3.1.4 Proteins

Question 1

what is the general structure of an amino acid?

Answer 1

-COOH carboxyl/ carboxylic acid group
-R variable side group consists of carbon chain and may include other functional groups e.g. 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) sulphate 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
differ only by side ‘R’ group

Question 4

how do dipeptides and polypeptides form?

Answer 4

condensation reaction forms peptide bond (-CONH-) & eliminates a molecule of water
dipeptides: 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 structure 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 structure of a protein

Answer 7

hydrogen bonds form between O delta negative attached to -C=O & H delta positive attached to -NH

Question 8

describe the two types of secondary protein structure

Answer 8

alpha helix
all N-H bonds on same side of protein chain
spiral shape
H-bonds parallel to helical axis
beta pleated sheet
N-H and C=O groups alternate from one side to another

Question 9

define tertiary structure of a protein and 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

disulfide bridges: strong covalent S-S bonds between molecules of the amino acid cysteine
ionic bonds: relatively strong bonds between charged R groups (pH changes cause these bonds to break)
hydrogen bonds: numerous & easily broken

Question 11

define quaternary structure of a protein

Answer 11

functional proteins 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 e.g. metal ions or phosphate groups

Question 12

describe the structure and function of globular proteins

Answer 12

spherical & compact
hydrophilic R groups face outwards & hydrophobic R groups face inwards = usually water-soluble
involved in metabolic processes e.g. enzymes & haemoglobin

Question 13

describe the structure and function of fibrous proteins

Answer 13

can form long chains or fibres
insoluble in water
useful for structure and support e.g. collagen in skin

Question 14

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

Answer 14

use capillary tube to spot mixture onto pencil origin line & place chromatography paper in solvent
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
use revealing agent or UV light to see spots
calculate Rf values & match to database

Question 15

what are enzymes?

Answer 15

biological catalysts for intra & extracellular reactions
specific tertiary structure determines shape of active site, complementary to a specific substrate
formation of enzyme-substrate (E-S) complexes lowers activation energy of metabolic reactions

Question 16

explain the induced fit model of enzyme action

Answer 16

shape of active site is not directly complementary to substrate & is flexible
conformational change enables E-S 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 sites 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 & peak of curve

Question 18

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

Answer 18

enzyme concentration
substrate concentration
concentration of inhibitors
pH
temperature

Question 18

how does substrate concentration affect the rate of reaction?

Answer 18

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 18

how does enzyme concentration affect rate of reaction?

Answer 18

given that substrate is in excess, rate increases proportionally to enzyme concentration
rate levels off when maximum number of ES complexes form at any given time

Question 19

how does temperature affect rate of reaction?

Answer 19

rate increases as kinetic energy increases & peaks at optimum temperature
above optimum, ionic and H-bonds in tertiary structure break = active site no longer complementary to substrate (denaturation)

Question 20

how does pH affect rate of reaction?

Answer 20

enzymes have a narrow optimum pH range
outside range, H+/OH- ions interact with H-bonds & ionic bonds in tertiary structure = denaturation

Question 20

what are the differences in competitive and non-competitive inhibitors

Answer 20

competitive inhibitors have a similar shape to substrate which means they bind to the active site whereas non-competitive inhibitors bind at allosteric binding sites
competitive inhibitors do not stop the reaction, E-S complex forms when inhibitor is released whereas non competitive inhibitors may permanently stop the reaction; trigger active site to change shape
competitive inhibitors are affected by increasing substrate concentration which decreases their affect whereas it has no effect in non competitive inhibitors

Question 21

outline how to calculate rate of reaction from a graph

Answer 21

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

Question 22

outline how to calculate rate of reaction from raw data

Answer 22

change in concentration of product or reactant / time

Question 22

why is it advantageous to calculate initial rate?

Answer 22

represents maximum rate of reaction before concentration of reactants decreases & ‘end product inhibition’

Question 23

state the formula for pH

Answer 23

pH = -log10 [H+]