learning objectives 3.1

Question 1

List and describe the 9 functional categories of proteins

Answer 1

1. transport proteins - transport ions and molecules
2. enzymes - catalyze cellular reactions
3. scaffold proteins - hold proteins together that interact in catalytic or signaling pathways
4. signaling proteins - cellular communication
5. structural proteins - provide mechanical support and structural organization
6. motor proteins - move along other molecules for transport or synthesis
7. storage proteins - repositories for ions and molecules
8. receptor proteins - signal detection and involved in transmission
9. regulatory proteins - regulate cellular processes

Question 2

Nonpolar amino acids (9)

Answer 2

Valine
Alanine
Methionine
Tryptophan
Proline (contains imino group)
Glycine
Leucine
Isoleucine
phenylalanine

Question 3

Polar Acid amino acids (2)

Answer 3

Aspartate/Aspartic Acid
Glutamate/Glutamic Acid
*Have a net charge of (-1) at ph 7

Question 4

Polar Basic amino acids (3)

Answer 4

Histidine (contains imidozal group)
lysine
Arginine (contains guanidium group)
*have a net charge of (+1) at ph 7

Question 5

Polar neutral amino acids (6)

Answer 5

Serine
Threonine
Asparagine
Glutamine
Cysteine (slightly polar)
Tyrosine (slightly polar)

Question 6

Aromatic amino acids

Answer 6

Tryptophan
Phenylalanine
Tyrosine

Question 7

Sulfur-containing amino acids

Answer 7

Methionine
Cysteine

Question 8

Carboxyl-containing amino acids (secondary carboxyl)

Answer 8

Aspartic Acid
Glutamic acid

Question 9

Hydroxyl-containing amino acids

Answer 9

Serine
Tyrosine
Threonine

Question 10

special amino acids

Answer 10

cysteine (forms disulfide bonds)
Glycine (R-group is just Hydrogen)
Proline (forms a bond to itself)

Question 11

Hydrophobic amino acids (8)

Answer 11

Alanine
Valine
Leucine
Isoleucine
Methionine
Phenylalanine
Tryptophan
Tyrosine

Question 12

Aliphatic

Answer 12

Valine
Leucine
Isoleucine
Methionine

Question 13

what are the groups that modify amino acids

Answer 13

acetyl
phosphate
hydroxyl
methyl
carboxyl
o-GlcNAc

Question 14

functional groups and linkages

Answer 14

Hydroxyl
Acyl
Carbonyl
Carboxyl
Sulfhydryl
Amino
Phosphate
Pyrophosphate
ester
ether
amide

Question 15

Describe alpha helices

Answer 15

• Right-handed (clockwise)
• H-bonds b/w peptide backbone
• H-bonding occurs b/w all peptides. Oxygen in Carbonyl bonds with w/ hydrogen in amino 4 peptides away
• turns every 3.6 residues
• h bonds run parallel to axis
• r-groups determine hydrophobic/hydrophilic character and formation
• stiff structure
• often found in membrane proteins
• contain amphipathic helices (hydrophobic and hydrophilic)

Question 16

What amino acid do you not see in alpha helices?

Answer 16

Proline, because they cannot fit and the steric hindrance

Question 17

What bonds stabilize alpha helices?

Answer 17

Hydrogen bonds within the backbone

Question 18

Where do the r-groups point in alpha helices and Beta sheets

Answer 18

Alpha helices: point outward
Beta sheets: point out top and bottom

Question 19

What makes up secondary structure?

Answer 19

alpha helices and beta sheets, turns

Question 20

Describe beta sheets

Answer 20

• can be parallel or anit-parallel
• are made of short segments of peptides
• Hydrogen bonding occurs between adjacent Beta sheets. they can be close by, a little distant, or in a different polypeptide
• flat but can be bent or twisted

Question 21

Describe beta turns

Answer 21

• 4 residues in a turn
• often found on the surface of globular proteins. This helps facilitate compact folding
• Glycine and Proline are commonly found
• stabilized by H bonds b/w residues 1 and 4

Question 22

describe beta loops

Answer 22

• loops are longer and more complex than turns
• do not have a regular structure. instead they are unique to each protein
• usually found on protein surface
• often involved in specific binding interactions

Question 23

Motifs

Answer 23

• 2 or more repeating structures
• can be small or large. (small: Helix-loop-helix)
  (large: Beta barrel)
• associated w/ specific function. Ex.) Helix-turn-helix motif of DNA binding proteins

Question 24

Helix-turn-helix motif

Answer 24

• 2 helices seperated by a turn
• found in DNA binding proteins
• found in Ca2+ binding proteins (EFhand)

Question 25

Coiled-coil motif

Answer 25

- 2 alpha helices wrapped around each other - stabilized by weak interactions b/w aliphatic side chains - amphipatic - protein family: fibrous proteins, some transcription factors

Question 26

Zinc finger motif

Answer 26

- a-helix + 2 antiparallel beta strands - stabilized by a central Zn2+ bound by 2 cys, and 2 HIs or 4 cys - zinc finger = C2H2 - found in DNA or RNA binding proteins

Question 27

list Protein structure

Answer 27

Primary secondary tertiary quaternary

Question 28

describe primary structure

Answer 28

- amino acid sequence - stabilized by peptide bonds - determines shape and function

Question 29

describe peptide bonds

Answer 29

- usually found in trans configuration - formed b/w Amino acids. - is a condensation rxn. yields H20 - two amino acids= 1 peptide bond - formed b/w the oxygen of the carboxyl group and the nitrogen of the amino group of the other A.A - uncharged. so it can pack tightly - NCC-NCC-NCC Backbone - formed N-terminus to C-terminus. (from left to right) - hydrogen bonding - small peptides still have biological activity - no rotation around peptide bond b/c of the double bond. rotation is possible around the alpha carbon - steric hinderance of R-groups affect protein folding

Question 30

describe secondary structure

Answer 30

- made of alpha helices and beta sheets - stabilized by H-bonding within the backbone - most common is a-helices and Beta sheets +turns

Question 31

describe tertiary structure

Answer 31

- folded protein structure. - stabilized by many interactions within the peptide r-groups/residues. (hydrophobic interactions, h-bonds, van der waals, salt bridges, disulfide bridges) - can be flexible or stiff

Question 32

describe quaternary structure

Answer 32

multiple subunits - stabilized by non-convalent bonds/interactions - often required for protein function - can be identical (homo-) or different (hetero) - dimer (2 subunits) - trimer (3 subunits) - tetramer (4 subunits)