Ch 1 - Amino Acids, Peptides, and Proteins Flashcards
What are the 4 groups attached to a central (alpha) carbon in an amino acid?
- an amino group (-NH2)
- a carboxylic acid group (-COOH)
- a hydrogen atom
- an R group (determines chemistry/function of AA)
What is the stereochemistry for the alpha carbon?
- L is for all chiral (4 different groups attached) amino acids in eukaryotes (all except cysteine have S configuration)
- all amino acids are chiral except glycine, which has a hydrogen atom as its R group
- D amino acids can exist in prokaryotes
Which side chains are non polar and aromatic?
glycine, (CH2) - Gly (G) alanine, (CH3) - Ala (A) valine, (CHCH3CH3) - Val (V) leucine, (CH2CHCH3CH3) - Leu (L) isoleucine, (CHCH3CH2CH3) - Ile (I) methionine, (CH2CH2SCH3) - Met (M) proline (pentagon, NH) - Pro (P)
Which side chains are aromatic?
tryptophan, - Trp (W)
phenylalanine, - Phe (F)
tyrosine - Tyr (Y)
Which side chains are polar?
serine, - Ser (S) threonine, Thr (T) asparagine, Asn (N) glutamine, - Glu (E) cysteine Cys (C)
Which side chains are negatively charged (acidic)?
aspartate, - Asp (D)
glutamate - Gln (E)
Which side chains are positively charged (basic)?
lysine, - Lys (K)
arginie, - Arg (R)
histidine - His (H)
What determines whether amino acids are hydrophobic or hydrophilic?
- long alkyl chain: hydrophobic
- with charges: hydrophilic
Amphoteric?
- can accept or donate protons
- ability of amino acids
pKa?
- the pH at which half of the species are deprotonated
[HA] - [A-]
How does pH level affect amino acids?
- at low (acidic), fully protonated
- at pH near the pI of the amino acid, neutral zwitterion
- at high (basic), fully deprotonated
Isoelectric point?
- pI
- without a charged side chain can be calculated by averaging the two pKa levels
How can amino acids be titrated?
- the titration curve is nearly flat at the pKa values of the amino acid
- the titration curve is nearly vertical at the pI of the amino acid
How is pI calculated in amino acids with charged side chains?
- they have an additional pKa value and their pI is calculated by averaging the 2 pKa values that correspond to the protonation and deprotonation of the zwitterion
- aa without charged side chains: pI around 6
- acidic aa: pI < 6
- basic aa: pI > 6
What is the difference between depeptides, tripeptides, oligopeptides, and polypeptides?
- di: have 2 aa residues
- tri: have 3 aa residues
- oligo: few aa residues (< 20)
- poly: many aa resides (>20)
What kind of reaction is forming a peptide bond?
- condensation or dehydration reaction (releasing one molecule of water)
- the nucleophilic amino group of one aa attacks the electrophilic carbonyl group of another amino acid
Why are amide bonds rigid?
because of resonance
What kind of reaction is breaking a peptide bond?
hydrolysis
Primary structure?
the linear sequence of aa in a peptide and is stabilized by peptide bonds
Secondary structure?
the local structure of neighboring amino acids and is stabilized by H-bonding between amino groups and nonadjacent carboxyl groups
What are the types of secondary structures?
- alpha helices: clockwise coils around a central axis
- beta pleated sheets: rippled strands that can be parallel or antiparallel
How can Proline interrupt secondary structures?
because of its rigid cycle structure
Tertiary structure?
- 3D shape of a single polypeptide chain, and is stabilized by hydrophobic interactions, acid-base interactions, H bonding, and disulfide bonds
Hydrophobic interactions?
- push hydrophobic R groups to the interior of a protein, which increases entropy of the surrounding water molecules and creates a negative Gibbs free energy
