Basics (Amino Acids, Proteins, Protein Analysis)

Question 1

1 A = ___ m

Answer 1

1 Angstrom = 1 x 10^-10 m

Question 2

How big is the radius of an atom on avg?

Answer 2

1-2 Angstroms

1-2 x 10^-10 m

Question 3

What is the average size of a protein?

Answer 3

150 residues

30-50 Angstroms

Question 4

Weight of 1 Hydrogen?

Answer 4

1 dalton

Question 5

What is the average weight of an amino acid?

Answer 5

110 daltons

Question 6

What is a covalent bond? How strong are they?

Answer 6

• A covalent bond is a bond in which electrons are shared between 2 atoms.
• They are strong (> 100 kcal/mol)
• Bring atoms close together (1-2 Angstroms)

Question 7

Order of electronegativity for elements found in proteins?

Answer 7

O > N > C = S > H

Question 8

What is electronegativity?

Answer 8

Ability of an atom to attract electrons in a chemical bond

Question 9

What is a hydrogen bond?

Answer 9

Bond formed between an H atom in a polar bond such as O-H or N-H and an electronegative atom like O and N.

• Weak (1-3 kcal/mol)
• Contribute to protein structure and stability

Question 10

Equation for pH

Answer 10

pH = -log[H⁺]

Question 11

Define pK_a

Answer 11

The pH at which the concentrations of HA and A^- are equal

Question 12

Describe the chemical structure of an amino acid in 2 parts

Answer 12

1. Set of atoms that make up the backbone of the protein chain
2. side chain atoms that make them unique

Question 13

Basic structure of an Amino Acid?

Answer 13

Question 14

What are the Nonpolar Amino Acids?

Answer 14

Gly, Ala, Val, Leu, Ile, Met, Pro, Phe, Trp

Question 15

What are the uncharged but polar amino acids?

Answer 15

Asn, Gln, Ser, Thr, Tyr, Cys

Question 16

What are the charged and polar amino acids?

Answer 16

Arg, Lys, Glu, Asp, His

Question 17

What is special about Cysteine?

Answer 17

• Can form covalent bonds (disulfide bonds) between 2 sulfurs
• Stabilize or constrain proteins
• Found in extracellular proteins

Question 18

Which amino acid forms disulfide bonds that stabilize or ocnstrain proteins?

Answer 18

Cysteine

Question 19

What is unique about Glycine?

Answer 19

• Glycine has no side chain
• Flexible, found in tight turns

Question 20

What is unique about Proline?

Answer 20

• Side chain bonds to the nitrogen along the peptide backbone and forms a ring structure
• Rigidifies a protein

Question 21

Gly

Answer 21

Question 22

Ala

Answer 22

Question 23

Val

Answer 23

Question 24

Ile

Answer 24

Question 25

Leu

Answer 25

Question 26

Phe

Answer 26

Question 27

Tyr

Answer 27

Question 28

Trp

Answer 28

Question 29

Met

Answer 29

Question 30

His

Answer 30

Question 31

Ser

Answer 31

Question 32

Thr

Answer 32

Question 33

Cys

Answer 33

Question 34

Asn

Answer 34

Question 35

Gln

Answer 35

Question 36

Pro

Answer 36

Question 37

Asp

Answer 37

Question 38

Glu

Answer 38

Question 39

Lys

Answer 39

Question 40

Arg

Answer 40

Question 41

pK_a values for Polar and Charged Amino Acids?

Answer 41

* 3.9 = Aspartic Acid (Asp, D) - NEGATIVE * 4.1 = Glutamic Acid (Glu, E) - NEGATIVE * 6.0 = Histidine (His, H) - NEUTRAL * 10.8 = Lysine (Lys, K) - POSITIVE * 12.5 = Arginine (Arg, R) - POSITIVE

Question 42

Amino Acid Abbrebiation: A

Answer 42

Alanine (Ala)

Question 43

Amino Acid Abbrebiation: C

Answer 43

Cysteine (Cys)

Question 44

Amino Acid Abbrebiation: D

Answer 44

Aspartic Acid (Asp)

Question 45

Amino Acid Abbrebiation: E

Answer 45

Glutamic Acid (Glu)

Question 46

Amino Acid Abbrebiation: F

Answer 46

Phenylalanine (Phe)

Question 47

Amino Acid Abbrebiation: G

Answer 47

Glycine (Gly)

Question 48

Amino Acid Abbrebiation: H

Answer 48

Histidine (His)

Question 49

Amino Acid Abbrebiation: I

Answer 49

Isoleucine (Ile)

Question 50

Amino Acid Abbrebiation: K

Answer 50

Lysine (Lys)

Question 51

Amino Acid Abbrebiation: L

Answer 51

Leucine (Leu)

Question 52

Amino Acid Abbrebiation: M

Answer 52

Methionine (Met)

Question 53

Amino Acid Abbrebiation: N

Answer 53

Asparagine (Asn)

Question 54

Amino Acid Abbrebiation: P

Answer 54

Proline (Pro)

Question 55

Amino Acid Abbrebiation: Q

Answer 55

Glutamine (Gln)

Question 56

Amino Acid Abbrebiation: R

Answer 56

Arginine (Arg)

Question 57

Amino Acid Abbrebiation: S

Answer 57

Serine (Ser)

Question 58

Amino Acid Abbrebiation: T

Answer 58

Threonine (Thr)

Question 59

Amino Acid Abbrebiation: V

Answer 59

Valine (Val)

Question 60

Amino Acid Abbrebiation: W

Answer 60

Tryptophan (Trp)

Question 61

Amino Acid Abbrebiation: Y

Answer 61

Tyrosine (Tyr)

Question 62

Abbreviations for 20 AAs?

Answer 62

Question 63

What is a polypeptide? Peptide bond?

Answer 63

Chain formed when amino acids polymerize through elimination of a water molecule. Pepdide bond is the CO-NH linkage.

Question 64

Number of amino acids in a protein?

Answer 64

between 40-4000 Amino Acids | (A few AA residues is called a peptide)

Question 65

Beginning of a polypeptide chain? End?

Answer 65

Beginning: N-terminus End: C-Terminus

Question 66

Condensation of 2 Amino Acids

Answer 66

Question 67

Primary, Secondary, Tertiary, and Quaternary structure of a protein?

Answer 67

1. **Primary** = amino acid sequence 2. **Secondary** = backbone arrangements (α-helices and β-strands) 3. **Tertiary** = 3D structure of chain 4. **Quaternary** = spatial arrangements of multiple polypeptide chains

Question 68

In an α-helix, residues separated by ___ positions form hydrogen bonds between their backbone atoms.

Answer 68

3