432 Exam 2

Between L and D amino acids, which is only found in proteins?

L amino acids

What amino acid is Ala?

Alanine

What amino acid is Arg?

Arginine

What amino acid is Asn?

Asparagine

What amino acid is Asp?

Aspartic acid

What amino acid is Cys?

Cysteine

What amino acid is Gln?

Glutamine

What amino acid is Glu?

Glutamic acid

What amino acid is Gly?

Glycine

What amino acid is His?

Histidine

What amino acid is Ile?

Isoleucine

What amino acid is Leu?

Leucine

What amino acid is Lys?

Lysine

What amino acid is Met?

Methionine

What amino acid is Phe?

Phenylalanine

What amino acid is Pro?

Proline

What amino acid is Ser?

Serine

What amino acid is Thr?

Threonine

What amino acid is Trp?

Tryptophan

What amino acid is Tyr?

Tyrosine

What amino acid is Val?

Valine

What amino acid is Asx?

Asparagine or aspartic acid

What amino acid is Glx?

Glutamine or glutamic acid

How is proline an exception to the typical amino acid structure?

It has a secondary amino group (not a second amino group); Nitrogen is bonded to both the alpha carbon and the side chain

What are the aromatic amino acids?

Phe, Tyr, Trp

What amino acids have aliphatic hydroxyl groups?

Ser, Thr

What amino acids have aliphatic side chains?

Val, Leu, Ile, Met

Which amino acid has cyclic structure?

Proline

Which amino acid has an indole?

Tryptophan

Which amino acids contain carboxamide

Asn, Gln

What is the difference between asparagine and glutamine?

Glutamine’s side chain is one methylene longer

Which amino acid can form disulfide bonds?

Cys

Between cys and ser, which is more reactive and why

Cys; -SH is more reactive than -OH

Which amino acids are basic?

Lys, Arg, His

What unique property does histidine have?

At physiological pH, it can bind or release protons

What amino acids have carboxylate side chains?

Asp and Glu

Is glycine chiral?

No, has 2 hydrogens

What amino acids contain sulfur?

Methionine and cysteine

Why does proline significantly affect protein structure?

Its ring structure makes it more conformationally restricted

Are amino acids containing hydroxyl groups hydrophilic or hydrophobic?

Hydrophilic

Which amino acid contains a guanidinium in its side chain?

Arginine

Which amino acid contains imidazole in its side chain?

Histidine

Under physiological pH, do amino acids with carboxylates have a positive or negative charge?

Negative charge

What is the most basic amino acid?

Arginine

Under physiological pH, do basic amino acids have positive or negative charge?

Positive charge

Which amino acids are acidic?

Asp, Glu

Which amino acids are essential?

Val, Leu, Ile, Phe, Trp, Met, Thr, Lys, His

Why is cysteine conditionally essential?

It is synthesized from methionine

Which amino acid is cysteine synthesized from?

Methionine

Why is arginine conditionally essential? 

It’s formed in the urea cycle and is essential for growing children

Why is tyrosine conditionally essential?

It’s essential for phenylketonuria patients

Under low pH, what ionization state are amino acids in?

Cation (both groups protonated)

Under high pH, what ionization state are amino acids in?

Anion (both groups deprotonated)

Under neutral pH, what ionization state are amino acids in?

Neutral (zwitterion)

How do you calculate the isoelectric point (pI) of an amino acid?

• Identify all ionizable groups and assign pKas

• Protonate each ionizable group and calculate the net charge

• Move up in pH to the first ionizable group’s pKa and deprotonate it; subtract 1 from the net charge

• Repeat until each group is deprotonated; this determines the pH at which each charged form of the molecule occurs

• Identify which form has a net charge of 0

• Average the pKa on either side of the neutral form to get pI

What is the isoelectric point (pI) of an amino acid?

The pH at which the charge of the molecule is 0

What is the basic structure of an amino acid?

Side chain, Hydrogen, primary amino group, and carboxyl group; all bonded to a chiral alpha carbon

What are the classifications of amino acid chains based on increasing length?

Peptide, polypeptide, and protein

How many amino acids long are peptides?

<10 amino acids

How many amino acids long are polypeptides?

10-50 amino acids

How many amino acids long are proteins?

>50 amino acids

What are the classifications of proteins based on shape?

Globular and fibrous

What protein shape class do enzymes, antibodies, transporters, and receptors fall under?

Globular proteins

What protein shape class do collagen, keratin, and elastin fall under?

Fibrous proteins

What is primary protein structure?

The amino acid sequence

What is secondary protein structure and its classes?

The folding of the primary structure

• α helices

• β sheets or strands

• β turns or reverse turns

What molecule is lost when joining 2 amino acids?

Water

Between separate amino acids and amino acids joined by a peptide bond, which is more thermodynamically stable and what does this mean?

Separate amino acids; Energy is needed to form peptide bonds

In what direction are amino acid sequences written/read?

Amino to carboxyl terminal residue (N to C)

What determines the 3D structure of proteins?

The amino acid sequence

Why are polypeptide chains flexible yet conformationally restricted?

The peptide bond has partial double bond character due to resonance that prevents it from rotating freely

Why are peptide bonds strong?

Resonance gives peptide bonds partial double bond character which decreases their length, increasing the amount of energy it takes to break

Which conformation of peptide bonds is favored and why?

Trans conformation decreases steric repulsion between side chains

Why can proline exist in equal amounts of cis and trans isomers?

Its cyclic ring already has high steric repulsion, decreasing the difference in energy between the cis and trans conformations

Are protein helices right or left handed?

Right handed

What intermolecular force maintains the structure of helices?

Hydrogen bonding

How many residues apart does H-bonding occur in helices?

4 residues apart

What is an α helical coiled coil?

Two helices wind around one another to form a superhelix

What function do superhelices serve?

Form stiff bundles of fibers and used in proteins that span biological membranes

How are superhelices held together?

Van der Wal forces between Leucine separated by 7 residues

How is a single strand of a collagen triple helix stabilized?

Steric repulsion of the pyrrolidine rings of the proline and hydroxyproline residues

What is the structure of collagen (triple helix)?

Each strand is h-bonded to the other two strands. Every 3rd residue is glycine because there is no space in the center of the helix. Pyrrolidine rings are on the outside.

Describe the structure of a β strand

Almost fully extended with the side chains of adjacent amino acids point in opposite directions

How are antiparallel β sheets held together?

H-bonds between single NH and CO groups

How are antiparallel β sheets held together?

2 H-bonds between each NH and CO group

How are β turns stabilized?

The CO group of residue i of the polypeptide chain is hydrogen

bonded to the NH group of residue i+3

What kind of amino acids are α helices made of?

Small aliphatic amino acids

What kind of amino acids are β sheets or strands made of?

Aromatic amino acids

What kind of amino acids are β turns or reverse turns made of?

Glycine and proline

Describe the properties of a peptide bond

• Resistance to hydrolysis

• Partial double bond character

• Has an H-bond donor and acceptor

• Neutral

What is native conformation?

When a protein can have many arrangements in space but only uses 1

What is a domain?

A stable unit of a 3* structure; The unit of protein folding

What are the components of a tertiary protein structure?

• 3D non-repetitive folding

• Domains and lobes

What are the components of a quaternary protein structure?

• 1+ polypeptides

• Subunits

Explain the advantage of having separate domains on a protein

• Efficient folding

• Larger folded proteins

• Flexibility and motion

• Union of new functions

What is a homodimer?

A protein consisting of 2 identical polypeptide chains

What is a heterodimer?

A protein consisting of 2 different polypeptide chains

What are the forces governing quaternary subunit association?

• Ionic interactions

• Hydrophobic interactions

• 2* structure

What is the only information required to specify the native conformation of a protein?

The sequence of its amino acid residues

What function does β-mercaptoethanol serve in denaturation?

Break or reduce disulfide bonds