Biochemistry Important Information

Question 1

What is an active site?

Answer 1

The area on an enzyme where a reaction occurs

Question 2

What is activation energy?

Answer 2

The minimum amount of energy needed for a reaction to start

Question 3

What is enzyme kinetics?

Answer 3

Measuring the rates of reaction of enzymes

Question 4

What happens in reversible inhibition?

3

Answer 4

The inhibitor can bind to and dissociate from the enzyme

Activity is lost when the inhibitor is bound

Must wait for the enzyme to become free to overcome this inhibition

Question 5

What happens in irreversible inhibition?

2

Answer 5

The enzyme is covalently modified and the activity is lost

Must replace the enzyme to overcome this inhibition

Question 6

What happens in competitive inhibition?

2

Answer 6

The inhibitor binds at the active site

This prevents the substrate from binding

Question 7

What are the three forms of reversible inhibition?

Answer 7

Competitive

Uncompetitive

Mixed

Question 8

What happens in mixed inhibition?

Answer 8

The inhibitor can bind to the free enzyme of the enzyme substrate complex

Question 9

How is Vmax and Km affected by competitive inhibition?

Binding to enzyme

Answer 9

Vmax is unchanged - i.e. it takes the same amount of enzyme to reach the max velocity

Km is increased - i.e. it takes more substrate to overcome the inhibitor

Question 10

How is Vmax and Km affected by uncompetitive inhibition?

binding to ES

Answer 10

Vmax is reduced -reduced amount of product

Km is reduced - the more substrate added to more IES made

Question 11

How is Vmax and Km affected by mixed inhibition?

Answer 11

Vmax is decreased

Hm is increased

Question 12

How does pH affect enzyme activity?

3

Answer 12

Denaturation can occur at unsuitable pH levels

Changes in the charged state of amino acid components of enzymes

Substrates can become charged which may influence which enzymes can act on it

Question 13

What is Beer Lambert’s Law?

Answer 13

Beer’s Law states that the concentration of a chemical solution is directly proportional to its absorption of light

Question 14

Describe an alpha helix

4

Answer 14

Secondary structure of a protein

Hydrogen bonding

3D structure - helix - spring

The CO group of each amino acid forms a hydrogen bond with the NH group of amino acid four residues earlier in the sequence.

Question 15

Describe a beta sheet.

5

Answer 15

Secondary structure of a protein

Hydrogen bonding

3D structure - sheets line up beside each other

The CO group of each amino acid forms a hydrogen bond with the NH group of amino acid

Either parallel = C -> N terminus matches up with another C -> N terminus chain or antiparallel = C -> N terminus matches up with N -> C chain

Question 16

What two components of amino acids is a hydrogen bond formed between?

Answer 16

The CO group of one amino acid forms a hydrogen bond with the NH group of another amino acid

Question 17

What are the consequences of resonance in the peptide bond?

3

Answer 17

The double bond is only a partial double bond - it resonates back and forth

It increases the polarity of the peptide bond

It restricts movement of the atoms in the bond (double bond is locked in position)

Question 18

What is tertiary structure of a protein?

Answer 18

Side chain bonding e.g. disulphide bridges, hydrogen bonds, salt bridges, van der Waals, hydrophobic interactions

Question 19

What are disulphide bonds?

Answer 19

Covalent link between the SH of two cysteine residues

Question 20

What is a steriosomer?

Answer 20

A molecule that are mirror images of their structure

Question 21

Define chirality

Answer 21

An object or a system is chiral if it is distinguishable from its mirror image; that is, it cannot be superimposed onto it.

Question 22

Define conditionally non-essential amino acids.

Answer 22

Amino acids produced by the body but in lower amounts and outside supplementation may be required e.g. in case of pregnancy

Question 23

Define essential amino acids.

2

Answer 23

Amino acids that cannot be produced by the body

They must be acquired via dietary or supplementary means

Question 24

Define non-essential amino acids.

Answer 24

Amino acids that can be produced by the body and therefore not required via dietary or supplementary means

Question 25

How do you know if an amino acid is hydrophilic or hydrophobic?

Answer 25

Hydrophilic amino acids will have an electronegative atom such as O, S or N as part of their variable group

Hydrophobic amino acids will have only carbons and hydrogens as part of their variable group

Question 26

How do you know if an amino acid is basic?

Answer 26

The presence of a nitrogen, hydrogen molecule with an overall positive charge

Question 27

What is a zwitterion?

Answer 27

A molecule that contains an equal number of positively and negatively charged functional groups

Question 28

What is pKa?
Give the equation
(3)

Answer 28

A measure of strength of an acid on the pH scale

pKa = -log10 Ka

The smaller the pKa, the stronger the acid

Question 29

Describe the ionisation state of an amino acid at a low pH

3

Answer 29

Low pH = plentiful H+

NH2 becomes NH3+

COOH can’t donate H+

Molecule has a positive charge

Question 30

Describe the ionisation state of an amino acid in an environment with an increasing pH
(3)

Answer 30

The COOH donates a H to become COO-

NH3+ remains

Zwitterion formed

Question 31

Describe the ionisation state of an amino acid in an environment with a high pH.
(3)

Answer 31

NH3+ loses its extra H+ and returns to NH2+

COO- remains

Overall negative charge

Question 32

Describe how the consequences of a single amino acid mutation in the context of a disease such as cystic fibrosis

Answer 32

This mutation is caused by the deletion of three base pairs of the CFTR gene leading to the loss of an amino acid called phenylalanine

Question 33

What is cystic fibrosis?

2

Answer 33

Severe damage to the lungs, digestive system and other organs in the body.

Cystic fibrosis affects the cells that produce mucus, sweat and digestive juices

Question 34

What is a chromophore?

Answer 34

An atom or group whose presence is responsible for the colour of a compound.

Question 35

What is a glycosidic bond?

4

Answer 35

A bond that forms between a C=O and a C-OH

This bond cyclises a glucose molecule (makes it a ring)

Separate glucose molecules can be linked in a similar way (condensation reaction between two cyclic glucose) using the OH of one and the OH of another - this leaves an O between the two structures

Can be alpha or beta bonds

Question 36

What is an alpha glycosidic bond?

Answer 36

An alpha bond links two sugars (rings) via a band below the plane of the ring, opposite to the configuration at C5

Question 37

What is a beta glycosidic bond?

Answer 37

A beta bond has the same configuration of the group at C5 are the same

Question 38

Write a general note on starch and glycogen

3

Answer 38

Same basic structure (alpha glyocisid bonds C1-4 branching)

Both use glucose as monomer

Different amounts of branching

Question 39

Write a note on glycogen.

5

Answer 39

Ball of glucose

C1-4 alpha bonds

Glycogenin acts as a seed to start the constriction of glycogen

About 3 times more branches compared to starch (amylopectin)

It is readily mobilized storage form of glucose

Question 40

Write a note on starch

3

Answer 40

Exists as one of two polysaccharides:
-amylose -> long unbranched chains -> linear chain or helical shape of glucose

-amylopectin -> branches -> a linear chain of glucose molecules with side chains branching off it

Stores excess glucose

Question 41

Write a note on cellulose

5

Answer 41

Polymer of glucose - thousands of glucose

Beta glycosidic bonds (B1-4)

Bond angle makes it more linear

Parallel strands interact via Hydrogen bonds

Structural polysaccharide