Protein Structure and Function

Question 1

What are the 4 levels of protein structure?

Answer 1

Primary, Secondary, Tertiary, Quaternary

Question 2

The number of possible conformations for each protein is almost infinite, why aren’t cells full of millions of different proteins?

Answer 2

2 theories
1. There is a energetically favorable way of folding
2. During evolution, the one that was the best survived and folding structure was passed on

Question 3

What is a protein’s primary structure?

Answer 3

Amino acid sequences.

Question 4

How are amino acids join together?

Answer 4

Through condensation reaction to form peptide bonds. The peptide binds the C-terminus on one amino acid to the N-terminus on the next amino acids.

Question 5

Why is the sequence of amino acids so important?

Answer 5

The order of amino acids is specific. The sequence makes the protein take different shapes and have different functions in your body.

Question 6

What is a protein’s secondary structure?

Answer 6

Folding of an amino acid chain into structure (alpha helix and beta sheet), from the hydrogen bonding interaction of the atoms in the backbone.

Question 7

How are the amino acids stabilize during folding?

Answer 7

By the hydrogen bonds forming between the amnio and carbonyl group (vertically). The R group are not involved in the binding.

Question 8

What is an alpha helix?

Answer 8

The coiled structural arrangement of many proteins consisting of a single chain of amino acids stabilized by hydrogen bonds

Question 9

How are alpha helix generated?

Answer 9

When a single polypeptide chain turns around itself to form a structurally rigid cylinder. A hydrogen bond is made between every fourth amino acid, linking the C=O of one peptide bond to the N–H of another

Example: the carbonyl of amino acid 1 would form a hydrogen bond to the N-H of amino acid 5

Question 10

What is a coil-coil alpha helix?

Answer 10

α-helical structures in which two or three helices are wound around each other to form superhelical bundles.

Question 11

How are coil coil α-helix form?

Answer 11

When the α helices have most of their non-polar side chains along one side, so they can twist around each other with their hydrophobic side chains facing inward. Usually found in aqueous environement.

Question 12

How can an α helix cross a membrane bilayer?

Answer 12

The hydrophilic polypeptide backbone is shielded from the hydrophobic lipid hydrocarbons. The hydrophobic side make contact with the hydrophobic hydrocarbon tails, while the hydrophilic form hydrogen bond with one another along the interior of the helix.

Question 13

What is a beta pleated sheet?

Answer 13

Structure made when hydrogen bonds form between segments of a polypeptide chain that folds side by side.

Question 14

How are anti-parallel beta pleated sheets form?

Answer 14

When the neighboring strands run in opposite direction and there is hydrogen bonding between H and the double stranded O

Question 15

How are parallel beta pleated strand forms

Answer 15

When the neighboring strands run parallel, and there is hydrogen bonding between H and the double stranded O.

Question 16

What is a protein tertiary structure?

Answer 16

One full, three-dimensional conformation formed by an entire polypeptide chain—
including the α helices, β sheets, and all other loops and folds that form between the N- and C-termini

Question 17

What are protein domains?

Answer 17

Protein domain is a region of the polypeptide chain of protein that is self-stabilising and folds independently from the rest.

Question 18

What is a ligand?

Answer 18

Any molecule that binds to a protein

Question 19

What is a quaternary structure?

Answer 19

Subunits that make up multi protein complexes; arrangement of the protein’s multiple subunits

Question 20

How does protein remain stabilized when they’re folding?

Answer 20

Thousands of weak non-covalent bonds between amino acids through intermolecular forces.

Question 21

What is common between the subunits that make up homo- quaternary structure?

Answer 21

The subunits are identical.

Question 22

What makes up a hetero- quaternary structure?

Answer 22

The polypeptide chain (subunits) in the quaternary structure are different.

Hemoglobin are composed of 2 beta-globin and 2 alpha-globin.

Question 23

How can protein form large complex structure?

Ex: Hollow tube, filament, spherical shell

Answer 23

Protein form large complex structure through multimerization.

Question 24

During folding, what helps with protein folding?

Answer 24

Chaperone proteins

Question 25

What is multimerization in protein?

Answer 25

The assembly of multimer, protein that are made of more than one polypeptide chain

Question 26

What are chaperone protein?

Answer 26

Protein that helps with the folding of other proteins. Because chaperones make folding more efficient and reliable, most protein have a certain way of folding, despite having an infinite way of folding.

Question 27

How does hydrophobic interaction constrain (force) protein folding?

Answer 27

In an aqueous setting, the hydrophobic molecules tend to be forced together to minimize their contact to water. Therefore, the hydrophobic effect of non-polar amino acids and water force the folding of protein where the non-polar side chains are packed into hydrophobic core region and the polar side chains can form hydrogen bonds to water.

Question 28

How are extracellular protein stabilized?

Answer 28

The protein can be stabilized through cross linking, meaning two amino acids from the same chain can join together.

Example: Disulfide Bond
Disulfide bonds do not change a protein’s conformation, but instead act as a sort of “atomic staple” to reinforce the protein’s most favored conformation in cysteine amino acids.

Question 29

What are the consequences of protein misfolding?

Answer 29

Normal protein can adopt an abnormal prion form. Then, the prion protein can induce formation of protein aggregates, causing disease.

Ex: Sickle cell is caused by a misfold by a hemoglobin from prior protein aggreagate.

Question 30

How does an enzyme know what ligand to bind to if it’s so specific?

Answer 30

If the surface contour of the ligand matches with the enzyme, binding is possible with the assistant of many simultaneously working weak, non-covalent interaction.

Question 31

What happens if the non-covalent bonds between a protein and ligand are broken?

Answer 31

The enzymes may denature because the hydrogen bonds are disturbed.

Question 32

What are three ways an enzyme can encourage a reaction?

Answer 32

1. Holding reacting substrates together in a precise alignment.
2. Rearranging the distribution of charge in a reaction intermediate
3. Altering bond angles in the substrate to increase the rate of a particular reaction

Question 33

How does an enzyme encourage a chemical reaction with the physical binding of two substrate molecules?

Answer 33

The enzyme binds to the two substrate molecules and orients them precisely to encourage a reaction to occur between them.

Question 34

How does an enzyme encourage a chemical reaction by rearranging the electrons in a substrate?

Answer 34

The enzyme binds to one substrate and rearrange the electron so that the substrate would have a partial positive and partial negative, encouraging a reaction.

Question 35

How does an enzyme encourage a chemical reaction with the physical manipulation of a substrate?

Answer 35

The enzyme strains the substrate into a transition state to favor a reaction.

Question 36

Why would an enzyme need to be regulated?

Answer 36

The cell can maintain itself in an optimal state, producing only those molecules it requires
to thrive under current conditions and ensuring that it does not deplete its energy reserves by accumulating molecules it does not need.

Question 37

What are the methods of regulating enzymes

Answer 37

1. Allosteric Effect
2. Phosphorylation
3. GTP Binding Protein

Question 38

What is an enzyme allosteric’s site?

Answer 38

Binding site that is different from the active site or where the substrate normally binds to the enzyme.

Question 39

What is feedback inhibition?

Answer 39

A negative regulation where an enzyme acting early in a reaction pathway is inhibited by a molecule produced later in that pathway.

Question 40

How does feedback inhibition control enzymes?

Answer 40

When there is a large amount of product that begins to accumulate, the product binds to an early enzyme, slowing down and preventing further entry of substrates.

Question 41

What is phosphorylation regulation of enzyme?

Answer 41

Attaching a phosphate group to an amino acid side chain to regulate the enzyme.

Question 42

How does phosphorylation regulate enzyme?

Answer 42

A phosphate group is added to an amino acid side chain. The two negative charge on the phosphate group can cause a conformational change to the enzyme, altering the protein’s activity.

The process can be reversed by removing the phosphate group by a second enzyme.

Question 43

What are protein kinase?

Answer 43

Protein that drives phosphorylation; adds a phosphate group from an ATP to the protein to make it active.

Question 44

What are protein phosphatase?

Answer 44

Protein that drives dephosphorylationn; removing phosphate group from a protein, making the protein inactive.

Question 45

What is GTP Binding Protein regulation?

Answer 45

Type of phosphorylation regulation where the phosphate group is part of the guanine nucleotide and binds to protein.

Question 46

How does GTP binding protein work?

Answer 46

The protein act as molecular switch in which the nucleotide binds to the protein to activate it. If GTP is hydrolyzed into GDP, the protein becomes inactive. The GDP finally dissociate from the protein.

Question 47

How can motor protein be driven?

Answer 47

Conformational change generate orderly movement of protein. This is done by coupling one of the conformational changes to the hydrolysis of an ATP molecule. ATP protein enters the motor protein and is hydrolyzed, causing the protein to undergo a conformational shape, which the change moves it forward.

Application: “muscle walking”
Muscle Contraction
Chromosomes Spindles
Organelle Movement