Protein Structure And Function

Question 1

What groups surround the alpha carbon in an amino acid?

Answer 1

Variable side chain
Amino group
H atom
Carboxyl group

Question 2

How are amino acids classified?

Answer 2

R groups

Question 3

Define AA residue.

Answer 3

Remnants of AA after it has been joined by a peptide bond to form a protein

Question 4

What angle is better the alpha carbon and C

Answer 4

Psi

Question 5

Name the angle between the alpha carbon and N

Answer 5

Phi

Question 6

Give features of peptide bond.

Answer 6

Partial double bond character 
Planar 
Rigidity- no rotation 
Resonance 
Stereoisomerism

Question 7

What is the primary structure?

Answer 7

AA sequence

Question 8

What is the secondary structure?

Answer 8

Locals spatial arrangement of polypeptide backbone

Alpha helix and beta sheet

Question 9

What is tertiary structure?

Answer 9

Overall 3D configuration of the protein

Question 10

What is the quaternary structure?

Answer 10

Association between different polypeptides to form multi subunit protein

Question 11

Define motif

Answer 11

Folding pattern of 1+ elements of secondary structure

Question 12

Domain

Answer 12

Polypeptide folded to distinct shape with functional role

Question 13

Define pI

Answer 13

The pH at which a protein has no overall net charge

Exists as a zwitterion

Question 14

Define pKA. What does pKa tell you about the side chain?

Answer 14

PKa is the pH at which there is 50% dissociation. Provides information about how strong an acid is.
High pKa = positively charged R group
Low pKa = negatively charged R group

Question 15

What happens if pH is smaller than the pKa of a amino acid?

Answer 15

Protonated

Question 16

What happens if pKa is greater than the pH ?

Answer 16

Deprotonated

Question 17

What does an Isoelectic point greater than 7 mean about the amino acids?

Answer 17

Basic protein

Increasing number of positive amino acids

Question 18

What happens if the isoelectric point is smaller than 7?

Answer 18

Acidic protein

Increasing number of negatively charged amino acids

Question 19

What plot is used to predict the secondary structures of a protein from it primary sequence?

Answer 19

Ramachandran

Question 20

What forces stabilise an alpha helix?

Answer 20

H bonds between N-H and C=O 4 amino acids apart

Question 21

What happens to the H bonds in a parallel beta sheet compared with a anti parallel beta sheet?

Answer 21

Same location however increased bio due angle and therefore weaker

Question 22

What is the Henderson - Hasselbach equation?

Answer 22

Henderson- Hasselbach = pH= pKa + log [A-]

[HA]

Question 23

How can you identify an acidic amino acid?

Answer 23

Side chain negatively charged- indicated H+ has been lost

Question 24

How can you identify a basic amino acid?

Answer 24

Side chain has positive charge indicating it has gained a proton

Question 25

What makes an amino acid polar or non-polar

Answer 25

Difference in electronegativity between atoms on side chain

Question 26

What makes an amino acid hydrophilic or hydrophobic?

Answer 26

``` Polar= hydrophilic Non-polar= hydrophobic ```

Question 27

What is an aliphatic amino acid?

Answer 27

Straight side chain with H and C

Question 28

What is an aromatic side chain?

Answer 28

Side chain with structure similar to that of benzene

Question 29

What is the hydrophobic effect?

Answer 29

Internalisation of hydrophobic aa’s leaving hydrophilic aa’s on the surface Not true from PM proteins

Question 30

What forces stabilise the primary structure?

Answer 30

Covalent peptide bonds

Question 31

What forces stabilise the secondary structure?

Answer 31

H bonds

Question 32

What forces stabilise the tertiary and quaternary structures?

Answer 32

``` Covalent disulphide bonds Ionic H bonds Vdw Hydrophobic effect ```

Question 33

Where do ionic interactions occur?

Answer 33

Between charged side chains form salt bridge

Question 34

Where do disulphide bonds form? Which proteins are they most commonly found in?

Answer 34

Between cysteine residues | Found in secreted proteins as extracellular environment is harsher

Question 35

Where do h bonds form?

Answer 35

Between electronegative atom and a H bound to another electronegative atom NOF

Question 36

What are vdw forces?

Answer 36

Dipole-dipole interactions that result form the transient localisation of electrons at any given moment. Intrinsic to any bond type

Question 37

What is the native conformation of a protein?

Answer 37

Folded protein that is functional

Question 38

How to detergents and organic solvents cause desaturation of a protein?

Answer 38

Disrupt hydrophobic interactions

Question 39

How does a change in pH alter protein structure?

Answer 39

Change in ionisation state of amino acids

Question 40

Outline how proteins fold

Answer 40

Ordered process as would take too long other wise Localised folding whereby stable conformations maintained Process driven by need to find most stable conformation

Question 41

Why does protein misfolding cause disease?

Answer 41

Misfolded proteins non functional therefore unable to work Can cause other proteins to misfold Accumulate in cells