Transcript Chemistry of Life

Chemistry of Life
Chapter 2
AN INTRO TO CHEMISTRY
Matter
• Substance that has mass and takes up space
– Compose all living things
• Generally found in 1 of 3 states
• Composed of 1 or more elements
Elements
• Can’t be broken down by ordinary chemical processes
• 92 occur naturally on Earth
– 96% of the human body is (CHON)
– 25 are essential to life
• Composed of atoms
Atoms
• Smallest particles that retains properties of an element
• Made up of subatomic particles:
– Protons (+) in nucleus
– Electrons (-) orbits nucleus
– Neutrons (no charge) in nucleus
• Protons and neutrons
– Mass of about 1
• Electrons
– Mass is negligible (1/2000)
Reading A Periodic Table
• Elements differ depending on the number of
subatomic particles
• Atomic symbol
– 1st letter or 2 (usually)
• Atomic number
– Determined by number of protons
– Element specific
• Mass number
– Determined by number of protons + neutrons
Chemical Properties of Atoms
• Electrons are key
– Move in orbitals called shells
– Repel one another, but attracted to protons
• Electron shells
– Outermost (valence) determines chemical properties
• Closer to the nucleus = lower energy and are filled first
– Holds up to 2 or 8 electrons (Octet Rule)
• Filled are unreactive
• Unfilled are reactive
– Number differs between atoms
• Chemical reactions are making and
breaking bonds
Electron Shell Models
SODIUM
11p+ , 11e-
CHLORINE
17p+ , 17e-
electron
proton
neutron
CARBON
6p+ , 6e-
OXYGEN
8p+ , 8e-
HYDROGEN
1p+ , 1e-
HELIUM
2p+ , 2e-
NEON
10p+ , 10e-
Chemical Bonds
• Hold 2 or more atoms together
– Complete outer shells
– By sharing, donating, or receiving electrons
• Form molecules (H2, I2, and O2) or compounds
(H20, NaCl, C6H12O6)
– Demonstrates emergent properties
• 2 H+ (gas) + O- (gas) = H2O (water)
• Na+ (metal) + Cl- (poisonous gas) = NaCl (table salt)
Ionic Bond
• One atom loses electrons  cation (charge?)
• Another atom gains these electrons  anion
(charge?)
• Charge difference attracts the two
– Very weak bond
– Table salt (NaCl)
cation
anion
Covalent Bonds
• Atoms share outer pair or pairs of valence electrons
– Single, double, or triple covalent bond
• Strong bonds
What’s Mine is Yours or Just Mine
Polar Covalent Bonds
• Electrons spend more time
• Electrons shared equally
near the nucleus with the
• Example: carbon dioxide(CO2),
most protons
hydrogen gas (H2)
(electronegativity)
• Example: water (H20)
Nonpolar Covalent Bonds
Hydrogen Bond
• Positive charge on H attracts
negative charge on another atom
• Individually weak, but often
numerous = strong
• Important to many biological
compounds
– E.g. water
• Makes up 70 – 90% of all living things
• Bonds create unique properties
Chemical Reactions
• Chemical equation: reactant(s) + reactant(s) = product(s)
– May be reversible
– Move to equilibrium
• Types
– Synthesis: (A + B  AB) usually anabolic and endergonic
– Decomposition: (AB  A + B) usually catabolic and exergonic
– Exchange: (AB + CD  AD + BC) may or may not be
endergonic/exergonic
– Redox: may gain or lose electrons
• Oxidized – loses electrons (LEO)
• Reduced – gains electrons (GER)
• Affected by temperature, concentration, catalysts, etc.
AN INTRO TO BIOCHEMISTRY
Biologically Important Compounds
• Inorganics lack carbon (generally)
– E.g. salts, water, acids, and bases
• Organics contain carbon, are covalently
bonded, and generally large
– E.g. carbs, lipids, proteins, and nucleic acids
Properties of Water
• High heat capacity
– Absorb and release water with little temp. change
– Environmental changes (internal and external)
• High heat of vaporization
– Lots of heat required to transform water to steam
– Sweating
• Polarity
– Slightly negative AND slightly positive ends
– Dissociation of salts, hydration layers, and transport
• Reactant
– Solubility
– Dehydration and hydrolysis
• Cushion/shock absorber
– Acts as a barrier/buffer
– CSF and joints
Electrolytes
• Ions able to conduct electrical current
– Kidneys regulate
• Salts contain ions other than H+ or OH– E.g. NaCl, KCl, and calcium phosphates
• Acids are hydrogen ion (H+) donors
– Concentration determines acidity of a solution
– E.g. pH < 7; HCl, H2CO3
• Bases are hydrogen ion (H+) acceptors
– Form water upon disassociation
– E.g. pH > 7; Mg(OH) 2, HCO3-, and NH3
• Buffers release H + with increasing pH and
accept H + when decreasing
– H2CO3
HCO3- + H+
Building Organic Molecules
• Monomers: small repeating units
– Universal, similar in all forms of life
• Polymers: chains of monomers, functional components
of cells (macromolecules)
– DNA is composed of 4 monomers (nucleotides)
• Variation based on arrangement
– Proteins are composed of 20 different amino acids (AA’s)
• Variation distinguishes within and between species
Making and Breaking Polymers
Dehydration reaction
• Links monomers
• Loss of water for each
monomer added
• Forms a covalent bond
1
2
Hydrolysis reaction
• Breaks polymers
• Addition of water for each
broken bond
4
3
1
1
2
3
2
3
4
4
1
2
3
4
Carbohydrates
• General (CH2O)n ratio, ends in ‘ose’
• Fuel source for cells
• Glycosidic bonds
– Dehydration vs. hydrolysis
• Monosaccharides
– Pentoses
– Glucose, fructose, & galactose
• Disaccharides
– Maltose, lactose, & sucrose
• Polysaccharides
– Glycogen
– Starch
Lipids
• Composed of fatty acids (long carbon chains) and a glycerol (3
carbons)
• Triglycerides
–
–
–
–
3 FA’s
Most usable form of energy
Fats (animal) and oils (plants)
Saturated or unsaturated (mono- or poly-)
• Phospholipids
– 2 FA’s and a phosphate group
– Amphipathic molecule
• Steroids
– Hydrocarbon rings
– Cholesterol and sex hormones
Proteins
• Chains of amino acids joined by peptide bonds
– 20 different types (alphabet)
– Peptides, polypeptides, and proteins (words) are all slightly different
• Structural levels
– Primary (1°) – sequence of amino acids
– Secondary (2°) – primary level folds to form alpha (α) – helixes and beta
(β) - pleated sheets
– Tertiary (3°) – folding of secondary structures on each other
– Quaternary (4°) – 2+ polypeptides interact to form a protein
• Denaturation destroys structure which alters or inhibits function
– Changes in pH and temperature
– Reversible or permanent depending on extend of change (fevers)
Protein Types
• Fibrous (structural proteins)
– Building materials of the body
• Keratin, elastin, and collagen
– Movement
• Actin and myosin
• Globular (functional proteins)
– Enzymes
– Transport
– Immunity
Enzymes
• Globular proteins acting as
catalysts to speed a reaction
– Lowers energy of activation (EA)
• End in ‘ase’ and named for substrate
• Mechanism of enzyme action:
– Enzyme binds substrate at its active site on the enzyme.
– Enzyme-substrate complex undergoes an internal
rearrangement that forms a product.
– Product released and now catalyzes another reaction
Nucleic Acids
• DNA and RNA
• Composed of nucleotides
with 3 components
– Pentose sugar
– Phosphate group (PO4)
– Nitrogenous base form
complementary pairs
How DNA and RNA Differ
DNA
(deoxyribonucleic acid)
• Directs protein synthesis;
replicates self; genetic
material
• Sugar is deoxyribose
– Has –H
• Bases are adenine (A),
cytosine (C), guanine (G), and
thymine (T)
• Double-stranded helix
• Only in nucleus
• 1 type
RNA
(ribonucleic acid)
• Carries out protein
synthesis
• Sugar is ribose
– Has -OH
• Bases are adenine (A),
cytosine (C), guanine (G),
and uracil (U)
• Single-stranded
• Not confined to nucleus
• 3 major types
Adenosine Triphosphate (ATP)
• RNA nucleotide with 3 phosphate groups
• Stores energy from break down of glucose
– Transfers phosphate groups to release energy =
phosphorylation
– Controls energy release