Unit 1 - Cells and Proteins

Question 1

What is the proteome?

Answer 1

The entire set of proteins expressed by a genome

Question 2

What makes the proteome larger that the genome?

Answer 2

Post-translational modification and alternative/RNA splicing

Question 3

What is alternative/RNA splicing?

Answer 3

The joining of exons after introns are removed from the primary transcript

Question 4

What are introns?

Answer 4

Non-coding regions of mRNA

Question 5

What is post-translational modification?

Answer 5

Changes made to polypeptides following translation

Question 6

Examples of post-translational modification.

Answer 6

Cutting the polypeptide chain and reassemble a modified version (insulin by cleavage (cutting) of proinsulin), add a functional group such as a carbohydrate or phosphate group (add carbohydrate to make glycoprotein)

Question 7

What are the distinguishing features of protein molecules?

Answer 7

Folded nature, ability to bind tightly and specifically to other molecules (ligands)

Question 8

Binding sites on the protein are complementary to the…

Answer 8

ligand

Question 9

What does the ligand binding do to the protein?

Answer 9

Causes a conformational change

Question 10

What does a conformational change do to the protein?

Answer 10

It can result in an altered function

Question 11

What do all amino acids have?

Answer 11

A central carbon with four groups attached (an amine (NH2)), a carboxylic acid (COOH), a hydrogen and a variable R group

Question 12

What does the R group on a protein do?

Answer 12

Determines the amino acids characteristics

Question 13

Hydrophilic molecules are…

Answer 13

Polar

Question 14

Hydrophobic molecules are…

Answer 14

Non polar

Question 15

R groups that are positively charged are…

Answer 15

Basic

Question 16

R groups that are negatively charged are…

Answer 16

Acidic

Question 17

What’s the key component of a negatively charged, hydrophilic amino acid?

Answer 17

Carboxylic acid group

Question 18

What’s the key component of a positively charged, hydrophilic amino acid?

Answer 18

Amine group

Question 19

What’s the key component of a polar, hydrophilic amino acid?

Answer 19

Carbonyl, hyrdoxyl, amine groups

Question 20

What’s the key component of a non-polar, hydrophobic amino acid?

Answer 20

Hydrocarbon group

Question 21

What are the four levels of protein structure?

Answer 21

Primary, secondary, tertiary, quaternary

Question 22

What is the primary structure of a protein?

Answer 22

The linear sequence of amino acids

Question 23

Example of primary structure.

Answer 23

Insulin, shapes to bind to receptor proteins in the plasma membrane of liver muscle and fat cells

Question 24

What is the secondary structure of a protein?

Answer 24

a-helix (alpha helix) and b-pleated (beta pleated) sheets are formed by hydrogen bonding

Question 25

What type of bonding is it and where on the protein is it on secondary structure?

Answer 25

Hydrogen, backbone of the protein

Question 26

The bond in a-helices form between what two chemicals?

Answer 26

N-H and C=O groups

Question 27

What are the two varieties of beta-pleated sheets?

Answer 27

Parallel and antiparallel

Question 28

What is the tertiary structure of a protein?

Answer 28

Final 3D shape of protein fored by interactions between R-groups

Question 29

What is the difference between hydrophobic and hydrophilic amino acids in tertiary structure?

Answer 29

Hydrophobic cluster together in the interior of the protien. Hydrophilic predominate at the surface of the protein

Question 30

What bonds are involved on tertiary structure?

Answer 30

Ionic (atoms are oppositely charged) , hydrogen and disulphide (covalent bond between two thiol groups) bonds

Question 31

What is Van der Waals interaction?

Answer 31

Caused by fluctuations in elecron clouds around molecules which cause them to become slightly positively or negatively charged. May result in attraction or repulsion between atoms

Question 32

What are prosthetic groups?

Answer 32

Non-protein parts

Question 33

What do prosthetic groups do?

Answer 33

Give proteins added function e.g. haem in myoglobin

Question 34

What is quaternary structure?

Answer 34

Several connected polypeptide subunits which are linked by bonds between R groups of the polypeptide chain

Question 35

Give an example of quaternary structure.

Answer 35

Haemoglobin

Question 36

What influences the interactions of the R groups?

Answer 36

pH and temperature

Question 37

What's the difference between integral and peripheral proteins?

Answer 37

Integral proteins are held within the membrane, peripheral proteins are loosely associated with the plasma membrane

Question 38

What does it mean if some integral proteins are transmembrane?

Answer 38

They span the entire width of the membrane

Question 39

Examples of transmembrane proteins.

Answer 39

Channels, transporters and receptors

Question 40

What is a ligand?

Answer 40

A substance that can bind to a protein

Question 41

What does the fluid mosaic model describe?

Answer 41

The structure of the plasma membrane

Question 42

What are membranes comprised of?

Answer 42

A phospholipid bilayer and a patchwork of protein molecules

Question 43

What are histones?

Answer 43

Packing proteins that DNA wraps around

Question 44

How are nucleosomes formed?

Answer 44

When DNA is wrapped around histones

Question 45

What are activator proteins?

Answer 45

They bind to specific DNA sequences and stimulate transcription

Question 46

What is needed to allow a reaction to occur?

Answer 46

Activation energy

Question 47

What happens to a reaction (the activation energy) when a catalyst is present?

Answer 47

The activation energy is lowered

Question 48

In living systems, how do enzymes lower the activation energy?

Answer 48

By forming an enzyme-substrate complex

Question 49

Describe induced fit in enzymes.

Answer 49

When the correct substrate binds to the enzyme a temporary change in the conformation occurs increasing the binding and interaction (affinity) with the substrate

Question 50

What is an allosteric enzyme?

Answer 50

One which changes conformation upon binding a modulator

Question 51

Where do modulators bind on an allosteric enzyme?

Answer 51

Secondary sites called allosteric sites

Question 52

What do negative modulators do?

Answer 52

Reduce the enzyme's affinity for the substrate

Question 53

What do positive modulators do?

Answer 53

Increase the enzyme;s affinity for the substrate

Question 54

How does haemoglobin show cooperativity?

Answer 54

When each polypeptide subunit (containing a haem group capable of binding to oxygen) the next one binds more easily and more easily. This is positive cooperativity.

Question 55

What does the cooperative binding of O2 with haemoglobin do?

Answer 55

It allows blood to carry about 60 times more O2 than it could if O2 dissolved in the plasma

Question 56

What happens to the saturation of oxyhaemoglobin when the temperture is decreased and the pH is increased?

Answer 56

It increases

Question 57

What happens to the saturation of oxyhaemoglobin when the temperture is increased and the pH is decreased?

Answer 57

It decreases

Question 58

What factors affect haemoglobin's ability to bind to oxygen?

Answer 58

Temperature and pH

Question 59

What do kinase enzymes do?

Answer 59

Responsible for the phosphorylation of other proteins

Question 60

What do phosphatase enzymes do?

Answer 60

Catalyse dephosphorylation

Question 61

What does the addition or removal of phosphate from particular R groups cause?

Answer 61

Reversible conformational changes in proteins

Question 62

What is a sarcomere?

Answer 62

A basic unit of muscle

Question 63

What proteins are in a sarcomere?

Answer 63

Actin and myosin

Question 64

What happens during muscle contraction?

Answer 64

Myosin have heads that act as cross bridges as they bind to actin. When ATP binds to myosin, the myosin head detaches from actin, swings forward and rebinds. The rebinding releases the ADP and a phosphate and drags the myosin along the actin filament (power stroke)