Amino Acids, Peptides, and Proteins Flashcards
What are the amino acids encoded in the genetic code called?
proteinogenic amino acids
Which amino acid is achiral?
glycine
Amino acids in eukaryotes are D or L?
L
Amino acids are all S/R except for ______?
S except for cysteine
Which two amino acids contain sulfur?
methionine and cysteine
Glycine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
nonpolar
neutral
nonaromatic
neither
Alanine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
nonpolar
neutral
nonaromatic
hydrophobic
Valine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
nonpolar
neutral
nonaromatic
hydrophobic
Leucine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
nonpolar
neutral
nonaromatic
hydrophobic
Isoleucine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
nonpolar
neutral
nonaromatic
hydrophobic
Methionine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
nonpolar
neutral
nonaromatic
neither
Proline Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
nonpolar
neutral
nonaromatic
neither
Tryptophan Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
nonpolar
neutral
aromatic
neither
Phenylalanine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
nonpolar
neutral
aromatic
hydrophobic
Tyrosine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
polar
neutral
aromatic
neither
Serine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
polar
neutral
nonaromatic
neither
Threonine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
polar
neutral
nonaromatic
neither
Asparagine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
polar
neutral
nonaromatic
neither
Glutamine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
polar
neutral
nonaromatic
neither
Cysteine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
polar
neutral
nonaromatic
neither
Aspartic Acid Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
polar
negative
nonaromatic
hydrophilic
Glutamic Acid Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
polar
negative
nonaromatic
hydrophilic
Lysine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
polar
positive
nonaromatic
hydrophilic
Arginine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
polar
positive
nonaromatic
hydrophilic
Histidine Polar/Nonpolar = Charge = Aromatic/Nonaromatic = Hydrophilic/Hydrophobic =
polar
positive
aromatic
hydrophilic
How many pKa values do amino acids have and what are they?
at least two
the first one is the deprotonation of the carboxyl group around 2
the second one is the deprotonation of the amino group around 9/10
At very acidic pH values, amino acids tend to be _____ charged.
positively
What is the isoelectric point?
the pH at which the molecule is electrically neutral
pI of a neutral amino acid
pKa amino group + pKa carboxylic acid / 2
pI of a acidic amino acid
pKa R group + pKa carboxylic acid / 2
pI of a basic amino acid
pKa amino group + pKa R group / 2
What is a peptide bond?
a specialized form of an amide bond, which form between the -COO- group of one amino acid and the NH3+ group of another amino acid
Peptides read from the _-terminus to the _-terminus.
N to C
How do hydrolytic enzymes hydrolyze peptides?
Break apart amide bond by adding a hydrogen atom to the amide nitrogen and an OH group to the carbonyl carbon
Where does trypsin cleave?
carboxyl end of arginine and lysine
Where does chymotrypsin cleave?
at the carboxyl end of phenylalanine, tryptophan and tyrosine
What is the primary structure of a protein?
the linear arrangement of amino acids coded in an organism’s DNA
What is the secondary structure of a protein?
the local structure of neighboring amino acids
What are two secondary structures?
alpha helix and beta sheets
Which bonds hold the secondary structure together?
hydrogen bonds
What is proline useful for?
found at the turns between beta sheets and start of alpha helix due to its kinking properties
What are fibrous proteins?
structures that resemble sheets or long strands
What are globular proteins?
structures that are spherical
What is tertiary structure?
three-dimensional shape
What determines the tertiary structure?
hydrophilic and hydrophobic interactions between the R groups
What are quaternary structures?
aggregate of smaller globular peptides (multiple polypeptides chains) that function as a protein
Four reasons for having quaternary structure?
(1) more stable by reducing the surface area of the protein complex
(2) reduce amount of DNA needed to encode the protein complex
(3) bring catalytic sites close together, allowing intermediates from one reaction to be directly shuttled to a second reaction
(4) Cooperativity/allosteric effects
What are conjugated proteins?
proteins with have covalently attached molecules known as prosthetic groups
What are lipoproteins?
proteins with lipid prosthetic groups
What are glycoproteins?
proteins with carbohydrate prosthetic groups
What are nucleoproteins?
proteins with nucleic acid prosthetic groups
What are prosthetic groups needed for?
- can direct protein to be delivered to a certain location
- affect activity of protein
Which amino acids have chiral carbons in their side chains?
serine and threonine
