protein

tính đối xứng của a.a ở việc alpha carbon được

is bonded to four different chemical groups.

Fill the blank: ____ can create disulfide bonds, while thioether group is a part of a side chain of ___.

cysteine and methionine

natural protein thì stereochemistry thường là

L stereochemistry

Two amino acids of the standard 20 contain sulfur atoms.

methionine and cysteine

Which one of the amino acids has an imino group?

Proline

amino acids have an aromatic side chain?

phenylalamine, tyrosine, tryptophan

ph<pl thì population of amino acids in solution will have:

positive charge

The formation of a peptide bond between two amino acids is an example of a(n) ______________ reaction.

B. condensation

định nghĩa của pl

độ ph mà a.a là zwitterion và có net charge = 0

The peptide bonds are formed through:

Condensation reaction

In the phenomenon of “Salting in” (at low salt concentrations), why does the solubility of

proteins increase?

Salt ions interact with the charged groups on the protein surface, helping to form a more stable hydration shell.

Why does protein precipitation occur at very high salt concentrations (Salting out)?

Because salt ions compete for water with the protein, exposing hydrophobic regions on the protein's surface.

muối nào thường dùng để salting out vì nó tan tốt trong nước

(NH4)2SO4

(Ammonium sulfate).

tính ứng dụng của salting out?

remove unwanted proteins, collect targetted proteins

What is the primary principle behind the Dialysis method in protein purification

seperation based on size

cái gì pass through semipermeable

small molecules

what is the driving force that move small molecules

concentration gradient (diffusion)

ứng dụng của dialysis

remove salt

primary factor used to separate proteins in Size Exclusion Chromatography?

The size and shape of the protein molecules.

In Size Exclusion Chromatography, what is the 'stationary phase' and mobile phase composed of?

stationary: beads and pores

mobile: buffer

trong size exclusion chroma thì protein nào nhanh nhất

thằng to hơn

tại sao trong size exclusion chroma thằng nhỏ lại chậm

vào lỗ nhỏ hơn trên pha tĩnh thì phải đi dài hơn tại lỗ từ to - bé

trong việc phân tách protein thì affinity chroma dựa vào nguyên tắc nào

binding giữa protein và ligand

ligand là gì

molecule có nhiệm vụ đi bind với targetted protein

In the Ni-NTA system, what is the role of the 'His-tag' attached to the protein?

A. To act as the specific binding site that coordinates with the Nickel

Which molecule is used to elute the His-tagged protein by 'competing' for the Nickel binding sites?

Imidazole.

advantage of using Ni-NTA chromatography

high specificity allowing high purity

basis for separating proteins in Ion-Exchange Chromatography?

magnitude of net electric charge

What is the specific charge of the stationary phase in Cation Exchange Chromatography?

C. Negative charge.

How does adding salt (e.g., NaCl) affect the bound proteins in the column?

The salt ions compete with the protein for binding the stationary phase.

In a Cation Exchange column, which protein binds most tightly?

The one with the highest net positive charge.

If you are using a Cation Exchanger and you increase the pH of the buffer, what generally happens to the protein's binding?

more negatively charged and release from the beads

primary physical basis for protein separation in electrophoresis?

dịch chuyển của charged protein

mục đích điện di không phải

làm tinh khiết protein

primary functions of SDS in SDS-PAGE technique?

It breaks hydrogen bonds, hydrophobic interactions, and ionic bonds to denature proteins.
It provides a uniform negative charge to the polypeptide chains.

It coats the linear polypeptide chains with a negative charge

allows proteins to be separated based on their molecular weight

break disulfide bonds

β- mercaptoethanol (or Dithiothreitol - DTT)

function of SDS-PAGE

To separate proteins primarily based on their size (molecular weight or length).

purpose of Isoelectric Focusing (IEF)?

To determine the isoelectric point (pI) of a protein based on its net charge.

function of two-dimensional (2D) electrophoresis

B. To separate proteins based on both their isoelectric point (pI) and molecular weight.

major limitation of using only SDS-PAGE compared to 2D electrophoresis?

It cannot separate proteins that have similar molecular weights but different charges.

It cannot separate proteins that have similar molecular weights but different charges.

1-Fluoro-2,4-dinitrobenzene (fdnb)

FDNB method applications

identifying the specific N-terminal amino acid,

The total number of polypeptide chains present in a protein.

function of the Edman degradation

To determine the entire amino acid sequence of a peptide by sequentially removing one

residue at a time from the N-terminal amino acid.

limitation of the Edman

to approximately 50 amino acid residues.

matching enzyme with their function

trypsin

chymotrysin

pepsin

cyanogen bromide

trypsin - lysine, arginine

chymotrypsin - phenylalamine, tyrosine, tryptophan

pepsin - hydrophobic & aromatic

cyanogen bromide - met

C∝—N

C∝—C

C∝—N: phi

C∝—C: psi

In the Ramachandran plot shown, what do the dark blue shaded regions represent?

"Allowed" regions representing favorable Ф and Ψ angles for secondary structures.

In an ∝ helix, which direction do the R groups residues

outward from the backbone

An idealized ∝ helix has how many amino acid residues per turn?

3.6

The ∝ helix is stabilized by a hydrogen bond between the carbonyl oxygen of the i residue

and the amino hydrogen of which residue?

i + 4

The rise along the helical axis for one complete turn of an idealized ∝ helix is:

Distance

5.4 Å

1.5 Å

Proline (Pro) considered an "∝ helix breaker"

quá pro, quá rigid structure

Glycine (Gly) rarely found in ∝ helices?

too flexible

Which of the following best defines the "net dipole" of an ∝ helical segment in a protein?

The macroscopic electric field created by the cumulative alignment of individual peptide bond dipoles.

In a beta conformation, what is the specific geometric shape of the polypeptide chain backbone?

zigzag

How do hydrogen bonds contribute to the formation of a beta sheet?

form between adjacent segments

What defines a 'parallel beta sheet' in terms of polypeptide chain orientation?

Adjacent chains run in the same N-terminal to C-terminal direction.

Matching phi, psi angles and repeat period corresponding to antiparallel and parallel B sheet:

-138 phi 135 psi 7 a: anti

-119 phi 113 psu 6.5 a

function of a beta turn in protein structure?

To connect the ends of two adjacent segments in an antiparallel beta sheet.

Which amino acid residues are most frequently found in β turns due to their unique structural properties?

glycine & proline

Which peptide bond configuration allows Proline to create a "kink" in the polypeptide chain, making it suitable for β turns?

cis

the primary function of a Beta loop

To connect adjacent segments of a parallel beta sheet, two alpha helices, or a beta sheet and an alpha helix.

how are the polypeptide chains in fibrous proteins typically arranged?

D. Arranged in long strands or sheets

Fibrous protein

Long strands or sheets

Consist largely of a single type of secondary structure

Insoluble in water

Support, shape, and external protection

globular

Compactly folded

Several types of secondary structures

soluble

Enzymes and regulatory proteins

Interior: hydrophobic R groups and Exterior:

hydrophilic R groups

Organized into complex multi-subunit globular complexes

function of the chaperonin complex?

To facilitate the correct folding of proteins that do not fold spontaneously.