Lecture 4 - Building Blocks of Proteins

Question 1

Zwitterion

Answer 1

Both positive and negative charges

Question 2

Non polar

Answer 2

hydrophobic

Question 3

Amino acids have

incl hows its classed

Answer 3

ionisable groups

Classed using pKa

Question 4

pKa

Answer 4

pH where an ionisable group is half ionized

Question 5

pI

isoelectric point

Answer 5

pH where the whole molecule has a charge of 0

Question 6

Amino acid properties

Answer 6

Amino Group (NH2)
Carboxyl Group (COOH)
Sidechain (R)

Question 7

Amino acid are

Answer 7

Chiral

Question 8

What do 20 amino acids have?

Answer 8

Same backbone
Different sidechains (R)

Question 9

Each amino acid has a different

Answer 9

name

Question 10

Sidechains of amino acids in proteins are arranged to

Answer 10

carry out chemical reactions

Question 11

Amino acid sidechain perform

Answer 11

biochem of proteins

attach to protein backbone

Question 12

Non polar amino acids

Answer 12

Glycine
Alanine
Valine
Leucine
Isoleucine
Methionine
F (Phenylalanine)
W (Tryptophan)
Cysteine
Proline

“Grandma Always Visits London In May For Winston’s Christmas Party”

Question 13

Negatively charged (acidic) polar amino acids

Answer 13

Aspartic acid (D)
Glutamic acid (E)

Question 14

Positively charged (basic) polar amino acids

Answer 14

K (Lysine)
R (Arginine)
Histidine

“Knights Riding Horses”

Question 15

Uncharged polar amino acids

Answer 15

Threonine (Thr)
Q (Glutamine, Gln)
Serine
Y (Tyrosine, Tyr)
N (Asparagine, Asn)

“The Queen Stole Your Nose”

Question 16

Why are 1 letter abbreviations for amino acids useful?

Answer 16

Sequence alignment

Describe mutations

Question 17

Why are 1 letter abbreviations for amino acids useful example
Old way
“From a glutamate to a valine at position 6”
whats the new way

Answer 17

E6V

1st letter - wild type or native amino acid
Number - Location of mutation
2nd letter - Mutated residue

Question 18

Some amino acids have

Answer 18

ionisable groups

Question 19

what parts of amino acids in solution are usually charged?

Answer 19

amino and carboxyl ends

Question 20

Some amino acid side chains are

Incl which contribute to?

Answer 20

ionisable

net charge of the amino acid

Question 21

How can ionisable side chains of amino acids be classified?

Answer 21

pKa value

Question 22

Amino acids ionisable side chains examples

Answer 22

Aspartic acid
Glutamic acid
Histidine
Lysine
Arginine
Cysteine
Tyrosine

Question 23

pKa value for an ionizable group on an amino acid or

protein is

Answer 23

pH at which the group is 50% ionized

Question 24

pI, or isoelectric point is

Answer 24

pH at which the net

charge on an amino acid (or protein) is zero

Question 25

all amino acids start out as

Answer 25

standard 20

Question 26

standard 20 of amino acids are

Answer 26

“translated” from RNA into proteins at the ribosome

Question 27

“post-translational modification”

Answer 27

amino acids modified after they are added to a | protein

Question 28

“post-translational modification” example

Answer 28

disulfide bond between 2 cysteines

Question 29

Other Amino Acid Modifications

Answer 29

1. Phosphorylation (add phosphate) 2. Hydroxylation (add hydroxyl) 3. Carboxylation (add carboxyl) 4. Metal Binding (add metal) 5. Iodination (add iodine) 6. Glycosylation (add glucose)

Question 30

Phosphorylation

Answer 30

control enzyme activity – | ON/OFF

Question 31

Hydroxylation

Answer 31

prevent connective tissues diseases and scurvy

Question 32

Carboxylation

Answer 32

need for blood clotting | metal binding

Question 33

Examples of Some Amino Acids that can be modified after translation

Answer 33

Phosphoserine Phosphothreonine Phosphotyrosine Glycosylation of Threonine

Question 34

How are proteins made?

Answer 34

joining amino acids together with a covalent peptide bond

Question 35

Peptide

Answer 35

short stretch of amino acids joined together by peptide bonds

Question 36

Protein

Answer 36

long chain of amino acids joined together with a biological function

Question 37

amino acid residues

Answer 37

amino acids bond together no longer complete, individual, amino acids.

Question 38

How did Linus Pauling and Robert Corey determine structure of peptide bond?

Answer 38

X ray Crystallography

Question 39

The Peptide Bond

Answer 39

Planar Trans Dipole

Question 40

What do we mean by “amino acids are chiral”?

Answer 40

exist in two forms have D- and L-isomers of amino acids. have at least one chiral centre. central carbon has four different groups attached

Question 41

What are the 4 main groups of amino acids, as discussed in the lecture?

Answer 41

Non Polar -'ve Polar (acid) +'ve Polar (basic) Uncharge Polar

Question 42

Where in a protein would you expect to find non-polar amino acid residues?

Answer 42

Interior hydrophobic away from water

Question 43

What chemical groups would we expect to find in the R-group of an ionizable amino acid?

Answer 43

``` Aspartic Acid (pKa = 4) Glutamic Acid (4) ``` Histidine (6) Lysine (10) Arginine (12.5) Cysteine (8) Tyrosine (10)

Question 44

What is the name of the bond that links amino acids in the polypeptide chain?

Answer 44

Peptide bond (Covalent bond)

Question 45

What are the key properties of peptide bond?

Answer 45

Planar, trans, dipole

Question 46

List some common examples of post-translational modifications.

Answer 46

1. Phosphorylation (add phosphate) 2. Hydroxylation (add hydroxyl) 3. Carboxylation (add carboxyl) 4. Metal Binding (add metal) 5. Iodination (add iodine) 6. Glycosylation (add glucose)

Question 47

What are some important functions of posttranslational modifications?

Answer 47

control enzyme activity – ON/OFF prevent connective tissues diseases and scurvy need for blood clotting metal binding