[Lec 3] Key Terms: Structure of Proteins

Question 1

Glycine

Answer 1

Gly, G; 1. neutral non-polar; 2. smallest amino acid, most flexible

Question 2

Alanine

Answer 2

Ala, A; neutral non-polar

Question 3

Valine

Answer 3

Val, V; neutral non-polar

Question 4

Isoleucine

Answer 4

Ile, I; neutral non-polar

Question 5

Tryptophan

Answer 5

Trp, W; neutral non-polar

Question 6

Phenylalanine

Answer 6

Phe, F; neutral non-polar

Question 7

Proline

Answer 7

Pro, P; 1. neutral non-polar; 2. covalent bond with amino group restricts conformational group, DISRUPTS ALPHA HELIX FORMATION

Question 8

Methionine

Answer 8

Met, M; neutral non-polar

Question 9

Leucine

Answer 9

Leu, L; neutral non-polar

Question 10

Aspartic Acid

Answer 10

Asp, D; acidic

Question 11

Glutamic Acid

Answer 11

Glu, E; acidic

Question 12

Lysine

Answer 12

Lys, K; basic

Question 13

Arginine

Answer 13

Arg, R; basic

Question 14

Histidine

Answer 14

His, H; basic

Question 15

Serine

Answer 15

Ser, S; neutral polar

Question 16

Threonine

Answer 16

Thr,T; neutral polar

Question 17

Cysteine

Answer 17

Cys, C; 1. neutral polar; 2. two cysteine resides can form a disulfide bond

Question 18

Tyrosine

Answer 18

Tyr, Y; 1. neutral polar; 2. contain both hydrophobic ring and -OH group; 3. sometimes known as aromatic of neutral polar

Question 19

Asparagine

Answer 19

Asn, N; neutral polar

Question 20

Glutamine

Answer 20

Gln, Q; neutral polar

Question 21

neutral non-polar

Answer 21

hydrophobic, inside lipid bilayer; in R, all contains methyl group, aromatic rings, or hydrogen alone. None are very electronegative so hydrogen bonds don’t form

Question 22

neutral polar

Answer 22

hydrophillic, outside lipid bilayer; in R, all contain electronegative oxygen or sulfur atoms which form hydrogen bond with molecules like water

Question 23

acidic

Answer 23

negative charge and contains an oxygen

Question 24

basic

Answer 24

positive charge and contains a nitrogen

Question 25

Alpha Helix

Answer 25

secondary structure; right handed helix; 1. 3.6 residues/turn; 2. H-bond between every 4th amino acid on backbone; 3. forms a rigid structure; 4. R-groups project out from helix ; 5. H-bonds are parallel to axis of helix; 6. side chains interact to hold two alpha helices together in coiled coil

Question 26

Leucine Zipper

Answer 26

motif; very stable; leucine in every 4th amino acid; alpha helix

Question 27

Beta-Pleated Sheets

Answer 27

secondary structure; 1. planar peptide bonds with bend at Carbon; 2. H-bonding between one beta strand and another between backbone; 3. R-groups alternate above and below sheet; 4. found parallel and antiparallel

Question 28

Tertiary Structure

Answer 28

1. folded structure of the entire polypeptide chain; 2. determined largely by primary structure

Question 29

Anifinsen Experiment

Answer 29

Showed that protein can fold correctly by itself. Primary structure is sufficient to produce correct tertiary structure

Question 30

chaperone proteins

Answer 30

help larger proteins fold properly

Question 31

motifs

Answer 31

important features smaller than domains

Question 32

structural motif

Answer 32

1. independently folding region; 2. continuous sequence of amino acids; 3. multiple domains possible

Question 33

functional domain

Answer 33

1. region or domain required for specific function; 2. structure of protein may not be known; 3. functional domain may be part of a larger structural domain or be made up of several smaller structural domains

Question 34

quaternary structure

Answer 34

arrangement of multiple subunits into larger complex

Question 35

subunits

Answer 35

each polypeptide of a multimeric unit; 1. often held together by non-covalent bonds, but disulfide bonds may form between subunits too; 2. multimeric proteins can be made up of identical (homo) or different (hetero) subunits

Question 36

subunit structure of a protein

Answer 36

the number and relative position of the subunits in multimeric proteins

Question 37

protein enzymes

Answer 37

catalyzes a chemical reaction

Question 38

Zinc finger motif

Answer 38

recognizes specific DNA sequences

Question 39

specificity

Answer 39

DNA binding can be "specific" (nucleotide sequence matters) or "nonspecific" (nucleotide sequence doesn't matter)

Question 40

affinity

Answer 40

how well proteins bind (higher affinity=tighter binding)

Question 41

competitive inhibitor

Answer 41

binds the active site

Question 42

allosteric inhibitor

Answer 42

changes active site by binding somewhere else

Question 43

Glycosylation

Answer 43

addition of sugar molecule; added to Asn, Ser, or Thr; can affect protein stability, conformation, and/or function

Question 44

Phosphorylation

Answer 44

addition of phosphate; added to Ser, Thr, Tyr; can affect protein stability, conformation, and/or function

Question 45

Acetylation

Answer 45

addition of acetyl group; added to many residue and backbone of N-terminus; can affect protein stability, conformation, and/or function

Question 46

Methylation

Answer 46

addition of a methyl group; added to Lys and Arg; can affect protein stability, conformation, and/or function