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64 Cards in this Set

  • Front
  • Back

What are polymers of amino acids?


What determines the function of a protein?

It's structure

What are five of the main functions of proteins?

1. Structural components

2. Motors for movement

3. Catalyzing chemical reactions

4. Mediate communication between cell and environment

5. Expression of genetic information

What are the four different levels of proteins?

1. Primary structure

2. Secondary structure

3. Tertiary structure

4. Quaternary structure

What is the primary structure of a protein?

The sequence of amino acid residues

What is the secondary structure of a protein?

The localized conformation of the polypeptide backbone

What is the tertiary structure of a protein?

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

What is the quaternary structure of a protein?

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

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

1. Nonpolar R groups

2. Polar uncharged R groups

3. Polar charged R groups

What type of R groups do hydrophobic amino acids have?

Nonpolar R groups

What type of R groups do hydrophilic amino acids have?

Polar R groups

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

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

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

Tryptophan is the only amino acid with a fused ring system

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

Cysteine residues can form disulfide bonds

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

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

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


What can tryptophan be used to determine?

The protein concentrations

How can tryptophan be used to determine protein concentrations?

Trp absorbs UV light at 280 nm

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

Beer's Law

What is the equation for Beer's Law?

What facilitates crosslinking?

Disulfide bonds

What can form intra-strand crosslinks?

Disulfide bonds

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

Disulfide bonds can also form inter-chain crosslinks

How are amino acids linked?

Via peptide bonds

What do amino acids link to form?

A polypeptide

T or F: Amino acids have many amino acid residues


What reaction links amino acids?

Condensation reaction

What does pK reveal?

The cutoff pH for protonation of species

What is the pH of this amino acid?

What is the pH of this amino acid?

pH < 3.5

What is the pH of this amino acid?

What is the pH of this amino acid?

3.5 < pH < 9

What is the pH of this amino acid?

What is the pH of this amino acid?

pH > 9

T or F: Amino acid structure does not affect solubility


What determines a molecules solubility?

The structure of the molecule

What does solubility of an amino acid refer to?

Polar, charged

Polar, uncharged


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

1. Insoluble

2. Made of mostly nonpolar amino acids

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

1. Soluble

2. Have hydrophilic amino acids on the surface

Why are secondary structures formed?

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

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

Alpha helix and beta sheet

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

The carbonyl oxygen and the amino hydrogen

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


How is the core of an alpha helix packed?


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


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

van der Waals

What is a beta sheet?

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

What are the two characteristics of alpha helixes backbone atoms?

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

2. Glycine and proline are rar

What does proline do to alpha helixes backbone atoms?

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

What does glycine do to alpha helixes backbone atoms?

Glycine is able to rotate too freely and distorts the helix

What amino acid is uncommon in beta sheets?


How are secondary structures linked?

Via polypeptide loops

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

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

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


What shape does a folded polypeptide assume?

A shape with a hydrophilic surface and a hydrophobic core

What is the stabilization of a protein structure?

Delicate balance between forces

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

Hydrophobic interaction




vdW interactions

Disulfide bonds

What are hydrophobic interactions?

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

Is a folded or unfolded protein more favorable?


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

Hydrogen bonds and charge/charge interactions

--> equally favor the unfolded and folded state

What are the characteristics of disulfide bonds?

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

Which interaction is the most important to consider?

Hydrophobic interaction

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

van der Waals interactio

What interactions are not as important to consider?



Disulfide bonds

What are the four steps for the protein folding process?

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

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

1. Another protein can help refold the misfolded protein

2. The misfolded protein is degraded

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

It can aggregate and cause diseases

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

Alzheimer's or Parkinson's