Amino Acids & Proteins

Question 1

What is a peptide?

Answer 1

A smaller unit of a protein

Question 2

What are amino acids?

Answer 2

The building blocks of peptides
They contain and amine and a carboxylic acid
The chemistry happens at the R group
Zwitterion (two ions)

Question 3

What form do amino acids normally appear in?

Answer 3

L amino acids are S

However there is one exception where L amino acid is R

Question 4

Name the aliphatic amino acids

Answer 4

Glycine (H)
Alanine (CH3)
Serine
Threonine

Question 5

Name the greasy hydrophobic amino acids

Answer 5

Valine (CH2(CH3)2)
Isoleucine (Ch2(CH3)Ch2(ch3)
Leucine (ch2ch2(ch3)2

Question 6

Name the aromatic amino acids

Answer 6

Phenylamine
Tyrosine- good for electron transfer
Tryptophan

Question 7

Name the carboxylic acids and their amides amino acids

Answer 7

Aspartic acid
Glutamic acid 
Aparagine
Glutamine 
(COOH)- provide H+

Histidine
Arginine
Lycine
(Amine)- basic side chains

Question 8

Name the sulfur containing and proline amino acids

Answer 8

Proline- links in peptide chains
Cystine- provides a thiol
Methionine- can be oxidised to protect against O2

Question 9

How are peptide bonds formed?

Answer 9

Condensation reaction between amino acids
Water is leaving group
(See mechanism)

Question 10

What makes the peptide bond planar?

Answer 10

The possible resonance forms makes the peptide bond planar

Question 11

Outline Chemical vs biological peptide bond formation

Answer 11

Chemical- acyl chlorides- cl- is a good leaving group
DCC + activated esters

Biological- activated esters from tRNA (good leaving group)
- see mechanism

Question 12

What is the primary structure?

Answer 12

The linear amino acid sequence

Question 13

Describe the process of Sanger sequencing

Answer 13

F is leaving group then H3O+

This is used to sequence polypeptide chains
See mechanism
Sangers reagent is used- bonds to chain- breaks off one amino acid

Question 14

What constrains the secondary structure

Answer 14

Planority of amide bond (resonance)
Available conformations due to free rotation around N-C and C-C bonds
NC is phi (dihedral angle)
CC is psi (dihedral angle)

Question 15

How can the secondary structure be estimated?

Answer 15

On the basis of the

1) planar peptide bond
2) estimated rotations around psi and phi
3) emerging 3D structures

Question 16

Describe the secondary structure alpha helix

Answer 16

Peptide coil shaped rod
Governed by H bonding- amide backbone can H bond to another amide bond
R groups are projected outwards

Question 17

Describe the secondary structure beta strand

Answer 17

Extended confirmation (120 torsional angle)
Side chains are projected in different directions
The B strands can align together to form a beta sheet (parallel or antiparallel) (NH2 terminus are on different sides)

Question 18

What is the secondary structure?

Answer 18

The arrangement into local folding units stabilised by hydrogen bonds

Question 19

What are examples of tertiary structure?

Answer 19

Beta barrel
Mix of B strands and alpha helix strands
Coiled coils- alpha helix

Question 20

Describe the oil drop model

Answer 20

This explains folding and structure
The chains fold to minimise interactions between hydrophobic regions and water (fold to protect hydrophobic chain on inside)
Hydrophilic region is on the outside

Question 21

What interactions provide stability to tertiary structure

Answer 21

1) hydrogen bonds
2) hydrophobic interactions between side chains
3) charged amino acids- electrostatic interactions
4) metal ion binding
5) disulfide bonding
- energetically driven to fold in water

Question 22

How do you form a disulfide bond?

Answer 22

Two SH groups react in oxidation reaction with O2 to form S-S bridge (+ 2H+ and 2e-)

See mechanism
- this requires an oxidising environment so happens extracellularly ( as there is little oxygen inside cells )

Question 23

What is quaternary

Answer 23

This is where two different proteins come together (dimers)
Proteins can also form strings
CTB= 5 individual same proteins- pentamer

Question 24

What do proteins need to be active and stable?

Answer 24

To be active proteins need to fold

To be stable they need interactions

Question 25

How can proteins cause disease?

Answer 25

Protein misfolding

Question 26

Why are co factors necessary?

Answer 26

They provide additional chemistry as many biological functions cannot be achieved with the standard 20 amino acids
Proteins recruit additional chemistry groups to aid functionalities

Question 27

Give examples of co factors?

Answer 27

Metals- redox chemistry
Haem group- carry O2
Diverse co factors derived from vitamins

Question 28

What is post translational modifications

Answer 28

These are chemical changes to a folded protein

They are covalent modifications of proteins to change its function

Question 29

Give examples of post translation modifications

Answer 29

Phosphorylation- phosphate attachment 
Glycoslation- sugar attachment 
Acylation- acyl attachment 
Alkylation- alkyl attachment 
Addition of other proteins

Question 30

What is protein phosphorylation?

Answer 30

-reversible
Attach a phosphate group using an enzyme
You can switch proteins on and off with enzymes (phosphorylation)
- some proteins may only be active when phosphorylated