proteins + enzymes

Question 1

explain how proteins are formed .

Answer 1

• proteins are polymers made from amino acids joined by peptide bonds .

Question 2

what is the general structure of an amino acid ?

Answer 2

• there are 20 diff amino acids found in living organisms
• each has a central carbon atom attached to a carboxyl group and an amine group are joined .
  —> the fourth bond on the carbon atom holds an R group or side chain, which varies between different amino acids .
• -COOH carboxyl / carboxylic acid group.
• -R variable side group consists of carbon chain + may include other functional groups
• -NH2 amine/ amino group

Question 3

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

Answer 3

• 20
• different only by side “R” group = influence how amino acid interacts with other amino acids so influence protein folding

Question 4

how do dipeptides and polypeptides form?

Answer 4

• condensation reaction forms peptide bond (-CONH-) and eliminates molecule of water .
• dipeptide : 2 amino acids
• polypeptide : long chain of amino acids (3 or more) .

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 + type of amino acids in the polypeptide .
• determined by the sequence of codons on mRNA.

Question 7

define “secondary structure” of a protein .

Answer 7

• not remain flat/ straight
• hydrogen bonds form between nearby amino acids (from amine group on one amino acid to carboxyl group of another ) to form either
  an alpha helix or a beta pleated sheet .

Question 8

describe the 2 types of secondary protein structure .

Answer 8

A-helix -
- all N-H bonds on same sides of protein chain
- spiral shape
- H-bonds parallel to helical axis
- polypeptide chain coiled and held in place by hydrogen bonding between NH and CO groups of amino acids

B-HELIX
- N-H & C=O groups alternate from one side to the other .
- no coupling but adjacent polypeptide chained are held together by hydrogen bonding .

Question 9

define “tertiary structure” of a protein. name the bonds present .

Answer 9

• 3D structure - further bending/folding and coming of the polypeptide chains to form specific shape involving :
• hydrogen bonds
• disulfide bridges
• ionic bonds
• shape determined by nature of R-groups of constituent amino acids + bonds form with other R- groups .

Question 10

describe each type of bond in the tertiary structure of proteins .

Answer 10

• disulfide bridges = strong solvent S-S bonds between molecules of amino acid cysteine
• ionic bonds = relatively strong bonds between charged R groups (pH changes cause these bonds to break)
• Hydrogen bonds = numerous and easily broken

Question 11

define “quaternary” structure of a protein.

Answer 11

• structure formed from interaction from interaction of multiple polypeptide chains - functional proteins may consist of more than one polypeptide .
• precise 3D structure held together by same types of bond = consists of 4 polypeptide chains (2 alpha and 2 beta) bonded together
• ## involve addition of prosthetic groups —each chain surround an iron- containing haem group

Question 12

describe the structure and function of globular proteins .

Answer 12

• spherical + compact
• hydrophilic R group face outwards + hydrophobic R groups face inwards = usually water soluble // transported easily from one part of cell to another .
• perform functional roles and involved in metabolic processes - (enzymes / haemoglobin)

Question 13

describe the structure and function of fibrous proteins

Answer 13

• long and thin (straight chain polypeptides), repetitive sequence of amino acids that lie side by side, held in place by hydrogen bonding .
• insoluble in water
• lots of disulphide bridges - resistance to physical/chemical attack .
• useful : structure and support = collagen in skin, keratin, and elastin.

-

Question 14

describe the structure and function of collagen.

Answer 14

• insoluble protein —> 3 polypeptide chains wrapped tightly around each other forming stable quaternary structure held by numerous hydrogen bonds .
• found : connective tissues - skin, muscle + bone. less sensitive then globular proteins to change temp/ph
• rope like structure - stretch which recoils when released

Question 15

what are enzymes ?

Answer 15

• proteins that act as biological catalysts for intra + extra cellular reactions .
• formation of enzyme-substrate complexes lowers activation energy of metabolic reactions .
• specific tertiary structure determines shape of active site - complementary to a specific substrate .

Question 16

define the meaning of activation energy .

Answer 16

• the minimum amount of energy needed for a reaction to happen .
• if less energy needed - reactions can take place as lower temps than would be needed without enzymes

Question 17

explain the induced fit model of enzyme action .

Answer 17

• shape of active site is not directly complementary to substrate + is flexible .
• conformational change enables ES complexes to form.
• this puts strain on substrate bonds, lowering activation energy .

Question 18

explain the induced fit model of enzyme action .

Answer 18

1) substrate binds to the enzymes active site , forming enzyme substrate complex .
2) enzyme converts substrate into product forming EP complex
3) - product is released from the enzymes active site .

• initially lock and key model = rigid shape of active site complementary to only 1 substrate .
• currently induced = explained why binding at allosteric sites can change activities site shape .

Question 19

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

Answer 19

• difference between free energy of substrate and peak of curve .

Question 20

compare the two models of enzyme action .

Answer 20

• explains why most enzymes display high specificity to their substrates .
  but not all enzymes catalyse single chemical reaction .
• induced = better explain how catalysis actually occurs - conformational change would place stress on bonds within substrate - bonds break so products form

Question 21

how does enzyme conc affect rate of reaction ?

Answer 21

• when increases, rate of reaction increases as more active sites will be available to bind to substrate molecules

—> more frequent collisions between enzyme and substrate - more formation of enzyme - substrate complexes.

—> can be limiting factor (availability of substrate) - not result in further increase in reaction rate .

Question 22

how does substrate conc affect rate of reaction ?

Answer 22

• as increases , rate of reaction increases as more substrate molecules to fill enzymes active site
• more frequent collision so more formation of ES complexes - “saturation” point reached = rate levels off when max no. EA complexes form at any given time

Question 23

how does enzyme substrate complex reduce activation energy.

Answer 23

• if 2 substrate molecules need to be joined - being attached to enzyme holds close together - reduce repulsion between molecules so bond more easily .
• if enzyme catalysing breakdown reaction : fitting into active site puts strain on bonds in substrate - substrate molecule easily breaks

Question 24

how does temp affect rate of reaction?

Answer 24

• at low temp - slow rate of reaction as enzyme and substrate have low amounts kinetic energy . = not many collisions so reduced formation of ES complexes .
• increased temp = no. collisions increases - in increasing formation of ES complexes + increasing rate of reaction
• hydrogen bonds begin break within protein - cause unravel + become denatured .
• denatured = lose shape of active sites so cannot bind to substrate - decrease rate of reaction

Question 25

how does pH affect the rate of reaction ?

Answer 25

• each enzyme has own optimum ph at which works best .
• deviations from optimum ph change the charge on the enzyme - affects ionic binding within structure
• deviation in ph also breaks hydrogen bonds (disrupted)
• cause to change shape + becomes denatured so decrease rate of reaction . - ph deviates from enzyme optimum conditions

Question 26

explain what is meant by competitive inhibitors .

Answer 26

• fit into the active site and prevent the normal substrate from binding .
• if the conc of the substrate is increased - theres better chance that the substrate molecule will get into active site before an inhibitor + the reaction rate increases

Question 27

explain what is meant by non- competitive inhibitors

Answer 27

• binds with the enzyme at a position other than its active site
• causes enzyme change its shape so active site no longer bind with substrate -
• increasing substrate conc has no effect on the reaction rate .

Question 28

constrast competitive + non competitive inhibitors .

Answer 28

COMPETITIVE .
- similar shape to substrate = bind to active site
- don’t stop reaction = ES complex forms when inhibitor is released
- increasing substrate conc decreases their effects .

NON-COMPETITIVE
- 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 29

state the formula of pH

Answer 29

• pH = -log10[H+]