Amino Acids and Protein Structure

Question 1

Which amino acids are nonpolar and aliphatic?

Answer 1

Glycine, Alanine, Proline, Valine, Leucine, and Isoleucine

Question 2

Which amino acids are aromatic?

Answer 2

nonpolar- Phenylalanine

more polar- Tyrosine and Tryptophan

Question 3

Which amino acids are polar, uncharged?

Answer 3

Asparagine, Glutamine, Serine, and Threonine

Question 4

Which amino acids are sulfur-containing?

Answer 4

Methionine and Cystine

Question 5

Which amino acids are acidic?

Answer 5

Aspartate and Glutamate

Question 6

Which amino acids are basic?

Answer 6

Arginine, Lysine, and Histidine

Question 7

Alteration of pH has effects on the ____ of amino acids, and therefore on _____.

Answer 7

charges, proteins

Question 8

For each protein, there is a certain ____ where the net charge on the protein is zero, this is the _____ of the protein.

Answer 8

pH, pI (isoelectric point)

Question 9

What type of bond does Cysteine form?

Answer 9

disulfide bonds between 2 cysteines

Question 10

Selenocysteine is found where?

Answer 10

in a few enzymes where it is essential for activity

Question 11

How can amino acids be modified?

Answer 11

carbohydrate additon, lipid addition, regulation, and modified amino acids

Question 12

Saccharides bound to proteins

Answer 12

Glycoproteins and proteoglycans

Question 13

O-linked

Answer 13

Serine, Threonine, and Tyrosine (saccharides bound to proteins)

Question 14

N-linked

Answer 14

Asparagine (saccharides bound to proteins)

Question 15

Lipid addition

Answer 15

fatty acylation or prenylation

• palmitoylation of cysteine residue
• myristoylation of a glycine residue
• prenylation of a cysteine residue
• may “anchor” a protein to a membrane, may also be involved in regulation

Question 16

Regulatory modifications

Answer 16

reversible

• phosphorylation (Serine, Threonine, Tyrosine)
• acetylation (lysine)
• ADP-ribosylation (arginine, glutamine, cysteine)

Question 17

Peptide bond

Answer 17

Bond between the alpha-carboxyl group of one amino acids and the alpha-amino group of another amino acid. Bond is planar. Adjacent R-groups are trans. Proteins are linear.

Question 18

Residue number 1 of the primary structure is called what?

Answer 18

amino-terminal (N-terminal)

Question 19

The last residue of the primary structure is called what?

Answer 19

carboxyl-terminal (C-terminal)

Question 20

Polymorphism (primary structure)

Answer 20

genetic variation in species, possible variation in phenotype

Question 21

Developmental variation (primary structure)

Answer 21

different protein isoforms or isozymes expressed at different developmental stages

Question 22

Tissue specific isoforms (primary structure)

Answer 22

different protein isoforms or isozymes are expressed at the same time but are restricted to different tissues
(ex. creatine kinase and lactate dehydrogenase)

Question 23

Secondary structure

Answer 23

recurring, localized structures found within regions of a polypeptide chain (alpha-helix and beta-pleated sheet)

Question 24

Alpha-helix

Answer 24

stabilized by hydrogen bonds between the amide hydrogen of an amino acyl residue and the carbonyl oxygen atom of a second acyl residue

Question 25

Beta-pleated sheet

Answer 25

- stabilized by hydrogen bonds between amide hydrogens and carbonyl oxygens - parallel sheets are oriented in the same direction relative to N and C termini

Question 26

Tertiary structure

Answer 26

the folding pattern of the secondary structural elements into a 3D conformation

Question 27

Forces involved in tertiary structure

Answer 27

hydrogen bonds, salt bridges, hydrophobic interactions, Van der Waals forces, and disulfide bridges

Question 28

Globular proteins

Answer 28

the "core" contains hydrophobic amino acyl resides while charged polar amino acyl resides are on the surface (these interact with the polar aquaous environment and form "salt bridges")

Question 29

Transmembrane proteins

Answer 29

usually alpha-helices with hydrophobic resides exposed to lipid environment

Question 30

Quaternary structure

Answer 30

association of individual polypeptide chain subunits into one functional protein

Question 31

Forces involved in quaternary structure

Answer 31

Globular proteins- hydrogen bonding, hydrophobic interactions, salt bridges and ionic bonds, rarely disulfide bonds Fibrous connective tissue- covalent linkages

Question 32

Functional aspects of quaternary structure

Answer 32

increased stability due to increased interactions, cooperativity between subunits, different subunits may have different activities which cooperate in overall function

Question 33

What specifies the folding of the mature protein?

Answer 33

the primary structure

Question 34

Do all proteins fold spontaneously?

Answer 34

No, some proteins require specific cellular processes that promote proper folding

Question 35

What cellular processes promote proper folding in proteins?

Answer 35

some heat shock proteins (hsp) prevent improper folding, some hsps require energy, and cis-trans isomerases and disulfide isomerases ensure proper folding

Question 36

What is chromatography?

Answer 36

separations of compounds based on relative affinity of compounds for a given stationary phase and for the mobile phase

Question 37

Types of chromatography

Answer 37

size exclusion (gel filtration), ion exchange, hydrophobic interaction, affinity, and high pressure liquid chromatography

Question 38

What is electrophoresis?

Answer 38

separation based on migration of charged molecules in an applied electrical field

Question 39

"Native" electrophoresis

Answer 39

used to separate proteins based on differences in charge (ex. hemoglobin isoforms)

Question 40

SDS-PolyAcrylamide Gel electrophoresis (PAGE)

Answer 40

SDS- sodium dodecyl sulfate, a detergent that disrupts non-covalent interactions of quaternary structure, based on size

Question 41

Iso-Electric Focusing (IEF)

Answer 41

special proprietary buffers are used to generate a pH gradient within a PA gel -the proteins with migrate to the pH which is equal to the protein's pI

Question 42

What is Western blot?

Answer 42

proteins separated by electrophoresis are transferred to a synthetic membrane that is incubated with an antibody to a specific protein, then a second antibody is added to visualize the specific protein

Question 43

What is Edman sequencing?

Answer 43

isolating and removing the N-terminal to determine the amino acid sequence of a peptide

Question 44

What is mass spectrometry?

Answer 44

seperates molecules based on thier mass with very high sensitivity