Amino acids & Proteins part 2

Question 1

Examples of post-translational modifications to amino acids?

Answer 1

Acetylation, Amidation, Phosphorylation, Hydroxylation, Methylation, Palmitoylation, Sulphation

Question 2

Post translational modification that occurs at the N-terminus is

Answer 2

Acetylation

Question 3

Post translational modification that happens to Ser, Tyr

Answer 3

Phosphorylation

Question 4

Hydroxylation occurs at which amino acid

Answer 4

Pro

Question 5

Methylation occurs at which amino acid(s)

Answer 5

Tyr, Lys

Question 6

Palmitoylation occurs at which amino acid(s)

Answer 6

Ser, Thr

Question 7

Are all amino acids except for glycine L or D?

Answer 7

All amino acids are L, except for glycine which is D

*all the amino acids have chiral carbons and exist as isomers…glycine is achiral b/c it has two Hydrogens attached to its central carbon

Question 8

Thalidomide

Answer 8

An example of how the body recognizes different enantiomers; one has tetrogenic affects and one has the effect it was designed for

Question 9

What does chirality describe?

Answer 9

The handedness of a molecule, the ability of a molecule to rotate the plane of polarized light either to the right, D, or to the left, L

Question 10

Which form (d or l) of amino acids is incorporated into proteins in mammalian cells?

Answer 10

L-form

Question 11

A chiral molecule and its mirror image molecule are called _______ or ______

Answer 11

Stereoisomers, or enantiomers

Question 12

What is an enantiomer?

Answer 12

A non superimposable mirror image

Question 13

What does it mean to be amphoteric?

Answer 13

The COOH and NH2 groups in amino acids are capable of ionizing. Since amino acids contain both a basic and an acidic group they are referred to as amphoteric

*The predominant form of the amino acid is dependent on the pH of the solution

Question 14

At physiological pH (7.4) what is happening to the carboxyl group of an amino acid and the amino group?

Answer 14

The carboxyl group is unprotonated, and the amino group is protonated

Question 15

Isoelectric point

Answer 15

The pH at which a molecule bears no net electric charge

Question 16

Zwitterion

Answer 16

At physiological pH, the amino group is protonated (positive charge) while the carboxyl group is unprotonated (negative charge) therefore that amino acid can act as both an acid or a base, which is referred to as a zwitterion

Question 17

Describe the titration of the non polar amino acid alanine with the use of a diagram

Answer 17

see notes

Question 18

How do amino acids link together?

Answer 18

Amino acids can link together by a covalent bond between the alpha-carboxyl end of one amino acid and the alpha amino end of another

Question 19

What type of reaction is the formation of a peptide bond?

Answer 19

A condensation reaction; water is lost

Question 20

Who were the two individuals who analyzed the geometry and dimensions of peptide bonds in the crystal structures of molecules containing one or a few peptide bonds?

Answer 20

Linus pauling and robert corey

Question 21

Pauling and corey rule #1

Answer 21

the peptidly C-N linkage and the four atoms to which the C and the N atoms are directly linked always form a planar structure as though the C-N linkages is a double bond

The C-N bond length of the peptide is 10% shorter than that found in usual C-N amine bonds as the peptide bond has some double bond character (40%) due to resonance which occurs with some amides

Question 22

Pauling and Corey rule #2

Answer 22

the peptide carbonyl and the amino groups always form the maximum number of hydrogen bonds.

Question 23

How to calculate the molecule weight of a peptide

Answer 23

Add the mass of the amino acids together then subtract the mass of a water molecule for each peptide bond formed

Question 24

The torsion angles phi and psi are at which bond?

Answer 24

alpha C-N bond is phi

alpha C-C bond is psi

Question 25

Primary structure

Answer 25

Linear sequence of amino acids that are joined together by peptide bonds.

Question 26

Secondary structure

Answer 26

Refers to the amount of structural regularity or shape that the polypeptide chain adopts.

Two main types: alpha helix and beta pleated sheet

Question 27

The alpha helix

Answer 27

The polypeptide folds by twisting into a right handed screw so that all the amino acids can form hydrogen bonds with each other. This high amount of hydrogen bonding stabilises the structure so that it forms a very strong rod-like structure.

Question 28

What amino acid residue tends to destabilize the alpha-helix structure? Any others?

Answer 28

Pro
A sequence of Asp or Glu residues together can also destabilize the helix because they are highly negatively charged and thus repel each other; these repulsions are stronger than the H-bonding

Question 29

How many residues are there per turn in an alpha helix?

Answer 29

3.6

Question 30

What is the rise/residue in an alpha helix?

Answer 30

1.5 Å units

Question 31

The beta sheet

Answer 31

More H-bonding is achieved by stretching out the polypeptide chain, and laying it side by side to form H-bonds between lengths of polypeptide chain. Thus providing both inter- and intra-H bonds.

The strands can run in opposite directions to give antiparallel beta-pleated sheet or they can run in same direction to give parallel beta-pleated sheets

Question 32

Tertiary Structure

Answer 32

Concerns how the secondary structure units associate within a single polypeptide chain to give a 3D structure

Question 33

Examples of tertiary structure

Answer 33

• disulfide bridges
• hydrogen bonding
• salt bridges
• hydrophobic interactions

Question 34

Quaternary structure

Answer 34

How two or more polypeptide chains associate to form a native protein structure. Proteins with more than one polypeptide chain are said to be oligomeric

Question 35

After folding into the quaternary structure what happens to the protein

Answer 35

The three dimensional, biologically active native conformation of the protein is maintained by hydrophobic interactions, electrostatic forces, Van der Waals forces, hydrogen bonding and if present covalent disulphide bonds, in addition to the peptide bonds between individual amino acids.

Question 36

How many disulfide bonds are found in human insulin?

Answer 36

3

Question 37

Name an example of a disease that is the result of a single amino acid change to a protein?

Answer 37

Sickle cell anemia

Question 38

Globular proteins

Answer 38

Relatively spherical in shape: egg albumin, hemoglobin, myoglobin, insulin

Question 39

Haemoglobin

Answer 39

Used to transport oxygen in the blood in red blood cells to tissue cells where it is used directly

-consists of 4 protein chains and 4 haem groups

Question 40

Myoglobin

Answer 40

Present in skeletal muscles as an extra storage protein to enable muscle cells to have a readily available supply of oxygen

-consists of a single protein chain with 153 amino acids and one haem group that stores oxygen in the muscles

Question 41

What metal ion is at the center of a haem group

Answer 41

Fe 2+

Question 42

Which has a stronger affinity for oxygen: haemoglobin or myoglobin?

Answer 42

Myoglobin