Peptides 1 & 2

Question 1

What does it mean that amino acids are amphoteric?

Answer 1

Accept or donate H+

Question 2

How many different R groups is there?

Answer 2

20

Question 3

Describe non-polar, neutral amino acids?

Answer 3

No charge or electronegative atoms to form H bonds
Not soluble in H2O
Glycine unique = achiral
Proline unique = cyclic

Question 4

Describe polar, neutral amino acids

Answer 4

Partial charges = form H bonds

Soluble in H2O

Question 5

Describe charged amino acids

Answer 5

Charged side chains = form H bonds + ionic bonds

Very soluble in H2O

Question 6

Describe chirality of amino acids

Answer 6

α-C in all amino acids = chiral

EXCEPT glycine

Question 7

Where are L amino acids found?

Answer 7

Proteins

Question 8

What do most L amino acids have?

Answer 8

Absolute configuration of S

Question 9

What does zwitterionic character help to calculate?

Answer 9

pI

Question 10

How do you calculate pI?

Answer 10

Draw out reaction charges 
Then find neutral species 
Then add pKa of molecule either side of species 
The divide by 2
= pI

Question 11

How can amino acids be separated?

Answer 11

pI separation by electrophoresis
By polarity-chromatography
Ion exchange chromatography

Question 12

How can amino acids be synthesised?

Answer 12

From α-halo acids

Strecker synthesis

Question 13

Describe synthesise from α-halo acids

Answer 13

Carboxylic acid + Br2, Pbr3, H2O —-> RBrCHCOOH + excess NH3 —-> amino acid

Question 14

Describe strecker synthesis

Answer 14

Aldehyde + trace acid, NH3 —-> imine + CN, HCl —-> RCHNH3CN + HCl, H2O —-> amino acid

Question 15

Describe synthesis of peptide

Answer 15

Carboxyl group + amino group —-> Amino acid with peptide bond

Question 16

Describe peptide bonds

Answer 16

Stabilised by resonance

e- shared unequally = greater density at O

Question 17

Describe synthesis of Gly-Ala

Answer 17

Protect N in glycine
Activate carbonyl group
Solid phase synthesis

Question 18

What happens in solid phase synthesis of Gly-Ala?

Answer 18

Use resin to attach to 1st amino acid
Deprotect N
Add to activated amino acid
Then cleave resin + BOC

Question 19

What is a peptide?

Answer 19

Fewer than 50 amino acids

Question 20

What is a protein?

Answer 20

One or more peptides arranged in biologically functional way

Question 21

Describe primary structure

Answer 21

Determined by mRNA

Can use cleavage agents to determine sequence

Question 22

Describe secondary structure

Answer 22

H bonding between peptide

Alpha helix or beta sheet

Question 23

Describe alpha helix

Answer 23

Narrow tube coiled in right hand sequence
H bonds run parallel to helix
Proline interrupts helix = sharp kink

Question 24

Describe beta sheets

Answer 24

2 or more lengths of polypeptide chains lie parallel to each other
R groups point above + below sheet
BUT C=O + NH point towards each other
H bonds between sections

Question 25

What is the Ramachadron plot?

Answer 25

A way to visualise angles of amino acids in protein structure

Question 26

Describe tertiary structure

Answer 26

Interactions between R groups of amino acids | Produce other folds/interactions to give final geometric shape

Question 27

What are the 4 types of interactions that give rise to tertiary structure?

Answer 27

Ionic bonds H bonds Hydrophobic interactions Disulphide bridges (covalent)

Question 28

How is a disulphide formed? | 1

Answer 28

Mild oxidation | Thiol ----> disulphide

Question 29

How is a disulphide formed? | 2

Answer 29

Reduction | Disulphide ----> thiol

Question 30

Describe quaternary structure

Answer 30

``` Not present in all proteins 2 or more polypeptide chains interact with each other Can include inorganic groups Forces between chains = same as tertiary Fibrous or globular ```

Question 31

Is denaturation irreversible or reversible?

Answer 31

Can be either

Question 32

Why do proteins fold the way thy do?

Answer 32

Energetically favourable

Question 33

What happens of you have a loss of structure?

Answer 33

Loss of activity