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Biochemistry Exam I Study Guide

Autor:   •  July 24, 2017  •  Coursework  •  17,391 Words (70 Pages)  •  338 Views

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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

...

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