Bio Chem Exam 2

Amino Acid Sequence of Bovine Insulin

Side chain A and B. Has a shared amount of six S groups. Occasionally, disulfide bonds are shown as a part of B as it is a covalent bond.

Alanine

Ala

Arginine

Arg

Asparagine

Asn

Aspartic acid (Aspartate)

Asp

Cysteine

Cys

Glutamic acid (Glutamate)

Glu

Glutamine

Gln

Glycine

Gly

Histidine

His

Isoleucine

Ile

Leucine

Leu

Lysine

Lys

Methionine

Met

Phenylalanine

Phe

Proline

Pro

Serine

Ser

Threonine

Thr

Tryptophan

Trp

Tyrosine

Tyr

Valine

Val

What is the amino terminus of the tripeptide Gly-Ala-Asp?

In any peptide the amino terminus (N-terminus) is the free –NH₂ group at the first amino acid in the sequence.

The carboxyl terminus (C-terminus) is the free –COOH group at the last amino acid in the sequence.

So the answer is Glycine (Gly)

What is the approximate molecular weight of a protein composed of 300 amino acids?

On average, one amino acid ≈ 110 daltons (Da) in a protein chain.
So: 300 amino acids x 110 Da/amino acid = 33,000 Da

Number of amino acids for a protein with a molecular weight of 110,000

110,000 Da/110 Da (amino acid) = 1,000 amino acids.

Where is rotation permitted in polypeptide chains?

The N-C_a bond and the C_a carbonyl bond

What determines the path of the polypeptide chain?

The rotation of the Φ and ψ bonds, called the torsion angles

Torsion angles of the polypeptide lie between…

-180 and +180 degrees.

Torsion angles are sometimes called…

Dihedral angles

Torsional angles describe the angle between…

Two planes formed by four atoms in a molecule

The bond angle defines the angle between the three atoms connected to…

one central common atom

The dihedral angle defines the angle between…

The groups attached to adjacent (C1 and C2) carbon atoms

Conformational change

A change in structure that arises solely from rotation about the covalent bonds.
No bonds are broken or reformed.

The +180° and –180° represent the same
physical conformation: just…

Two ways of describing a full half-turn

The range is centered around 0°, which
corresponds to the…

Eclipsed conformation also called “syn”

A dihedral angle of +180 is called…

“anti”

___________ mean rotation in one direction (clockwise), and ___________ mean rotation in the opposite direction (counter clockwise)

Positive and negative angles

A range of _ and _ is not used as -180 and +180 is better for specificity

0 and 360 degrees

Occurs when the bonds on adjacent atoms are directly aligned with each other. This causes a steric clash and is a high-energy, unstable state

Eclipsed conformation

Occurs when the bonds on adjacent atoms are staggered, or twisted, relative to each other. This minimizes steric hindrance and is a low-energy, stable state

Staggered conformation

The polypeptide chain is made up of a series of planes linked at _________. In the backbone of a polypeptide chain, the two most important single bonds for rotational freedom are those around the __.

α carbons

Dihedral/Torsion angles are also called______

Ramachandran angles

Torsion angles control __________. Freedom of rotation about two bonds of each amino acids allows the protein to fold in several ways.

protein folding

Some φ and ψ combinations are very unfavorable because of ______________ of backbone atoms with other atoms in the backbone or side chains.

steric crowding

Some φ and ψ combinations are more favorable because of chance to form favorable ________ along the backbone.

H--bonding interactions

A __________ shows the distribution of φ and ψ dihedral angles that are found in a
protein.

Ramachandran plot

Ramachandran plots also

• shows the common secondary structure elements
• reveals regions with unusual backbone structure

Example of Ramachandran plot

(guaranteed question on this)

Certain combinations of φ and ψ angles result in ________ conformations where atoms on adjacent residues ______ with each other.

eclipsed-like, clash

These high-energy conformations are ____________________ on the Ramachandran plot

sterically disallowed and appear as empty regions

________ are different conformations of a side
chain, defined by its χ (chi) torsional angles.

Rotamers

Each _______ corresponds to a specific set of
dihedral angles (χ1, χ2, etc.) that describe how the side chain atoms are _____ around their bonds

rotamer, rotated

PTMs like _____________________ introduce new atoms or functional groups, which can shift the preferred rotameric states.

phosphorylation, methylation, and acetylation

PTMs are __________________

Post translational modifications

Proteins have irregular 3D structures as they lack _______, designed to ________________, and have functional _____________

symmetry, interact and recognize thousands of molecules, diversity

Despite the irregularity protein structures still have ______________

regular features

________ is a frequent cause for bronchitis in young children

hMPV F glycoprotein

The structures of over _________ proteins are known

137,000

describes the spatial arrangement of the main-chain atoms
in a segment of a polypeptide chain

Secondary structure

Common types

α helix,
β sheets,
β turn, random coils.

α helix and β sheets are the architectural elements of protein structure.

α helix

Simplest arrangement, maximum number of hydrogen bonds.

___________ protrude out from the backbone

R groups

Each helical turn is

3.6 residues, ∼5.4 Å

The average residues in most helices is 

∼10

The influenza protein

Hemagglutinin

Approximately how many residues are there per influenza protein

54

________________ R groups protruding away from the helical backbone are the most common

Right handed

_____________ theoretically less stable, not observed in proteins

Extended left-handed

Where are the Interhelical Hydrogen Bonds and what do they add to the structure

• Between the hydrogen atom attached to the electronegative nitrogen atom of residue n and the electronegative carbonyl oxygen atom of residue n + 4.

• Confers significant stability.

These hydrogen bonds are _________________ meaning they occur within the same polypeptide chain

intrachain/intrahelical

How do intrahelical bonds maintain the helical shape?

By pulling the backbone into a tight coil

The R side chains (________) of the amino acids project outward from the helix, allowing interactions with the ___________ or _____________

R-groups, environment or other molecules

H-bond donor involving side chains

Residue n-NH

H-bond acceptor involving side chains

Residue n+4-C=O

Amino Acid Sequence Affects Stability of the

α Helix

Amino acid residues have an intrinsic propensity to form

an α helix

Interactions between R chains spaced ________ residues apart can stabilize or destabilize _______

3-4, α helix

Regarding the interactions between R chains the charge, size, and shape of R chains can _________ and the formation of _________ and __________ can stabilize

destabilize, ion pairs and hydrophobic effect can stabilize

Proline and Glycine Occur Infrequently in an

α Helix

Proline

introduces destabilizing kink in helix

Regarding Proline:

nitrogen atom is part of rigid ring - _________

rotation about  _________ bond is not possible

This restricts the ____________ of rotation, making it incompatible with the regular geometry of an α-helix

no H-bond donor, N—Cα, φ (phi) angle

Glycine regarding an α Helix

high conformational flexibility, take up coiled structures.

The flexibility of glycine allows it to have many confirmations which destabilizes the regular ____________

geometry of the helix

Helix dipole effect

plays a role in helix stability, protein folding, and molecular interactions.

Small electric dipoles in each peptide bond align the hydrogen bonds. Each peptide bond has a small dipole moment due to the partial

positive charge on the amide hydrogen (–NH) and partial negative charge on the
carbonyl oxygen (C=O)

N-terminus of the α-helix has a ___________ due to the allignment of the dipoles (NH₃ ⁺terminus).

Therefore, ______________ (like
Aspartate, Glutamate) are often found near the N-
terminus to stabilize this charge.

partial positive charge, negatively charged amino acids

C-terminus has a _____________

Therefore _________ amino acids (like
Lysine, Arginine) are often found near the ___________ for stabilization.

partial negative charge, positively charged amino acids, C-terminus

A β-sheet consists of multiple β-strands lying side-by-side.
Strands can be: ________ _________

Parallel and Antiparallel

Hydrogen bonds form between the carbonyl oxygen of ____

one

define the rotation around the backbone bonds regarding polypeptide chains

Dihedral angles φ and ψ

In β-sheets:
• φ ≈ ___________
• ψ ≈ ___________

–60° to –150°

+90° to +180°

The β-sheets values allow the backbone to adopt a

highly extended conformation, ideal for sheet confirmation

Adjacent Polypeptide Chains in a β Sheet Can Be

Antiparallel or Parallel

β-Strand

A single extended segment of polypeptide in β-conformation

In a B strand the backbone is _______ out in a zigzag pattern

The average length is _______-

The arrows on the plot point from _______

stretched, 6 amino acids, N to C

Antiparallel - opposite orientation ________________

occurs more ___________

More _______ and _________ due to linear to hydrogen bonds

Maybe separated by a minimum of 4 amino acids in a ________. Strands can be _______ or _________ in amino acid sequences.

N to C and C to N, frequent, stable, beta turn, distant, close

Parallel - same orientation. Strands must be __________ in amino acid sequences

Less stable due to __________________

All R groups are _____ or _____ the plane of strands

distant, angled hydrogen bonds, above, below

β turns are common in proteins and connect the ends of two __________________

adjacent antiparallel β-strands in a β-sheet

common names regarding the B turns in proteins

reverse turn, tight turn

regarding reverse turn, tight turn

____° turn

involves _ residues

residue 1: _______

residue 4: _______

Hydrogen bond froms between _______________ reside

180, 4, start of the turn, end of the turn, first and fourth

10 types of turns are found in proteins. The most common is a _________

β turn.