Biological molecules (proteins)

Question 1

What is the general sturcture of an amino acid?

Answer 1

-COOH carboxyl/carboxylic acid group
-R variable side group consists of carbon chain and may include other functiona groups (benzene ring or -OH alcohol)
-NH2 amine/amino group

Question 2

Describe how to test for proteins in a sample

Answer 2

Biuret test confirms presence of peptide bond
1. Add equal volume of sodium hydroxide to sample at room temperature.
2. Add drops of dilute copper (II) sulfate solution. Swirl to mix.
(steps 1 & 2 make Biuret reagent)
3. Positive result: colour changes from blue to purple
Negative result: solution remains blue

Question 3

How many amino acids are there and how do they differ from one another?

Answer 3

20 (naturally occuring)
differ only by side R group

Question 4

How do dipeptides and polypeptides form?

Answer 4

• Condensation reaction forms peptide bond (-CONH-) & eliminates molecule of water
• Dipeptide: 2 amino acids
• Polypeptide: 3 or more amino acids

Question 5

How many levels of protein structure are there?

Answer 5

4

Question 6

Define primary struture of a protein

Answer 6

.Sequence, number and type of amino acids in the polypeptide
.Determined by sequence of codons on mRNA

Question 7

Define secondary struture of a protein

Answer 7

.Hydrogen bonds form between O- (slightly negative) attatched to -C=O and H+ (slightly positive) attatched to -NH

Question 8

Describe the 2 types of secondary protein structure

Answer 8

a-helix:
* all N-H bonds on same side of protein chain
* spiral shape
* H-bonds parallel to helical axis

ẞ-pleated sheet:
* N-H & C=O groups alternate from one side to the other

Question 9

Define tertiary structure of a protein. Name the bonds present

Answer 9

3D structure formed by further folding of polypeptide
.disulfide bridges
.ionic bonds
.hydrogen bonds

Question 10

Describe each type of bond in the tertiary structure of proteins

Answer 10

.Disilfide bridges- strong covalent S-S bonds between molecules of the amino acid cysteine
.Ionic bonds- relatively strong bonds between charged R groups (pH changes causes these bonds to break)
.Hydrogen bonds- numerous and easily broken

Question 11

Define quarternary structure of a protein

Answer 11

.Functional proeteins may consist of more than one polypeptide
.Precise 3D structure held together by the same types of bond as tertiary structure
.May involve addition of prosthetic groups (metal ions/phosphate groups)

Question 12

Describe the structure and function of globular proteins

Answer 12

.Spherical and compact
.Hydrophilic R groups face outwards and hydrophobic R groups faced inwards= usually water-soluble
.Involved in metabolic processes (enzymes and haemoglobin)

Question 13

Describe the structure and function of fibrous proteins

Answer 13

.Can form long cahins or fibres
.Insoluble in water
.Ueful for structure and support (collagen in skin)

Question 14

Outline how chromatography could be used to identify the amino acids in a mixture

Answer 14

1. Use capillary tube to spot mixture onto pencil origin line & place chromatography paper in solvent
2. Allow solvent to run until it almost touches other end of paper. Amino acids move different distances based on relative attraction to paper & solubility in solvent.
3. Use revealing agent or UV light to see spots.
4. Calculate R, values & match to database

Question 15

What are enzymes?

Answer 15

.Biological catalysts for intra and extracellular reactions
.Specific tertiary structure determines shape of active site, complementary to a specific substrate
.Formation of enzyme-substrate complexes lowers activation energy of metablic reactions

Question 16

Explain the induced fit model of enzyme action

Answer 16

.Shape of active site is not directly complementary to substrate and is flexible
.Conformational change enables ES complexes to form
.This puts strain on substrate bonds,lowering activation energy

Question 17

How have models of enzyme action changed?

Answer 17

.Initially lock and key model: rigid shape of active site complementary to only 1 substrate
.Currently induced fit model: also explains why binding at allosteric sities can change shape of active site

Question 18

How could a student identify the activation energy of a metabolic reaction from an energy level diagram?

Answer 18

Difference between free energy of substrate and peak of curve

Question 19

Name 5 factors that affect the rate of enzyme-controlled reactions

Answer 19

.enzyme concentration
.substrate concentration
.concentration of inhibitors
.pH
.temperature

Question 20

How does substrate concentration affect rate of reaction?

Answer 20

Given that enzyme concentration is fixed, rate increases proportionally to substrate concentration

Rate levels off when maximum number of ES complexes form at any given time

Question 21

How does temperature affect rate of reaction?

Answer 21

Rate increases as kinetic energy increases and peaks at optimum temperature

Above optimum, ionic and H-bonds in 3 degress struture break= active site no longer complementary to substrate (denaturation)

Question 22

How does pH affect rate of reaction?

Answer 22

Enzymes have a narrow optimum pH range

Outside range H+/OH- ions interact with H-bonds and ionic bonds in 3 degrees structure= denaturation

Question 23

Contrast competitive and non-competitive inhibitors

Answer 23

Competitive inhibitors

similar shape to substrate = bind to active site

do not stop reaction; ES complex forms when inhibitor is released

increasing substrate concentration in decreases their effect

Non-competitive inhibitors

bind at allosteric binding site

may permanently stop reaction; triggers active site to change shape

increasing substrate concentration has no impact on their effect

Question 24

Outline how to calculate rate of reaction from a graph

Answer 24

.calculate gradient of line or gradient of tangent to a point
.initial rate: draw tangent at t=0

Question 25

Outline how to calculate rate of reaction from raw data

Answer 25

.Change in concentration of product or reactant/time

Question 26

Why is it advantageous to calculate initial rate?

Answer 26

Represents maximum rate of reaction before concentration of reactants decreases and end product inhibition

Question 27

State the formula for pH

Answer 27

pH= -log10(H+)