Transcript The Molecules of Life

The Molecules of Life
Chapter 2
2.1 The atom is the fundamental unit of matter.
Chemistry: study of matter
Matter: anything that takes up space and has weight/mass
•
made up of elements
Elements:
pure substances that can not be broken
down further
• 92 naturally occurring elements
• Listed in Periodic Table of Elements
• C, Na, Ca
• 25 elements required for life
• 96% of life made of COHN
ATOMS
 Elements are made up of tiny units called atoms
 the smallest complete unit of an element
 Atoms contain 3 smaller units called subatomic particles
Subatomic particle
location
symbol
Proton
nucleus
p+
Neutron
n
Electron
e-
charge
+1 each
0
-1 each
 Mass of 1dalton = 1d = 1.67 x 10 -24 g
mass
1d
1d
nucleus
0
orbiting
CHARACTERISTICS OF AN ATOM
Atomic number: equal to the # p+
6 C; shown top/top left of symbol
in an electrically neutral atom, #p+ = # e identity of element (never changes)
Periodic Table is organized by atomic number
Atomic mass: combined weights of p+ and n
12.01 C; shown bottom/bottom left of symbol
mass = # p + # n
n = mass – atomic number
NOTE: mass can vary, because number of n can
vary
Isotopes: atoms of same element with different masses
same atom; different #n
12 C, 13 C, 14 C
CARBON ATOM
Atomic # = ?
Atomic mass = ?
#n=?
ORBITALS AND SHELLS
e- orbit nucleus in regions called orbitals
7 energy levels or electron shells
Corresponds to 7 periods of Periodic
Table
ENERGY LEVELS (SHELLS) OF ELECTRONS
 There are 7 known energy levels or electrons shells
 Correspond to 7 periods in the Periodic Table of Elements
 7 horizontal rows = 7 energy levels = 7 electron shells
 1 st Energy Level: holds a maximum of 2 e  2 nd Energy Level: holds a maximum of 8 more e  3 rd Energy Level: holds a maximum of 8 more e  The first 18 elements are in order by atomic number in the
first 3 periods/e- shells
PERIODIC TABLE
Organized by atomic number into 7 periods or energy shells
1st shell: max 2 e-;
2nd & 3rd shells: max 8 e- each
READING THE PERIODIC TABLE
Elements in a row (period) are in the
same outermost energy level
Valence shell = outermost energy level
All in 2nd energy level with 3 to 10 e- each
(remembering that
1st shell has 2)
PERIODIC TABLE
Elements in a column are called a group. Same # e- in outermost/valence shell
Noble elements
He (2e-)
Ne (10e-)
Ar (18e-)
All inert;
Valence shells
are filled;
“happy”
QUICK CHECK
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P has an atomic # = 15.
How many protons?
How many e- ?
How are e- organized?
Which is valence shell? How many e - missing from
maximum (“holes”)?
QUICK CHECK ANSWERS
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P has an atomic # = 15.
15p+
15 e2e- in 1 st shell, 8e- in 2 nd shell, 5e- in 3 rd shell
Valence shell is 3rd shell; has a maximum of 8e Therefore, the “valence” (number of missing e -; or “holes”)
is 3e This means that the bonding capacity for P is 3
Valence (missing e- or “holes”) = bonding capacity
CHEMICAL BONDS
2.2 Atoms can combine to form molecules linked by chemical
bonds.
Molecule: A substance made up of 2 or more atoms
Chemical bond: attractions when atoms fill each others’ valence shell
• What determines chemical bonding? e- in valence shell (outermost)
• Atoms try to complete each other’s valence shells
3 Types of Chemical Bonds:
• Covalent: polar and nonpolar
• Hydrogen
• Ionic
COVALENT BOND
Formed by sharing 1 or more
pairs of valence electrons;
Very strong bond
Tends to be groups closer to
the middle of the Periodic Table
H-H
Valence: bonding capacity of an
atom; number of covalent
bonds needed to complete
outer valence shell; # of “holes”
Valence for H = 1, O = 2; N = 3;
C=4
COVALENT BONDING
Atoms try to complete each others valence shells (fill it to max)
1st shell = 2e2nd shell = 8 more e3rd shell = 8 more e-
Electronegativity
An atom’s ability to attract and hold shared
electrons
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O >>>H…..think H 2 O (water)
O>>>C…..think CO 2 (carbon dioxide)
N>>>H…..think NH 3 (ammonia)
C = H……think CH 4 (methane)
NONPOLAR COVALENT BOND
Nonpolar Covalent Bonds :
electrons
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formed by equal sharing of
nonpolar = nonpulling
Both atoms are equally electronegative
Molecule has no charge
H 2 , O 2 , Cl 2 , CH 4
Gasoline, fat, grease, butter
POLAR COVALENT BONDS
Polar Covalent Bonds: formed by large differences in electronegativity
Unequal sharing (polar = pulling)
Creates partial + and - changes
Bonds inside of H2O; NH3, CO2
Examples of Polar and Nonpolar Covalent
Bonds
HYDROGEN BONDS
Weak attractions that help stabilize biological molecules
Between H2O molecules, between strands of DNA, between polar mol
IONIC BONDS
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Ionic Bonds: transferring electrons
When 2 atoms are very different in electronegativities
Groups closest to the right or left side of Periodic Table
Ion: charged atom
 # p + does not equal #e  Result is a positively charged atom (cation) and a negatively charged atom
(anion)
 Cation (e- donor)….hint: remember ca + ion
 Positively charged atom
 Has more p + than e  Na + , Mg + , K + , Ca +2
 Anion (e-acceptor)
 Negatively charged atom
 Has more e- than p+
 Cl - , Br - , F -
 The attraction between the two ions of opposite charges is the
ionic bond; called “salts”; they are fairly strong bonds as crystals
but fragile in water
IONIC BOND/SALTS
Bond made by transferring electrons between two charged atoms
Ion= charged atom
Cation
Anion
Called salts
Fairly strong bonds as crystals; fragile in water
A CHEMICAL REACTION
Involves breaking and forming chemical bonds
WATER CHEMISTRY
2.3 Water is abundant
and essential for life.
•Life evolved in water
•Cells 70-95%
•Covers 75% of Earth
•Polar molecule
•Good solvent
Water is a Polar Molecule
 Hydrogen bonding between water molecules is basis for all of water ’s
unusual properties
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Cohesion (high surface tension)
High specific heat (resists changes in temperature)
High heat of vaporization
Water expands when it freezes
Water is a versatile solvent
 Hydrophilic: water loving compounds
 Dissolve in water
 Polar
 Ionic
 Hydrophobic: water fearing compounds
 Do not dissolve in water (separate)
 Nonpolar
 Oil, gasoline, butter, CH4
HYDROGEN BONDING IN WATER
(LIQUID AND SOLID)
H bonds close together
H bonds farther apart & lock
Water is characterized by extensive hydrogen bonding
pH is a Measure of the Concentration of
Protons in Solution
 About 1 molecule of water in 550 million spontaneously and reversibly
ionizes
 H 2 O = [H + ] + [OH - ]
 At equilibrium, [H + ] = [OH - ] = 10 –7 M, or pH = 7;
neutral solution
 If [H + ] > [OH - ] = acidic (10 -2 or pH = 2)
 If [H + ] < [OH - ] = basic (10 -8 or pH = 8)
 pH is a way to express [H + ] of acidic & basic solutions
 pH = -log 10 [H + ]
 Most biological fluids are pH 6 – 8; except for stomach acid 1.5
 Each pH unit is a 10-fold difference (because scale is
logarithmic)
pH scale goes from 0 to 14
CARBON: LIFE’S CHEMICAL BACKBONE
2.4 Carbon is the backbone
of organic molecules
CARBON & COVALENT BONDS
Each C atom can form up to 4 covalent bonds
DIVERSITY IN CARBON-CONTAINING
MOLECULES
•Bonding capacity of 4 leads to tremendous
diversity of C molecules
•Commonly bonds to O, H, N
•Can also bond to other C’s …carbon skeletons
CARBON DOUBLE BONDS
Hydrocarbons: only C’s and H’s
Hydrophobic due to C-C and C-H bonds being nonpolar
Remember: C has atomic # of 6; therefore bonding capacity of 4
ISOMERS
Functional Groups
Small chemically reactive groups of atoms frequently bonded to C skeletons
 Hydroxyl –OH , alcohols, i.e. ethanol; polar, found in sugars,
dissolve in water
 Carbonyl aldehyde –COH ; i.e. formaldehyde; polar, found in
sugars
 Carbonyl ketone –CO; i.e. acetone; polar; found in sugars
 Carboxyl –COOH, carboxylic acids; i.e.acetic acid (vinegar);
found in amino acids
 Amino –NH 2 , amines, bases; found in amino acids
 Phosphate – PO 4 , organic phosphates; important in ATP &
cellular energy
 Sulfhydryl –SH; thiols, sulhydryl bridges in
proteins
FUNCTIONAL GROUPS
POLYMERS & THEIR MONOMERS
2.5 Large organic molecules (polymers) include proteins, nucleic acids,
carbohydrates, and lipids, each of which is built from simpler repeating units
(monomers).
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Proteins (amino acids)
Nucleic acids (nucleotides)
Carbohydrates (sugars)
Lipids (fatty acids)
Dehydration Synthesis & Hydrolysis
 Dehydration Synthesis: the way to link monomers to make
polymers
 Remove 1 H 2 O molecule for each covalent bond made
 Process requires energy and enzymes (anabolic)
 i.e. store excess food in body as fats
 Hydrolysis: the way to break down polymers into monomers
 Add 1 H 2 O molecule for every bond broken
 Releases energy stored in bonds (catabolic)
 i.e. digestive enzymes hydrolyze food
 4 polymers of life use both techniques
AMINO ACIDS
= monomer of proteins
(side chain; 20 diff. kinds)
PROTEIN
1 or more
Covalent bond in
proteins
monomers
Proteins act as catalysts and provide structure to cell
NUCLEOTIDES
•Monomers of nucleic acids (which store/transmit
heredity)
•Composed of 3 components:
•5-carbon/pentose sugar
•Nitrogenous base
•PO4
•DNA = Deoxyribonucleic Acid
•Hereditary material contains coded info
•Named for its pentose sugar: deoxyribose
•Nitrogenous bases: A, T, C, G
•Raw material for hundreds of thousands of
genes in chromosomes
•RNA = Ribonucleic Acid
•Synthesizes protein
•Follows instructions of DNA
•Named for pentose sugar: ribose
•Nitrogenous bases: A, U, C, G
NITROGENOUS BASES IN NUCLEIC ACIDS
(All Goats eat Purina)
THE BOND IN THE NUCLEIC ACIDS
•Nucleotides linked together by phosphodiester bonds
•Joins PO4 of one nucleotide to sugar of next
•Makes a polynucleotide (NA)
•1 strand polynucleotide = RNA
•2 strand polynucleotide = DNA
STRUCTURE OF DNA
Double-stranded polynucleotide
Purine--Pyrimidine
Purines
Backbone =
Sugar-PO4 pattern
(ladder)
Pyrimidines
Hydrogen bonds
(rungs of ladder)
Base-pairing rule: A-T; G-C
CARBOHYDRATES
Sugars & their polymers in a ratio of 1:2:1 C:H:O; short-term fuel source
Monosaccharies
Carbs provide short term energy and make up the cell wall of plants, bacteria, algae
NAMING SUGARS
Monosaccharides  One/simple sugar; (CH2O)n where n = 3-7; major nutrient
for cells, especially glucose
i.e. apples…..fructose,mannose
Disaccharides  Two sugars linked together; covalent bond is glycosidic bond
• Sucrose…..i.e. table sugar, sugar in plants, candy
• Lactose…..i.e. sugar in milk
• Maltose…. i.e. sugar in beer, barley
Polysaccharides  Many sugars linked together
• Energy Storage: …….starch (plants); glycogen (animals,humans)
• Structural Support:……cellulose (plant cell wall/fiber); chitin
(exoskeleton of arthropods)
Complex carbohydrates  Long, branched chains of monosaccharides;
commonly refers to whole plant foods high in starch & fiber
CYCLIC MONOSACCHARIDES
GLYCOSIDIC BONDS
LIPIDS
Chemically diverse group of hydrophobic molecules
Fatty Acids; components of fat
Phospholipids: components of
membranes
Steroids : lipid hormones
Lipids store energy, act as signaling molecules, and make up plasma membranes
FATS =TRIACYLGLYCEROL
•1 glycerol……forms backbone of fat
•3 fatty acid “tails”
•Covalent bonds called esters
•Long-term energy storage
SATURATED VS. UNSATURATED FATS
unsaturated
kinks
One or more double bonds
Kinks at double bond
Liquid…plant fats
i.e. corn oil, olive oi, avocados, nuts
Healthier form of fat (LDL)
VAN der WAALS FORCES
• Weak forces
• Length of hydrocarbon chains
increases these forces.
• Kinks caused by unsaturated carbons
(double-bonded carbons)
reduce tightness, causing a lower
melting point.
PHOSPHOLIPIDS
•Modified fat
•1 glycerol, 2 f.a., 1 PO4 &
small chemical grp
•One end hydrophilic
•Other end hydrophobic
•Major component of cell
membranes
•Hydrophilic “heads” face out
•Hydrophobic “tails” face in
COULD THESE BUILDING BLOCKS HAVE BEEN
GENERATED ON EARLY EARTH?
2.6 Life likely originated
on Earth by chemical reactions
that gave rise to the molecules
of life.
1953: Miller & Urey experiments
Showed that a.a. can be generated
in lab under conditions of Early Earth
HOW DID BUILDING BLOCKS FORM
MACROMOLECULES?