Biochemistry

Question 1

What is the primary structure of proteins in an amino acid sequence?

Answer 1

The primary protein refers to the number and sequence of amino acids in its polypeptide chain.

Question 2

What is the secondary structure of proteins?

Answer 2

This refers to the folding of the polypeptide chain as a result of hydrogen bonding.

Question 3

What influences the configuration of the secondary structures?

Answer 3

The R groups along the chains and so differs the proteins and even in different sections of the same protein.

Question 4

What are the two different main types of secondary structures?

Answer 4

α-helix, β-pleated sheet

Question 5

What is α-helix?

Answer 5

An α-helix is a regular coiled configuration of the polypeptide chain resulting from hydrogen bonds forming between two peptide bonds four amino acid units apart. This twists the chain into a tightly coiled helix.

Question 6

What are the properties of α-helix?

Answer 6

They are flexible and elastic as the intra-chain hydrogen bonds easily break and re-form as the molecule is stretched.

Question 7

What is β-pleated sheet?

Answer 7

A structure composed of ‘side by side’ polypeptides which are in extended form, not tightly coiled as in the α-helix.

Question 8

How are the β-pleated sheets arranged?

Answer 8

They are arranged in pleated sheets that are cross-linked by inter-chain hydrogen bonds.

Question 9

What are the properties of β-pleated sheets?

Answer 9

They are flexible but inelastic.

Question 10

What is the tertiary structure of proteins?

Answer 10

This refers to the further twisting, folding and coiling of polypeptide chain as a result of interactions between the R groups, known as side chains. This results in a very specific compact three-dimensional structure, known as the proteins conformation. This is the most stable arrangement of the protein.

Question 11

What is the importance of the conformation in the tertiary structure?

Answer 11

The conformation is particulaily important in the globular proteins, which include all the enzymes and proteins hormones.

Question 12

Why are globular proteins water soluble?

Answer 12

They are water soluble because of their structure positions nearly all of the polar (or hydrophilic) side-chains in the interior out of contact with water.

Question 13

What is a hydrophobic interation?

Answer 13

An interaction between non-polar side chains.

(Ex. two alkyl side chains in valine; these weak interactions based on London (dispersion) forces between induced dipoles, produce non-polar regions in the interior of proteins)

Question 14

What is hydrogen bonding?

Answer 14

Between polar side chains

(Ex. Between the -CH2OH group in serine and the -CH2COOH group in aspartic acid)

Question 15

What is ionic bonding?

Answer 15

Between ide chains carrying a charge

(Ex. between the -(CH2)4NH3+ group in lysine and the -CH2COO- group in aspartic acid.

Question 16

What are disulfide bridges?

Answer 16

Between the sulfur-containing amino acid cysteine. These are covalent bonds and hence the strongest of these interactions

*DIAGRAM on pg 466 of textbook

Question 17

What does denaturing of a protein mean?

Answer 17

The interactions of hydrophobic interactions, hydrogen bonding, ionic bonding and disulfide bridges can all be upsetted by disruptions such as changes in temperature, pH or the presense of metal ions.

When a protein loses its specific tertiary structure as a result of such disruptions, it is said to be denatured. The denaturation of enzymes renders them biologically inactive, which is one of the reasons why intracellular conditions must be tightly controlled.

Question 18

What is the quaternary structure of proteins?

Answer 18

Some proteins comprise of more than one polypeptide chain, these associations between these chains are known as quaternary structure. This association involves similar forces and bonds to those found in the tertiary structure

Question 19

What are enzymes?

Answer 19

Enzymes are biological catalysts that control every reaction in biochemistry. Enzymes are specific for each reaction and can be individually controlled, they determine the cell’s reactivity at the molecular level.

Question 20

What shape are enzymes?

Answer 20

Enzymes are in compact spherical shapes when in aqueous solution in cells. Their well-defined tertiary structure gives them a specific three-dimensional shape, which is essential for enzyme activity. They are typically large molecules, containing several hundred amino acids, and some having quarternary structure.

Question 21

What are co-factors in referencing enzymes?

Answer 21

Some enzymes require non-protein molecules to be bound for activity. These are co-factors and may be organic, when they are known as coenzymes, or inorganic, such as metal ions. Common examples include vitamins, many of which act as precursors for coenzymes

Question 22

What is a substrate?

Answer 22

Enzymes are catalysts and so increase the rate of a chemical reaction without themselves undergoing permanent chemical change. The reactant in the reaction catalyzed by the enzyme is known as the substrate.

Question 23

What is an enzyme-substrate complex?

Answer 23

The action of the enzyme is due to its ability to form a temporary binding to the substrate where it is held by relatively weak forces of attraction, forming an enzyme-substrate complex.

Question 24

What is the reason for the active site in enzymes?

Answer 24

The enzyme and the substrate temporarily bind together on the active site, which s typically a pocket or groove on the surface of the protein.

Question 25

What is the substrate compared to the enzyme? Why is this?

Answer 25

The substrate is usually a much smaller molecule than the enzyme, and therefore able to fit within it.

Question 26

What is the reason for ‘chemical fit’?

Answer 26

The chemical fit impacts the formation of the complex. Its also the compatibility between the substrate and the side chains of the amino acids at the active site of the enzyme.

Question 27

What is the equation of the enzyme and enzyme substrate?

Answer 27

E+S = E-S = E-P = E+P

(Enzyme = E , Substrate = S , Product = P)

Question 28

Why are enzymes specific?

Answer 28

Enzymes are very specific to their substrate. This is resulted from its conformation, as this determines the arrangement of the side chains of the amino acids at its active site and therefore its ability to bind precisely with the substrate.

Question 29

What does a graph of substrate conformation against the rate of reaction show?

Answer 29

This graph show the distinctive shape of saturation.

Question 30

What points can be deduced from a graph showing the shape of saturation?

Answer 30

a) At low substance concentration, the rate of reaction is proportional to the substrate concentration. Enzyme is available to bind to the substrate

b) As the substrate concentration is increased the rate decreases and is no longer proportional to the substrate concentration. Some of the enzymes has its active sites occupied by substrate and is not available

c) At high substrate concentration the rate is constant and independent of substrate concentration. At this point the enzyme is saturated with substrate.

All enzymes show this but vary widely with respect to the substrate concentration.

Question 31

How does temperature effect the enzyme activity?

Answer 31

At a high temperature the enzymes are denatured and cannot be put back together and therefore the reactions cannot happen.

With too low of a temperature they are deactivated, and will not work.

All enzymes have a a designated temperature point where they work. This is why body temperature changes can be so dangerous and therefore you can die.

*Graph in the textbook on page 471

Question 32

How does pH effect the enzyme activity?

Answer 32

It influences the state of ionization of acidic or basic groups in the side chains of the protein. We can predict that at low pH, acidic and basic groups become protonated and at high pH they become deprotonated.

The precise influence of pH depends on the R groups of the amino acids in the enzyme, and so varies in different enzymes.

pH pretty much just messes with the H concentration of the enzymes.

Question 33

What is the effect of heavy metal ions on enzymes?

Answer 33

When they react they react with the -SH groups, displacing the hydrogen ion. This disrupts the folding of the protein, and may change the shape of the active site and its ability to bind substrate. This is a form of inhibition