Protein Structure, Ligand Binding and Conformational Change 1.2

Question 1

what does amino acid sequence determine?

Answer 1

protein structure

Question 2

what do allosteric proteins with multiple subunits show?

Answer 2

co-operativity

Question 3

what is co-operativity?

Answer 3

where changes in binding at one subunit alters the affinity of the remaining subunits

Question 4

what do modulators do?

Answer 4

they regulate the activity of the enzyme when they bind to the allosteric site

Question 5

give an example of co-operativity

Answer 5

the binding and release of oxygen in haemoglobin

Question 6

what factors lower the affinity of haemoglobin for oxygen?

Answer 6

decreased pH and increased temperature

Question 7

what can the addition/removal of phosphate cause?

Answer 7

it can cause reversible conformational change in proteins

Question 8

what do protein kinases do?

Answer 8

they catalyse the transfer of a phosphate group to other proteins

Question 9

where is the terminal of ATP transferred?

Answer 9

to specific R groups

Question 10

what do protein phosphates do?

Answer 10

they catalyse the reverse reaction

Question 11

what does phosphorylation do and what does it affect

Answer 11

it brings about conformational change
- affects a proteins activity

Question 12

give two examples of cellular proteins that are regulated through reversible binding of phosphate

Answer 12

enzymes and receptors

Question 13

what happens to proteins that are not activated by phosphorylation

Answer 13

others are inhibited

Question 14

where do allosteric interactions occur

Answer 14

between spatially distinct sites

Question 15

what do many allosteric proteins consist of?

Answer 15

multiple subunits (have quaternary structure)

Question 16

describe quaternary structure

Answer 16

exists in proteins with two or more connected polypeptide subunits

Question 17

what is a prosthetic group?

Answer 17

a non-protein unit tightly bound to a protein and necessary for its function

Question 18

what can interactions of R groups be influenced by?

Answer 18

temperature and pH

Question 19

what do binding sites have towards ligands

Answer 19

complementary shape and chemistry

Question 20

what is a ligand?

Answer 20

a substance that can bind to a protein

Question 21

what do R groups that are not involved in protein folding allow?

Answer 21

binding to ligands

Question 22

what happens as a ligand binds to a protein binding site?

Answer 22

conformation of the protein changes

Question 23

describe the secondary structure

Answer 23

hydrogen bonding along the backbone of the protein strand results in regions of secondary structure.

examples: alpha helices, anti-parallel/parallel, beta-pleated sheets or turns

Question 24

what is the primary structure?

Answer 24

a sequence in which amino acids are synthesised into the polypeptide

Question 25

how do R groups vary?

Answer 25

-size
-shape
-charge
-hydrogen
-capacity
-chemical reactivity

Question 26

how are amino acids classified?

Answer 26

according to they R groups

Question 27

give examples of R groups

Answer 27

basic (positively charged)
- contains an amino acid side chain (-NH2)

acidic (negatively charged)
- contains carboxylic acid side chain (-COOH)

polar
- carbonyl (-CO), hydroxyl (-OH), amine (-NH2)

hydrophobic
- hydrocarbon group (-CH3)

Question 28

why can a wide range of functions be carried out by proteins?

Answer 28

because of the diversity of R groups

Question 29

describe the structure of amino acids

Answer 29

they have the same basic structure, differing only in the R group present

Question 30

name the two functional groups that amino acids contain

Answer 30

• amine (-NH2)
• carboxylic acid (-COOH)

Question 31

what is a peptide bond?

Answer 31

a strong covalent bond between a carbon atom of one amino acid and a nitrogen atom of another

Question 32

what are amino acids linked by and what do they form?

Answer 32

they are linked by peptide bonds and they form polypeptides

Question 33

describe tertiary structure

Answer 33

the polypeptide folds into a tertiary structure - this change is stabilised by interactions between R groups:
-hydrophobic interactions
-ionic bonds
-LDFs
-disulfide bridges
-hydrogen bonds

Question 34

what happens due to the binding of a modulator?

Answer 34

conformation of the enzyme changes and alters the affinity of the active site for the substrate

Question 35

what are proteins polymers of?

Answer 35

amino acid monomers