Biochemistry Exam I Study Guide

Biochemistry Exam I Study Guide

CHEMISTRY REVIEW

• Chemical Bonding

• Electrovalent or Ionic Bonds

• Valence electrons are transferred  from atom to another
• Forms charged atoms (ions)

• Atom that loses electrons becomes a cation (+ positively charged)
• Atom that gains electrons becomes an anion (negatively charged)

• NaCl

• Na+ has 1 valence electron
• Cl- has 7 valence electrons
• Na’s valence electron is transferred to Cl to complete octet and becomes cation; Cl = anion

• Bonds are formed by attraction on + and – charges
• Weaker than covalent bonding
• Bonds dissociate when dissolved in water (b/c water is a polar solvent; “like dissolves like”)

• Covalent Bonds

• Bonds that are formed when atoms share valence electrons
• Can be polar or nonpolar

• Nonpolar

• Share electrons equally
• i.e. H2 or O2

• Polar

• Share electrons unequally
• Creates dipole – have + and - polarity
• Electrons are pulled toward the more electronegative atom
• i.e. H2O

• Coordinate Covalent

• Bond formed when one atom provides both electrons in a shared pair
• i.e. NH3 has a lone pair of electrons that can partially contribute to make another bond

• Hydrogen Bonds

• When H forms polar bond with another atom it takes on a slight + charge (dipole), which makes it attracted to any nearby negatively charged atoms
• Forms between adjacent H2Os
• All life is due to Hydrogen bonding

• Water as a solvent

• Dissolves polar compounds due to its polar activity
• Amphipathic – chemical compound possessing both hydrophilic (lipophobic) and hydrophobic (lipophilic) properties

• Hydrophilic/lipopobic compounds are dissolvable in water
• Hydrophobic/lipophilic compounds are not dissolvable in water

• Tonicity

• If a cell is placed in a hypertonic solution, the cell shrinks as water moves outside of the cell due to increased solute concentration outside the cell
• If a cell is placed in a hypotonic solution, the cell inflates and could potentially burst as water moves inside the cell due to the decreased solute concentration outside the cell
• If a cell is placed in an isotonic solution, water is moving in and out of the cell as equal rates and is considered to be in equilibrium

• Acids

• Compounds that release protons (H+) in a solution
• Proton “donors”
• Strong acids – acids that quickly and completely dissociate when placed in H2O

• HCl
• H2SO4
• H3PO4

• Weak acids – acids that dissociate slowly when placed in H2O

• ***regulators in changes of alkalinity/acidity in the human system***
• H2CO3 

• Bases

• Compounds that accepts protons (H+) or lowers H+ levels of a solution or releases hydroxyl ions (OH-)
• Proton “acceptors”
• Strong bases 

• NaOH
• Ca(OH)2

• Weak base

• NH4OH

• Buffers

• Solution composed of a weak acid and its conjugate base
• When small amounts of strong acids or bases are added to it, the pH only changes a little by combining with or releasing H+
• Important buffer systems (help regulate pH inside the body (pH = 7.4 ± 1.0))

• Hemoglobin buffer
• Bicarbonate buffer

• H2CO3  ⬄ H+ + HCO3-

weak acid             conj. Base

• Phosphate buffer
• Protein buffer

• Dissociation constant (Ka)

• Ka = [H+] [A-]        OR        Ka = [product]
             [HA]                                [reactant]
• pKa = -log Ka
  
  
• Henderson-Hasselbalch Equation:

• pH = pKa + log [A-]        OR         pH = pKa + log [proton acceptor]
                          [HA]                                      [proton donor]

• ***if [A-] = [HA], then pH = pKa (b/c log (1) = 0)***

• Functional Groups[pic 1]
• Oxidation/Reduction Reactions

• OIL RIG – “Oxidation is loss of electrons; Reduction is gain of electrons”
                          (or addition of oxygen)                   (or removal of oxygen)

• 1o alcohols are oxidized to aldehydes
• 2o alcohols are oxidized to ketones
• Aldehydes are oxidized to carboxylic acids
• Carboxylic acids are reduced to aldehydes
• Aldehydes/ketones are reduced to 1o/2o alcohols, respectively

• Other important chemical reactions

• Acid + Alcohol = Ester                    
• Acid + Sulfhydryl group = Thioester
• Acid + Amine = Amide
• Phosphoric Acid + Alcohol = Phosphoester

AMINO ACIDS

• General Structure

• zwitterionic (dipolar) form predominates at a neutral pH

[amino group carries slight (+) charge]

[carboxyl group carries slight (-) charge]

• can act as either

• an acid (proton donor)  and have negative charge
  OR
• a base (proton acceptor) and have a positive charge

• AMPHOTERIC: both acidic and basic

• standard amino acid has no net charge at pH=7 (if side chain R not polar)

• if R = acidic, net charge > 0
• if R = basic, net charge <0

• isoelectric pH (pI) – pH of a specific amino acid in which its net charge = 0

• if the charge of an amino acid is changed, the molecule can be activated or inactivated[pic 2]

• Main components:

• α-Carbon (chiral – central Carbon atom is bonded to four different groups)

• 1o amino group
• carboxyl group
• variable side chain (R)

• Stereoisomerism

• Levorotatory (L-) rotate light to the left
• Dextrorotatory (D-) rotate light to the right
• Only L-amino acids are used to make proteins in the human system

• Classification

• different chemical properties of amino acids are due to the presence of difference side chains or R-groups

• they can be:

• polar
• nonpolar
• aromatic
• positively charged (acidic)
• negatively charged (basic)

• both the amino and the carboxyl groups can ionize

• carboxyl group donates H+ more readily than the amino group

• R-groups of some amino acids can ionize
  
• Nonpolar, aliphatic R groups (neutral) - VPGMAIL

*glycine is the simplest amino acid; does not have a chiral center[pic 3]

*One H-atom of glycine is replaced by methyl group (CH3) to make alanine

*valine, leucine, and isoleucine are branched chain amino acids

[pic 4]

                Polar, Uncharged R-Groups GCAST[pic 5]

*serine, threonine, and tyrosine contain a hydroxyl (OH-) group as their side chain ~ important for attachment of phosphate group in cellular signaling