UNIT 1 EXAM 🧫

Chapter 1: Evolution, the Themes of Biology, and Scientific Inquiry

Learning Goals
 Describe the characteristics shared by all living organisms
 Organize and identify life’s hierarchical levels
 Describe the role of DNA information on reproduction, growth, and development
 Explain the food and energy interactions between species in an ecosystem
 Explain how interactions between molecules, cells, and organs lead to homeostasis
and regulation for the survival of organisms
 Explain the role of adaptations and natural selection in the evolution of populations
 Compare and contrast the three Domains of Life
 Explain the role of deductive reasoning, formulating and testing hypothesis in the
scientific method
 Identify the components of a controlled experiment, including predictions,
hypotheses dependent and independent variables in an experiment
 Discuss the applications and limitations of the scientific method

Biology: the scientific study of life

 Properties of life:
o Order
o Energy processing
o Growth and development
o Evolutionary adaptation
o Response to environment
o Regulation
o Reproduction

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Unifying themes of biology
1. Organization: structure fits function (as explained by natural selection)
o Reductionism: reduces complex systems into simpler, manageable components to study –
provides an incomplete view of life
o Emergent properties: novel properties that emerge due to the arrangement and
interactions of parts as complexity increases
 Example: photosynthesis occurs in an intact chloroplast but will not take place if
chloroplast molecules are simply mixed into a test tube – organization of the
molecules matters!
o Systems biology: explores systems through analyzing the interactions of its parts –
complements reductionism to understand emergent properties
o Example:
 Biosphere: all life on earth and places where life exists
 Ecosystem: living things in a particular area, along with non-living components –
tropical forest/grassland
 Communities: array of species in a particular ecosystem
 Populations: individuals of a species that interbreed in a specific area
 Organisms: individual living things
 Organs: part of organism made up of multiple tissues that performs a specialized
function
 Tissues: group of cells that perform a specialized function
 Cells: fundamental unit of structure and function in life
 Smallest unit of organization that performs all activities required for life
 Cell Theory developed in 1800s: all living organisms are made of cells, the
basic unit of life
 Prokaryotic cells: smaller, single-celled organisms lacking a nucleus
(unenclosed DNA) and other membrane-enclosed organelles – bacteria
and archaea
 Eukaryotic cells: larger cells containing membrane-enclosed organelles –
organelles may be universal (nucleus containing DNA) or specific to a cell
(chloroplasts)
 Organelles: functional components of cells
 Molecules: chemical structure consisting of two or more atoms

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2. Information: encoded into DNA
o Each chromosome contains one long deoxyribonucleic acid (DNA) molecule, containing
thousands of genes
 Genes are units of inheritance
o DNA is arranged in a double helix, containing two strands of nucleotides (A/T/C/G)
 Sequences of nucleotides encode specific genes, which are often a blueprint for
specific proteins
 RNA: an intermediary in encoding proteins -- genes’ nucleotides are transcribed
into mRNA, which is then translated into a series of amino acids
 Amino acids: the building blocks of proteins
 Gene expression: process by which information in a gene directs the manufacture
of cellular products
o All forms of life employ the same genetic code: the same sequence of nucleotides means
the same thing in different organisms
 Same proteins amongst different organisms draws to the relationship of species
o Some RNA is translated to proteins, some RNA manufactures proteins, some RNA can
regulate protein-coding genes
o Genome: library of genetic instructions that an organism inherits
 Human cell: two sets of chromosomes, 3 billion nucleotide pairs of DNA per set
 Genomics: study of whole sets of genes/DNA
 Proteomics: study of whole sets of proteins and properties
 Proteome: entire set of proteins expressed by a given cell, tissue, or
organism
3. Energy and matter: flow of energy and cycling of matter
o Movement, growth, reproduction, and cellular activities require energy
o Producers: photosynthetic organisms that utilize energy from sunlight, which is then
converted into chemical energy
o Consumer: feeds on other organisms
o Utilization of chemical energy results in some loss of energy as heat, thus energy flows
through the ecosystem in one direction: enters as sunlight and exits as heat
o Chemicals cycle within the ecosystem: used and recycled

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4. Interactions: within organisms and between organisms in a system
o Self-regulation through feedback regulation: output or product of a process regulates that
very process
 Negative feedback: most common, response reduces initial stimulus
 Example: increase in blood glucose stimulates pancreas to secrete insulin,
which causes the body cells to take up glucose and the liver to store it,
decreasing blood glucose levels, eliminating the stimulus for insulin
secretion
 Positive feedback: less common, response increases initial stimulus
 Example: blood vessel damage results in platelet aggregation, platelets
release chemicals that stimulate more platelet aggregation, resulting in
clot formation
o Organisms interact within ecosystems
 mutualism, commensalism, predation, parasitism, and competition between
organisms
 Interaction with factors in the environment
 Example: climate change has caused the deterioration of some species’
habitats, resulting in extinction
5. Evolution: a process of biological change in which species accumulate differences from their
ancestors as they adapt to different environments over time (through natural selection)
o Explains the unity and diversity between species
o Species named by their genus and name unique to the species
 Example: Homo sapiens
o Three Domains of Life: Bacteria, Archaea, Eukarya
 Bacteria and Archaea: single-celled, prokaryotic organisms
 Eukarya: eukaryotes (containing eukaryotic cells)
 Further classified as kingdoms Plantae, Fungi, Animalia (organized by
modes of nutrition) AND the protists (most numerous, diverse)

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 o The Theory of Natural Selection and Charles Darwin
 As species adapt to different environments, they accumulate differences from
their ancestors
 Natural selection is the cause for this descent with modification
 Three observations: individuals in a population vary in traits which are
heritable, a population can produce far more offspring than can survive to
reproduce offspring of their own, species are generally suited/adapted to
their environment
 A natural environment consistently selects the propagation of certain traits

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 o Tree diagrams: map ancestral species and descendants
 Organisms descend from a common ancestor
 Cumulative effects of natural selection over time can cause a split into two or
more descendant species – possibly due to a fragmentation into subpopulations in
different environments
Science: an approach to understanding the natural world
 Inquiry: search for information and explanations of natural phenomena
o Process: repetitive cycle of observations, hypotheses (logical and testable explanations),
and experimentation
 Observation and exploration: observe the natural world and explore scientific
literature
 Gathering and analyzing data: quantitative or qualitative
 Inductive reasoning: derive generalizations from a large number of specific
observations
 Forming and testing hypotheses: an explanation based on observations and
assumptions that leads to a testable prediction
 Experiment: scientific test carried out under controlled conditions
 Deductive reasoning: predictions of results that will be found if a
hypothesis is correct
o “If . . . then . . .”
 Hypothesis can never be proved beyond all doubt, experimentation simply
allows one to prove that a hypothesis is not incorrect
o Repeated testing results in increased confidence in a hypothesis’
validity
o Flexibility of the scientific process: not linear
 Experimentation
o Controlled experiment: compare experimental group with a control group
o Variables: factor that is manipulated and factor that is measured
 Independent: manipulated factor
 Dependent: factor that is measured and predicted to be affected by the
independent variable

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  Theory
o Scientific theory: broader than hypotheses, general enough to produce new testable
hypotheses, supported by a greater body/accumulation of evidence
 Example: theory of natural selection or gravity
 Teamwork
o Model organism: species easy to grow in lab and lends itself well to the questions being
investigated

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Chapter 2: The Chemical Context of Life

Learning Goals
 Identify the primary elements in living organisms
 Describe the structure of atoms
 Differentiate between atoms, molecules, and compounds
 Compare and contrast ionic and covalent bonds
 Describe the relevance of Van der Waals interactions in biology
 Explain how hydrogen bonding determines water’s cohesion, adhesion, surface
tension and ability to dissolve other substances
 Explain how each of the following water properties are essential to sustain life
1. Adhesion
2. Cohesion
3. Surface tension
4. Regulation of temperature
5. Solvent property
 Describe acids, bases and the effect pH on cells

Properties of matter
 Matter: made of elements
o Element: chemical substance in its pure form, cannot be broken down into to other
substances by chemical reactions
 92 elements occur in nature, signified by the first one or two letters of its name
 Elements of life
 20-25% of the 92 natural elements are essential to life – 25 elements are
essential to humans, but only 17 are essential to plants
 Oxygen, carbon, hydrogen, and nitrogen make up 96% of living matter, the
remaining 4% is mainly calcium, phosphorus, potassium, and sulfur
 Trace elements are needed in minute quantities, such as iron in all
organisms, but iodine in vertebrates only (thyroid gland)
 Some elements are toxic to organisms, such as arsenic
 An element contains a certain type of atom exclusive to the element
 Atom: smallest unit of matter than retains the properties of an element
o Identity based on number of protons (oxygen has 8 protons)

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Properties of compounds
 Compound: made of atoms joined by bonds
o Electron distribution: the electron distribution of an atom determines the ability to form
bonds (O2 has space for 2 electrons, allowing 2 bonds to form)
o Overall, a compound’s properties depend on the atoms and how they are bonded
together
o Consist of two or more elements combined in a fixed ratio
 H2O (two hydrogen to one oxygen atoms) or NaCl
Subatomic particles
 More than 100 types of particles from atoms exist, but only neutrons, protons, and electrons are
relevant to biology
o Protons (+) are electrons (-) are electrically charged
o Atomic nucleus: protons and neutrons are packed together tightly in a dense core at the
center of the atom
 Protons give the nucleus a
positive charge
 Electrons move rapidly
around the nucleus, through
attraction to an opposite
charge
o Neutrons and protons are similar in
mass: 1.7x10-24g or 1 Dalton
 Also measured in
Daltons/atomic mass unit (amu)
o Electrons have a mass equal to 1/2000 of a neutron or proton, so they can be ignored in
calculating total mass
 Atomic number: elements vary in their number of subatomic particles and have the same
number of protons in the nuclei
o Written to the left of the element in subscript: 2He
 An atom of helium contains 2 protons in the nucleus
 Unless otherwise indicated, an atom is neutral in charge, thus the atomic number
also indicates the number of electrons surrounding the nucleus

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  Mass number: indicates the total number of protons and neutrons in an atom, which can be used
to deduce the number of neutrons
o Written to the left of an element in superscript: 23Na
 An atom of sodium contains 23 protons and neutrons
 The atomic number for sodium is 11 (protons); therefore 23 – 11 = 12 neutrons
 Atomic mass: total mass of an atom; since almost all of an atom’s mass is concentrated in the
nucleus and the mass of electrons are negligible, it is very close to the mass number
 Isotopes: elements with varying atomic forms, in the number of neutrons
o Behave identically in chemical reactions although their masses are different
o Element with more than one naturally occurring isotope: atomic mass is an average of
those isotopes weighted by their abundance
o Stable isotopes: nuclei do not have a tendency to lose subatomic particles through a
process called decay
o Radioactive isotope: nucleus decays spontaneously, giving off particles and energy
 If it results in a change in number of protons, the atom is transformed into a
different element
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 C is a radioactive isotope in which a neutron decays into a proton,
producing 14N
 Radioactive tracers: used as diagnostic tools in medicine, cells can use radioactive
atoms just like nonradioactive isotopes, metabolism is tracked through these
tracers, sometimes used in conjunction with imaging
 Example: analyzing tracers in urine to determine kidney dysfunction
 Radiometric dating: used to identify the age of a fossil through measuring
different isotopes and calculating how many half-lives have passed since an
organism was fossilized or a rock was formed
 Half-life: time it takes for 50% of the parent isotope to decay into the
daughter isotope, not affected by temperature, pressure, or any other
environmental factors

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  Energy levels of atoms: atoms are mostly empty space; when two atoms approach each other in
a reaction, their nuclei do not come close enough to interact; electrons are the only subatomic
particles directly involved in chemical reactions
o Electrons are attracted to the positively charged nucleus
o Energy: the capacity to cause change, electrons vary in the amount of energy they
possess
o Potential energy: energy matter possesses because of its location or structure (water in a
reservoir of a dam)
 Matter has a tendency to move toward the lowest possible state of potential
energy
 Electrons have potential energy due to their distance from the nucleus
 The further away an electron is from the nucleus, the greater the potential
energy
 Changes in potential energy of electrons can only occur in steps of fixed
amounts
 Electron shells: an electron’s energy level relates to its average distance
from the nucleus; thus, there is a characteristic average distance and
energy level at each shell
o First shell is closest to the nucleus, with the least amount of
potential energy
o Electrons can move from one shell to another by absorbing or
losing an amount of energy equal to the difference in potential
energy between its position in the old shell and in the new shell
 Electrons that absorb more energy move farther away from
the nucleus
 Lost energy is usually released into the environment as
visible light or UV radiation
o The chemical behavior of an atom is determined by the electron distribution in the atom’s
electron shells, particularly the outermost shell
 The periodic table displays the electron distribution for the first 18 elements, from
1H to 18Ar, arranged in three rows/periods/electron shells, with the left-to-right

sequence corresponding to the addition of electrons and protons

 The first shell can only hold two electrons, the second shell holds eight:
electrons per shell = 2(n2)
 Valence electrons and shell: electrons in the outmost shell

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  Atoms with the same
number of electrons in
their balance shells
exhibit similar
chemical behavior: F (7
valence electrons, 2nd
shell) and Cl (7
valence electrons, 3rd
shell) both form
compounds when
combined with Na
 Atoms with
completed valence
shells are
unreactive/inert, at
the far right of the
periodic table
(helium, neon,
argon)
o Orbital: three-dimensional space in
which an electron is found 90% of
the time, representation of an
electron shell
 First electron shell is a
spherical orbital called 1s,
the second shell has four
orbitals total with one called 2s
(spherical) and three called 2p
(dumbbell-shaped)
 No more than 2 electrons
can occupy a single orbital
 The reactivity of an atom arises from the presence of unpaired electrons in one or
more orbitals, to complete their valence shells
Formation and function of molecules
 Chemical bonds: atoms with incomplete valence shells can interact with certain other atoms to
complete their valence shells through the transfer of valence electrons
 The strongest kinds of chemical bonds are covalent bonds in molecules and ionic bonds in dry
ionic compounds

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  Covalent bonds: sharing of a pair of valence electrons by two atoms, constituting a molecule
o Single bond: pair of shared electrons (H–H)
o Double bond: two pairs of shared electrons (O==O)
o Valence: number of electrons needed to complete the atom’s outermost valence shell
o Electronegativity: the attraction of a particular atom for the electrons in a covalent bond
 The more electronegative an atom is, the more strongly it pulls shared electrons
towards itself
 Nonpolar covalent bond: electronegativity between atoms is equal, such as
covalent bond between two atoms of the same element (electrons are shared
equally)
 H2 or O2
 Polar covalent bond: covalent bonds that vary in polarity (electrons are not shared
equally)
 H2O
 Oxygen is one of the most electronegative elements (electrons spend more time
near oxygen nucleus in an H2O molecule)
 Oxygen is denoted with a partial negative charge (delta minus) and
hydrogen is denoted with a partial positive charge (delta plus)
 Ionic bonds/compounds/salts: two atoms are so unequal in their attraction for valence electrons
that the more electronegative atom strips an electron completely away from its partner,
producing oppositely charged atoms/molecules called ions; cations are positively charged, anions
are negatively charged; opposite charges attract to form an ionic bond
o An electron transfer does not need to occur; any two ions of opposite charge can form an
ionic bond
 Na+ and Cl- form an ionic bond: Na gives up its extra electron in the outer valence
shell to chlorine, causing Na to have 11 protons but 10 electrons (+ charge) and Cl
to have 17 protons but 18 electrons (- charge)
o Unlike covalent compounds, ionic compounds do not consist of definite molecules in a
specific size and number of atoms, but are rather a ratio of elements
o Ion also applies to entire molecules that are electrically charged
o Environmental conditions affect the strength of bonds: dry salt crystal has strong bonds,
but dissolved in water, the bonds are weaker because each ion is partially shielded
through its interactions with water molecules
 Drugs marketed as salts due to stability in dry conditions and dissociation in water

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  Weak chemical interactions: most of the strongest bonds in organisms are covalent, however,
large biological molecules in their functional form are often held together by weak interactions
o The reversibility of the weak interaction can allow two molecules to affect each other,
while still being able to separate easily – an example of this is the ionic bond
 Hydrogen bonds: central to the chemistry of life – noncovalent attraction to an
electronegative atom: when a hydrogen atom is covalently bonded to an
electronegative atom, the hydrogen bond has a partial positive charge that allows
it to be attracted to different
electronegative atoms with a
partial negative charge nearby
 The electronegative atoms
are typically oxygen (to
form water) or nitrogen (to
form ammonia) atoms
 Van der Waals interactions:
electrons are not always evenly
distributed and molecules with
nonpolar covalent bonds may have
positively and negatively charged regions, allowing molecules and atoms to stick
to each other
 Individually weak, occur only with atoms and molecules are close together
 Allow geckos to walk up the wall
o The cumulative effect of weak reactions is to reinforce the three-dimensional shape of
the molecule
 Molecular shape and function: molecules have characteristic shapes and sizes, key to the
function in a living cell
o Molecules consisting of two atoms are always linear, but the shapes of molecules with
more than two atoms are determined by the positions of their orbitals
 When atoms form covalent bonds, the orbitals in its valence shell undergo
rearrangement
o Molecular shape determines how biological molecules recognize and respond to one
another with specificity, molecules bind only if their shapes are complementary
 Opiates have shapes similar to endorphins that can bind to endorphin receptors in
the brain

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Chemical reactions
 Reactants: starting materials
 Products: resulting materials
 Coefficients: number of molecules involved
 Matter is conserved in chemical reactions: bonds can be made or broken, but all atoms must be
accounted for
 All chemical reactions are theoretically reversible, indicated by the opposite headed arrows
 Factors affecting the rate of a reaction: concentration of reactions
o Greater concentration results in more frequent collision; however, eventually forward
and reverse reactions occur at the same rate and relative concentrations of products and
reactants stop changing, resulting in chemical equilibrium

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Chapter 3: Water and Life

Hydrogen bonding
 Polar covalent bonds: electrons spend more time closer to oxygen than hydrogen due to its
electronegativity
 Polar molecule: unequal sharing of electrons, charge is unevenly distributed
 Hydrogen bonds: hold molecules of water together, the partially positive hydrogen is attracted to
the partially negative oxygen
o Liquid state: fragile, 1/20th the strength of covalent bond
 Water is constantly forming new hydrogen bonds
Four emergent properties
 Cohesive behavior
o Cohesion: hydrogen bonds hold the substance together
o Surface tension: high in water due to its cohesion; measure of how difficult it is to stretch
or break the surface of a liquid
 Asymmetry between bonds of water and lack of bonding to the air gives water
unusually high surface tension
o Adhesion: occurs in water due to hydrogen bonds, counter the downward pull of gravity
with water conducting cells; clinging of one substance to another
 Ability to moderate temperature
o Absorbs heat from air that is warmer and releasing stored heat to air that is cooler
o Temperature and heat
 Kinetic energy: energy of motion; atoms and molecules are always moving and
therefore have kinetic energy
 Faster = greater kinetic energy
 Thermal energy: total kinetic energy associated with random movement of atoms
or molecules, based on volume
 Temperature: average kinetic energy of the molecules in a body of matter,
regardless of volume
 Water in a swimming pool may have a lower temperature than a pot of
coffee, but the swimming pool has higher thermal energy due to its volume

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  Two objects of different temperatures brought together: thermal energy
passes from the warmer to the cooler object until equilibrium is achieved
o Ice absorbs thermal energy from the liquid as it melts
 Heat: thermal energy in transfer from one body of matter to another
 Calorie: unit of heat, amount of heat it takes to raise the temperature of 1g of
water by 1 degree Celsius/the amount of heat 1g of water releases when it cools
by 1 degree Celsius
 Kilocalorie: 1000 calories, the quantity of heat required to raise the temperature
of 1kg of water by 1 degree Celsius
 Joule: equal to 0.239 calories
 Specific heat: ability of water to stabilize temperature, amount of heat that must
be absorbed or lost for 1g of that substance to change its temperature by 1
degree Celsius, measure of how well a substance resists changing its temperature
when it absorbs or releases heat
 Water: 1 cal/(g x degree Celsius) – unusually high specific heat, water will
change its temperature less than other liquids when it absorbs or loses a
given amount of heat
o Heat must be absorbed in order to break hydrogen bonds, but heat
is released when hydrogen bonds form, helping water to resist
changes in temperature
o A large body of water can absorb and store more heat during the
daytime while maintaining its temperature, but then warm up the
air as it cools at night
 Moderates air temperature in coastal areas and stabilizes
ocean temperatures for marine life
 Organisms similarly utilize water to resist changes in
temperature
 Vaporization/evaporation: molecules moving fast enough can overcome attraction
to other molecules and depart the liquid to enter into the air as gas (or vapor);
transformation from liquid to gas
 Temperature is the average kinetic energy of molecules and the speed of
molecular movement varies; therefore, some evaporation occurs at any
temperature
o Heated liquids have a higher kinetic energy and evaporate more
quickly

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  Heat of vaporization: quantity of heat a liquid must absorb for 1g of it to be
converted from liquid to gas
o Water has a high specific heat: 580 calories of heat are needed to
evaporate 1g of water at 25 degrees Celsius
 Hydrogen bonds must be broken prior to molecules exiting
from liquid state
 Helps to moderate earth’s climate: solar heat is absorbed by
the sea during evaporation of the surface water; as moist air
circulates poleward; it releases heat as it condenses and
forms rain
 Evaporative cooling: as a liquid evaporates, the surface of the liquid that remains
behind cools down and its temperature decreases
 Hottest molecules with greatest kinetic energy are most likely to leave as
gas, resulting in the average kinetic energy of the remaining molecules to
decline
 Evaporation of sweat from the skin dissipates body heat and prevents
overheating
 Expansion upon freezing
o Water is one of the few substances less dense as a solid than as a liquid, allowing it to
float on liquid water
 Water expands as it solidifies due to its hydrogen bonds
 At 0-4 degrees Celsius, water begins to freeze as the molecules are moving
too slowly to break the hydrogen bonds
 At 0 degrees Celsius the molecules become locked into a crystalline
structure and each water molecule is hydrogen bonded to each other; the
hydrogen bonds keep the molecules far apart, making ice 10% less dense
than water
 As the temperature rises above 0 degrees Celsius, hydrogen bonds are
disrupted, the crystal collapses, there are fewer hydrogen bonds, so
molecules slip closer together
 At 4 degrees Celsius, water reaches its greatest density and begins to
expand as molecules move faster
 If ice sank, then eventually large bodies of water could freeze solid, making life
impossible
 When a deep body of water cools, ice floats, insulating the water below,
preventing it from freezing

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 o Global warming has resulting in ice to form later in the year, melt earlier, and cover a
smaller area
 Ice acts as a solid habitat for some animals
 Versatility as a solvent
o Solution: liquid that is a completely homogenous mixture of two or more substances
o Solvent: dissolving agent
o Solute: substance that is dissolved
o Aqueous solution: solute is dissolved in water and water is the solvent
 Water is a versatile solvent d/t the polarity of the water molecule: ions are
exposed to the solvent, ions and regions of water molecules are attracted to each
other due to their opposite charges, water molecules surround the individual ions,
separating them, eventually dissolving all ions
 A compound does not need to be ionic to dissolve in water: nonionic polar
molecules are also soluble d/t water molecules surrounding each of the solute
molecules and forming hydrogen bonds
 Proteins can dissolve in water if they have ionic and polar regions on their surface
o Hydration shell: sphere of water molecules around each dissolved ion
o Hydrophilic: substance with an affinity for water
 May not necessarily dissolve; some molecules are too large
 Cotton is made up of giant cellulose molecules and can form hydrogen
bonds with water, water adheres to the fibers

o Hydrophobic: nonionic and nonpolar substances cannot form hydrogen bonds repel
water
 High number of nonpolar covalent bonds in oils
 Major ingredient of cell membranes
o Molecular mass: sum of masses of all the atoms in a molecule
 Multiply the number of atoms by the atomic mass of each element
o Mole: one mole (mol) of a substance is 6.02x1023 molecules, known as Avogadro’s number
– grams vary
o Molarity: the number of moles of a solute per liter of a solution
 1 mol of sucrose dissolved in 1 L of water is 1 M (1 molar solution of sucrose)

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Evolution of life on other planets
 Astrobiologists look for evidence of water on other planets as a sign of life
o Mars has an ice cap at both poles and enough water vapor exists in the atmosphere for
frost to form, in addition to finding flowing water and a large reservoir one mile below
the surface ice
Acidic and basic conditions that affect living organisms
 Hydrogen ion: occasionally a hydrogen atom participating in bonding between two water
molecules will shift from one molecule to another, adding on a single proton with a charge of 1+
o Does not exist on its own in an aqueous solution and is always associated with a water
molecule
 Hydroxide ion: a molecule that has lost a proton, with an extra electron (OH-)
 Hydronium ion: a molecule that has gained a proton (H3O+)
 Water molecules dissociate at the same rate they are being reformed from H+ and OH- -- at this
equilibrium point, the concentration of water molecules greatly exceeds the concentration of
ions
o The ions are very reactive, and their concentration can drastically affect a cell’s proteins
and other complex molecules
o Adding solutes like acids and bases can disrupt the balance
 Acids and bases:
o Acid: substance that increases the hydrogen ion concentration of a solution
 Acidic solution: more H+ than OH-
 Strong acid: dissociates completely when mixed with water (single arrow)
 Weak acid: binding and release of hydrogen ions is reversible (double arrow)
o Base: substance that reduces that hydrogen ion concentration of a solution
 Accept hydrogen ions or dissociate to form hydroxide ions, which combine with
hydrogen ions and form water
 Basic solution: more OH- than H+
 Strong base: dissociates completely when mixed with water (single arrow)
 Weak base: binding and release of hydrogen ions is reversible (double arrow)
 pH scale: numerical method of expressing the range of H+ concentrations, compresses range of
H+ concentrations using logarithms due to mol/L being inadequate
o pH=-log[H+]
 Decreases as H+ concentration increases

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  pH of a neutral aqueous solution is 7 (less is acidic, more is basic)
 Most biological solutions range from 6-8
 A solution at a pH of 3 is 1000 times more acidic than a solution at a pH of 6
o In any aqueous solution at 25 degrees Celsius, the product of the H+ and OH-
concentrations is constant at 10-14 – [H+][OH-]=10-14, constant relationship of acids and
vases in an aqueous solution
 Buffer: internal pH of most living cells is close to 7, with the pH of human blood being 7.4 (slightly
basic); blood changes pH less rapidly due to buffers, allowing it to maintain a relatively constant
pH
o Buffers accept hydrogen ions from the solution when they are in excess, but donate them
when they are depleted
o Contain a weak acid and a base, which combine reversibly with ions
o Carbonic acid-bicarbonate buffering system: carbonic acid (H2CO3) is formed with CO2
reacts with water in blood plasma and dissociates into bicarbonate and hydrogen
 If H+ concentration in the blood falls, more carbonic acid dissociates, replenishing
hydrogen ions
 If H+ concentration in the blood
rises, more HCO3- removes
hydrogen ions from the solution,
forming carbonic acid
 Ocean acidification: the burning of fossil fuels releases CO2 into the atmosphere, resulting in
global warming
o 25% of the human-generated CO2 is absorbed by the ocean
o When CO2 dissolves in seawater, it reacts with water to form carbonic acid, lowering the
ocean pH
 The extra hydrogen ions combine with carbonate ions to form bicarbonate ions,
reducing the carbonate ion concentration
 40% decrease in carbonate ions by 2100
 Carbonate ions are necessary for calcification, production of calcium carbonate by
many marine organisms
 Reef-building corals and animals with shells
 Coral reefs are in danger
o The pH of the ocean is 0.1 pH lower than at any time in the past 420,000 years, with
another 0.3-0.5 pH drop by the end of the century

21
Chapter 4: Carbon and the Molecular Diversity of Life

Learning Goals
 Explain the importance of carbon to biological molecules
 Identify the functional groups present in biological molecules
 Describe how organic molecules are synthesized by cells
 Explain how polymers are broken down to monomers
 Describe the types of carbohydrates
 Explain the functions of carbohydrates
 Describe the types and functions of lipids
 Evaluate the role of proteins in the cell
 Compare the roles of DNA and RNA

Carbon is the basis for all biological molecules

 Carbon can form four bonds, bond to other carbon molecules
o Commonly bonds to hydrogen, oxygen, and nitrogen
o Properties depend on arrangement of the carbon skeleton and its chemical groups
Organic chemistry
 Organic chemistry: the study of compounds containing carbon
 Origin of life: abiotic (non-living) synthesis of organic compounds
o Stanley Miller designed in experiment and found that complex organic molecules could
arise spontaneously under conditions that existed on early earth
 Close system with a flask of water to simulate the sea, heat to cause vaporization
and produce an atmosphere, sparks to mimic lightning: produced organic
molecules
o Carbon-based compounds found in Mars crater where a Lake once existed: potential
relics of life-forms
o Major elements of life (C, H, O, N, S, P) are uniform from one organism to another
reflecting a common evolutionary origin

22
  Unique chemical versatility of the carbon atom: carbon’s ability to form four bonds produces an
inexhaustible variety of organic molecules
o Different species and individuals are distinguished by variations in the types of organic
molecules they make
Carbon can bond to four other atoms
 Bond formation: carbon has 6 electrons with 2 in the first electron shell and 4 in the second shell,
producing 4 valence electrons in a shell that can hold up to 8 electrons
o Carbon completes its shell by sharing 4 electrons with another atom so that 8 electrons
are present: single or double covalent bonds in organic molecules

o Four main atoms in organic molecules: H, O, N

 CO2: two double bonds have the same number of shared electrons as four single
bonds
 Often considered inorganic due to lack of hydrogen

23
  Molecular diversity from carbon skeleton variation: carbon chains often form the basis of most
organic molecules
o Hydrocarbons: organic molecules consisting of only carbon and hydrogen
 Major components of petroleum, which is a fossil fuel
 Not prevalent in most living organisms but some of a cell’s organic molecules have
regions consisting of only carbon and hydrogen
 Fats have long hydrocarbon tails
 Neither petroleum nor fat dissolves in water, both are hydrophobic: great majority
of their bonds are relatively nonpolar carbon-to-hydrogen linkages
 Can undergo reactions that release a relatively large amount of energy
o Isomers: same number of atoms of the same
elements but different structures, resulting in
different properties
 Structural isomers: differ in covalent
arrangements of carbon skeletons
 Increased complexity of carbon
skeleton results in an increased
number of possible isomers
 Cis-trans isomers: also known as
geometric isomers; same covalent
bonds but differ in their spatial
arrangement due to the inflexibility of
double bonds
 Occurs if a double bond joins 2
carbon atoms but each carbon
has 2 different atoms or groups
of atoms attached to it: 2
potential isomers
 Enantiomers: mirror images that
different shape due to the presence of
an asymmetric carbon, attached to
four different atoms or groups of atoms
 Usually only one isomer is biologically active because only that form can
bind to specific molecules in an organism

24
 o Two enantiomers of a drug may not be equally effective (meth is an
example)
Chemical groups
 May participate in chemical reactions or may contribute to function indirectly by their effects on
molecular shape
 Functional groups: chemical groups that are directly involved in chemical reactions
o Chemical groups most important to biology: [hydroxyl, carbonyl, carboxyl, amino,
sulfhydryl, phosphate], and methyl groups
 First 6 are chemically reactive, all but sulfhydryl and methyl groups are hydrophilic
and increase the solubility of organic compounds in water
 Methyl groups serve as tags on biological molecules
 Carboxyl and amino group are ionized at normal cellular pH

25
  ATP: adenosine triphosphate is a complex organic phosphate
o Organic molecule adenosine connected to three phosphate groups
o One phosphate group may split off as a result of a reaction with water, producing ADP or
adenosine diphosphate
o The process of a phosphate group splitting from ATP results in the release of energy than
can be used by the cell

26
Chapter 5: The Structure and Function of Large Biological Molecules

Four classes of biological molecules, three are polymers

 Polymers: long chains of monomer units
o Carbohydrates: source of energy and structural support
o Proteins: catalyze reactions and transport substances in and out of cells
o Nucleic acids: store genetic information and function in gene expression
 Lipids: not polymers or macromolecules -- hydrophobic -- provide energy, make up cell
membranes, act as hormones
Macromolecules
 Macromolecules: large carbohydrates, proteins, nucleic acids
 Polymer: long molecule consisting of many similar or identical building blocks linked by covalent
bonds
o Monomer: repeating units that serve as building blocks of a polymer
o Each class of the polymer is made up of a different type of monomer
o Synthesis (polymerization) and breakdown
 Enzymes: responsible for synthesis and breakdown of polymers -- specialized
macromolecules that speed up reactions
 Condensation reaction: the reaction that connects a monomer to another
monomer or polymer through covalent bonds, which results in the loss of a
small molecule
o Dehydration reaction: water molecule is lost
 Formation of carbohydrate and protein polymers
 Each reactant provides part of an H20 molecule:
hydroxyl group (OH-) and a hydrogen ion (H+)

27
  Hydrolysis: reaction that dissembles polymer, reverse of dehydration
reaction
o Bond between monomers is broken by the addition of a water
molecule
 Digestion: organic material in our food is in the form of
polymers, which are too big to enter the cells – various
enzymes break down the polymers into monomers, which
are released into the bloodstream, and then reassembled
into new polymers within the cell by dehydration reaction
o Diversity
 Small differences in polymers, particularly DNA and proteins, within relatives –
more extensive amongst those who are not related and different species
 Most polymers are constructed from 40-50 common monomers, diversity stems
from their arrangement in a linear sequence
 Proteins are built from 20 amino acids and are typically hundreds of amino acids
long
 Molecular structure and function can still be grouped by class

28
Carbohydrates
 Carbohydrates: sugars and polymers of sugars
 Sugars
o Monosaccharides: simplest carbohydrates, sugar
monomers
 Usually, a multiple of the unit CH2O
 Glucose (C6H12O6) is most common
 Trademarks:
 Carbonyl group (>C=O)
o Aldose (aldehyde sugar):
carbonyl group at end of
carbon skeleton
 Glucose and
galactose
o Ketose (ketone sugar):
carbonyl group within
carbon skeleton
 Fructose (isomer of
glucose)
 Multiple hydroxyl groups (-OH)
 Diversity:
 Size of carbon skeleton: 3-7
carbon atoms
 Spatial arrangement around asymmetric carbons (glucose vs galactose)
 Linear depictions of glucose are inaccurate: in aqueous solutions, glucose and
other simple sugars for 5-6 carbon atoms form rings, this is their most stable form
 Purpose
 Major nutrients for cells through cellular respiration: cells extract energy
by breaking glucose molecules down
 Carbon skeletons serve as raw material for synthesis of small organic
molecules such as amino acids and fatty acids
 Monosaccharides not immediately used are incorporated into
disaccharides and polysaccharides

29
 o Disaccharides: two monosaccharides joined by a covalent bond
 Glycosidic linkage: covalent bond formed between two monosaccharides by
dehydration reaction
 Sucrose (table sugar) is most common: glucose and fructose monomers
 Lactose: glucose and galactose monomers
 Lactose intolerance: lack enzyme lactase, cannot break down the
disaccharide
o Broken down by intestinal bacteria, resulting in cramping and gas
o Either take lactase supplement or drink dairy treated with lactase
 Must be broken down into monosaccharides to be used for energy by organisms
o Polysaccharides: carbohydrate macromolecules/polymers
 Serve as storage material and hydrolyzed as needed or building materials
 Architecture and function determined by monosaccharides and glycosidic linkages
 Storage polysaccharides:
 Starch: storage of glucose monomers by plants, take the form of granules
in plastids (such as chloroplasts)
o Withdrawn by plants through hydrolysis
o Most organisms, including humans, have enzymes that can
hydrolyze plant starch
o Most of the glucose monomers are joined by 1-4 linkages
o Simplest form is amylose, which is unbranched
o Glucose monomers have an alpha configuration
 Glycogen: storage of glucose monomers by animals
o Extensively branched
 Branches allow for easier breakdown
o Vertebrates store glycogen in mainly liver and muscle cells:
breakdown results in release glucose in respond to increased
energy demands
 In humans, stores are depleted within a day unless they’re
replenished by eating – low carb diets can lead to weakness
and fatigue

30
  Structural polysaccharides:
 Cellulose: component of tough walls that enclose plant cells, most
abundant organic compound on earth
o Polymer of glucose, with 1-4 glycosidic linkages
o Glucose monomers have a beta configuration
o Straight molecule, never branched, some hydroxyl groups are free
to hydrogen-bond with hydroxyls on parallel cellulose molecules
 Parallel cellulose molecules are called microfibrils
 Major constituent of paper and cotton, imparting
strength
o Enzymes that can hydrolyze alpha linkages cannot hydrolyze beta
linkages
 Insoluble fiber for humans
 Cows and termites harbor cellulose-digesting prokaryotes
and protists in the gut
 Chitin: carbohydrate used by arthropods to build exoskeletons
o Embedded in proteins, harden when protiens link to each other or
encrusted with calcium carbonate
o Similar to cellulose: beta linkages, but with nitrogen-containing
attachment

31
Lipids

 Lipids: not true polymers and not big enough to be considered macromolecules
o Hydrophobic: consist mostly of hydrocarbons
o Fats, phospholipids, and steroids
 Fats: large molecules assembled from smaller molecules by dehydration reactions – glycerol
molecule joined to three fatty acids – glycerol is an alcohol, each
of its three carbons bears a hydroxyl group
o Fatty acid: long carbon skeleton, 16 to 18 carbon atoms
in length, carbon at one end is a carboxyl group
(functional group), the rest is a hydrocarbon chain, each
fatty acid is joined to glycerol by dehydration reaction
resulting in an ester linkage between hydroxyl and
carboxyl groups
 Saturated: no double bonds between carbon
atoms composing a chain, hence the chain is saturated with hydrogen 
saturated fat: flexibility of single bonds allows the molecules to pack together
tightly, resulting in a solid formation at room temperature
 Hydrogenated fat: unsaturated fat converted to saturated fat by adding
hydrogen, allowing them to solidify
 Contribute to atherosclerosis
 Unsaturated: one or more double bonds, with fewer hydrogen atoms 
unsaturated fat: less flexible due to cis double bonds, resulting in liquid formation
at room temperature
 Nearly every double bond is a cis double bond, resulting in kinks in the
hydrocarbon chain
o Trans fats: hydrogenating fats can also produce trans double bonds. Which contribute to
coronary heart disease
o Major function is energy storage
 A gram of fat stores more than twice as much energy as a gram of polysaccharide
like starch
 Compact reservoir of fuel: stored in adipose cells, which swell and shrink – also
insulate and cushion

32
  Phospholipids: major constituents of cell membranes
o Two fatty acids attached to glycerol, with a hydroxyl group (negative charge) and another
polar molecule
 Phosphate group and its attachments form a hydrophilic head – assemble into
double layered sheet in water, called a bilayer, that shields the hydrophobic fatty
acid tails
 Arranged in similar bilayer at the surface of cells

 Steroids: lipids characterized by a carbon skeleton consisting of four fused rings

o Distinguished by particular chemical groups attached to the rings
o Cholesterol is common in animals:
component of cell membranes and a
precursor for other steroids, like sex
hormones
 Synthesized in the liver and
obtained from diet
 Can contribute to
atherosclerosis

33
Proteins
 Proteins: account for more than 50% of dry mass of most cells, instrumental in almost all activity
o Most enzymes are proteins, which regulate metabolism
 Catalysts: chemical agent that selectively speed up chemical reactions without
being consumed in a reaction
o The most structurally sophisticated molecules known, each type of protein has a unique
three-dimensional shape
o Constructed from the same set of 20 amino acids, linked in unbranched polymers
 Bond between amino acids is a peptide bond
 Polypeptides: amino acid polymers
 Protein: biologically active molecule made up of one or more polypeptides, each
folded and coiled into a specific three-dimensional structure
 Amino acids (monomers): organic molecule with both an amino group and a carboxyl group
o The center of an amino acid contains an asymmetric carbon atom called an alpha carbon
 Four partners are an amino group, carboxyl group,
hydrogen atom, and a variable group or R, also called a
side chain (differs in each amino acid)
o Amino acids are grouped by the properties of the side chains
 Nonpolar (hydrophobic), polar (hydrophilic), acidic
(negative charge due to presence of carboxyl group
dissociated at cellular pH, hydrophilic), basic (positive
charge, hydrophilic)

34
35
  Polypeptides (amino acid polymers)
o When two amino acids are positioned so that the carboxyl group is adjacent to the amino
group, they become joined through dehydration reaction, resulting in a covalent peptide
bond
o Polypeptide backbone: repeating sequence of atoms
 Different side chains extend from the backbone
 Range in length from a few to >1000 amino acids
 Each polypeptide has a unique linear sequence of amino acids
 Ends of polypeptides have free amino group (N-terminus) and free carboxyl group
(C-terminus)
 Chemical nature is determined by the kind and sequence of the side chains,
resulting in a unique folding pattern, shape, and chemical characteristics
o Structure and function: a functional protein is not just a polypeptide chain, but one or
more polypeptides folded into a molecule with a unique shape – the amino acid sequence
determines what three-dimensional structure the protein will have
 Structure results in function: ability to recognize and bind to another molecule
 Morphine and other opiates can mimic endorphins d/t their shape and
thus fit into and bind the endorphin receptors (proteins) in the brain
 Four levels:
 Primary structure: linear chain of amino acids
o Determined by inherited genetic information
o Dictates secondary structure through alpha helices and beta
pleated sheets
o Dictates tertiary structure through chemical nature of the backbone
and side chains
 Secondary structure: regions stabilized by hydrogen bonds between atoms
of the polypeptide backbone
o Coils and folds due to hydrogen bonds between repeating
constituents of the polypeptide backbone
 Oxygen has a partial negative charge and hydrogen atoms
attached to the nitrogen have a partial positive charge,
resulting in hydrogen bonds between the atoms
o Alpha helix: hydrogen bonds between every fourth amino acid

36
 o Beta pleated sheet: two or more segments of polypeptide chain
lying side by side are connected by hydrogen bonds
 Tertiary structure: three-dimensional shape stabilized by interactions
between side chains
o Hydrophobic interaction: amino acids with hydrophobic side chains
cluster at the core of the protein, out of contact with water
 Van der Waals interactions hold nonpolar amino acid side
chains together
o Disulfide bridges: covalent bonds reinforce the shape of the protein
– two cysteine monomers are brought closely together by the
folding of the protein, the sulfurs of each cysteine bond, resulting in
rivets in the protein
 Quaternary structure: arises when protein consists of two or more
polypeptide chains
o Collagen: three identical helical polypeptides intertwined into a
larger helix, producing strong fibers
o Hemoglobin: four polypeptide subunits – alpha and beta, each
subunit has a non-polypeptide component called heme, containing
an iron atom that binds oxygen
 Sickle cell disease: a change in the primary structure due to a substitution
of amino acid valine for glutamic acid at the sixth amino acid in the primary
structure of hemoglobin (protein that carries O2 in the RBCs)
o Hemoglobin aggregates into chains, deforming RBCs – sickle cell
crisis occurs when the cells clog vessels
 Protein folding: usually occurs as the protein is being synthesized in the
cell, but also depends on the physical and chemical conditions of the
environment
o Changes in pH, salt [ ], temperature, and other aspects of the
environment can alter the weak chemical bonds, resulting in
denaturation (biologically inactive)
 Denaturation can occur when a protein is transferred from
an aqueous environment to a nonpolar solvent, resulting in
hydrophobic regions to shift outward
o Difficult to determine folding process of proteins due to
intermediate structures and various stages of folding

37
  Misfolding of polypeptides is a problem responsible for
conditions like CF, Alzheimer’s, Parkinson’s and mad cow
disease
 X-ray crystallography: used to determine 3-D structure of a
protein
 Not entirely accurate: significant number of proteins
(20-30%) do not have distinct 3-D structure until
they interact with a target protein or other molecule
o Flexibility can contribute to binding with
different targets at different times
o Referred to as intrinsically disordered
proteins
Nucleic acids
 Nucleic acids: polymers made of monomers called nucleotides
o Gene: program sequence of polypeptides, unit of inheritance
 Consist of DNA, which is a type of nucleic acid
 Roles:
o DNA and RNA: enable living organisms to reproduce
o Gene expression: DNA directs DNA and RNA synthesis, controlling protein synthesis
through RNA
o Proteins are needed to implement genetic programs
o A given gene along a DNA molecule can direct synthesis of a type of RNA called mRNA,
which interacts with the cell’s protein synthesizing ribosomes to direct production of a
polypeptide, which folds into proteins
 mRNA transports genetic information for building proteins from the nucleus to the
cytoplasm
 Components:
o Polynucleotides: nucleic acids/macromolecules
o Nucleotides: monomers of polynucleotides
 Composed of a five-carbon sugar (pentose), nitrogen-containing base, and one to
three phosphate groups
 Beginning monomer has three phosphate groups, but two are lost during
polymerization – portion of nucleotide w/o phosphate groups is called a
nucleoside (nitrogenous base + sugar)

38
  Nitrogenous bases have one or two rings that include nitrogen atoms (take up H+
from the solution)
 Pyrimidine: one six-membered ring of carbon and nitrogen atoms
o Cytosine, thymine, and uracil
 Purines: larger, six-membered ring fused to a five-membered ring
o Adenosine and guanine
 Differ in chemical groups attached to the rings
 A, G, C found in both DNA and RNA, but T is found in only DNA, whereas U
is found in only RNA
 Sugar: DNA contains deoxyribose (missing oxygen atom on the second carbon)
and RNA contains ribose

 Nucleotide polymers: linkage of nucleotides involves condensation reaction, adjacent nucleotides

are joined by a phosphodiester linkage – phosphate group that covalently bonds to sugars of two
nucleotides, resulting in repeating sugar-phosphate backbone
o Free ends of the polymer are different: one has phosphate attached to the 5’ carbon and
the other end has a hydroxyl group attached to the 3’ carbon
 Built from 5’ to 3’
o Number of base sequences is limitless

39
  DNA and RNA structures:
o Double helix: two polynucleotides that form a DNA molecule
 Sugar-phosphate backbones run in opposite directions (5’ 3’) or antiparallel, on
the outside of the helix
 Nitrogenous bases are paired on the interior of the helix, through hydrogen bonds
 Compatible bases: AT and GC
 Complementary strands
o RNA molecules: single strands, complementary base pairing can occur between regions of
two RNA molecules or stretches of nucleotides in the same molecule, allowing it to take
on a specific shape necessary for function
 Transfer RNA (tRNA): brings amino acids to the ribosome for synthesis of a
polypeptide, ~80 nucleotides in length
 AU pairing instead of AT
Genomics and proteomics
 Bioinformatics: use of computer software to analyze large biological data sets
 Genomics: analyzing large sets of genes or even comparing whole genomes of different species
 Proteomics: analysis of large sets of proteins, including their sequences
 Evolution: compare similarity in genomes

40
Chapter 6: A Tour of the Cell

Learning Goals
 Apply the cell theory principles to the study of cells
 Explain the upper and lower limits to cell size.
 Evaluate the proper use of each type of light microscope and electron microscope
 Identify the features that are shared by all cells
 Compare the differences between eukaryotic and prokaryotic cells
 Identify the differences between plant and animal cells
 Identify the organelles of a cell based on their structure
 Describe the function of all the organelles seen in eukaryotic cells
 Explain the molecular composition and function of each type of cytoskeleton fiber
 Compare and contrast cilia and flagella
 Explain the external components of plant cells
 Describe the role of the extracellular matrix and junctions of animal cells

Microscopy and biochemistry

 Microscopy: invented in 1590 – parameters: magnification, resolution, contrast
o Resolution is inversely related to the wavelength of light (or electrons)
o Important to cytology: the study of cell structure
 Function of each cell requires an understanding of biochemistry: study of chemical
processes within cells
o Light microscope: visible light is passed through the specimen, through a glass lens, which
refracts (bends the light in such a way that the image of the specimen is magnified as it is
projected into the eye or into a camera)
 Magnification: x1000, resolution: 200 nanometers, contrast: staining
 Barrier to viewing organelles (low resolution)
 Better technology has been produced to view cell molecules and structures with
fluorescent markers

41
 o Electron microscope: introduced in the 1950s, focuses a beam of electrons through the
specimen or onto its surface
 Shorter wavelength of electrons than visible light = greater resolution (2
nanometers)
 Pros: reveal subcellular structures
 Cons: prep methods of specimens can kill the cells and produce artifacts
 Scanning electron microscope (SEM): detailed study of the topography of a
specimen, utilizes electromagnets as a lens to bend the path of the electrons,
electron beam scans the surface of a sample coated with thin film of gold, exciting
surface electrons, which are detected by a device that translates them into an
electronic signal sent to a video screen, producing a 3-D images
 Transmission electron microscope (TEM): internal structure of cells, utilizes
electromagnets as a lens to bend the path of the electrons, electron beam
through thin section of a specimen stained with heavy metal atoms that attach to
specific cell structures (increased electron density in those areas), electrons are
scatters more in the denser regions, so fewer electrons are transmitted, image
displays pattern of electrons
 Cryo-electron microscopy: preserve specimens at low temperatures, view
specimens in their cellular environments
o Complements X-ray crystallography: reveal protein complexes and
substructures
 Cell fractionation: takes cells apart, separates organelles from one another through the use of a
centrifuge (differential centrifugation) to identify structures that cannot be seen otherwise

42
43
Eukaryotic membranes
 Prokaryotic vs eukaryotic cells
o All cells have a plasma membranes, cytosol, chromosomes, and ribosomes
o Eukaryotic cells: DNA within nucleus, which is bound by a double membrane
 Membrane-bounded structures: organelles
 Larger: the logistics of carrying out cellular metabolism sets limits on cell size
o Prokaryotic cells: DNA in a region called the nucleoid, not membrane-enclosed
 Reactions may take place within specific regions surrounded by proteins
 Plasma membrane: selective barrier that allows passage of O2, nutrients, and wastes
o Ratio of SA to volume is critical: as a cell increases in size its SA grows proportionately less
than its volume
 Smaller cell has greater SA than volume
 Need a SA large enough to accommodate the volume: some cells (neurons are
elongated), others are microscopic
 Some cells require high SA to volume to aid in the exchange of material with their
surroundings: intestinal cells have microvilli
o Internal membranes: incompatible processes occur simultaneously

44
  Plasma and organelle membranes participate in cell metabolism: enzymes and
proteins built into membranes
 Membrane compositions are unique, suited to their function
Eukaryote genetic materials
 Most genes are located within the nucleus, in addition to the mitochondria and chloroplasts
o Nucleus is enclosed by nuclear envelope: double membrane – two lipid bilayers,
continuous pores perforating both membranes lined by protein known as a pore complex
(regulates entry and exist of proteins, RNA, and large macromolecules)
 Nuclear side of nuclear envelope: lined by nuclear lamina at the pores – maintains
shape of nucleus through protein filaments – and a nuclear matrix
o DNA organized into chromosomes carrying one long DNA molecule
 Chromosomes made up of chromatin: DNA and proteins (including histones)
 Human cells have 46 chromosomes in their nucleus (except for gametes, which
have 23)
o Nucleolus within the nucleus: rRNA is synthesized from genes in the DNA, proteins
imported from the cytoplasm are assembled with rRNA into subunits of ribosomes that
travel out of the nucleus and form ribosomes
 Multiple nucleoli can exist
 Can play a role in controlling cell division and life span
o Protein synthesis: nucleus synthesizes mRNA (carrying DNA info), transported to
ribosome, which translates the message into a specific polypeptide
 Ribosomes, made of ribosomal RNA and proteins, produce proteins
o Not membrane-bounded, therefore not an organelle
o Number of ribosomes and size of nucleoli correspond to protein synthesis by cell
o Two cytoplasmic regions in which protein synthesis takes place:
 Free ribosomes suspended in cytosol
 Bound ribosomes attached to the outside of the ER or nuclear envelope
 Depend on function: free ribosomes make proteins that function within the
cytosol, whereas bound ribosomes make proteins that go in membranes or
organelles
Endomembrane system
 Endomembrane system: includes nuclear envelope, ER, Golgi apparatus, lysosomes,
vesicles/vacuoles, and the plasma membrane

45
 o Synthesis of proteins, transport of proteins, metabolism and movement of lipids,
detoxification of poisons
o Membranes related through direct physical continuity or transfer of membrane segments
as tiny vesicles
o Structure varies and can change throughout the membrane’s lifespan
 ER: biosynthetic factory
o ER: extensive network of membranes, makes up ½ of the membranes in cells
 Network of tubules/sacs called cisternae
o ER membrane: separates ER lumen from the cytosol
 Continuous with the nuclear envelope
 Smooth ER: outer surface lacks ribosomes
 Diverse metabolic processes: synthesis of lipids, metabolism of carbs,
detoxification, storage of calcium ions depending on the cell type
o Enzymes synthesize lipids, including steroids, and detoxify poisons
by adding hydroxyl groups to molecules (water solubility makes
them easier to flush out)
 Drugs stimulate proliferation of the smooth ER and
detoxification enzymes, resulting in greater detoxification
and increased tolerance to drugs
o Store calcium ions for use by the cells
 Rough ER: studded with ribosomes
 Cells may secrete proteins produced by ribosomes attached to rough ER
o Polypeptide chain grows from bound ribosome  threaded into ER
lumen by a pore in the membrane  folds into functional shape 
ER membrane keeps them separate from proteins in cytosol
(produced by free ribosomes)  depart from ER wrapped in
vesicles that bud from the transitional ER (transport vesicles)
 Most secretory proteins are glycoproteins (proteins
covalently bonded to carbohydrates): enzymes in the ER
membrane facilitate their bonding
 Membrane factory for the cell: adds membrane proteins and phospholipids
to its own membrane  inserted into ER membrane and anchored by the
hydrophobic portions  ER membrane expands are portions are
transferred through transport vesicles to other membranes

46
  Golgi apparatus: shipping and receiving
o Products of the ER are modified and stored and sent out: cells specialized for secretion
o Consists of cisternae (flattened membranous sacs) and vesicles within close vicinity
 Cisternae vary on each side in thickness and composition
 Cis face: located near ER, RECEIVE INFO, transport vesicles move material
from the ER to the Golgi by fusing with the Golgi membrane
 Trans face: TRANSPORT INFO, produce transport vesicles
o Products are sorted and targeted for different parts of the cell
 Contain unique enzymes
o Products are modified during transport from cis to trans regions
o Manufactures some macromolecules like polysaccharides
o Transport vesicles fuse with the plasma membrane after use
 Lysosomes: digestive compartments
o Membrane is sacs of hydrolytic enzymes: used to digest (hydrolyze) macromolecules
o Lysosomal enzymes work best in acidic environments (within the lysosome)
 Small leakages from the lysosome have no effect due to the cytosol’s neutral pH,
but large amounts of enzymes can result in autodigestion
o Hydrolytic enzymes and membranes produced by rough ER  Golgi apparatus  some
lysosomes bud from trans face  inner membrane and enzymes are spared from
destruction by 3-D shape of proteins
o Intracellular digestion: some cells engulf things through phagocytosis, food vacuole fuses
with a lysosome
 Products pass into the cytosol
o Recycle cell’s own organic material through autophagy: double membrane arises,
lysosome fuses with outer membrane, dismantle inner membrane and closed material,
organic compounds released  cell can continually renew itself
o Some conditions involve inherited lysosomal storage diseases w/ a lack of hydrolytic
enzymes (Tay-Sachs – lipid overgrowth in brain)
 Vacuoles: diverse
o Large vesicles derived from ER and Golgi apparatus
o Selective transport

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 o Food vacuoles that form by phagocytosis, contractile vacuoles that pump excess water
out of the cell, enzymatic hydrolysis, reserves of organic compounds (water), store toxins
o Central vacuoles: exist in mature plant cells, coalescence of smaller vacuoles, cell sap
within the vacuole: main repository of inorganic ions

Mitochondria and chloroplasts

 Convert energy to forms cells can use
 Endosymbiont theory: similarities to bacteria -- early ancestor of eukaryotic cell engulfed an
oxygen-using, non-photosynthetic prokaryotic cell, formed a relationship with a host cell,
becoming endosymbiont (cell living within another cell) – merged into a single organism:
eukaryotic cell with a mitochondrion
o Another engulfed a photosynthetic prokaryotic cell, becoming a eukaryotic cell with
chloroplasts
o Both surrounded by two membranes rather than one: engulfed ancestor prokaryotes had
two outer membranes
o Mitochondria and chloroplasts contain ribosomes, like prokaryotes, and circular DNA
molecules, like bacterial chromosomes
 The DNA programs the synthesis of organelle proteins on ribosomes

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 o Both are fairly autonomous organelles: grow and reproduce within the cell
 Mitochondria: sites of cellular respiration – O2 to drive generation of ATP by extracting energy
from sugars, fats, etc.
o Found in almost all Eukaryotic cells (plants, animals, fungi, some protists)
 Single large mitochondria or up to thousands depending on the cell’s metabolic
activity
o Both membranes surrounding the mitochondria are phospholipid bilayers, the inner
membrane has cristae (infoldings) whereas the outer membrane is smooth – the inner
membrane divides the mitochondrion into two compartments: the intermembrane space
and mitochondrial matrix, containing enzymes, mitochondrial DNA, and ribosomes
 Enzymes: catalyze cellular respiration, function in respiration (produce ATP)
 Cristae: large SA, increased productivity
o Mitochondria change rapidly and form a branched tubular network
 Chloroplasts: found in plants and algae, sites of photosynthesis: solar energy to chemical energy
o Contain green pigment chlorophyll, enzymes, and other molecules that function in
photosynthetic production of sugar
o Two membranes around the chloroplasts: more flattened, interconnected membranes
inside the chloroplasts called thylakoids – each stack is a granum, the surrounding fluid is
known as the stroma
 The stroma contains chloroplast DNA, ribosomes, and enzymes
 Three spaces: intermembrane space, the stroma, and the thylakoid space
 Convert light to chemical energy during photosynthesis
o Can transform in shape and size, can reproduce, move along tracks of the cytoskeleton
o Chloroplast: specialized member of a family of closely related plant organelles called
plastids – amyloplast (colorless organelle that stores amylose starch in tubers and roots)
and chromoplast (pigments that give fruits and flowers orange and yellow hues)
 Peroxisomes: specialized metabolic compartment bounded by single membrane, contain
enzymes that remove hydrogen atoms from substrates and transfer them to O2, resulting in the
production of hydrogen peroxide (hence the name)
o Use oxygen to break down fatty acids that are transported to mitochondria and used as
fuel for cellular respiration
o Hydrogen peroxide can be used to detoxify substances
o Glyoxysomes: specialized peroxisomes found in fat-storing tissues of plant seeds

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  Contain enzymes responsible for initiating conversion of fatty acids to sugar, which
the seedlings use to source of energy and carbon prior to photosynthesis
Cytoskeleton
 Network of fibers extending throughout the cytoplasm that hold organelles in place
o Present in eukaryotes, but also some bacterial cells
 Roles: support (animal cells lack walls) and motility (changes in cell location and movement of
cell parts)
o Can be quickly dismantled and reassembled in different areas of the cell
o Interaction between cytoskeleton and motor proteins: cytoskeletal elements, motor
proteins, and the plasma membrane allow cells to move along fibers outside of the cell –
inside of the cell, vesicles and organelles use motor proteins to transport along tracks of
the cytoskeleton
o Cytoskeleton is responsible for the inward movement of the cell to form vacuoles and
phagocytic vesicles
 Components: microtubules (thickest), microfilaments (aka actin filaments – thinnest), and
intermediate filaments
o Microtubules: in all eukaryotic cells, hollow rods constructed from globular proteins
called tubulins – each is a dimer, containing two polypeptides: alpha and beta tubulins --
the overall microtubule grows by adding dimers or disassembles and rebuilds elsewhere –
one end is more active than the other – shape, support, and serve as tracks for motility
 Centrosomes and centrioles: microtubules grow out of centrosomes in animal cells
– a region near the nucleus – the centrioles is the center of the centrosome,
composed of 9 sets of triplet microtubules, arranged in a ring
 Cilia and flagella: cellular extensions that contain microtubules, act as locomotor
appendages
 Cilia usually occur in large numbers, whereas flagella are limited and longer
o Differ in beating patterns (flagella have undulating motion, cilia
have alternating power and recovery strokes)
o A single primary cilium can act as an antenna, which transmit
molecular signals from the cell’s environment to its interior
 Common structure: growth of microtubules sheathed in an extension of
the plasma membrane -- 9 pairs of microtubules in a ring with two single
microtubules in the center of nearly all eukaryotic flagella and cilia
 Basal body: anchors the microtubule assembly to the cell, similar to a
centriole

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  Dynein: large motor protein that aids the flagella and cilia in bending
motion, utilizes ATP for energy
o Microfilaments: present in all eukaryotes -- thin, solid rods – twisted double chain of actin
subunits – can form structural networks when proteins join filaments together – bear
tension – 3D structure formed inside plasma membrane supports the cell’s shape
 Actin: globular protein that builds microfilaments
 Cortex: outer cytoplasmic layer of a cell – semisolid consistency d/t microfilaments
 May make up the core of microvilli (increase cell SA)
 Myosin: protein that works with actin filaments cause contraction of muscle cells
 Pseudopodia: cellular extensions arising from actin filaments + myosin
 Cytoplasmic streaming: circular flow of cytoplasm within cells d/t actin-protein
interactions
o Intermediate filaments: only found in cells of some animals – diverse, contain types of
protein subunits that are related to keratin
 More permanent – can persist after cell death
 Reinforce cell and fix the position of organelles

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Extracellular components
 Cell wall: extracellular structure of pant cells and some prokaryotes – protects the plant cell,
maintains shape, prevents excessive uptake of water
o Thicker than plasma membrane, varied composition, but all contain microfibrils of
polysaccharide cellulose, which are synthesized by enzyme called cellulose synthase and
excreted to the extracellular space, embedded in the matrix
o Primary cell wall: initial wall in young plant, thin
o Middle lamella: between primary adjacent walls, layer of sticky polysaccharide pectin,
acts as glue
o Secondary cell well: some cells add another wall between the plasma membrane and
primary wall – deposited in several laminated layers
 Extracellular matrix of animal cells: animal cells do not have cell walls, but have an ECM,
consisting of glycoproteins
o Collagen: most abundant glycoprotein, 40% of total protein in human body
o Proteoglycans: secreted by cells, collagen fibers are embedded into this woven network
 Small core protein with many carb chains covalently attached (up to 95% carb)
 Hundreds of proteoglycan molecules can become bonded to a long polysaccharide
molecule
o Fibronectin: a glycoprotein that attaches cells to ECM – bind to cell-surface receptor
proteins called integrins
 Integrins span the cell membrane and bind on the cytoplasmic side to associated
proteins, which are attached to microfilaments of the cytoskeleton
 Transmit signals between the ECM and cytoskeleton: regulate cell behavior
o Mechanical and chemical pathways to transmit information to the nucleus: mechanical
through fibronectin/integrins/microfilaments of the cytoskeleton, resulting in changes to
the cytoskeleton, leading to signaling pathways in the cell, changing protein synthesis and
overall cell function
 Cell junctions: neighboring cells adhere, interact, and communicate via sites of direct physical
contact
o Plasmodesmata: perforate plant cell walls, lined by membrane
 Plasma membranes of adjacent cells line the channel of each plasmodesma,
producing a continuous connection

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  Channels are filled with cytosol, allowing cells to share the same internal chemical
environment – unify the plant structure, allowing substances to pass from cell to
cell
o Cell junctions: especially common in the epithelium
 Tight junctions: most like plasmodesmata, but lined with proteins extending from
the cellular membrane that form pores

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