ABIO 365 EXAM #2

Alanine

Valine

Leucine

Isoleucine

Methionine

Phenylalanine

Tryptophan

Tyrosine

Glycine

Proline

Cysteine

Asparagine

Glutamine

Serine

Threonine

Lysine

Arginine

Histidine

Aspartic Acid

Glutamic Acid

Characteristics of Alanine

(Ala, A) Nonpolar hydrocarbon; hydrophobic

Characteristics of Valine

(Val, V) Nonpolar hydrocarbon; hydrophobic

Characteristics of Leucine

(Leu, L) Nonpolar hydrocarbon; hydrophobic

Characteristics of Isoleucine

(Ile, I) Nonpolar hydrocarbon; hydrophobic

Characteristics of Phenylalanine

(Phe, F) Nonpolar hydrocarbon; hydrophobic

Characteristics of Methionine

(Met, M) Hydrophobic; contains sulfur

Characteristics of Tryptophan

(Trp, W) Hydrophobic; aromatic

Characteristics of Tyrosine

(Tyr, Y) Hydrophobic in this chart; aromatic

Characteristics of Glycine

(Gly, G) Special amino acid

Characteristics of Proline

(Pro, P) Special amino acid

Characteristics of Cysteine

(Cys, C) Special amino acid

Characteristics of Asparagine

(Asn, N) Polar hydrophilic

Characteristics of Glutamine

(Gln, Q) Polar hydrophilic

Characteristics of Serine

(Ser, S) Polar hydrophilic

Characteristics of Threonine

(Thr, T) Polar hydrophilic

Characteristics of Lysine

(Lys, K) Basic hydrophilic

Characteristics of Arginine

(Arg, R) Basic hydrophilic

Characteristics of Histidine

(His, H) Basic hydrophilic

Characteristics of Aspartic acid

(Asp, D) Acidic hydrophilic

Characteristics of Glutamic acid

(Glu, E) Acidic hydrophilic

Why do proteins have greater structural diversity than nucleic acids?

Proteins use 20 standard amino acids, whereas nucleic acids use 4 standard nucleotide types

How many possible sequences can a protein of 100 amino acids have?

20^100, approximately 10^130 possible sequences

What does pI stand for?

Isoelectric point

What does the isoelectric point represent?

The pH at which a molecule has zero net electrical charge

Which pKa values are averaged to calculate the pI of a neutral amino acid?

pI = (pK1 + pK2)/2

How is the pI calculated for an acidic amino acid such as Asp or Glu?

pI = (pK1 + pKR)/2

Which pKa values determine the pI of a basic amino acid such as Lys, Arg, or His?

pI = (pK2 + pKR)/2.

What happens to protein solubility at its isoelectric point?

Solubility is generally minimal, making precipitation more likely.

How does isoelectric focusing separate proteins?

By differences in their isoelectric points

How many standard amino acids are used to build proteins?

20 standard amino acids.

What makes an amino acid essential?

The body cannot synthesize enough of it, so it must be obtained from the diet.

What two functional groups react to form a peptide bond?

The amino group (NH2) of one amino acid and the carboxyl group (COOH) of another.

In which direction is a polypeptide synthesized?

From the N-terminus toward the C-terminus.

What does a peptide bond connect?

Adjacent amino acid residues in a polypeptide chain.

Why is a peptide bond planar?

Resonance gives the C-N bond partial double-bond character.

Why can't a peptide bond freely rotate?

Its partial double-bond character restricts rotation around the peptide C-N bond.

Which backbone atoms provide flexibility around a peptide unit?

The alpha-carbon bonds, described by the phi (Φ) and psi (Ψ) angles.

What do phi (Φ) and psi (Ψ) angles describe?

The rotational conformation of the protein backbone around the alpha-carbon bonds.

What makes a chiral compound optically active?

It can rotate the plane of polarized light.

Which standard amino acid is achiral?

Glycine, because its alpha-carbon has two hydrogen atoms.

What is a racemic mixture?

A 50:50 mixture of two enantiomers.

Why does a racemic mixture show zero net optical rotation?

The equal and opposite rotations of its enantiomers cancel.

What does a protein's primary structure describe?

The linear sequence of amino acid residues.

Which structural level includes alpha helices, beta sheets, and turns?

Secondary structure.

What is a super-secondary structure?

A recurring association or arrangement of multiple secondary-structure elements.

What is a protein domain?

A compact, self-contained structural unit within a protein.

What does tertiary structure describe?

The overall three-dimensional fold of a single polypeptide chain.

What does quaternary structure describe?

The assembly of multiple polypeptide subunits into one functional protein complex.

What is a homooligomer?

A protein complex containing multiple copies of the same type of subunit.

What is a heterooligomer?

A protein complex containing more than one type of subunit.

What covalent linkage can stabilize a protein's folded structure?

A disulfide (S-S) bond between two cysteine residues.

How can a disulfide bond connect two separate polypeptide chains?

It covalently links cysteine residues on different chains, such as chains A and B.

What are two important biological roles of alpha helices?

DNA binding and membrane spanning.

How can an alpha helix recognize a specific DNA sequence?

It can fit into the major groove of double-stranded DNA and form sequence-specific hydrogen bonds.

What region of DNA does a DNA-binding alpha helix fit into?

The major groove of double-stranded DNA.

What type of amino acid side chains predominate in the membrane-spanning region of an alpha helix?

Hydrophobic side chains that interact favorably with the membrane's lipid interior.

Why can a membrane-spanning alpha helix cross a lipid bilayer?

Its hydrophobic exterior interacts with the membrane's nonpolar core.

What type of interaction connects neighboring strands in a beta sheet?

Hydrogen bonding between backbone carbonyl (C=O) and amide (N-H) groups.

What are the two main types of beta sheets?

Parallel and antiparallel beta sheets.

What distinguishes parallel from antiparallel beta sheets?

The direction in which their neighboring polypeptide strands run.

What is a beta turn?

A short backbone reversal that helps a polypeptide change direction.

Which residues form a characteristic hydrogen bond in a beta turn?

The backbone C=O of residue 1 and N-H of residue 4.

How do Type I and Type II beta turns differ in the course notes?

By the orientation of the side chains at positions 2 and 3.

How are side chains arranged in a Type I beta turn according to these notes?

The R groups point toward the same side.

How are side chains arranged in a Type II beta turn according to these notes?

The R groups point toward opposite sides.

Which amino acid is commonly found at position 3 of a Type II beta turn?

Glycine.

How many amino acid residues are involved in a gamma turn?

Three residues.

Which amino acid is associated with gamma turns in these notes?

Proline.

Which backbone atoms hydrogen-bond in a gamma turn?

The C=O of residue 1 and the N-H of residue 3.

What is alpha-keratin?

A fibrous structural protein found in hair, nails, and parts of the skin.

What is the basic monomeric structural element of alpha-keratin?

A long alpha helix.

What is the hydrophobic pattern described for alpha-keratin's helix?

Every fourth residue is hydrophobic.

What stabilizes the coiled-coil arrangement of alpha-keratin?

Hydrophobic interactions between the helices.

How are two alpha helices arranged in the keratin coiled-coil?

They wind around each other to form a two-helix dimer.

What higher-level structures form when keratin dimers assemble?

Higher-order fibrous structures.

What mechanical properties do alpha-keratin fibers provide?

High strength combined with flexibility.

Why is cysteine abundant in some alpha-keratins?

Its side chains form disulfide bonds that help stabilize the filaments.

What does a phylogenetic tree show for proteins?

Evolutionary relationships among protein sequences.

What can sequence comparison reveal about two proteins?

Whether they are homologous and may share a common evolutionary ancestor.

What does it mean for two proteins to be homologous?

They share evolutionary ancestry.