Biochem Notes

LECTURE NOTES 1: Foundations of Biochemistry - 1 open ended and 5 MC

Properties of living organisms
- self-replication & self-assembly
- sensing and resonding to changes in environment
- define function for each component and regulation
-
Classification of organisms based on where they get their energy
Phototrophs (take energy from sun light)
Chemotrophs (take energy from food in environment) - organotrophs (bacteria) - not photosynthetic

Biological
1) Cellular
a. nucleus (eukaryotes) & nucleoids (bacteria), cytoplasm, plasma membrane
b. Eukaryotic cells > nucleus > bacteria > mitochondrion > viruses > ribosome > proteins > lipids > small molecules > atoms
- Structure of a Bacterial Cell
a. NO NUCLEUS, MITOCHONDRIA,
b. ribosomes, nucleoid, Pili, flagella, cell envelope (cell wall around bacteria)

- Structure of an Animal Cell (eukaryotic cell)
a. Nucleus - contains genetic material
b. Mitochondrion - oxidizes fuel to produce ATP!
c. Ribosomes - protein synthesizing machines
d. Lysosome - breaks down intracellular debris
e. Cell membrane BUT NO CELL WALL

Structure of a Plant cell
a. Thylakoids - site of light-driven ATP synthesis
b. Vacuole - degrades and recycles macromolecules
c. Cell Wall
d. Chloroplasts; but also have mitochondria

** Difference b/t Prokaryotic & Eurkaryotic cells
Prokaryotic Cell
a. generally small (1-10 nanometers)
b. DNA w/ nonhistone protein; genome in nucleoid, not surrounded by membrane
c. no mitosis; only fission or budding
d. no membrane-bounded organelles
e. photosynthesis
f. no mitochondria, cytoskeleton, or intracellular movement

Eukaryotic Cell
a. generally large (5-100 nanometers)
b. DNA w/ histone & nonhistone proteins; membranous envelope!
c. mitosis (miotic spindle, centrioles)
d. mitochondria, chloroplasts, endoplasmic reticulum, golgi, lysosomes, etc.
e. absorption, ingestion, and photosynthesis
f. mitochondria, complex cytoskeleton, vesicle transport

2) Genetic - DNA strands are complimentary - DNA (( RNA ( Protein - translation on the ribosome of RNA sequence into protein sequence then folding of protein into conformation

3) Evolutionary
a. Archaebacteria ( Eukaryotic cells ( Eubacteria - BUT prokaryotic cells are the oldest and from them came eukaryotic cells
b. RNA World Hypothesis - creation of nucleotides from atmosphere ( prod. of short RNA molecules w/ random seqs. ( selective replication & duplication of RNA segments ( synthesis of specific peptides, catalyzed by RNA ( increasing role of peptides in RNA replication (coevolution of RNA & protein) ( translation system develops ( Genomic RNA copied into DNA ( DNA genome translated on Ribosome w/ protein catalysts

c. DNA mutations produce evolutionary change
d. Prokaryotes originated eukaryotes - bacteria engulfed by eukaryotic cell gave rise to mitochondria and other organelles & same with plant cells

Chemical
- Carbon: BASE of chemistry ( can form bonds with other elements; tetrahedral 109.5 degrees; accepts large amount of functional groups a. carbon forms chiral molecules
- configuration: can’t superimpose molecules ( stereoisomers
- conformation: same position of atoms; rotate freely around a single bond
- 70% of body is made from water; 15% proteins; 1% DNA; 3% RNA

Physical
a. Laws of Therodynamics 1. energy is constant 2. entropy (total disorder) is continuously increasing
c. We (humans) take food as our energy ( take one form of energy and convert it into another form
d. ATP = Central Energy source!
e. Energonic and Exergonic reactions - Energonic: need energy - Exergonic: releases energy
e. Metabolism - Catabolism: reactions the produce less complex substrates - antabolism; reactions that form more complex - metabolic pathways are regulated - final product of reaction is inhibiting the first enzyme to save energy

What forces keep macromolecules together?
a. Carbon-Carbon bonds are more stable; though Si-O is stable, it takes too much energy to break the bond.
b. WANT REVERSIBLE BONDS
c. Non-covalent bonds - charge-charge interaction (IONIC interaction): strongest out of the other non-cov. forces - dipole-dipole charge: H20 is a good example of permanent dipole - induced dipole: temporary - Van der Waals interaction: minimum distance atoms must be from each other = different radii
d. Hydrogen bond - explains structure of proteins

LECTURE NOTES 2: WATER - 1 open ended and 5 MC questions
Properties of water pH Buffers
Biological importance of water

A. Properties 1. Angle of 104 degrees instead of 109 degrees 2. High boiling point; melting point; heat of vaporization; surface tension - why? 3. High dielectric constant: ability of H20 molecules to surround ions and diminish attraction of opposite charges for each other 4. Maximum density found in liquid state (NOT SOLID STATE) 5. Negative volume of melting = ice takes up more space than liquid
- as kinetic energy increases (higher temp) liquid forms; lower K.E. = ice a. Water forms network of hydrogen bonds b. Interactions 3. Amphiphilic molecules - fatty acids/lipids - 2 characteristics: polar head & hydrophobic tail they form MICELLES in water (micelles look like a circle w/ polar heads outside & tails inside) 2. Hydrophobic interactions form a cage-like structure around molecules called clathrate
6. Lipid portions at the edge of cluster force ordering of water molecules ( fewer H2O molecules are ordered; entropy increases

C. pH 4. some bacteria that lives in acidic environments 5. electrolytes - molecules that when in water, form ions 6. Henderson-Hasselbalch Equation: [HA] = [A-], pH = pKa

G. Buffers 8. solutions that tend to resist changes in their pH as acid or base is added 9. made up of weak acid and conjugate base 10. solution of weak acid has pH ~ pKa H+ + A- ( HA OH- + HA ( A- + H2O 4. pH buffer curve: adding base, but pH isn’t changing as rapidly ( buffer. Select buffer than has pKa closest to pH. 1 unit away from pK of molecule, you’re less likely to maintain pH 5. each molecule that has a group that can be ionized = different pK’s for each group

F. Biological importance 7. gas exchange in blood ( a carbonate buffer system in blood that helps carry CO2 from blood to outside 8. pH is important for enzymatic activity 9. Isotonic solution - no net water movement 10. Hypertonic solution - water moves out and cell shrinks 11. Hypotonic solution - water moves in and cell swells up and may burst

LECTURE NOTES 3: AMINO ACIDS - 2 open ended and 8 MC

Structure, Stereochemistry, Classes, Peptides (Peptide bond, Ramachandran Plot), Polypeptides (Primary, secondary, tertiary, quaternary structures), Protein Folding

A. Structure 2. Primary structure - composition/sequence of amino acids to create protein; ORDER OF A.A.’S MATTERS! c. Amino Acids 1. Structure: 20 amino acids: Essential (can’t synthesize, must ingest) and Non-essential - 2 groups that can ionize: (Carboxyl) acidic group around 2 pK, amine group around 9 pK - 7 total groups that can ionize

2. Stereochemistry: L configuration of an amino acid (H in back, and then left is NH3+, right is COO-, top is R group ( focus is on 2 stereoisomers of amino acids - Zwitterions: between fully protonated and fully deprotonated

3. Classes of A.A.: aliphatic, hydroxl or sulfur-containing, aromatic, basic, acid & their amide - Guanidinium & Imidazole: H leaves and molecule is less + charged as acid decreases & base increase

4. Peptides: Short polymers of two or more amino acids in which the carboxyl group of one AA is linked to the amino group of another AA - Peptide bond: chemical bond formed b/t the carboxyl group of one AA and the amino group of another AA - peptide bond is PLANAR w/ double bond character - Tetrapeptides: 4 or more amino acids joined by peptide bonds - polyampholytic behavior of a tetrapeptide -( KNOW THIS DIAGRAM - ALSO KNOW PEPTIDE RESONANCE! - Torsion angle: dihedral angle; measure of rotation around a bond; defined by 4 atoms around measured bond - RAMACHANDRAN PLOT - represents areas of steric exclusion in the polypeptide chain

5. Polypeptides: A long continuous, unbranched chain of peptides

2. secondary structure - intermediate state a. Beta-strand:

3. tertiary structure defines the function of the protein 4. quaternary structure - more than one protein coming together