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A.P. Biology Final Backup
Chemistry
The properties of carbon that influence it’s role in biological systems include its normal valence
of 4, equally distributed charges, and ability to form long chains.
Functional groups are clusters of elements typically found together in particular molecules, and
they are usually involved in chemical reactions.
The building blocks of proteins are amino acids.
Amino groups and carboxyl groups are the main functional groups of proteins.
Side chains (variable groups) distinguishes one amino acid from another.
The Primary structure is its sequence of amino acids.
A protein’s amino acids are linked by peptide bonds involving the amino group of one amino
acid and the carboxyl of another.
A protein’s secondary structure describes how hydrogen bonds form between amino acids that
are fairly close together, usually as a helix or pleated sheet.
A protein’s tertiary structure describes the folding of a protein molecule due to other attractions
within the molecule, often involving the variable (R) groups.
A protein’s quaternary structure describes the bonding of two or more polypeptide chains, such
as in hair or the collagen in connective tissues.
Functions of proteins include parts of plasma membranes (channels, gates, enzymes, facilitators
of diffusion, etc), enzymes, and transport molecules (such as hemoglobin).
Carbohydrates are often simply referred to as sugars, but are often much more complex (such as
cellulose or starch).
Monosaccharides are single sugar units of 3 to 5 carbon atoms long.
Monosaccharide functions including energy sources, markers on cell surfaces, and are the
identifying factor of ABO blood groups.
In aldehyde sugars (end in –ose) such as glucose and ribose, the terminal carbon on the adlehyde
group has a double bonded oxygen and a hydrogen attached.
In ketone sugars (end in –ulose) such as levulose (usually called fructose), the ketone group has
the double bonded carbon and oxygen between two other carbons.
Disaccharides are double sugar units that serve as energy sources.
Polysaccharides have multiple sugar units that function as energy sources, cell wall components
(cellulose; pectin; etc.), and energy storage (starch in plants or glycogen in animals).
Lipids are organic molecules in cells that are not water soluble, and include fats, oil, waxes, and
steroids.
Triglycerides consist of three fatty acids and one glycerol, and function in energy storage.
Fatty acids are said to be saturated (with hydrogen) if all the carbons in the chain have single
bonds between them in saturated fatty acids.
In unsaturated fatty acids, some of the carbons have double bonds between them, so there are
fewer hydrogen atoms.
Steroids are based on cholesterol molecules, and include hormones such as the sex hormones.
Steroid hormones are lipid soluble, and that means they pass freely through the plasma
membrane and are able to act directly on DNA to turn genes on or off.
Phospholipids are composed of two fatty acids, a phosphate group (among other things) and one
glycerol molecule.
Phospholipids are the major component of the plasma membrane.
The phosphate group is on the hydrophilic head portion of the molecule, while the fatty acids
constitute the hydrophobic tails.
The function of enzymes and its active site are influenced by temperature, pH and ion
concentration, and inhibitors.
Enzymes are catalysts that usually consist of proteins.
In an enzyme reaction, the rate of reaction increases as the temperature increases until the
optimal temperature is reached. After that, the rate of reaction decreases as the enzyme
denatures.
Most enzymes become totally denatured at 60o C.
Enzymes are also affected by the pH of the environment.
Most enzymes work best around a pH of 7. Enzymes can be denatured by deviations from the
optimal pH.
Competitive inhibitors are similar in shape to the normal substrate and bond with the active site
of the enzyme.
Reversible competitive inhibitors can be overcome by administering a large dose of substrate.
Noncompetitive inhibitors link to the enzyme molecule at a site other than the active site,
changing the shape of the active site making it unavailable.
Cells
Cell size is largely influenced by the ratio of surface area to volume, which affects gas and
nutrient exchange.
The cell membrane (the plasma membrane) encloses the cell.
The plasma membrane regulates all that enters and leaves a cell.
The cytoplasm is everything inside the cell, outside the nucleus.
The cells structures within the cytoplasm are often suspended in a series or web of protein fibers
(microtubules and microfilaments) called the cytoskeleton.
All cells have ribosomes, which serve as the site for synthesis of proteins.
All cells have DNA, which provides the instructions for making proteins, regulating cell
activities, and enabling cells to reproduce.
The nucleus directs cell activities and stores DNA.
There are many small openings or channels on the nuclear membrane called nuclear pores, which
allow ribosomal proteins and RNA to leave the nucleus.
The ribosomal proteins are manufactured in the nucleolus and form ribosomes when they are
assembled in the cytoplasm.
Eukaryotes store DNA in the nucleus, and the DNA is in long stands wound tightly around
proteins.
Just before the cell divides, however, the DNA strands wind up into dense, compact structures
called chromosomes.
An Endoplasmic Reticulum (ER) processes proteins made by ribosomes
Ribsomes in the cytoplasm make proteins that are designed to remain in the cell to make new
organelles.
Ribosomes attached to the surface of the rough endoplasmic reticulum make proteins that are
designed to be exported from the cell.
The ER is a network of membranes that move proteins and other substances through the cell.
The ER membranes are also made of a lipid bilayer with embedded proteins. As a protein is
made, it crosses the ER membrane and that portion of the ER pinches off and forms a sac called
a vesicle that protects the protein from other proteins in the cytoplasm.
The smooth portion of the ER lacks ribosomes and appears smooth in an electron microscope,
and it functions in making lipids and breaking down toxic substances.
The Golgi Apparatus (Bodies) packages and distributes the proteins
Vesicles from the ER carry the proteins to the Golgi apparatus, which appear as flattened sacs.
Enzymes in the Golgi apparatus modify the proteins, which are then encased in new vesicles that
bud from the surface of the Golgi.
Some of the vesicles produced by the Golgi are lysosomes, which are small spherical organelles
that contains the cell’s digestive enzymes.
Lysosomes digest and recycle the cells used components by breaking down macromolecules
(lipids, carbos, nucleic acids and proteins).
Mitochondria produce ATP through cellular respiration (including the Kreb’s cycle, the electron
transport chain, and oxidative phosphylation).
Nearly all eukarotic cells contain mitochondria, and cells with high energy needs (e.g., muscle
cells) have many (hundreds or thousands) mitochondria.
Mitochondria also have two membranes. The outer is smooth, and the inner membrane has
many folds. The two compartments formed by these membranes are where the chemical
reactions take place.
Mitochondria also have nucleic acids (DNA) and ribosomes.
Membranes
In the Fluid mosaic model , the plasma membrane consists of two layers of phospholipids with a
scattering of proteins within it.
The fatty acid tails (hydrophobic tails) of the phospholipids are toward the inside of the
membrane, while the phosphate group, and asssociated atoms, are on the outsides (hydrophilic
heads).
The membrane functions to regulate the passage of substances into and out of the cell, providing
selective permeability.
Substances that can diffuse freely through the plasma membrane are nonpolar (hydrophobic)
molecules as well as very small molecules such as water, carbon dioxide and oxygen. In general,
charged particles do not pass freely through the membrane.
The ability of specific ions and polar molecules to pass through the membrane depends on
transport proteins that are within the membrane.
Simple diffusion is a type of passive transport in which a substance travels through the
membrane from areas of high concentration to areas of low concentration.
Facilitated diffusion is a type of passive transport in which membrane proteins assist some
substances through the membrane along the concentration gradient.
Active transport requires energy to transport substances against the diffusion gradient, allowing
the cells to concentrate substances inside or outside.
An example of active transport is the sodium-potassium pump.
Uniport transport proteins -- carry a single substance through the membrane
Symport transport proteins -- carry two different substances in the same direction at the same
time.
Antiport transport proteins -- carry two different substances in opposite directions.
Cellular respiration
Glycolysis takes place in the cytosol, splitting a 6 carbon sugar to two, three carbon pyruvate
molecules without using oxygen.
Glycolysis produces 2 NADH and a net gain of 2 ATP through substrate level phosphorylation.
Glycolysis is regulated by feedback inhibition, involving the enzyme phosphofructokinase.
The Krebs cycle takes place in the matrix of the mitochondrion.
In the Krebs cycle, pyruvate is reacted with coenzyme A (CoA), carbon dioxide is released,
hydrogen ions are harvested in NADH and FADH and one ATP is generated per cycle by
substrate level phosphorylation.
The Electron transport chain takes place in the inner membrane of the mitochondrion, where
hydrogen ions are actively transported between the membranes of the mitochondrion.
The electron transport chain creates an electrochemical gradient that provides the energy for the
production of ATP.
As electrons are passed down the electron transport chain, molecular oxygen accepts the
hydrogen ions and electrons, forming water.
Lactic acid fermentation occurs in skeletal muscle cells with insufficient oxygen and produces
lactic acid, causing muscle fatigue and an oxygen debt.
When resting, lactic acid is carried to the liver via the bloodstream where it is converted back to
pyruvate for use in other body functions.
Alcoholic fermentation occurs in yeast and some bacterial cells, producing ethanol (ethyl
alcohol) which eventually poisons the cells.
Photosynthesis
Photosynthesis is production of sugar by using sunlight energy.
The reactions of photosynthesis are summarized as 6H2O + 6CO2 –(light) C6H12O6+ 6O2
Photosynthesis occurs in membranes of thylakoids, which are sacs in stacks called grana,
surrounded by the stroma of the chloroplast.
The thylakoid sacs are the location of the light reactions of photosynthesis that produces ATP
and NADPH.
Stroma is comparable to the cytoplasm of the cell, and serves as the location of the Calvin cycle,
in which ATP and NADPH provide energy and hydrogen ion electrons for the production of
sugar, independent of light.
Photosynthetic pigments include the primary pigment, chlorophyll a, and the accessory pigments
carotenoids and chlorophyll b.
The accessory pigments protect chlorophyll a from damage from UV light and absorb light at
wavelengths not absorbed by chlorophyll a.
The energy absorbed by accessory pigments are transferred to chlorophyll a in the photosystems,
broadening the absorption spectrum for photosynthesis.
The O2 released during photosynthesis comes from water (H2O).
The mesophyll of the leaf are involved in photosynthesis.
In C3 plants (most plants), most of the photosynthesis occurs in the palaside mesophyll (palisade
parenchyma) located on the upper side of the leaf.
Spongy mesophyll is toward the lower side of the leaf, and is responsible for only some
photosynthesis, but serves primarily in gas exchange with the atmosphere through openings
called stomata.
The stomata are regulated by guard cells, which are triggered by CO2 concentration.
In C3 plants, the stomata open during the day and close at night. CAM plants in arid regions
open their stomata at night to conserve water.
Photosystem I donates electrons that end up in NADPH
Photosystem II splits water, and donates electrons that restore photosystem I, and water is
ultimately the source of electrons that end up in NADPH.
The light-independent reactions (also known as the dark reactions or the Calvin cycle) use
NADPH from the light reactions to provide energy and hydrogen ions needed to produce sugar
from carbon dioxide.
In the light-independent reactions the carbon dioxide acceptor is RuBP in a reaction catalyzed by
the enzyme rubisco that eventually forms PGA.
In the light-independent reactions the first stable compound, PGA, reacts with NADPH to
produce PGAL, which is converted to glucose, and RuBP is restored with a series of reactions
involving ATP and NADPH.
Photorespiration occurs when the stomata of the leaf are closed and there is a shortage of carbon
dioxide for photosynthesis. The enzyme rubisco reacts RuBP with oxygen instead of carbon
dioxide to produce needed carbon dioxide.
C3 plants are capable of trapping (fixing) carbon in the Calvin cycle only.
C4 plant utilize the Calvin cycle, but have a series of added on reactions that allow carbon
dioxide to be trapped in the early morning or late evening.
CAM plants are desert plants that trap CO2 at night and store it as crassulacean acid to prevent
water loss through the stomata since the stomata only open at night.
The light-dependent reactions occur only during the day; the light-independent reactions occur
only during the night.
The light-dependent reactions utilize CO2 and H2O; the light -independent reactions produce CO2
and H2O.
The light-dependent reactions produce ATP and NADPH; the light-independent reactions use
energy stored in ATP and NADPH.
If plants are grown for several days in an atmosphere containing 14CO2 in place of 12CO2, one
would expect to find very little radioactivity in the growing leaves.
If plants are grown for several days in an atmosphere containing 14CO2 in place of 12CO2, one
would expect to find large amounts of radioactive water released from the stomata.
If plants are grown for several days in an atmosphere containing 14CO2 in place of 12CO2, one
would expect to find a large increase in 14C in the starch stored in the roots.
Carbohydrate-synthesizing reactions of photosynthesis directly require products of the light
reactions.
The carbon that makes up organic molecules in plants is derived directly from carbon fixed in
photosynthesis.
The Cell Cycle
In the cell cycle, interphase refers to the G1, S and G2 phases collectively.
The G1 phase features normal cell function and growth; and cells that do not pass the G1
checkpoint remain permanently in G1, sometimes referred to as G0.
The S phase features the synthesis of DNA known as DNA replication.
The G2 phase features additional production of proteins, and preparation for mitosis.
Mitosis occurs in diploid somatic (body) cells and results in two identical daughter cells with the
same number of somatic cells as the parent cell.
Prophase of mitosis includes the disappearance of the nuclear membrane, the appearance of the
replicated chromosomes, an in animal cells the replication of the centromere and migration of the
duplicated centromeres to the opposite poles of the cell.
Metaphase of mitosis features sister chromatids meeting along the equatorial plate of the cell
and spindle fibers attaching to each chromatid.
In anaphase of mitosis, chromatids are separated as the spindle fibers shorten.
Telophase of mitosis features the formation of new nuclei.
Division of the cell is called cytokinesis.
Meiosis
Meiosis occurs in reproductive cells and reduces the diploid parent cell to two haploid daughter
cells, and then splits the daughter cells again to result in four haploid daughter cells.
Mitosis and meiosis are both divisions of the nucleus, but serve different purposes.
Mitosis most closely resembles the second stage of meiosis.
Crossing over takes place between prophase I and metaphase I of meiosis.
Crossing over provides opportunities for variation between gametes.
The independent assortment of chromosomes during metaphase I of meiosis provides
opportunities for variation between gametes.
The steps of meiosis below are in the correct order:
a.
b.
c.
e.
f.
g.
d.
h.
The nuclei in step d. are haploid.
The nuclei in step e. are haploid.
The nuclei in step h. are haploid.
Genetics
Alleles are alternative forms of a gene.
Dominance is the expression of one allele masking the expression of another .
Homozgyous individuals have identical alleles for a gene.
Heterozygous individuals have two different alleles.
Pleiotropy describes when one gene influences several other traits.
A test cross is a cross between an individual displaying the dominant trait and one that is a
known homozygous recessive.
Mendel’s Law of Segregation states that allele pairs separate during gamete formation (meiosis)
and then randomly combine with the fusion of gametes during fertilization.
Mendel’s Law of Independent Assortment states that the inheritance of one trait does not
influence the inheritance of another as long as alleles for the trait are on separate chromosomes.
If a couple’s first two children are female, the probability that the couple’s third child will be
male is roughly 50%.
If a couple’s first two children are female, the probability that all three of the couple’s children
will be female is roughly 1/8 or 12.5%.
A couple has 5 children, all sons. If the woman gives birth to a sixth child, the probability that
the sixth child will be a son is 50%.
Molecular Genetics
Nucleotides are composed of a phosphate group, 5-carbon sugar (deoxyribose or ribose) and a
nitrogenous base (adenine, guanine, cytosine, thymine, uracil).
The phosphate of a nucleotide is attached to the 3' carbon of one sugar and the 5'carbon of the
next, and the nitrogenous bases are linked to the 1' carbon of the sugar.
In DNA, the nitrogenous bases are linked to each other by hydrogen bonds (cytosine with
guanine; adenine with thymine).
Adenine and guanine are purines, and are larger than thymine, cytosine and uracil, which are all
pyrimadines.
To form a double strand, one side of the DNA molecule must be upside down and backwards in
relation to the other, which is referred to as antiparallel.
In eukaryotes, DNA replication involves the creation of replication bubbles at various places in
the DNA strand by the enzyme helicase, which breaks the hydrogen bonds between nitrogen
bases.
In DNA replication, RNA primase places a short sequence of RNA nucleotides called an RNA
primer.
In DNA replication on the leading strand, DNA polymerase adds nucleotides beginning at the 5'
end of the newly forming strand that complements the leading strand.
In DNA replication on the lagging strand, DNA polymerase adds nucleotides beginning at the 5'
end but it builds short segments called Okazaki segments which are joined by the enzyme ligase.
Protein Synthesis
The genetic code is read as triplets of bases called a codon, and each codon codes for one amino
acid.
Because there are four bases, but are read only three at a time, there are 64 possible
combinations.
There are only 20 amino acids, so some of the codes are repetitive, and others do not code for
anything and function as stop codons.
Transcription takes place in the nucleus.
In transcription, the genetic code of the DNA is transcribed into a messenger RNA (mRNA)
molecule.
RNA differs from DNA because it contains ribose rather than deoxyribose, it contains the
nitrogenous base uracil rather than thymine, and it is singled-stranded.
After transcription, RNA processing removes noncoding portions called introns from the mRNA
molecule.
At the end of RNA processing, the coding portions called exons are joined by spliceosomes.
After mRNA leaves the nucleus, it becomes attached to the ribosome between the subunits.
The synthesis of protein from the mRNA is called translation.
Amino acids are activated when attached to a tRNA molecule.
In translation,, the anticodons of tRNA bond with a complementary mRNA codon at the
ribosome, where the amino acid is attached to a growing chain of other amino acids.
Evolution
Linnaeus developed the system of binomial nomenclature for the classification of living things,
giving each a specific scientific name (genus and species), usually in Latin and descriptive.
Cuvier proposed that fossils are the remains of organisms that once lived and are found in
sedimentary rocks.
Hutton proposed that changes in the physical features of the earth were gradual (such as the
formation of canyons), and Lyell said that the forces behind such events continue today.
Lamarck believed that organisms have changed over time, but he hypothesized that an organism
needing a specific trait can acquire it and then passed it on to the offspring.
The basic ideas behind Charles Darwin's theory of natural selection include that there are more
offspring produced than can be supported.
Darwin believed that variations exist in any population of organisms.
Darwin believed that organisms compete with each other for essentials, such as food, water,
mates, etc., and the individuals that are best fit (most adapted) tend to survive and have more
offspring.
Fossils represent ancestors of presently living organisms.
Evidence that supports evolution includes comparative anatomy, which supports that related
organisms have similar body parts.
Evidence that supports evolution includes comparative embryology, which shows that related
organisms have similar patterns of development.
Evidence that supports evolution includes comparative biochemistry, which shows that related
organisms have similar chemical pathways and chemical composition.
Population genetics
The Hardy-Weinberg principle provides the conditions under which evolution occurs, but
assumes that the population must be large, isolated without migration, with no natural selection
or sexual selections, and no mutations.
If p + q = 1 and p2 + 2 pq + q2 = 1, and p=.30, then 42% of the population are heterozygous.
The Founder effect describes how an isolated small group of organisms leaves the main
population to colonize in a new area, and changes to allele frequencies could occur.
Genetic drift describes how random events in a small population can change allele frequencies. .
Gene flow describes how migrants can influence allele frequencies in the populations they visit.
Prezygotic reproductive isolating mechanisms leading to speciation include gametic isolation,
behavioral isolation, temporal isolation, mechanical isolation, and habitat isolation.
Postzygotic isolating mechanisms include reduced hybrid viability, reduced hybrid fertility, and
hybrid breakdown.
Allopatric speciation involves reproductive isolation from a geographic barrier.
Sympatric speciation involves reproductive isolation from a radical change in the genome of a
population subgroup.
Adaptive divergence or adaptive radiation is the result of the introduction of new environmental
stresses presenting new problems and opportunities.
Convergent evolution is the independent development of similar characteristics in different
species as a result of similar ecological roles and selection pressures.
Analogous structures are most closely associated with convergent evolution.
Homologous structures are most closely associated with divergent evolution.