NBME Biochemistry- Protein Structure and Function
what is an ionizable example of a hydrophilic amino acid?
-COOH of aspartate
the -OH of which 3 amino acids is important for regulation of enzyme activity?
-OH of serine, tyrosine, & threonine
How many and what type of amino acids are the building blocks of human/mammalian proteins?
20- alpha amino acids
what are the abbreviations for Alanine?
Ala = A
What are the nonessential amino acids?
Alanine Asparagine Aspartate Cysteine Glutamate Glutamine Glycine Proline Serine Tyrosine
Can make pyruvate
Alanine, Cysteine, Glycine, Serine, Threonine, Tryptophan
what is a common extracellular protein that is stabilized by disulfide bonds?
Albumin
what are the abbreviations for Arginine?
Arg = R
What are the basic amino acids?
Arginine Lysine Histidine
can make alpha keto glutarate
Arginine, Glutamate, Glutamine, Histadine, Proline
What are the abbreviations for asparagine?
Asn = N
What are the abbreviations for Aspartate?
Asp = D
Can make Oxalaoacetate
Aspartate, Asparagine
What is the abbreviation for aspartate or asparagine?
Asx = B
What are the abbreviations for cysteine?
Cys=C
What are the abbreviations for glutamine?
Gln= Q
What are the abbreviations for Glutamate?
Glu = E
what are the abbreviations for glutamate or glutamine?
Glx = Z
What are the abbreviations for Glycine?
Gly = G
What are the aliphatic amino acids?
Glycine Alanine Valine Leucine Isoleucine
What are the hydrophobic amino acids?
Glycine Alanine Valine Leucine Isoleucine Methionine Proline Phenylalanine Tryptophan
What are the abbreviations for Histidine?
His=H
what are the abbreviations for isoleucine?
Ile = I
Can make succinyl CoA
Isolecine, Methionine, Threonine, Valine
What are the Essential amino acids?
Isoleucine Leucine Lysine Methionine Phenylalanine Threonine Trytophan Valine Arginine Histidine
Can make Acetyl CoA
Isoleucine, Leucine, Tryptophan
All the amino acids found in proteins are in the L or D configuration?
L
What are the abbreviations for Leucine?
Leu = L
Can make Acetoacetyl CoA
Leucine, Lycine, Phenyalanine, Tryptophan, Tyrosine
what is the abbreviation for lysine?
Lys = K
which amino acid has an ε -amino group?
Lysine
What are the hydrophilic amino acids?
Lysine Arginine Aspartate Glutamate Asparagine Glutamine Tyrosine Serine Threonine Cysteine
what are the abbreviations for methionine?
Met = M
neutral polar example of a hydrophilic amino acid?
OH of serine
Essential amino acid mnemonics
PVT TIM HALL Any Help In Learning These Little Molecules Proves Truly Valuable Phenylalanine (Phe - F) Valine - (Val - V) Threonine - (Thr - T) Tryptophan (Trp- W) Isoleucine (Ile - I) Methionine (Met -M) Histidine (His - H) Arginine (Arg - R) Leucine (Leu - L) Lysine (Lys - K)
what are the abbreviations for phenylalanine?
Phe = F
Can make Fumarate
Phenylalanine, Tyrosine
What are the abbreviations for Proline?
Pro = P
Amino acid metabolism cofactors
Pyridoxal phosphate - transamination ractions Tetrahydrobiopterin (BH4) - ring hydroxylation reactions. Teyrahydrfolate (FH4) - one carbon metabolism
what are the abbreviations for serine?
Ser = S
What are the hydroxy amino acids?
Serine Threonine
which amino acids are nucleophiles?
Serine (-OH) Cysteine (-SH)
what is the term for the 20 amino acids coded for by DNA?
Standard amino acids
What are the abbreviations for threonine?
Thr = T
what are the abbreviations for Tryptophan?
Trp = W
what are the abbreviations for tyrosine?
Tyr = Y
what are the abbreviations for Valine?
Val = V
what are the branched chain amino acids?
Valine Leucine Isoleucine
what does an α-amino acid consist of?
a central carbon atoms called the α-carbon linked to an amino group, a carboxylic acid group, a hydrogen atom, a distinctive R group
what is cystine?
a dimer formed by the oxidation of the SH groups of 2 cysteines
what does cystine contain?
a disulfide bond
what is an amphoteric molecule?
a molecule that can act as either an acid or a base
separation of plasma proteins by electrophoresis is done at what pH?
a pH above the isoelectric pH, so the charge on proteins is negative
what is isoelectric focusing?
a specialized form of electrophoresis where proteins are separated on the basis of isoelectric pH
which amino acid has a guanido group?
arginine
What are the acidic amino acids and amides?
aspartic acid asparagine glutamic acid glutamine
how do carboxyl and amino groups of amino acids exist at physiologic pH?
at pH 7.4: carboxyl groups exist as COO- amino groups exist as NH3+
how does electrophoresis separate charged biomolecules?
based on the rate of migration in a charged electrical field
How are the standard amino acids incorporated into proteins?
by translation
What are the sulfur containing amino acids?
cysteine methionine
Ketogenic
essential: Leucine Lysine
is R-COOH a stronger or weaker acid than R-NH3+?
far stronger
Which is the smallest amino acid, the one found where peptides bend sharply?
glycine
which amino acid does not exhibit chirality?
glycine
which amino acid is optically inactive?
glycine
what is the equation used to analyze the titration curve of amino acids?
henderson-hasselbach equation pH=pKa + log ([A-]/[HA])
which amino acid has an imidazole group?
histidine
where are hydrophobic amino acids typically found in a polar environment?
in interior of proteins
What is special about the pka of the imidazole group of histidine?
it can be acid or base at neutral pH
What is an aliphatic example of a hydrophobic amino acid?
methyl group of alanine
what are zwitterions?
molecules that contain both positive and negative charges on them
what is the non-protein function of glutamate?
neurotransmitter
Glucogenic and Ketogenic
non essential: Tyrosine (Tyr - Y) essential: Isoleucine (Ile - I) Phenylalanine (Phe - F) Tryptophan (Trp - W)
Glucogenic only (13)
non-essential : Alanine - (Ala - A) Arginine - (Arg - R) Asparagine - (Asn - N) Aspartate - (Asp - D) Cysteine - (Cys - C) Glutamate (Glu - E) Glutamine (Gln - Q) Histidine (His - H) Proline (Pro - P) Serine (Ser - S) Essential: Methionine - (Met - M) Threonine - (Thr - T) Valine - (Val - V)
Where are hydrophobic amino acids typically found in a hydrophobic environment like the cell membrane
on the outside surface of the protein
DNA codes for how many amino acids?
only 20
what is an aromatic example of a hydrophobic amino acid?
phenyl group of phenylalanine
what are the aromatic amino acids?
phenylalanine Tyrosine tryptophan
what does the net charge on an amino acid depend on?
pka of its functional groups pH of the surrounding medium
What is the mechanism that creates non standard amino acid derivatives in human proteins?
post translational modifications
What is the non-protein function of Tyrosine?
precursor to thyroid hormones
what is the only amino acid with a secondary amino group?
proline
which amino acid is an IMINO acid?
proline
what are the special optical properties of tryptophan and tyrosine used for?
quantitative estimation of proteins if their trp and tyr content is known
what are the 2 major functions of charged R groups in basic and acidic amino acids?
stabilize protein conformations through salt bonds "charge relay systems" in catalysis and electron transport
What change in amino acids causes the pathology of sickle cell disease?
substitution of polar glutamate by non-polar valine in the beta-subunit of hemoglobin
which of the groups bound to the α-carbon of an amino acid is known as the side chain?
the R group
What is the net charge on an amino acid?
the algebraic sum of all the positively and negatively charged groups present
which side groups of amino acids can serve as sites of attachment for oligosaccharide chains in glycoproteins?
the amide group of asparagine, as well as the hydroxyl group of serine or threonine
what is the isoelectric species of an amino acid?
the form of the molecule that has an equal number of positive and negative charges and thus is electrically neutral
what does the unique geometry of proline contribute to?
the formation of the fibrous structure of collagen interruptions in the alpha-helices found in globular proteins
What is the isoelectric pH?
the pH midway between the pKa values on either side of isoelectric species
Which side groups of amino acids typically serve as a site of attachment for phosphate groups?
the polar hydroxyl groups of serine, threonine, and rarely tyrosine
in which direction does a protein move during electrophoresis?
the protein is negatively charged so it moves toward the positive electrode
which amino acid has an indole ring?
tryptophan
which amino acids contain aromatic rings whose pi electrons absorb ultraviolet light?
tryptophan tyrosine
are a-COOH and -NH3+ weak acids or weak bases?
weak acids
are -COO- and -NH2 weak acids or weak bases?
weak bases
are amino acids amphoteric molecules?
yes
are there other amino acids, and if so what is their function?
yes, they exist in free or combined states and can be non-protein associated amino acids and/or perform specialized functions
