Protein Structure and Chemistry

Question 1

What is the structure of membrane bound proteins?

Answer 1

They have hydrophobic regions that allow them to embed within hydrophobic lipid bi layers of a cell membrane.

Question 2

What is the structure of water soluble proteins?

Answer 2

Mostly composed of hydrophilic amino acids and cannot interact with hydrophobic environment of cell membrane.

Question 3

What are the functions of membrane bound proteins?

Answer 3

Transporters, receptors, channels and enzymes.

Question 4

What are the functions of water soluble proteins?

Answer 4

They are involved in various cellular processes including enzymatic reactions, structural support and signal transduction.

Question 5

Where are membrane bound proteins found?

Answer 5

Embedded within lipid bi layer of a cell membrane and are found in both plasma membrane and intra cellular organelles.

Question 6

Where are water soluble proteins found?

Answer 6

Primarily located in the cytoplasm or extracellular fluids.

Question 7

Interactions of membrane bound proteins?

Answer 7

They interact with lipids and other membrane bound proteins.

Question 8

Interactions of water soluble proteins?

Answer 8

Interact with other soluble proteins and other molecules in cytoplasm.

Question 9

Overall of membrane bound proteins and water soluble proteins?

Answer 9

MBP have evolved to function within unique environments of a cell membrane.

WSP have evolved to function in aqueous environments in cytoplasm

Question 10

What is an enzyme?

Answer 10

A biological catalyst made up of proteins.

Question 11

What is chemical basis of enzymatic catalysis?

Answer 11

Involves the ability of enzymes to bind substrates in a way that stabilizes the transition state of a reaction, thereby lowering the activation energy and increasing the rate of the reaction.

Question 12

How do enzymes catalyse?

Answer 12

by binding to the reactants, or substrates, in a specific orientation and conformation that promotes the formation of the transition state.

Question 13

How is binding facilitated?

Answer 13

By the complementary shape of the enzyme’s active site and the substrate, as well as by specific interactions, such as hydrogen bonds, van der Waals forces, and electrostatic interactions.

Question 14

What is drug inhibition?

Answer 14

It refers to the way in which a drug binds to an enzyme and affects its activity.

Question 15

What are the three modes of drug inhibition?

Answer 15

competitive, noncompetitive, uncompetitive

Question 16

How is data analysed within drug inhibition?

Answer 16

Lineweaver-Burk plot, which is a graphical representation of the enzyme kinetics.

Question 17

What is competitive inhibition?

Answer 17

The inhibitor competes with the substrate for binding to the active site of the enzyme.
This can be observed in enzyme kinetics as an increase in the apparent Km or in the presence of the inhibitor, with no change in the Vmax.

Question 18

What is Km?

Answer 18

The concentration of substrate required to achieve half of the maximum reaction rate

Question 19

What is VMax?

Answer 19

Maximum Reaction Rate

Question 20

What is noncompetitive inhibition?

Answer 20

the inhibitor binds to a site on the enzyme that is distinct from the active site, and the binding of the inhibitor alters the conformation of the enzyme, thereby reducing its activity.
This can be observed in enzyme kinetics as a decrease in the Vmax in the presence of the inhibitor, with no change in the Km.

Question 21

What is an uncompetitive inhibition?

Answer 21

The inhibitor binds only to the enzyme-substrate complex, thereby preventing the reaction from proceeding.
This can be observed in enzyme kinetics as a decrease in both the Vmax and the Km in the presence of the inhibitor.

Question 22

Why is enzyme kinetic studies important?

Answer 22

It can provide important information about the mode of drug inhibition and help in the development of effective drugs that can selectively target specific enzymes.

Question 23

What is a protein?

Answer 23

A polymer consisted of amino acids.

Question 24

What is an amino acid?

Answer 24

A monymer that forms the protein.

Question 25

When you have a lot of amino acids what is this called?

Answer 25

Polypeptide, each bond that connects with another amino acid is called a peptide bond.

Question 26

What is the smallest chains of AA called?

Answer 26

Oligopeptides

Question 27

What are the larger chains called?

Answer 27

Polypeptides but proteins are largest of them all.

Question 28

What are the four levels of protein structure?

Answer 28

Primary and secondary structure, Tertiary and Quaternary structure.

Question 29

What is the primary structure?

Answer 29

Sequence of amino acids that make up a protein.
It is the first level of protein structure and represents the specific arrangement of amino acids in a polypeptide chain, determined by the DNA sequence of the gene that codes for the protein.

Question 30

What groups are contained in an amino acid?

Answer 30

Amino group, R group (side chain) , carboxyl group.

Question 31

What is the secondary structure?

Answer 31

Alpha helix and beta pleated sheets.
It is the local spatial arrangement of the polypeptide chain that is stabilized by hydrogen bonding between the amino acid residues.

Question 32

What is the most common type of secondary structure ?

Answer 32

Alpha helices, beta sheets, and random coils.

Question 33

What is the Alpha Helix in a secondary structure cell?

Answer 33

The polypeptide chain forms a right-handed helical structure with a tightly coiled backbone.
The backbone is stabilized by hydrogen bonds formed between the carbonyl oxygen of one amino acid residue and the amino hydrogen of another amino acid residue, which are located four residues apart along the polypeptide chain.

Question 34

What is the Beta sheet in a secondary structure cell?

Answer 34

In a beta sheet, the polypeptide chain forms an extended sheet-like structure, where the peptide strands are arranged side-by-side and are held together by hydrogen bonds formed between the carbonyl and amino groups of neighboring strands.

Question 35

Why is the secondary structure important?

Answer 35

Secondary structures are important for the overall three-dimensional structure of a protein and play a crucial role in determining its stability and function.

Question 36

What is the tertiary level in protein structure?

Answer 36

The tertiary structure is responsible for the overall shape of a protein and determines its functional properties.

Question 37

What contributes to the formation of the tertiary structure?

Answer 37

Hydrophobic interactions, Hydrogen bonds, Electrostatic interactions, Disulfide bonds and Van der waals forces.

Question 38

What is a hydrophobic interaction?

Answer 38

Hydrophobic interactions occur between nonpolar amino acid residues, which tend to cluster together in the protein’s interior away from the surrounding water molecules.

Question 39

What are hydrogen bonds?

Answer 39

Hydrogen bonds form between polar amino acid residues, such as those in the side chains, and can help stabilize the protein’s structure by forming local structural motifs.

Question 40

What is an electrostatic interaction?

Answer 40

Electrostatic interactions occur between charged amino acid residues, such as acidic and basic residues, and can contribute to the folding and stability of the protein.

Question 41

What is a disulphide bond?

Answer 41

Disulfide bonds are covalent bonds that form between cysteine residues in the protein, creating bridges that can help stabilize the tertiary structure.

Question 42

Van der waals forces?

Answer 42

Van der Waals forces are weak attractive forces that occur between all atoms and molecules and can contribute to the packing and stability of the protein’s structure.

Question 43

Why is the tertiary structure critical?

Answer 43

It determines the protein’s specific three-dimensional shape, which in turn dictates its interactions with other molecules in the cell.

Question 44

What is the quaternary level in protein structure?

Answer 44

refers to the arrangement and interaction of multiple protein subunits, also known as protein chains or polypeptide chains, to form a functional protein complex.

Question 45

What is the quaternary structure held by?

Answer 45

held together by various types of noncovalent interactions, such as hydrogen bonds, hydrophobic interactions, electrostatic interactions, and van der Waals forces, as well as occasionally by covalent bonds.

Question 46

What techniques can be used to analyse the quaternary structure?

Answer 46

X-ray crystallography, cryo-electron microscopy, and other structural biology methods are commonly used to study the quaternary structure of protein complexes and elucidate their functional mechanisms.