Biochemistry Chapter 2: Amino Acids and Proteins Flashcards
arginine (R) ARG
Asparagine (N) ASN
Average weight for an amino acid residue
110 Da or 110 Da
1 AMU = ___ Da
1 AMU = 1 Da
Amino acids that can be phosphorylated
Serine (Ser, S) – The most commonly phosphorylated amino acid.
Threonine (Thr, T) – Also frequently phosphorylated, often alongside serine.
Tyrosine (Tyr, Y) – Less common but crucial in signaling pathways (e.g., receptor tyrosine kinases).
catecholamines
neurotransmitters derived from tyrosine that include dopamine and norepinephrine.
D
asparatic acid
what would a reducing agent do to an amino acid?
Disrupt disulfide bridges
Amino Acids with amide group
Asparagine and glutamine
Amino acids with additional amino groups
Lysine, Arginine and histidine
Protein secondary structure is characterized by the pattern of hydrogen bonds between:
backbone amide protons and carbonyl oxygens.
Secondary structure is NOT stabilized by side chain interactions, only tertiary & quaternary structure are stabilized by side chain interactions.
Histidine contains what kind of ring
imidazole ring
Histidine (His) is what kind of AA
Polar and weakly basic (because of nitrogen containing ring)
Q Amino Acid
Glutamine, Gln polar, uncharged amino acid
Difference between methonine and cysteine
methonine = has a methyl at the end (S is not exposed)
Cysteine = terminal SH group and can form disulfide bridges
Ubiquitinated
refers to a protein that has been tagged with ubiquitin, a small regulatory protein involved in protein degradation, signaling, and trafficking within the cell.
Ubiquitin vs ubiquinone
Ubiquitin is a protein that regulates other proteins in the body (Tags proteins for degradation), while ubiquinone is a form of coenzyme Q10 that helps generate energy in cells
R vs N amino acids
R = Arginine is positively charged at physiological pH and plays a role in electrostatic interactions and protein stability.
N = Asparagine is polar but uncharged, often involved in hydrogen bonding and protein folding.
D vs E amino acids
D = aspartic acid
E = glutamic acid
At physiological pH (~7.0), the positively charged amino acids are:
✅ Histidine (H)
✅ Lysine (K)
✅ Arginine (R)
At physiological pH (~7.0), the positively charged amino acids are:
✅ Histidine (H)
✅ Lysine (K)
✅ Arginine (R)
at physiological pH (~7.0), the only negatively charged amino acids are:
✅ Aspartate (D)
✅ Glutamate (E)
at physiological pH (~7.0), the only negatively charged amino acids are:
✅ Aspartate (D)
✅ Glutamate (E)
What Happens in Disulfide Bond Reduction
To break a disulfide (-S-S-) bond, we must reduce it back to two free thiols (-SH).
This means we need a reducing agent to donate electrons.
Uncharged polar Amino Acids
Serine (Ser, S) – contains a hydroxyl (-OH) group
Threonine (Thr, T) – contains a hydroxyl (-OH) group
Asparagine (Asn, N) – contains an amide (-CONH2) group
Glutamine (Gln, Q) – contains an amide (-CONH2) group
Cysteine (Cys, C) – contains a sulfhydryl (-SH) group (important in disulfide bonds)
salt bridge
is an electrostatic interaction between oppositely charged amino acid side chains (e.g., acidic and basic residues) that helps stabilize protein structure or protein-ligand binding.
Tryptophan is a recrusor to what NT
Serotonin
primary covalent interactions within and between proteins
Disulfide Bonds (Cysteine - Most Common)
Serine vs threonine vs tyrosine
All polar AAs with OH group
When two amino acids are joined via a peptide bond, what is the mass of the byproduct of this reaction? (Note: Assume that the amino acids were not modified by protecting groups.)
When a peptide bond forms between two amino acids, there is a loss of water (18 amu).
amu vs g/mol
AMU describes the mass of a single atom/molecule, while g/mol describes the mass of one mole of those atoms/molecules, but their numerical values are the same.
6 because 3! = 6
Are proline kinks found in alpha helices or beta sheets
How many amino acids per turn in an alpha helix?
3.6
types of turns in secondary structure of proteins and where the hydrogen bonds are
A γ-turn: i and i + 2
A β-turn: i and i + 3
α-turn i and i + 4
A π-turn: i and i + 5
