1.2- Proteins (after prelim)

Question 1

4 structures of protein

Answer 1

primary, secondary, tertiary, quaternary

Question 2

amino acids link by ….. bonds to form …..

Answer 2

peptide, polypeptides

Question 3

Primary structure of protein

Answer 3

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

Question 4

Due to the make up of AAs, the primary sequence has an ……… at one end and a ……. at the other

Answer 4

N-terminus, C-terminus (amino & carboxyl)

Question 5

Secondary structure of protein

Answer 5

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

Question 6

3 types of secondary structure

Answer 6

alpha helix
beta sheets
turns

Question 7

Alpha helix (secondary structure)

Answer 7

formed by twisting the polypeptide chain into a spiral and then stabilising with hydrogen bonding
The R groups stick out

Question 8

Beta sheet (secondary structure)

Answer 8

have parts of the chain running alongside each other, forming a sheet
The R groups sit above and below the sheet

Question 9

Anti-parallel beta sheets

Answer 9

the chains run in opposite directions from each other

Question 10

Tertiary structure

Answer 10

the final folded shape of the polypeptide

is stabilised by many different interactions between the R groups of AAs

Question 11

Possible R group interactions for tertiary structure

Answer 11

hydrophobic interactions
ionic bonds
LDFs
hydrogen bonds
disulphide bridges

Question 12

What do turns (secondary structure)

Answer 12

They reverse the direction of the polypeptide chain and the chain folds back on itself.

Question 13

hydrophobic interactions (tertiary)

Answer 13

hydrophobic amino acids tend to cluster together on the interior of a protein, away from the surface (and away from water)

Question 14

Ionic bonds (tertiary)

Answer 14

when atoms that are oppositely charged are held by an electrostatic attraction
COOH and NH2 become COO- and NH3+, they are strongly charged and attracted to each other

Question 15

LDFs (tertiary)

Answer 15

weak interactions between the electron cloud of atoms

may result in an attraction/repulsion between atoms

Question 16

Hydrogen bonds (tertiary)

Answer 16

weak

electrostatic attractive interaction between a H atom and an electronegative atom (oxygen, nitrogen)

Question 17

Disulphide bridges (tertiary)

Answer 17

covalent bond between R groups containing sulphur

Question 18

Quaternary structure

Answer 18

exists in proteins with two or more connected polypeptide subunits which are linked by bonds between the R groups

Question 19

Quaternary structure describes the ……… arrangement of the subunits

Answer 19

spacial arrangement

Question 20

prosthetic group

Answer 20

a non-protein unit tightly bound to a protein and necessary for its function
e.g., haem in haemoglobin. The ability of haemoglobin to bind oxygen is dependent upon the non-protein haem group.

Question 21

interactions of the R groups can be influenced by

Answer 21

pH and temperature

This is why pH and temperature will affect the structure (and function) of a protein.

Question 22

Increasing temperature disrupts the interactions that hold the protein in…

Answer 22

shape

The protein begins to unfold, eventually becoming denatured.

Question 23

As pH increases/decreases from the optimum, the normal ……………….. between charged groups are lost

Answer 23

ionic interactions

which gradually changes the conformation of the protein until it becomes denatured

Question 24

ligand

Answer 24

a substance that can bind to a protein

Question 25

R groups not involved in protein folding can allow binding to

Answer 25

ligands

Question 26

Binding sites will have …………. to the ligand

Answer 26

complementary shape and chemistry

Question 27

As a ligand binds to a protein-binding site the ………of the protein …….

Answer 27

conformation of the protein changes

This change in conformation causes a functional change in the protein

Question 28

When developing drugs researchers use

Answer 28

molecular modelling techniques

Question 29

allosteric enzyme

Answer 29

an enzyme whose activity is regulated by altering its conformation

Question 30

Many allosteric proteins consist of multiple…

Answer 30

subunits (have quaternary structure)

Question 31

Allosteric interactions occur between

Answer 31

spatially distinct sites

Active site = substrate, allosteric site = substance other than substrate

Question 32

Modulators

Answer 32

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

Question 33

Following binding of a modulator, the conformation of the enzyme…

Answer 33

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

Question 34

Negative modulators -

Answer 34

reduce the enzyme’s affinity for the substrate = decrease activity

Question 35

Positive modulators -

Answer 35

increase the enzyme’s affinity for the substrate = increase activity

Question 36

Allosteric proteins with multiple subunits show ……. in binding…..

Answer 36

show co-operativity in binding, in which changes in binding at one subunit alter the affinity of the remaining subunits

Question 37

The binding of a substrate molecule to one active site of an allosteric enzyme

Answer 37

increases the affinity of the other active sites for binding of subsequent substrate molecules.

Question 38

Allosteric enzymes contain a second type of

site, called an

Answer 38

allosteric site

Question 39

The binding and release of oxygen in

haemoglobin shows

Answer 39

co-operativity

Question 40

Changes in binding of oxygen at one subunit

alter the

Answer 40

affinity of the remaining subunits for

oxygen.

Question 41

A decrease in pH or an increase in temperature lowers the …….. of haemoglobin for oxygen,

Answer 41

A decrease in pH or an increase in temperature lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced.

Question 42

Reduced pH and increased temperature in actively respiring tissue will reduce the binding of oxygen to

Answer 42

haemoglobin promoting increased oxygen delivery to tissue

Question 43

Phosphorylation of proteins is a common form of

Answer 43

post-translational modification.

Question 44

post-translational modification

Answer 44

This is when a phosphate group is added to the protein.

Question 45

The addition or removal of phosphate can cause…

Answer 45

reversible conformational changes in proteins.

Question 46

Protein Kinases

Answer 46

Catalyse the transfer of a phosphate group from ATP to other proteins
The terminal phosphate of ATP is transferred to specific R groups

Question 47

Protein Phosphatases

Protein phosphatases catalyse the

Answer 47

reverse reaction

They catalyse the transfer of a phosphate group from proteins onto ADP to regenerate ATP

Question 48

Phosphorylation brings about

Answer 48

conformational changes, which can affect a protein’s activity.
The activity of many cellular proteins, such as enzymes and receptors, is regulated in this way.

Question 49

Some proteins are …… by phosphorylation while others are……

Answer 49

activated, inhibited