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AP BIO - THE BIG IDEAS
BIOCHEM
Living organisms are integral parts of the physical universe and must obey the fundamental laws of chemistry and
physics.
Covalent bonds are strong bonds: they can be broken apart only with relatively large amounts of energy; hence
covalently bound molecules are stable.
In a polar covalent bond the charge is distributed unequally among the atoms involved. Bonds to atoms such as
nitrogen and oxygen are often polar, while bonds between carbon atoms and between carbon and hydrogen are
essentially nonpolar.
Weak chemical bonds play a crucial role in stabilizing the shape of many of the large molecules found in living matter
and holding them together.
Water molecules are polar and have a strong tendency to form hydrogen bonds with one another; the consequent
cohesive forces between the water molecules gives water many of its special properties, making it the medium of life.
All complex molecules are composed of many simpler building-block molecules, bonded together by condensation
reactions; they can be broken down by hydrolysis.
Proteins may act as important enzymes in chemical reactions or as structural components of cells.
The amino acid content and sequence of a protein determine its three-dimensional shape; The R groups of amino acids
largely determine the structure and properties of proteins. Of particular importance is the fact that some R groups are
hydrophilic, while others are hydrophobic. Weak bonds between these groups play a crucial role in determining the
three-dimensional structure of proteins. Alteration in the shape of a protein can lead to a change in its biological
function.
Nucleic acids make up the genes that determine the structural and functional characteristics of living things.
The course of a chemical reaction depends on whether the free energy in the covalent bonds in the reactants is greater
or less than the free energy in the covalent bonds in the products. If the reaction results in the products with less free
energy , the reaction is exergonic and will proceed spontaneously. If, however, the covalent bonds of the products
have more free energy than the reactants, the reaction will require a net input of energy and is said to be endergonic.
Enzymes, like all catalysts, lower the activation energy needed for all reactions. An enzyme effectss only the rate of
the reaction but does not alter the direction of the reaction, its final equilibrium, or the reaction energy involved.
Most enzymes are highly specific, and each can interact only with those reactants or substrates that fit spatially and
chemically into the active site of the enzyme. Anything that alters the shape of the enzyme will alter its activity.
CELLS
The fundamental organizational unit of life is the cell. All living things are composed of cells; all cells come from
preexisting cells.
A cell's interaction with its environment is crucial; materials necessary for life must be obtained from the
environment, and waste products must be released into it.
Membranes are barriers between cells and around certain entities within cells. All substances moving into or out of a
cell must pass through a membrane barrier, and the membrane of each cell can be quite specific about what is to pass
through, at what rate, and in which direction.
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The plasma membrane consists of a bilayer of phospholipids oriented with their hydrophobic tails toward the interior
of the membrane and their hydrophilic heads toward the aqueous surfaces. The proteins are distributed both on the
surfaces and in the interior of the membrane.
The phospholipid bilayer creates an effective barrier between the inside of the cell and the surrounding medium.
Highly specialized channels and pumps control the passage of molecules into and out of the cell.
A living cell is an extraordinarily complex unit with an intricate internal structure; its activities are precisely
integrated and controlled.
There are two fundamental types of cells, procaryotic and eucaryotic cells. Procaryotic cells lack a membraneenclosed nucleus, as well as other intracellular membranous organelles present in eucaryotic cells..
The first cells were probably procaryotic; eucaryotic cells may have originated from a symbiotic union of ancient
procaryotic cells of several types.
ENERGY - RESPIRATION
Within a living cell, a constant supply of energy is required to drive the various chemical reactions that maintain life.
The ultimate energy source for most organisms is sunlight; green plants transform light energy into energy-rich
compounds like glucose, which can be used directly or passed to other organisms.
The energy stored in complex organic molecules must be transformed into the energy of ATP - the universal energy
currency of living organisms - in order to be used by the cell; this transformation must occur in every living cell.
The energy stored in complex organic molecules is not liberated through a single large reaction; rather, the universal
catabolic process by which the molecules are broken down occurs as a series of small reactions, each catalyzed by its
own specific enzyme.
All living cells break down sugars by the process of glycolysis. The glycolytic pathway consists of a series of
coupled reactions in which the product of one reaction becomes the substrate for the next. In such reactions, the
exergonic steps push or pull endergonic steps, with the favorable net free-energy change of the steps taken together
enabling the sequence of reactions to proceed.
Fermentation enables a cell to continue reactions of glycolysis in the absence of oxygen, by providing reactions in
which NAD is regenerated from NADH.
Considerable more energy can be extracted from glucose if oxygen is present that if it is absent; consequently a
plentiful supply of oxygen is essential for most organisms if their energy demands are to be met.
Cells living under aerobic conditions obtain most of their energy from cellular respiration, a process in which pyruvic
acid is oxidized to acetyl-CoA, which is then oxidized in the Krebs citric acid cycle.
The NADH and FADH synthesized in the oxidation of glucose pass their electrons to oxygen indirectly by way of a
series of electron carrier molecules (cytochromes). The energy thus liberated is used to pump H+ ions from the
matrix into the outer compartment of the mitochondrion, creating a chemiosmotic gradient across the inner membrane.
ATP is produced when H+ move back across the membrane.
The metabolic breakdown of high-energy compounds is an inefficient process; more that half the available energy is
lost as heat. Some animal have evolved mechanisms for retaining this heat and can thus maintain a uniformly high
body temperature and metabolic rate (endothermic).
ENERGY - PHOTOSYNTHESIS
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The ultimate energy source for most organisms is sunlight; green plants transform light energy into energy-rich
compounds like glucose, which can be used directly or passed to other organisms.
When a photon of light is absorbed by a chlorophyll molecule, the photon's energy raises an electron to a higher
energy level and this excited state is passed through the photosystem. The energy released in the transfer of excited
electrons from one acceptor to the next is converted into a form that can be used by the cell.
During cyclic photophosphorylation, light energy is used to move electrons from chlorophyll, through a series of
electron acceptor molecules, and back to the chlorophyll molecule. The free energy released in the electron transfer is
indirectly converted into ATP.
During noncyclic photophosphorylation, light energy is used to pull electrons and hydrogen away from water. The
electrons are passed through two electron-transport chains, eventually reaching the final acceptor, NADP.
The energy released as the electrons flow along the electron-transport chains is used to move H+ ions into the inside
of the thylakoid. ATP is synthesized when the H+ ions flow back through special channels in the membrane, down
the concentration gradient.
A series of reactions, the Calvin cycle, is used to reduce CO2 to form carbohydrate.
The hydrogen and electrons necessary for the reduction of CO2 come from water. When water is split, the oxygen is
not needed and is released as a gas.
Under certain conditions, the RuBP necessary for the Calvin cycle is oxidized in the process called photorespiration.
The RuBP is thus unavailable for the Calvin cycle.
Some plants have evolved structural and biochemical adaptations that enable them to fix CO2 in a different manner
(C4, CAM), circumventing the photorespiration process.
CELL DIVISION
When a cell divides, it must make a complete copy of the genetic information in its nucleus and then, as it divides,
give one complete set to each daughter cell.
Mitosis produces new cells with exactly the same chromosomal endowment as the parent.
Meiosis reduces the number of chromosomes in a cell by half, so that when the egg and sperm unite in fertilization,
the normal diploid number is restored.
Sexual reproduction increases variation in the population by making possible genetic recombination.
GENETICS - GENERAL
Somatic cells have pairs of homologous chromosomes, a pair consisting of one chromosome from each parent. Each
gene is found in two copies, one on each chromosome of the homologous pair, at corresponding loci.
In meiosis, each gamete receives a copy of only one chromosome from each homologous pair, and hence only one of
the two alleles.
Genes do not alter one another; they remain distinct and segregate unchanged when meiosis occurs.
When two or more pairs of genes located on different chromosomes are involved in a cross, the members of one pair
are inherited independently of the other.
Characteristics are often determined by many genes acting together.
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The expression of a gene depends both on the other genes present and on the physical environment. All organisms are
the product of the inheritance and their environment.
A gene may exist in any number of allelic forms in a population, but a given individual can possess no more than two
alleles.
Mutational changes in genes occur at random; most of the mutations that have a phenotype effect are deleterious.
The inheritance patterns for characteristics controlled by genes on the X chromosomes are quite different from those
for characteristics controlled by autosomal genes.
GENETICS - MOLECULAR
DNA is the genetic material that makes up the genes; it contains all the information needed for the cell's growth and
division into two similar cells.
During replication, a faithful copy of the DNA is made by base pairing.
When DNA is replicated, the strands are copied in only one direction; the replicating enzymes move along one of the
parental strands from 3' to 5', generating a complimentary strand that goes from 5' to 3'.
The information encoded in DNA is used to produce both the proteins that form cellular structure and the enzymes
that direct cellular metabolism; these determine the phenotypic characteristics of the organism.
During transcription, the information in the DNA is faithfully copied into RNA (base pairing).
In eucaryotes, specific regions within the transcript must be removed in the nucleus to create a functional mRNA
molecule.
The sequence of the bases in DNA determines the sequence in which amino acids will be linked in protein synthesis.
The genetic code consists of triplet coding units; a combination of three nucleotides specifies one amino acid. The
code is degenerate and nonoverlapping.
Translation of the information contained in DNA into functional proteins is indirect, involving several types of RNA.
Although every cell in the body of a multicellular organism has identical genetic information, individual cells have
different structural and functional characteristics. Various control mechanisms determine when and how each cell
will act on its inherited genetic instructions.
Each gene can make only one kind of messenger RNA; regulators determine if and when each gene will synthesize its
particular RNA.
ECOLOGY
Ecology is the study of the interactions between organisms and their environment. The various ecosystems are linked
by biological, chemical, and physical processes.
Many natural populations show an initial period of exponential growth at low densities, followed by a deceleration in
growth at higher densities, and by an eventual leveling off as the density approaches the carrying capacity of the
environment. Such a population is limited by influences that provide feedback control in that they depend at least
partially on the density of the population itself.
In natural populations, growth is subject to a number of limitations; the regulation of population density can occur in
different ways in different populations.
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The niche is the function and position of an organism in the ecosystem. The more the niches of two different species
overlap, the more intense the competition between them will be.
A species does not exist as an isolated entity; it is always interacting in a variety of ways with other species in the
community to which it belongs.
The biotic community formed by the various species in an area can be considered a unity of life, with its own
structure and functional interrelationships.
The trend of most ecological successions is toward a more complex and stable ecosystem, in which less energy is
wasted and hence a greater biomass can be supported without further increase in the supply of energy.
Most ecological successions eventually reach a climax stage that is more stable than the stages preceding it. The more
complex organizations of the climax community, and its larger organic structure and more balanced metabolism,
enable it to buffer its own physical environment to such an extent that it can perpetuate itself as long as the
environment remains essentially the same.
The movement of energy and materials knits a community together and binds it with the physical environment to form
a functioning system.
Radiant energy from the sun is the ultimate energy source for life on earth. This energy is captured by the producers
and passed on to the consumers.
Energy is constantly drained from an ecosystem as it is passed along the links of a food chain. Energy flow is always
noncyclic.
The water and mineral components of the biosphere are used over and over again; they cycle through an ecosystem,
and can be passed around it indefinitely.
The sun is the ultimate energy source for life, and the distribution of its energy helps determine the distribution of
living things. Because the earth's surface curves away from the path of incident light, areas of different latitudes
receive different amounts of sunlight and precipitation.
A limited number of major categories of climax formations, called biomes, can be recognized; classification of a
region as belonging to a particular biome is determined by which climax community is the most common in the
region.
The distribution of biomes is a consequence of climate, physiography, and other environmental factors.
Since its intrinsic rate of increase always exceeds the carrying capacity of the environment, a population is always
under pressure to expand its niche or to extend its range. To spread successfully into a new area, a species must have
the physiological potential to survive and reproduce there, an ecological opportunity, and physical access.
EVOLUTION
Modern evolutionary theory is based on two concepts; that the genetically determined characteristics of living things
change with time, and that this change is directed by natural selection.
The evolutionary raw material is genetic variation in a population. Natural selection can act on genetic variation only
when it is expressed as phenotypic variation.
Evolutionary change means change in allelic frequencies (and hence in genotypic ratios) in populations of organisms,
not individuals.
By natural selection, we mean nonrandom reproduction, or, more specifically, reproduction that is to some degree
correlated with genotype.
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Evolutionary change is not automatic; it occurs only when something disturbs the genetic equilibrium. Mutation
pressure and selection pressure are always disturbing this equilibrium, and migration and genetic drift may also do so.
Adaptations are genetically determined characteristics that enhance an organism's chances of perpetuating its genes in
future generations.
In the modern view, a species is a genetically distinctive group of natural population s that share a common gene pool
and that are reproductively isolated from all other such groups.
Divergent speciation usually begins when two sets of populations are separated geographically by external barriers; as
the two population systems evolve independently, they accumulate differences that lead in time to the development of
intrinsic isolating mechanisms.
Sympatric speciation does not involve geographical isolation. Species that arise by polyploidy are genetically
distinctive and are reproductively isolated for the parent species. Habitat preference, host-specificity, and certain
behavioral isolating mechanisms can also produce reproductive isolation leading to speciation.
ORIGIN OF LIFE
Life arose spontaneously from nonliving matter under the conditions prevailing on the early earth; from these
beginnings all present life on earth has descended.
All of the events now hypothesized as contributing to the origin of life, and all the known characteristics of life, seem
to fall well within the general laws of the universe; no supernatural event was necessary for the origin of life on earth.
There was no abrupt transition from "nonliving' prebionts to "living" cells; the attributes associated with life were
acquired gradually.
Living organisms, one they arose, changed their environment and thus destroyed the conditions that had made
possible the origin of life.
VIRUSES AND MONERA
Viruses are on the border between life and nonlife; they lack the metabolic machinery to make ATP and proteins, and
they cannot reproduce themselves in the absence of a host; but they have nucleic acid genes that encode the
information for their reproduction.
Bacterial cells are procaryotic; they lack a nuclear membrane and most other membranous organelles and thus are
fundamentally different from all other living organisms.
The Monera are an extraordinarily successful group of organisms; their great metabolic versatility and enormous
reproductive potential have enabled them to survive in a wide variety of habitats.
The Cyanobacteria are procaryotic cells that produce O2 as a by-product of their photosynthesis; they may have
initiated the oxygen revolution some 2.3 billion years ago.
Many bacteria are beneficial; all other organisms depend directly or indirectly on the activities of the bacteria.
PROTISTA
The Protista include the eucaryotic organisms that are primarily unicellular or colonial.
The Protista can be separated into three evolutionary lines: the animal-like, fungus-like, and plantlike Protista.
However, there are also many similarities among them.
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Each protozoan should be regarded not as equivalent to a cell of a more complex animal but as a complete organism
with the same properties and characteristics as multicellular animals.
FUNGI
The fungi are a diverse group of sedentary, absorptive heterotrophic organisms; they have great economic importance,
and play a vital role as decomposers.
The cells of fungi are eucaryotic. They have calls but are usually organized into threadlike hyphae in which the
cellular partitions may be absent or incomplete.
The characteristics of sexual reproduction are significant in distinguishing among the several divisions of fungi
PLANTAE - EVOLUTION
The green algae are regarded as the group from which the land plants evolved.
In the life cycle of the most primitive plants, the haploid stages are dominant; this apparently was the ancestral
condition.
The evolution of most plants groups shows a tendency toward reduction of the gametophyte (multicellular haploid
stage) and increasing importance of the sprorophyte (multicellular diploid stage). The evolutionary move from an
aquatic existence to a terrestrial one was not simple for the terrestrial environment is in many ways hostile to life.
Plants evolved a number of characteristics that enabled them to survive on land.
The Bryophytes represent the most conspicuous exception to the evolutionary trend toward reduction of the
gametophyte and increasing importance of the sporophyte.
The evolution of the tracheophytes is best understood in terms of adaptations for life in the terrestrial environment.
The angiosperms are the most successful land plants because they have evolved the most efficient adaptations for
living and reproducing on land.
PLANTAE - PHYSIOLOGY
Autotrophic organisms manufacture their own organic compounds from inorganic raw materials absorbed directly
from the environment.
On order to carry out their life processes, all organisms require prefabricated high-energy compounds or the raw
material from which these compounds can be synthesized.
Because of the presence of the Casparian strip, all materials absorbed by the root must pass through the living
endodermal cells to reach the vascular tissue, and the plant can exercise some control over the movement of
substances into the vascular tissue.
The successful exploitation of the land environment by plants was dependent on the evolution of specialized
conducting tissues that would transport water and nutrients from one part of the plant to another.
All tissues produced by the apical meristem are primary tissues. All tissues derived from the cambium (secondary
meristem) are secondary tissues; they contribute to growth in diameter.
The two main types of plant vascular tissue are xylem, which conducts water and inorganic ions upward from the
roots to the arterial parts of the plant; and phloem, which conducts water and organic solutes from one part of the
plant to another, both upwards and downwards.
According to the cohesion theory, water lost by transpiration from the aerial parts of plants is replaced by withdrawal
of water from the water column in the xylem, and in the process the whole column is pulled upward.
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According to the pressure-flow, or mass flow, hypothesis, there is a mass flow of solutes under pressure through the
sieve tubes of phloem from an area of high concentration to an area of low concentration.
Chemical control mechanisms play an important role in the coordination of the myriad functions of living organisms.
Hormonal control is common to plants.
Plant hormones are not highly specific in their action but rather participate in some fashion in nearly all aspects of
growth and development.
A plant's response to a given hormone depends on the tissue, the concentration of the hormone, and the concentration
of other plant hormones that may be present.
Plant cell division is stimulated by cytokinins and auxins, and by other factors that enhance their activity.
Control of cell enlargement involved substances such as auxins and gibberellins, which promote cell elongation.
The various plant hormones, by their mutual interactions and other differential effects on various parts of the plant
body, help integrate and coordinate the development of form and function.
In most plants, flowering is affected by photoperiodism, the response to the duration and timing of light and darkness.
ANIMALIA
Characteristics such as level of organization, type of symmetry, presence or absence of segmentation, nature of
embryonic development, and form of larva, if any, have been used to establish hypothetical relationships among the
various animal groups.
The Porifera differ greatly from other multicellular animals, and are believed to have evolved on a line of their own.
The Cnidaria are radially symmetrical animals with bodies that are relatively simple in structure.
The Platyhelminthes and Nemertea are thought to be the most primitive bilaterally symmetrical animals; in each, the
body is composed of three well-developed germ layers, and is acoelomate.
A major split probably occurred in the animal kingdom soon after the emergence of a bilateral organism. One
evolutionary line led to the phyla in which the blastopore become the mouth: these are called Protostomia. The other
line led to the phyla in which the blastopore become the anus and a new mouth is formed: these are called the
Deuterostomia.
In some protostome phyla, the body cavity is not completely enclosed by mesoderm; it is a pseudocoelom. All the
other protostome phyla have true coeloms; in most groups these arise as a split in the initially solid mass of
mesoderm.
The Arthropods are generally regarded as the most highly evolved representatives of the protostome line.
The phylum Echinodermata, the most primitive of the major deuterostome phyla, is linked in important ways to the
Chordata.
All chordates possess, at some time in their life cycle, a notochord, pharyngeal slits, and a dorsal hollow nerve cord.
The members of the subphylum Vertebrata may be regarded as the most highly evolved representatives of the
deuterostome line.
The acquisition of hinged jaws was one of the most important events n the history of vertebrates since it made
possible the development of a variety of feeding methods and life styles.
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Any fish that had appendages better suited for land locomotion than those of their fellows would have been able to
exploit the ecological opportunities open to them on land more fully; through selection pressure exerted over millions
of years, the fins of these first vertebrates to walk on land would slowly have evolved into legs.
The evolution of the amniotic egg, which provides a fluid -filled chamber in which the embryo may develop even
when the egg itself is in a dry space, was an important evolutionary advance in the conquest of land.
Fossil evidence indicates that the members of the class Mammalia arose from small, shrewlike insectivores.