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BIOMOLECULES

ATOMS and ELEMENTS

A. Atoms
- basic units of all matter
1. Three Major Components
- negatively charged electrons
- positively charged protons
- uncharged neutrons
2. Protons and Neutrons
- heaviest components
- found in the nucleus (heaviest part of the atom)
- number of protons normally equals the number of electrons  atom as a whole is uncharged
3. Electrons
- very light
- orbit the nucleus
- arranged in orbitals of differing energy levels
a. Electrons Farthest from the Nucleus
- travel the fastest
- highest energy level
- can move from one orbital to another as they gain or lose energy
b. Orbitals
- each can contain only a certain number of electrons
i. 1st Orbital
- closest to the nucleus
- contains a maximum of 2 electrons
ii. 2nd Orbital
- contains 8 electrons (octet rule)
iii. 3rd Orbital
- contains 8 electrons (octet rule)
- other atoms (little biological importance) have additional electrons
- each orbital must be filled (starting with the one closest to the nucleus) before
electrons can occupy the next outer orbital
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B. Element
- substance that consists of a single type of atom
1. Identified by Two Numbers
a. Atomic Number
- is the number of protons which equals the number of electrons
- ex: Hydrogen
- 1 proton  atomic number is 1
Oxygen - 8 protons  atomic number is 8
b. Atomic Weight or Mass
- sum of the number of protons and neutrons (electrons are too light to contribute to the
weight)
- ex: Hydrogen (1H)
- 1 proton and no neutrons  atomic weight is 1
Oxygen (16O)
- 8 protons and 8 neutrons  atomic weight is 16
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CHEMICAL BONDS and the FORMATION of MOLECULES

- outer orbital must contain the maximum number of electrons  very stable atom
- if an atom does not have its outer orbital full  tends to fill its outer orbital by bonding with other atoms
 maximally stable
- most atoms do not have their outer orbitals filled with the maximum number of electrons
- to fill their outer orbitals  atoms can either gain electrons from, or lose electrons to, other atoms
- the number of electrons that an atom must gain or lose to fill its outer orbital is its valence
- number of covalent bonds that the atom can form
1. Compound
- consists of two or more different elements
2. Molecular Weight of a Molecule or Compound
- sum of the atomic weights of the component atoms
- ex: molecular weight of water is 18 (1+1+16)
A. Covalent Bonds
- atoms often achieve stability by sharing electrons with other atoms  fill the outer orbitals of both
atoms simultaneously  creates strong bonds (covalent bonds)
- all covalent bonds are strong
- covalent bonds do not break unless they are exposed to strong chemicals or large amounts of energy
generally as heat
- never break apart spontaneously at temperatures compatible with life
1. Carbon
- frequently involved in covalent bonding
- has four electrons but requires a total of eight to fill its outer orbital
2. Hydrogen
- has one electron
- requires an additional one to fill its outer orbital
- carbon atom can fill its outer orbital by sharing electrons with four hydrogen atoms
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B. Non-Polar and Polar Covalent Bonds

- two atoms connected by a covalent bond may exert the same or different attractions for the shared
electrons of the bond
1. Non-Polar Covalent Bonds
- both atoms have a similar attraction for electrons
2. Polar Covalent Bonds
- one atom has a much greater attraction for electrons than the other  the electrons are
shared unequally
- one part of the molecule has a slightly positive charge and another part a slightly negative
charge
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3. Water
- oxygen atom has a greater attraction for the shared electrons than do the hydrogen atoms
- oxygen atom has a slight negative charge and the hydrogen atoms a slight positive charge
C. Ionic Bonds
- join ions together
- electrons from one atom are attracted very strongly by another nearby atom  electrons completely
leave the first atom  become a part of the outer electron orbital of the second without any
sharing (loss or gain of electrons)  electrically charged atom (ions)
- attraction of the positively charged atom to the negatively charged atom  bond formation
- atom that gains electrons  negatively charged (anions)
- atom that loses electrons  positively charged (cations)

- superscript number
- difference between the number of protons and electrons in the ion
- common among the weak forces holding ions, atoms, and molecules together
- readily broken at room temperature
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D. Hydrogen Bonds
- weak bonds formed by the attraction (electrostatic interactions) of a positively charged hydrogen
atom in a polar molecule to a negatively charged atom, frequently oxygen (O) or nitrogen (N) in
another polar molecule

- oxygen of water can form hydrogen bonds with two other water molecules, so that each water
molecule is hydrogen-bonded to approximately four close neighboring water molecules
in a fluid three-dimensional lattice

- a single hydrogen bond is too weak to bind molecules together

- a large number can hold molecules together firmly
- intermolecular or intramolecular
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1. Formation

2. Bond Strength
- weaker than covalent bonds
- strong enough to dissolve polar molecules in water and to separate charges
- weak enough to allow movement of water and solutes
- approximately 4 kcal, roughly 1/20th of the strength of the covalent O-H bond in the water
molecule  dynamic extensive water lattice with many strained bonds that are
continuously breaking and reforming  hydrogen bonds between water molecules and
polar solutes continuously dissociate and reform (constantly being formed and broken
at room temperature because the energy produced by the movement of water is enough to
break these bonds)  solutes to move through water and water to pass through channels
in cellular membranes
3. Function
- stabilize 3D structures of proteins and nucleic acids
- enzyme catalysis

BIOMOLECULES
- products of evolutionary selection
- fittest possible molecules for their biological reaction
- interact with each other
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The BIOLOGICAL FITNESS of ORGANIC COMPOUNDS
A. Some Chemical Elements are More Fit Than the Others
1. About 30 of the more than 90 naturally occurring chemical elements are essential to organisms
- most of the elements in living matter have relatively low atomic numbers
- only five have atomic numbers above that of selenium (34)
2. Elements Essential in Nutrition
- of one or more species but not all essential for every specie
a. Elements of Organic Matter
-C
- O2
-S
- H2
- N2
-P
b. Monoatomic Ions
- Na+
- Mg++
- Cl-
- K+
- Ca++
c. Trace Elements
- Mn
- Co
- Zn
- Al
- Mo
- Si
- Ni
-F
- Fe
- Cu
-B
-V
-I
- Sn
- Cr
- Se
- represent a miniscule fraction of the weight of the human body
- essential to the function of specific proteins  essential to life usually because
- oxygen-transporting capacity of the hemoglobin molecule is absolutely
dependent on four iron ions that make up only 0.3% of its mass
B. Four Most Abundant Elements in Living Organisms (In Terms of Percentage of Total Number of Atoms)
- 99% of the mass of most cells
- lightest elements capable of forming one, two, three, and four bonds
- the lightest elements form the strongest bonds in general
- readily form covalent bonds by electron-pair sharing
1. Carbon
- needs 4 electrons
2. Hydrogen
- needs 1 electron
3. Oxygen
- needs 2 electrons
4. Nitrogen
- needs 3 electrons
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The HIERARCHY of the MOLECULAR ORGANIZATION of CELLS

A. Precursors from the Environment
- CO2
- NH3
- H2O
- N2
B. Metabolic Intermediates
- pyruvate
- malate
- citrate
- glyceraldehydes-3-phosphate
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C. Building-Blocks
- nucleotides
- monosaccharides
- glycerol
- amino acids
- fatty acids
D. Macromolecules
- nucleic acids
- polysaccharides
- proteins
- most prominent
- over 50% of the dry weight of the cell
- lipids
E. Supramolecular Assemblies
- ribosomes
- enzyme complexes
- contractile systems
- microtubules
F. Organelles
- nucleus
- chloroplasts
- mitochondria
- Golgi bodies
G. Supramolecular Complexes
- not covalently bonded to each other
- nucleic acid and proteins of ribosomes
- held together by weak non-covalent forces
- hydrogen bonds
- hydrophobic interactions
- van der Waals interactions

The PRIMORDIAL MOLECULES

A. 20 Amino Acids
- glycine - threonine
- aspartic acid - alanine
- phenylalanine - asparagine
- valine - tyrosine
- glutamic acid - leucine
- tryptophan - glutamine
- isoleucine - cysteine
- histidine - serine
- proline - arginine
- methionine - lysine
B. 5 Nitrogenous Bases
1. Pyrimidines
- uracil
- thymine
- cytosine
2. Purines
- adenine
- guanine
C. 1 or More Fatty Acids
- palmitic acid
D. 2 Sugars
- -D-glucose
- -D-ribose
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E. Sugar Alcohol
- glycerol
F. Nitrogenous Alcohol
- choline

BIOMOLECULES
A. Biomolecules Are Compounds of Carbon with a Variety of Functional Groups
1. Carbon
- form single bonds with hydrogen atoms
- form single and double bonds with oxygen and nitrogen atoms
- ability to form very stable carbon-carbon single bonds
- each carbon atom can form single bonds with up to four other carbon atoms
- two carbon atoms also can share two (or three) electron pairs  forming double (or triple)
bonds
- the four single bonds that can be formed by a carbon atom are arranged tetrahedrally
- free rotation around each single bond
- very large or highly charged groups attached to both carbon atoms  restrict
rotation
- form covalent bonds with H, O, N, S

- double bond formed

- shorter
- rigid
- allows little rotation about its axis
2. Carbon, Oxygen and Nitrogen
- can share 1 or 2 electron pairs to yield single or double bonds
3. Covalently Linked Carbon Atoms in Biomolecules
- form linear chains, branched chains, and cyclic structures
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B. Functional Groups
- confer specific chemical properties on the molecule
- most biomolecules can be regarded as derivatives of hydrocarbons
- hydrogen atoms replaced by a variety of functional groups  different families of organic
compounds
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- many biomolecules are polyfunctional

- containing two or more different kinds of functional groups each with its own chemical
characteristics and reactions
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C. Major Classes of Biomolecules

- identical functions in all species of cells
1. Proteins
- direct products and effectors of gene action
- catalytic activity (enzymes)
- structural elements
2. Nucleic Acids
- store and transmit genetic information
3. Polysaccharides
- storage forms of energy-yielding fuel
- extracellular structural elements
4. Lipids
- storage forms of energy-rich fuel
- major structural component of membranes

The SPECIATION and DIFFERENTIATION of BIOMOLECULES

- more complex biomolecules evolved from the primordial biomolecules
A. Arginine
- ornithine
- citrulline
B. Proline
- 3-hydroxyproline
- 4-hydroxyproline
- 4-hydroxymethylproline
- 4-methyleneproline
- 4-ketoproline
C. Leucine
- -hydroxyleucine
- -hydroxyleucine
- N-methylleucine
- -dihydroxyleucine
- -hydroxyleucine
D. Guanine
- 1-methyguanine
- 2-methylguanine
- 2-dimethylguanine
- 2-O-methylguanine
- 7-methyguanine
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E. D-Glucose
- D-mannose
- D-fructose
- D-galactose
- N-acetylglucosamine
- D-glucuronic acid
- D-glucose 6-phosphate
- ascorbic acid
- inositol
- sucrose
- maltose
- lactose
F. Palmitic Acid
- oleic acid
- stearic acid
- lauric acid
- palmitoleic acid
- palmitaldehyde
- stearaldehyde