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The Science of Life
Jacqueline Basallo
INTRODUCTION
a. EXPLAIN WHY YOU ARE ALREADY A SCIENTIST
Science is the state of knowledge; knowledge as a system testing
the truths of accepted laws through the scientific method. Daily, we
interact with living organisms, matter, atoms, compounds, et cetera, all
which arose from theories which were once tested. Unknowingly, we put
the scientific method to work to solve menial problems in everyday life
and for this reason, I, and every human being, is already a scientist.
b. DESCRIBE CAREER GOAL
Futuristically thinking, I aspire to some day become a successful
architect. After schooling for approximately 5 years, I seek to be
employed in a very successful firm and to change the being of the citizens
of the nation and the world.
c. PERSONAL VIEW TOWARDS EDUCATION
I feel that education is a critical part to society. Ignorance is one of
the wrongs with human kind and by education we help to prevent that.
Education leads to success. It is through education that society can change
its being and challenge the individual, stimulate ingenuity and
resourcefulness and yields a rewarding sense accomplishment.
d. DESCRIBE WHAT KEEPS YOU MOTIVATED IN LIFE
My motivation lies in my own self-content. Looking forward to the
happiness I can create for myself by completing a proposed goal is what
keeps me motivated.
CHAPTER ONE OBJECTIVES (SELF-MONITOR)
a. Briefly describe unifying themes that pervade the science of biology.
The science of biology is pervaded by unifying themes. Themes as such
include: the structural level on which life is organized which has emergent
properties; Cells are the basic units of structure and function of an
organism; the continuity of life is based on heritable information in the
form of DNA; a feeling for organisms enriches the study of life; structure
and function are correlated at all levels of biological organization; organisms
interact continuously with their environments; the dual faces of life on
Earth are diversity and unity; the core theme of biology is evolution;
science as a process of inquiry often involved hypothetico-deductive
thinking; science and technology are functions of society; biology is a
multidisciplinary adventure.
b. Diagram the hierarchy of structural levels in biology.
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c. Explain how the properties of life emerge from complex organization.
The properties of life emerge from complex organization. Firstly, atoms
are ordered into complex biological molecules. These molecules of life are
then arranged into structures called organelles, which are the components
of cells. Although some organisms consist of single cells, multi-cellular
organisms have its similar cells grouped into tissues and the specific
arrangement of tissues form organs. It is through this hierarchy that all
biological processes transcend and life emerges.
d. Describe seven emergent properties associated with life.
Seven emergent properties associated with life include:
1. Order: all other characteristics of life emerge from an organisms complex
organization.
2. Reproduction: Organisms reproduce their own kind.
3. Growth and development: Heritable programs in the form of DNA
direct the pattern of growth
and development.
4. Energy utilization: Organisms take in energy and transform it to
do many kinds of work.
5. Response to the environment: Organisms reponse to
environmental stimulus as protection.
6. Homeostasis: Regulatory mechanisms maintain an organism's
internal environment withing
tolerable limits, although the external
environment may fluctuate.
7. Evolutionary adaptation: Life evolved as a result of the
interaction of organisms with one
another and their environments.
e. Explain how technological breakthroughs contributed to the formulation
of the cell theory and our
current knowledge of the cell.
Technological breakthroughs have aided in the formulation of the cell
theory and our current knowledge of the cell. A powerful instrument
called the electron microscope has been able to expose the complex
structure of cells. This instrument proved an improvement to the
discoveries of the English scientist, Robert Hooke, and his contemporary,
Anton van Leeuwenhoek. The electron microscope showed that all cells are
enclosed by a membrane that regulates the passage of materials between
the cell and its surroundings and that every cell, at some point in its life
span, contains DNA.
f. Distinguish between prokaryotic and eukaryotic cells.
I already know the distinguished factors between prokaryotic and
eukaryotic cells as I familiarized myself with it when I took Biology Honors.
g. Explain, in their own words, what is meant by "form fits function."
By “form fits function“, I believe that it is meant that the
biological structure of an organism hinders what an organism does and how
it works. Likewise, knowing a structures function can give insight on its
construction.
h. List the five kingdoms of life and distinguish among them.
I know the five kingdoms of life and can distinguish among them as I
learned it in my 9th grade Biology Honors class.
i. Outline the scientific method.
I can outline the scientific method as every science class since grade
school, which I have taken, has placed emphasis on the scientific method.
h. Distinguish between inductive and deductive reasoning.
I can distinguish between inductive and deductive reasoning as there
have been many hands on classes I’ve taken which have introduced the
difference. For example, my Honors Biology course, Honors Chemistry
Course and Honors Physics Course placed an emphasis on the differences
between the reasoning.
i. Explain how science and technology are interdependent
Science is a process used to test accepted truths and answer
questions in relation to nature. Technology allows scientists to answer and
work on questions that were previously unanswered or unapproachable.
CHAPTER TWO OBJECTIVES (SELF-MONITOR)
a. Define element and compound.
An element is a substance that cannot be broken down to other
substances by chemical reactions. A compound is produced when two or
more elements may combine in a fixed ratio and can be broken down.
b. State four elements essential to life that make up 96% of living
matter.
Four elements essential to life that make up 96% of living matter
are:
carbon, oxygen, hydrogen, nitrogen
c. Describe the structure of an atom.
The atom is the smallest unit of an element. An atom is made up
of closely packed together protons, which carry a positive charge and
neutrons which are neutral to form the nucleus. The electrons, in the
atoms outer shells, move about this nucleus.
d. Define and distinguish among atomic number, mass number, atomic
weight, and valence.
The atomic number of an atom is the number of protons in its
nuclei, each unique to a certain element. The atomic number is written is
a subscript to the left of the symbol for the element.
The mass number is the sum of protons plus neutrons in the
nucleus of an atom. The mass number is written as a superscript to the
left of an element's symbol.
The atomic weight of an element is what is technically the total
atomic mass or mass number. The atomic weight tells us the approximate
mass of the whole atom.
Valence is the bonding capacity - a certain number of covalent bonds
that must be formed for the atom to have a full complement of valence
electrons - of each atom sharing electrons.
e. Given the atomic number and mass number of an atom, determine the
number of neutrons.
Helium:
Atomic number: 2
Mass number: 4
Number of neutrons = 2
f. Explain the octet rule and predict how many bonds an atom might
form.
The octet rule states that When atoms react, they tend to achieve
an outer shell having eight electrons. The octet rule can be used to
explain the number of covalent bonds an atom forms. This number
normally equals the number of electrons that atom needs to have a total
of eight electrons (an octet) in its outer shell.
g. Define electronegativity and explain how it influences the formation of
chemical bonds.
According to this concept, each kind of atom has a certain
attraction for the electrons involved in a chemical bond. This "electronattracting" power of each atom can be listed numerically on an
electronegativity scale. When atoms react with each other, they
"compete" for the electrons involved in a chemical bond. The atom with
the higher electronegativity value, will always "pull" the electrons away
from the atom that has the lower electronegativity value. The degree of
"movement or shift" of these electrons toward the more electronegative
atom is dependent on the difference in electro negativities between the
atoms involved.
h. Distinguish among non-polar covalent, polar covalent and ionic bonds.
In a non-polar covalent bond, electrons are shared equally. In a polar
covalent bond, one atom is more electronegative than the other, and so
electrons of this bond will not be shared equally. In an ionic bond, cations
- a positive charged ion- and anions - a negatively charged ion - attract
each other.
i. Describe the formation of a hydrogen bond and explain how it differs
from a covalent or ionic bond.
A hydrogen bond occurs when a hydrogen atom covalently bonded to
one electronegative atom is also attracted to another electronegative
atom. It differs from a covalent or ionic bond in that the hydrogen bond
is a weak electrical attraction between a negatively charged atom and a
positively charged atom in which the contact between molecules can be
brief.
THEMES
Cells are an organisms basic units of structure and function
Chapter 2 exemplifies how about 25 of the 92 natural elements are
known to be essential to life. Elements, like cells, are required by
organisms. Just four of the natural elements - carbon, oxygen, hydrogen
and nitrogen, make up 96% of living matter. The chemical context of life
is the most fundamental branch of life.
Structure and function are correlated at all levels of biological
organization.
Chapter 2 emphasized the correlation of structure and function as it
discusses the atom. When speaking of the atom, it is evident, for
instance, the number of bonds the atom will form by the number of
electrons required to complete that atom's valence shell.
Evolution is the core theme of Biology.
Chapter 2 explained the chemical conditions on the early Earth that set
the stage for the origin and evolution of life. "Chemical reactions and
physical processes on the early Earth created an environment that made
life possible. And life, once it began, transformed the planet's chemistry,"
stated Chapter 2 (pp 38) As the definition its definition states,
evolution is the change of a species over time, with relation to other
organisms and its environment. This chapter provided an introduction to
how chemical evolution on the early Earth made the origin of life possible.
Organisms are open systems that interact continuously with their
environments.
This chapter provided how atoms combine and interact by chemical bonding
to form molecules. Molecules consist of two or more bonded atoms. It
likewise emphasized how when an ionic bond combines with a water
atmosphere, it becomes relatively weak, exposing how organisms are
affected through their interaction with environments.
Science as a process
Chapter 2 exemplified the theme of "Science as a process" as it outlines
the structure of an atom, moving on to the process undertaken to
essentially determine the number of subatomic particles in each atom.
CHAPTER THREE OBJECTIVES (SELF-MONITOR)
a. Describe how water contributes to the fitness of the environment to
support life.
Life adapts to its environment through natural selection, but for
life to exist at all in a particular location, the environment must first be
a suitable abode. Water contributes to Earth's habitability by moderating
temperatures.
b. Describe the structure and geometry of a water molecule, and explain
what properties emerges as a result of this structure.
The water molecule is deceptively simple: two hydrogen atoms are joined
to the oxygen atom by a single covalent bond. Because hydrogen is more
elcetronegative than hydrogen, the electrons of the polar bonds spend
fractionally more time closer to the oxygen atoms. This results in the
oxygen region of the molecule having a slight negative charge and hydrogens
having a slight positive charge.
The anomalous properties of water arise from attractions among these
polar molecules. The molecules are thus held together by a hydrogen bond.
Collectively, these hydrogen bonds are responsible for: water's cohesive
behavior, its ability to stabilize temperature, it's expansion among freezing
and its versatility as a solvent for life.
c. 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.
d. List five characteristics of water that are emergent properties resulting
from hydrogen bonding.
Five characteristics of water that are emergent properties resulting from
hydrogen bonding include:
Cohesion
Adhesion
Surface Tension
Specific Heat
and it's versatility as a solvent for life.
e. Describe the biological significance of the cohesiveness of water.
Water molecules stick together as a result of hydrogen bonding. When
water is in liquid form, its hydrogen bonds are very fragile. They form,
break and re-form with great frequency. Water molecules are constantly
forming new bonds with a succession of partners. Thus, at any instant, a
substantial amount of water molecules are bonded to their neighbors,
giving water more structure than most liquids - cohesion.
f. Distinguish between heat and temperature
Heat is a measure of the total quantity of kinetic energy due to
molecular motion in a body of matter.
Temperature measures the intensity of heat due to the average kinetic
energy of the molecules.
g. 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 poleward, 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.
h. 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
charged and polar substances. When ions or polar substances are
surrounded by water molecules, they dissolve and are called solutes.
i. Write the equation for the dissociation of water, and explain what is
actually transferred from one molecule to another.
H2O Û 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
(OH-).
j. Explain the basis for the pH scale.
The basis of the pH scale is the H+ and OH- concentrations. The pH
scale compresses the range of H+ and OH- concentrations by employing a
common mathematical device: logarithms.
k. Explain how acids and bases directly or indirectly affect the hydrogen
ion concentration of a solution.
Acids donate additional H+ in aqueous solutions as bases donate OH- or
accept H+ in solutions. In an acidic solution, [H+] is greater than [OH-],
and the pH is less than 7. In a basic solution, [H+] is less than [OH-], and
the pH is greater than 7.
Themes:
Organisms interact continuously with their environments.
Life adapts to its environment through natural selection, but for
life to exist at all in a particular location, the environment must first be
a suitable abode. Water contributes to Earth's habitability by moderating
temperatures.
The structural level on which life is organized which has emergent
properties,
Water has five characteristics that are emergent properties resulting
from hydrogen bonding include:
Cohesion
Adhesion
Surface Tension
Specific Heat
and it's versatility as a solvent for life.
Structure and function are correlated at all levels of biological organization
The water molecule is deceptively simple: two hydrogen atoms are
joined to the oxygen atom by a single covalent bond. Because hydrogen is
more elcetronegative than hydrogen, the electrons of the polar bonds
spend fractionally more time closer to the oxygen atoms. This results in
the oxygen region of the molecule having a slight negative charge and
hydrogens having a slight positive charge.
The anomalous properties of water arise from attractions among these
polar molecules. The molecules are thus held together by a hydrogen bond.
Collectively, these hydrogen bonds are responsible for: water's cohesive
behavior, its ability to stabilize temperature, it's expansion among freezing
and its versatility as a solvent for life.
Science and technology are functions of society
The science of acids and bases led to the technology of creating a
scale which would determine how acidic or basic a substance is, thus the
pH scale.
A feeling for organisms enriches the study of life
It is our organisms we must keep in mind if our explorations of cells
or ecosystems is to be meaningful. Considering the dependence of all life
on water, Chapter 3 exemplifies this theme through the discussion of one
of the most serious assaults on water quality-acid precipitation
CHAPTER FOUR OBJECTIVES (SELF-MONITOR)
a. 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.
b. 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,
c. Recognize the major functional groups, and describe the chemical
properties of organic molecules in which they occur.
The major functional groups include:
*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:
The dual faces of life on Earth are diversity and unity
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.
Structure and function are correlated at all levels of biological organization
The key to the chemical characteristics of an atom is the
distribution of electrons determining the number of bonds and atom will
form. Carbon atoms are the most versatile building blocks of molecules.
Carbon has a total of six electrons. Each carbon atom acts as an
intersection point from which a molecule can branch off in up to four
directions because having four valence electrons, Carbon has little tendency
of gaining or losing electrons.
Organisms interact continuously with their environments
The continuous interaction with environments is one of the core
themes of Biology. Functional groups interact with their environment to
perform their role in an organism. Functional groups consist of specific
groups of atoms that covalently bond to carbon skeletons and give the
overall molecule distinctive chemical properties.
Biology is a multidisciplinary adventure.
Upon applying the concepts of molecular complexity, we begin to see
organic chemistry, the specialized study of carbon compounds, entwined in
the study of biology.
CHAPTER 5 OBJECTIVES (SELF-MONITOR)
a. List the four major classes of biomolecules.
*Carbohydrates
*Lipids
*Proteins
*Nucleic acids
b. Explain how organic polymers contribute to biological diversity.
c. Describe how covalent linkages are formed and broken in organic
polymers.
d. 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)
Store energy in chemical bonds; g) Carbon skeleton raw
material for other organic molecules; h) Monomers for di- and
polysaccharides
4. Disaccharides: a) Double sugars; b) Two
monosaccharides
5. Polysaccharides: a) Polymers of 100s to 1000s of
monosaccharidesb)
e. List four characteristics of a sugar.
1. -OH group attached to each carbon except 1
2. Carbon without -OH group doubled bonded to oxygen
3. Aldehydes
4. Carbon skeleton
f. 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.
g. Describe the important biological functions of polysaccharides.
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.
h. Distinguish between the glycosidic linkages found in starch and cellulose,
and explain why the difference is biologically important.
Glycosidic linkages in starch and cellulose:
1. Starch
a) Monomer = a-glucose
b) -OH on carbon 1 below plane of ring
c) a 1_4 linkages
2. Cellulose
a) Monomer = b-glucose
b) -OH on carbon 1 above plane of ring
c) b 1_4 linkages
3. Significance
a) Different shape
b) Enzyme that breaks a 1_4 linkage cannot break b 1_4 linkage
i. Explain what distinguishes lipids from other major classes of
macromolecules.
Lipids are distinguished from other major classes of macromolecules by
their trait of having little or no affinity for water.
j. Describe the unique properties, building block molecules and biological
importance of the three important groups of lipids: fats, phospholipids and
steroids.
* Fats are high-energy, compact storage molecules also known as
triaclyclycerols. They are
constructed by joining a glycerol molecule
to three fatty acids. The major function of fats is energy
storage.
* Phospholipids substitute the third fatty acid of fats with a negatively
charged phosphate group,
which may be joined, in turn, to another
small molecule. Such bonding introduces hydrophilic
behavior to this
part of the molecule. Phospholipids are ideally suited for contruction of
cell
membranes.
* Steriods are lipids characterized by a carbon skeleton consisting of four
interconnected rings.
Different steriods vary in the functional groups
attached to this ensemble of rings, their building blocks. An important
steriod is cholesterol, a commonc component of the membranes of animal
cells.
k. Identify an ester linkage and describe how it is formed.
A bond between a hydroxyl group and a carboxyl group. The product is a
fat, or a triarcyclycerol, which consists of three fatty acids linked to one
glycerol molecule.
*Dehydration synthesis*
a) Water molecule removed to form bond between glycerol and fatty
acid
(1) H from -OH group on glycerol
(2) -OH from carboxyl group on fatty acid
l. Distinguish between a saturated and unsaturated fat
If fatty acids are saturaterd with hydrogen, a fat is said to be saturated.
Unsaturated fatty acids have one or more double bonds with carbons,
formed by the removal of hydrogen atoms from the carbon skeleton.
m. 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
n. List and recognize four major components of an amino acid.
Four major components:
a) -COOH group
b) -NH2 group
c) R (side chain)
d) H
o. Identify a peptide bond and explain how it is formed.
Peptide bonds
a) Covalent bond
b) Formed by dehydration synthesis
c) Links two amino acids together
d) Water molecule removed to form bond between amino acids
(1) H+ comes from the amino group on one amino acid
(2) -OH comes from carboxyl group of the other amino acid
p. Explain what determines protein conformation
Protein conformation and levels of protein structure
1. Conformation = 3-D shape
2. Native conformation
a) Shape under normal biological conditions
b) Conformation important
(1) Directly related to function
(2) Example - recognition between
(a) Hormone and its receptor
(b) Enzyme and its substrate
(c) Antibody and its antigen
c) Determined by amino acid sequence
d) Stabilized by bonds between neighboring regions of folded protein
q. Define primary structure
Primary structure
(1) Sequence of amino acids
(2) Determined by genes (DNA base sequence)
(3) Slight changes can affect conformation and function
(a) Example - Sickle-cell hemoglobin
r. Describe the two types of secondary protein structure
Secondary structure
(1) Regular, repeated folding of polypeptide chain
(2) Folds stabilized by hydrogen bonds
a) helix
(i) Helical coil
(ii) Found in fibrous proteins & some portions of globular
proteins
(b) pleated sheets
(i) Antiparallel sheets folded into accordion pleats
(ii) Make up dense core of many globular proteins
(iii) Major portion of some fibrous proteins (e.g. silk)
s. Explain how weak interactions and disulfide bridges contribute to
tertiary protein
structure.
Tertiary structure
(1)
Globular proteins
(2) Irregular contortions
(3) Bonds contributing to tertiary structure
(a) Weak interactions
(i) Hydrogen bonds
(ii) Ionic bonds
(iii) Hydrophobic interactions
(b) Covalent linkage
(i) Disulfide bridges
(ii) Located between two cysteine monomers
(iii) Strong
t. Describe quaternary protein structure.
Quaternary structure
(1) Interaction among several polypeptides
(2) Examples
(a) Collagen
(i) Found in connective tissue
(ii) Fibrous protein
(iii) Consists of three helical polypeptides forming a triple
helix
(b) Hemoglobin
(i) Globular
(ii) Consists of four subunits
(a) Two a chains
(b) Two b chains
u. Define denaturation and explain how proteins may be denatured.
Denaturation
1. Alters protein's native conformation
2. Change in shape = change in activity
3. How proteins may be denatured
a) Transfer to organic solvent
(1) Disrupts hydrophobic interactions
(2) Result = change in shape
b) Chemical agents
(1) Disrupts hydrogen bonds, ionic bonds, and disulfide bridges
(2) Example
(a) Change pH
(b) Change ion concentration in solution
(c) Change interactions that maintain shape of protein
c) Excessive heat
(1) Increase thermal agitation
(2) Disrupts bonds
(3) Result = change in shape
v. Describe the characteristics that distinguish nucleic acids from the other
major groupsof 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.
w. Summarize the functions of nucleic acids.
There are two types of nucleic acids:
deoxyribonucleic acid (DNA), stores information for the synthesis of
specific proteins.
ribonucleic acid (RNA), links this genetic information to the protein
synthesizing machinery.
x. List the major components of a nucleotide
a) Five-carbon sugar (deoxyribose)
b) Nitrogenous base
c) Phosphate group
y. Distinguish between a pyrimidine and a purine.
1) Pyrimidines
a) Single ring
b) 6-membered ring of carbon and nitrogen atoms
c) Cytosine & thymine
2) Purines
a) Double ring
b) 5-membered ring fused with 6-membered ring
c) Adenine & guanine
z. List the functions of nucleotides.
Nucleotides, the monomers of nuclide acids, are themselves
composed of three smaller molecular building blocks: a phosphate groups, a
pentose sugar, and a nitrogenous base, either a purine of a pyramidine. In
DNA the pentose is deoxyribose and the possible bases are cytosine,
thymine, adenine, and guanine.
In a DNA strand, each nucleotide monomer has its phosphate group
bonded to the sugar of the next nucleotide. The polynomer has a regular
sugar-phosphate backbone with variable appendages, the four kinds of
nitrogenous bases.
z(2). Briefly describe the three-dimensional structure of DNA.
1. Consists of 2 strands wound in double helix (twisted ladder)
2. Sugar-phosphate backbones form outside of helix (sides of ladder)
3. Paired bases
a) Form rungs of ladder
b) Covalently bonded to sugar
c) Bases held together by hydrogen bonds
4. Base pairing rule
a) Adenine always pairs with thymine
(1) Form 2 hydrogen bonds
b) Cytosine pairs with guanine
(1) Form 3 hydrogen bonds
5. Two strands are antiparallel
Themes:
The continuity of life is based on heritable information in the form of
DNA
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.
Cells are the basic units of structure and function of an organism
Cells make macromolecules by linking relatively small molecule
together, forming chains called polymers. A polymer is a large molecule
consisting of many identical or similar building blocks linked by bonds. The
subunits that serve as the building blocks of a polymer are called
monomers.
The dual faces of life on Earth are diversity and unity
Lipids are mostly hydrophobic molecules with diverse functions. The
major function of fats is energy storage. Phospholipids are ideally suited
for construction of cell membranes. An important steroid is cholesterol, a
common component of the membranes of animal cells.
The core theme of biology is evolution
DNA and proteins are used as tape measures for evolution.
Structure and function are correlated at all levels of biological organization
A protein’s function depends on its specific conformation. Protein
conformation can be described by three or four hierarchal levels. The
structure and function of a protein are sensitive to conditions such as pH,
salt concentration, and temperature.
CHAPTER 6 OBJECTIVES (SELF-MONITOR)
a. 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.
b. Distinguish between kinetic and potential energy.
Kinetic energy is the energy of motion. Potential energy is energy
at standstill in relation to possible motion.
c. Distinguish between open and closed systems.
I am familiarized with the difference between open and closed
systems as I learned this in my Biology Honors Course.
d. Explain, in their own words, the First and Second Laws of
Thermodynamics.
The first Law of Thermodynamics is that energy cant be created nor
destryed. The second Law of Thermodynamics states that energy changes
in forms.
e. 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 an entropy change isnt evident, their energy
is being transformed into heat.
f. Distinguish between entropy and enthalpy.
Entropy is 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.
g. Write the Gibbs equation for free energy change.
changeF = changeH - Tchange in S
h. 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.
i. 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.
j. 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.
k. 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.
l. 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.
m. List the three components of ATP and identify the major class of
macromolecules of which it belongs.
ATP is composed of Adenine, Ribose and Phosphates. ATP belongs
to the nucleic acid class of macromolecules.
n. Explain how ATP performs cellular work.
ATP performs cellular work by transfering a phosphate group from
ATP to some other molecule.
o. Describe the function of enzymes in biological systems.
Enzymes speed metabolic reactions by lowering energy barriers.
1. Problem
a) Reactions too slow at cellular temperature
b) Molecules cannot absorb enough heat energy
2. Solution
a) Enzymes
b) Lower activation energy
p. Explain the relationship between enzyme structure and enzyme
specificity.
Relationship between enzyme structure and enzyme specificity
1. Specificity depends upon enzyme shape
2. Substrate binds to enzyme’s active site
3. Substrate must fit into enzyme’s active site
4. Active site
a) Pocket or groove on protein’s surface
b) Determines enzymes specificity
c) Changes shape in response to substrate
q. 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 enzyme-substrate 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.
r. 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
4. Side chains of amino acids may participate in reaction
s. Explain how substrate concentration affects the rate of an enzymecontrolled
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
t. Explain how enzyme activity can be regulated or controlled by
environmental
conditions, cofactors, enzyme inhibitors and allosteric regulators.
Regulation and control of enzyme activity
1. Environmental conditions
a) Temperature
(1) Optimal temperature
(2) Allows for greatest number of collisions without
denaturing enzyme
is 35oC to 40 C
o
b) PH
(3) Humans – optimal temperature
(1) Optimal range 6 to 8
(2) Exception – stomach enzymes
c) Ionic concentration
(1) Ions can interfere with ionic bonds within enzyme
(2) Result = disrupts shape
2. Cofactors
a) Description
(1) Small nonprotein molecules
(2) Required for proper enzyme catalysis
b) Action
(1) May bind tightly to active site
(2) May bind loosely to active site and substrate
c) Some inorganic
(1) Metals
(2) Zinc, iron, copper
d) Some organic
(1) Coenzymes
(2) Vitamins
3. Enzymes inhibitors
a) Description
(1) Chemicals that inhibit enzyme activity
(2) May be irreversible (attach by covalent bonds)
(3) May be reversible (attach by weak bonds)
b) Competitive inhibitors
(1) Resemble substrate
(2) Compete with substrate for active site
(3) If reversible
(a) Increase substrate concentration
(b) Overcomes inhibition
c) Noncompetitive inhibitors
(1) Don’t attach to active site
(2) Causes enzyme to change shape
(3) Substrate cannot bind to active site
(4) May act as metabolic poisons
(a) Example – DDT
(b) Example – Antibiotics
4. Allosteric regulation
a) Allosteric enzymes
(1) Have two conformations
(2) One active – one inactive
(3) If activator binds to allosteric site
(a) Active conformation stable
(b) Enzyme active
(4) If inhibitor binds to allosteric site
(a) Inactive conformation stable
(b) Enzyme inactive
c) Enzyme activity dependent upon concentration of
activator and
inhibitor
u. 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.
v. Explain how metabolic pathways are regulated.
Regulating metabolic pathways
1. By controlling enzyme activity
2. Feedback inhibition
a) End products inhibits enzyme activity
b) Increase product – decrease enzyme activity
3. Structural order
a) Compartmentalization
b) Confines enzymes to specific location within cell
THEMES:
Organisms interact continuously with their environments
All cell’s chemical and physical environment affects enzyme activity.
As proteins, enzymes are very sensitive to environmental conditions that
influence their three-dimensional structure. Each enzyme has optimal
conditions of temperature and pH.
Biology is a multidisciplinary adventure.
Biology, in Chapter 6, begins to deal with the Chemistry of life and
its organization into metabolic pathways.
Structure and function are correlated at all levels of biological organization
Each enzyme has a uniquely shaped active site, giving it specificity in
combining with its particular substrate. The active site of an enzyme can
lower activation energy in a number of ways: by providing a template for
substances to come together in proper orientation, by binding to the
substrate in such way that critical bonds of the substance are strained,
and by providing suitable microenvironments.
The structural level on which life is organized which has emergent
properties
In this unit, it is displayed how increasing levels of organization
result in the emergence of properties that are different from those of
the lower levers. Organization is the key to the chemistry of life.
Metabolic order emerges from the cell’s regulatory systems and structural
organization.
Cells are the basic units of structure and function of an organism
The living cell is a chemistry industry in miniature, where thousands
of reactions occur within microscopic space. Small molecules are assembled
into polymers, which may later by hydrolyzed as the needs of the cell
change. Cells export chemical products that are used in other parts of the
organism. The chemical process known as cellular respiration drives the
cellular economy by extracting the energy stored in sugars and other fuels.