Amino Acids, Peptides, & Proteins

Question 1

What are four basic functions of proteins?

Answer 1

Motion, Catalysis, Transport, & Structure

Question 2

All amino acids in proteins are in which isomer form?

Answer 2

“L” isomer

Question 3

What is the Henderson-Hasselbalch equation?

Answer 3

pKa = pH + log([Acid]/[Base])

Question 4

What is the general structure of an amino acid?

Answer 4

A carbon center with an attached R group, H atom, COO- group, and NH3+ group

Question 5

Which two aromatic side-chained amino acids absorb UV light?

Answer 5

Tryptophan & Tyrosine

Question 6

What is the isoelectric point of a protein?

Answer 6

A characteristic property of a protein; the pH at which a molecule carries no electric charge

Question 7

What is ubiquitination and what’s its function?

Answer 7

An enzymatic, protein post-translational modification process in which ubiquitin is tagged on. This is used to modify function of protein or to mark it for degradation.

Question 8

What is a peptide bond?

Answer 8

The bond between two amino acids; between the carboxyl group of one and the amino group of another.

Question 9

What kind of bonds are responsible for higher-order protein structure?

Answer 9

Non-covalent interactions such as H bonds, Van der Waals, hydrophobic interactions, and ionic interactions.

Question 10

Describe an alpha helix

Answer 10

H bonds between backbone carbonyl (CO) and imido (NH) within a polypeptide chain forms the alpha-helix; creates a right-handed screw

Question 11

Describe a beta sheet

Answer 11

Made of hydrogen bonds between neighboring strands; side chains protrude from the sheet alternating up and down; can be antiparallel or parallel

Question 12

What are the three polar and positively-charged amino acids?

Answer 12

Histidine, Lysine, Arginine

Question 13

What are the two polar and negatively-charged amino acids?

Answer 13

Aspartate, Glutamate

Question 14

About how many nonstandard amino acids exists?

Answer 14

About 300

Question 15

What is glycosylation of proteins?

Answer 15

A post-translational modification that involves adding sugars to amino acids; can be O-linked or N-linked

Question 16

What are four other methods of post-translational modification?

Answer 16

Acetylation, methylation, ubiquitination, & phosphorylation

Question 17

What is primary protein structure?

Answer 17

Primary structure is basically the o

Question 18

Describe the formation of a peptide bond

Answer 18

The amino group of one amino acid covalently bonds with the carboxyl group of the next

Question 19

Are proteins made in the N’ to C’ direction or C’ to N’?

Answer 19

N’ to C’

Question 20

What is the difference between a peptide and a protein?

Answer 20

Proteins are made up of only the 20 “protein” amino acids, while peptides are made of these 20 plus many more.

Question 21

What do proteases and peptidases do?

Answer 21

Digest proteins and peptides

Question 22

Are most peptide bonds in the trans or cis configuration?

Answer 22

Trans

Question 23

What catalyzes proline isomerization?

Answer 23

Prolyl isomerases

Question 24

Which two residues are often used for twists and turns in protein structure?

Answer 24

Glycine and Proline

Question 25

Why is carbon monoxide lethal?

Answer 25

It fits into the same binding site on heme groups that Oxygen fits into, but it binds over 20,000 times better! This prevents hemoglobin from transporting oxygen to cells.

Question 26

Describe the R and T states of hemoglobin

Answer 26

The Relaxed state is when the heme groups are not bound to Oxygen - oxygen binding affinity increases. The Tense state is when the heme groups are bound to Oxygen - oxygen binding affinity decreases.

Question 27

Does oxygen bind to hemoglobin better at higher or lower pHs?

Answer 27

Binds better at higher pH (lungs have a higher pH)

Question 28

What are Hsp70/Hsp 40 (eukaryotes) / DnaK/DnaJ (prokaryotes)?

Answer 28

Chaperones and protein folders! They are induced at elevated temperatures and bind to hydrophobit regions of unfolded proteins to prevent aggregation. They help transport some proteins across membranes in unfolded states.

Question 29

What does protein disulfide isomerase (PDI) do?

Answer 29

Reduces improper disulfide bonds and reforms them correctly.

Question 30

What does Peptide Prolyl Isomerase (PPI) do?

Answer 30

Makes proline be in cis conformation; some proteins need proline in cis conformation for proper folding

Question 31

What causes Cystic Fibrosis?

Answer 31

A mis-folded CFTR protein - usually a deletion of F58

Question 32

Describe the healthy and diseased Prion protein (PrP)

Answer 32

The diseased PrP has more beta sheets, is insoluble, and resistant to protease