REVIEWER

 PHYSICAL SCIENCE

Proton – positive electrical charge. Electron – negative electrical charge. Neutron – neutral.
Nucleus – protons and neutrons.
Nucleosynthesis – process of element (nuclei) formation.
 Three types – Big Bang nucleosynthesis
– Stellar (star) nucleosynthesis Nucleosynthesis that are occurring
– Supernova nucleosynthesis in our universe.

Nuclear Fusion – smaller nuclei collide together to make larger nuclei, and energy is released in the
form of electromagnetic radiation.
– requires extremely high temperatures and pressures.
– involves only the nuclei of atoms.
– at the temperatures at which fusion can occur, matter exists as a plasma.
– plasma is a super high energy, electrically charged gas.
– when nuclei collide, some of the mass of the nuclei is converted to energy by
Einstein’s famous equation E=mc2.

ELECTROMAGNETIC SPECTRUM

 WAVELENGTH

Radio Waves – 5,000,000,000

Microwaves – 10,000
Infrared – 10,000
Visible Light – 500
Ultraviolet – 250
X-rays – 0.5
Gamma Rays – 0.0005 nanometers

 ENERGY

Gamma Rays – 2,480,000 electron volts

X-rays – 2480
Ultraviolet – 4.96
Visible Light – 2.48
Infrared – 0.124
Microwaves – 0.124
Radio Waves – 0.000000248

Big Bang Nucleosynthesis (formation of light elements 1-2)

– the most widely accepted scientific theory about the origin of the universe.
– energetic explosion that initiated the expansion of the universe.
– the age of the universe is calculated at about 13.7 billion years old. Our
sun and its surrounding planets are 4.65 billion years old.
– all hydrogen and most helium in the universe were produced during the
event.
– ceased within few minutes after the event because the universe had
expanded and cooled sufficiently by then such that the temperatures and
pressures were too low to support additional nuclear fusion
reactions.

Stellar Nucleosynthesis (formation of heavier elements He-Fe)

– a star is a very hot ball of gas (plasma).
– star create elements by combining lighter nuclei into heavier nuclei via
nuclear fusion reactions in their cores and releasing energy in the process.
– our sun is only large enough to fuse hydrogen into helium within its
core.
– stars much larger than our sun can fuse heavier elements from lighter
elements.
– the heaviest element that can be made in a star is iron.
STARS BASED ON THEIR TEMPERATURE

Spica (blue) – the hottest. Vega (white) – less hot than spica. Sun (yellow) – less hot than vega.
Aldebaran (orange) – less hot than sun. Betelgeuse (red) – less hot than aldebaran.

Supernova Nucleosynthesis (formation of heavier elements Co-U)

– elements heavier than iron (Z=26) are made primarily when giant stars
explode in supernovae.
– when a star runs out of nuclear fuel (lighter nuclei) and can no longer
undergo fusion reactions, gravity causes the star to collapse. The
gravitational collapse triggers a phenomenally large explosion called
supernova.
– make elements with atomic numbers 27-92 (Cobalt to Uranium).
– since only the largest stars can explode in supernovae events, elements
with atomic numbers 27-92 are rarer than elements with atomic number
1-26.

Synthetic Elements – 24 known chemical elements that do not occur naturally on earth.
– created by human.
– ‘synthetic’, ‘artificial’, or ‘man-made’.
– elements with atomic number 95-118.

ELEMENTS IN PERIODIC TABLE

 Nuclide – atomic species characterized by the specific constitution of its nucleus.

 Discovered or synthesized
 94 natural occurring elements
 24 synthetic elements

Synthetic Elements – chemical element that does not occur naturally on earth.
– created artificially.
– radioactive and decay rapidly into lighter elements.
– only occur on earth as the product of atomic bomb or experiments.
– atomic number 95-118.

Isotopes – atoms of the same elements with different number of neutrons.

MACHINES THAT CAN MAKE SYNTHETIC ELEMENTS

 Nuclear Reactor
 Particle Accelerator

Nuclear Reaction – causes a nuclide to change by bombarding it with energetic particle.

– involves heavy target nucleus and a light bombarding particle.
– produces heavier product nucleus.
– emits a very high electromagnetic energy.
– process in which two nuclei, or a nucleus and an external subatomic particle,
collide to produce one or more new nuclides.
– transformation of at least one nuclide to another.
– involving changes in the nucleus of atoms.
– release much more energy than chemical reactions (deals with electrons only).

NUCLEAR REACTION INVOLVED IN SYNTHESIS OF NEW ELEMENT IN THE LABORATORY

1. Capture reaction 2. Fission reaction 3. Fusion reaction

NUCLEAR REACTION

 Nuclear Fission
– process in which a heavy/large unstable nucleus splits into smaller and more
stable nuclei with the release of energy.
– neutrons and energy are released.
– used in nuclear weapons and power plants (U-235).
  Nuclear Fusion
– two or more nuclei come close enough to form one or more different atomic
nuclei and subatomic particles (neutrons or protons).
– two light atomic nuclei fuse together to create a larger/heavier nucleus and in
the process release energy.
– releases far more energy than nuclear fission (3-4 times more).
– the sun’s (stars) energy comes form the fusion of hydrogen atoms into helium
atoms.
– the hydrogen bomb is a fusion weapon.

Thermonuclear Fusion – uses extremely high temperature.

– temperature is a measure of the average kinetic energy of a particle.

Molecule – a group of two or more atoms held together by chemical bonds.

Example:
Water, Salt, Ozone, Nitrogen, Ethyl Alcohol, Isopropyl Alcohol, Sugar, Coffee

Polarity – refers to the distribution of electric charge around atoms, chemical groups, or molecules.

 2 FACTORS THAT DETERMINE THE POLARITY OF MOLECULES

1. Polarity of the bonds between atoms which can be studies based on electronegativity.
2. Geometrical shape of the molecule which can be predicted via the valence shell electron
pair repulsion (VSEPR) theory.

POLARITY OF MOLESCULES
 All compounds can be classified based on what type of chemical bond formed when the
atoms combined.
 Classification of the compound can be used to determine whenever a molecule is polar or
non-polar.
 Two classifications of compounds are covalent and ionic.

Covalent Compound – a molecule formed by covalent bonds, in which the atoms share one or
more pairs of valence electrons.

Ionic Compounds – are made up of ions rather than molecules. Instead of sharing electrons in
covalent bonds, ionic compound atoms transfer electrons from one atom to
another to form an ionic bond that relies on electrostatic attraction to keep the
atoms together.

Electronegativity (EN) – the measure of relative tendency of an atom to attract electrons to itself
when chemically combined with another atom.
– the higher the value of electronegativity, the more it tends to attract
electron toward itself.

Molecular Polarity – when there are no polar bonds in a molecule, there Is no permanent charge
difference between one part of the molecule and another, and the molecule is
nonpolar.
– a molecule can possess polar bonds and still be nonpolar. If polar bonds are
evenly (or symmetrically) distributed, the bond dipoles cancel and do not create
a molecular dipole.
– a water molecule is polar because its O-H bonds are significantly polar, and it
bent geometry makes the distribution of those polar bonds asymmetrical.

Polarity – separation of electric charge leading to a molecule or its chemical groups having an
electric dipole or multiple moment.
– polar molecules interact through dipole-dipole intermolecular forces and hydrogen bonds.
– molecular polarity is dependent on the difference in electronegativity between atoms in
compound and the asymmetry of the compound’s structure.

Dipole Moments – occur when there is a separation of charge.

– can occur between two ions in an ionic bond or between atoms in a covalent
bond; dipole moments arise from differences in electronegativity.
– the larger the difference in electronegativity, the larger the dipole moment.
What are polar molecules?
– molecules in which the charge is not distributed symmetrically among the shape
of the molecules.
– the polarity of a molecule is dependent on the presence of polar bonds and
the shape of the molecule.

How does polarity affect the shape of molecules?

– if it’s polar the shape of the molecule should have a structure which do
not cancel out dipole moment.
– if it’s non-polar the shape of the molecule should have a structure which
do cancel out dipole moment.

Valence Electrons – the electrons in an element’s outermost shell (valence shell).

Electronegativity – the measure of the tendency of an atom to attract electrons, the higher its value,
the higher its tendency to attract electrons.

Chemical Bonding – interactions that account for the association of atoms into molecules, ions,
crystals, and other stable species that make up the familiar substance.

Chemical Bond – a lasting attraction between atoms, ions, or molecules that enables the formation
of chemical compounds.
– the bond may result from the electrostatic force of attraction between oppositely
charged ions as in ionic bonds; or through the sharing of electrons as in covalent
bonds.

Ionic Bond – formed when valence electron/s transfer from one atom (metal) to another (non-metal).
– results to formation of ions (cation and anion).
– electronegativity difference between the two atoms involved is greater than 1.8 (>1.8).

Covalent Bond – formed when valence electrons are shared by atoms (usually both non-metals).
– results to formation of covalent compounds.
 – electronegativity is between 0-1.8.

TYPES OF CHEMICAL BOND

Nonpolar Covalent Bond – if the electronegativity difference is less than 0.4 (<0.4).

Polar Covalent Bond – if the electronegativity difference is between greater than 0.4 (>0.4) and 1.8,
polar covalent is formed.

Metallic Bond – the electrostatic force that holds the particles together in a metal.
– results from the attraction between metal cations and the surrounding “sea of
electron”.
– valence electrons do not belong to any one atom.

NONPOLAR VS. POLAR VS. IONIC BOND

Macromolecule – a very large molecule important to biological processes, such as a protein or

nucleic acid.
– composed of thousands of covalent bonded atoms.
 – most are polymers.
 Polymer – large molecule consisting of many identical or similar building blocks linked by
bonds.
 Monomer – subunits that serve as building blocks for polymers.

“CHON” – stands for carbon, hydrogen, oxygen, and nitrogen.

– come together and interact to form biomolecules.
– make up more than 95% of the mass of biological systems.
WHY ARE MACROMOLECULES IMPORTANT TO THE HUMAN BODY?

 Carbohydrates are the body’s main source of energy.

 Lipids provide stored energy reserves. This allows us to survive when carbohydrates are not
being supplied to the body.
 Protein helps us stay strong, by forming new bones and muscles, and helping us fight
diseases.
 Nucleic acids are responsible for making each person functional and unique; they are the
blueprint for our genetic structure.

HOW CELLS USE ORGANIC COMPUNDS?

 Biological organisms use the same kinds of building blocks.

 All macromolecules (large, complex molecules) have specific functions in cells.
 Other than water, macromolecules make up the largest percent mass of a cell.

Carbohydrates – refers to any of the group of organic compounds consisting of carbon, hydrogen,
and oxygen.
– usually in the ratio of 1:2:1, hence the general formula: Cn (H₂O)n.
– composition gives carbohydrates their name: they are made up of carbon (carbo-)
plus, water (-hydrate).m
– the most abundant among the major classes of biomolecules.
– used as fuels and building material.
– carbs are sugar and their polymers.
– main types: monosaccharides, disaccharides, and polysaccharides.

Monosaccharides – generally have molecular formulas in some multiple of CH2O.

– glucose (C6 H12 O6) most common.
– in aqueous solution may form rings.
– major nutrients for cells.

Disaccharides – two monosaccharides joined by glyosidic linkages.

– glyosidic linkage
– a covalent bond formed between monosaccharides.
– sucrose is most prevalent.

Polysaccharides – 100s to 1000s of monosaccharides long.

– Starch
 Storage polysaccharides of plants.
– Glycogen
 Storage polysaccharides of animals.
– Cellulose
 Structural polysaccharides which is a major component of tough plant cell
wall.
– Chitin
 Structural polysaccharides used by arthropods to build exoskeletons.

Lipids – are fatty, waxy, or oily compounds that are soluble in organic solvents and insoluble in
polar solvents such as water.
– broad group of organic compounds which include fats, waxes, sterols, fat-soluble vitamins
(such as vitamins A, D, E, and K), monoglycerides, diglycerides, phospholipids, and others.
– its functions are storing energy, signaling, and acting as structural components of cell
membranes.

– have applications in cosmetic and food industries, and in nanotechnology.

– mostly hydrophobic molecule with diverse functions.
– little or no affinity for water.
 – used for energy storage and structure.
– main types: fats, phospholipids, and steroids.

Fats – large molecules, but not polymers.

– Fatty acid
A long carbon skeleton with carboxyl group head and a hydrocarbon tail.

Triacylglycerol (triglyceride) – three fatty acids linked glycerol molecule.

Saturated fatty acids – containing no double bonds between the carbon atoms composing the tail.

– solids at room temperature.

Unsaturated fatty acids – has one or more double bonded carbons in the tail.

Phospholipids – two fatty acid tails linked to one glycerol molecule.

– ambivalent behavior towards water.
– when in contact with water they form a micelle (cluster).

Cholesterol – important steroid that is a common component of the membranes of animal cells.
– many hormones are steroids produced from cholesterol.

Proteins – the molecular tools for most cellular functions.

– used for: structural support, storage, transport of other substances, signaling from
one part of the organism to the other, movement, and defense against foreign
substance.
– Conformation
 Unique 3-D shape of a protein.

Protein Polypeptides – polymers of amino acids connected in a specific sequence.

– Amino acids
 organic molecules possessing both carboxyl and amino groups.
– acidity is determined by side chains.

Peptide Bonds – formed when an enzyme joins amino acids by means of condensation.

Polypeptide – chains of amino acids linked by peptide bonds.

Protein Conformation (shape) – determines function and is the result of the linear sequence of
amino acids in polypeptide.
– folding, coiling and the interactions of multiple polypeptide chains
create a functional protein.
– 4 levels of conformation: primary, secondary, tertiary, and
quaternary.

Primary Structure – unique, liner sequence of amino acids in a protein.

Secondary Structure – hydrogen bonding occurs between amino and carbonyl groups of amino
acids.

Tertiary Structure – irregular contortions from bonding between side chains of various amino acids.

Quaternary Structure – overall protein structure that results from aggregation of tertiary subunits.

Denaturation – unravelling and loss of native conformation of a protein.

– can be due to heat, pH, salts, etc.
– some can renature exactly, others cannot.
– example: cooking and egg.

Nucleic Acids – store and transmit hereditary information.

– Gen
a unit of inheritance.
 – DNA and RNA
 Deoxyribonucleic acid and Ribonucleic acid
 DNA is like a computer software, proteins are the hardware
 Genetic into flows from DNA to RNA to protein.

DNA Structure – a polymer with an information-rich sequence of nucleotides.

– Pyrimidine
 6 membered rings made of carbon and nitrogen atoms.
 Cytosine and thymine
– Purine
 6 membered rings fused to a five membered ring.
 Adenine and guanine
– Phosphodiester
 Covalent bonds holding nucleotides together.
– Double Helix
 Two chains of nucleotides that spiral around an imaginary axis.
– Hydrogen Bonds
 Hold two chains of nucleotides together.
– Adenine pairs with thymine
– Cytosine pairs with guanine
– Two strands of DNA double helix are complimentary

RNA STRUCTURE – single stranded

– four kinds of nucleotide monomers (A, U, C, G)
– key player in the protein-building processes
– mRNA, tRNA, rRNA

IMPOTANCE OF DNA AND RNA

– Inheritance is based on precise replication of DNA.

– We can use DNA and proteins as “tape measure” of evolution.
 Linear sequences of nucleotides in DNA molecules are passed from parents
to offspring.
 More distantly related species have chains that are less similar.