AP Biology Review


Contents:

Part I:  Chemistry
Part II:  Enzymes
Part III: Membranes
Part IV:  Cellular respiration
Part V:  Photosynthesis
Part VI:  Mitosis and Meiosis
Part VII: Mendelian Genetics
Part VIII:  Molecular Genetics
Part IX: Evolution
Part X: Plant physiology
Part XI:  Vertebrate physiology

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Chemistry


Properties of carbon
    Normal valence of 4
    Charges are equally distributed around the carbon atom
     Carbon compounds tend to be nonpolar
    Carbon atoms can form long chains

Macromolecules in cells:  Text chapters 4 and 5
    Functional groups:  clusters of elements typically found together in particular molecules.  They are usually involved in chemical reactions.

Macromolecule structure and function lab

    Proteins
        Building blocks = amino acids.
            Functional groups -- amino and carboxyl
            Each amino acid has a side chain (variable group) that distinguishes one amino acid from another.
        Structures of proteins
           Primary structure = sequence of amino acids.  The amino acids are linked by peptide bonds involving the amino group  of one amino acid and the carboxyl of another.  Dictated by the genetic code.
            Secondary structure = hydrogen bonds form between amino acids that are fairly close together.  Two main kinds of
                                               structures result --
                                                    alpha helix
                                                    beta pleated sheet
            Tertiary structure = folding of a protein molecule due to other attractions within the molecule - often involve the
                                          variable (R) groups.
            Quaternary structure =  bonding together of two or more polypeptide chains.  Examples include hair and collagen (in
                                          in connective tissues.

        Functions of proteins:
                Parts of plasma membranes (channels, gates, enzymes, facilitators of diffusion, etc)
                Enzymes
                Transport molecules (such as hemoglobin)

   Carbohydrates -- polyhydroxy- aldehydes; ketones; amines or acids OR anything made from them
        Monosaccharides - single sugar units;  may be 3 to 5 carbon atoms long.
                Functions:  energy sources
                                 markers on cell surfaces
                                 ABO blood groups
            Aldehyde sugars
                The aldehyde group involves a terminal carbon has a double bonded oxygen and a hydrogen attached.  Examples of aldehyde sugars include glucose and ribose.  The names of aldehyde sugars typically end in -ose.

            Ketone sugars
            The ketone group has the double bonded carbon and oxygen between two other carbons.  Examples of ketone sugars (ketosugars) include levulose and ribulose.  The names of ketone sugars typically end in -ulose.  However, sometimes the name of a sugar was given before the rule was applied.  Therefore, levulose is often referred to as fructose.

               Disaccharides - double sugar units
              Functions:  energy sources

               Polysaccharides -  multiple sugar units
            Functions:  energy sources
                             cell wall components (cellulose; pectin; etc.)
                             energy storage (starch -- plants;  glycogen  -- animals)

Lipids = organic molecules in cells that are not water soluble.
    Triglycerides = fats and oils. Consist of three fatty acids + one glycerol
            Fatty acids may be saturated or unsaturated (with hydrogen).  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.
              Functions of triglycerides:  energy storage and energy sources.
    Steroids
        Based on cholesterol.
        Some are hormones such as the sex hormones.
        Steroid hormones are lipid soluble.  That is, they pass freely through the plasma membrane.  Therefore, steroid hormones
                are able to act directly on DNA to turn genes on or off.

    Phospholipids
        Composition -- two fatty acids, phosphate group (among other things) and one glycerol molecule
        Major component of the plasma membrane
        The phosphate group is on the hydrophilic head protion of the molecule, while the fatty acids constitute the hydrophobic
                tails.

Enzymes
              Function of enzymes
              Active site function
              Kinetics
              Influence of temperature, pH and ion concentration
              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.

Inhibitors:
    Competitive inhibitors are similar in shape to the normal substrate and bond with the active site of the enzyme.  Therefore, the enzyme cannot work on the normal substrate.   This affects the Km 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.  The result is that the active site changes shape and is unavailable to the substrate.  This kind of inhibitor affects the Vmax of the enzyme.


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Membranes

Chapter 8 (Biology, Campbell, et.al)

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) are toward the inside of the membrane, while the phosphate group, and asssociated atoms, are on the outsides (hydrophilic heads).

Membrane function - to regulate the passage of substances into and out of the cell - 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. 

Lab -- Demonstrating the Effects of Stress on a Plasma Membrane - see your online textbook


Membrane transport:
    Passive

        Simple diffusion -  Substance able to get through the membrane travel from areas of high concentration to areas of low
                                    concentration
        Facilitated diffusion - membrane proteins assist some substances through the membrane following the diffusion gradient.
                                        There are specific proteins for specific substances.  Example:  P450 in the lung alveoli assist the
                                        diffusion of oxygen into the blood stream.  Oxygen diffuses 30% faster due to this substance.
                                        (see link)
    Active transport - energy is used to transport substances against the diffusion gradient.  This allows the cells to concentrate
                                substances inside or outside. (See link)
      

   An example of active transport is the sodium-potassium pump. 

    Protein carriers in plasma membranes:
            Uniport proteins -- carry a single substance through the membrane 

            Symport proteins -- carry two different substances in the same direction at the same time.

            Antiport proteins -- carry two different substances in opposite directions.


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Cellular respiration

Vocabulary
Free energy changes (D G)
       + D G means that additional energy is required in order for an chemical reaction to take place
        -D G means that energy is liberated from the reaction.
The D G values of coupled reactions are additive.  Therefore, if the amount of energy liberated by one reaction is greater than the energy absorbed by another, one reaction can drive the other.  In cells, the hydrolysis of ATP to ADP generally drives other reactions.

Aerobic respiration 

 Animation of repiration

Process Location Major events
Glycolysis


Cytosol Splitting of 6 carbon sugar to two, three carbon pyruvate molecules.
Produces 2 NADH and a net gain of 2 ATP.
ATP is produced by substrate level phosphorylation.
Oxygen is not involved.
Regulated by feedback inhibition -- involves the enzyme phosphofructokinase.  Tied up by ATP or citrate.
Krebs cycle Matrix of the mitochondrion Pyruvate is reacted with coenzyme A (CoA).  Carbon dioxide is released and NADH is formed.  The result is the two carbon acetyl group that links with coenzyme A forming Acetyl-CoA.
Acetyl-CoA reacts with oxaloacetate (a 4 carbon molecule) to form a six carbon citrate.
In the cycle, carbon dioxide is removed, and the hydrogen ions are harvested in NADH and FADH.
One ATP is generated per cycle by substrate level phosphorylation.
Electron transport chain Inner membrane of the mitochondrion Hydrogen ions are actively transported between the membranes of the mitochondrion.  The result is an electrochemical gradient that provides the energy for the production of ATP.
Electrons are passed down the chain.
Molecular oxygen is the ultimate acceptor of hydrogen ions and electorns.

Fermentation:
    Beginning steps -- glycolysis.
    Pyruvate (or a derivative of it) becomes the final acceptor of hydrogen ions and electrons from NADH.
    NAD is an oxidizing agent in glycolysis in the conversion of PGAL (phosphoglyceraldehyde) to 1,3 bisphosphoglycerate.
            Lactic acid fermentation
                Occurs in skeletal muscle cells
                Pyruvate is the direct acceptor of H+ and electrons from NADH
                Produces lactic acid
                Accumulation of lactic acid causes 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.  Pyruvate is then used for another purpose.

            Alcoholic fermentation
                Occurs in yeast and some bacterial cells
                Pyruvate loses a carbon in the form of CO2 producing acetaldehyde.  Acetaldehyde becomes the acceptor of H+ and electrons from NADH
                Produces ethanol (ethyl alcohol) which eventually poisons the cells.

Sample AP Exam questions:

Within the cell, many chemical reactions that, by themselves, require energy input (have a positive free-energy change) can occur becuase the reactions
(A) may be coupled to the hydrolysis of ATP
(B)  take place very slowly
(C)  take place when the cells are at unusually high temperatures
(D) are catalyzed by enzymes
(E) are aided by various metal ions that act as catalysts.

Answer and explanation

Which of the following is a characteristic of mitochondria and chloroplasts that
 supports the endosymbiotic theory?
(A)  Both have bacteria-like polysaccharide cell walls.
(B)  Both can reproduce on their own outside of the cell
(C)  Both contain DNA molecules
(D)  Both contain endoplasmic reticulum and Golgi bodies
(E)  Both contain ribosomes that are identical to ribosomes of the eukaryotic cytoplasm.

Answer and explanation


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Photosynthesis

Objectives:
A.    P. Biology
Chapter 10 – Photosynthesis

Photosynthesis Lab - see your online textbook

Production of sugar by using sunlight energy.

6H2O + 6CO2 ----------> C6H12O6+   6O2

Organelle involved - chloroplast
Structure of chloroplast -

                                        Thylakoid sacs - location of the light reactions of photosynthesis that produces ATP and
                                                                  NADPH.
                                         Stroma is comparable to the cytoplasm of the cell.  This is where the Calvin cycle occurs.
                        ATP and NADPH are the needed energy sources as well as hydrogen ion and electron sources for the
                        production of sugar in the Calvin cycle (light independent reactions).

        Photosynthetic pigments:
                Primary pigment = chlorophyll a.  This is the pigment that takes direct part in the light dependent reactions.
                Accessory pigments = carotenoids and chlorophyll b.  Functions - protect chlorophyll a from damage from
                                                    UV light and absorb light at wavelengths that are not absorbed by chlorophyll a.
                                                    Electrons are transferred to chlorophyll a in the photosystems.  This broadens the
                                                    absorption spectrum for photosynthesis. (see link)

Leaf structure
                Mesophyll = tissues involved in photosynthesis.  In C plants, the palaside mesophyll (also known as palisade        parenchyma) is located on the upper side
                                    of the leaf.  Most of the photosynthesis occurs in this tissue.
                                    Spongy mesophyll is toward the lower side of the leaf.  Some photosynthesis occurs in this tissue.
                                    However, this the main tissue that allows for gas exchange with the atmosphere.
                Stomata = openings in the leaf epidermis that allow for the exchange of oxygen and carbon dioxide between the leaf
                                and the atmosphere.  The stomata are regulated by guard cells.  The opening and closing of the stomata
                                is regulated by CO concentration.  In C3 plants, the stomata open during the day and close at night.

Light reactions  (animation 1)  (animation 2) Occurs in the thylakoid membranes.  All pigments and enzymes are embedded in the membranes.
                Noncyclic electron flow
                        Basically, electrons are passed from water to NADPH.  Water is split releasing molecular oxygen as a waste
                        product.  The hydrogen ions are passed into the thylakoid sacs producing an electrochemical gradient that
                        ultimately produces ATP.

                        Two photosystems involved.
                        Photosystem I donates electrons that end up in NADPH
                        Photosystem II splits water, and donates electrons that restore photosystem I.  Therefore, water is ultimately
                        the source of electrons that end up in NADPH.
                        Review animation

Light independent reactions (also known as the dark reactions or the Calvin cycle) (animation)
                       The products of the light reactions provide the energy and the hydrogen ions needed to produce sugar from
                       carbon dioxide.  The carbon dioxide acceptor is RuBP (ribulose 1,5 bisphosphate). The enzyme rubisco                                      (ribulose bisphosphosphate carboxylase) catalyzes the reaction between RuBP and carbon dioxide.  The first                               stable compound is PGA (a three carbon compound -- 3 phosphoglycerate). PGAL (glyceraldehyde 3                                       phosphate) is produced as a result of reacting PGA with NADPH (from the light reactions).   PGAL is                                       converted to glucose, and RuBP is restored as a result of 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, which normally reacts RuBP with carbon dioxide, reacts oxygen with RuBP instead.  the result is the decompostion of RuBP to 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.  (See link)

CAM plants:  desert plants.  Trap CO2 at night and store it as crassulacean acid.  The plants carry out the Calvin cycle during the day by removing CO2 from crassulacean acid.  This prevents water loss through the stomata since the stomata only open at night.  In cactus, the leaves are reduced to needles, thus reducing surface area.
 
 

Sample AP Exam questions:

The O2 released during photosynthesis comes from
(A)  CO2
(B) H2O
(C) NADPH
(D) RuBP (RuDP)
(E)  C6H12O6

Answer and explanation

Which of the following is an important difference between light-dependent and light-independent reactions of photosynthesis?
(A)  The light-dependent reactions occur only during the day; the light-independent reactions occur only during the night.
(B)  The light-dependent reactions occur in the cytoplasm; the light-independent reactions occur in the chloroplasts.
(C)  The light-dependent reactions utilize CO2 and H2O; the light -independent reactions produce CO2 and H2O.
(D)  The light-dependent reactions depend on the presents of both photosystems I and II;  the light-independent reactons require only photosystem I.
(E)  The light-dependent reactions produce ATP and NADPH; the light-independent reactions use energy stored in ATP and NADPH.

Answer and explanation

If plants are grown for several days in an atmosphere containing 14CO2 in place of 12CO2, one would expect to find
(A) very little radioactivity in the growing leaves
(B) large amounts of radioactive water released from the stomates
(C) a large increase in 14C in the starch stored in the roots
(D) a large decrease in the rate of carbon fixation in the guard cells
(E) an increase in the activity of RuBP carboxylase (rubisco) in the photosynthetic cells.

Answer and explanation

Carbohydrate-synthesizing reactions of photosynthesis directly require
(A) light
(B) products of the light reactions
(C) darkness
(D) O2 and H2O
(E)  chlorophyll and CO2

Answer and explanation

The carbon that makes up organic molecules in plants is derived directly from
(A)  combustion of fuels
(B) carbon fixed in photosynthesis
(C) carbon dioxide produced in respiration
(D)  carbon in the lithosphere
(E) coal mines

Answer and explanation



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Mitosis and Meiosis

Objectives:  As a result of this unit, you should be able to:
1.  State the evidence that proves that the genetic material is actually DNA. (See pages 278-283)
2.   Explain how the cell cycle is regulated.
3.  State the importance of the processes of mitosis and meiosis.
4.  State the differences between the two processes in terms of:
    A.  the kinds of cells involved
    B.  the number of daughter cells produced
    C.  the purpose of each process
 5.  Explain the events that take place in each of the processes.
   

Comparison of mitosis and meiosis
    Both are divisions of the nucleus

Mitosis Meiosis
Purpose Maintain the same number of chromosomes in the cells of the body. Maintain the number of chromosomes from one generation to the next in a sexually reproducing population.
Cells involved Somatic (body) cells Reproductive cells
Number of daughter cells 2 4
Chromosome number in the daughter cells Same number as in the parent cell 1/2 the number of chromosomes as the parent cell
Number of divisions of the nucleus one two
Number of times the chromosomes are replicated one one

Stages of the cell cycle
    Interphase
        G1 -- normal cell function; growth of the cell; restriction point -- decision to divide
        S -- synthesis of DNA
        G2 -- production of protiens, etc. in preparation for mitosis

   Mitosis
            Prophase - disappearance of the nuclear membrane;  condensation of the replicated chromosomes; (in animal cells)
                              replication of the centromere and migration of the duplicated centromeres to the opposite poles of the cell.

            Metaphase - sister chromatids line up along the equatorial plate of the cell;  spindle fibers attach to each chromatid

            Anaphase - chromatids are separated as the spindle fibers shorten

            Telophase - formation of new nuclei.  The cell may or may not divide.

Division of the cell is called cytokinesis.

Photomicrographs of plant cell mitosis (see link)

Meiosis

Prophase I:  Sister chromatids and homologous chromosomes condense and line become tangled together.  Homologs exchange parts -
               crossing over.
                    Crossing over provides variety among the gametes.

Metaphase I:  Modified sister chromatids and their homologs line up together along the equatorial plate of the cell.

Anaphase I:  Homologs separate, but the sister chromatids stay together.

Telophase I:  Temporary formation of nuclei

Prophase II:  Condensation of chromatids

Metaphase II:  Sister chromatids line up along the equatorial plate

Anaphase II:  Chromatids separate

Telophase II:  Formation of new nuclei.  Each one is different due to crossing over in prophase I.



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Genetics

 
Definitions:
    Allele - alternative forms of a gene
    Codominant (incomplete codominance) - the expression of two alleels is a blend of traits
    Dominant - the expresson of one allele masks over that of another
    Epistasis - one gene prevents the expression of another gene that is not one of its allele
    Homozgyous - having identical alleles for a gene
    Heterozygous - having two different alleles
    Pleiotropy - one gene influences several other traits
    Test cross - a cross between an individual displaying the dominant trait and one that is a known homozygous recessive.

Mendelian laws
    Segregation - during gamete formation (meiosis) the alleles for each trait separate;  each gamete has one set of
                          chromosomes.  Therefore, each gamete has one allele for each trait.

    Independent assortment - the inheritance of one trait does not influence the inheritance of another.  This is true as
                                            long as the genes are on separate chromosomes.


 
Due the fact that there are thousand of traits, but a limited number of chromosomes (for example, 23 pairs in humans), chromosomes contain thousands of genes.  The closer the genes for two different traits are to each other on the same chromosome, the greater is the chance that they will be inherited together.  A way to test for this is a test cross of known heterozygotes.  If the two genes are on separate chromosomes, the test cross should result in a nearly 1:1:1:1 phenotypic ratio.
Test cross results that are very far off from this may indicate chromosome linkage.  The only way that variety can show up in terms of the arrangement of the two traits in question is if crossing over happens.  The closer two genes are to each other, the less frequently crossing over occurs.

Rule of addition -- The probability of an event that can occur in two or more ways is the sum of the separate probabilities.
Rule of multiplication -- The probability of two events occurring at the same is the product of the individual probabilities.

-------------------------

Sample AP exam questions:

Achondroplastic dwarfism is a dominant genetic trait that causes severe malformation of the skeleton.  Homozygotes for this condition are spontaneously aborted (hence, the homozygous condition is lethal) but heterozygotes will develop to be dwarfs.
   Matthew has a family history of the condition, although he does not express the trait.  Jane is an achondroplastic dwarf.  Matthew and Jane are planning a family of several children and want to know the chances of producing a child with achondroplastic dwarfism.

The genotypes of Matthew and Jane are best represented as
        Matthew                        Jane
(A)  AA                                Aa
(B)  Aa                                  aa
(C)  aa                                   aa
(D)  aa                                   Aa
(E)  Aa                                   Aa

Answer and explanation

The probablility that Matthew and Jane's first child will be an achrondroplastic dwarf is
    (A)  0%
    (B)  25%
    (C) 50%
    (D)  75%
    (E)  100%

Answer and explanation

If three children are born to Matthew and Jane, what are the chances that the first two children will not express the trait but that the third child will be an achrondroplastic dwarf?
    (A)  5/8
    (B)  4/8
    (C)  3/8
    (D)  1/8
    (E)  1/16

Answer and explanation

A male fruit fly (Drosophila melanogaster) with red eyes and long wings was mated with a female with purple eyes and vestigial wings.  All of the offspring in the F1 generation had red eyes and long wings.
    These F1 flies were test crossed with purple-eyed, vestigial-winged flies.  Their offspring, the F2 generation, appeared as indicated below.

                             F2 Generation
                        125 red eyes, long wings
                        124 purple eyes, vestigial wings
                          18 purple eyes, long wings
                          16 red eyes, vestigial wings

                        283 total

If in the F1 and F2 generations the same characteristics appeared in both males and females, it would be safe to assume that these traits for eye color and wing length
        (A)  are sex-linked
        (B)  vary in dominance according to sex
        (C)  are sex-influenced characteristics
        (D)  are autosomal characteristics
        (E)  follow the Mendelian rule of independent assortment.

Answer and explanation

In the F2 generation, the results are best explained by the fact that
        (A)  the test cros with the F1 flies resulted in sterile offspring
        (B)  these genes for eye color and wing shape do not pass through the F1 generation
        (C)  these genes for eye color and wing shape are found on the same chromosome
        (D)  crossing-over decreases variability
        (E)  the genes are sex-linked

Answer and explanation

If a single locus controls wing shape, then the alleles for this gene act as
    (A) dominant-recessive alleles
    (B)  incomplete-dominance alleles
    (C)  codominant alleles
    (D)  multiple alleles
    (E) variable alleles.

Answer and explanation

A couple has 5 children, all sons.  If the woman gives birth to a sixth child, what is the probability that the sixth child will be a son?
(A)  5/6
(B)  1/2
(C)  1/5
(D) 1/6
(E) 1/64

Answer and explanation
   

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Molecular Genetics

Structure of nucleic acids::

    Nucleotides:
        Composition -- phosphate group, 5-carbon sugar (deoxyribose or ribose) and a nitrogenous base (adenine, guanine,
                                cytosine, thymine, uracil)
    Nucleotides are linked together.  The phosphate is attached to the 3' carbon of one sugar and the 5'carbon of the next.  The nitrogenous bases are linked to  the 1' carbon of the sugar.  In DNA, the bases are linked to each other by hydrogen bonds (cytosne with guanine; adenine with thymine).  To do this, one side of the DNA molecule must be upside down and backwards in relation to the other.  This is referred to as antiparallel.

    DNA replication
    In eukaryotes, replication involves the creation of replication bubbles at various places in the DNA strand.  This is accomplished by the enzyme helicase that breaks the hydrogen bonds between nitrogen bases.  RNA primase places a short sequence of RNA nucleotides.  This sequence is the RNA primer.  DNA polymerase adds nucleotides beginning at the 5' end of the newly forming strand.

The genetic code
The genetic code is read as triplets of bases.  Every three bases codes for one amino acid.  Since there are four bases, but are read only three at a time, there are 64 possible combinations.  There are only 20 amino acids.  Therefore, some of the codes are repetitive, and others do not code for anything and are stop codons.

Protein synthesis
1.  Transcription of the genetic code into mRNA molecules.
     A.  RNA contains the sugar ribose rather than the deoxyribose of DNA.
     B.  RNA contains the nitrogenous base uracil rather than thymine.
     C.  Modification of the RNA is necessary.  The RNA first generated contains coding and noncoding portions.  The noncoding portions (introns) must be removed, and the coding portions (exons) are joined.  A cap and tail are added before the RNA becomes messenger RNA.
2.  mRNA becomes attached to the ribosome between the subunits.
3.  The amino acids must be activated.  That is, attached to a tRNA molecule.
4.  The anticodons of the tRNA form a bond with the complementary codons of the mRNA at the ribosome.
5.  The tRNA's bring the amino acids close enough to each other to have the peptide bond made by the enzyme peptidyl transferase.
The synthesis of protein from the RNA is called translation.

Gene regulation in prokaryotes

Gene regulation in eukaryotes


Sample questions from AP Exams:

1.  The process in which protein is assembled at a ribosome is
    (A)  Transcription
    (B)  Translation
    (C)  Transformation
    (D)  Replication
    (E)  Reverse transcription

    Answer and explanation

2.  The process in which naked DNA is taken up by a bacterial or yeast cell is known as
    (A)  Transcription
    (B)  Translation
    (C)  Transformation
    (D)  Replication
    (E)  Reverse transcription

    Answer and explanation
 


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Evolution-- Chapters 22 - 25 (Campbell, et.al.)
 
Part I:  Natural selection

        Historical perspective:  (Influences on Darwin)
           Linnaeus devised the system of binomial nomenclature for the classification of living things.
           Every living thing has a specific scientific name. The name is in Latin or is Latinized and is
           descriptive.  The scientific name consists of the genus name and the species adjective.
           A scientific name is either underlined or written in italics.)
 

           Cuvier -- Fossils are the remains of organisms that once lived and are found in sedimentary rocks.
            The different strata of rocks may have the remains of different kinds of organisms in them.  He
            speculated that there were natural disasters that caused an end to each era.

            Hutton -- Changes in the physical features of the earth were gradual (such as the formation of canyons).

            Lyell -- The forces that caused mountain building, eroding, etc. in the past are the same as the forces
                         doing the same things today.

            Lamarck -- Organisms have changed over time.  Lamarck's theory was based on the observations of
                               fossils and contemporary organisms.  Lamarck hypothesized that if an organism needs a
                               trait for survival, the trait can be acquired and then passed on to the offspring.  Features
                               that are not necessary are gradually lost.

            Malthus -- Human populations will eventually become so large that there will be competition among people.
                             The result will be wars and famine.

Charles Darwin's theory of natural selection.

           Basic ideas:
             1.  There are more offspring produced than can be supported.
                   2.  Variations exist in any population of organisms.
                   3.  Organisms compete with each other for essentials, such as food, water, mates, etc.
                   4.  The individuals that are best fit (most adapted) tend to survive and have more offspring than
                        those who are less adapted.
 
            Darwin borrowed ideas from others.  According to Darwin, evolution is a slow and steady process (gradualism).
            Fossils represent ancestors of presently living organisms.

            Evidence that supports evolution:
                    Comparative anatomy -- related organisms have similar body parts.
                    Comparative embryology -- related organisms have similar patterns of development.
                    Comparative biochemistry -- related organisms have similar chemical pathways and chemical composition.

Population genetics:
      The Hardy-Weinberg principle provides the conditions under which evolution occurs.  These conditions are:
            1.  The population must be large
            2.  The population must be isolated -- no migration
            3.  No particular characterisitic is favored over another (no natural selection)
            4.  All phenotypes must be represented in the reproducing population (random mating)
            5.  Mutations cannot occur.

    The following equations represent the frequencies of the alleles, and genotypes:
            p = frequency of the dominant allele in the population
            q = frequency of the recessive allele in the population
        p +  q = 1

        p2 + 2 pq +  q2 = 1

        p2 = frequency of the homozygous dominant genotype in the population

        2pq = frequency of the heterozygous individual in the population

        q2 = frequency of the homozygous recessive in the population

Founder effect
     A small group of organisms leaves the main population to colonize in a new area.  If the colony does not interbreed with the
    parent population, it will evolve along its own lines due to the fact that the allelic frequecies of the colony are not the same
    as the parent population.

Genetic drift
    The frequency can change by random events in a small population.

Gene flow
    The frequency of alleles can change when organisms immigrate to an established population.  The migrants may carry alleles
    new to the established population.

Cline (example)
    A variation in the phenotype of a species over a geographical region.

Gene fixation
     All of the alternative alleles of a particular gene are eliminated except for one.  All members of the population have the
    allele.

Speciation
    Caused by reproductive isolation
               Prezygotic isolating mechanisms
                            Gametic isolation
                            Behavioral isolation
                            Temporal isolation
                            Mechanical isolation
                            Habitat isolation
               Postzygotic isolating mechanisms
                            Hybrid inviability
                            Reduced hybrid fertility
                            Hybrid breakdown
    Defnitions of species
              Morphospecies
              Biological species
              Ecological species
              Recognition species
              Cohesion species
    Allopatric speciation
    Sympatric speciation
                Autopolyploidy
                Allopolyploidy
    Adaptive divergence
    Convergent evolution   

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Plant physiology

Anatomy of flowering plants:

         Tissues, cell types and other definitions:


Root structure;
r
 
 



Stem structure:                     Monocot stems have scattered vascular bundles.  The cells surrounding the vascular bundles are called pith.
                    Pith consists of parenchyma cells (thin walled).
                    The stems of dicots have the vascular bundles in rings.  A herbaceous dicot generally has a single ring of
                    vascular bundle.  In woody dicots, the wood consists of xylem cells.  The phloem is limited to the bark of the tree.
 
 



Leaf structure
 

Flower structure:
 

Double fertilization results in the formation of the seed embryo (2N) and the endosperm (3N).

Water transport in plants.
Transpiration
                    The evaporation of water from the leaf surface pulls water up the xylem cells from the root.  This is because of the attraction of water molecules to each
                    other (cohesion -- caused by hydrogen bonds between molecules) and the attraction of water moleculesto to the molecules in the walls of the xylem cells
                    (adhesion).

Sugar transport (Pressure flow hypothesis)

Plant responses:
Phototropism
       Growth response toward light.  Stems grow toward light (positive phototropism), while roots grow away from light
        (negative phototropism).  The response is due to the action of auxin. In stems, the cells nearest the apical meristem
        elongate in response to the presence of auxin.  (Auxin is produced by the apical meristem).
        Hypothesis I:  Auxin on the bright side of  the stem is destroyed by light.  Therefore, the shaded side of the stem
                                elongates faster, and the stem bends toward light.
        Hypothesis II:  Chemical messengers that inhibit cell elongation accumulate on the bright side of the stem.
 


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Vertebrate physiology
           Digestive system
           Circulatory system
                            (follow all links)
                        Synchronization of the heart beat
                                (Scroll down to the appropriate illustration.  Click on the animation button)
                        Hypertension
                       Dissection of fetal pig showing the circulatory system
                Respiratory system
              Immune system  (follow the links)
                                    Immune system animations
            Excretory system
                                    Animation
             Endocrine system
                Muscles 
                Nervous system

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Ecology

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