Protein Intro

Question 1

What is a proteome?

Answer 1

Full set of proteins encoded by the human genome (NOT same as number of genes as 1 gene doesn’t equal 1 protein)

Question 2

What are single nucleotide polymorphisms (SNPs)? What do they give rise to?

Answer 2

Changes in a single base. Give rise to proteins that differ by one amino acid (function slightly differently)

Question 3

What is the function of enzymes?

Answer 3

Required to catalyse metabolic reactions, digestive enzymes break down nutrients into small pieces that can be readily absorbed

Question 4

What is phenylketonuria?

Answer 4

Enzymes can’t break down phenylalanine (important amino acid found it many proteins in diet)

Question 5

What is haemophilia?

Answer 5

The ability of the blood to clot is severely reduced, causing the sufferer to bleed severely from even a slight injury.

Question 6

What is haemophilia typically caused by?

Answer 6

The condition is typically caused by a hereditary lack of a coagulation factor, most often factor VIII.

Question 7

What is ferritin?

Answer 7

A blood protein that contains iron

Question 8

What is an example of a disease caused by faulty transport proteins?

Answer 8

Sickle cell anaemia; Hb isn’t synthesised correctly so problems with transport of oxygen around body

Question 9

What is myosin an example of?

Answer 9

Muscle/motor protein

Question 10

What is Duchenne muscular dystrophy?

Answer 10

Protein dystrophin is absent/ineffective so lose ability to use muscles

Question 11

What is type 2 diabetes?

Answer 11

Non-insulin dependent diabetes –> insulin receptor is faulty so can’t bind insulin properly

Question 12

What is type 1 diabetes?

Answer 12

Insulin lacking as cells in pancreas which synthesise it have been destroyed

Question 13

What is myasthenia gravis?

Answer 13

Body creates antibodies that bind to neurotransmitter receptor which leads to difficulty in getting muscles to respond to neurological signals

Question 14

How are amino acids joined?

Answer 14

By peptide bonds to make a polypeptide chain during a condensation reaction (water is eliminated)

Question 15

Peptide bonds have partial double bond characteristics. What does this mean?

Answer 15

• limited rotation around bond

- bond resonates between 2 forms; makes bonds quite rigid

Question 16

What is the 1ary structure?

Answer 16

The order of amino acids (sequence)

Question 17

What is the 1ary structure determined by?

Answer 17

The gene that codes for the protein

Question 18

What does the 1ary structure determine?

Answer 18

Structure and function of final folded protein (order of amino acids and R groups they contain)

Question 19

What is the backbone?

Answer 19

Amino acid chain (consist of alpha carbons of each amino acids connected by peptide bonds)

Question 20

What is a residue?

Answer 20

An amino acid in the polypeptide chain

Question 21

Why does a polypeptide chain have direction?

Answer 21

As amino acids have different ends (C and N terminus)

Question 22

What is 2ary structure of protein?

Answer 22

Describes local spatial arrangements of amino acids in peptide chain

Question 23

What is 2ary structure affected by?

Answer 23

Hydrogen bonds between amino acids in chain

Question 24

What do hydrogen bonds form between?

Answer 24

Between N-H and C=O groups (intrachain H bonds; occur between different parts of same chain)

Question 25

What do these hydrogen bonds do to the chain?

Answer 25

Make chain coil into alpha helix or fold into beta pleated sheet

Question 26

Describe an alpha helix

Answer 26

Formed by backbone of chain and side chains extend outside helix - H bonds lie parallel to helix

Question 27

Describe beta pleated sheet

Answer 27

Polypeptide chains run alongside one another - stabilised by H-bonding between strands - may be several strands making up sheet which are part of same chain (intrachain) or between different amino acid chains (interchain) - R grounds lie outside plane of sheet - strands can run parallel or anti-parallel

Question 28

Describe rigidity of beta pleated sheet

Answer 28

Fully extended polypeptide chain; no elasticity (rigid)

Question 29

Describe rigidity of alpha helix

Answer 29

H bonds lie parallel to helix; gives helix some elasticity

Question 30

What is the 3ary structure?

Answer 30

Overall 3D protein shape of 1ary and 2ary structures (how protein folds)

Question 31

How do soluble proteins fold?

Answer 31

Fold so interior is hydrophobic and exterior is hydrophilic

Question 32

What is 4ary structure?

Answer 32

Only some proteins consist of more than one polypeptide chain; sub-units 4ary describes spatial arrangement of sub-units

Question 33

What are the strongest forces holding structures together? Why?

Answer 33

Disulphide bonds --> strongest as covalent between pairs of Cys (sulphur containing amino acid) N.B. the 2 Cys may be in different polypeptides so attach 2 chains covalently together

Question 34

What is Cys?

Answer 34

Cysteine - sulphur containing amino acid Contains a thiol (-SH) group and can form covalent bonds with other cysteines

Question 35

What happens when 2 Cys residues are brought close together in a folded protein?

Answer 35

The 2 SH groups may react to form sulphide bond

Question 36

What is the 2nd strongest force holding structures together?

Answer 36

Electrostatic interactions (ionic bonds)

Question 37

What are ionic bonds?

Answer 37

Attraction between oppositely charged side chains This is called an ion pair and interaction is called a salt bridge

Question 38

What do ionic bonds do?

Answer 38

Stabilises structure (chains with same charge would repel and destabilise)

Question 39

What are dipoles?

Answer 39

A range of weak process that occur in electrically neutral molecules (permanent dipoles, dipole-induced interactions, London dispersion forces)

Question 40

Where do dipoles occur?

Answer 40

Occur across covalent bonds between atoms of different electronegativity so attract shared electrons in bond to different degrees

Question 41

What do dipoles lead to?

Answer 41

Polar molecules

Question 42

Why does a C=O have a dipole?

Answer 42

O has high EN so slightly -ve charge C has slightly +ve charge

Question 43

What are hydrogen bonds?

Answer 43

- Example of bond created by dipole formation - Attraction between H atom of donor group (e.g -OH and =NH) and non-bonding electrons on acceptor group (e.g O=C-) - Stabilise 3ary and 4ary interaction

Question 44

What are Van der Waal's?

Answer 44

Temporary induced dipoles. May occur by chance of be induced by proximity of another charged atom

Question 45

What interactions are most important in stabilising proteins?

Answer 45

Hydrophobic interactions

Question 46

How do hydrophobic interactions force folding of the chain?

Answer 46

- Drives hydrophobic molecules together | - Drives polar amino acids (hydrophilic) to surface of protein