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
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 = .
Functional groups -- amino and carboxyl
Each amino acid has a side chain that distinguishes one amino acid from another.
= 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)
-- 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
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
-
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
+ 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.
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
tails.
Function of enzymes
Active site function
Kinetics
Influence of temperature, pH and ion concentration
Inhibitors
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
- 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)
- 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
Protein carriers in plasma membranes:
-- carry a single substance through the membrane
| Process | Location | Major events |
| 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. |
|
| 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. |
|
| 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.
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,
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.
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.
6H2O + 6CO2 ----------> C6H12O6+ 6O2
Organelle involved - chloroplast
Structure of
-
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).
:
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.
(
1) () Occurs in the thylakoid membranes. All pigments and
enzymes are embedded in the membranes.
Noncyclic electron flow
Basically, electrons are passed from water to .
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.
(also known as the dark reactions or
the Calvin cycle) ()
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. 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
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
require
(A) light
(B) products of the light reactions
(C) darkness
(D) O2 and H2O
(E) chlorophyll and CO2
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
| 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 |
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
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.
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
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%
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
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.
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
gene
act as
(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
son?
(A) 5/6
(B) 1/2
(C) 1/5
(D) 1/6
(E) 1/64
:
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.
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.
1.
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.
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 from the RNA is called .
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
Historical
perspective: (Influences on Darwin)
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.)
--
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.
-- Changes in the physical features of the earth were gradual (such as the formation of canyons).
-- The forces that caused mountain building, eroding, etc.
in the
past are the same as the forces
doing the same things today.
--
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.
-- 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.
The frequency of alleles can change when organisms
immigrate
to an established population. The migrants may carry alleles
new to the established population.
Cline ()
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.
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
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
(adhesion).
Sugar transport ()
Plant responses:
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.
Back to top