Bring on the Biochemistry

Question 1

Dipolar Amino Acid (Zwitterion)

Answer 1

Amino acids exist as dipolar at neutral pH.
Amino group: protonated
Carbonyl group: ionized

Low pH: both groups protonated

Question 2

Non polar, hydrophobic amino acids

Answer 2

9 amino acids:

Glycine 
Alanine 
Valine
Leucine
Isoleucine
Phenylalanine 
Tryptophan 
Proline 
Methionine

Question 3

Polar uncharged, Neutral Amino Acids

Answer 3

6 amino acids, slightly hydrophilic

Cysteine 
Asparagine 
Threonine
Glutamine 
Tyrosine 
Serine

Question 4

Positively charged amino acids

Answer 4

3 amino acids, very hydrophilic

Lysine
Arginine
Histidine

Question 5

Negatively charged amino acid

Answer 5

2 amino acids

Aspartate
Glutamate

Question 6

Primary structure

Answer 6

Peptide bonds are very stable because of amide covalent bonds.

Resistant to hydrolysis

Question 7

Secondary structure

Answer 7

Alpha helix:

1. Regularly repeating patterns.
   - caused by hydrogen bonding between amino and carbonyl groups.
2. Coiled structures
3. 4 amino acids is closer than 2 amino acids in terms of hydrogen bonding
4. Right or left screwed

Beta pleated sheet and turn:

1. Can run in parallel or anti parallel
2. Forms due to competition between H bonds (steric clash) of alpha helix.

Question 8

Tertiary structure

Answer 8

1. Formed through interaction of side chains
2. Combinations of motifs
   - motifs are secondary structure found within tertiary structure
3. Hydrophobic portions fold within the core or found in interior.
4. Bonds: disulfide linkages and ionic bonds.

Solvation layer describes solvent surrounding protein; crucial for tertiary shape.

Question 9

Quarternary structure

Answer 9

1. Arrangement of multiple subunits ( multiple tertiary structures)
2. Held together by same type of bonds found in tertiary structure
3. Named according to number of subunits
   - dimer
   - trimer
   - tetramer

Question 10

Protein folding

Answer 10

Protein folding is protein self assembly=> amino acids develop secondary, tertiary or quaternary structures.

Native state is when protein fully folded.
- determined by amino acid sequence

Chaperones are proteins that stabilize folding and prevent aggregation.
- many are nonspecific.

Protein folding is a spontaneous reaction.

Question 11

DNA vs RNA

Answer 11

RNA: extra hydroxyl group
- extra OH results in less stability—> single helix, shorter strands, more susceptible to alkaline hydrolysis

DNA: absent OH group
- absent OH contributes to stability —> double helix; built to protect the nucleobases.

Question 12

Enzyme kinetics Michaelis- Menton Model

Answer 12

V= Vmax * [substrate]/ [substrate] + Km

V: rate of formation of the product
Vmax: reaction rate when enzyme saturated with substrate
Km: concentrations of substrate when reaction rate is half Vmax.

Question 13

Amino acids isomers

Answer 13

Exist as the L or D isomer

• Only L amino acids are used to make proteins
• almost all L amino acids have an absolute S configuration.

Question 14

Isoelectric point

Answer 14

Amino acid charge depends on pH

Isoelectric point (pI)pH at which net charge is 0

• below pI, protein is net + charged
• above pI, protein is net - charged