Proteins - Characteristics and Engineering Lecture Flashcards

Flashcards covering protein structure, stability, folding, engineering, and enzyme kinetics based on the provided lecture notes.

Amino acids are linked via __________ bonds, which exhibit no free rotation due to resonance.

peptide

In a peptide bond, a total of __________ atoms are located within the same plane.

six

For sterical reasons, most peptide bonds are found in the __________ configuration rather than the cis configuration.

trans

The __________ diagram is a plot used to visualize the energetically allowed regions for backbone dihedral angles $\phi$ and $\psi$.

Ramachandran

A right-handed $\alpha$-helix contains __________ amino acids per turn, corresponding to a pitch of $5.4\,\text{\AA}$.

3,6

In an $\alpha$-helix, hydrogen bonds form between the $(N-H)_i$ and the $(C=O)_{i-4}$ (or $(N-H)_{i+4}$ and $(C=O)_i$ according to transcript notation), while in a $\beta$-strand, the distance between amino acids is __________ $\text{\AA}$.

3,5

The __________ effect drives protein folding by increasing the entropy of the system through the release of water molecules.

hydrophobic

According to the Lambert-Beer law, absorbance ($A$) is equal to $\varepsilon \times c \times d$, where $\varepsilon$ represents the __________ coefficient.

molar absorbance

In Circular Dichroism (CD) spectroscopy, the __________ bond acts as the chromophore.

peptide

The __________-__________ equation is used to calculate protein stability ($\Delta G_{FU}$) as a function of temperature ($T$).

Gibbs-Helmholtz

The __________ paradox states that proteins cannot fold by sampling all possible conformations, as the time required would exceed the age of the universe.

Levinthal's

In the folding of HisF, the __________ intermediate (IBP) is characterized by high secondary structure content and a compact conformation.

burst-phase

The molecular chaperone __________ works in cooperation with Hsp10 (GroES) in an ATP-dependent manner to assist protein folding.

GroEL

__________ design for protein engineering requires detailed information about the protein structure to plan specific amino acid exchanges.

Rational

Unlike rational design, __________ evolution typically involves random mutagenesis and requires a high-throughput screening or selection system.

directed

The yeast-two-hybrid (Y2H) system is used to identify protein-protein interactions, which are specifically monitored in the cell's __________.

nucleus

__________ measures the change in the refractive index at the backside of a metal film when a prey protein binds to an immobilized bait protein.

Surface plasmon resonance (SPR)

In Isothermal Titration Calorimetry (ITC), the binding signal measured is the __________ ($\Delta H$) released or absorbed during complex formation.

heat

The efficiency of Fluorescence Resonance Energy Transfer (FRET) is inversely proportional to the __________ power of the distance between the donor and acceptor.

sixth

According to the Transition State Theory, enzymes accelerate reactions by lowering the __________ energy ($\Delta G^{\neq}$).

activation

In the Michaelis-Menten equation, $K_M$ represents the substrate concentration at which the reaction velocity is __________ $\times V_{max}$.

0.5

Enzymes for which the specificity constant ($k_{cat}/K_M$) is close to the diffusion-controlled rate are described as __________ perfect.

kinetically

The __________ technique is a rapid kinetic method used to study pre-steady-state reactions by mixing reactants in syringes and monitoring optical signals.

stopped flow

In tryptophan synthase (TS), the ancestral reconstruction of the __________ (LBCA-TS) showed high similarity to the structure from $S.\,typhimurium$.

Last Bacterial Common Ancestor

In the IGPS reaction, a biphasic __________ diagram for the turnover number ($k_{cat}$) suggests a change in the rate-limiting step at approximately $35\,^{\circ}\text{C}$.

Arrhenius