Chapter 4 - Protein Structure

Front 1

What are polymers of amino acids?

Back 1

Proteins

Front 2

What determines the function of a protein?

Back 2

It's structure

Front 3

What are five of the main functions of proteins?

Back 3

1. Structural components

2. Motors for movement

3. Catalyzing chemical reactions

4. Mediate communication between cell and environment

5. Expression of genetic information

Front 4

What are the four different levels of proteins?

Back 4

1. Primary structure

2. Secondary structure

3. Tertiary structure

4. Quaternary structure

Front 5

What is the primary structure of a protein?

Back 5

The sequence of amino acid residues

Front 6

What is the secondary structure of a protein?

Back 6

The localized conformation of the polypeptide backbone

Front 7

What is the tertiary structure of a protein?

Back 7

The three-dimensional structure of an entire polypeptide, including its side chain

Front 8

What is the quaternary structure of a protein?

Back 8

The spatial arrangement of polypeptide chains in a protein with multiple subunits

Front 9

What are the three categories of R groups for amino acids?

Back 9

1. Nonpolar R groups

2. Polar uncharged R groups

3. Polar charged R groups

Front 10

What type of R groups do hydrophobic amino acids have?

Back 10

Nonpolar R groups

Front 11

What type of R groups do hydrophilic amino acids have?

Back 11

Polar R groups

Front 12

What is unique about the amino acid proline (Pro, P)?

Back 12

Proline is the only amino acid whose side chain loops back onto its own backbone

Front 13

What is unique about the amino acid tryptophan (Trp, W)?

Back 13

Tryptophan is the only amino acid with a fused ring system

Front 14

What is unique about the amino acid cysteine (Cys, C)?

Back 14

Cysteine residues can form disulfide bonds

Front 15

What is unique about the amino acid methionine (Met, M)?

Back 15

Methionine is one of only two amino acids with a sulfur in its R group

Front 16

What amino acid do most proteins contain at least one of?

Back 16

Tryptophan

Front 17

What can tryptophan be used to determine?

Back 17

The protein concentrations

Front 18

How can tryptophan be used to determine protein concentrations?

Back 18

Trp absorbs UV light at 280 nm

Protein concentrations can be determined based on detection of Trp in proteins

Beer's Law

Front 19

What is the equation for Beer's Law?

Back 19

Front 20

What facilitates crosslinking?

Back 20

Disulfide bonds

Front 21

What can form intra-strand crosslinks?

Back 21

Disulfide bonds

Front 22

What can occur when a protein contains more than one polypeptide chain?

Back 22

Disulfide bonds can also form inter-chain crosslinks

Front 23

How are amino acids linked?

Back 23

Via peptide bonds

Front 24

What do amino acids link to form?

Back 24

A polypeptide

Front 25

T or F: Amino acids have many amino acid residues

Back 25

True

Front 26

What reaction links amino acids?

Back 26

Condensation reaction

Front 27

What does pK reveal?

Back 27

The cutoff pH for protonation of species

Front 28

What is the pH of this amino acid?

Back 28

pH < 3.5

Front 29

What is the pH of this amino acid?

Back 29

3.5 < pH < 9

Front 30

What is the pH of this amino acid?

Back 30

pH > 9

Front 31

T or F: Amino acid structure does not affect solubility

Back 31

False

Front 32

What determines a molecules solubility?

Back 32

The structure of the molecule

Front 33

What does solubility of an amino acid refer to?

Back 33

Polar, charged

Polar, uncharged

Nonpolar

Front 34

What are the two characteristics of structural proteins (collagen, keratin)?

Back 34

1. Insoluble

2. Made of mostly nonpolar amino acids

Front 35

What are the two characteristics of proteins that need to function in the cell?

Back 35

1. Soluble

2. Have hydrophilic amino acids on the surface

Front 36

Why are secondary structures formed?

Back 36

To minimize steric strain and maximize the hydrogen bonds between the polar groups of the backbone

Front 37

What are common secondary structures that are characterized by hydrogen bonding between backbone groups?

Back 37

Alpha helix and beta sheet

Front 38

What does an H-bond in an alpha helix form between?

Back 38

The carbonyl oxygen and the amino hydrogen

Front 39

How many residues are there per turn for an alpha helix?

Back 39

3.6

Front 40

How is the core of an alpha helix packed?

Back 40

Densley

Front 41

What is the value of a pitch of an alpha helix?

Back 41

5.4A

Front 42

What type of interactions are there between the backbone atoms of an alpha helix?

Back 42

van der Waals

Front 43

What is a beta sheet?

Back 43

Aligned strands of polypeptides hydrogen bond with neighboring strands that are either parallel or antiparallel to each other

Front 44

What are the two characteristics of alpha helixes backbone atoms?

Back 44

1. H-bones: C=O bonds with NH that is four positions away

2. Glycine and proline are rar

Front 45

What does proline do to alpha helixes backbone atoms?

Back 45

Proline introduce destabilizing kink, lacks N-H for H-bonding

Front 46

What does glycine do to alpha helixes backbone atoms?

Back 46

Glycine is able to rotate too freely and distorts the helix

Front 47

What amino acid is uncommon in beta sheets?

Back 47

Proline

Front 48

How are secondary structures linked?

Back 48

Via polypeptide loops

Front 49

What type of structure do loops that link beta-strands and alpha-helices have?

Back 49

Irregular secondary structure: does not adopt a defined secondary structure, but is not random

Front 50

T or F: Proteins can have limited combinations of secondary structures

Back 50

False

Front 51

What shape does a folded polypeptide assume?

Back 51

A shape with a hydrophilic surface and a hydrophobic core

Front 52

What is the stabilization of a protein structure?

Back 52

Delicate balance between forces

Front 53

What interactions should be considered for the stabilization of a protein structure?

Back 53

Hydrophobic interaction

H-bonds

Electrostatic

Charge/charge

vdW interactions

Disulfide bonds

Front 54

What are hydrophobic interactions?

Back 54

The aggregation/association of nonpolar molecules due to the hydrophobic effect

Front 55

Is a folded or unfolded protein more favorable?

Back 55

Folded

Front 56

What bonds are able to form in the folded or unfolded state?

Back 56

Hydrogen bonds and charge/charge interactions

--> equally favor the unfolded and folded state

Front 57

What are the characteristics of disulfide bonds?

Back 57

Rare and have been demonstrated to not be essential for stabilizing protein structures in which they are present. May help prevent unfolding in harsh conditions, but do not have a strong effect on stability in normal conditions

Front 58

Which interaction is the most important to consider?

Back 58

Hydrophobic interaction

Front 59

What is the other interaction, along with hydrophobic interaction, that needs to be considered?

Back 59

van der Waals interactio

Front 60

What interactions are not as important to consider?

Back 60

H-bonds

Charge/charge

Disulfide bonds

Front 61

What are the four steps for the protein folding process?

Back 61

1. Folding of a protein is not random!

2. Protein folds through one or a few alternate pathways

3. Small element of the secondary structure form first

4. Hydrophobic effect causes secondary structures to coalesce with a hydrophobic core

Front 62

What one or two pathways occur if a misfolded protein is detected?

Back 62

1. Another protein can help refold the misfolded protein

2. The misfolded protein is degraded

Front 63

What happens if a misfolded protein is not detected or degraded?

Back 63

It can aggregate and cause diseases

Front 64

What are two examples of diseases that can be caused when a misfolded protein is not detected or degraded?

Back 64

Alzheimer's or Parkinson's