Properties of carbon
Normal valence of 4
Charges are equally distributed around the carbon atom
Carbon compounds tend to be nonpolar
Carbon atoms can
Macromolecules in cells: Text chapters 4 and
Functional groups: clusters of elements typically found together in particular molecules. They are usually involved in chemical reactions.
Macromolecule structure and function lab
Building blocks =
Functional groups -- amino and carboxyl
Each amino acid has a side chain
Secondary structure = hydrogen bonds form between amino acids that are fairly close together. Two main kinds of
structures result --
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)
Transport molecules (such as hemoglobin)
Monosaccharides - single sugar units; may be 3 to 5 carbon atoms long.
Functions: energy sources
markers on cell surfaces
ABO blood groups
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.
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.
Functions: energy sources
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 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.
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.
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
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.
Function of enzymes
Active site function
Influence of temperature, pH and ion concentration
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
Simple diffusion -
Substance able to get through the membrane travel from areas of high
to areas of low
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.
substances inside or outside. (See link)
An example of active transport is the
Protein carriers in plasma membranes:
|Cytosol||Splitting of 6 carbon sugar to two, three carbon pyruvate
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.
|Matrix of the mitochondrion||Pyruvate is reacted with coenzyme A (CoA). Carbon
released and NADH is formed. The result is the two carbon acetyl
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.
|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.
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.
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.
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,
energy input (have a positive free-energy change) can occur becuase the
(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.
Which of the following is a characteristic of mitochondria and
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.
6H2O + 6CO2 ----------> C6H12O6+ 6O2
Organelle involved - chloroplast
Thylakoid sacs - location of the light reactions of photosynthesis that
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).
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)
Mesophyll = tissues involved in photosynthesis. In C3 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 CO2 concentration. In C3 plants, the stomata open during the day and close at night.
Noncyclic electron flow
Basically, electrons are passed from water to
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.
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
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
This prevents water loss through the stomata since the stomata only
at night. In cactus, the leaves are reduced to needles, thus
Sample AP Exam questions:
The O2 released during photosynthesis comes from
(D) RuBP (RuDP)
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.
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.
Carbohydrate-synthesizing reactions of photosynthesis directly
(B) products of the light reactions
(D) O2 and H2O
(E) chlorophyll and CO2
The carbon that makes up organic molecules in plants is derived directly
(A) combustion of fuels
(B) carbon fixed in photosynthesis
(C) carbon dioxide produced in respiration
(D) carbon in the lithosphere
(E) coal mines
|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|
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
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.
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.
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
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
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
(A) AA Aa
(B) Aa aa
(C) aa aa
(D) aa Aa
(E) Aa Aa
The probablility that Matthew and Jane's first child will be an
achrondroplastic dwarf is
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 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.
125 red eyes, long wings
124 purple eyes, vestigial wings
18 purple eyes, long wings
16 red eyes, vestigial wings
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.
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
If a single locus controls wing shape, then the alleles for this
(A) dominant-recessive alleles
(B) incomplete-dominance alleles
(C) codominant alleles
(D) multiple alleles
(E) variable alleles.
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
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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.
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 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.
A. RNA contains the sugar ribose rather than the deoxyribose of DNA.
B. RNA contains the nitrogenous base uracil rather than thymine.
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.
Sample questions from AP Exams:
1. The process in which protein is assembled at a ribosome is
(E) Reverse transcription
Answer and explanation
2. The process in which naked DNA is taken up by a bacterial
cell is known as
(E) Reverse transcription
perspective: (Influences on Darwin)
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.)
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.
doing the same things today.
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.
The result will be wars and famine.
Charles Darwin's theory of natural selection.
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.
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
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
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.
The frequency can change by random events in a small population.
The frequency of alleles can change when organisms immigrate to an established population. The migrants may carry alleles
new to the established population.
A variation in the phenotype of a species over a geographical region.
All of the alternative alleles of a particular gene are eliminated except for one. All members of the population have the
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Caused by reproductive isolation
Prezygotic isolating mechanisms
Postzygotic isolating mechanisms
Reduced hybrid fertility
Defnitions of species
Water transport in plants.
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
Sugar transport (
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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