3.13 - Amino Acids, Proteins and DNA

Question 1

What are the 2 functional groups of amino acids?

Answer 1

NH2 and COOH
Amine and carboxylic acid

Question 2

How many naturally occurring amino acids are there in the body?

Answer 2

20

Question 3

What type of amino acids are found in the body? What does this mean about their structure?

Answer 3

a-amino acids (alpha)
It means that the NH2 is always on the carbon next to the COOH

Question 4

Draw a general formula for a-amino acids

Answer 4

search it up
or
pmt slide 9

Question 5

Are a-amino acids chiral? Why?

Answer 5

Yes, one carbon has 4 different substituents. Except glycine, where R=H

Question 6

Which enantiomer do a-amino acids exist as in nature?

Answer 6

(-) enantiomer

Question 7

How can amino acids be synthesised industrially?

Answer 7

RCHO + NH4CN —> RCH(NH2)CN via nucleophillic addition.
RCH(NH2)CN + HCl + 2H20 —> RCH(NH2)COOH + NH4Cl
(Hydrolysis, HCl is dilute)
Need to reflux the reaction mixture

Question 8

Is the product from amino acids being synthesised naturally optically active? Why?

Answer 8

No, a racemic mixture is formed as the CN- ion can attack from above or below the planar C=O bond with equal likelihood. An equal amount of each enantiomer is formed so net effect on plane polarised light.

Question 9

In what form do amino acids exist as solids? What consequences does this have?

Answer 9

Zwitterions (ionic lattice) - high MP and BP

Question 10

What colour solids are most zwitterions at room temperature?

Answer 10

White solids

Question 11

Do zwitterions dissolve in water? Non-polar solvents? Why?

Answer 11

Yes, but not in non-polar solvents due to ionic nature/ polar bonds.

Question 12

Define a zwitterion.

Answer 12

Ions which have both a permanent positive and negative charge, but are neutral overall.

Question 13

How do zwitterions can occur in amino acids?

Answer 13

COOH is deprotonated –> COO-
NH2 is protonated –> NH3+

Question 14

What amains to amino acids in acidic conditions?

Answer 14

Gains a proton on the NH2 group

Question 15

What happens to amino acids in alkaline conditions?

Answer 15

Loses a proton from COOH group

Question 16

What is the peptide linkage?

Answer 16

-CONH-

Question 17

What is a dipeptide?

Answer 17

Two amino acids bonded together

Question 18

What name is given to chains of amino acids up to 50 amino acids?

Answer 18

Polypeptides

Question 19

What name is given to chains of amino acids with more than 50?

Answer 19

Proteins

Question 20

What are polypeptides and proteins found in?

Answer 20

• Enzymes
• Wool
• Hair
• Muscles

Question 21

What is the process called by which polypeptides or proteins can be broken down into their constituent amino acids?

Answer 21

Hydrolysis

Question 22

What conditions are needed for hydrolysis to occur?

Answer 22

• 6 moldm-3
• reflux for 24 hours

Question 23

What is the primary structure of a protein? How is it bonded?

Answer 23

The sequence of amino acids along the protein chain. Bonded by covalent bonds.

Question 24

How is the primary structure represented?

Answer 24

Sequence of 3 letter abbreviations of the amino acids

Question 25

How can the primary structure of a protein be broken up?

Answer 25

Hydrolysis 6M HCl 24 hour reflux

Question 26

What is the secondary structure of a protein?

Answer 26

The shape of the protein chain

Question 27

What are the two options for the secondary structure?

Answer 27

Alpha-helix shape or beta-pleated sheets

Question 28

How is the secondary structure held together?

Answer 28

Hydrogen bonding between C=O and H-H groups

Question 29

What is the tertiary shape of a protein?

Answer 29

Alpha-helix or beta-pleated sheet is folded into a complex 3D shape.

Question 30

How is the tertiary structure held together?

Answer 30

* Hydrogen bonding - Ionic interactions between R groups - Sulfur-sulfure bonding (disulfide brideges) - Van der Waals forces of attraction.

Question 31

Why is the tertiary structure important?

Answer 31

The shape od protein molecules is vital in their function e.g. for enzymes.

Question 32

How can amino acids bond/ be attracted to each other (3 main ways) ?

Answer 32

- Hydrogen bonding - Ionic interactions between groups on sie chains - Sulfur-sulfur bonds; 2 S atoms oxidised to form an S-S bond

Question 33

What is wool? How is it held together?

Answer 33

Protein fibre with secondary alpha-helix structure; held together by hydrogen bonds

Question 33

What does wool's structure and bonding mean for wool's properties?

Answer 33

- Can be stretched, H bonds extend. - Release it and it returns to its original shape - Wash too hot and H bonds permanently break so garment loses its shape.

Question 34

What is a TLC plate made of?

Answer 34

Plastic sheet coated with silica, SiO2. This is the stationary phase. (The solvent is in the mobile phase).

Question 35

Describe how you would carry out Thin Layer Chromatography

Answer 35

1. Spot the samples onto a pencil line a few cm above the base of the TLC plate. 2. Place this in a beaker with solvent level below the pencil line. Ensure there is a lid on the beacker to keep the inside saturated with solvent vapour. 3. Wait until the solvent front is almost at the top of the TLC plate; then remove from the beaker and analyse.

Question 36

Why does the TLC separate amino acids or other molecules?

Answer 36

Solvent carries amino acids up the TLC plate. The rate of the movement depends on the balance between that amino acids affinity for the solvent (solubility in it) and affinity for the stationary phase (attraction to the silicon with hydrogen bonding).

Question 37

What do you often have to do to enable the amino acids to be seen on the chromatogram?

Answer 37

Spray with ninhydrin (amino acids colourless, ninhydrin turns their spots purple) Or shine UV light on them

Question 38

How do you calculate an Rf value?

Answer 38

Distance moved by that substance divided by the distance moved by the solvent front.

Question 39

How can Rf values verify which amino acid is which?

Answer 39

Compare the experimental Rf values to known/ accepted values in the same solvent. Or run pure amino acids in the same solvent and compare results to identify amino acids.

Question 40

What is the 2D TLC?

Answer 40

Uses a square TLC plate. Spot the amino acids in one corner, then run TLC in first solvent. Flip the plate through 90° and repeat TLC in a second, different solvent.

Question 41

What are the benefits of 2D TLC (2 main ones)?

Answer 41

- Separates the spots more - it is extremely unlikely that 2 amino acids will have identical Rf values in 2 solvents. - Gives you 2 Rf values for each amino acids; you can be more confident in verifying the identity of the amino acids when comparing to known values, as 2 Rf values can be verified.

Question 42

How do you find the primary structure of a protein?

Answer 42

Reflux with 6M HCl and reflux for 24 hours Carry out TLC to find the number and type of amino acids present

Question 43

How do you find the secondary and/ or tertiary structure of a protein?

Answer 43

Various techniques e.g. X-Ray Diffraction

Question 44

What is an enzyme?

Answer 44

Protein bases catalysts that speed up reactions in the body by factors of upto 10^10

Question 45

How many reactions is each enzyme designed to catalyse?

Answer 45

One reaction - they are very specialised

Question 46

What is the structure of an enzyme?

Answer 46

Globular protein with an active site. Has a very particular shape.

Question 47

How does its structure help the function of the enzyme? What is the hypothesis known as?

Answer 47

The reacting molecules fit precisely into the active site and are held at exactly the right orientation to react. This is the lock and key hypothesis.