Enzymes and Proteins

Question 1

what structures can be part of enzymes to help them work properly?

Answer 1

cofactors and coenzymes

Question 2

what is the main function of enzymes?

Answer 2

increase the rate of spontaneous reactions
reduce activation energy for a reaction
speed up the time it takes to reach reaction equilibrium

Question 3

in what ways do enzymes reduce the activation energy of a reaction?

Answer 3

decreasing entropy (create more order)
induced fit
desolvation

Question 4

what is the active site of an enzyme complementary to and why?

Answer 4

it’s complementary to the transition state

if it was complementary to the substrate, it would be stable and not cause a reaction

Question 5

what is Vmax?

Answer 5

it is the maximum reaction speed of an enzyme when it is saturated with substrate

Question 6

what is Km in the context of enzymes and what do its values mean?

Answer 6

it’s the ratio of rate constant of breaking vs formation of an enzyme-substrate complex
high Km means poor affinity (unstable complex)
low Km means high affinity (stable complex)

Question 7

how can Km be calculated from a V0 (initial velocity)/S (substrate) plot?

Answer 7

it’s calculated as half of Vmax

Question 8

what is the basis of the Michaelis-Menten (M-M) equation?

Answer 8

that the first part of an enzyme/substrate reaction (E+S = ES) is reversible and faster than the second one (ES = E + S)

Question 9

what are isoenzymes?

Answer 9

different enzymes that catalyse the same reaction

Question 10

what are the mechanisms for multiple substrates to bind to an enzyme?

Answer 10

ternary complex formation (random or ordered)
no ternary complex (sequential, one substrate after the other)
ping pong reaction (simultaneous group transfers)

Question 11

what is an allosteric enzyme?

Answer 11

an enzyme where substrate binding to one subunit will cause other subunits to have more affinity to substrate

Question 12

what are three factors that can affect enzyme function?

Answer 12

temperature
pH
inhibitors

Question 13

what are two ways allosteric enzymes can function, and what are they classed as?

Answer 13

allosteric enzymes = regulatory enzymes
concerted model (all subunits bind at the same time)
sequential model (one subunit+substrate triggers the others to open)

Question 14

what are different types of enzyme inhibitors?

Answer 14

competitive (binds in place of substrate)
uncompetitive (binds to enzyme and changes its shape)
noncompetitive (binds after substrate to trap it)

Question 15

what are possible ways for enzymes to be modulated?

Answer 15

allosteric enzymes (concerted or sequential)
covalent modification (phosphorylation)
proteolytic cleavage (eg prodrugs)

Question 16

what can be used to study enzymes?

Answer 16

gel electrophoresis

Question 17

what is the structure of an amino acid?

Answer 17

amino group
carboxylic acid group
R side chain (gives unique properties to protein)

Question 18

what is primary amino acid structure and what bonds are present?

Answer 18

linear arrangement of polypeptides
covalent bond (peptide bonds)

Question 19

what is the secondary amino acid structure and what bonds are present?

Answer 19

spatial arrangement of linear polypeptides close to eachother
alpha helix (HN-OC) hydrogen bonds, helical shape
beta sheet (HN-OC) hydrogen bonds

Question 20

what is the tertiary amino acid structure and what bonds are present?

Answer 20

spatial arrangement of linear polypeptides far away from eachother
bonded by: disulphide bridges, hydrogen bonds, ionic bonds, hydrophobic reactions, vd Waals forces

Question 21

what is a quaternary amino acid structure?

Answer 21

arrangement of tertiary structures in subunits

Question 22

what is protein denaturation and digestion, and what can cause them?

Answer 22

denaturation - loss of secondary and tertiary structure
causes: heat, pH, chemicals, solvents
digestion - loss of primary covalent bond
causes: enzymes that cleave strong peptide bonds

Question 23

what is the effect of denaturation on a protein?

Answer 23

loss of shape
loss of function
less soluble/altered water solubility

Question 24

how can proteins be classified in seven classes?

Answer 24

aliphatic
aromatic
sulphur-containing
acids
bases
uncharged polar
other

Question 25

what are the different structural differences in proteins, and what functions can they have?

Answer 25

globular proteins - hemoglobin (enzymes, transporters, hormones, signalling)
fibrous proteins - collagen (ECM, tendons, connective tissue, bone)
membranous proteins - LDL receptor (cell-cell signalling, recognition, structure, transporters)

Question 26

what is collagen composed of?

Answer 26

three polypeptides attached with hydrogen bonds

Question 27

what are possible disorders caused by abnormalities in protein structure?

Answer 27

globular - sickle cell anaemia (Hb structure abnormal)
fibrous - scurvy, osteogenesis imperfecta (collagen weak)
membranous - familiar hypercholesterolaemia (LDL receptor mutation)

Question 28

what are some of the molecules proteins can be attached to for different functional purposes?

Answer 28

lipids - lipoproteins (carry insoluble compounds)
metals - metalloproteins (metals often needed by enzymes to carry out function)
glucose - glycoprotein (variety of functions)

Question 29

what is glycosylation and where does it occur?

Answer 29

addition of glucose molecule to protein

occurs in ER and Golgi complex

Question 30

what is the result of amino acids joining together?

Answer 30

covalent bond (peptide bond)
condensation (loss of one water molecule)