Chapter 1: Amino Acids, Peptides, and Proteins Flashcards
What are the two functional groups contained in amino acids?
- Amino group (NH2)
- Carboxyl group (COOH)
What is attached to the alpha carbon? (4)
- Amino group (NH2)
- Carboxyl group (COOH)
- Hydrogen
- Side chain (R group)
Do amino acids need to have both the amino and carboxyl groups bonded to the same carbon?
No
What are proteinogenic amino acids?
The 20 amino acids encoded by the human genetic code
Which amino acid is the only achiral one?
Glycine
Are all amino acids optically active?
Yes, except glycine
Are amino acids used in eukaryotes L or R?
L-amino acids
Which amino acids have an S absolute configuration? Which has an R configuration?
S: almost all chiral amino acids
R: cysteine
Which amino acids make up the nonpolar, nonaromatic side chains? (7)
Glycine, alanine, valine, leucine, isolucine, methionine, proline
Which amino acid is a cyclic amino acid? How many members does its ring have?
- Proline
- 5-membered ring
Which amino acids make up the aromatic side chains? (3)
Phenylalanine, tryptophan, tyrosine
Which amino acids contain an OH group?
Tyrosine, serine, threonine
Which amino acids make up the polar side chains? (5)
Serine, threonine, asparagine, glutamine, cysteine
In which amino acids do amide nitrogens NOT gain or lose protons with changes in pH?
Asparagine and glutamine
Which amino acid has a thiol group? What is a thiol group?
- SH
- Cysteine
Which amino acids make up the negatively charged (acidic) side chains?
Aspartic acid (aspartate) and glutamic acid (glutamate)
What is physiological pH?
7.4
What is the difference between aspartate and aspartic acid?
Aspartate is the deprotonated form of aspartic acid
Which amino acids make up the positively charged (basic) side chains?
Lysine, arginine, histidine
Which amino acid has an imidazole ring?
Histidine
When is histidine protonated?
When pH < pKa (around 6), the nitrogen atom can become protonated
Classifying amino acids as hydrophobic and hydrophilic is complex. Which amino acids are definitely hydrophobic? Where would they be found?
- Long alkyl side chains: alanine, isoleucine, leucine, valine, and phenylalanine
- Found in the interior of proteins
Classifying amino acids as hydrophobic and hydrophilic is complex. Which amino acids are definitely hydrophilic? Where would they be found?
- Charged side chains
- Amides: asparagine and glutamine
- Found in the surface of proteins, in contact with water
Define amphoteric species. Give an example.
They can accept or donate protons (ex: amino acids)
How do ionizable groups tend to react under acidic conditions? What about under basic conditions?
Acidic: gain protons (protonation)
Basic: lose protons (deprotonation)
What is the pKa? What is the concentration of HA equivalent to?
The pH at which half of the species is deprotonated
HA) = (A-
If the pH is below the pKa, what will happen? If the pH is above the pKa, what will happen?
pH < pKa: protonation
pH > pKa: deprotonation
What is pKa1? What is pKa2?
pKa1: pKa for the carboxyl group
pKa2: pKa for the amino group
How many pKas are there for amino acids?
- 2 if there is no ionizable side chain
- 3 if there is an ionizable side chain
What is the overall charge of amino acids under acidic conditions (assuming no ionizable side chains)?
+1 (fully protonated)
What is the overall charge of amino acids under basic conditions (assuming no ionizable side chains)?
-1 (fully deprotonated)
How is the amino acid when the pH is near the pI of the amino acid?
Neutral zwitterion
Define zwitterions. What are they also called?
- Dipolar ions
- Has both a positive and negative charge
What is the equation to calculate the pI of a neutral amino acid?
(pKa (NH3+ group) + pKa (COOH group)) / 2
What is the pH equal to when the concentrations of a fully protonated amino acids are equal to its zwitterion? How many equivalents of base needed to be added?
- pH = pKa1
- 0.5 equivalents of base
What is the optimal buffering point? What is the buffering region?
pH = pKa
pKa +/- 1
What is the isoelectric point (pI)? How many equivalents of base needed to be added to reach this point?
- The pH at which the molecule is electrically neutral
- 1 equivalent of base
What is the pH equal to when the concentration of the zwitterion form equals the concentration of the fully deprotonated form? How many equivalents of base needed to be added?
- pH = pKa2
- 1.5 equivalents of base
How much base equivalents need to be added to fully protonate an amino acid?
2 equivalents of base
How can you calculate the pI of an acidic amino acid?
(pKa (R group) + pKa (COOH group)) / 2
How can you calculate the pI of a basic amino acid?
(pKa (NH3+ group) + pKa (R group)) / 2
How do the pI values compare between acidic side chains and basic side chains?
Acidic side chains: below 6
Basic side chains: above 6
How many resides are contained in oligopeptides? What about polypeptides?
Oligopeptides: 3-20
Polypeptides: more than 20
A peptide bond forms between the ____ group of one amino acid and the ____ group of another amino acid.
–COO- and NH3+
What kind of reaction drives peptide bond formation?
Condensation/Dehydration: loss of water
How is a peptide bond formed?
- Electrophilic carbonyl carbon on AA1 is attacked by the nucleophilic amino group on AA2
- After, the hydroxyl group of the carboxylic acid is kicked off
- Result: formation of a peptide bond
Why do amide groups exhibit resonance?
Delocalizable pi electrons in the carbonyl and in the lone pair on the amino nitrogen
What does the resonance of amide groups cause?
The C-N bond in the amide has a partial bond character
In what order are peptides drawn in?
In the same order that it is synthesized by ribosomes: from the N-terminus to the C-terminus
What is the result of the partial bond character in the C-N bond of a peptide?
Rotation of the protein backbone around its C-N amide bond is restricted
Give examples of hydrolytic enzymes.
Trypsin and chymotrypsin
Where does trypsin cleave?
At the carboxyl end of arginine and lysine
Where does chymotrypsin cleave?
At the carboxyl end of phenylalanine, tryptophan, and tyrosine
How do hydrolytic enzymes break apart the amide bond?
By adding a hydrogen atom to the amide nitrogen and an OH group to the carbonyl carbon
Define primary structure.
Linear sequence of amino acids in chain
Define secondary structure.
Local structure determined by nearby amino acids
Define tertiary structure.
Three-dimensional shape of protein
Define quaternary structure.
Interaction between separate subunits of a multisubunit protein
What is the stabilizing bond of primary structure?
Peptide (amide) bonds
What is the stabilizing bond of secondary structure?
Hydrogen bonds
What is the stabilizing bond of tertiary and quaternary structures?
van der Waals forces, hydrogen bonds, ionic bonds, covalent bonds
What are the subtypes of secondary structure? (2)
- a-helix
- B-pleated sheet
What are the subtypes of tertiary structure? (3)
- Hydrophobic interactions
- Acid-base/salt bridges
- Disulfide links
How can the primary structure of a protein be determined in a laboratory setting?
Through sequencing
Do the peptide chains in an a-helix coil clockwise or counter clockwise?
Clockwise
The a-helix is stabilized by intramolecular hydrogen bonds between a ________ atom and an ______ atom _ residues down the chain
- Carbonyl oxygen
- Amide hydrogen
- 4 residues
The a-helix is an important component in which structure?
Keratin
Where is proline found/not found in secondary structures?
Found: turns between chains of a B-pleated sheet
Not found: middle of pleated sheets or a-helices
* Creates kinks in a-helices and turns in B-sheets
_____, the primary protein component of silk fibres, is composed of B-pleated sheets
Fibroin
How can proteins be broadly divided?
Fibrous proteins (collagen) and globular proteins (myoglobin)
How do disulfide bonds form?
When two cysteine molecules become oxidized to form cystine
What do disulfide bonds create in the protein chain?
Loops
What does forming a disulfide bond require?
The loss of two protons and two electrons (oxidation)
What are molten globules?
The intermediate state between secondary and tertiary structures
What is denaturation?
The loss of a protein’s tertiary structure, which makes it lose its function
What explains hydrophobic folding?
Increases entropy by allowing water molecules on the surface of the protein to have more possible positions and configurations (positive deltaS, deltaG <0, stabilizes the protein)
Do all proteins have tertiary structure? What about quaternary structure?
Tertiary: yes
Quaternary: no
What are the 4 roles of quaternary structures?
1) Be more stable (reducing the surface area of the protein complex)
2) Reduce the amount of DNA needed to encode the protein complex
3) Bring catalytic sites together
4) Induce cooperativity or allosteric effects
What are conjugated proteins?
Proteins with covalently attached molecules
What is the attached molecule on a conjugated protein called? What can it be?
- Prosthetic group
- Metal ion, vitamin, lipid, carbohydrate, or nucleic acid
What is the prosthetic group in hemoglobin’s subunits?
Heme (contains an iron atom in its core)
What denatures proteins? (2)
- Heat
- Solutes
Why does heat denature proteins?
By increasing their average kinetic energy, thus disrupting hydrophobic interactions
Why do solutes denature proteins?
By disrupting elements of secondary, tertiary, and quaternary structure
How many distinct tripeptides can be formed from three amino acids?
3 x 2 x 1 = 6
Which amino acids are likely to be found in a transmembrane portion of an a-helix?
Hydrophobic amino acids
Which two amino acids have chiral carbons in their side chains?
Threonine and isoleucine
Which amino acid is likely to be found in high concentrations in collagen?
Glycine
