Cells/Proteins KA2 Proteins

Question 1

What is the proteome?

Answer 1

The entire set of proteins expressed by a genome

Question 2

Why is the proteome larger than the number of genes?

Answer 2

Due to alternative RNA splicing and post translational modification

Question 3

Not all genes are expressed as…

Answer 3

Proteins in a particular cell

Question 4

What does amino acid sequence determine…

Answer 4

Protein structure

Question 5

Proteins are polymers of…

Answer 5

Amino acid monomers

Question 6

What do amino acid link by? What does this form?

Answer 6

AA link by peptide bonds to form polypeptides

Question 7

What is the primary structure?

Answer 7

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

Question 8

Hydrogen bonding along the … results in … ?

Answer 8

Along the backbone of the protein strand results in regions of secondary structure

Question 9

Name the types of secondary structure;

Answer 9

Alpha helices
Parallel or anti-parallel beta sheets
Turns

Question 10

Identify the structure of amino acids;

Answer 10

Basic - positively charged
Acidic - negatively charged
Polar - hydrophobic

Question 11

Polypeptide fold into a … ? What causes this confirmation?

Answer 11

Folds into a tertiary structure
This conformation is caused by bonding - such as interactions of the R groups in hydrophobic regions, ionic bonds, van der waals interactions - including hydrogen bonds and disulphides bridges

Question 12

What is a prosthetic group?

Answer 12

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

Question 13

When does quaternary structure exist?

Answer 13

In proteins with several connected polypeptide subunits

Question 14

What can interactions of the R groups be influenced by?

Answer 14

Temperature and pH

Question 15

What do R groups at the surface of a protein determine?

Answer 15

Its location within a cell

Question 16

Hydrophilic R groups will predominate…

What will hydrophobic R groups do in these proteins?

Answer 16

At the surface of a soluble protein found in the cytoplasm

Hydrophobic R groups may cluster at the centre to form a globular structure

Question 17

Describe the fluid mosaic model…

Answer 17

?

Question 18

What do regions of hydrophobic R groups allow for?

Answer 18

Allow strong hydrophobic interactions that hold integral proteins within the phospholipid bilayer

Question 19

Some integral proteins are … ?

Give some examples

Answer 19

Transmembrane

For example, channels, transporters and many receptors

Question 20

Peripheral proteins have fewer… ?

Answer 20

Hydrophobic R groups interacting with the phospholipids

Question 21

What is a ligand?

Answer 21

A substance that can bind to a protein

R groups not involved in protein folding can allow binding to these other molecules

Question 22

DNA binds to…

Answer 22

A number of proteins

Question 23

What do positively charged Histone proteins bind to?

Answer 23

Negatively charged sugar-phosphate backbone of DNA in eukaryotes

The DNA is wrapped around histones to form nucleosomes packing the DNA in chromosomes

Question 24

Other proteins have binding sites that are specific to…

Answer 24

Particular sequences of double stranded DNA and when bound to can either stimulate or inhibit initiation of transcription

Question 25

As a ligand binds to a protein binding site or as a substrate binds to an enzyme’s active site, what happens?

Answer 25

The conformation of the protein changes, this change in conformation causes a functional change in the protein

Question 26

When does induced fit occur in enzymes?

Answer 26

When the correct substrate starts to bind resulting in a temporary change in shape of the active site increasing the binding and interaction with the substrate

Question 27

(During induced fit) what happens to the conformation of the enzyme?

Answer 27

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

Question 28

In enzymes, what is related to induced fit? What does the chemical environment do?

Answer 28

Specificity between the active site and substrate is related to induced fit

The chemical environment produced lowers the activation energy required for the reaction

Question 29

Describe the difference between positive and negative modulators with relation to the substrate

Answer 29

Positive modulators increase the enzyme affinity whereas negative modulators reduce the enzyme’s affinity for the substrate

Question 30

Once catalysis takes place, what happens to the original enzyme?

Answer 30

The original enzyme conformation is resumed and products are released from the active site

Question 31

What do some proteins with quaternary structure show?

Answer 31

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

Question 32

Describe cooperativity in the binding and release of oxygen in haemoglobin and the influence of temperature and pH

Answer 32

?

Question 33

Describe the effect of temperature on haemoglobin’s ability to bind oxygen

Answer 33

As temperature increases, affinity for oxygen decreases

This is because hardworking tissues produce heat

Question 34

Describe the effect of pH on haemoglobin’s ability to bind oxygen

Answer 34

As pH decreases, affinity for oxygen decreases

This is because hardworking tissues make carbon dioxide which decreases the pH

As a result oxygen is released to tissues

Question 35

The addition or removal of phosphate from particular R groups can be used for?

Answer 35

Used to cause reversible conformational changes in proteins

Question 36

The addition or removal of phosphate from particular R groups is a common form of?

Answer 36

Post translational modification

In this way the activity of many cellular proteins such as enzymes and receptors are regulated

Question 37

What is kinase responsible for?

Answer 37

Often responsible for phosphorylation of other proteins

Question 38

What is the role of phosphatase?

Answer 38

Phosphatase catalyses dephosphorylation

Question 39

Some proteins (ATPases) use ATP for ?

Answer 39

Phosphorylation

Question 40

Give an example of how ATPases use ATP for their phosphorylation

Answer 40

Eg. Myosin has heads that act as cross bridges as they bind to actin

When ATP binds to myosin, the myosin head detaches from actin, swings forwards and rebinds

The rebinding releases ADP and a phosphate ion drags the myosin along the actin filament