Lecture 4 - building blocks of proteins

Question 1

are amino acids usually found in the L or D form in biological systems

Answer 1

L form

Question 2

are amino acids chiral

Answer 2

yes

Question 3

what is a zwitterion

Answer 3

when they have both a positive and negative charge

Question 4

are non polar side chains hydrophobic or hydrophilic

Answer 4

hydrophobic

Question 5

how to tell if the amino acid is non polar

Answer 5

if it has only C or H at the end of their side chain

Question 6

how to tell if the amino acid is polar

Answer 6

if it also has -OH, -NH2 or -O in their side chain
if it is able to form bonds with other atoms

Question 7

are polar amino acids hydrophilic or hydrophobic

Answer 7

hydrophilic

Question 8

how to know if a amino acid is positively charged polar

Answer 8

same as polar but has + charge at pH 7

Question 9

how to know if a amino acid is negatively charged polar

Answer 9

same as polar but has - charge at pH 7

Question 10

how to know if something is ionisable or not

Answer 10

• its polar
• has an H atom that can participate in acid base reactions
• donates and accepts electrons

Question 11

what does the pKa of an ionisable group on amino acid or protein equal

Answer 11

the pH at which the group is 50% ionised

Question 12

what does the pI or isoelectric point equal

Answer 12

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

Question 13

what is post translational modification

Answer 13

a chemical group can be added to an amino acid residue AFTER translation has occurred

Question 14

what happens due to post translational modification

Answer 14

the protein is modified which can switch it on or off

Question 15

what amino acid is different to the others in terms of post translational modification

Answer 15

cystine = forms a disulfide bond instead of adding something

Question 16

what type of bond is a peptide bond

Answer 16

a covalent bond

Question 17

what are other features of a peptide bond that are important for preventing steric hinderance

Answer 17

planar = flat
trans = a-carbons go on opposite sides
dipole = ends have opposite charges

Question 18

what is special about the peptide bond in terms of the double bond

Answer 18

it has partial double bond character (when the double bond can switch from the O to the N ?)

Question 19

what do amino acids have

Answer 19

An alpha carbon, amino group, carboxyl group and side chain (R)

Question 20

what are enantiomers

Answer 20

non superimposable mirror images

Question 21

what is cystine commonly found in

Answer 21

proteases

Question 22

what is glycines R group

Answer 22

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 23

What does the R group in proline do?

Answer 23

Bends back to the main chain N forming a 5 membered covalently closed ring. This makes it rigid and an imino acid rather than an amino acid as it contains an amine

Question 24

How are negatively charged polar (acidic) amino acids shown?

Answer 24

As the conjugate base where the protons are already donated

Question 25

how is the peptide bond formed

Answer 25

via dehydration between C-terminal of one amino acid and N-terminal of another

Question 26

what is a peptide

Answer 26

short stretch of amino acids joined by peptide bonds

Question 27

what is a polypeptide

Answer 27

a longer stretch of amino acids joined by peptide bonds

Question 28

what is a protein

Answer 28

longer chain of amino acids, usually with a biological function

Question 29

what is an amino acid residue

Answer 29

amino acids that are covalently joined together in peptide of a protein

Question 30

When will disulphide bonds form?

Answer 30

In an oxidising environment

Question 31

When will disulphide bonds break?

Answer 31

In a reducing environment

Question 32

what are types of post translational modification

Answer 32

Phosphorylation, hydroxylation, carboxylation, metal ending, iodination, glycosylation and many others