week 4 - amino acids & proteins

• Amino acids

  • Every amino acid has an amine group (NH2), a carboxyl group (COOH), and an R group (side chain) bonded to a central carbon atom.
  • alpha carbon: the central carbon, connecting the 3 groups
• peptide bonds

  • bond formed when 2 amino acids form
  • specifically the C - N bond

  
• amino acid properties

  • contains: acidic (-COOH) group & basic (-NH2) group
  • at certain pH levels, these amino acids can act as SALTS
  • salts have: high melting points, water solubility
  • zwitterion: a neutral ion

  A) zwitterion

  
• chirality - D&L

  • All naturally occurring amino acids are in the L -form
  • unlike sugars, where only "D - form" is natural

  
• amino acids facts

  • out of the 20 amino acids, 9 are essential to humans (we don't produce in body, must consume in diet)
  • Each amino acid has a three - letter code
  • proline is the only amino acid without separate groups on alpha-carbon (ie. its amine group is part of a ring)

  A) proline

  
• non polar amino acids

  • 9 of them
  • polarity depends on the polarity of side chain

  A) alanine

  B) glycine

  C) valine

  D) leucine

  E) isoleucine

  F) phenylalanine

  
• polar amino acids

  • 6 of them

  A) asparagine

  B) cysteine

  C) glutamine

  D) serine

  
• Acidic and basic amino acids

  • 5 of them (2 acidic, 3 basic)

  A) aspartic

  B) glutamic

  C) histidine

  D) lysine

  E) arginine

  
• Acid-Base Properties

  • In acidic solution, zwitterions ACCEPT a proton to form a carboxyl group (overall +1 charge)
  • In basic solution, zwitterions DONATE a proton to form an amine group (overall -1 charge)

  A) acidic

  B) basic

  
• pKa of amino acids

  • the lower the pKa, the stronger the acid
  • the higher the pKa, the weaker the acid
  • these numbers are used to calculate the Isoelectric point (pl)

  
• isoelectric point (pI)

  • the pH where an amino acid has equal amounts of positive and negative charges (ie. neutral charge)
  • where the zwitterion occurs (not always at 7 pH)
  • the pl for every amino acid is different due to the different side chains
  • calculation: the avg pKa values

  
• titration curve for amino acids

  • isoelectric point is at pH of 6.06
  • acidic: protonated
  • basic: deprotonated

  
• Electrophoresis

  • process which separates amino acids & proteins
  • molecules at their isoelectric points don't move

  1. mark sample in middle of paper
  2. submerge the ends of paper in buffer solution (with electrodes in the solution too, connected to power supply)
  3. negatively charged particles move toward the anode (+)
  4. positively charged particles move toward the cathode (-)
  5. dry the paper

  A) +

  B) buffer

  C) -

  
• definitions

  • peptide: a short polymer of amino acids
  • Polypeptide: A macromolecule containing many amino acids
  • Protein: a macromolecule of 5000 g/mol or greater, consisting of one or more polypeptide chains
• primary structure

  • the sequence in which amino acids are connected
  • it's the "backbone" of the protein

  A) primary

  B) tertiary

  
• primary structure continued

  • 2 amino acids can form 2 different dipeptides, X—Y and Y—X
  • how to write sequence of amino acids:
  • aminoterminal amino acid (N-terminal) on the LEFT
  • carboxyl-terminal amino acid (C-terminal) on the RIGHT

  A) N

  B) C

  
• resonance - primary structure

  • N has a lone pair of e's which can be pushed off and form a pi bond (making it C = N)
  • in the C = O group, the pi bond will be pushed to the O atom, making it C - O with 6 valence electrons (more -ve)
  • this results in a +ve N atom and -ve O atom which are resonance structures.
  • the C=N now has no rotation due to double bond

  
• resonance - primary structure

  • N has a lone pair of e's which can be pushed off and form a pi bond (making it C = N)
  • in the C = O group, the pi bond will be pushed to the O atom, making it C - O with 6 valence electrons (more -ve)
  • this results in a +ve N atom and -ve O atom which are resonance structures.
  • the C=N now has no rotation due to double bond (flat molecule)

  
• structures of proteins

  • Primary: the sequence of amino acids in a protein chain.
  • Secondary: the repeating arrangement of adjacent segments of protein chains (helix & beta)
  • Tertiary: the overall 3D shape from the bending and folding of the protein chain.
  • Quaternary: the overall structure of proteins composed of more than one polypeptide.

  A) quarternary

  
• secondary structure - alpha helix

  • R groups (side chain) point outwards
  • H-bonds form between the C=(O) and N-(H), creating helix structure
  • 3.6 amino acids per turn of helix

  A) R group

  B) oxygen

  C) hydrogen

  
• secondary structure - beta sheets

  • R groups on each chain alternate above and below the sheet (shown in image)
  • H-bonds form between the C=O and N-H of same chain
  • Each peptide bond is planar, and α-carbons are trans to each other

  
• Tertiary structure

  • types of bonds: disulfide, H-bonds, ionic, dipole-dipole, ion-dipole, dispersion
  • disulfide link: formed between 2 "-SH" groups through oxidation and reversed through reduction

  A) oxidation

  B) reduction

  
• quarternary structure

  • made from 2 or more polypeptides
  • eg Hemoglobin consists of 4 polypeptide chains, 2x a-chains and 2x b-chains held by dispersion forces
  • a-chain has 141 amino acids\, b-chain has 146

  A) heme

  B) hemoglobin