Module 4 - The Chemical Basis of Life (Part 2)

OTHER IMPORTANT ORGANIC COMPOUNDS

Carbohydrates - are the most abundant class of organic compounds found in living organisms.
- major source of metabolic energy, both for plants and for animals that depend on plants for food
- the formulas of many carbohydrates can be written as carbon hydrates, Cn(H2O)n, hence their name.
- divided into four: monosaccharides, disaccharides, oligosaccharides, and polysaccharides.

Protein - are organic compounds made of amino acids (see figure below) arranged in a linear chain and folded into a globular form

- proteins are essential parts of organisms and participate in virtually every process within cells
- many proteins are enzymes that catalyze biochemical reactions and are vital to metabolism
- proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape

Fats - consist of a wide group of compounds that are generally soluble in organic solvents and largely insoluble in water.
- may be either solid or liquid at room temperature, depending on their structure and composition.
- "oils" is usually used to refer to fats that are liquids at normal room temperature, while "fats" is usually used to refer to fats that are solids at normal room temperature
- play a vital role in maintaining healthy skin and hair, insulating body organs against shock, maintaining body temperature, and promoting healthy cell function
- serve as energy stores for the body

- proteins are essential parts of organisms and participate in virtually every process within cells
- many proteins are enzymes that catalyze biochemical reactions and are vital to metabolism
- proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape

Fats - consist of a wide group of compounds that are generally soluble in organic solvents and largely insoluble in water.
- may be either solid or liquid at room temperature, depending on their structure and composition.
- "oils" is usually used to refer to fats that are liquids at normal room temperature, while "fats" is usually used to refer to fats that are solids at normal room temperature
- play a vital role in maintaining healthy skin and hair, insulating body organs against shock, maintaining body temperature, and promoting healthy cell function
- serve as energy stores for the body

Nucleic acids -  macromolecule composed of chains of monomeric nucleotides (see figure below)
 -  macromolecule composed of chains of monomeric nucleotides (see figure below)

- these molecules carry genetic information or form structures within cells
- most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)


Enzymes – catalyze specific chemical reactions
- increase the speed of a chemical reaction without being consumed by the reaction.
- mostly proteins
- lowers the EA of a chemical reaction

EA (energy of activation) – energy required to break the existing bonds and begin the reaction

Some enzymes have two components
Apoenzyme – protein
Cofactor – chemical component that maybe inorganic or organic

Inorganic cofactors are usually trace elements like Fe, Cu and Mn

Examples of organic cofactors (also called coenzymes)  are vitamins.

Vitamins – organic compounds required in the diet in relatively small amounts for normal biochemical functioning.

Module 4 - The Chemical Basis of Life

Matter – anything that takes up space and has mass

Greeks believed that matter arises from 4 basic elements: air, water, fire and earth.

Element – is a substance that cannot be broken down to other substances by chemical reactions
-    116 named and unnamed elements to date.
-    92 are naturally occurring and only 25 are known essential to life.

Atom – is the smallest unit of matter that still retains the properties of an element

Sub-atomic particles
1. Neutron – neutral charged particles
2. Proton – positively charged particles
3. Electron – negatively charged particles and form a cloud around the nucleus (proton + neutron)

Compounds – is a substance consisting of two or more different elements combined in a fixed ratio.

Molecule – two or more atoms held together by covalent bonds.

Chemical bonds – attractions that result in atoms staying close together

4 Types of chemical bonds
1. Covalent bonds
2. Ionic bonds
3. Hydrogen bonds
4. Van der Waals Interactions

COVALENT BONDS
- is the sharing of a pair of valence electrons by two atoms with comparable electronegativity
- bond in which two electrons are shared by two atoms

Valence electron – number of electrons in the outermost shell/orbital

Orbital – a region in space about the nucleus where there is a high probability of finding a given electron.

Electronegativity – attraction of an atom for the electrons of a covalent bond.
- ability of an atom to attract toward itself the electrons in a chemical bond.

Types of Covalent Bonding
1. Non-polar – electrons are shared equally.
- ex. O2, H2

2. Polar – one atom is bonded to a more electronegative atom, the electrons of the bond will not be shared equally
- ex. H2O

IONIC BOND
- two atoms are so unequal in their attraction for valence electrons that the more electronegative atom strips an electron completely from its partner
- usually formed between metals and non metals
-atoms with valence electrons = 1, 2, 3 tend to lose electrons to other atoms called CATIONS (positively charged)
- atoms with valence electrons = 5, 6, 7 tend to gain from other atoms called ANIONS (negatively charged)

HYDROGEN BOND
- forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

VAN DER WAALS INTERACTIONS
- weak attractions between molecules or parts of molecules that are brought about by localized charged fluctuations.

Characteristics of Water
1. The polarity of water molecules results in hydrogen bonding and being a versatile solvent (Water is the solvent of life)
2. Cohesive (Organisms depend on the cohesion of water molecules)
3. High specific heat (Water moderates temperature on Earth)
4. Density (Oceans and lakes don’t freeze solid because ice floats)

TWO TYPES OF COMPOUNDS
1. Inorganic compounds
2. Organic compounds

INORGANIC COMPOUNDS
- usually do not contain carbon
- usually do not contain C-H bonds
- usually contain metal atoms
- exceptions carbon monoxide (CO¬), carbon dioxide (CO2), carbon disulfide (CS2), compounds containing the cyanide (-CN-), carbonate (-CO32-) and bicarbonate (-HCO3-) groups. i.e

4 Categories
1. Ionic Compounds
2. Molecular Compounds
3. Acids and Bases
4. Hydrates

Ionic compounds – formed due to ionic bonding
- made up of cations and anions
- usually formed by metals and nonmetals
Ex. NaCl, KBr (potassium bromide), ZnI2 (zinc iodide)

Molecular compounds – contain discrete molecular units
- usually composed of nonmetallic elements
Ex. HCl (hydrogen chloride), CO2 (carbon dioxide)

Acids – substances that yields hydrogen ions (H+) when dissolved in water
- contain one or more hydrogen atoms as well as an anionic group
Ex. HI (hydroiodic acid; I-, anion), H2SO4 (sulfuric acid; SO4-, anion)

Bases – substance that yields hydroxide ions (OH-) when dissolved in water.
Ex. NaOH (sodium hydroxide), KOH (potassium hydroxide)

Hydrates – compounds that have a specific number of water molecules attached to them.
Ex. CaSO4•2H2O (Gypsum, calcium sulfate dehydrate), MgSO4•7H2O (Epsom salt, Magnesium sulfate heptahydrate)
*the water can be driven off by heating and the resulting compound will then be called anhydrous

ORGANIC COMPOUNDS
 - contain carbon
- usually in a combination with elements such as hydrogen, oxygen, nitrogen and sulfur
- can be classified according to functional groups
- derived from a group of compounds known as hydrocarbons (made up of only hydrogen and carbon)

Functional group – group of atoms that is largely responsible for the chemical behavior of the parent molecule.

2 Main Classes of Organic Compounds
1. Aliphatic Hydrocarbon
2. Aromatic Hydrocarbon

Aliphatic hydrocarbon – do not contain the benzene group or the benzene ring
- simple hydrocarbon chains
- divided into alkanes, alkene and alkynes (cycloalkanes are a type of alkane).

Aromatic hydrocarbon – contain one or more benzene ring
- usually chemically unreactive

Benzene – colorless, flammable liquid obtained chiefly from petroleum and coal tar.
- is relatively inert (unreactive)

Alkane – only single covalent bonds are present
Ex. CH4 (methane) – natural product of the anaerobic bacterial decomposition of vegetable matter under matter; “marsh gas”

Cycloalkanes – carbon atoms are joined in rings

Alkenes – also called olefins
- contain at least one carbon-carbon double bond
Ex. C2H4 (ethylene), used in organic polymers (plastics) and in agricultural purposes.

Alkynes- contain at lease one carbon-carbon triple bond
Ex. C2H2 (ethyne or acetylene), colorless gas and with oxygen used to weld metals

Alcohols – contain the hydroxyl (-OH) groups.
Ex. CH3CH2OH (ethanol, ethyl alcohol)

Ethers – contain the R—O—R’, where R and R’ are a hydrocarbon (aliphatic or aromatic) group.
Ex. CH3OCH3 (diethyl ether), a known anesthetic

Aldehyde – has a carbonyl group (C double bonded to O) and at least has one hydrogen atom is bonded to the carbon in the carbonyl group.
Ex. H2C=O (formaldehyde), preservative for animal specimens

Ketone -  has a carbonyl group (C double bonded to O) and the carbon atom in the carbonyl group is bonded to two hydrocarbon groups
Ex. Acetone as solvent (see below)

Carboxylic Acids – acids that contain the carboxyl group, —COOH.

Ex. HCOOH (Formic Acid) exceted by ants as defense mechanism
 
Ester – R’COOR, where R’ can be H or a hydrocarbon group and R is a hydrocarbon group
- used in the manufacture of perfumes and as flavoring agents in the confectionery and soft-drink industries.

Amines – organic bases with the functional group,  –NH3
- are used mainly in the manufacture of dyes

Module 3 – Variety of Organisms

Taxonomy – the branch of biology concerned with naming and classifying the diverse forms of life.

Carolus Linnaeus/Carol von Linnae (1707-1778)
 - Swedish physician and botanist
 - sought to discover order in the diversity of life “for the greater glory of the Lord”
 - divided life between plants and animals
 - developed the two part or binomial system of naming organisms according to genus and species that is still used today

Robert H. Whittaker (1969)
-    led a team of researcher from Cornell University.
-    proposed a 5-kingdom system: Monera, Protista, Plantae, Fungi, and Animalia

Carl Woese (1977)
- added Archaea as a sixth kingdom
- redefined his classification to three domains in 1990: Bacteria, Archaea and Eukarya.

* taken from wikipedia.com

Taxonomic Classification
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species

Mnemonic: Do Kings Play Chess On Fine Grain Sand? 

2 Types of cells
1. Prokaryotes – no nucleus and has single loop of DNA
2. Eukaryotes – has nucleus, DNA is longer and contain more information, has a lot of organelles

Bacteria/Eubacteria – Prokaryotes
-    Rarely have organelles
-    Often motile using pili or flagella
-    Peptidoglycan (a kind of protein) in cell wall
-    Can be found in many different shapes and sizes
-    Can be found in almost any environment
-    Ex. E. coli

Archaea – Prokaryotic organisms
-    Mostly inhabit extreme environments (extremophiles)
-    Archaean groups based on environmentsal criteria
1.    Methanogens – obtain energy using CO2 to oxidize H2 producing methane; live mostly in swamps and marshes where there is little oxygen
2.    Halophiles – live in saline places. Some just tolerate salinity while some require a degree of salt to be present to survive.
3.    Thermophiles – thrive in hot environments
4.    Alkaliphiles/Acidophiles – thrive in basic or acidic environments.
- ex. Sulfulobulos

Protists – mostly unicellular eukaryotes
-    maybe several kingdoms within Domain Eukarya
-    Some make food by photosynthesis (algae)
-    Some are heterotrophic and eat bacteria and other protests
-    Can be heterotrophic or autotrophic
-    Some protests are fungus-like
-    Ex. Amoeba, brown algae, Diatoms, Trypanosoma

Fungi – heterotrophic eukaryotes that digest their food externally and absorb externally and absorb the nutrients.
-    usually consists of a mass of threadlike hyphae called a mycelium
-    ex. Yeast, Button mushrooms, truffles

Plants – multicellular eukaryotes that make organic molecules by photosynthesize.
-    have fortified cell well (lignin)
-    obtain nutrients in two media (air and water)
-    ex. Trees, shrubs, grasses

Animalia – are multicellular, heterophic and lack cell walls
-    held together by extracellular structural proteins and by unique type of multicellular junctions
-    reproduce sexually

Modes of Nutrition among Living organisms.

Comparisons among the three domains

Module 2 – Origin of Life

Theories on the Origin of Life
1. Creationism – religious belief that humanity, life, the Earth and the universe are the creation of a supernatural agency
2. Spontaneous generation (abiogenesis) – organic life could and does arise from inorganic matter
- disproved in 1668 by Francisco Redi and in 1859 by Louis Pasteur
3. Gold’s “Deep-Hot Biosphere” Model – 1970 by Thomas Gold
- life first developed not on surface of the Earth but several kilometers below the surface
4. Extraterrestrial formation – Organic material came from space specifically Mars
- supported by Francis Crick of DNA fame
5. Panspermia – is the hypothesis that seeds of life exists already all over the Universe, that life on Earth may have originated through these seeds (comets)

Evolution – change in lines of descent
-    as the process by which populations of organisms change over time
-    theorized by Charles Darwin in 1859 in his book “On the Origin of Species by Natural Selection; or the Preservation of Favoured Races in the Struggle for Life”.

Pre-Darwinian Ideas about Evolution
Aristotle (384-322 BCE)
-    saw much evidence of natural affinities among organisms
-    visualized organisms as being “imperfect but moving toward a more perfect state”
-    did not discuss mechanism

Leonardo da Vinci (1452-1519)
-    correctly interpreted unexpected fossil finds as the remains of animals that had existed in previous ages but had become extinct.

Jean Baptiste de Lamarck (1744-1829)
-    first scientist to propose that organisms undergo change over time as a result of some natural phenomena rather than divine intervention.
-    Shrink and disappear.
-    Theory of use and disuse

Darwin’s book had 2 concepts
1.    Darwin argued convincingly from several lines of evidence that contemporary species arose from a succession of ancestors through a process of “descent with modification”, his phrase for evolution.
2.    Mechanism of evolution is called Natural Selection

Natural Selection – differential survival and reproduction of individuals in a population that differs in the details of their habitable traits.

Process of Natural Selection
1. A natural population tends to increase in size. As it does, the individuals of the populations competes more for food, shelter, and other limited resources.
2. Individuals of a population differ from one another in the details of shared traits. Such traits have a heritable basis.
3. Adaptive forms of traits make their bearers more competitive, so those forms tend to become more common over generations.

Module 1 - Nature of Science

Module 1 – Nature of Science

Science
-    systematic study of nature
-    from the Latin “to know”
-    is a process of inquiry that includes repeatable observations and testable hypothesis
-    is a way of thinking and a method of investigation the natural world in systematic manner

Critical Thinking
-    judging information before accepting it

Types of Science
 Physics – study of the laws of the Universe that govern matter, energy, space and time.
Chemistry – deals with matter at the macromolecular scale observing its reactions, transformations and combinations
Astronomy – study of celestial objects
Geology – study of the Earth
Microbiology - study of microscopic organisms
Psychology – study of behavior and mental processes
Oceanography – study of how the ocean works.
Ecology – study of the biota and the environment and their interactions.
Botany – study of plants

Scope and Limits of Science
1.    only that which is observable
2.    does not answer subjective questions i.e. “Why do I exist?”
3.    Does not address the supernatural or anything that is “beyond nature”
4.    Reductionism

Scientist use two types of systematic thought processes
1. Deduction – begin with supplied information (premise)
    - proceeds from general principles to specific conclusions
    - helps us discover relationships among known facts.
Fact – info or knowledge based on evidence

2. Induction – opposite of deduction
    - begin with specific observations and draw a conclusion or discover a general principle

Scientific Method
1.    Observation
2.    Question
3.    Hypothesis
4.    Predictions
5.    Test/Experiment
6.    Conclusion

Hypothesis – tentative answer to some questions
-    educated guess
-    testable statement

Prediction – deductive logical consequence of a hypothesis

Sampling error – is a difference between results from a subset and results from the whole

Theory – is an integrated explanation of some aspect of the natural world that is based on a number of hypothesis, each supported by consistent results from many observations or experiments.