Download gil, virginia

BIO 101
Virginia Gil
A. We are already considered scientists because of how we apply our basic science skills
in our everyday life. We use elements of science on almost an everyday basis, in most if
not all of what we do, such as the scientific method to get an answer to a specific
problem. We are also considered scientists because we are surrounded by science in one
form or another, and we interact with these scientific elements.
A career goal of mine is to someday become a Pharmacist or pursue a similar career in
the medical field.
C. I think education is the basis of any well-rounded human being. Education opens the
doors to a plethora of opportunities.
D. Wanting to succeed in life and one day providing for my family as they have done for
me keeps me motivated.
Objectives:

Briefly describe unifying themes that pervade the science of biology.
Unifying themes that pervade in the science of biology include the structural level
by which life is organized, cell and their structure and function, study of life and heritable
information such as that of DNA and organisms and their interaction with their
environment.
Diagram the hierarchy of structural levels in biology.
Figure 0110

Explain how the properties of life emerge from complex organization.
Properties of life emerge from complex organisms such as that of atoms. These
are ordered into complex biological molecules. Molecules are then arranged into
organelles, which consist of cells. From this complex organization life is able to emerge.

Describe seven emergent properties associated with life.
Seven emergent properties associated with life include order, reproduction,
growth and development, energy utilization, response to the environment, homeostasis,
and evolutionary adaptation.

Explain how technological breakthroughs contributed to the formulation of the
Cell theory and our current knowledge of the cell.
I know this because I learned it in Honors Biology.

Distinguish between prokaryotic and eukaryotic cells.
I know this because I learned this in Honors Biology.

Explain, in their own words, what is meant by "form fits function."
“Form fits function” as far as the given shape of any organism assists them in
carrying out certain actions. There exists a correlation between structure and function.
For example, a bird’s build makes flight possible.

List the five kingdoms of life and distinguish among them.
The five kingdoms consist of Monera, Protista, Plantae, Fungi, and Animalia.
Monera is the kingdom of prokaryotes. Prostista consists of unicellular eukaryotes.
Plantae is the plant kingdom, or those that carry out the process of photosynthesis. Fungi
are organisms that absorb nutrients after decomposing organic refuse. Animalia consists
of unicellular eukaryotes that ingest other organisms.

Outline the scientific method.
I know this because I learned this in Honors Biology.

Distinguish between inductive and deductive reasoning.
Induction is reasoning from a set of specific observations to reach a general
conclusion. In deduction one uses a general conclusion to derive specific observations.

Explain how science and technology are interdependent.
Science is a process many use to come up with answers to any questions
concerning nature and technology enables scientists to answer and work on questions that
were previously unanswered or unapproachable.
Chapter 2 Objectives:

Define element and compound.
I know this because I learned this in Chemistry.
 State four elements essential to life that make up 96% of living matter.
Four elements essential to life are Oxygen, Nitrogen, Hydrogen, and Carbon.
 Describe the structure of an atom.
An atom consists of protons and neutrons in the nucleus and electrons in the
electron cloud.
 Define and distinguish among atomic number, mass number, atomic weight, and
valence.
Atomic number is the number of protons, mass number is the sum of protons and
neutrons, atomic weight is another term for mass number, and valence is the atom’s
bonding capacity.
 Given the atomic number and mass number of an atom, determine the number of
neutrons.
One would subtract the atomic number from the mass number to determine the
atom’s neutrons.
 Explain the octet rule and predict how many bonds an atom might form.
I know this because I learned this in Chemistry.
 Define electronegativity and explain how it influences the formation of chemical
bonds.
Electronegativity is the attraction of an atom for the electrons of a covalent bond.
Electronegativity determines the type of bond between atoms.
 Distinguish among nonpolar covalent, polar covalent and ionic bonds.
A nonpolar covalent bond occurs when both atoms are electronegative and a polar
covalent bond occurs between two electro negatively charged atoms. An ionic bond
occurs when one atom is transferred from one atom to another.
 Describe the formation of a hydrogen bond and explain how it differs from a
covalent or ionic bond.
A hydrogen bond takes place when a hydrogen atom is also attracted to another
electronegative atom. A hydrogen bond is weaker than a covalent or ionic bond.
Themes expressed in Chapter:
I. Science
1. Describe how water contributes to the fitness of the environment to support life.
I already know this because I learned it in Honors Biology.
2. Describe the structure and geometry of a water molecule, and explain what properties
emerge as a result of this structure.
Water's hydrogen bonds result in cohesion and surface tension, as well as a high
specific heat. Water is also less dense at a solid state than a liquid state. Lastly, water is
an unusually versatile solvent.
3. Explain the relationship between the polar nature of water and its ability to form
hydrogen bonds.
The water molecule is a polar molecule, meaning that it has opposite charges on
opposite ends. The anomalous properties of water arise from attraction among these
polar molecules. The attraction is electrical; a slightly positive hydrogen of one molecule
is attracted to a slightly oxygen of a nearby molecule. The molecules are thus held
together by a hydrogen bond.
List five characteristics of water that are emergent properties resulting from
hydrogen
bonding.
-Cohesion
-Adhesion
-Surface Tension
-High Specific Heat
-Less Dense at a solid state
4. Describe the biological significance of the cohesiveness of water.
Water's cohesiveness allows it to be transported upwards in microscopic vessels of
plants.
5. Explain how water's high specific heat, high heat of vaporization and expansion
upon freezing affect both aquatic and terrestrial ecosystems.
The high specific heat of water makes ocean temperatures quite stable, creating a
favorable environment for marine life. The water that covers most of planet Earth
keeps temperature fluctuations within the limits that permit life. Also, because
organisms are made primarily of water, they are more reliable to resist changed in
their own temperatures than if they were made of a liquid with a lower specific
heat.
Water's high heat of vaporization helps moderate Earth's climate. A
considerable amount of solar heat absorbed by tropical seas is consumed during
the evaporation of surface water. Then, as moist tropical air circulates pole ward,
it releases heat as it condenses to form rain. As substances evaporate, the surface
of the liquid that remains behind cools down. This evaporative cooling of water
contributes to the stability of temperature in lakes and ponds and also provides a
mechanism that prevents terrestrial organisms from overheating.
The ability of ice to float because of the expansion of water as it solidifies
is an important factor in the fitness of the environment. If ice sank, then
eventually all ponds, lakes, and even oceans would freeze solid making life, as we
know it impossible on Earth. The floating ice insulates the liquid water below,
preventing it from freezing and allowing life to exist under the frozen surface.
6. Explain how the polarity of the water molecule makes it a versatile solvent.
Water is an unusually versatile solvent because its polarity attracts it to
change polar substances.
7. Write the equation for the dissociation of water, and explain what is actually
transferred from one molecule to another.
H2O <---> H+ + OHOccasionally, a hydrogen atom is shared between two water molecules in a
hydrogen bond shifts from one molecule to another. When this happens, the
hydrogen atom leaves its electron behind, and what is actually transferred is a
hydrogen ion. The water molecule that lost a proton is now a hydroxide ion (OH8. Explain the basis for the pH scale.
The pH scale ranges from 1-14, where solutions ranging from 1-6 are acidic,
and those ranging from 8-14 are basic. Solutions classified as 7 are neutral.
Chapter 4 Objectives
1. Explain how carbon's electron configuration determines the kinds and number of bonds carbon will
form.
Carbon has a total of six electrons, with two in the first electron shell and four in the second shell.
Having four valence electrons in a shell that holds eight, carbon has little tendency to gain or lose electrons
and form ionic bonds; it would have to donate or accept for electrons to do so. Instead, a carbon atom
completes its valence shell by sharing electrons with other atoms in four covalent bonds. Each carbon thus
acts as an intersection point from which a molecule can branch off in up to four directions.
2. Describe how carbon skeletons may vary, and explain how this variation contributes to the diversity and
complexity of organic molecules.
Carbon chains form the skeletons of organic molecules. The skeletons vary in length and may be
straight, branched or arranged in closed rings. Some carbon skeletons have double bonds, which vary in
number and location. Such variation in carbon skeletons is an important source of the molecular
complexity and diversity that characterize living matter. Hydrocarbons for example, are organic molecules
consisting only of carbon and hydrogen, illustrating the diversity of carbon skeletons of organic molecules.
Such compounds too include isomers (structural, geometric, and enentiomers) which are compounds with
the same molecular formula but different structures,
3. Recognize the major functional groups, and describe the chemical properties of organic molecules in
which they occur.
The major functional groups incllude:
*the hydroxyl group (OH-), found in alcohols, has a polar covalent bond, which helps alcohols dissolve in
water
*the carbonyl group (ñCO), can be either at the end of a carbon skeleton (aldehyde) or within the
skeleton (ketone)
*the carboxyl group (-COOH), is found in carboxylic acids. The hydrogen of this group can dissociate
to some extent, making the molecule a weak acid.
*the amino group (-NH2) can accept an H+, thereby acting as a base.
*the sulfhydryl group (-SH), helps stabilize the structure of some proteins.
*the phosphate group can bond to the carbon skeleton by one of its oxygen atoms and has an important
role in the transfer of cellular energy.
Themes:
I. This chapter illustrates cells as the basic units of structure and function of an organism by outlining their
composition and properties.
II. Structure and function correlate where he structure of each cell classifies them into different groups,
thus, affecting their function. For instance, carbon skeletons affect the complexity of organic molecules.
II. The idea that the structural level on which life is organized which has emergent properties is also
evident where cells categorized according to properties and such.
III. The continuity of life is based on DNA. The building blocks of DNA are cells and the various bonds.
IV. The dual faces of life on earth are diversity and unity as is seen through the study of cells where each
are diverse yet all are still classified as cells.
CHAPTER 5 OBJECTIVES
1. List the four major classes of biomolecules.
-Lipids, carbohydrates, proteins, and nucleic acids
2. Describe how covalent linkages are formed and broken in organic polymers.
3. Describe the distinguishing characteristics of carbohydrates, and explain how they are
classified.
Characteristics of carbohydrates:
1. Polymers of simple sugars
2. Classified according to number of simple sugars
a) Monosaccharides = 1 simple sugar
b) Disaccharides = 2 simple sugars
c) Polysaccharides = many simple sugars
3. Monosaccharides
a) Simple sugars
b) 3 to 7 carbons
c) Carbon to hydrogen to oxygen ratio is 1 to 2 to 1
d) Major nutrient for cells
e) Glucose most common
f) Other examples
(1) Ribose
(2) Deoxyribose
(3) Galactose
(4) Fructose
g) Store energy in chemical bonds
h) Carbon skeleton raw material for other organic molecules
i) Monomers for di- and polysaccharides
4. Disaccharides
a) Double sugars
b) Two monosaccharides
5. Polysaccharides
a) Polymers of 100s to 1000s of monosaccharides
4. Identify a glycosidic linkage and describe how it is formed.
A glycosidic linkage is a covalent bond formed between two monosacharrides. For
example, maltose is a disaccharide formed by a glysodic linkage between two molecules
of glucose.
5. Describe the important biological functions of polysaccharide
1. . Storage: some polysaccharides are storage material, hydrolyzed as needed to provide
sugar for cells.
2. Structure: polysaccharadies serve as building material for structures protecting
the cell or the whole organism.
6. Explain what distinguishes lipids from other major classes of macromolecules.
Lipids are the one class of large biological molecules that does not include polymers.
7. Describe the unique properties, building block molecules and biological importance of
the three important groups of lipids: fats, phospholipids and steroids.
-Fats store large amounts of energy. There are saturated and unsaturated fats.
Phospholipids are major components of cell membranes. They have a negatively charge
phosphate group. Steroids have a basic structure of four fused rings of carbon atoms.
Steroids include cholesterol and certain hormones
8. Distinguish between a saturated and unsaturated fat.
Saturated fats have the maximum numbers of hydrogen atoms. Unsaturated fats have
one or more double bonds between their carbons.
9. Describe the characteristics that distinguish proteins from the other major classes of
macromolecules, and explain the biologically important functions of this group.
1. Characteristics
a)
Polymers of amino acids
b)
Vary in structure
c)
Each has unique 3-D shape
d)
20 different amino acids (see Figure 5.17 p.75)
2.
Importance
a)
Major component of cell parts
b)
Provide structural support
c)
Storage of amino acids
d)
Receptor proteins - involved in cellular response to chemical
stimuli)
Contractile proteins - movement)
Antibodies - defense against foreign substances)
Enzymes - catalysts
10. Define primary structure.
Primary structure is a unique sequence of amino acids.
11. Explain how weak interactions and disulfide bridges contribute to tertiary protein
structure.
12. Describe quaternary protein structure.
Quaternary protein structure is the particular shape of a complex, aggregate
protein, defined by the characteristic three-dimensional arrangement of its constituent
subunits, each a polypeptide.
13. Define denaturation and explain how proteins may be denatured.
Denaturation is a process in which a protein unravels and loses its native
conformation. Denaturation occurs under extreme conditions of pH, salt concentration,
and temperature.
14. Describe the characteristics that distinguish nucleic acids from the other major
groups of macromolecules.
Nucleic acids store and transmit hereditary information. Nucleic acids are the
molecules that enable living organisms to reproduce their complex equipment from one
generation to the next.
15. Summarize the functions of nucleic acids.
Nucleic acids store and transmit heredity information. A nucleic acid strand is a
polymer of nucleotides. Also, inheritance is based on replication of the DNA double
helix.
16. List the major components of a nucleotide.
Nucleotides are composed of three parts: phosphate group, which is joined by a
pentose (five-carbon sugar), which in turn is bonded to an organic molecule called a
nitrogenous base.
17. Distinguish between a pyrimidine and a purine.
Pyrimidine is characterized by a six-membered ring made up of carbon and
nitrogen atoms. Purines are larger, with the six-membered rings fused to a fivemembered ring.
18. Briefly describe the three-dimensional structure of DNA.
DNA is a helical, double stranded macromolecule with bases projecting into the
interior of the molecule. DNA strands are complementary to each other (A=T, C=G).
One strand of Dna can serve as a template for the formation of the other.
Themes:
I. The continuity of life is based on heritable information obtained through DNA.
DNA’s complex double helix structure allows it to carry vital information of all living
things.
II. Cells are the basic unit of structure and function. For instance, carbohydrates are
essential to a functioning organism, proving for energy and such.
II. The structural level of these has emergent properties. Characteristics of each cell or
molecule have properties that affect its function.
IV. Organisms interact continuously with their environment. As mentioned before,
carbohydrates exhibit this behavior in the reactions that occur once interaction takes
place.
V. The dual faces of life on earth are unity and diversity. The diverse molecules are
categorized differently and are composed differently yet all aid in chemical processes that
take place in the body.
Chapter 6 Objectives
1. Explain the role of catabolic and anabolic pathways in the energy exchanges of
cellular metabolism.
Catabolic pathways are that where energy is released, or broken down while anabolic
pathways accounts for the energy absorbed or built up in the exchange of energy in
cellular metabolism.
2. Distinguish between kinetic and potential energy.
Kinetic eneregy is energy of motion while potential energy is energy at standstill in
relation to possible motion.
3. Distinguish between open and closed systems.
4. Explain, in their own words, the First and Second Laws of Thermodynamics.
The first Law of Thermodynamics is that energy cant be created nor destroyed. The
second Law of Thermodynamics states that energy changes in forms.
5. Explain why highly ordered living organisms do not violate the Second Law of
Thermodynamics.
Ordered living organisms do no violate the Second Law of Thermodynamics because
while entropy change isn’t evident, their energy is being transformed into heat.
6. Distinguish between entropy and enthalpy.
Entropy is a measure of disorder or randomness while enthalpy is the sum of the
internal energy of a body and the product of its volume multiplied by the pressure.
7. Write the Gibbs equation for free energy change.
changeF = changeH - Tchange in S
8. Explain how changes in enthalpy, entropy and temperature influence the
maximum amount of usable energy that can be harvested from a reaction.
9. Explain the usefulness of free energy.
Free energy is the energy available for work. Organisms can only live at the expense
of free energy acquired from the surroundings.
10. List two major factors capable of driving spontaneous processes.
In order for a process to occur spontaneously, the system must either give up energy or
give up order.
11. Distinguish between exergonic and endergonic reactions.
An exergonic reaction proceeds with a net release of free energy, in other words,
those reactions that occur spontaneously. An endergonic reaction is one that absorbs free
energy from its surroundings, these reactions are nonspontaneous.
12. Describe the relationship between equilibrium and free energy change for a
reaction.
An unstable system is rich in free energy. It has a tendency to change spontaneously
to a more stable state, and it is possible to harness this downhill change in order to
perform work.
13. Describe the function of ATP in the cell.
ATP is the cell's energy shuttle. ATP drives endergonic reactions by transfer of the
phosphate group to specific reactants, making them more reactive.
14. List the three components of ATP and identify the major class of
Macromolecules of which it belongs.
15. Explain how ATP performs cellular work.
ATP performs cellular work by transfering a phosphate group from ATP to some
other molecule.
16. Explain why chemical disequilibrium is essential for life.
17. Describe the energy profile of a chemical reaction including activation energy (EA )
free energy change (DG) and transition state.
18. Describe the function of enzymes in biological systems.
Enzymes speed metabolic reactions by lowering energy barriers.
19. Explain the relationship between enzyme structure and enzyme specificity.
The specificity of an enzyme is attributed to a compatible fit between the shape of
its active site and the shape of the substrate.
20. Explain the induced fit model of enzyme function and describe the catalytic
cycle of an enzyme.
Induced fit brings chemical groups of the active site into positions that enhance
their ability to work on the substrate and catalyze the chemical reaction.
In an enzymatic reaction, the substrate binds to the active site to form an enzymesubstrate complex. In most cases, the substrate is held in the active site by weak
interactions, such as hydrogen bonds and ionic bonds. Side chain of a few of the amino
acids that make up the active site catalyze the conversion of substrate to product, and the
product departs from the active site.
21. Describe several mechanisms by which enzymes lower activation energy.
Ways enzymes lower activation energy
1. Bring reactants together in proper orientation
2. Bonds in substrate distorted during induced-fit
3. Provides microenvironment conducive to reaction
a) Localized low pH
b) Caused by acidic side chains
22. Explain how substrate concentration affects the rate of an enzyme-controlled
reaction.
Effect of substrate concentration on rate of enzyme-controlled reaction
1. Increase substrate concentration – increase rate of reaction
2. If substrate level high
a) Enzymes become saturated
b) Reaction rate dependent on how fast active sites convert substrate into product
23. Explain how enzyme activity can be regulated or controlled by environmental
conditions, cofactors, enzyme inhibitors and allosteric regulators.
The velocity of an enzymatic reaction increases with increasing temperatures. At
some point on the temp. scale, however, the speed of the enzymatic reaction drops
sharply with additional temp. increases. Cofactors are ions are molecules present in order
for some enzymes to function properly. Enzyme inhibitors reduce enzyme function and
allosteric sites are specific receptor sites on an enzyme remote from the active site.
Molecules bind to the site and change the shape of the active site.
24. Distinguish between allosteric activation and cooperativity.
Allosteric activation is when the molecules that naturally regulate enzyme activity
bind to an allosteric site, a specific receptor site on some part of the enzyme molecule
remote from the active site. Cooperativity is the mechanism that amplifies the response
of enzymes to substrates: One substrate molecule primes an enzyme to accept additional
substrate molecules.
25. Explain how metabolic pathways are regulated.
Themes:
I. The idea that science is a process of inquiry and reasoning is evident in the study of
enzymes and catalysts for instance. Further understanding of these can easily be obtained
through experiments and such.
II. Science and technology are functions of society and technology is needed for a better
understanding of concepts. Experiments performed in order to better understand topics
like that of enzymes are in need of technology in order to be successful.
III. Organisms interact continuously with their environment and these are seen in energy
where energy interacts with the environment and causes various reactions.
IV. A theme of biology is evolution and evolution of ideas is key in understanding
concepts.