Protein Structure, Ligand Binding And Conformational Change

Question 1

What are proteins

Answer 1

Polymers of amino acid monomers

Question 2

How are amino acids linked

Answer 2

Peptide bonds to form polypeptides

Question 3

What do a,ion acids share and not share

Answer 3

Have the same basic structure but differing r groups present

Question 4

What do different r groups have

Answer 4

Different size, shape, charge, hydrogen bonding capacity, chemical reactivity

Question 5

How are amino acids classified

Answer 5

According to r groups basic, acidic, polar and hydrophobic groups

Question 6

What does the wide range of functions carried out by proteins result in

Answer 6

The diversity of amino acid R groups

Question 7

What is the primary structure

Answer 7

Sequence in which the amino acids are synthesised into the polypeptide

Question 8

What results in a secondary structure

Answer 8

Hydrogen bonding along the backbone of the protein strand

Question 9

What do secondary structures have

Answer 9

Alpha helices
Parallel or antiparellel beta pleated sheets
Turns

Question 10

LEARN HOW TO LABEL SECONDSRY STRUCTURE

Question 11

What’s a tertiary structure

Answer 11

The polypeptide folds into a tertiary structure. This conformation is stabilised by interactions betweeen R groups

Question 12

Give examples of R groups

Answer 12

Hydrophobic interactions
Ionic bonds
LDFs
Hydrogen bonds

Question 13

What’s a quaternary structure

Answer 13

Exists in proteins with two or more connected polypeptide subunits. It describes the spatial arrangement of the subunits

Question 14

What’s a prosthetic group

Answer 14

Non protein unit tightly bound to a protein necessary for its function e.g in the molecule haemoglobin

Question 15

What’s haemoglobin definition

Answer 15

Iron containing oxygen transporting protein present in the red blood cells of almost all vertebrates

Question 16

What is the ability of haemoglobin to bind to oxygen dependant on

Answer 16

Non protein haem group

Question 17

What influences interactions of R groups

Answer 17

Temperature and ph

Question 18

What happens when temperature is increase in R group

Answer 18

Disrupts the interactions that hold the protein shape. The protein begins to unfold, eventually becoming denatured

Question 19

What happens to R groups as Ph increases or decreases

Answer 19

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

Question 20

What’s a ligand definition

Answer 20

A substance that can bind to a protein

Question 21

What can R groups do that are not involved in protein folding

Answer 21

Allow binding to ligands

Question 22

What do bonding sites of R groups have when binding to ligand

Answer 22

Complementary shape and chemistry to ligand

Question 23

What happens as the ligand binds to the protein binding site

Answer 23

The conformation of the protein changes. This change I’m conformation causes functional change in the protein

Question 24

What’s allosteric definition

Answer 24

Interactions which occur between spatially distinct sites

Question 25

What does the binding of a substrate molecule of one active site of an allosteric enzyme do

Answer 25

Increases the affinity of the other active sites for binding subsequent substrate molecules

Question 26

What can the activity of allosteric enzymes do

Answer 26

Vary greatly with small changes in substrate concentrations

Question 27

What do many allosteric proteins have

Answer 27

Multiple subunits which means they have a quaternary structure

Question 28

What do allosteric proteins with multiple subunits do

Answer 28

Show cooperatively In binding which changes in binding at one subunit alter the affinity of the remaining subunits

Question 29

What sites do allosteric enzymes have

Answer 29

Active site and allosteric site

Question 30

What do modulators do

Answer 30

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

Question 31

What happens after the binding of a modulator

Answer 31

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

Question 32

What do positive and negative modulators do

Answer 32

Positive modulators increase the enzymes affinity for the substrate Negative modulators decrease the enzymes affinity

Question 33

Give examples if negative and positive modulators

Answer 33

Negative-inhibition Positive-activation

Question 34

What shows cooperatively

Answer 34

The binding and release of oxygen in haemoglobin

Question 35

What does changes if oxygen at one subunit do

Answer 35

Alter the affinity of the remaining subunits for oxygen

Question 36

What is the binding of oxygen to haemoglobin affected by

Answer 36

Ph and temperature

Question 37

Describe the effect of ph in binding of oxygen to haemoglobin

Answer 37

Decrease-decreases the affinity for oxygen Increase-increases affinity for oxygen

Question 38

Describe the effect of temperature on binding of oxygen to haemoglobin

Answer 38

Decrease- increases affinity for oxygen Increase-decreases affix y for oxygen

Question 39

What can an addition of removal of a phosphate cause

Answer 39

Reversible conformational changes in proteins, this is a common form of post translation modification

Question 40

What do protein kinases to

Answer 40

Catalyse the transfer of a phosphate group to other proteins

Question 41

What is transferred to a specific R group of proteins

Answer 41

Terminal phosphate or ATP

Question 42

What catalyses the reverse reaction of phosphate

Answer 42

Protein phosphates

Question 43

What does phosphorylation do

Answer 43

Brings about conformational changes which can affect a proteins activity

Question 44

What happens to proteins in phosphorylation

Answer 44

Some are activated others are inhibited

Question 45

What does adding a phosphate group do

Answer 45

Adds negative charges

Question 46

What is disrupted in unphosphorylated proteins

Answer 46

Ionic interactions