Background Assumed for Upper Division Courses:

1. Hierarchical organization of living systems

SUBATOMIC PARTICLES => ATOMS => SMALL MOLECULES => MACROMOLECULES => MACROMOLECULAR ASSEMBLIES=>CELL ORGANELLES => CELLS => TISSUES => ORGANS => ORGAN SYSTEMS => ORGANISMS

2. Chemical Bonds
A. Form so atoms become STABLE = have full outer ELECTRON SHELL
B. Strong bonds = COVALENT bonds & IONIC bonds
C. Weak bonds = HYDROGEN bonds, HYDROPHOBIC bonds & Van der Waals forces
I. POLAR & NONPOLAR covalent bonds
II. HYDROPHOBIC and HYDROPHILIC molecules

D. STRONG BONDS exist between atoms & small molecules
I. CONDENSATION and HYDROLYSIS
II. require ENZYMES to form & break inside cells
 
E. WEAK BONDS exist between macromolecules, macromolecular assemblies and within macromolecules
I. chemical environment within cell causes these to form and break
II. chemical environment acts through EQUILIBRIUM CONSTANT affect concentrations of REACTANTS and PRODUCTS
 
3. Functional Groups in Biological Molecules
A. Acetyl, Amino, Carbonyl, Carboxyl, Hydroxyl, Methyl, Phosphate, Sulfhydryl
B. recognize FORMULA, POLARITY
C. SULFHYDRYL common covalent crosslinker within/between polypeptide chains

4. Water
A. Importance to living systems
 I. it's everywhere
II. HYDROGEN BOND formation => solubility, cohesion, specific heat, surface tension,
III. dissociation => two reactive ions = H+ & OH-

B. PH = - LOG[H+]
I. [H+][OH-] = 10-14M
II. appreciate that pH = very important part of chemical environment w/i cell (cf. 2.E.II, above)
III. approximate pH ranges for physiological, acid & basic conditions
 
 
Small Molecules & Macromolecules of the Cell

1. Small molecules = MONOMERS linked together to form macromolecules = POLYMERS
 
2. For each of the four types of macromolecules

A. NAME
B. nature of MONOMER
C. RECOGNIZE STRUCTURE of monomer & of polymer
D. general FUNCTION
E. general LOCATION w/i cell
F. GENERAL NATURE of macromolecule -hydrophobic vs. hydrophilic vs. charged vs. neutral under physiological conditions
 
3. For CARBOHYDRATES
A. general chemical & structural formulae for MONOSACCHARIDES
I. HYDROPHILIC & therefore water soluble
B. polysaccharides = linear or branched
C. FUNCTIONS of polysaccharide
I. animal: energy storage = glycogen & structure = chitin
II. plant: energy storage = starch & structure = cellulose
D. can be COVALENTLY LINKED TO protein or lipid to form GLYCOPROTEINS or GLYCOLIPIDS
 
4. LIPIDS
A. built of FATTY ACID CHAIN
 I. alkyl (CH2) chains
II. very hydrophobic
 
B. glycerol w/ three fatty acids = TRIGLYCERIDE
 I. long term energy storage
 
C. glycerol w/two fatty acids and a phosphate link to an "R" = PHOSPHOLIPID
 I. structural component of cell membranes
II. AMPHIPATHIC
a. molecule w/areas of 2 different properties
b. HYDROPHOBIC fatty acid chains
c. HYDROPHILIC HEAD (glycerol, phosphate & "R")
 
D. STEROIDS
I. Four interconnected carbon rings
II. Cholesterol: plasma membrane component
III. Hormones
 
5. PROTEINS
A MONOMER = amino acid
I. general structure of an AMINO ACID
II. 20 common ones
III. backbone vs. "R" groups
IV. classes of "R" groups: nonpolar, neutral polar, acidic polar, basic polar
 
B. POLYMER = PROTEIN
I. amino acids linked by PEPTIDE BONDS
 
C. LEVELS OF ORGANIZATION
I. PRIMARY = amino acid sequence
II. SECONDARY = a-helix, b-sheet & random coil
III. TERTIARY = spatial arrangement of regions of secondary structure
IV. QUATERNARY = spatial arrangement of polypeptides in multimeric proteins
D DOMAINS of proteins
I. each domain = piece of polypeptide w/unique function/structure
II. each domain from different portion of genome
a. evolution of gene/protein by movement of these regions of DNA
b. production of multidomain protein by transcript processing
 
E. IMPORTANT FEATURE is 3D shape & flexibility which => function

F. FUNCTIONS w/i cell = "tools" of the cell

I. receptors, transport channels, motors, enzymes, structural elements, carriers

6. NUCLEIC ACIDS
A. MONOMER = NUCLEOTIDE
I. phosphate, sugar & base
II. four kinds of bases in RNA & in DNA
III. role of EACH CARBON IN THE SUGAR
IV. DEOXYRIBOSE vs. RIBOSE
 
B. POLYMER = NUCLEIC ACID
I. monomers linked by phosphodiester bond between sugar & phosphate
II. information "written" in base sequence of the monomers
III. DNA
a. 2 molecules hydrogen bonded in a double helix
b. BASE SEQUENCE of carries genetic information
IV. RNA
a. several types
b. each has specific role in converting genetic information of DNA
into amino acid sequence of protein
 

1. Spontaneous Reactions & The Laws of Thermodynamics
A. FIRST LAW & SECOND LAWS OF THERMODYNAMICS
I. energy cannot be created or destroyed, but converted from one form to another
II. all systems spontaneously move to their lowest free energy condition (most disordered)
 
B. Reversible reactions & EQUILIBRIUM CONSTANTS
I. Keq = [P]/[S] = constant for a given reaction
 
C. ENDERGONIC and EXERGONIC reactions
I. ENERGY DIAGRAMS
II. REACTION COUPLING: energy released from exergonic drive endergonic
2. ATP = energy currency of the cell

3. Role of ENZYMES in Biological Reactions

A. enzymes act on ACTIVATION ENERGY of chemical reactions
B. Characteristics:
I. BRIEFLY COMBINE w/S
II. UNCHANGED after catalyzing reaction of S => P
III. each catalyzes a SPECIFIC reaction
IV. SATURATED by high [S] e. many contain COFACTORS
C. Catalytic Mechanisms
aI. ACTIVE SITE = location in enzyme at which reaction occurs
II. transition state bound best in active site
III. SAME ENZYME CATALYZES BOTH DIRECTIONS OF A REVERSIBLE REACTION
 
D. Factors Affecting Enzyme Activity
I. SUBSTRATE CONCENTRATION
II. INHIBITORS: competitive & noncompetitive
III. TEMPERATURE & pH
E. ALLOSTERY: allosteric enzymes have >1 binding site

F. COVALENT MODIFICATION

EXTREMELY IMPORTANT CONCEPT
I. minor chemical modification has major effects on protein activity
II. common modifiers: Ca+2, PO4, CH3, COCH3
III. KINASES & PHOSPHATASES
 
4. RNA-BASED CATALYSIS
A. RNA splicing & processing
B. Impact on concepts of evolution of life
 

1. Form of the genetic information = structure of DNA double helix

A. Single DNA molecule = nucleotide linked by covalent bonds between sugar of one & phosphate of next
B. BACKBONE of DNA
I. sugar-phosphate w/base of each nucleotide perpendicular to backbone
II. POLARIZED; one end has phosphate & other end has sugar
C. Double helix
I. two DNA molecules
II. ANTIPARALLEL = 3' => 5' on one molecule next to 5' => 3' on other
III. hydrogen bonding between COMPLEMENTARY BASE PAIRS
D. Knowing sequence of one molecule = TEMPLATE, provides sequence of the other

A. SEMICONSERVATIVE
B. DNA POLYMERASE
C. Role of complementary base pairing
D. DISCONTINUOUS on one strand & continuous on the other because 3'=>5' on each molecule

A. TRANSCRIPTION
I. part of one DNA molecule = template for mRNA synthesis
II. 3'=>5'
III. complementary base pairing

B. TRANSCRIPT PROCESSING

I. conversion of TRANSCRIPT into mRNA
a. removal of INTRONS
b. addition of cap & poly A tail
c. transport into cytoplasm

 
C. TRANSLATION
I. sequence of events
a.mRNA binds to SMALL RIBOSOMAL SUBUNIT
b. LARGE RIBOSOMAL SUBUNIT joins complex
c. AMINOACYL TRNA SYNTHETASE "charges" each tRNA with amino acid
d. charged tRNAs join RIBOSOME
e. peptide bond forms as amino acid released from tRNA
f. free tRNA leaves ribosome
g. TERMINATION CODON binds termination factor, not a charged tRNA
h. complex dissociates, releasing polypeptide
 
II. genetic code
a. CODON = 3 nucleotide sequence of mRNA
b. each codon brings in tRNA bearing only one specific amino acid
c. ANTICODON = 3 nucleotide sequence of tRNA that base pairs with the codon
 

1. Biological Membranes

A. FLUID MOSAIC MODEL
2D phospholipid bilayer with embedded (INTEGRAL) and associated (PERIPHERAL) proteins

B. INTEGRAL VS. PERIPHERAL PROTEINS

I. operationally defined by extraction with hydrophobic or hydrophilic solvents
II. determined by extent & nature of associations with phospholipids of bilayer

C. Properties of membranes

I. asymmetry: phospholipids, proteins & carbohydrates
II. types of mobility: lateral, rotational & flip-flop

Copyright 1997 Western Oregon University.
Direct suggestions, comments, and questions about this page to Dr. Turner.
Web page construction by Lindsay Turner, Dec., 2001