Lecture: Biochemistry
I. Inorganic Compounds
A. Water (H2O) - 60-80% of cells
1. heat capacity - ability to store lots of heat
2. heat of vaporization - lots of heat to evaporate
3. polarity/solvency - ability to dissolve reactants
I. salts and large macromolecules normally in solution
ii. ideal medium for cellular transport
4. reactivity - essential for many chemical reactions
I. hydrolysis - water added to break down molecules
glycogen + H2O ----> glucose + glucose + glucose + ...........
ii. dehydration - water removed to synthesize
glucose + glucose + glucose + ... ---> glycogen + H2O
B. Salts - cations (Na+) and anions (Cl-) other than H+/OH1. salts dissociate in the presence of water (solution)
2. called electrolytes because they are charged atoms
3. Examples of Important Salts in Body
I. Na+, Cl-, K+, Ca++ - membrane potential on cell
ii. Ca++ and PO4- - calcium phosphates for bone
iii. Fe++, Mg++, Zn+, Cu+ - blood and enzymes
4. Kidneys are essential for water and salt homeostasis
C. Acids and Bases - H+ donors and H+ acceptors
1. Acids - compounds that release H+ in solution and increase H+
i. HCl - hydrochloric acid released in stomach
HCl ---> H+ + Clii. HC2H3O2 - acetic acid in vinegar
2. Bases - compounds that receive H+ or produce OH- acceptors
i. hydroxides - release OH- (hydroxides ions)
NaOH (sodium hydroxide - lye)
MgOH (magnesium hydroxide - milk of magnesia)
NaOH ---> Na+ + OH-
OH- + H+ ---> H2O
ii. ammonia - nitrogenous waste --> urea (urine)
NH3 + H+ -----> NH4+
3. pH - a measure of H+ concentration in a solution
H2O <=====> H+ + OHI. 1 of 107 water molecules dissociate in pure H2O
ii. H+ concentration is 1/10,000,000 = 10-7
iii. pH = -log10[H+]
iv. pure water pH = -log10[10-7] = 7.0
<---------------------------------------------------------------->
1 2 3 4 5 6 7 8 9 10 11 12 13 14
ACIDIC
Neutral
BASIC
4. Neutralization - acid and base combine
HCl + NaOH ---> H2O + NaCl
5. Buffers - dampen the fluctuation of pH in the body
I. pH of blood serum = 7.35 to 7.45 (slightly basic)
ii. strong acids - completely dissociate (HCl)
weak acid - partial dissociate (carbonic acid)
iii. strong base - completely dissociate (NaOH)
weak base - partial dissociate (bicarbonate)
6. Carbonic Acid - Bicarbonate Buffer System
H2CO3 <===========> HCO3- + H+
H2CO3 <------------ HCO3- + H+
(H+ + Cl- <------- HCl)
ACID
BASE (NaOH ----> Na+ + OH-) H2CO3 -----> HCO3- Na+ + H+ + OH- (H2O)
I. acid condition - reaction goes to the left
ii. base condition - reaction goes to the right
II. Organic Compounds
A. Characteristics of Organic (Carbon containing) Compounds
1. Exceptions:
CO (carbon monoxide)
CO2 (carbon dioxide)
C (graphite and diamond)
2. carbon forms 4 covalent bonds (not ions)
3. carbon is relatively electroneutral (not e-neg)
4. carbon easily forms bonds with H, O, N
5. carbon can form single, double, and triple bonds
B. Carbohydrates (C - carbo; H - hydr; O - ates)
1. monosaccharide (one sugar) simple sugars
a. can exist in chain or ring form
b. 5-carbon sugars
i. ribose - in Ribose Nucleic Acid (RNA)
ii. deoxyribose - in Deoxyribose N A (DNA)
c. 6-carbon sugars
i. glucose - main monosaccharide in blood
ii. galactose - glucose isomer (OH changes)
iii. fructose - glucose isomer
2. disaccharide (two sugar) double sugars
a. results from dehydration sythesis of 2 monosacs
b. glucose - fructose = sucrose (table sugar)
glucose - glucose = maltose (malt sugar)
glucose - galactose = lactose (milk sugar)
3. polysaccharide (many sugar) chains of sugars
a. starch - long chains of glucose in plants
b. glycogen - long chains of glucose in animals
i. stored in liver and muscle cells
4. Functions of Carbohydrates
a. quick energy - glucose primary fuel to make ATP
b. energy storage - glycogen for storage purpose
c. structural - glycolipids for cell identity
C. Lipids (fats, phospholipids, steroids)
1. neutral fats (triglycerides) - common fats and oils
a. composed of glycerol and 3 fatty acid chains
i. non-polar fatty acid side chains make them insoluable in water
b. different fats = different fatty acid chains
c. saturated fats - all single bonds for carbons
i. generally solid at room temperature
d. unsaturated fats - one/more double bonds
ii. generally liquid at room temperature
e. functions - insulation, protection, and long term energy storage (more calories/gram)
2. Phospholipids
a. glycerol, 2 fatty acid chains, and phosphate
b. "tail" - non-polar fatty acids (hydrophobic)
c. "head" - polar phosphate group (hydrophilic)
d. major component of the plasma membrane of cell
3. Steroids
a. ring-like structure
b. cholesterol - precursor of all other steroids
i. easily dissolved in neutral fats
ii. essential to maintain membrane rigidity
c. other steroids derived from cholesterol
i. Vitamin D - sunlight; for bone growth
ii. sex hormones - estrogen, progesterone, testosterone
iii. other hormones - cortisol (stress signal) and aldosterone (salt/water balance)
D. Proteins
1. Molecular Structure of Proteins
a. 20 different amino acids (same in all life)
i. amino end (NH2)
ii. acid group (COOH)
iii. R-group unique for each amino acid
b. dehydration synthesis joins amino acids
i. called a peptide bond
ii. dipeptide - 2 amino acids
iii. tripeptide - 3 amino acids
iv. polypeptide - many amino acids
2. Levels of Protein Structure
a. Primary Structure
i. actual linear combination of amino acids
b. Secondary Structure
i. alpha-helix: coiling of the polypeptide
ii. beta-pleated sheet: chains side by side
c. Tertiary Structure
i. secondary structures form 3-D shape important for correct function
d. Quaternary Structure
i. two or more polypeptides together
ii. hemoglobin: 2 alpha and 2 beta polypeps
3. Functions of Proteins
Fibrous Proteins
a. Structural
i. collagen - bone, tendon, ligamnents
ii. keratin - hair, nails, skin
iii. elastin - trachea and joints
b. Movement
i. actin & myosin - muscle cells
ii. microtubules - cilia and flagella
Globular Proteins
a. Enzymes - Catalysis of Chemical Reactions
i. peroxidase - converts H2O2 to H2O
ii. amylase - breaks down starch to glucose
b. Transport
i. hemoglobin - binds and carries oxygen
ii. K+ Channel - allows K+ into a cell
c. pH Buffer
i. albumin - acid & base buffer in blood
d. Hormonal Function
i. insulin - regulates blood glucose level
ii. growth hormone - regulates human growth
e. Neurotransmitter
i. enkephalins - regulate pain in spinal cord
f. Immunity
i. antibodies - attach to foreign molecules
ii. complement proteins - enhance response
4. Enzymes and Enzyme Function
a. enzyme - a protein that catalyzes a reaction
i. increase the rate of a natural reaction
b. cofactor or coenzyme - essential for function
i. could be a metal like Fe, Cu, Zn
ii. many derived from Vitamins (like Vit B)
c. induced fit model - subtrate fits into enzyme
i. active site - area where substrate fits
ii. enzyme lowers activation energy threshold
d. sometimes enzymes must be activated to work
5. Denaturation of Proteins
a. disrupting delicated 3-D shape of the protein
i. excessive heat (fever)
ii. excessive pH (too acidic or too basic)
b. reversible - protein can reassume its shape
c. irreversible - protein is permanently damaged
i. cooking albumin in egg white
d. can disrupt active site and enzyme activity
E. Nucleic Acids (DNA & RNA)
1. nucleotide - basic unit forming the DNA & RNA chains
a. base - nitrogen containing ring structure
i. adenine (A)
ii. cytosine (C)
iii. guanine (G)
iv. thymine (T) {uracil (U) in RNA}
b. sugar - pentose (ribose RNA : deoxyribose DNA)
c. phosphate group
2. nucleotide attraction by Hydrogen Bonding of bases
a. A = T (A = U in RNA)
b. C = G
3. DNA forms a double helix
4. genetic code - sequence of nucleotides dictates sequence of amino acids for a protein
5. gene - a sequence of nucleotides of DNA molecule that codes for one protein
F. ATP as "Energy Currency"
1. glycogen and lipids = energy in savings bond ($5,000)
2. glucose = energy as a large check ($100)
3. ATP = energy that can actually be spent by cells ($1)
a. high energy phospate bonds
ATP <======> ADP + Pi + ENERGY
(Breaking bond releases useable energy)