Week 8 (Proteins I)

Question 1

What are proteins?

Answer 1

A linear polymer of amino acids (Amino acids joined together to form long chains)

Question 2

How many different amino acids are there?

Answer 2

20

Question 3

How do amino acids differ?

Answer 3

Amino acids all have the same basic structure, but with one side chain that differs

Question 4

Which isomers are found in proteins?

Answer 4

Only L-amino acids are found in proteins

Question 5

How to amino acid side chains vary?

Answer 5

Side chains vary in size, shape, charge, polarity and chemical reactivity

Question 6

Which amino acid isn’t chiral?

Answer 6

Glycines variable group is ‘H’ so does not have 4 different groups attached to the central carbon atom

Question 7

Which amino acid links to itself?

Answer 7

Proline

Question 8

what is the 1 letter code for Glycine?

Answer 8

G (Gly)

Question 9

what is the 1 letter code for Alanine?

Answer 9

A (Ala)

Question 10

what is the 1 letter code for Valine?

Answer 10

V (Val)

Question 11

what is the 1 letter code for Leucine?

Answer 11

L (Leu)

Question 12

what is the 1 letter code for Isoleucine?

Answer 12

I (Ile)

Question 13

what is the 1 letter code for Methionine?

Answer 13

M (Met)

Question 14

what is the 1 letter code for Proline?

Answer 14

P (Pro)

Question 15

what is the 1 letter code for Phenylalanine?

Answer 15

F (Phe)

Question 16

what is the 1 letter code for Tryptophan?

Answer 16

W (Trp)

Question 17

what is the 1 letter code for Serine?

Answer 17

S (Ser)

Question 18

what is the 1 letter code for Threonine?

Answer 18

T (Thr)

Question 19

what is the 1 letter code for Cysteine?

Answer 19

C (Cys)

Question 20

what is the 1 letter code for Tyrosine?

Answer 20

Y (Tyr)

Question 21

what is the 1 letter code for Asparagine?

Answer 21

N (Asn)

Question 22

what is the 1 letter code for Glutamine?

Answer 22

E (Gln)

Question 23

what is the 1 letter code for Aspartic Acid?

Answer 23

D (Asp)

Question 24

what is the 1 letter code for Glutamic Acid?

Answer 24

E (Glu)

Question 25

what is the 1 letter code for Lysine?

Answer 25

K (Lys)

Question 26

what is the 1 letter code for Arginine?

Answer 26

R (Arg)

Question 27

what is the 1 letter code for Histidine?

Answer 27

H (His)

Question 28

What is each amino acid within a polypeptide chain called?

Answer 28

A residue

Question 29

How do you know which is residue number 1?

Answer 29

* Chain has an amino or N – terminus and a carboxyl or C – terminus. * Always go from amino to carboxyl * the N-terminal residue is numbered 1.

Question 30

What is the primary structure?

Answer 30

The primary structure of a protein is simply the amino acid sequence in the polypeptide chain Every protein has a unique, precisely defined sequence The function of a protein is dependent upon its amino acid sequence

Question 31

What determines the 3D structure of a protein?

Answer 31

Proteins fold up into complex 3-D shapes/structures which are essential for their function, and the structure is determined by the amino acid sequence.

Question 32

Describe folding of the polypeptide chain

Answer 32

- The polypeptide chain is quite flexible and can fold up to form structures - 3 types of non-covalent bond help to stabilise the folded structure

Question 33

What is the secondary structure?

Answer 33

Secondary structure is when the sequence of amino acids are linked by hydrogen bonds (between the amino hydrogen N-H and carboxyl oxygen C=O atoms in the peptide backbone) to form repeating structures: - **α-helices** - **β-sheets** -**Turns & loops**

Question 34

Describe an alpha helix

Answer 34

- The polypeptide chain forms a helical coil - Hydrogen bonding stabilises the structure - Amino acid side chains protrude on the outside of the helix

Question 35

What are important measurements characteristic of alpha helices?

Answer 35

Right-handed helix - you go from left to right as you go up the helix 36 amino acids per 10 turns = 3.6 amino acids per turn Pitch - distance along the long axis for one turn of the helix = 0.54 nm - Rise per amino acid = 0.15 nm - The C=O group of a residue i hydrogen bonds with the N-H group of residue i+4 along the sequence

Question 36

Describe the properties of beta sheets

Answer 36

- Comprised of 2 or more polypeptide β-strands - Hydrogen bonding between the strands holds them together in a sheet - Strands can be parallel or anti-parallel - Amino acid side chains are alternately above and below the plane of the β-sheet - Sometimes referred to as β-pleated sheet

Question 37

What are beta turns?

Answer 37

- Many amino acids are found in turns or loops - Particularly common are β-turns or hairpin turns, which connect the ends of two adjacent segments of an antiparallel β-sheet - Commonly contain proline residues (its unique structure allows a tighter turn) and glycine (small and flexible)

Question 38

What is the single letter code for each amino acid?

Answer 38