Ch 1 - amino acids

Question 1

proteinogenic amino acids

Answer 1

• 20 alpha amino acids that are coded for by the human genome
• alpha - amino group is bound to the alpha carbon of the carboxylic acid
  
  • R group or side chain also bound to alpha group

Question 2

stereochemistry

Answer 2

• all amino acids are chiral except glycine
  
  • optically active because they are chiral
• L amino acids in eukaryotes
  
  • amino group on left side of fischer projection
  • S configuration almost always
    
    • except cysteine, which is an L amino acid with an R configuration
• D amino acids exist in nature
  
  • amino group on right side of fischer

Question 3

nonpolar, nonaromatic side chains

Answer 3

• glycine, alanine, valine, leucine, isoleucine, proline, methionine
• methionine has a methyl group attached so its nonpolar
• proline - cyclic amino acid
  
  • amino nitrogen as part of the ring
  • effects secondary protein structure due to lack of flexibility

Question 4

aromatic side chains

Answer 4

• tryptophan - doble ring with N
• phenylalanine
• tyrosine - phenylalanine with -OH
  
  • relatively polar

Question 5

Polar, nonaromatic side chains

Answer 5

• serine and threonine -OH
• asparagine and glutamine -amide
  
  • do not gain or lose protons with pH change
• cysteine -thiol (-SH)
  
  • prone to oxidation

Question 6

negative charge side chains

Answer 6

• aspartic and glutamic acid
• aspartate is deprotonated aspartic acid
• glutamate is deprotonated gultamic acid
• carboxylate groups

Question 7

positively charged side chains

Answer 7

• lysine - terminal primary amine
• arginine - 3 N terminal group, positive charge over all 3 N
• histidine - imidazole (aromatic with 2 N)
  
  • positive charge when both N are protonated, below pH 6

Question 8

Hydrophobic/philic amino acids

Answer 8

• hydrophobic - interior of proteins, alkyl chains
  
  • alanine, isoleucine, leucine, valine, phenyalanine
• hydrophilic - surface amino acids, charged
  
  • histidine, arginine, lysine, glutamate, aspartate, asparagine, glutamine
• neither
  
  • cysteine, threonine, serine, tyrosine, tryptophan, proline, methionine, glycine

Question 9

Amino acid mutation shorthand

Answer 9

E6V

sixth amino acid that was glutamic acid has been replaced by valine

Question 10

amphoteric species

Answer 10

• can accept or donate a proton
• protonated at low pH and deprotonated at high pH
• at pka it is half protonated and half deprotonated
• first pka is around 2 for the carboxyl group
• second pka around 9 or 10 for amino group
• third pka for ionizable R group

Question 11

zwitterions

Answer 11

electrically neutral

dipolar ions

• positive at lower pH
• negative at higher pH
• isoelectric point (pI)
  
  • electrically neutral
  • determine by averaging the 2 pka values
  • around 6 for nonionizable amino acids
  • titration curve vertical at this point

Question 12

ionizable side chains, titration

Answer 12

• acidic side chains have low pI
• basic side chains have high pI
• determine pI by averaging 2 pkas that surround the neurtral species
• good buffer around the pka, horizontal titration curve

Question 13

peptides

Answer 13

• made of amino acids called residues
• dipeptides
• tripeptides
• oligopeptide - up to 20
• polypeptides - more than 20
• joined by peptide bonds
  
  • between carboxyl and amino groups
• drawn N to C terminus

Question 14

peptide bond formation

Answer 14

• electrophilic carbonyl carbon is attacked by the nucleophilic amino group
• hydroxyl group leaves
• condensation or dehydration reaction - loss of water
• partial double bond character due to pi electrons in carbonyl and lone pair on N
  
  • resonance
  • limited rotation and more rigid

Question 15

peptide hydrolysis

Answer 15

• hydrolytic enzymes
• break amide bond by affing H to N and OH to C

Question 16

Primary structure

Answer 16

• linear arrangement of amino acids, sequence
• N to C terminus
• stabilized by peptide bonds
• primary structure is all that is required for folding of protein
  
  • other structures are most energetically favorable for the environment
• can be determined using sequencing

Question 17

Secondary structure

Answer 17

• intramolecular hydrogen bonding to form alpha helices and beta pleated sheets
• local structure of neighboring amino acids

Question 18

alpha helix

Answer 18

• rod like
• peptide chain coils clockwise
• H bond between carbonyl O and amide H that are 4 residues apart
• side chains point away from core
• important in structure of keratin
  
  • hair, fingernails, skin
• proline typically only found in helices that cross the cell membrane
  
  • found as residue that starts the helix or
  • cyclic structure causes a kink

Question 19

Beta pleated sheets

Answer 19

• parallel or antiparallel
• chains form rows next to each other
• H bonds between carbonyl O on one chain and amide H of other chain
• pleated shape for more H bonds
• R groups above and below the plane of the sheet
• important for fibrin - silk fibers
• proline common in turns between chains
  
  • uncommon in the chain due to kink

Question 20

overall protein shape

Answer 20

• fibrous - sheet or long strand
  
  • collagen
• globular - sphere
  
  • myoglobin
• due to 3 and 4 structure

Question 21

Tertiary structure

Answer 21

• 3D shape
• determined by hydrophobic and hydrophilic interactions between R groups
• hydrophobic interior - N-H and C-O of those amino acids form electrostatic interactions and hydrogen bonds that stabilize protein
• hydrophobic not found on surface
• salt bridges between charged R groups
• disuldife bonds - between two cysteine, oxidize to become cystine
  
  • create loops in the chain
  • determines hair curliness
  • requires oxidation

Question 22

Protein folding

Answer 22

• primary structure than secondary structure than hydrophobic interactions and H bonds cause protein to collapse into 3D shape
• molten globules - intermediate shapes
• rapid process
• denaturation - unfold and lose function

Question 23

salvation layer

Answer 23

• solvent forms salvation layer around a solute
• nonpolar side chains disrupt hydrogen bonding and rearrangement occurs to maximize H bonding
  
  • rearrangement leads to structure that has more order and less options
    
    • increases order and is unfavorable
• hydrophilic side chains can form H bonds with water and the entropy increases
  
  • favorable and maximum stability
  • more conformational states and therefore more disorder
  • delta S > 0

Question 24

Quaternary Structure

Answer 24

• only for proteins with more than one polypeptide
• aggregate of smaller peptides or subunits
• can be more stable by reducing surface area
• reduce DNA needed to code for complex
• bring catalytic sites closer
• induce allosteric effects or cooperativity - one subunit changes and that changes the activity of other subunits

Question 25

conjugated proteins

Answer 25

• get function from prosthetic groups that are covalently attached
  
  • organic molecules, vitamins, metal ions
• lipoproteins, glycoproteins (attached to carb), nucleoproteins (attached to nucleic acid)
• can direct protein to certain location
• major role in determining function of protein

Question 26

denaturation

Answer 26

• protein loses 3D shape
• often irreversible
• cannot catalyze reactions
• heat -
  
  • increase kinetic energy and overcome hydrophobic interactions
• solutes -
  
  • interfere with forces that hold proteins together
  • break disulfide bonds - reduce cystine to cysteine
  • overcome H bonds in secondary structures