Transcript Fundamentals of Chemistry

What are the Different Forms of
Matter?
• Matter: anything that has mass and occupies space
• Elements: pure substances that cannot be broken down
chemically into simpler forms of matter
– Some share properties and reactivity  grouped (Dmitri Mendeleyev,
1869); symbols used (see Periodic Table of Elements)
– About 30 are important for living things (see handout); carbon,
oxygen, hydrogen, and nitrogen ≈ 90% mass of living things
• Atom: simplest particle that retains all the properties of
the particular element (atomic structure a “model”)
– Nucleus: consists of protons (+) and neutrons (neutral) of equal
mass (atomic number = number of protons = element’s identity)
– Electrons (-): low mass, arranged in shells around nucleus (outer
shells reactive, high energy, can be attracted to other nuclei)
– Isotopes: different forms of same element (re. number of neutrons)
– Ions: charged atoms (lose electron  cation; gain electron  anion)
How do Atoms Combine to Make
Compounds?
• Compound: pure substance made up of two or more
elements (vs. mixtures of multiple compounds)
• Chemical Bonds: elements with unfilled outer shells
reactive (stable octet; Noble gases not reactive)
– Elements valence (number of bonds will form) determined by the
number of outer-shell electrons (= group number)
• Example: carbon (group IV) forms four bonds, often with other carbon
atoms, forming chains and rings
• Groups 5-7 form 3 bonds, 2 bonds, and 1 bond, respectively
– Ionic Bond: transfer of electron from one element to another (from
opposite sides of Periodic Table), and subsequent attraction
between resulting cation (+) and anion (-); salts (ex. NaCl)
– Covalent Bond: sharing of electrons between multiple nuclei 
molecules; example: H2O (water)
• Intermolecular Forces: between (vs. within) molecules
– Hydrogen Bond: attraction between partial positive H atom (of one
molecule) and unbound electrons or partial negative atom (of a
separate molecule)
How are Matter and Energy Related?
• Energy: ability to do work or cause change
• States of matter: solid, liquid, and gas
– All compounds transition at specific temperatures
(melting and boiling points)
– From solid to gas, atoms/molecules increase in motion,
and distances increase (Brownian Motion: atoms and
molecules always in motion  can meet and react)
• Energy and Chemical Reactions
– Chemical reactions involve breaking and forming of
chemical bonds (movement/transfer of electrons)
– Reaction Equations: reactants  products
• Example: CO2 + H2O  H2CO3
– Catalysts: lower activation energy of reactions; re-used
– Redox Reactions: involve loss (oxidation) or gain
(reduction) of electrons (ex., electron transport chains)
Why is Water so Important for Life?
• Properties of Water (favorable for life)
– Good solvent: water is polar (negative and positive ends)
 breaks ionic bonds and makes ions available for
organisms (ex. calcium from calcium carbonate, sodium
from sodium chloride)
– Cohesive: molecules of water “stick together” (results
from hydrogen bonds)  good medium for chemistry
and high surface tension
• Top mm of ocean/lakes with highest abundance of photosynthetic
microbes, many organisms can float on surface
– High thermal capacity: resists temperature changes;
stable for life
– Unique density: becomes less dense upon freezing (ice
floats); allows life to exist under ice when air is far
below freezing
Fig. 2.2
Fig. 2.3
Fig. 2.5
Fig. 2.4
What are Mixtures, Solutions,
Acids, and Bases?
• Mixtures: combinations of multiple substances
• Solutions: mixture where one or more substances (solutes) are
uniformly distributed in another substance (solvent)
– Example: seawater (water: 96.5%, salts: about 3.5%, plus dissolved
gases and organic matter)
• Acids, Bases, and the pH Scale
– Acid: any substance that increases the concentration of protons (H+)
in solution (increases hydronium ion, H3O+); sour tastes, corrosive
• Examples: sulfuric, nitric, hydochloric acids
– Base: any substance that decreases proton concentration (or
increases hydroxide ion, OH-) in solution; bitter tastes, feel slippery,
but can be as dangerous as acids when concentrated
• Examples: sodium hydroxide, calcium carbonate
– pH Scale: measurement of proton concentration (natural logarithm);
relative degree of acidity/basicity
• Ranges from 0 to 14; 7 is neutral (pure water), <7 acids, >7 bases
• Buffers: substances that stabilize pH changes
What are the Major Groups of Biochemicals?
• Organic Chemicals: have carbon; methane (CH4) simplest
– Life on Earth based on carbon compounds; several identified in outer
space
– Vital Force Theory (organic compounds only produced by living
organisms) disproved in 1828 when Frederick Wöhler synthesized
urea (CH4N2O) from simpler compounds
• Major groups of organic biochemicals
– Carbohydrates: monosaccharides (ex. glucose), disaccharides (ex.
sucrose), polysaccharides (examples: starch, glycogen, cellulose)
• Main sources of metabolic energy for living things
– Lipids: large proportion of C-C and C-H bonds
• Component of cell membranes; energy sources, natural fats, oils,
pigments, and steroid hormones
– Proteins: polymers of amino acids (20 types); many functions:
• Enzymes (organic catalysts), structural functions, antibodies, cell
recognition and messenger molecules (hormones and receptors)
– Nucleic Acids: polymers of nucleotides (characterized by nitrogenous
bases, a sugar, and an inorganic phosphate group)
• Hereditary (DNA, RNA) and energy (ATP) functions
Fig. 2.8
Fig. 2.6b
Fig. 2.9
Fig. 2.10
Fig. 2.13
Fig. 2.14
Fig. 2.15
What are Condensation and
Hydrolysis Reactions?
• Polymerization
– Condensation of monomers  polymers and water (by-product)
– Examples: glucose  starch (or cellulose, or glycogen); amino
acids  proteins
• Hydrolysis
– Polymers + water  subunits
– Example: digestion of proteins or polysaccharides (enzymes
involved)
• Energy Currency
– Adenosine triphosphate (ATP) is the molecule involved in the
transfer of energy for most metabolic reactions (ATP  ADP 
AMP or vice versa)
– Other energy compounds: NADH, NAD, FADH (redox factors)
– All reactions require energy, but can produce a net gain in
energy (or can require net energy input from another source)
The Origin of Life: How? When? Where?
•
From the Pre-biotic Soup to Proto-cells (Oparin-Haldane)
1.
2.
3.
•
Formation of large organic compounds from “interstellar-type”
compounds (amino acids formed from methane, water,
ammonia, and hydrogen gas with electric spark as energy
source - Stanley Miller, 1953)
Formation of organic polymers (biochemicals) from large organic
compounds (some polymerize in presence of metal
catalysts, but small yields)
Internalization of metabolites within lipid membrane (phospholipids and fatty acids spontaneously form hollow spheres
in water, and internalize certain compounds)
The Importance of RNA
–
–
RNA a simpler compound than DNA, can do cellular work (like an
enzyme), and can evolve in response to selection
Ribosomal RNA is conserved in all living things; RNA nucleotides
involved in the energy systems of all cells (ex., ATP)
Fig. 2.16
Fig. 2.17
The Origin of Life: How? When? Where?
• The Heterotroph Hypothesis: first living cells were likely
heterotrophic vs. autotrophic (complex metabolism)
• The Fossil Record for Early Life
– Oldest confirmed fossils of cells ~ 2 billion years old (stromatolites);
older fossils (~ 3.5 billion years old) relatively controversial
– Indirect indications of life (bioindicators) suggest life present by 3.5
billion years ago
• Graphite particles rich in carbon-12 from rocks in Greenland
• Banded iron formations (redbeds) suggest that oxygen gas reached
~ 15% of present-day level by 2.5 billion years ago (regarding
formation of rust in presence of iron, water, and oxygen gas)
• Where did Life Originate?
– Pre-biotic soup (“warm little pond” or “cold pond”?); water is the
“matrix of life” (properties conducive for life)
– Hydrothermal vents and springs: both home to ancient forms of
microbes (chemosynthetic thermophiles)
– Panspermia Hypothesis: first cells arrived via meteorite?
Fig. 2.1
Fig. 2.20
Fig. 2.19
Is There Life in Outer Space?
• The Search for Life in Outer Space (astrobiology)
– Existence of extra-terrestrial microbes thought to be more likely than
in past, due to diversity of extremophiles on Earth (“life finds a
way”), and presence of organic compounds, water, and energy
sources in outer space (vs. “Goldilocks argument”)
• Bacteria omnipresent: found in all extreme environments on Earth
– Temperature: -2 to 121°C (ice caps, hydrothermals; experimental evidence)
– Pressure: up to 1600 MPa (experimental); microbes cultured from deep-sea
and from crustal fluids
– Dryness: endolithic microbes in deserts of Peru and Antarctica (0% humidity)
– Salinity: 15-37% NaCl (soda lakes)
– pH: as low as 0.7 (sulfur springs) and as high as 12.5 (soda lakes)
– Locations of Interest: Mars (polar ice caps, recent evidence of more
widespread water in past); Europa (Jovian moon – “snowball” with
liquid beneath ice, likely volcanic activity and magnetic field)
• The Search for Intelligent Life in Outer Space
– Search for Extra-Terrestrial Intelligence (SETI)
• Drake Equation: formulated by Frank Drake in 1961 as an estimate of
the number of communicating civilizations in the Milky Way galaxy;
estimates range from 1 to 1,000,000 (C. Sagan); Drake’s ~ 10
• Listen for abnormal signals of extra-terrestrial origins via radio telescopes;
digital signals sent out in 1974 and 1999; Voyager spacecraft (2)
contain messages on discs (now beyond solar system);
SETI@home project allows individuals to help analyze data (noise)