Chapter 2 - Proteins

Question 1

Proteins are

Answer 1

Linear polymers built of amino acids which are linked end to end

Question 2

Secondary structures

Answer 2

Three dimensional structure formed by hydrogen bonds between amino acids near one another

Question 3

Amino acids are

Answer 3

The building blocks of proteins

Almost all amino acids are chiral

Question 4

L amino acid

Answer 4

Became more dominant in solution due to its solubility

Question 5

Amino acids in solution at neutral pH exist as

Answer 5

Diplomat ions or zwitterions where the amine group is protonated and the carbonyl group is deprotonated

Question 6

Amino acid R groups can be characterized as

Answer 6

Hydrophobic amino acids with no polar groups
Polar amino acids with neutral R groups
Positively charged (basic)
Negatively charged (acidic)

Question 7

The formation of a dipeptide from two amino acids is accompanied by

Answer 7

A loss of water molecule

Question 8

Peptides are kinetically stable becaus

Answer 8

The rate of hydrolysis is extremely slow

Question 9

The amino acid sequence is

Answer 9

The link between the genetic message in DNA and the three-dimensional structure that performs a proteins biological function

Question 10

The molecular weight of an amino acid

Answer 10

110g/mol

Question 11

Disulfide bonds are formed by

Answer 11

The oxidation of a pair of cysteine residues

Question 12

Polypeptides are flexible yet constricted

Answer 12

Resonance causes the peptides to be rigid and planar because it makes it less reactive and more stable. Due to the partial double bond character

Question 13

Why are almost all peptides trans?

Answer 13

Due to steric clashes between R groups. Proline is usually cis.

Question 14

Freedom of rotations

Answer 14

Allows proteins me to fold in different ways.

Question 15

Psi angle

Answer 15

Bond between the C and O

Question 16

Phi angle

Answer 16

Bond between the C and N

Question 17

Ramachandran plot

Answer 17

Shows favored confirmations of the proteins

Question 18

Two types of secondary structures

Answer 18

Alpha helix

Beta sheets

Question 19

Alpha helices

Answer 19

Rodlike structure, stabilized by hydrogen bonds between the NH and C groups.
Rise of amino acid - 1.5A
Residues per turn - 5.6A

Question 20

In the alpha helix

Answer 20

The CO group of each amino acid forms a hydrogen bond with the NH that is situated 4 residues ahead of the sequence

Question 21

Not good for alpha helices

Answer 21

Proline, valine, threonine, isoleucine, serine, aspartame, asparagine and glycine

Question 22

Beta sheet

Answer 22

Fully extended. The distance between adjacent amino acid is 3.5A

Question 23

Antiparallel confirmation

Answer 23

Stronger that parallel due to hydrogen bond allignment

Question 24

Omega loop

Answer 24

The CO residue i of the polypeptide chain is hydrogen bonded to the NH group of the residue i + 3 to stabilize the turn

Question 25

Alpha keratin

Answer 25

Have covalent disulfide bonds that hold the, together and make them very rigid

Question 26

Structure of proteins

Answer 26

3 dimensional structure
Fulfills biological conformation (native fold)
Cost of conformational entropy

Question 27

Motifs

Answer 27

Certain combination of secondary structures

Question 28

Protein folding

Answer 28

Is driven by the strong tendency of hydrophobic residues trying to be excluded from water.

Question 29

Tertiary structure

Answer 29

The interior consists of almost entirely no polar residues such as leucine, valine, methionine and phenylalanine. Polar charged chains are on the surface

Question 30

Two major classes of tertiary structures

Answer 30

Fibrous proteins

Globular proteins

Question 31

Quaternary structures

Answer 31

Each polypeptide is called a subunit. Refers to the spatial arrangement of subunits and the nature of their interactions

Question 32

Ribonuclease

Answer 32

Is a single polypeptide that has 124 amino acid residues cross linked by four disulfide bonds

Question 33

Protein stability

Answer 33

Depends on its three dimensional structure

Integrity - denaturation

Question 34

Urea and mercaptoethanol

Answer 34

Disrupt the noncovalent bonds. They replace water as the molecule solvating the proteins and disrupt the van der Waals

Question 35

Scientist Annfisten

Answer 35

Made the critical observation that the denatured ribonuclease, freed of urea and mercapto by dialysis, slowly regained enzymatic activity