1.2.3 protein structure, ligand binding, conformational change

Question 1

what determines protein structure

Answer 1

amino acid sequence

Question 2

what are proteins

Answer 2

polymers of amino acid monomers

Question 3

what are amino acids linked with to form polypeptides

Answer 3

peptide bonds

Question 4

do amino acids have the same basic structure

Answer 4

yes

Question 5

how do amino acid structures differ

Answer 5

the R group present

Question 6

how do R groups of amino acids vary

Answer 6

• size
• shape
• charge
• hydrogen bonding capacity
• chemical reactivity

Question 7

how are amino acids classified

Answer 7

according to their R groups

Question 8

what are the different amino acid classifications

Answer 8

• basic (positively charged)
• acidic (negatively charged)
• polar
• hydrophobic

Question 9

what does the diversity of the R groups of amino acids result in

Answer 9

the amino acids having a wide range of functions carried out by their proteins

Question 10

what is the primary structure

Answer 10

the sequence in which the amino acids are synthesised into the polypeptide

Question 11

what results in the secondary structure

Answer 11

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

Question 12

what are examples of the secondary structures

Answer 12

• alpha helices
• parallel beta-pleated sheets
• anti-parallel beta-pleated sheets
• turns

Question 13

what does the polypeptide structure fold into

Answer 13

tertiary structure

Question 14

what stabilizes the tertiary structure (give examples)

Answer 14

interactions between R groups

• hydrophobic interactions
• ionic bonds
• london dispersion forces
• hydrogen bonds
• disulfide bridges

Question 15

what are disulfide bridges

Answer 15

covalent bonds between R groups containing sulfur

Question 16

when does a quaternary structure exist

Answer 16

in proteins with two or more connected polypeptide subunits

Question 17

what is a quaternary structure

Answer 17

the spatial arrangement of the subunits

Question 18

what is a prosthetic group

Answer 18

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

Question 19

what is the ability of haemoglobin to bind oxygen dependent on

Answer 19

the non protein haem group

Question 20

what can influence the interactions of the R groups

Answer 20

• temperature
• pH

Question 21

what happens to proteins when you increase the temperature

Answer 21

• the increased temperature disrupts the interactions that hold the protein in shape
• the protein begins to unfold, eventually becoming denatured

Question 22

what can pH affect in relation to proteins

Answer 22

the charges on acidic and basic R groups

Question 23

why does pH affect the charges on acidic and basic R groups

Answer 23

• as pH increases or decreases from the optimum, the normal ionic interactions between charged groups are lost, which gradually changes the conformation of the protein until it becomes denatured

Question 24

what does ligand binding change

Answer 24

the conformation of a protein

Question 25

what is a ligand

Answer 25

a substance that can bind to a protein

Question 26

which R groups can allow binding to ligands

Answer 26

those that are not involved in protein folding

Question 27

why can ligands attach to binding sites

Answer 27

they have complementary shape and chemistry to the ligand

Question 28

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

Answer 28

the conformation of the protein changes

Question 29

what does protein conformation cause

Answer 29

a functional change in the protein

Question 30

where do allosteric interactions occur

Answer 30

between spatially distinct sites

Question 31

what does the binding of a substrate molecule to one active site of an allosteric enzyme cause

Answer 31

an increase in the affinity of the other active sites for binding of subsequent substrate molecules

Question 32

why is the binding of substrate molecules to one active site of an allosteric enzyme of biological importance

Answer 32

the activity of the allosteric enzymes can vary greatly with small changes in substrate concentration

Question 33

what do many allosteric proteins consist of? and what does this mean for their structure?

Answer 33

multiple subunits, so they have a quaternary structure

Question 34

what does cooperativity in binding mean (when looking at allosteric proteins with quaternary structures)

Answer 34

changes in binding at one subunit alter the affinity of the remaining subunits

Question 35

what is the name of the other site on allosteric enzymes

Answer 35

allosteric site

Question 36

what do modulators do

Answer 36

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

Question 37

what happens following the binding of a modulator

Answer 37

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

Question 38

what do positive modulators do

Answer 38

they increase the enzymes affinity for the substrate

Question 39

what do negative modulators do

Answer 39

they reduce the enzymes affinity for the substrate

Question 40

what does the binding and release of oxygen in haemoglobin show

Answer 40

cooperativity

Question 41

what does the change in binding of oxygen at one subunit alter

Answer 41

the affinity of the remaining subunits for oxygen

Question 42

does temperature and pH have an influence on the binding of oxygen

Answer 42

yes

Question 43

what lowers the affinity of haemoglobin for oxygen, therefore causing a reduction in the binding of oxygen

Answer 43

- decrease in pH | - increase in temperature

Question 44

what reduces the binding of oxygen to haemoglobin, promoting increased oxygen delivery to tissue?

Answer 44

- reduced pH | - increased temperature

Question 45

what can the addition or removal of a phosphate cause

Answer 45

reversible conformational change in proteins

Question 46

is phosphorylation a form of post translational modification

Answer 46

yes

Question 47

what do protein kinases do

Answer 47

they catalyse the transfer of a phosphate group to other proteins

Question 48

where is the terminal phosphate of ATP transferred to

Answer 48

specific R groups

Question 49

what do protein phosphotases do

Answer 49

catalyses the reverse reaction of phosphorylation (removes, rather than adds)

Question 50

what does phosphorylation bring about

Answer 50

conformational changes, which can affect a proteins activity

Question 51

how is the activity of many cellular proteins, such as enzymes and receptors, regulated?

Answer 51

through phosphorylation

Question 52

is it true that all proteins are activated by phosphorylation

Answer 52

no. some are inhibited

Question 53

does adding a phosphate group add negative or positive charges

Answer 53

negative

Question 54

can ionic interactions in the unphosphorylated protein remain undisrupted

Answer 54

no, they can get disrupted and new ones will then get created