evolution: the process by which living species become gradually modified and adapted to
their environment in more and more sophisticated ways
Present day cells all inherited their genetic instructions from the same common ancestor
d. Genes Provide the Instructions for Cell Form, Function, and Complex Behavior
i. Genome: a cells entire sequence of nucleotides in an organisms DNA
Provides a genetic program that instructs the cell how to behave
e. The Invention of the Light Microscope Led to the Discovery of Cells
i. Cell theory: all living cells are formed by the growth and division of existing cells
f. Light Microscopes Allow Examination of Cells and Some of Their Components
i. Extracellular matrix: a dense material often made of protein fibers embedded in a
polysaccharide gel
g. The Fine Structure of a Cell is Revealed by Electron Microscopy
i. Organelles: separate, recognizable substructures with specialized functions
ii. Plasma membrane: the membrane that separates the interior of the cell from its external
environment
iii. Internal membranes: membranes surrounding organelles
h. The Prokaryotic Cells
i. Prokaryotic cells do not have a nucleus to hold its DNA or any complex organelles
They are also small, spherical, rodlike, or corkscrew shaped
They have a tough, protective coat or cell wall surrounding the plasma membrane
They are able to evolve fast due to their large numbers, rapid growth rates, and ability to
exchange genetic material by a process akin to sex
ii. Eukaryotic cells are organisms whose cells do have a nucleus
i. Prokaryotes Are the Most Diverse and Numerous Cells on Earth
i. Prokaryotes exploit an enormous range of habitats and they vastly outnumber all eukaryotic
organisms on Earth
 ii. Mitochondria are thought to have evolved from aerobic bacteria that took to living inside the
anaerobic ancestors of todays eukaryotic cells
This created a symbiotic relationship in which the host eukaryote and the engulfed
bacterium helped one another to survive and reproduce
Chloroplasts have evolved from photosynthetic bacteria that long ago found home inside
the cytoplasm of a plant ancestor
j. The World of Prokaryotes Is Divided into Two Domains: Bacteria and Archaea
2. The Eukaryotic Cell
i. The Nucleus Is the Information Store of the Cell
Nucleus: is enclosed within two concentric membranes that form the nuclear envelope
and it contains molecules of DNA
These DNA molecules become visible as chromosomes when they become more
compact before a cell divides into two daughter cells
ii. Mitochondria Generate Usable Energy from Food to Power the Cell
Mitochondria: are generators of chemical energy for the cell
They harness the energy from the oxidation of food molecules to produce ATP, the
basic chemical fuel that powers most of the cells activities
They contain their own DNA and reproduce by dividing in two
Cellular respiration: fueled by mitochondrion that consume oxygen and release carbon
dioxide in cells
Without mitochondria, cells would be unable to use oxygen to extract the energy they
need from the food molecules
iii. Chloroplasts Capture Energy from Sunlight
Chloroplasts: only found in the cells of plant and algae
Have two surrounding membranes as well as internal stacks of membranes containing
the green pigment chlorophyll
They carry out photosynthesistrapping the energy of sunlight in their chlorophyll
molecules and using this energy to drive the manufacture of energy rich sugar
moleculeplants then extract this stored energy by oxidizing the sugars in their
mitochondria and generate ATP
iv. Internal Membranes Create Intracellular Compartments with Different Functions
Endoplasmic Reticulum: irregular maze of interconnected spaces enclosed by a
membrane
Where most cell membrane components and materials destined for export from the
cell are made
Golgi apparatus: stacks of flattened, membrane enclosed sacs
Modifies and packages molecules made in the ER that are destined to be secreted
from or transported in the cell
Lysosomes: small, irregularly shaped organelles in which intracellular digestion occurs,
releasing nutrients from ingested food particles and breaking down unwanted molecules
for either recycling within the cell or excretion from the cell
Peroxisomes: small, membrane enclosed vesicles that provide a safe environment for a
variety of reactions in which hydrogen peroxide is used to inactivate toxic molecules
Transport vesicles: ferry materials between one membrane enclosed organelle and
another
 Endocytosis and exocytosis: when vesicles fuse with plasma membrane and either
release their contents into the external medium or carry material from outside
v. The Cytosol Is a Concentrated Aqueous Gel of Large and Small Molecules
Cytosol: the site of many chemical reactions that are fundamental to the cells existence
and is like a water-based gel
vi. The Cytoskeleton Is Responsible for Directed Cell Movements
Cytoskeleton: system of protein filaments that are composed by three major filament
types that gives the cell mechanical strength, controls its shape, and drives and guides its
movements. In otherwords, it governs the internal organization of the cell as well as its
external features
Actin filament: abundant in all eukaryotic cells but occur largely in muscle cells for
muscle contraction
Microtubules: thickest filaments in the cytosol that pull the duplicated chromosomes
in opposite directions and distribute them equally to the two daughter cells
Intermediate filaments: serve to strengthen the cell
vii. The Cytoplasm is Far from Static
Motor proteins: use the energy stored in molecules of ATP to trundle along these tracks
and cables, carrying organelles and proteins through the cytoplasm.
viii. Eukaryotic Cells May Have Originated as Predators
The ancestral eukaryotic cell was a predator that fed by capturing other cells
Such a way of life requires a large size, flexible membrane, and a cytoskeleton
This primitive cell was most likely the sort of cell that engulfed the free-living,
oxygen consuming bacteria that were the likely ancestors of the mitochondria
Protozoans: microorganisms that can be photosynthetic or carnivorous, motile or
sedentary
Their anatomy is elaborate and includes sensory bristles, photoreceptors, beating
cilia, stalk like appendages, mouth parts, stinging darts, and muscle like bundles
b. Model Organisms
i. Molecular Biologists Have Focused on E. coli
They are small, rod shaped cell that normally lives in the gut of humans and other
vertebrates that used to study fundamental mechanisms of life
ii. Brewers Yeast is a Simple Eukaryotic Cell
Microorganism that is used for brewing beer and baking bread
It is a single celled fungus that reproduces very fast
iii. Arabidopsis Has Been Chosen as a Model Plant
Can produce very fast, flowering plant, weed
iv. Model Animals Include Flies, Fish, Worms, and Mice
v. Biologists Also Directly Study Human Beings and Their Cells
vi. Comparing Genome Sequences Reveals Lifes Common Heritage
vii. Genomes Contain More Than Just Genes
Cao, Jasmin

BIOL 151

Prof. Vetrone

Chapter 3: Energy, Catalysis, and Biosynthesis

A. Energy, Catalysis, and Biosynthesis

1. Catalysis allows the cell to control its metabolismthe sum total of all the chemical reactions it
needs to carry out to survive, grow, and reproduce
2. Cells obtain energy from their environment and use it to create order
3. Catabolic pathway: break down foodstuffs into smaller molecules
a. Anabolic pathway: use energy harnessed by catabolism to drive the synthesis of molecules that
form the cell
B. The Use of Energy by Cells
1. Biological Order Is Made Possible by the Release of Heat Energy from Cells
a. Second Law of Thermodynamics: in the universe or in any isolated system, the degree of
disorder can only increase
b. Entropy: measure of a systems disorder
c. Heat is energy in its most disordered form
i. cells reactions generate heat that increases the thermal motions of nearby molecules and
increase entropy of the system
d. Cells take in energy from its environment in the form of food, inorganic molecules or photons
from the sun and it uses this energy to generate order within itself by forging are chemical bonds
and building large macromolecules
2. Cells Can Convert Energy from One Form to Another
a. First Law of Thermodynamics: energy cannot be created or destroyed but it can be converted
from one form to another
b. Cells benefit from the heat energy it produces because heat generating reactions are directly
linked to processes that maintain molecular order inside the cell
i. increase order inside cell causes increased disorder outside cell
3. Photosynthetic Organisms Use Sunlight to Synthesize Organic Molecules
a. Animals live on energy stored in the chemical bonds of organic molecules
i. Food molecules also provide the atoms that animals need to construct new living matter
b. Photosynthesis: a process that converts the electromagnetic energy into sunlight into chemical
bond energy in cells
i. Photosynthetic organisms use the energy they derive from sunlight to synthesize small
chemical building blocks such as sugars, amino acids, nucleotides, and fatty acids
These small molecules are then converted into macromolecules that form the plant
ii. 1st stage of photosynthesis: energy from sunlight is captured and stored as chemical bond
energy in specialized molecules called activated carriers
2nd stage: the activated carriers are used to help drive a carbon fixation process, in which
sugars are manufactured from carbon dioxide gas
4. Cells Obtain Energy by the Oxidation of Organic Molecules
 a. Energy is extracted from food molecules by a process of gradual oxidation
i. Cellular respiration: cell obtains energy from organic molecules by allowing carbon and
hydrogen atoms in these molecules to combine with oxygen
5. Oxidation and Reduction Involve Electron Transfers
a. Oxidation: addition of oxygen atoms to a molecule
i. occurs in any reaction in which electrons are transferred from one atom to another
ii. refers to the removal of electrons from an atom
b. Reduction: involves the addition of electrons to an atom
c. Because the number of electrons is conserved in a chemical reaction, oxidation and reduction
always occur simultaneously: if one molecule gains, the other loses an electron
d. Hydrogenation: when a molecule picks up both an electron and a proton at the same time
e. Dehydrogenation: oxidation reactions unlike hydrogenation
i. Reduction occurs when the number of C-H bonds increases whereas oxidation occurs when
the number of C-H bonds decreases
C. Free Energy and Catalysts
1. Catalysis: the acceleration of the specific chemical reactions needed to sustain life
2. Chemical Reactions Proceed in the Direction that Causes a Loss of Free energy
a. Free energy: energy that can be harnessed to do work or drive chemical reactions
3. Enzymes Reduce the Energy Needed to Initiate Spontaneous Reactions
a. Activation energy: energy required to start a reaction
b. Catalyst: speeds up the reaction by lowering the activation energy
c. Substrates: molecules that the enzyme or specialized proteins binds to and holds in a way that
greatly reduces the activation energy needed to facilitate a chemical interaction between them
d. Enzymes are highly selective: they direct each of the many different molecules in a cell along
specific reaction pathways, producing the compounds that the cell actually needs
4. The Free Energy Change for a Reaction Determines Whether It Can Occur
a. Disorder increases when useful energy that can be harnessed to do work is dissipated as heat
b. Energetically favorable reactions are those that create disorder by decreasing the free energy of
the system to which they belong; they have a negative delta G
i. A reaction can occur spontaneously only if delta G is negative
c. Energetically unfavorable reactions create order in the universe; they have a positive delta G
i. Such reactions cannot occur spontaneously; they take place when they are coupled to a
second reaction with a negative delta G large enough to make net delta G negative
5. Delta G Changes As a Reaction Proceeds Towards Equilibrium
a. Because delta G changes as products accumulate and substrates are depleted, chemical reactions
will generally proceed until they reach a state of equilibrium
i. Equilibrium: when the rates of the forward and reverse reactions are equal or when delta G is
equal to zero
This is rare because states of chemical inactivity would be incompatible with life
6. The Standard Free Energy Change or delta G Makes it Possible to Compare the Energetics of
Different Reactions
a. Standard free energy change of a reaction or delta G with degree sign, is independent of
concentration; it is based on their behavior under ideal conditions where the concentrations of all
the reactants are set to the same fixed value of 1 mole/liter
b. Delta G= Delta G with degree sign + RTln ([X]/[Y])
7. The Equilibrium Constant Is Directly Proportional to delta G with degree sign
a. K= equilibrium constant
i. K= ([X]/[Y])where X is the concentration of the product and Y is substrate at equilibrium
ii. The more energetically favorable the reaction, the more product will accumulate if the
reaction proceeds to equilibrium
8. In Complex Reactions, the Equilibrium Constant Includes the Concentrations of All Reactants and
Products
a. K= [AB]/[A][B]
i. The concentrations of both reactants are multiplied because the formation of product AB
depends on the collision of A and B, and these occur at a rate that is proportional to [A][B]
9. The Equilibrium Constant Indicates the Strength of Molecular Interactions
a. Noncovalent interactions include binding of substrates to enzymes, the binding of gene
regulatory proteins to DNA, and the binding of one protein to another to make the many
different structural and functional protein complexes
i. Two molecules will bind to each other if the free energy change for the interaction is
negative: free energy of resulting complex is less than the sum of free energy of the unbound
partners
ii. K becomes larger as the binding energy or the energy released in the binding interaction
increases
10. For Sequential Reactions, the Changes in Free Energy Are Additive
a. Enzymes catalyze reactions that are energetically unfavorable by directly coupling energetically
unfavorable reactions with energetically favorable ones
i. They do this to make the overall pathway energetically favorable
b. Fortunately, there are other, more general ways of using enzymes to couple reactions involving
the production of activated carriers that can shuttle energy from one reaction site to another
11. Thermal Motion Allows Enzymes to Find Their Substrates
a. Enzymes and their substrates are both present in relatively small amount in the cytosol, yet an
enzyme can capture and process about a thousand substrate molecules every second
i. Rapid binding is caused by fast molecular motions that are a result of health energy
ii. As the molecules in a liquid collide and bounce off one another, the molecules move in ways
called random walks
iii. Small organic molecules can diffuse through cytosol nearly as much as water
b. Because proteins diffuse through the cytosol much more slowly than do small molecules, the
rate at which an enzyme will encounter its substrate depends on the concentration of the
substrate
c. Random encounters between an enzyme and its substrate often lead to the formation of an
enzyme substrate complex
i. This association is stabilized by the formation of multiple,, weak bonds between the enzyme
and the substrate
These interactionswhich can include hydrogen bonds, van der waals, and electrostatic
attractions persist until random thermal motion causes molecules to dissociate again
When two colliding molecules have poorly matching surfaces, few non covalent bonds
are formed, and they dissociate as rapidly as they come together
This prevents incorrect associations rom forming
12. V max and Km Measure Enzyme Performance
 a. To catalyze a reaction, an enzyme must first bind its substrate
i. The substrate then undergoes a reaction to form the product, which initially remains bound to
the enzyme
Finally, the product is released and diffuses away, leaving the enzyme free to bind
another substrate molecule and catalyze another reaction
b. At first, the concentration of the enzyme substrate complex and therefore, the rate at which
product is formed rises in a linear fashion in direct proportion to substrate concentration
i. However, as more and more enzyme molecules become occupied by substrate, this rate
increase tapers off, until at a very high concentration of substrate it reaches a maximum
valued termed V max
At this point, the active sites of all enzyme molecules in the sample are fully occupied by
substrate, and the rate of product formation depends only on how rapidly the substrate
molecule can undergo a reaction to form the product
For many enzymes, this turnover number is of the order of 1000 substrate molecules per
second, although turnover numbers between 1 and 100,000 have been measured
c. Because there is no clearly defined substrate concentration at which the enzyme can be deemed
fully occupied, biochemists instead use a different parameter to gauge the concentration of
substrate needed to make the enzyme work efficiently. This value is called Michaelis constant or
Km
i. The Km of an enzyme is defined as the concentration of substrate at which enzyme works at
half its maximum speed
A small Km mean a substrate binds very highly to the enzyme and a large Km indicates
weak binding
d. Although an enzyme lowers the activation energy for a reaction, it will also lower the energy for
the reverse reaction
i. Thus, equilibrium point and delta G remains unchanged
D. Activated Carriers and Biosynthesis
1. Energy is stored as chemical bond energy in a set of activated carriers, small organic molecules that
contain one or more energy rich covalent bonds
a. These molecules diffuse rapidly and carry their bond energy from the sites of energy generation
to the sites where energy is used for biosynthesis or for other energy requiring cell activities
b. Activated carriers store energy in an easily exchangeable form, either as a readily transferable
chemical group or as readily transferable electrons
c. Most important activated carriers are ATP, NADPH, and NADH.
2. The Formation of an Activated Carrier Is Coupled to an Energetically Favorable Reaction
a. When a fuel molecule such as glucose is oxidized in a cell, enzyme catalyzed reactions ensure
that a large part of the free energy released is captured in a chemically useful form
i. In cells, energy capture is achieved by means of a coupled reaction, in which an energetically
favorable reaction is used to drive an energetically unfavorable one that produces an
activated carrier or some other useful molecule which requires enzymes
3. ATP is the Most Widely Used Activated Carrier
a. ATP is synthesized in an energetically unfavorable phosphorylation reaction, in which a
phosphate group is added to ADP
i. When required, ATP gives up this energy packet in an energetically favorable hydrolysis to
ADP and inorganic phosphate
 The regenerated ADP is then available to be used for another round of the
phosphorylation reaction that forms ATP, creating an ATP cycle in the cell
Phosphorylation reactions are examples of condensation reactions and they occur in
many important cell processes:
They activate substrates, mediate the exchange of chemical energy, and serve as the
key constituents of intracellular signaling pathways
ii. ATP helps power the many pumps that actively transport substances in the cell
It also powers the molecular motors that enable muscle cells to contract and nerve cells to
transport materials along their axons
4. Energy Stored in ATP Is Often Harnessed to Join Two Molecules Together
a. Condensation reactions, which is energetically unfavorable, are forced to occur by being coupled
to ATP hydrolysis in an enzyme catalyzed reaction pathway
5. NADH and NADPH Are Both Activated Carriers of Electrons
a. Both NADH and NADPH carry energy in the form of two high energy electrons plus a proton,
which together form a hydride ion or H-
i. When these activated carriers pass their energy to a donor molecule, they become oxidized to
form NAD+ and NADP+
ii. During a special set of energy yielding catabolic reactions, a hydride ion is removed from the
substrate molecule and added to the nicotinamide ring of NADP+ to form NADPH
The hydride ion carried by NADPH is give up in a subsequent oxo-red reaction because
the ring can achieve a more stable arrangement of electrons without it
In this subsequent reaction, which regenerates NADP+, the NADPH becomes
oxidized and the substrate becomes reducedthus completing the NADPH cycle
6. NADPH and NADH Have Different Roles in Cells
a. NADPH and NADH differ in a single phosphate group and have different conformations
i. This difference makes it possible for the two carriers to bind as substrates to different sets of
enzymes and deliver electrons to different target molecules
ii. Why is there a division of labor between the two molecules?
Because there is a need to regulate two sets of electron transfer reactions independently.
NADPH operates with enzymes that catalyze anabolic reactions, supplying the high
energy electrons needed to synthesize energy rich molecules
NADH has a role as an intermediate in the catabolic system of reactions that generate
ATP through the oxidation of food molecules
There is a lot of NAD+ in the cell to act as oxidizing agents and plenty NADPH to act
as reducing agents for catabolism and anabolism
7. Cells Make Use of Many Other Activated Carriers
a. FADH2 carries hydrogen and high energy electrons
b. Coenzyme A can carry an acetyl group in a readily transferable linkage
i. This activated carrier called acetyl CoA is used to add two carbon units in the biosynthesis of
the hydrocarbon tails of fatty acids
c. Activated carriers are usually generated in reactions coupled to ATP hydrolysis
8. The Synthesis of Biological Polymers Requires an Energy Input