Lecture 4 - Building Blocks of Proteins: Amino Acids

Question 1

What do all amino acids contain:

Answer 1

An alpha carbon, Amino group, Carboxyl group, Side (R) Chain

Question 2

An alpha carbon with 4 different groups is called what?

Answer 2

Chiral

Question 3

What forms can amino acids exist in?

Answer 3

L or D (predominantly L form)

Question 4

What are enantiomers?

Answer 4

Non-superimposable mirror images

Question 5

What is the predominant form of amino acids in solution?

Answer 5

Zwitterion (COOH deprotonated and NH2 protonated)

Question 6

What are common in the 20 amino acids?

Answer 6

The backbone

Question 7

What are different in the 20 amino acids?

Answer 7

The side chains

Question 8

What does each amino acid have (naming)

Answer 8

A full name, abbreviated 3 letter name, 1 letter name.

Question 9

What do the amino acids have due to their different side chains?

Answer 9

Different chemical properties

Question 10

What do amino acid side chains do in proteins?

Answer 10

Carry out the biochemical reactions for which proteins are known

Question 11

How are amino acids classified?

Answer 11

Based on their chemical properties

Question 12

What are most non-polar amino acids?

Answer 12

Hydrophobic

Question 13

Where are hydrophobic amino acids found?

Answer 13

Typically on the inside of a protein stabilising the structure (forming the hydrophobic core)

Question 14

What is glycine’s R group?

Answer 14

A hydrogen making it non-chiral, flexible because its R group is small meaning it is found in regions which need to get tight and close together

Question 15

What is cysteine commonly found in?

Answer 15

Proteases

Question 16

What do phenylalanine and tryptophan have?

Answer 16

Aromatic side chains (resonance structures)

Question 17

What does the R group in proline do?

Answer 17

Bends back to the main chain N forming a 5 membered covalently closed ring. This makes it rigid.

Question 18

What side chain do negatively charged polar (acidic) amino acids have?

Answer 18

One containing an acidic carboxyl group

Question 19

What side chain do positively charged polar (basic) amino acids have?

Answer 19

One containing a basic amine group

Question 20

What are common in non-polar side chains?

Answer 20

Have either C or H groups at end of side chain.

Question 21

What are common in polar side chains?

Answer 21

Have either -OH, -NH2, or -O at the end of their side chains.

Question 22

Non-polar amino acids are?

Answer 22

Hydrophobic

Question 23

Polar amino acids are?

Answer 23

Hydrophilic

Question 24

What are the three types of polar amino acids?

Answer 24

Uncharged, Positively charged, Negatively charged

Question 25

What is the pKa value?

Answer 25

pH at which the ionisable group is 50% ionised.

Question 26

What is the pI or Isoelectric point?

Answer 26

pH at which the net charge on an amino acid is zero

Question 27

The smaller the pKa...

Answer 27

the stronger the acid

Question 28

For non-ionisable amino acids the pKa is the ____ as the pI

Answer 28

Same

Question 29

pH < pKa = ?

Answer 29

Protonation (extra H atom)

Question 30

pH > pKa = ?

Answer 30

Deprotonation (is missing an H atom)

Question 31

Where is the RNA translated into proteins

Answer 31

ribosomes

Question 32

What is post translational modification?

Answer 32

Modification of amino acids after they are added to a protein.

Question 33

Cysteine can sometimes form a covalent bond with another nearby cysteine via?

Answer 33

Disulfide bonds.

Question 34

What are the main amino acid modification methods?

Answer 34

Phosphorylation, Hydroxylation, Carboxylation Metal binding, Iodination, Glycosylation.

Question 35

Peptide cleavage:

Answer 35

Shortening of a peptide to ensure correct folding

Question 36

Cysteine - Cysteine disulfide bond formation allows?

Answer 36

Stability of protein structure

Question 37

Phosphorylation is...

Answer 37

addition of a phosphate, often acts as a switch, turning a protein on or off.

Question 38

Glycosylation is...

Answer 38

addition of glucose/sugars, increases stability and reduces flexibility of proteins

Question 39

Hydroxylation is...

Answer 39

addition of a hydroxyl group, converts hydrophobic residues into hydrophilic residues

Question 40

Carboxylation is...

Answer 40

addition of a carboxyl group, mostly occurs in blood clotting proteins

Question 41

What is the name of the covalent bond in joining amino acids?

Answer 41

Peptide bond

Question 42

What are the characteristic of the peptide bond

Answer 42

Planar, Trans, Dipole. 40% double bond character leads to planairty, rotational barrier of -80KJ/mol.

Question 43

What are amino acid residues?

Answer 43

amino acids that are covalently bonded, leading to them being no longer complete, individual amino acids.