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